Ontology for Biomedical Investigation
type: Ontology
version info: 2012-07-01
date: 2012-07-09
comment: This file is based on checkout of our SVN repository revision $Revision: 3641 $
default language: en
version info: $Revision$
Contributor: Alan Ruttenberg
Source: Pierre Grenon and Barry Smith: "SNAP and SPAN: Towards Geospatial Dynamics"
Contributor: Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester
creator: Allyson Lister
comment: An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at http://code.google.com/p/information-artifact-ontology/
subject: An ontology for the annotation of biomedical and functional genomics experiments.
Contributor: Andrew Spear
creator: Barry Smith
creator: Bill Bug
Contributor: Chris Mungall
creator: Bjoern Peters
creator: Carlo Torniai
creator: Chris Mungall
comment: This document was an early experimental prototype of bfo2, not blessed by the working group. It is archived because it was used by some projects. There was very little change other than ids relative to earlier versions of BFO, and ids used here will be used in the ultimate release
creator: Alan Ruttenberg
creator: Chris Stoeckert
creator: Chris Taylor
creator: Cristian Cocos
creator: Daniel Rubin
creator: Daniel Schober
creator: Dawn Field
creator: Dirk Derom
creator: Elisabetta Manduchi
creator: Eric Deutsch
creator: Frank Gibson
creator: Gilberto Fragoso
creator: Helen C. Causton
creator: Helen Parkinson
creator: Holger Stenzhorn
creator: James Malone
creator: Jay Greenbaum
creator: Jeffrey Grethe
creator: Jennifer Fostel
creator: Jessica Turner
creator: Jie Zheng
creator: Joe White
creator: John Westbrook
creator: Kevin Clancy
creator: Larisa Soldatova
creator: Lawrence Hunter
creator: Liju Fan
creator: Luisa Montecchi
creator: Matthew Pocock
creator: Melanie Courtot
creator: Melissa Haendel
creator: Mervi Heiskanen
creator: Monnie McGee
creator: Norman Morrison
Format: OWL-DL
creator: Philip Lord
creator: Philippe Rocca-Serra
creator: Pierre Grenon
creator: Richard Bruskiewich
creator: Richard Scheuermann
creator: Robert Stevens
creator: Ryan R. Brinkman
creator: Stefan Wiemann
creator: Susanna-Assunta Sansone
creator: Tanya Gray
description: The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific.
creator: Tina Hernandez-Boussard
creator: Trish Whetzel
creator: Yongqun He
Rights Management: free, no license required.
version IRI: obi.owl

2012 summer release
type: Thing
type: Version
file-release: obi.owl
file-release: Ontology for Biomedical Investigation
revision: SVN $Revision: 3641 $

Description
type: AnnotationProperty
comment: An account of the content of the resource.
description: Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content.

term replaced by
type: AnnotationProperty
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
definition: Use on obsolete terms, relating the term to another term that can be used as a substitute
editor preferred term: term replaced by
has curation status: IAO_0000125

Contributor
type: AnnotationProperty
comment: An entity responsible for making contributions to the content of the resource.
description: Examples of a Contributor include a person, an organisation, or a service. Typically, the name of a Contributor should be used to indicate the entity.

curator note
type: AnnotationProperty
definition: An administrative note of use for a curator but of no use for a user
term editor: PERSON:Alan Ruttenberg
editor preferred term: curator note
has curation status: IAO_0000122

OBO foundry unique label
type: AnnotationProperty
editor note: The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .
definition: An alternative name for a class or property which is unique across the OBO Foundry.
definition source: GROUP:OBO Foundry <http://obofoundry.org/>
editor preferred term: OBO foundry unique label
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Bjoern Peters
term editor: PERSON:Chris Mungall
term editor: PERSON:Melanie Courtot
has curation status: IAO_0000125

has obsolescence reason
type: AnnotationProperty
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Melanie Courtot
definition: Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.
editor preferred term: has obsolescence reason

Creator
type: AnnotationProperty
comment: An entity primarily responsible for making the content of the resource.
description: Examples of a Creator include a person, an organisation, or a service. Typically, the name of a Creator should be used to indicate the entity.

Subject and Keywords
type: AnnotationProperty
comment: The topic of the content of the resource.
description: Typically, a Subject will be expressed as keywords, key phrases or classification codes that describe a topic of the resource. Recommended best practice is to select a value from a controlled vocabulary or formal classification scheme.

IEDB alternative term
type: AnnotationProperty
definition: An alternative term used by the IEDB.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
sub property of: alternative term
has curation status: IAO_0000122

FGED alternative term
type: AnnotationProperty
definition: An alternative term used by the Functional Genomics Data (FGED) Society.
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: Penn Group
sub property of: alternative term
has curation status: IAO_0000122

axiom id
type: AnnotationProperty

Resource Identifier
type: AnnotationProperty
comment: An unambiguous reference to the resource within a given context.
description: Recommended best practice is to identify the resource by means of a string or number conforming to a formal identification system. Example formal identification systems include the Uniform Resource Identifier (URI) (including the Uniform Resource Locator (URL)), the Digital Object Identifier (DOI) and the International Standard Book Number (ISBN).

Date
type: AnnotationProperty
comment: A date associated with an event in the life cycle of the resource.
description: Typically, Date will be associated with the creation or availability of the resource. Recommended best practice for encoding the date value is defined in a profile of ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format.

Title
type: AnnotationProperty
description: Typically, a Title will be a name by which the resource is formally known.
comment: A name given to the resource.

Relation
type: AnnotationProperty
description: Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system.
comment: A reference to a related resource.

adjacent to
type: AnnotationProperty
editor preferred term: adjacent to
editor note: belongs in BFO?
definition: x adjacent to y if and only if x and y share a boundary
imported from: ro.owl
type: ObjectProperty
range: independent continuant
domain: independent continuant
sub property of: spatially disjoint from

expand expression to
type: AnnotationProperty
term editor: Chris Mungall
definition: A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones
example of usage: ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
editor preferred term: expand expression to

has_specified_input
type: AnnotationProperty
editor note: 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
term editor: PERSON: Bjoern Peters
term editor: PERSON: Larry Hunter
term editor: PERSON: Melanie Coutot
editor preferred term: has_specified_input
definition: A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
term editor: PERSON: Alan Ruttenberg
example of usage: see is_input_of example_of_usage
type: ObjectProperty
sub property of: has participant
domain: planned process

definition
type: AnnotationProperty
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
term editor: PERSON:Daniel Schober
definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
editor preferred term: definition
has curation status: IAO_0000122

editor note
type: AnnotationProperty
definition: An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
definition source: GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
term editor: PERSON:Daniel Schober
editor preferred term: editor note
has curation status: IAO_0000122

in branch
type: AnnotationProperty
definition: An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.
term editor: GROUP:OBI
definition source: OBI_0000277
editor preferred term: in branch

has ID prefix
type: AnnotationProperty
definition: Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created.
term editor: Person:Alan Ruttenberg
example of usage: Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"

has curation status
type: AnnotationProperty
definition source: OBI_0000281
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Bill Bug
term editor: PERSON:Melanie Courtot
editor preferred term: has curation status

Language
type: AnnotationProperty
comment: A language of the intellectual content of the resource.
description: Recommended best practice is to use RFC 3066 [RFC3066], which, in conjunction with ISO 639 [ISO639], defines two- and three-letter primary language tags with optional subtags. Examples include "en" or "eng" for English, "akk" for Akkadian, and "en-GB" for English used in the United Kingdom.

definition source
type: AnnotationProperty
definition source: Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
term editor: PERSON:Daniel Schober
editor preferred term: definition source
definition: formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
has curation status: IAO_0000122

Resource Type
type: AnnotationProperty
comment: The nature or genre of the content of the resource.
description: Type includes terms describing general categories, functions, genres, or aggregation levels for content. Recommended best practice is to select a value from a controlled vocabulary (for example, the DCMI Type Vocabulary [DCMITYPE]). To describe the physical or digital manifestation of the resource, use the Format element.

antisymmetric property
type: AnnotationProperty
term editor: Alan Ruttenberg
editor preferred term: antisymmetric property
example of usage: part_of antisymmetric property xsd:true
definition: use boolean value xsd:true to indicate that the property is an antisymmetric property

first order logic expression
type: AnnotationProperty
term editor: PERSON:Alan Ruttenberg
editor preferred term: first order logic expression

has_specified_output
type: AnnotationProperty
term editor: PERSON: Bjoern Peters
term editor: PERSON: Larry Hunter
term editor: PERSON: Melanie Courtot
editor preferred term: has_specified_output
definition: A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
term editor: PERSON: Alan Ruttenberg
type: ObjectProperty
sub property of: has participant
domain: planned process
inverse of: is_specified_output_of

term editor
type: AnnotationProperty
editor note: 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition: Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
term editor: PERSON:Daniel Schober
editor preferred term: term editor
has curation status: IAO_0000122

expand assertion to
type: AnnotationProperty
definition: A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
term editor: Chris Mungall
example of usage: ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
editor preferred term: expand assertion to

alternative term
type: AnnotationProperty
definition: An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
term editor: PERSON:Daniel Schober
editor preferred term: alternative term
has curation status: IAO_0000125

Source
type: AnnotationProperty
comment: A reference to a resource from which the present resource is derived.
description: The present resource may be derived from the Source resource in whole or in part. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system.

editor preferred term
type: AnnotationProperty
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
term editor: PERSON:Daniel Schober
definition: The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
editor preferred term: editor preferred term
has curation status: IAO_0000122

example of usage
type: AnnotationProperty
definition: A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
term editor: PERSON:Daniel Schober
editor preferred term: example
has curation status: IAO_0000122

Publisher
type: AnnotationProperty
comment: An entity responsible for making the resource available
description: Examples of a Publisher include a person, an organisation, or a service. Typically, the name of a Publisher should be used to indicate the entity.

Coverage
type: AnnotationProperty
description: Coverage will typically include spatial location (a place name or geographic coordinates), temporal period (a period label, date, or date range) or jurisdiction (such as a named administrative entity). Recommended best practice is to select a value from a controlled vocabulary (for example, the Thesaurus of Geographic Names [TGN]) and that, where appropriate, named places or time periods be used in preference to numeric identifiers such as sets of coordinates or date ranges.
comment: The extent or scope of the content of the resource.

is denotator type
type: AnnotationProperty
term editor: Alan Ruttenberg
editor note: In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')
definition: relates an class defined in an ontology, to the type of it's denotator
editor preferred term: is denotator type

has ID policy for
type: AnnotationProperty
definition: Relating an ontology used to record id policy to the ontology namespace whose policy it manages
term editor: Person:Alan Ruttenberg
example of usage: Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"

has ID range allocated to
type: AnnotationProperty
term editor: Person:Alan Ruttenberg
example of usage: Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300]
definition: Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms

imported from
type: AnnotationProperty
definition: For external terms/classes, the ontology from which the term was imported
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Melanie Courtot
editor preferred term: imported from
has curation status: IAO_0000125

has ID digit count
type: AnnotationProperty
example of usage: Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"
term editor: Person:Alan Ruttenberg
definition: Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits)

Format
type: AnnotationProperty
comment: The physical or digital manifestation of the resource.
description: Typically, Format may include the media-type or dimensions of the resource. Format may be used to determine the software, hardware or other equipment needed to display or operate the resource. Examples of dimensions include size and duration. Recommended best practice is to select a value from a controlled vocabulary (for example, the list of Internet Media Types [MIME] defining computer media formats).

Rights Management
type: AnnotationProperty
description: Typically, a Rights element will contain a rights management statement for the resource, or reference a service providing such information. Rights information often encompasses Intellectual Property Rights (IPR), Copyright, and various Property Rights. If the Rights element is absent, no assumptions can be made about the status of these and other rights with respect to the resource.
comment: Information about rights held in and over the resource.

is part of
type: ObjectProperty
type: TransitiveProperty
editor note: There is controversy about this relation intended to represent the relation between some arbitrary physical thing that is used as a represention/proxy/pointer to something else
alternative term: part of
alternative term: part_of
domain: entity
range: entity
inverse of: has part
sub property of: is located in

domain of part of
type: Axiom
annotated target: entity
annotated source: is part of
axiom id: BFO_0010001
annotated property: domain

has part
type: ObjectProperty
type: TransitiveProperty
alternative term: has_part

inheres in
type: ObjectProperty
type: FunctionalProperty
alternative term: inheres_in
range: independent continuant
domain: dependent continuant
inverse of: is bearer of
sub property of: s depends on

is bearer of
type: ObjectProperty
alternative term: bearer of
alternative term: bearer_of
domain: independent continuant
range: dependent continuant

is realized by
type: ObjectProperty
alternative term: realized by
alternative term: realized_by

realizes
type: ObjectProperty
domain: process
range: realizable entity
inverse of: is realized by

participates in
type: ObjectProperty
alternative term: participates_in

has participant
type: ObjectProperty
alternative term: has_participant
range: continuant
domain: process
inverse of: participates in
property chain axiom: realizes
property chain axiom: inheres in

is concretization of
type: ObjectProperty
alternative term: concretization of
alternative term: concretization_of
range: specifically dependent continuant
domain: generically dependent continuant

concretizes
type: ObjectProperty
domain: specifically dependent continuant
range: generically dependent continuant
inverse of: is concretization of

is immediately preceded by
type: ObjectProperty
type: FunctionalProperty
alternative term: immediately preceded by
alternative term: immediately_preceded_by
sub property of: is preceded by

immediately precedes
type: ObjectProperty
type: FunctionalProperty
alternative term: immediately_precedes
domain: process
range: process
inverse of: is immediately preceded by
sub property of: precedes

is preceded by
type: ObjectProperty
type: TransitiveProperty
alternative term: preceded by
alternative term: preceded_by

precedes
type: ObjectProperty
type: TransitiveProperty
range: process
domain: process
inverse of: is preceded by

is course of
type: ObjectProperty
alternative term: course of
alternative term: course_of
sub property of: has participant

has course
type: ObjectProperty
alternative term: has_course
domain: continuant
range: process
sub property of: participates in
inverse of: is course of

occurs in
type: ObjectProperty
alternative term: occurs_in
range: independent continuant
domain: process
inverse of: has site of
property chain axiom: is part of

has site of
type: ObjectProperty
alternative term: has_site_of

begins to exist during
type: ObjectProperty
alternative term: begins_to_exist_during
domain: continuant
range: process
sub property of: participates in

ceases to exist during
type: ObjectProperty
alternative term: ceases_to_exist_during
domain: continuant
range: process
sub property of: participates in

s depends on
type: ObjectProperty
alternative term: s_depends_on
range: independent continuant
domain: specifically dependent continuant

has granular part
type: ObjectProperty
alternative term: has_granular_part
sub property of: has part

has granular process part
type: ObjectProperty
alternative term: has_granular_process_part
sub property of: has part

is granular part of
type: ObjectProperty
alternative term: granular part of
alternative term: granular_part_of
range: material entity
domain: material entity
sub property of: is part of
inverse of: has granular part

is granular part of process
type: ObjectProperty
alternative term: granular part of process
alternative term: granular_part_of_process
domain: process
range: process
sub property of: is part of
inverse of: has granular process part

is aggregate of
type: ObjectProperty
alternative term: aggregate of
alternative term: aggregate_of
sub property of: is part of

is fiat part of
type: ObjectProperty
alternative term: fiat part of
alternative term: fiat_part_of
sub property of: is part of

has participant beginning to exist
type: ObjectProperty
alternative term: has_participant_beginning_to_exist
sub property of: has participant
inverse of: begins to exist during

has participant ceasing to exist
type: ObjectProperty
alternative term: has_participant_ceasing_to_exist
sub property of: has participant
inverse of: ceases to exist during

is function of
type: ObjectProperty
alternative term: function of
alternative term: function_of
domain: function
sub property of: inheres in

is quality of
type: ObjectProperty
alternative term: quality of
alternative term: quality_of
domain: quality
sub property of: inheres in

is role of
type: ObjectProperty
alternative term: role of
alternative term: role_of
domain: role
sub property of: inheres in

is located in
type: ObjectProperty
alternative term: located in
alternative term: located_in

is located at
type: ObjectProperty
alternative term: located at
alternative term: located_at

g depends on
type: ObjectProperty
alternative term: g_depends_on
range: independent continuant
domain: generically dependent continuant

has function
type: ObjectProperty
alternative term: has_function

has quality
type: ObjectProperty
alternative term: has_quality

has role
type: ObjectProperty
alternative term: has_role

has measurement unit label
type: ObjectProperty
type: FunctionalProperty
sub property of: has part
range: measurement unit label

obsolete_specifically denotes
type: ObjectProperty
editor note: 8/6/2009 Alan Ruttenberg: The suggestions is to deprecate specific and generically denotes in favor of a single denote relationship that corresponds to the generic sense
term editor: Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
example of usage: The process of creation is, for example, writing down on paper the name of a friend by deliberately creating a certain pattern using ink. Here the ink + paper is the independent continuant and the carrier is the pattern in the ink. c = pattern in the ink b = paper + ink r = friend
definition: c specifically denotes r =def r is a portion of reality & c is a particular quality & c depends specifically on some independent continuant b & b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly. Marked means there is a changed or additional quality of the bearer - the quality is the information carrier. Case 1 Memory trace as mark created when reading some description of some friend. The trace can denote. Case 2 Pattern of ink arrayed on paper as mark when writing down a friend's name Case 3 Pattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file.
editor note: see http://code.google.com/p/information-artifact-ontology/issues/detail?id=25&q=denote
has obsolescence reason: IAO_0000103
has curation status: IAO_0000125
sub property of: ObsoleteProperty

is about
type: ObjectProperty
editor note: 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
example of usage: This document is about information artifacts and their representations
definition: is_about is a (currently) primitive relation that relates an information artifact to an entity.
term editor: person:Alan Ruttenberg
domain: information content entity
has curation status: IAO_0000125

mentions
type: ObjectProperty
editor note: 7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity)
editor note: 7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation "mentions" in it's (logical) definition
definition: An information artifact IA mentions an entity E exactly when it has a component/part that denotes E
term editor: PERSON: Jonathan Rees
term editor: Person: Alan Ruttenberg
has curation status: IAO_0000125
sub property of: is about

denotes
type: ObjectProperty
editor note: 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r
example of usage: A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named.
definition source: Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
definition: denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically
term editor: person:Alan Ruttenberg
sub property of: is about

obsolete_materially denotes
type: ObjectProperty
editor note: see http://code.google.com/p/information-artifact-ontology/issues/detail?id=25&q=denote
has obsolescence reason: IAO_0000103
sub property of: ObsoleteProperty

is quality measurement of
type: ObjectProperty
editor note: 8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later
term editor: Alan Ruttenberg
editor note: From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. -- From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] unit of measure is a quality, e.g. the length of a ruler. [We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] [Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] a represents b means either a denotes b or a describes describe: a describes b means a is about b and a allows an inference of at least one quality of b We have had a long discussion about denotes versus describes.
editor note: From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality.
editor note: From the second meeting on IAO: An attempt at defining assay using Barry's "reliability" wording assay: process and has_input some material entity and has_output some information content entity and which is such that instances of this process type reliably generate outputs that describes the input.
editor note: This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details.
definition: m is a quality measurement of q at t when q is a quality there is a measurement process p that has specified output m, a measurement datum, that is about q
range: quality
domain: measurement datum
sub property of: is about

obsolete_describes
type: ObjectProperty
has obsolescence reason: IAO_0000103
sub property of: ObsoleteProperty

obsolete_represents
type: ObjectProperty
has obsolescence reason: IAO_0000103
sub property of: ObsoleteProperty

has coordinate unit label
type: ObjectProperty
type: FunctionalProperty
comment: relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point
sub property of: has part
domain: cartesian spatial coordinate datum
range: UO_0000001

is duration of
type: ObjectProperty
term editor: Person:Alan Ruttenberg
definition: relates a process to a time-measurement-datum that represents the duration of the process
range: process
has curation status: IAO_0000120
sub property of: is about
domain: time measurement datum

is quality measured as
type: ObjectProperty
editor note: 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship
term editor: Person:Alan Ruttenberg
definition: inverse of the relation of is quality measurement of
has curation status: IAO_0000120
inverse of: is quality measurement of

is quality specification of
type: ObjectProperty
term editor: Person:Alan Ruttenberg
term editor: Person:Bjoern Peters
definition: a relation between a data item and a quality of a material entity where the material entity is the specified output of a material transformation which achieves an objective specification that indicates the intended value of the specified quality.
has curation status: IAO_0000120
sub property of: is about

quality is specified as
type: ObjectProperty
editor note: 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship
term editor: Person:Alan Ruttenberg
term editor: Person:Bjoern Peters
definition: inverse of the relation of is quality specification of
has curation status: IAO_0000120
inverse of: is quality specification of

has time stamp
type: ObjectProperty
type: FunctionalProperty
term editor: Alan Ruttenberg
definition: relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken
sub property of: has part
has curation status: IAO_0000123
range: time measurement datum
domain: time stamped measurement datum

has measurement datum
type: ObjectProperty
term editor: Alan Ruttenberg
definition: relates a time stamped measurement datum to the measurement datum that was measured
sub property of: has part
has curation status: IAO_0000123
domain: time stamped measurement datum
range: Class
  intersection of: measurement datum
  intersection of: Class
    complement of: time measurement datum

provides_service_consumer_with
type: ObjectProperty
sub property of: has part
domain: service

is_supported_by_data
type: ObjectProperty
definition source: Philly 2011 workshop
definition: The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process
example of usage: The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA.
range: data item
domain: conclusion textual entity

obsolete_is_concretization_of
type: ObjectProperty
definition: Is a relationship between a generically dependent continuant and a specifically dependent continuant. A generically dependent continuant may inhere in more than one entity. It does so by virtue of the fact that there is, for each entity that it inheres, a specifically dependent *concretization* of the generically dependent continuant that is specifically dependent. For instance, consider a story, which is an information artifact that inheres in some number of books. Each book bears some quality that carries the story. The relation between this quality and the generically dependent continuant is that the former is the concretization of the latter.
term editor: PERSON: Alan Ruttenburg
term editor: PERSON: Barry Smith
editor preferred term: is_concretization_of
editor note: replaced by: http://purl.obolibrary.org/obo/BFO_0000059
deprecated: true
has obsolescence reason: IAO_0000228
sub property of: ObsoleteProperty

is_specified_input_of
type: ObjectProperty
term editor: PERSON:Bjoern Peters
editor preferred term: is_specified_input_of
definition: A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
term editor: Alan Ruttenberg
example of usage: some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
sub property of: participates in
range: planned process
inverse of: has_specified_input

obsolete_is_concretized_as
type: ObjectProperty
definition: Is a relationship between a specifically dependent continuant and a generically dependent continuant. A generically dependent continuant may inhere in more than one entity. It does so by virtue of the fact that there is, for each entity that it inheres, a specifically dependent *concretization* of the generically dependent continuant that is specifically dependent. For instance, consider a story, which is an information artifact that inheres in some number of books. Each book bears some quality that carries the story. The relation between this quality and the generically dependent continuant is that the former is the concretization of the latter.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Barry Smith
editor preferred term: is_concretized_as
editor note: replaced by: http://purl.obolibrary.org/obo/BFO_0000058
deprecated: true
has obsolescence reason: IAO_0000228
sub property of: ObsoleteProperty

obsolete_has_quality
type: ObjectProperty
definition: A relation between an entity and a quality. For types: E has_quality Q iff: for any eEt, exists qQt such that q inheres_in e at t. For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Quality [GOC:cjm]
term editor: GROUP:OBI:<http://obi.sourceforge.net>
term editor: PERSON: Chris Mungall
editor preferred term: has_quality
editor note: replaced by: http://purl.obolibrary.org/obo/BFO_0000086
deprecated: true
has curation status: IAO_0000122
has obsolescence reason: IAO_0000228
sub property of: ObsoleteProperty

obsolete_is_realized_by
type: ObjectProperty
term editor: GROUP:OBI:<http://obi.sourceforge.net>
term editor: PERSON: Chris Mungall
definition: Relation between a realizable and a process. Reciprocal relation of realizes [GOC:cjm]
alternative term: executed_during
alternative term: has_realization
alternative term: is_realized_as
editor preferred term: is_realized_by
editor note: replaced by http://purl.obolibrary.org/obo/BFO_0000054: 'is realized by'
deprecated: true
has curation status: IAO_0000122
has obsolescence reason: IAO_0000228
sub property of: ObsoleteProperty

obsoleted_has_specified_output_information
type: ObjectProperty
term editor: PERSON: Frank Gibson
editor preferred term: obsoleted_has_specified_output_information
deprecated: true
definition: A relation between a participant in a process, that produces a data set . The process is the realization of a concretization of a realizable information entity (objective specification or plan specification). In general, not all data present at the end of the process are specified_data.
term editor: PERSON: Alan Ruttenberg
sub property of: ObsoleteProperty

is_manufactured_by
type: ObjectProperty
term editor: Alan Ruttenberg
term editor: Liju Fan
definition: c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the "Manufacturer Role", and those people/and or machines were members or of directed by the organization to do this.
alternative term: has_make
alternative term: has_manufacturer
example of usage: http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities)
editor preferred term: is_manufactured_by
domain: material entity
range: Class
  union of: Homo sapiens
  union of: organization

obsolete_has_function
type: ObjectProperty
term editor: GROUP:OBI:<http://obi.sourceforge.net>
term editor: PERSON: Chris Mungall
definition: Relation between an independent continuant and a function.
editor preferred term: has_function
example of usage: heart has_function to-pump-blood
editor note: replaced by: http://purl.obolibrary.org/obo/BFO_0000085
deprecated: true
has curation status: IAO_0000122
has obsolescence reason: IAO_0000228
sub property of: ObsoleteProperty

obsoleted_is_reagent_in
type: ObjectProperty
editor preferred term: obsoleted_is_reagent_in
deprecated: true
term editor: Alan Ruttenberg
definition: Relationship between a substance and a protocol application in which it participates, where the substance has a ReagentRole
example of usage: some Triton X-100 (Sigma-Aldrich) is_reagent_in instance of Chromium Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
sub property of: ObsoleteProperty

obsolete_realizes
type: ObjectProperty
term editor: GROUP:OBI:<http://obi.sourceforge.net>
term editor: PERSON: Chris Mungal
definition: Relation between a process and a function, where the unfolding of the process requires the execution of the function. Class level: P realizes F iff: given any p that instantiates P, there exists some f, t such that f instantiates F at t and p *realizes* f. Here, *realizes* is the primitive instance level relation [GOC:cjm]
example of usage: example of usage: The process of 'histidine catabolism' (GO:0006548) realizes the function 'histidine ammonia lyase activity' (GO:0004397) (note: here 'activity' denotes a function and not a process). We leave open the possibility of defining in future the sub-relations directly_realizes (as bewteen a function and it's functioning) and indirectly_realizes.
alternative term: executes
alternative term: has_function_part
alternative term: involves_execution_of
alternative term: is_realization_of
editor preferred term: realizes
editor note: replaced by http://purl.obolibrary.org/obo/BFO_0000055: 'realizes'
deprecated: true
has curation status: IAO_0000122
has obsolescence reason: IAO_0000228
sub property of: ObsoleteProperty

obsoleted_utilizes_reagent
type: ObjectProperty
editor preferred term: obsoleted_utilizes_reagent
deprecated: true
term editor: Alan Ruttenberg
definition: Relationship between a protocol application and a substance that has role reagent that participates in the protocol application
example of usage: see example_of_usage for is_reagent_in
sub property of: ObsoleteProperty

obsoleted_is_device_for
type: ObjectProperty
editor preferred term: obsoleted_is_device_for
deprecated: true
term editor: Alan Ruttenberg
definition: Relationship between a device and a protocol application in which it participates
example of usage: some LKB 1272 Clinigamma counter is_device_for instance of Chromium Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
sub property of: ObsoleteProperty

is_specified_output_of
type: ObjectProperty
term editor: PERSON:Bjoern Peters
editor preferred term: is_specified_output_of
definition: A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
term editor: Alan Ruttenberg
sub property of: participates in
range: planned process

obsoleted_utilizes_device
type: ObjectProperty
editor preferred term: obsoleted_utilizes_device
deprecated: true
term editor: Alan Ruttenberg
definition: Relationship between protocol application and an intrument in which it participates
example of usage: see example_of_usage for is_device_for
sub property of: ObsoleteProperty

is_proxy_for
type: ObjectProperty
editor preferred term: is_proxy_for
editor note: A relation between continuant instances c1 and c2 where within a protocol application, measurement of c1 is related to a what would be the measurement of c2. (another definition)
definition: A relation between continuant instances c1 and c2 where within an experiment/ protocol application, measurement of c1 is used to determine what a measurement of c2 would be.
term editor: Alan Ruttenberg
example of usage: position on a gel is_proxy_for mass and charge of molecule in an western blot. Florescent intensity is_proxy_for amount of protein labeled with GFP. Examples: A260/A280 (of a DNA sample) is_proxy_for DNA-purity. NMR Sample scan is a proxy for sample quality. Within the assay mentioned here: https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay level of radioactivity is_proxy_for level of toxicity
range: continuant
domain: continuant

obsoleted_has_specified_input_information
type: ObjectProperty
term editor: PERSON: Frank Gibson
alternative term: consumes data
editor preferred term: has specified input information
deprecated: true
definition: A relation between a process and a participant in that process, that consumes a data set . The process is the realization of a concretization of a directive information entity (objective specification or plan specification). In general, not all data present at the beginning of the process are specified_data.
term editor: PERSON:Alan Ruttenberg
sub property of: ObsoleteProperty

obsolete_has_role
type: ObjectProperty
definition: A relation between a continuant C and a role R. The reciprocal relation of role_of.
term editor: GROUP:OBI:<http://obi.sourceforge.net>
term editor: PERSON:Chris Mungal
editor preferred term: has_role
editor note: replaced by: http://purl.obolibrary.org/obo/BFO_0000087
deprecated: true
has curation status: IAO_0000122
has obsolescence reason: IAO_0000228
sub property of: ObsoleteProperty

obsolete_results_from
type: ObjectProperty
editor note: 2009/11/23: BP, dev call:o bsoleted as discussed in tracker https://sourceforge.net/tracker/?func=detail&aid=2899860&group_id=177891&atid=886178 . Should be replaced by instead creating defined classes for materials, which are specified output of the process that conveys the
editor preferred term: obsolete_results_from
deprecated: true
has obsolescence reason: IAO_0000103
sub property of: ObsoleteProperty

achieves_planned_objective
type: ObjectProperty
example of usage: A cell sorting process achieves the objective specification 'material separation objective'
term editor: BP, AR, PPPB branch
definition source: PPPB branch derived
definition: This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.
editor preferred term: achieves_planned_objective
curator note: modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
range: objective specification
domain: planned process

obsoleted_is_specified_information_output_of
type: ObjectProperty
definition: A relation between a data set and the process in which it participates and was produced. Inverse of outputs_specified_data relation.
definition source: Editor
term editor: PERSON: James Malone
editor note: is replaced by has_specified_output_of
editor preferred term: is_specified_information_output_of
deprecated: true
sub property of: ObsoleteProperty

has grain
type: ObjectProperty
definition source: PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
editor preferred term: has grain
definition: the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car.
editor note: Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form
term editor: PERSON: Alan Ruttenberg
sub property of: has part

obsoleted_is_specified_information_intput_of
type: ObjectProperty
definition: Is the inverse relation of has_specfied_input_information
editor note: is replaced by is_specified_intput_of
editor preferred term: obsoleted_is_specified_information_intput_of
deprecated: true
sub property of: ObsoleteProperty

is grain of
type: ObjectProperty
editor preferred term: is grain of
definition source: Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
term editor: PERSON: Alan Ruttenberg
sub property of: is part of

supplies
type: ObjectProperty
definition: A relation between an organisation or person and a material entity who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner.
term editor: GROUP: Relations branch
editor preferred term: supplies

has_supplier
type: ObjectProperty
definition: A relation between a material entity and an organisation or person who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner.
term editor: PERSON: Alan Rutternberg
term editor: PERSON: Cristian Cocos
term editor: PERSON: Frank Gibson
term editor: PERSON: Melanie Courtot
editor preferred term: has_supplier
domain: material entity
has curation status: IAO_0000120
inverse of: supplies
range: Class
  union of: Homo sapiens
  union of: organization

objective_achieved_by
type: ObjectProperty
definition: This relation obtains between a a objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
editor note: definition needs clean up to indicate directionality
editor preferred term: objective_achieved_by
domain: objective specification
range: planned process
inverse of: achieves_planned_objective

is member of organization
type: ObjectProperty
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
editor note: 2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a population
editor note: JZ: Discussed on May 7, 2012 OBI dev call. Bjoern points out that we need to allow for organizations to be members of organizations. And agreed by the other OBI developers. So, human and organization were specified in 'Domains'. The textual definition was updated based on it.
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
definition source: Person:Helen Parkinson
term editor: Person:Helen Parkinson
definition: Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization.
editor preferred term: is member of organization
range: organization
domain: Class
  union of: Homo sapiens
  union of: organization

has category label
type: ObjectProperty
editor preferred term: has category label
sub property of: has part
domain: categorical measurement datum
range: categorical label

has disposition to bind
type: ObjectProperty
type: SymmetricProperty
definition: A relationship between two material entitites that each have disposition to form a complex with the other.
definition source: IEDB
editor note: This is a shortcut relation, and should expand to say that the two material entities have dispositions, point to the process in which they from a complex that realizes those dispositions, and points to the complex in which the two entities are 'bound to' each other
editor preferred term: has disposition to bind
domain: material entity
range: material entity

has organization member
type: ObjectProperty
term editor: Person: Jie Zheng
definition: Relating an organization to a legal person or organization.
editor note: See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_id=177891&atid=886178
domain: organization
inverse of: is member of organization
range: Class
  union of: Homo sapiens
  union of: organization

process is result of
type: ObjectProperty
term editor: IEDB
term editor: PERSON:Bjoern Peters
example of usage: The production of IFN-gamma by effector T cells is a process result of T cell stimulation through the TCR
definition: is a relationship between a process and a preceding occurrent that directly caused the later one to occur
editor preferred term: process is result of
range: occurrent
domain: occurrent
sub property of: is immediately preceded by

obsolete_is_described_by
type: ObjectProperty
editor preferred term: is_described_by
deprecated: true
has obsolescence reason: IAO_0000103
sub property of: ObsoleteProperty

bound_to
type: ObjectProperty
editor preferred term: bound_to

derives from
type: ObjectProperty
editor preferred term: derives from
range: independent continuant
domain: independent continuant
imported from: ro.owl
sub property of: topObjectProperty

spatially disjoint from
type: ObjectProperty
editor preferred term: spatially disjoint from
expand expression to: BFO_0000051 exactly 0 (BFO_0000050 some ?Y)
definition: A is spatially_disjoint_from B if and only if they have no parts in common
term editor: Chris Mungall
imported from: ro.owl

surrounded by
type: ObjectProperty
editor preferred term: surrounded by
definition: x surrounded_by y if and only if x is adjacent to y and for every region r that is adjacent to x, r overlaps y
sub property of: adjacent to
imported from: ro.owl

temporal relation
type: ObjectProperty
editor note: move to BFO?
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
definition source: Allen
range: occurrent
has curation status: IAO_0000125

starts
type: ObjectProperty
definition: inverse of starts with
term editor: Chris Mungall
definition source: Allen
sub property of: is part of
has curation status: IAO_0000125
sub property of: temporal relation

starts with
type: ObjectProperty
type: TransitiveProperty
alternative term: started by
definition: x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
example of usage: Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
sub property of: has part
has curation status: IAO_0000125
sub property of: temporal relation
inverse of: starts

has measurement value
type: DatatypeProperty
type: FunctionalProperty
domain: scalar measurement datum
range: float

has x coordinate value
type: DatatypeProperty
type: FunctionalProperty
domain: cartesian spatial coordinate datum
range: float

has z coordinate value
type: DatatypeProperty
type: FunctionalProperty
domain: cartesian spatial coordinate datum
range: float

has y coordinate value
type: DatatypeProperty
type: FunctionalProperty
domain: cartesian spatial coordinate datum
range: float

has_feature_value
type: DatatypeProperty
editor preferred term: has_feature_value
term editor: James Malone
definition: has_feature_value datatype property is used to describe the feature values which the feature class can contain, for example has_base can have feature values of nonNegativeInteger values.
domain: OBI_0200140

entity
type: Class
subclass of: Thing
disjoint with: ObsoleteClass
editor preferred term: entity

continuant
type: Class
subclass of: entity
definition: An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
example of usage: a heart
example of usage: a person
example of usage: a symphony orchestra
editor preferred term: continuant
alternative term: endurant
example of usage: the color of a tomato
example of usage: the disposition of blood to coagulate
example of usage: the lawn and atmosphere in front of our building
example of usage: the mass of a cloud

occurrent
type: Class
subclass of: entity
definition: An entity that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants.
example of usage: a surgical operation as processual context for a nosocomical infection
editor preferred term: occurrent
alternative term: perdurant
example of usage: the life of an organism
example of usage: the most interesting part of Van Gogh's life
example of usage: the spatiotemporal context occupied by a process of cellular meiosis
example of usage: the spatiotemporal region occupied by the development of a cancer tumor

independent continuant
type: Class
subclass of: continuant
definition: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
example of usage: a chair
example of usage: a heart
example of usage: a leg
example of usage: a person
example of usage: a symphony orchestra
example of usage: an organism
editor preferred term: independent continuant
alternative term: substantial entity
example of usage: the bottom right portion of a human torso
example of usage: the lawn and atmosphere in front of our building

dependent continuant
type: Class
subclass of: continuant
definition: A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities.
editor preferred term: dependent continuant

spatial region
type: Class
subclass of: continuant
definition: A continuant that is neither bearer of quality entities nor inheres in any other entities.
editor note: All instances of continuant [snap:Continuant] are spatial entities, that is, they enter in the relation of (spatial) location with spatial region [snap:SpatialRegion] entities. As a particular case, the exact spatial location of a spatial region [snap:SpatialRegion] is this region itself.
editor note: An instance of spatial region [snap:SpatialRegion] is a part of space. All parts of space are spatial region [snap:SpatialRegion] entities and only spatial region [snap:SpatialRegion] entities are parts of space. Space is the entire extent of the spatial universe, a designated individual, which is thus itself a spatial region [snap:SpatialRegion].
editor note: Space and spatial region [snap:SpatialRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of space is sometimes called "absolutist" or "the container view". In BFO, the class site [snap:Site] allows for a so-called relational view of space, that is to say, a view according to which spatiality is a matter of relative location between entities and not a matter of being tied to space. The bridge between these two views is secured through the fact that while instances of site [snap:Site] are not spatial region [snap:SpatialRegion] entities, they are nevertheless spatial entities.
example of usage: parts of the sum total of all space in the universe
editor preferred term: spatial region
example of usage: the sum total of all space in the universe

process
type: Class
subclass of: occurrent
definition: A processual entity that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities.
editor preferred term: process
example of usage: the life of an organism
example of usage: the process of cell-division
example of usage: the process of sleeping

temporal region
type: Class
subclass of: occurrent
editor note: All instances of occurrent [span:Occurrent] are temporal entities, that is, they enter in the relation of (temporal) location with temporal region [span:TemporalRegion] entities. As a particular case, the exact spatiotemporal location of a temporal region [span:TemporalRegion] is this region itself. Continuant [snap:Continuant] entities are not temporal entities in the technical sense just explained; they are related to time in a different way, not through temporal location but through a relation of existence at a time or during a period of time (see continuant [snap:Continuant].
editor note: An instance of temporal region [span:TemporalRegion] is a part of time. All parts of time are temporal region [span:TemporalRegion] entities and only temporal region [span:TemporalRegion] entities are parts of time. Time is the entire extent of the temporal universe, a designated individual, which is thus a temporal region itself.
definition: An occurrent that is part of time.
editor note: Time and temporal region [span:TemporalRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of time can be called "absolutist" or "the container view" in analogy to what is traditionally the case with space (see spatial region [snap:SpatialRegion].
editor preferred term: temporal region
example of usage: the duration of a surgical procedure
example of usage: the moment of death
example of usage: the time it takes to run a marathon

two dimensional region
type: Class
subclass of: spatial region
definition: A spatial region with two dimensions.
example of usage: the surface of a cube-shaped part of space
example of usage: the surface of a rectilinear planar figure-shaped part of space
example of usage: the surface of a sphere-shaped part of space
editor preferred term: two dimensional region

disposition
type: Class
subclass of: realizable entity
definition: A realizable entity that essentially causes a specific process or transformation in the object in which it inheres, under specific circumstances and in conjunction with the laws of nature. A general formula for dispositions is: X (object has the disposition D to (transform, initiate a process) R under conditions C.
editor preferred term: disposition
example of usage: the disposition of a patient with a weakened immune system to contract disease
example of usage: the disposition of a vase to brake if dropped
example of usage: the disposition of blood to coagulate
example of usage: the disposition of metal to conduct electricity
example of usage: the disposition of vegetables to decay when not refrigerated

realizable entity
type: Class
subclass of: specifically dependent continuant
definition: A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
editor note: If a realizable entity [snap:RealizableEntity] inheres in a continuant [snap:Continuant], this does not imply that it is actually realized.
editor preferred term: realizable entity
example of usage: the disposition of blood to coagulate
example of usage: the disposition of metal to conduct electricity
example of usage: the function of the reproductive organs
example of usage: the role of being a doctor

zero dimensional region
type: Class
subclass of: spatial region
definition: A spatial region with no dimensions.
example of usage: a point
editor preferred term: zero dimensional region

quality
type: Class
subclass of: specifically dependent continuant
definition: A specifically dependent continuant that is exhibited if it inheres in an entity or entities at all (a categorical property).
editor preferred term: quality
example of usage: the ambient temperature of air
example of usage: the circumference of a waist
example of usage: the color of a tomato
example of usage: the mass of a piece of gold
example of usage: the shape of a nose
example of usage: the weight of a chimpanzee

specifically dependent continuant
type: Class
subclass of: dependent continuant
definition: A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
alternative term: mode
alternative term: property
editor preferred term: specifically dependent continuant
example of usage: the color of a tomato
example of usage: the disposition of fish to decay
example of usage: the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc.
example of usage: the liquidity of blood
example of usage: the mass of a cloud
example of usage: the role of being a doctor
example of usage: the smell of mozzarella
alternative term: trope

temporal instant
type: Class
subclass of: connected temporal region
definition: A connected temporal region comprising a single moment of time.
example of usage: right now
editor preferred term: temporal instant
example of usage: the moment at which a child is born
example of usage: the moment at which a finger is detached in an industrial accident
example of usage: the moment of death

connected temporal region
type: Class
subclass of: temporal region
definition: A temporal region every point of which is mediately or immediately connected with every other point of which.
editor preferred term: connected temporal region
example of usage: the 1970s years
example of usage: the time from the beginning to the end of a heart attack
example of usage: the time taken up by cellular meiosis

role
type: Class
subclass of: realizable entity
definition: A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
editor preferred term: role
example of usage: the role of a biological grandfather as legal guardian in the context of a system of laws
example of usage: the role of a chemical compound in an experiment
example of usage: the role of a patient relative as defined by a hospital administrative form
example of usage: the role of a person as a surgeon
example of usage: the role of a student in a university
example of usage: the role of a woman as a legal mother in the context of system of laws
example of usage: the role of ingested matter in digestion

object boundary
type: Class
subclass of: independent continuant
definition: An independent continuant that is a lower dimensional part of a spatial entity, normally a closed two-dimensional surface. Boundaries are those privileged parts of object entities that exist at exactly the point where the object is separated off from the rest of the existing entities in the world.
editor note: Boundaries are theoretically difficult entities to account for, however the intuitive notion of a physical boundary as a surface of some sort (whether inside or outside of a thing) will generally serve as a good guide for the use of this universal.
editor preferred term: object boundary
alternative term: substance boundary
example of usage: the outer surface of a cell or cell wall
example of usage: the surface of the earth
example of usage: the surface of the interior of the stomach
example of usage: the surface of the skin

one dimensional region
type: Class
subclass of: spatial region
definition: A spatial region with one dimension.
example of usage: an edge of a cube-shaped part of space
editor preferred term: one dimensional region
example of usage: the part of space that is a line stretching from one end of absolute space to the other

three dimensional region
type: Class
subclass of: spatial region
definition: A spatial region with three dimensions.
example of usage: a cube-shaped part of space
example of usage: a sphere-shaped part of space
editor preferred term: three dimensional region

site
type: Class
subclass of: independent continuant
definition: An independent continuant consisting of a characteristic spatial shape in relation to some arrangement of other continuant entities and of the medium which is enclosed in whole or in part by this characteristic spatial shape. Site entities are entities that can be occupied by other continuant entities.
editor note: An instance of Site [snap:Site] is a mixture of independent continuant [snap:IndependentContinuant] entities which act as surrounding environments for other independent continuant [snap:IndependentContinuant] entities, most importantly for instances of object [snap:Object]. A site [snap:Site] is typically made of object [snap:Object] or fiat object part [snap:FiatObjectPart] entities and a surrounding medium in which is found an object [snap:Object] occupying the site [snap:Site]. Independent continuant [snap:IndependentContinuant] entities may be associated with others (which, then, are sites) through a relation of "occupation". That relation is connected to, but distinct from, the relation of spatial location. Site [snap:Site] entities are not to be confused with spatial region [snap:SpatialRegion] entities. In BFO, site [snap:Site] allows for a so-called relational view of space which is different from the view corresponding to the class spatial region [snap:SpatialRegion] (see the comment on this class).
example of usage: Maria's nostril or her intestines for a variety of bacteria
example of usage: a particular room in a particular hospital
editor preferred term: site

generically dependent continuant
type: Class
subclass of: dependent continuant
definition: A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
example of usage: a certain PDF file that exists in different and in several hard drives
editor preferred term: generically dependent continuant

scattered temporal region
type: Class
subclass of: temporal region
definition: A temporal region every point of which is not mediately or immediately connected with every other point of which.
editor preferred term: scattered temporal region
example of usage: the time occupied by the individual games of the World Cup
example of usage: the time occupied by the individual liaisons in a romantic affair

function
type: Class
subclass of: disposition
definition: A realizable entity the manifestation of which is an essentially end-directed activity of a continuant entity in virtue of that continuant entity being a specific kind of entity in the kind or kinds of contexts that it is made for.
editor preferred term: function
example of usage: the digestive function of the stomach to nutriate the body
example of usage: the function of a birth canal to enable transport
example of usage: the function of a computer program to compute mathematical equations
example of usage: the function of a hammer to drive in nails
example of usage: the function of a judge in a court of law
example of usage: the function of an automobile to provide transportation
example of usage: the function of reproduction in the transmission of genetic material
example of usage: the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc.

process boundary
type: Class
subclass of: occurrent
definition: A processual entity that is the fiat or bona fide instantaneous temporal process boundary.
example of usage: birth
example of usage: death
editor preferred term: process boundary
example of usage: the detaching of a finger in an industrial accident
example of usage: the final separation of two cells at the end of cell-division
example of usage: the forming of a synapse
example of usage: the incision at the beginning of a surgery
example of usage: the onset of REM sleep

temporal interval
type: Class
subclass of: connected temporal region
definition: A connected temporal region lasting for more than a single moment of time.
example of usage: any continuous temporal duration during which a process occurs
editor preferred term: temporal interval

material entity
type: Class
subclass of: independent continuant
definition: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
editor note: Examples: collection of random bacteria, a chair, dorsal surface of the body
editor note: Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology.
editor preferred term: material entity

portion of organism substance
type: Class
subclass of: gross anatomical part
definition: Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.
editor preferred term: portion of organism substance
imported from: caro.owl

portion of tissue
type: Class
subclass of: gross anatomical part
definition: Anatomical structure, that consists of similar cells and intercellular matrix, aggregated according to genetically determined spatial relationships. [database_cross_reference: CARO:MAH]
editor preferred term: portion of tissue
imported from: caro.owl

multi-tissue structure
type: Class
subclass of: gross anatomical part
definition: Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types.
editor preferred term: multi-tissue structure
imported from: caro.owl

epithelium
type: Class
subclass of: portion of tissue
definition: Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina.
editor preferred term: epithelium
imported from: caro.owl

gross anatomical part
type: Class
subclass of: material entity
definition: Anatomical structure that is part of a multicellular organism and is at the gross anatomical level, e.g. above the level of a cell. Included are portions of organism substances such as blood, multi-cell-part structures such as axon tracts, acellular anatomical structures such as hair, and organism subdivisions such as head. Excluded is the whole organism and more granular parts of the organism, such as atoms, molecules, macromolecular complexes and cells.
editor preferred term: gross anatomical part
imported from: caro.owl

water
type: Class
subclass of: molecular entity
definition: An inorganic hydroxy compound that has formula H2O.
editor preferred term: water
imported from: chebi.owl

biotin
type: Class
subclass of: molecular entity
subclass of: Restriction
  on property: has role
  some values from: label role
definition: A biotin that has formula C10H16N2O3S.
editor preferred term: biotin
imported from: chebi.owl

peptide
type: Class
subclass of: macromolecule
definition: Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid.
editor preferred term: peptide
imported from: chebi.owl

deoxyribonucleic acids
type: Class
subclass of: nucleic acid
definition: High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
editor preferred term: deoxyribonucleic acids
imported from: chebi.owl

hydrogensulfite
type: Class
subclass of: molecular entity
definition: A sulfur oxoanion that has formula HO3S.
editor preferred term: hydrogensulfite
imported from: chebi.owl

glucose
type: Class
subclass of: molecular entity
editor preferred term: glucose
imported from: chebi.owl

5'-adenylyl sulfate
type: Class
subclass of: molecular entity
editor preferred term: 5'-adenylyl sulfate
definition: An acyl sulfate that has formula C10H14N5O10PS.
imported from: chebi.owl

molecular entity
type: Class
subclass of: material entity
definition: Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
editor note: We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well
editor preferred term: molecular entity
imported from: chebi.owl

cytochalasin
type: Class
subclass of: molecular entity
editor preferred term: cytochalasin
imported from: chebi.owl

N-ethyl-N-nitrosourea
type: Class
subclass of: molecular entity
editor preferred term: N-ethyl-N-nitrosourea
imported from: chebi.owl

proton
type: Class
subclass of: molecular entity
definition: Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u.
editor preferred term: proton
imported from: chebi.owl

luciferin
type: Class
subclass of: molecular entity
definition: A low-molecular-mass compound present in bioluminescent organisms that emits light when oxidized in presence of enzyme luciferase.
editor preferred term: luciferin
imported from: chebi.owl

sodium chloride
type: Class
subclass of: molecular entity
definition: An inorganic chloride salt that has formula ClNa.
editor preferred term: sodium chloride
imported from: chebi.owl

lead(0)
type: Class
subclass of: molecular entity
definition: An elemental lead that has formula Pb.
editor preferred term: lead(0)
imported from: chebi.owl

acrylamide
type: Class
subclass of: molecular entity
definition: An acrylamide that has formula C3H5NO.
editor preferred term: acrylamide
imported from: chebi.owl

hydroxyl
type: Class
subclass of: molecular entity
definition: A reactive oxygen specy that has formula HO.
editor preferred term: hydroxyl
imported from: chebi.owl

ruthenium
type: Class
subclass of: molecular entity
definition: An iron group element that has formula Ru.
editor preferred term: ruthenium
imported from: chebi.owl

fluorescein
type: Class
subclass of: molecular entity
subclass of: Restriction
  on property: has role
  some values from: label role
definition: A xanthene dye that has formula C20H12O5.
editor preferred term: fluorescein
imported from: chebi.owl

gadodiamide hydrate
type: Class
subclass of: molecular entity
editor preferred term: gadodiamide hydrate
imported from: chebi.owl

gadoteridol
type: Class
subclass of: molecular entity
editor preferred term: gadoteridol
imported from: chebi.owl

phenolsulfonphthalein
type: Class
subclass of: molecular entity
editor preferred term: phenolsulfonphthalein
imported from: chebi.owl

sodium citrate dihydrate
type: Class
subclass of: molecular entity
editor preferred term: sodium citrate dihydrate
imported from: chebi.owl

rhodium
type: Class
subclass of: molecular entity
definition: A cobalt group element that has formula Rh.
editor preferred term: rhodium
imported from: chebi.owl

gadolinium
type: Class
subclass of: molecular entity
definition: A lanthanoid that has formula Gd.
editor preferred term: gadolinium
imported from: chebi.owl

terbium
type: Class
subclass of: molecular entity
definition: A lanthanoid that has formula Tb.
editor preferred term: terbium
imported from: chebi.owl

nucleic acid
type: Class
subclass of: macromolecule
definition: A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
editor preferred term: nucleic acid
imported from: chebi.owl

ribonucleic acids
type: Class
subclass of: nucleic acid
definition: Naturally occurring polyribonucleotides.
editor preferred term: ribonucleic acids
imported from: chebi.owl

amino acids
type: Class
subclass of: molecular entity
definition: Carboxylic acids containing one or more amino groups.
editor preferred term: amino acids
imported from: chebi.owl

macromolecule
type: Class
subclass of: molecular entity
definition: A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
editor preferred term: macromolecule
alternative term: polymer
imported from: chebi.owl

gadolinium molecular entities
type: Class
subclass of: molecular entity
editor preferred term: gadolinium molecular entities
imported from: chebi.owl

gadodiamide
type: Class
subclass of: molecular entity
definition: A gadolinium coordination entity that has formula C16H26GdN5O8.
editor preferred term: gadodiamide
imported from: chebi.owl

sodium phosphates
type: Class
subclass of: molecular entity
editor preferred term: sodium phosphates
imported from: chebi.owl

phosphorus-32
type: Class
subclass of: molecular entity
subclass of: Restriction
  on property: has role
  some values from: label role
definition: The radioactive isotope of phosphorus with relative atomic mass 31.973907 and half-life of 14.26 days.
editor preferred term: phosphorus-32
imported from: chebi.owl

phosphorus-33
type: Class
subclass of: molecular entity
subclass of: Restriction
  on property: has role
  some values from: label role
definition: The radioactive isotope of phosphorus with relative atomic mass 32.971725, half-life of 25.34 days and nuclear spin (1)/2.
editor preferred term: phosphorus-33
imported from: chebi.owl

Cy3 dye
type: Class
subclass of: molecular entity
subclass of: Restriction
  on property: has role
  some values from: label role
editor preferred term: Cy3 dye
imported from: chebi.owl

Cy5 dye
type: Class
subclass of: molecular entity
subclass of: Restriction
  on property: has role
  some values from: label role
editor preferred term: Cy5 dye
imported from: chebi.owl

digoxigenin
type: Class
subclass of: molecular entity
subclass of: Restriction
  on property: has role
  some values from: label role
definition: A 12beta-hydroxy steroid that has formula C23H34O5.
editor preferred term: digoxigenin
imported from: chebi.owl

ethylenediaminetetraacetic acid
type: Class
subclass of: molecular entity
definition: A tetracarboxylic acid that has formula C10H16N2O8.
editor preferred term: ethylenediaminetetraacetic acid
imported from: chebi.owl

double-stranded DNA
type: Class
subclass of: deoxyribonucleic acids
editor preferred term: double-stranded DNA
imported from: chebi.owl

5-bromo-2-deoxyuridine
type: Class
subclass of: molecular entity
editor preferred term: 5-bromo-2-deoxyuridine
imported from: chebi.owl

chromium-51
type: Class
subclass of: molecular entity
definition: A synthetic radioactive isotope of chromium having a half-life of 27.7 days and decaying by electron capture with emission of gamma rays (0.32 MeV); it is used to label red blood cells for measurement of mass or volume, survival time, and sequestration studies, for the diagnosis of gastrointestinal bleeding, and to label platelets to study their survival.
editor preferred term: chromium-51
imported from: chebi.owl

Alexa Fluor 532
type: Class
subclass of: molecular entity
subclass of: Restriction
  on property: has role
  some values from: label role
editor preferred term: Alexa Fluor 532
definition: An organosulfonic acid that has formula C34H33N3O11S2.
imported from: chebi.owl

Alexa Fluor 546
type: Class
subclass of: molecular entity
subclass of: Restriction
  on property: has role
  some values from: label role
editor preferred term: Alexa Fluor 546
definition: An organic heteropentacyclic compound that has formula C44H45Cl3N4NaO14S3.
imported from: chebi.owl

Alexa Fluor 555
type: Class
subclass of: molecular entity
subclass of: Restriction
  on property: has role
  some values from: label role
definition: A fluorescent dye of absorption wavelength 555 nm and emission wavelength 565 nm, derived from a 3,6-diaminoxanthene-4,5-disulfate.
editor preferred term: Alexa Fluor 555
imported from: chebi.owl

tritiated thymidine
type: Class
subclass of: molecular entity
definition: 3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 3,5-dibromo-4-hydroxyphenyl groups. It is used as a laboratory indicator, changing from yellow below pH 3 to purple at pH 4.6, and as a size marker for monitoring the progress of agarose gel and polyacrylamide gel electrophoresis. It has also been used as an industrial dye.
editor preferred term: tritiated thymidine
imported from: chebi.owl

Dimethyl sulfate
type: Class
subclass of: molecular entity
editor preferred term: Dimethyl sulfate
definition: The dimethyl ester of sulfuric acid
imported from: chebi.owl

Diethylpyrocarbonate
type: Class
subclass of: molecular entity
editor preferred term: Diethylpyrocarbonate
definition: The diethyl ester of dicarbonic acid
imported from: chebi.owl

1,1-dihydroxy-3-ethoxy-2-butanone
type: Class
subclass of: molecular entity
editor preferred term: 1,1-dihydroxy-3-ethoxy-2-butanone
definition: A butanone derivative having two hydroxy substituents at the 1-position and an ethoxy substituent at the 3-position.
imported from: chebi.owl

N-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimide
type: Class
subclass of: molecular entity
definition: A carbodiimide having cyclcohexyl and 2-(4-morpholinyl)ethyl as the two N-substituents.
editor preferred term: N-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimide
imported from: chebi.owl

N-methylisatoic anhydride
type: Class
subclass of: molecular entity
definition: A 3,1-benzoxazin-1,4-dione having an N-methyl substituent.
editor preferred term: N-methylisatoic anhydride
imported from: chebi.owl

Fe-BABE
type: Class
subclass of: molecular entity
definition: A tetracarboxylic acid consisting of ethylenediaminetetraacetic acid having a 4-bromoacetamidobenzyl group at the C1-position and (S)-configuration.
editor preferred term: Fe-BABE
imported from: chebi.owl

EDTA methidiumpropylamide
type: Class
subclass of: molecular entity
definition: A combined intercalating and chelating reagent. The iron chelate, prepared by adding Fe(NH4)2(SO4)2, effects random oxidative cleavage of DNA in the presence of O2 and a reducing agent. This activity is useful as a footprinting probe.
editor preferred term: EDTA methidiumpropylamide
imported from: chebi.owl

bromophenol blue
type: Class
subclass of: molecular entity
definition: A combined intercalating and chelating reagent. The iron chelate, prepared by adding Fe(NH4)2(SO4)2, effects random oxidative cleavage of DNA in the presence of O2 and a reducing agent. This activity is useful as a footprinting probe.
editor preferred term: bromophenol blue
imported from: chebi.owl

tris
type: Class
subclass of: molecular entity
definition: A compound widely used as a biological buffer substance in the pH range 7--9; pKa = 8.3 at 20 degreeC; pKa = 7.82 at 37 degreeC.
editor preferred term: tris
imported from: chebi.owl

cell
type: Class
subclass of: material entity
definition: Anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
example of usage: PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .."
editor preferred term: cell
imported from: cl.owl

fibroblast
type: Class
subclass of: cell
definition: A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped.
editor preferred term: fibroblast
imported from: cl.owl

epithelial cell
type: Class
subclass of: cell
definition: A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina.
editor preferred term: epithelial cell
imported from: cl.owl

T cell
type: Class
subclass of: lymphocyte
definition: A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex.
editor preferred term: T cell
imported from: cl.owl

mast cell
type: Class
subclass of: cell
definition: A cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. Progenitors leave bone marrow and mature in connective and mucosal tissue. Mature mast cells are found in all tissues, except the bloodstream. Their phenotype is CD117-high, CD123-negative, CD193-positive, CD200R3-positive, and FceRI-high. Stem-cell factor (KIT-ligand; SCF) is the main controlling signal of their survival and development.
editor preferred term: mast cell
imported from: cl.owl

hepatocyte
type: Class
subclass of: epithelial cell
definition: The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated.
editor preferred term: hepatocyte
imported from: cl.owl

erythrocyte
type: Class
subclass of: cell
definition: A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen.
editor preferred term: erythrocyte
imported from: cl.owl

macrophage
type: Class
subclass of: cell
definition: A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells.
editor preferred term: macrophage
imported from: cl.owl

B cell
type: Class
subclass of: lymphocyte
definition: A lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
editor preferred term: B cell
imported from: cl.owl

dendritic cell
type: Class
subclass of: cell
definition: A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative).
editor preferred term: dendritic cell
imported from: cl.owl

lymphocyte
type: Class
subclass of: mononuclear cell
definition: A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin.
editor preferred term: lymphocyte
imported from: cl.owl

CD4-positive, alpha-beta T cell
type: Class
subclass of: alpha-beta T cell
definition: A mature alpha-beta T cell that expresses an alpha-beta T cell receptor and the CD4 coreceptor.
editor preferred term: CD4-positive, alpha-beta T cell
imported from: cl.owl

CD8-positive, alpha-beta T cell
type: Class
subclass of: alpha-beta T cell
definition: A T cell expressing an alpha-beta T cell receptor and the CD8 coreceptor.
editor preferred term: CD8-positive, alpha-beta T cell
imported from: cl.owl

basophil
type: Class
subclass of: cell
definition: Any of the immature or mature forms of a granular leukocyte that in its mature form has an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse, bluish-black granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. A basophil is CD123-positive, CD193-positive, CD203c-positive, and FceRIa-positive.
editor preferred term: basophil
imported from: cl.owl

plasma cell
type: Class
subclass of: B cell
definition: A terminally differentiated, post-mitotic, antibody secreting cell of the B cell lineage with the phenotype CD138-positive, surface immunonoglobulin-negative, and MHC Class II-negative. Plasma cells are oval or round with extensive rough endoplasmic reticulum, a well-developed Golgi apparatus, and a round nucleus having a characteristic cartwheel heterochromatin pattern and are devoted to producing large amounts of immunoglobulin.
editor preferred term: plasma cell
imported from: cl.owl

alpha-beta T cell
type: Class
subclass of: T cell
definition: A T cell that expresses an alpha-beta T cell receptor complex.
editor preferred term: alpha-beta T cell
imported from: cl.owl

CD8-positive, alpha-beta cytotoxic T cell
type: Class
subclass of: CD8-positive, alpha-beta T cell
definition: A CD8-positive, alpha-beta T cell that is capable of killing target cells in an antigen specific manner with the phenotype perforin-positive and granzyme B-positive.
editor preferred term: CD8-positive, alpha-beta cytotoxic T cell
imported from: cl.owl

mature NK T cell
type: Class
subclass of: alpha-beta T cell
definition: A mature alpha-beta T cell of a distinct lineage that bears natural killer markers and a T cell receptor specific for a limited set of ligands. NK T cells have activation and regulatory roles particularly early in an immune response.
editor preferred term: mature NK T cell
imported from: cl.owl

mononuclear cell
type: Class
subclass of: cell
definition: A leukocyte with a single non-segmented nucleus in the mature form.
editor preferred term: mononuclear cell
imported from: cl.owl

soil
type: Class
subclass of: material entity
definition: Any material within 2 m from the Earth's surface that is in contact with the atmosphere, with the exclusion of living organisms, areas with continuous ice not covered by other material, and water bodies deeper than 2 m.
editor preferred term: soil
imported from: envo.owl

podzol
type: Class
subclass of: soil
definition: Podzols are soils with a typically ash-grey upper subsurface horizon, bleached by loss of organic matter and iron oxides, on top of a dark accumulation horizon with brown, reddish or black illuviated humus and/or reddish Fe compounds. Podzols occur in humid areas in the boreal and temperate zones and locally also in the tropics.
editor preferred term: podzol
imported from: envo.owl

environmental material
type: Class
subclass of: material entity
definition: Material in or on which organisms may live.
editor preferred term: environmental material
imported from: envo.owl

geographical location
type: Class
subclass of: site
definition: A reference to a place on the Earth, by its name or by its geographical location.
imported from: gaz.owl

antibody-dependent cellular cytotoxicity
type: Class
subclass of: biological_process
definition: Cytolysis of target cells by natural killer cells, eosinophils, neutrophils, monocytes, or macrophages following engagement of antibodies bound to the target cells by Fc receptors on the effector cells.
editor preferred term: antibody-dependent cellular cytotoxicity
imported from: go.owl

type IV hypersensitivity
type: Class
subclass of: hypersensitivity
definition: An inflammatory response driven by T cell recognition of processed soluble or cell-associated antigens leading to cytokine release and leukocyte activation.
editor preferred term: type IV hypersensitivity
imported from: go.owl

cytokine production
type: Class
subclass of: biological_process
definition: The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: cytokine production
imported from: go.owl

cell killing
type: Class
subclass of: biological_process
definition: Any process in an organism that results in the killing of its own cells or those of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions.
editor preferred term: cell killing
imported from: go.owl

T cell mediated cytotoxicity
type: Class
subclass of: cell killing
editor preferred term: T cell mediated cytotoxicity
definition: The directed killing of a target cell by a T cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors.
imported from: go.owl

adaptive immune response
type: Class
subclass of: immune response
definition: An immune response based on directed amplification of specific receptors for antigen produced through a somatic diversification process, and allowing for enhanced response to subsequent exposures to the same antigen (immunological memory).
editor preferred term: adaptive immune response
imported from: go.owl

cytokine production involved in immune response
type: Class
subclass of: cytokine production
definition: The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus contributing to an immune response, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: cytokine production involved in immune response
imported from: go.owl

platelet activating factor production
type: Class
subclass of: cytokine production
definition: The synthesis or release of platelet activating factor following a stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: platelet activating factor production
imported from: go.owl

tolerance induction
type: Class
subclass of: biological_process
definition: A process that directly activates any of the steps required for tolerance, a physiologic state in which the immune system does not react destructively against the components of an organism that harbors it or against antigens that are introduced to it.
editor preferred term: tolerance induction
imported from: go.owl

B cell tolerance induction
type: Class
subclass of: tolerance induction
definition: A process involving any mechanism for tolerance induction in B cells.
editor preferred term: B cell tolerance induction
imported from: go.owl

T cell tolerance induction
type: Class
subclass of: tolerance induction
definition: A process involving any mechanism for tolerance induction in T cells.
editor preferred term: T cell tolerance induction
imported from: go.owl

hypersensitivity
type: Class
subclass of: biological_process
definition: An inflammatory response to an exogenous environmental antigen or an endogenous antigen initiated by the adaptive immune system.
editor preferred term: hypersensitivity
imported from: go.owl

cytokine production involved in inflammatory response
type: Class
subclass of: cytokine production
definition: The synthesis or release of a cytokine following a inflammatory stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: cytokine production involved in inflammatory response
imported from: go.owl

molecular_function
type: Class
subclass of: function
definition: Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
editor preferred term: molecular_function
imported from: go.owl

antigen binding
type: Class
subclass of: process
definition: Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.
editor preferred term: antigen binding
imported from: go.owl

catalytic activity
type: Class
subclass of: molecular_function
definition: Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
editor preferred term: catalytic activity
imported from: go.owl

RNA-directed DNA polymerase activity
type: Class
subclass of: catalytic activity
definition: Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time.
editor preferred term: RNA-directed DNA polymerase activity
imported from: go.owl

ion-channel activity
type: Class
subclass of: cellular process
definition: The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates.
editor preferred term: ion-channel activity
imported from: go.owl

cellular_component
type: Class
subclass of: material entity
definition: The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
editor preferred term: cellular_component
imported from: go.owl

chromosome
type: Class
subclass of: cellular_component
definition: A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. Source: ISBN:0198547684
editor preferred term: chromosome
imported from: go.owl

glucose metabolic process
type: Class
subclass of: biological_process
definition: The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
editor preferred term: glucose metabolic process
imported from: go.owl

chromatin remodeling
type: Class
subclass of: cellular process
definition: Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation. Source: GOC:jid, PMID:12697820
editor preferred term: chromatin remodeling
imported from: go.owl

phagocytosis
type: Class
subclass of: biological_process
definition: An endocytosis process that results in the engulfment of external particulate material by phagocytes. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles.
editor preferred term: phagocytosis
imported from: go.owl

immune response
type: Class
subclass of: process
subclass of: response to stimulus
definition: Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
editor preferred term: immune response
imported from: go.owl

response to DNA damage stimulus
type: Class
subclass of: response to stimulus
definition: Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
editor preferred term: response to DNA damage stimulus
imported from: go.owl

cell cycle
type: Class
subclass of: biological_process
definition: The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
editor preferred term: cell cycle
imported from: go.owl

blood coagulation
type: Class
subclass of: biological_process
definition: The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
editor preferred term: blood coagulation
imported from: go.owl

biological_process
type: Class
subclass of: process
disjoint with: planned process
definition: Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
editor preferred term: biological_process
imported from: go.owl

opsonization
type: Class
subclass of: phagocytosis
definition: The process in which a microorganism (or other particulate material) is rendered more susceptible to phagocytosis by coating with an opsonin, a blood serum protein such as a complement component or antibody.
editor preferred term: opsonization
imported from: go.owl

cell proliferation
type: Class
subclass of: biological_process
definition: The multiplication or reproduction of cells, resulting in the expansion of a cell population.
editor preferred term: cell proliferation
imported from: go.owl

fertilization
type: Class
subclass of: biological_process
definition: The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy).
editor preferred term: fertilization
imported from: go.owl

cellular process
type: Class
subclass of: biological_process
definition: Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
editor preferred term: cellular process
imported from: go.owl

gene expression
type: Class
subclass of: biological_process
definition: The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
editor preferred term: gene expression
imported from: go.owl

vascular endothelial growth factor production
type: Class
subclass of: cytokine production
definition: The appearance of vascular endothelial growth factor production due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: vascular endothelial growth factor production
imported from: go.owl

immunoglobulin mediated immune response
type: Class
subclass of: biological_process
definition: An immune response mediated by immunoglobulins, whether cell-bound or in solution.
editor preferred term: immunoglobulin mediated immune response
imported from: go.owl

immunoglobulin complex
type: Class
subclass of: protein complex
definition: A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.
editor preferred term: immunoglobulin complex
imported from: go.owl

B cell receptor complex
type: Class
subclass of: OBI_1110022
definition: An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins.
editor preferred term: B cell receptor complex
imported from: go.owl

antigen processing and presentation
type: Class
subclass of: biological_process
definition: The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex.
editor preferred term: antigen processing and presentation
imported from: go.owl

protein domain specific binding
type: Class
subclass of: OBI_0001588
definition: Interacting selectively and non-covalently with a specific domain of a protein. Source: GOC:go_curators
editor preferred term: protein domain specific binding
imported from: go.owl

actin filament polymerization
type: Class
subclass of: biological_process
definition: Assembly of actin filaments by the addition of actin monomers to a filament. Source: GOC:mah
editor preferred term: actin filament polymerization
imported from: go.owl

hemopoiesis
type: Class
subclass of: biological_process
definition: The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates.
editor preferred term: hemopoiesis
imported from: go.owl

connective tissue growth factor production
type: Class
subclass of: cytokine production
definition: The appearance of connective tissue growth factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: connective tissue growth factor production
imported from: go.owl

chemokine production
type: Class
subclass of: cytokine production
definition: The appearance of a chemokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: chemokine production
imported from: go.owl

granulocyte macrophage colony-stimulating factor production
type: Class
subclass of: cytokine production
definition: The appearance of granulocyte macrophage colony-stimulating factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: granulocyte macrophage colony-stimulating factor production
imported from: go.owl

hepatocyte growth factor production
type: Class
subclass of: cytokine production
definition: The appearance of hepatocyte growth factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: hepatocyte growth factor production
imported from: go.owl

type I interferon production
type: Class
subclass of: cytokine production
definition: The appearance of type I interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
editor preferred term: type I interferon production
imported from: go.owl

interferon-beta production
type: Class
subclass of: cytokine production
definition: The appearance of interferon-beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: interferon-beta production
imported from: go.owl

interferon-gamma production
type: Class
subclass of: cytokine production
definition: The appearance of interferon-gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon-gamma is also known as type II interferon.
editor preferred term: interferon-gamma production
imported from: go.owl

interleukin-1 alpha production
type: Class
subclass of: interleukin-1 production
definition: The appearance of interleukin-1 alpha due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: interleukin-1 alpha production
imported from: go.owl

interleukin-1 beta production
type: Class
subclass of: interleukin-1 production
definition: The appearance of interleukin-1 beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: interleukin-1 beta production
imported from: go.owl

interleukin-1 production
type: Class
subclass of: cytokine production
definition: The appearance of interleukin-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: interleukin-1 production
imported from: go.owl

interleukin-10 production
type: Class
subclass of: cytokine production
definition: The appearance of interleukin-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: interleukin-10 production
imported from: go.owl

interleukin-11 production
type: Class
subclass of: cytokine production
definition: The appearance of interleukin-11 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: interleukin-11 production
imported from: go.owl

interleukin-12 production
type: Class
subclass of: cytokine production
definition: The appearance of interleukin-12 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: interleukin-12 production
imported from: go.owl

interleukin-13 production
type: Class
subclass of: cytokine production
definition: The appearance of interleukin-13 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: interleukin-13 production
imported from: go.owl

interleukin-14 production
type: Class
subclass of: cytokine production
definition: The appearance of interleukin-14 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: interleukin-14 production
imported from: go.owl

interleukin-15 production
type: Class
subclass of: cytokine production
definition: The appearance of interleukin-15 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: interleukin-15 production
imported from: go.owl

interleukin-16 production
type: Class
subclass of: cytokine production
definition: The appearance of interleukin-16 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: interleukin-16 production
imported from: go.owl

interleukin-17 production
type: Class
subclass of: cytokine production
definition: The appearance of any member of the interleukin-17 family of cytokines due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: interleukin-17 production
imported from: go.owl

interleukin-18 production
type: Class
subclass of: cytokine production
definition: The appearance of interleukin-18 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: interleukin-18 production
imported from: go.owl

interleukin-19 production
type: Class
subclass of: cytokine production
definition: The appearance of interleukin-19 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: interleukin-19 production
imported from: go.owl

interleukin-2 production
type: Class
subclass of: cytokine production
definition: The appearance of interleukin-2 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: interleukin-2 production
imported from: go.owl

interleukin-20 production
type: Class
subclass of: cytokine production
definition: The appearance of interleukin-20 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: interleukin-20 production
imported from: go.owl

interleukin-21 production
type: Class
subclass of: cytokine production
definition: The appearance of interleukin-21 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: interleukin-21 production
imported from: go.owl

interleukin-22 production
type: Class
subclass of: cytokine production
definition: The appearance of interleukin-22 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: interleukin-22 production
imported from: go.owl

interleukin-23 production
type: Class
subclass of: cytokine production
definition: The appearance of interleukin-23 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: interleukin-23 production
imported from: go.owl

interleukin-24 production
type: Class
subclass of: cytokine production
definition: The appearance of interleukin-24 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: interleukin-24 production
imported from: go.owl

interleukin-25 production
type: Class
subclass of: cytokine production
definition: The appearance of interleukin-25 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: interleukin-25 production
imported from: go.owl

interleukin-26 production
type: Class
subclass of: cytokine production
definition: The appearance of interleukin-26 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: interleukin-26 production
imported from: go.owl

interleukin-27 production
type: Class
subclass of: cytokine production
definition: The appearance of interleukin-27 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: interleukin-27 production
imported from: go.owl

interleukin-3 production
type: Class
subclass of: cytokine production
definition: The appearance of interleukin-3 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: interleukin-3 production
imported from: go.owl

interleukin-4 production
type: Class
subclass of: cytokine production
definition: The appearance of interleukin-4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: interleukin-4 production
imported from: go.owl

interleukin-5 production
type: Class
subclass of: cytokine production
definition: The appearance of interleukin-5 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: interleukin-5 production
imported from: go.owl

interleukin-6 production
type: Class
subclass of: cytokine production
definition: The appearance of interleukin-6 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: interleukin-6 production
imported from: go.owl

interleukin-7 production
type: Class
subclass of: cytokine production
definition: The appearance of interleukin-7 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: interleukin-7 production
imported from: go.owl

interleukin-8 production
type: Class
subclass of: cytokine production
definition: The appearance of interleukin-8 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: interleukin-8 production
imported from: go.owl

interleukin-9 production
type: Class
subclass of: cytokine production
definition: The appearance of interleukin-9 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: interleukin-9 production
imported from: go.owl

TRAIL production
type: Class
subclass of: cytokine production
editor preferred term: TRAIL production
definition: The appearance of TRAIL due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

tumor necrosis factor production
type: Class
subclass of: tumor necrosis factor superfamily cytokine production
alternative term: TNF alpha production
definition: The appearance of tumor necrosis factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: tumor necrosis factor production
imported from: go.owl

lymphotoxin A production
type: Class
subclass of: tumor necrosis factor superfamily cytokine production
alternative term: TNF beta production
definition: The appearance of lymphotoxin A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: lymphotoxin A production
imported from: go.owl

transforming growth factor beta1 production
type: Class
subclass of: cytokine production
definition: The appearance of transforming growth factor-beta1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: transforming growth factor beta1 production
imported from: go.owl

transforming growth factor beta2 production
type: Class
subclass of: cytokine production
definition: The appearance of transforming growth factor-beta2 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: transforming growth factor beta2 production
imported from: go.owl

transforming growth factor beta3 production
type: Class
subclass of: cytokine production
definition: The appearance of transforming growth factor-beta3 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: transforming growth factor beta3 production
imported from: go.owl

macromolecule localization
type: Class
subclass of: biological_process
definition: Any process in which a macromolecule is transported to, or maintained in, a specific location.Source: GOC:mah
editor preferred term: macromolecule localization
imported from: go.owl

DNA polymerase activity
type: Class
subclass of: catalytic activity
definition: Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a nucleic acid template and primer.
editor preferred term: DNA polymerase activity
imported from: go.owl

type III interferon production
type: Class
subclass of: cytokine production
definition: The appearance of type III interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Type III interferons are members of the interferon-lambda gene family.
editor preferred term: type III interferon production
imported from: go.owl

chemokine (C-X-C motif) ligand 9 production
type: Class
subclass of: chemokine production
definition: The appearance of chemokine (C-X-C motif) ligand 9 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: chemokine (C-X-C motif) ligand 9 production
imported from: go.owl

helper T cell enhancement of adaptive immune response
type: Class
subclass of: adaptive immune response
definition: Positive regulation of an adaptive immune response mediated via cytokine production by helper T cell.
editor preferred term: helper T cell enhancement of adaptive immune response
imported from: go.owl

helper T cell enhancement of T cell mediated immune response
type: Class
subclass of: helper T cell enhancement of adaptive immune response
definition: Positive regulation of a T cell mediated immune response mediated via cytokine production by a helper T cell.
editor preferred term: helper T cell enhancement of T cell mediated immune response
imported from: go.owl

helper T cell enhancement of B cell mediated immune response
type: Class
subclass of: helper T cell enhancement of adaptive immune response
definition: Positive regulation of a B cell mediated immune response mediated via cytokine production by a helper T cell.
editor preferred term: helper T cell enhancement of B cell mediated immune response
imported from: go.owl

granzyme A production
type: Class
subclass of: biological_process
definition: The appearance of granzyme A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: granzyme A production
imported from: go.owl

perforin production
type: Class
subclass of: biological_process
definition: The appearance of a perforin protein due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: perforin production
imported from: go.owl

granulysin production
type: Class
subclass of: biological_process
definition: The appearance of granulysin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: granulysin production
imported from: go.owl

regulation of gene expression, epigenetic
type: Class
subclass of: regulation of molecular function, epigenetic
definition: Any process that modulates the frequency, rate or extent of gene expression; the process is mitotically or meiotically heritable, or is stably self-propagated in the cytoplasm of a resting cell, and does not entail a change in DNA sequence. Source: PMID:10521337, PMID:11498582
editor preferred term: regulation of gene expression, epigenetic
imported from: go.owl

regulation of molecular function, epigenetic
type: Class
subclass of: biological_process
definition: Any heritable epigenetic process that modulates the frequency, rate or extent of protein function by self-perpetuating conformational conversions of normal proteins in healthy cells. This is distinct from, though mechanistically analogous to, disease states associated with prion propagation and amyloidogenesis. A single protein, if it carries a glutamine/asparagine-rich ('prion') domain, can sometimes stably exist in at least two distinct physical states, each associated with a different phenotype; propagation of one of these traits is achieved by a self-perpetuating change in the protein from one form to the other, mediated by conformational changes in the glutamine/asparagine-rich domain. Prion domains are both modular and transferable to other proteins, on which they can confer a heritable epigenetic alteration of function; existing bioinformatics data indicate that they are rare in non-eukarya, but common in eukarya. Source: GOC:dph, GOC:ems, GOC:tb, PMID:10611975, PMID:11050225, PMID:11447696, PMID:11685242, PMID:11782551
editor preferred term: regulation of molecular function, epigenetic
imported from: go.owl

T cell proliferation
type: Class
subclass of: cell proliferation
editor preferred term: T cell proliferation
definition: The expansion of a T cell population by cell division. Follows T cell activation.
imported from: go.owl

T cell receptor complex
type: Class
subclass of: OBI_1110022
definition: A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains.
editor preferred term: T cell receptor complex
imported from: go.owl

T cell activation
type: Class
subclass of: biological_process
editor preferred term: T cell activation
definition: The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
imported from: go.owl

immunoglobulin complex, circulating
type: Class
subclass of: immunoglobulin complex
subclass of: OBI_1110022
alternative term: antibody
definition: An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component.
editor preferred term: immunoglobulin complex, circulating
imported from: go.owl

DNA polymerase complex
type: Class
subclass of: protein complex
subclass of: enzyme
subclass of: Restriction
  on property: has function
  some values from: DNA polymerase activity
definition: A protein complex that possesses DNA polymerase activity and is involved in template directed synthesis of DNA.
editor preferred term: DNA polymerase complex
imported from: go.owl

peptide antigen binding
type: Class
subclass of: antigen binding
definition: Interacting selectively and non-covalently with an antigen peptide.
editor preferred term: peptide antigen binding
imported from: go.owl

MHC protein complex
type: Class
subclass of: protein complex
definition: A transmembrane protein complex composed of an MHC alpha chain and, in most cases, either an MHC class II beta chain or an invariant beta2-microglobin chain, and with or without a bound peptide, lipid, or polysaccharide antigen.
editor preferred term: MHC protein complex
imported from: go.owl

membrane-bounded organelle
type: Class
subclass of: cellular_component
definition: Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
editor preferred term: membrane-bounded organelle
imported from: go.owl

protein complex
type: Class
subclass of: material entity
subclass of: Restriction
  on property: has part
  some values from: PR_000000001
example of usage: A ribosome is a protein complex
definition: Any macromolecular complex composed of two or more polypeptide subunits, which may or may not be identical. Protein complexes may have other associated non-protein prosthetic groups, such as nucleotides, metal ions or other small molecules.
editor preferred term: protein complex
imported from: go.owl

cytotoxic T cell degranulation
type: Class
subclass of: cell killing
definition: The regulated exocytosis of secretory granules containing preformed mediators such as perforin and granzymes by a cytotoxic T cell.
editor preferred term: cytotoxic T cell degranulation
imported from: go.owl

sequence-specific DNA binding
type: Class
subclass of: OBI_0001588
definition: Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
editor preferred term: sequence-specific DNA binding
imported from: go.owl

regulation of DNA methylation
type: Class
subclass of: regulation of molecular function, epigenetic
definition: Any process that modulates the frequency, rate or extent of the covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine. Source: GOC:jl
editor preferred term: regulation of DNA methylation
imported from: go.owl

cellular developmental process
type: Class
subclass of: biological_process
definition: A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition.
editor preferred term: cellular developmental process
imported from: go.owl

response to stimulus
type: Class
subclass of: biological_process
definition: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
editor preferred term: response to stimulus
imported from: go.owl

chromosome organization
type: Class
subclass of: biological_process
definition: Any process that modulates the frequency, rate or extent of gene expression; the process is mitotically or meiotically heritable, or is stably self-propagated in the cytoplasm of a resting cell, and does not entail a change in DNA sequence. Source: PMID:10521337, PMID:11498582
editor preferred term: chromosome organization
imported from: go.owl

actin polymerization-dependent cell motility
type: Class
subclass of: biological_process
definition: A process involved in the controlled movement of a bacterial cell powered by the continuous polymerization of actin at one pole of the cell. Source: GOC:mah, PMID:15773977
editor preferred term: actin polymerization-dependent cell motility
imported from: go.owl

transforming growth factor beta production
type: Class
subclass of: cytokine production
definition: The appearance of any member of the transforming growth factor-beta family of cytokines due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Transforming growth factor-beta family members include TGF-B1, TGF-B2, and TGF-B3.
editor preferred term: transforming growth factor beta production
imported from: go.owl

monocyte chemotactic protein-1 production
type: Class
subclass of: chemokine production
definition: The appearance of monocyte chemotactic protein-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: monocyte chemotactic protein-1 production
imported from: go.owl

chemokine (C-C motif) ligand 4 production
type: Class
subclass of: chemokine production
definition: The appearance of chemokine (C-C motif) ligand 4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: chemokine (C-C motif) ligand 4 production
imported from: go.owl

macrophage inflammatory protein-1 gamma production
type: Class
subclass of: chemokine production
definition: The appearance of macrophage inflammatory protein-1 gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: macrophage inflammatory protein-1 gamma production
imported from: go.owl

macrophage inflammatory protein-1 alpha production
type: Class
subclass of: chemokine production
definition: The appearance of macrophage inflammatory protein 1 alpha due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: macrophage inflammatory protein-1 alpha production
imported from: go.owl

chemokine (C-C motif) ligand 5 production
type: Class
subclass of: chemokine production
definition: The appearance of chemokine (C-C motif) ligand 5 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: chemokine (C-C motif) ligand 5 production
imported from: go.owl

chemokine (C-C motif) ligand 1 production
type: Class
subclass of: chemokine production
definition: The appearance of chemokine (C-C motif) ligand 1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: chemokine (C-C motif) ligand 1 production
imported from: go.owl

granulocyte colony-stimulating factor production
type: Class
subclass of: cytokine production
definition: The appearance of granulocyte colony-stimulating factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: granulocyte colony-stimulating factor production
imported from: go.owl

IP-10 production
type: Class
subclass of: chemokine production
editor preferred term: IP-10 production
definition: The appearance of IP-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

granzyme B production
type: Class
subclass of: biological_process
definition: The appearance of granzyme B due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: granzyme B production
imported from: go.owl

tumor necrosis factor superfamily cytokine production
type: Class
subclass of: cytokine production
definition: The appearance of any member of the TNF superfamily due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: tumor necrosis factor superfamily cytokine production
imported from: go.owl

tumor necrosis factor (ligand) superfamily member 11 production
type: Class
subclass of: tumor necrosis factor superfamily cytokine production
definition: The appearance of tumor necrosis factor superfamily member 11 (TNFSF11; RANKL) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: tumor necrosis factor (ligand) superfamily member 11 production
imported from: go.owl

interleukin-17A production
type: Class
subclass of: interleukin-17 production
definition: The appearance of interleukin-17A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: interleukin-17A production
imported from: go.owl

interleukin-17F production
type: Class
subclass of: interleukin-17 production
definition: The appearance of interleukin-17F due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
editor preferred term: interleukin-17F production
imported from: go.owl

complement-dependent cytotoxicity
type: Class
subclass of: cell killing
definition: Lysis of a cell resulting from triggering of the complement cascade. An example can be seen with complement activation and subsequent lysis of a bacterial cell as a result of the binding of IgM to the cell surface followed by the binding of complement proteins to that antibody.
editor preferred term: complement-dependent cytotoxicity
imported from: go.owl

histamine secretion mediated by immunoglobulin
type: Class
subclass of: immune response
definition: Histamine release triggered by the binding of an antigen to an immunoglobulin bound to the cell surface.
editor preferred term: histamine secretion mediated by immunoglobulin
imported from: go.owl

immune complex formation
type: Class
subclass of: immunoglobulin mediated immune response
definition: The process that gives rise to an immune complex. Immune complexes are clusters of antibodies bound to antigen, to which complement may also be fixed, and which may precipitate or remain in solution. Examples are the clumping of cells such as bacteria or red blood cells in the presence of an antibody, precipitation of a toxin after an antibody binds to it, and clumping of viral particles as a result of antibody binding to the virus.
editor preferred term: immune complex formation
imported from: go.owl

immunoglobulin-mediated neutralization
type: Class
subclass of: immunoglobulin mediated immune response
definition: The inhibition of an antigen's biological effects by antibody binding to it. An example is neutralization of diphtheria toxin by preventing its entry into human cells via the binding of antibody specific for diphtheria toxin.
editor preferred term: immunoglobulin-mediated neutralization
imported from: go.owl

Insulin resistance
type: Class
subclass of: disposition
editor preferred term: Insulin resistance
definition: `Increased resistance` (PATO:0001650) towards `insulin` (PRO:000009054).
imported from: hp.owl

conditional specification
type: Class
subclass of: directive information entity
definition source: OBI branch derived
definition source: OBI_0000349
term editor: PlanAndPlannedProcess Branch
definition: a directive information entity that specifies what should happen if the trigger condition is fulfilled
editor preferred term: conditional specification
has curation status: IAO_0000120

measurement unit label
type: Class
subclass of: datum label
editor note: 2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term.
editor note: 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
definition: A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
example of usage: Examples of measurement unit labels are liters, inches, weight per volume.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot
editor preferred term: measurement unit label
has curation status: IAO_0000125

objective specification
type: Class
subclass of: directive information entity
editor note: 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."
editor note: Answers the question, why did you do this experiment?
definition source: OBI Plan and Planned Process/Roles Branch
definition source: OBI_0000217
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Barry Smith
term editor: PERSON: Bjoern Peters
term editor: PERSON: Jennifer Fostel
definition: a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
editor preferred term: objective specification
example of usage: purpose of a study; support of hypothesis, discovery of new information
has curation status: IAO_0000125

narrative object
type: Class
subclass of: information content entity
editor note: 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion
definition: A narrative object is an information content entity that is a set of propositions.
example of usage: Examples of narrative objects are reports, journal articles, and patents submission.
definition source: OBI_0000013
editor note: agree - DENRIE. Issue(alan) do we only mean text? What about a story told by mime. Does music count? (no) what about an oral report. Regarding definition, saying it is a set of propositions means we loose the idea that wording matters. Maybe adjust saying a narrative object has some relationshop to a set of propositions
definition source: group:OBI
editor preferred term: narrative object
term editor: person:Chris Stoeckert
has curation status: IAO_0000124

action specification
type: Class
subclass of: directive information entity
term editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch
example of usage: Pour the contents of flask 1 into flask 2
definition: a directive information entity that describes an action the bearer will take
has curation status: IAO_0000123

obsolete_artifact
type: Class
subclass of: ObsoleteClass
has obsolescence reason: IAO_0000103

datum label
type: Class
subclass of: information content entity
curator note: 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum.
definition: A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
term editor: GROUP: IAO
editor preferred term: datum label
editor note: http://www.golovchenko.org/cgi-bin/wnsearch#4n
has curation status: IAO_0000123

software
type: Class
subclass of: plan specification
definition source: GROUP: OBI
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Melanie Courtot
definition: Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit.
editor note: see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178
editor preferred term: software
has curation status: IAO_0000120

obsolete2_digital entity
type: Class
subclass of: ObsoleteClass
definition source: OBI_0000261
editor note: 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Superclass was 'digitial quality'
definition: A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical.
definition source: group:OBI
editor preferred term: obsolete_digital entity
term editor: person:Chris Stoeckert
has obsolescence reason: IAO_0000103

journal article
type: Class
subclass of: report
example of usage: Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number.
definition source: OBI_0000159
definition: a report that is published in a journal
definition source: group:OBI
editor preferred term: journal article
term editor: person:Alan Ruttenberg
term editor: person:Chris Stoeckert
has curation status: IAO_0000120

information carrier
type: Class
equivalent class: Class
  intersection of: quality
  intersection of: Restriction
    on property: concretizes
    some values from: information content entity
subclass of: quality
editor note: 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'.
definition: A quality of an information bearer that imparts the information content
term editor: PERSON: Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
example of usage: The pattern in ink on a page of a paperback novel.
editor preferred term: information carrier
has curation status: IAO_0000125

model number
type: Class
subclass of: symbol
definition: A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
term editor: Person: Alan Ruttenberg
editor note: manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers
editor preferred term: model number
has curation status: IAO_0000125

obsolete_material_entity
type: Class
subclass of: ObsoleteClass
has obsolescence reason: IAO_0000226

obsolete2_binary digital entity
type: Class
subclass of: ObsoleteClass
definition source: OBI_0000244
editor note: 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Superclass was 'digital entity'
definition: A binary digital entity is a digital entity that is encoded in a way that is not easily human readable and that contains other than text characters.
example of usage: MS Word document, ZIP file, DICOM file, JPEG file
editor preferred term: binary digital entity
editor note: digital_entity
definition source: group:OBI
term editor: person:Chris Stoeckert
has obsolescence reason: IAO_0000103

obsolete_unit of measure
type: Class
subclass of: ObsoleteClass
term editor: Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
example of usage: The length of a ruler.
definition: a unit of measure is the quality of some material entity compared to which another quality is some multiple of.
has obsolescence reason: IAO_0000103

programming language
type: Class
subclass of: plan specification
definition: A language in which source code is written, intended to executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it.
definition source: OBI_0000058
example of usage: R, Perl, Java
definition source: group:OBI
term editor: person:Alan Ruttenberg
term editor: person:Chris Stoeckert
editor preferred term: programming language
has curation status: IAO_0000120

data item
type: Class
subclass of: information content entity
editor note: 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
editor note: 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
editor note: 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
example of usage: Data items include counts of things, analyte concentrations, and statistical summaries.
editor note: JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jonathan Rees
definition: a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
alternative term: data
editor preferred term: data item
has curation status: IAO_0000125

symbol
type: Class
subclass of: information content entity
editor note: 20091104, MC: this needs work and will most probably change
term editor: PERSON: Jonathan Rees
definition: a smallish, word-like datum...
editor preferred term: symbol

numeral
type: Class
subclass of: symbol
definition: A symbol that denotes a number.
term editor: PERSON: Jonathan Rees
editor preferred term: numeral

information content entity
type: Class
subclass of: generically dependent continuant
subclass of: Restriction
  on property: is about
  some values from: entity
example of usage: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
definition source: OBI_0000142
term editor: PERSON: Chris Stoeckert
definition: an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity
editor preferred term: information content entity
editor note: information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
has curation status: IAO_0000125

integer numeral
type: Class
subclass of: numeral
term editor: PERSON: Jonathan Rees
definition: a numeral that denotes an integer
editor preferred term: integer numeral

scalar measurement datum
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: has measurement unit label
  min cardinality: 1
subclass of: Restriction
  on property: has measurement value
  min cardinality: 1
example of usage: 10 feet. 3 ml.
editor note: 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot
editor note: Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.
definition: a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
has curation status: IAO_0000120

directive information entity
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is about
  some values from: realizable entity
editor note: 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
editor note: 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
definition: An information content entity whose concretizations indicate to their bearer how to realize them in a process.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
editor note: Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
has curation status: IAO_0000123

time trigger
type: Class
subclass of: conditional specification
definition source: OBI branch derived
definition source: OBI_0000331
term editor: PlanAndPlannedProcess Branch
definition: revisit?
editor preferred term: time trigger
has curation status: IAO_0000124

obsolete_study interpretation
type: Class
subclass of: ObsoleteClass
editor note: 2009-03-16: definition was "A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application."
editor note: 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
definition source: OBI_0000005
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot
alternative term: conclusion
definition: A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses
term editor: Lawrence Hunter
term editor: PERSON: Jennifer Fostel
editor note: The obsoleting of narrative object required a modest change in the definition of this term. Circularity with "interpretation... interprets" has been removed, using "about the implications" instead.
editor preferred term: obsolete_study interpretation
has obsolescence reason: IAO_0000103
has curation status: IAO_0000125

dot plot
type: Class
subclass of: graph
definition: A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions.
example of usage: Dot plot of SSC-H and FSC-H.
definition source: OBI_0000123
editor preferred term: dot plot
definition source: group:OBI
term editor: person:Allyson Lister
term editor: person:Chris Stoeckert
has curation status: IAO_0000002

graph
type: Class
subclass of: diagram
definition: A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way.
definition source: OBI_0000240
term editor: PERSON: Lawrence Hunter
editor preferred term: graph
definition source: group:OBI
term editor: person:Alan Ruttenberg
term editor: person:Allyson Lister
has curation status: IAO_0000125

obsolete2_text based digital entity
type: Class
subclass of: ObsoleteClass
definition source: OBI_0000132
definition source: group:OBI
editor note: 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digital document'
definition: A text based digital entity is a digital entity that is encoded so that it only contains text characters.
example of usage: XML file, C++ source code file
editor note: digital_entity
term editor: person:Chris Stoeckert
editor preferred term: text based digital entity
has obsolescence reason: IAO_0000103

rule
type: Class
subclass of: conditional specification
editor note: MSI
definition source: OBI_0500021
definition source: PRS
term editor: PRS
definition: a rule is an executable which guides, defines, restricts actions
example of usage: example to be added
editor preferred term: rule
has curation status: IAO_0000124

contour plot
type: Class
subclass of: graph
example of usage: Contour plot of SSC-H, FSC-H, and FL1-H.
definition source: OBI_0000246
editor preferred term: contour plot
editor note: generically_dependent_continuants
definition source: group:Flow Cytometry community
term editor: person:Allyson Lister
term editor: person:Chris Stoeckert
has curation status: IAO_0000002

obsolete2_report figure
type: Class
subclass of: ObsoleteClass
definition source: OBI_0000027
definition: A report figure is a report display element that has some aspect of illustration, but may be a composite of figures, images, and other elements
editor note: I prepended the 'report ' to make it clear that we mean parts of reports here. We may want a more generic version of 'figure', in which case this would become a defined class - figure and part_of some report
editor note: Replaced by defined version of figure
definition source: group:OBI
term editor: person:Alan Ruttenberg
term editor: person:Allyson Lister
editor preferred term: report figure
has obsolescence reason: IAO_0000103
has curation status: IAO_0000124

algorithm
type: Class
subclass of: plan specification
definition: A plan specification which describes inputs, output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
definition source: OBI_0000270
example of usage: PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
term editor: Philippe Rocca-Serra
term editor: PlanAndPlannedProcess Branch
definition source: adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
editor preferred term: algorithm
has curation status: IAO_0000120

software interpreter
type: Class
subclass of: algorithm
definition: A software interpreter is a software application that executes some specified input software.
editor note: Do we care? Jennifer: Yes, there was a particular version of R that had a bug and it was fixed later. That would imply that we mean specific version of an interpreter. So an instance of this would be a particular version of the interpreter
definition source: OBI_0000199
example of usage: R program, Perl interpreter, Java virtual machine
definition source: group:OBI
term editor: person:Alan Ruttenberg
term editor: person:Chris Stoeckert
editor preferred term: software interpreter
has curation status: IAO_0000120

curation status specification
type: Class
equivalent class: Class
  one of: IAO_0000124
  one of: IAO_0000423
  one of: IAO_0000125
  one of: IAO_0000122
  one of: IAO_0000123
  one of: IAO_0000428
  one of: IAO_0000120
  one of: IAO_0000121
  one of: IAO_0000002
subclass of: data about an ontology part
editor note: Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition source: OBI_0000266
term editor: PERSON:Bill Bug
definition: The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
editor preferred term: curation status specification
has curation status: IAO_0000125

density plot
type: Class
subclass of: graph
definition: A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel.
example of usage: Density plot of SSC-H and FSC-H.
definition source: OBI_0000179
editor preferred term: density plot
definition source: group:Flow Cytometry community
term editor: person:Allyson Lister
term editor: person:Chris Stoeckert
has curation status: IAO_0000002

report
type: Class
subclass of: document
editor note: 2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on something that has completed." Should it be restricted to those things that are completed? For example, a progress report is (usually) about something that definitely has *not* been completed, or may include (only) projections. I think the definition would not suffer if the whole sentence is deleted.
editor note: 2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so.
editor note: 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
editor note: 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion
example of usage: Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article.
definition source: GROUP: OBI
definition source: OBI_0000099
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot
term editor: PERSON:Chris Stoeckert
definition: a document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record)
editor note: disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification
editor preferred term: report
has curation status: IAO_0000125

obsolete_report element
type: Class
subclass of: ObsoleteClass
editor note: 2009-03-16: needs some more work (clarify relations).
editor note: 2009-03-16: was report display element with definition: A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements.
editor note: 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
editor note: 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion
definition source: OBI_0000001
term editor: PERSON: Melanie Courtot
editor note: Replaced by textual entity and figure
definition: A report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page).
definition source: GROUP:OBI
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Allyson Lister
editor note: There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text
editor preferred term: report element
has obsolescence reason: IAO_0000103
has curation status: IAO_0000120

obsolete2_binary executable
type: Class
subclass of: ObsoleteClass
definition source: OBI_0000222
editor note: 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digital entity'
definition: Binary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions. (derived from Wikipedia, Nov 1, 2007)
editor preferred term: binary executable
definition source: group:OBI
term editor: person:Jennifer Fostel
has obsolescence reason: IAO_0000103

source code module
type: Class
subclass of: directive information entity
definition: A source code module is a directive information entity that specifies, using a programming language, some algorithm.
definition source: OBI_0000039
example of usage: The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script.
definition source: group:OBI
term editor: person:Alan Ruttenberg
term editor: person:Chris Stoeckert
editor preferred term: source code module
has curation status: IAO_0000124

obsolete_report table
type: Class
subclass of: ObsoleteClass
editor note: 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity table'. Alan restored as there are OBI dependencies and this merits further discussion
definition source: OBI_0000265
definition: A report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content
definition source: group:OBI
term editor: person:Alan Ruttenberg
term editor: person:Allyson Lister
editor preferred term: report table
has curation status: IAO_0000002
has obsolescence reason: IAO_0000103

data format specification
type: Class
subclass of: directive information entity
editor note: 2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes information. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file"
definition: A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file
definition source: OBI branch derived
definition source: OBI_0000187
term editor: PERSON: Alan Ruttenberg
term editor: PlanAndPlannedProcess Branch
editor preferred term: data format specification
has curation status: IAO_0000123

data set
type: Class
subclass of: data item
editor note: 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type
definition: A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
example of usage: Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
definition source: OBI_0000042
editor preferred term: data set
definition source: group:OBI
term editor: person:Allyson Lister
term editor: person:Chris Stoeckert
has curation status: IAO_0000120

image
type: Class
subclass of: figure
definition: An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface.
definition source: OBI_0000030
definition source: group:OBI
editor preferred term: image
term editor: person:Alan Ruttenberg
term editor: person:Allyson
term editor: person:Chris Stoeckert
has curation status: IAO_0000122

data about an ontology part
type: Class
subclass of: data item
term editor: Person:Alan Ruttenberg
definition: data about an ontology part is a data item about a part of an ontology, for example a term

plan specification
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: has part
  some values from: objective specification
subclass of: Restriction
  on property: has part
  some values from: action specification
comment: 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them
editor note: 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
term editor: Alan Ruttenberg
editor note: Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
definition source: OBI Plan and Planned Process branch
definition source: OBI_0000344
example of usage: PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
definition: a directive information entity that when concretized it is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified. Plan specifications includes parts such as objective specification, action specifications and conditional specifications.
editor preferred term: plan specification
has curation status: IAO_0000120

obsolete2_digital document
type: Class
subclass of: ObsoleteClass
definition source: OBI_0000195
editor note: 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digial entity'
definition: A digital document is a digital entity consisting of an electronic file which can be rendered into human-readable form by one or more computational applications. The digital document does not refer to the information content of the document but to an instance of the file.
editor preferred term: digital document
definition source: group:OBI
term editor: person:Jennifer Fostel
has obsolescence reason: IAO_0000103

measurement datum
type: Class
subclass of: data item
editor note: 2/2/2009 is_specified_output of some assay?
definition: A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
example of usage: Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
definition source: OBI_0000305
definition source: group:OBI
editor preferred term: measurement datum
term editor: person:Chris Stoeckert
has curation status: IAO_0000120

obsolete_identifier
type: Class
subclass of: ObsoleteClass
editor note: _identifier is a container under information content entity for collecting types of terms to indicate a specific instance or clas of what was used or participated in an investigation. Identifiers are borne by a product or its packaging, and can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. Note: everybody agreed that identifier is probably a too general term. We however felt that it would be appropriate to group "identifiying" terms under some kind of umbrella. We therefore propose to use _identifier for that purpose. As per OBI conventions, the _ prefixing identifier indicates that this is a helper class and shouldn't be considered as final.
has curation status: IAO_0000121
has obsolescence reason: IAO_0000226

version number
type: Class
subclass of: symbol
definition: A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name.
term editor: GROUP: IAO
editor note: Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version
editor preferred term: version number
has curation status: IAO_0000124

serial number
type: Class
subclass of: symbol
definition: A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
term editor: GROUP: IAO
editor note: Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-)
editor preferred term: serial number
has curation status: IAO_0000124

lot number
type: Class
subclass of: symbol
definition: A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots.
term editor: GROUP: IAO
alternative term: batch number
editor preferred term: lot number
has curation status: IAO_0000124

setting datum
type: Class
subclass of: data item
editor note: 2/3/2009 Feedback from OBI This should be a "setting specification". There is a question of whether it is information about a realizable or not. Pro other specification are about realizables. Cons sometimes specifies a quality which is not a realizable.
definition: A settings datum is a datum that denotes some configuration of an instrument.
editor note: Alan grouped these in placeholder for the moment. Name by analogy to measurement datum.
has curation status: IAO_0000124

obsolete_digital quality
type: Class
subclass of: ObsoleteClass
editor note: Need to rework digital entity. Digital quality was suggested by Barry.
editor note: 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4
has obsolescence reason: IAO_0000103

conclusion textual entity
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is_supported_by_data
  some values from: data item
subclass of: Restriction
  on property: is_specified_output_of
  some values from: interpreting data
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
editor note: 2009/10/23 Alan Ruttenberg: We need to work on the definition still
definition: A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers.
term editor: Person:Alan Ruttenberg
editor preferred term: conclusion textual entity
example of usage: that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660
has curation status: IAO_0000120

material information bearer
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: is bearer of
    some values from: Restriction
      on property: concretizes
      some values from: information content entity
subclass of: material entity
definition: An information bearer is a material_entity in which a concretization of an information content entity inheres.
term editor: GROUP: IAO
example of usage: a hard drive, a piece of paper with writing on it, a brain
editor preferred term: material information bearer
has curation status: IAO_0000120

histogram
type: Class
subclass of: graph
definition: A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes.
definition source: GROUP:OBI
term editor: PERSON:Chris Stoeckert
term editor: PERSON:James Malone
term editor: PERSON:Melanie Courtot
editor preferred term: histogram
has curation status: IAO_0000122

heatmap
type: Class
subclass of: graph
definition: A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map.
definition source: GROUP:OBI
term editor: PERSON:Chris Stoeckert
term editor: PERSON:James Malone
term editor: PERSON:Melanie Courtot
editor preferred term: heatmap
has curation status: IAO_0000122

Venn diagram
type: Class
subclass of: graph
definition: A Venn diagram is a report graph showing all hypothetically possible logical relations between a finite collection of sets.
term editor: PERSON:Chris Stoeckert
term editor: PERSON:James Malone
term editor: PERSON:Melanie Courtot
editor preferred term: Venn diagram
definition source: WEB: http://en.wikipedia.org/wiki/Venn_diagram
has curation status: IAO_0000122

obsolete_survival curve
type: Class
subclass of: ObsoleteClass
definition: A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time.
term editor: PERSON:Chris Stoeckert
term editor: PERSON:James Malone
term editor: PERSON:Melanie Courtot
definition source: WEB: http://www.graphpad.com/www/book/survive.htm
editor preferred term: obsolete_survival curve
has obsolescence reason: IAO_0000103
has curation status: IAO_0000122

dendrogram
type: Class
subclass of: graph
definition: A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm.
example of usage: Dendrograms are often used in computational biology to illustrate the clustering of genes.
term editor: PERSON:Chris Stoeckert
term editor: PERSON:James Malone
term editor: PERSON:Melanie Courtot
definition source: WEB: http://en.wikipedia.org/wiki/Dendrogram
editor preferred term: dendrogram
has curation status: IAO_0000122

scatter plot
type: Class
subclass of: graph
definition: A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis.
example of usage: Comparison of gene expression values in two samples can be displayed in a scatter plot
term editor: PERSON:Chris Stoeckert
term editor: PERSON:James Malone
term editor: PERSON:Melanie Courtot
definition source: WEB: http://en.wikipedia.org/wiki/Scatterplot
editor preferred term: scatter plot
alternative term: scattergraph
has curation status: IAO_0000122

photograph
type: Class
subclass of: image
definition: A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc.
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Joanne Luciano
term editor: PERSON:Melanie Courtot
definition source: WEB: http://en.wiktionary.org/wiki/photograph
has curation status: IAO_0000122

photographic print
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: is bearer of
    some values from: Restriction
      on property: concretizes
      some values from: photograph
subclass of: material information bearer
definition: A photographic print is a material entity upon which a photograph generically depends.
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Melanie Courtot
editor preferred term: photographic print
has curation status: IAO_0000125

obsolescence reason specification
type: Class
equivalent class: Class
  one of: IAO_0000227
  one of: IAO_0000228
  one of: IAO_0000226
  one of: IAO_0000103
  one of: IAO_0000229
subclass of: data about an ontology part
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot
editor note: The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
definition: The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
editor preferred term: obsolescence reason specification
has curation status: IAO_0000125

textual entity
type: Class
subclass of: information content entity
definition: A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc.
editor note: AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc.
editor note: MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities.
term editor: PERSON: Lawrence Hunter
example of usage: Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
alternative term: text
editor preferred term: textual entity

citation
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: document
term editor: PERSON: Lawrence Hunter
example of usage: Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183.
definition: a textual entity intended to identify a particular publication
editor preferred term: citation
has curation status: IAO_0000125

author identification
type: Class
subclass of: written name
definition: A textual entity intended to identify a particular author
example of usage: L. Hunter
term editor: PERSON: Lawrence Hunter
editor preferred term: author identification
has curation status: IAO_0000125

institutional identification
type: Class
subclass of: textual entity
definition: A textual entity intended to identify a particular institution
term editor: PERSON: Lawrence Hunter
example of usage: University of Colorado Denver School of Medicine
editor preferred term: institutional identification
has curation status: IAO_0000125

caption
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: figure
definition: A textual entity that describes a figure
example of usage: Figure 1: A system diagram describing the modules of the Hanalyzer. Reading methods (green) take external sources of knowledge (blue) and extract information from them, either by parsing structured data or biomedical language processing to extract information from unstructured data. Reading modules are responsible for tracking the provenance of all knowledge. Reasoning methods (yellow) enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. All knowledge sources, read or reasoned, are assigned a reliability score, and all are combined using that score into a knowledge network (orange) that represents the integration of all sorts of relationship between a pair of genes and a combined reliability score. A data network (also orange) is created from experimental results to be analyzed. The reporting modules (pink) integrate the data and knowledge networks, producing visualizations that can be queried with the associated drill-down tool.
term editor: PERSON: Lawrence Hunter
editor preferred term: caption
has curation status: IAO_0000125

document title
type: Class
subclass of: textual entity
definition: A textual entity that names a document
term editor: PERSON: Lawrence Hunter
example of usage: Textual characteristics of traditional and Open Access scientific journals are similar
editor preferred term: document title
has curation status: IAO_0000125

table
type: Class
subclass of: textual entity
definition: A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions
term editor: PERSON: Lawrence Hunter
editor preferred term: table
example of usage: | T F --+----- T | T F F | F F
has curation status: IAO_0000125

table of abbreviations
type: Class
subclass of: table
definition: A table where the constituent texts are abbreviations and their expansions
example of usage: IAO information artifact ontology OBI ontology of biomedical investiations GO gene ontology
term editor: PERSON: Lawrence Hunter
editor preferred term: table of abbreviations
has curation status: IAO_0000125

figure
type: Class
subclass of: information content entity
definition: An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
example of usage: Any picture, diagram or table
term editor: PERSON: Lawrence Hunter
editor preferred term: figure
has curation status: IAO_0000120

diagram
type: Class
subclass of: figure
definition: A figure that expresses one or more propositions
example of usage: A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.
term editor: PERSON: Lawrence Hunter
editor preferred term: diagram
has curation status: IAO_0000120

document
type: Class
subclass of: information content entity
definition: A collection of information content entities intended to be understood together as a whole
example of usage: A journal article, patent application, laboratory notebook, or a book
term editor: PERSON: Lawrence Hunter
editor preferred term: document
has curation status: IAO_0000120

publication
type: Class
subclass of: document
definition: A document that has been accepted by a publisher
example of usage: A journal article or book
term editor: PERSON: Lawrence Hunter
editor preferred term: publication
has curation status: IAO_0000120

publication about an investigation
type: Class
subclass of: publication
subclass of: Restriction
  on property: is about
  some values from: investigation
definition: A publication that is about an investigation
example of usage: Most scientific journal articles
term editor: PERSON: Lawrence Hunter
editor preferred term: publication about an investigation
alternative term: scientific publication
has curation status: IAO_0000120

patent
type: Class
subclass of: document
definition: A document that has been accepted by a patent authority
term editor: PERSON: Lawrence Hunter
example of usage: US Patent 6,449,603
editor preferred term: patent
has curation status: IAO_0000120

document part
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is part of
  some values from: document
example of usage: An abstract, introduction, method or results section.
term editor: PERSON: Lawrence Hunter
definition: an information content entity that is part of a document
editor preferred term: document part
has curation status: IAO_0000120

abstract
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: document
definition: A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes.
term editor: PERSON: Lawrence Hunter
example of usage: The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or biomedical language processing to extract information from unstructured data, and track knowledge provenance. Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data.
editor preferred term: abstract
has curation status: IAO_0000120

introduction to a publication about an investigation
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: objective specification
definition: A part of a publication about an investigation that is about the objective specification (why the investigation is being done)
term editor: PERSON: Lawrence Hunter
example of usage: Section labelled 'introduction' of a typical scientific journal article
alternative term: introduction
editor preferred term: introduction to a publication about an investigation
has curation status: IAO_0000120

methods section
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: OBI_0500000
definition: A part of a publication about an investigation that is about the study design of the investigation
term editor: PERSON: Lawrence Hunter
example of usage: The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article.
editor preferred term: methods section
has curation status: IAO_0000120

results section
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: study design execution
definition: A part of a publication about an investigation that is about a study design execution
term editor: PERSON: Lawrence Hunter
example of usage: The section labelled 'results' in a typical scientific journal article
editor preferred term: results section
has curation status: IAO_0000120

discussion section of a publication about an investigation
type: Class
subclass of: document part
definition: A part of a publication about an investigation that is about the study interpretation of the investigation
term editor: PERSON: Lawrence Hunter
alternative term: discussion section
editor preferred term: discussion section of a publication about an investigation
has curation status: IAO_0000120

references section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: citation
definition: A part of a document that has citations as parts
term editor: PERSON: Lawrence Hunter
example of usage: The list of citations found at the end of a scientific publication, grant proposal or patent application, sometimes called "literature cited" or "bibliography"
editor preferred term: references section
has curation status: IAO_0000120

author list
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: author identification
example of usage: Lawrence Hunter and Kevin Brettonel Cohen
term editor: PERSON: Lawrence Hunter
editor preferred term: author list
definition: part of a document that enumerates the authors of the document
has curation status: IAO_0000120

institution list
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: institutional identification
term editor: PERSON: Lawrence Hunter
example of usage: The University of Colorado Denver School of Medicine and the University of Colorado Boulder.
editor preferred term: institution list
definition: part of a document that has parts that are institution identifications associated with the authors of the document
has curation status: IAO_0000120

author contributions section
type: Class
subclass of: document part
definition: A part of a publication that is about the specific contributions of each author
example of usage: LH conceived of the hypothesis, designed the study and contributed to the writing of the manuscript. KBC executed the experiments, analyzed the data, and contributed to the writing of the manuscript.
term editor: PERSON: Lawrence Hunter
editor preferred term: author contributions section
has curation status: IAO_0000120

acknowledgements section
type: Class
subclass of: document part
term editor: PERSON: Lawrence Hunter
definition: Part of a publication that is about the contributions of people or institutions other than the authors.
example of usage: The authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscript
editor preferred term: acknowledgements section
has curation status: IAO_0000120

footnote
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: document part
definition: A part of a document that is about a specific other part of the document. Usually footnotes are spatially segregated from the rest of the document.
term editor: PERSON: Lawrence Hunter
example of usage: The referent in the text is usually indicated by a special typographic character such as * or a superscripted number, which is also used to indicate the footnote that refers to that text.
alternative term: endnote
editor preferred term: footnote
has curation status: IAO_0000120

supplementary material to a document
type: Class
subclass of: document part
term editor: PERSON: Lawrence Hunter
alternative term: appendix
definition: part of a document that is segregated from the rest of the document due to its size
alternative term: supplementary material
editor preferred term: supplementary material to a document
has curation status: IAO_0000120

table of contents
type: Class
subclass of: table
definition: A table that relates document parts to specific locations in a document (usually page numbers). This is also a document part (subsumption there should be inferred).
term editor: PERSON: Lawrence Hunter
editor preferred term: table of contents
has curation status: IAO_0000125

table of figures
type: Class
subclass of: table
definition: A table that relates figures in a document to specific locations in that document (usually page numbers). This is also a document part (subsumption there should be inferred).
term editor: PERSON: Lawrence Hunter
editor preferred term: table of figures
has curation status: IAO_0000125

running title
type: Class
subclass of: document title
definition: A shorter version of a document title
term editor: PERSON: Lawrence Hunter
editor preferred term: running title
has curation status: IAO_0000125

copyright section
type: Class
subclass of: document part
definition: A document part that describes legal restrictions on making or distributing copies of the document
term editor: PERSON: Lawrence Hunter
example of usage: This work is licensed under a Creative Commons Attribution-Share Alike 3.0 United States License.
editor preferred term: copyright section
has curation status: IAO_0000120

cartesian spatial coordinate datum
type: Class
subclass of: data item
subclass of: Restriction
  on property: denotes
  some values from: zero dimensional region
subclass of: Restriction
  on property: has coordinate unit label
  cardinality: 1
editor note: 2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617
definition: A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude
term editor: Alan Ruttenberg
has curation status: IAO_0000120

one dimensional cartesian spatial coordinate datum
type: Class
subclass of: cartesian spatial coordinate datum
subclass of: Restriction
  on property: has x coordinate value
  cardinality: 1
subclass of: Restriction
  on property: denotes
  some values from: Class
    intersection of: zero dimensional region
    intersection of: Restriction
      on property: is part of
      some values from: one dimensional region
comment: A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region
term editor: Alan Ruttenberg
has curation status: IAO_0000124

two dimensional cartesian spatial coordinate datum
type: Class
subclass of: cartesian spatial coordinate datum
subclass of: Restriction
  on property: has x coordinate value
  cardinality: 1
subclass of: Restriction
  on property: has y coordinate value
  cardinality: 1
subclass of: Restriction
  on property: denotes
  some values from: Class
    intersection of: zero dimensional region
    intersection of: Restriction
      on property: is part of
      some values from: two dimensional region
comment: A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region
term editor: Alan Ruttenberg
has curation status: IAO_0000124

three dimensional cartesian spatial coordinate datum
type: Class
subclass of: cartesian spatial coordinate datum
subclass of: Restriction
  on property: has z coordinate value
  cardinality: 1
subclass of: Restriction
  on property: has x coordinate value
  cardinality: 1
subclass of: Restriction
  on property: denotes
  some values from: Class
    intersection of: zero dimensional region
    intersection of: Restriction
      on property: is part of
      some values from: three dimensional region
subclass of: Restriction
  on property: has y coordinate value
  cardinality: 1
comment: A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region
term editor: Alan Ruttenberg
has curation status: IAO_0000124

length measurement datum
type: Class
subclass of: scalar measurement datum
subclass of: Restriction
  on property: has measurement unit label
  some values from: UO_0000001
subclass of: Restriction
  on property: is quality measurement of
  some values from: PATO_0000122
definition: A scalar measurement datum that is the result of measurement of length quality
term editor: Alan Ruttenberg
has curation status: IAO_0000123

denotator type
type: Class
equivalent class: Class
  one of: IAO_0000410
  one of: IAO_0000420
  one of: IAO_0000421
subclass of: data about an ontology part
definition: A denotator type indicates how a term should be interpreted from an ontological perspective.
term editor: Alan Ruttenberg
definition source: Barry Smith, Werner Ceusters
example of usage: The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.

mass measurement datum
type: Class
subclass of: scalar measurement datum
subclass of: Class
  intersection of: Restriction
    on property: has measurement unit label
    all values from: UO_0000002
  intersection of: Restriction
    on property: is quality measurement of
    all values from: PATO_0000125
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A scalar measurement datum that is the result of measurement of mass quality
term editor: Person:Alan Ruttenberg
has curation status: IAO_0000123

hypothesis textual entity
type: Class
subclass of: textual entity
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A textual entity that expresses an assertion that is intended to be tested.
term editor: Person:Alan Ruttenberg
editor preferred term: hypothesis textual entity
example of usage: that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660
has curation status: IAO_0000120

time measurement datum
type: Class
subclass of: scalar measurement datum
subclass of: Class
  intersection of: Restriction
    on property: has measurement unit label
    all values from: UO_0000003
  intersection of: Restriction
    on property: is duration of
    all values from: process
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A scalar measurement datum that is the result of measuring a temporal interval
term editor: Person:Alan Ruttenberg
has curation status: IAO_0000123

postal address
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: geographical location
definition: A textual entity that is used as directive to deliver something to a person, or organization
editor note: 2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue http://code.google.com/p/information-artifact-ontology/issues/detail?id=59

email address
type: Class
subclass of: information content entity
editor note: Alan Ruttenberg 1/3/2012 - Provisional id, see issue at http://code.google.com/p/information-artifact-ontology/issues/detail?id=130&thanks=130&ts=1325636583
term editor: Person:Alan Ruttenberg
term editor: Person:Chris Stoeckart
editor preferred term: email address
has curation status: IAO_0000123

author role
type: Class
subclass of: role
definition: A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot
editor preferred term: author role
has curation status: IAO_0000125

data item extraction from journal article
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: data item
subclass of: Restriction
  on property: has_specified_input
  some values from: journal article
definition: a planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing
term editor: Person:Alan Ruttenberg
has curation status: IAO_0000120

documenting
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: information content entity
subclass of: Restriction
  on property: has_specified_output
  some values from: document
editor note: 6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape
term editor: Bjoern Peters
example of usage: Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
definition: a planned process in which a document is created or added to by including the specified input in it.
definition source: wikipedia http://en.wikipedia.org/wiki/Documenting
has curation status: IAO_0000125

line graph
type: Class
subclass of: graph
definition: A line graph is a type of graph created by connecting a series of data points together with a line.
definition source: GROUP:OBI
term editor: PERSON:Chris Stoeckert
term editor: PERSON:Melanie Courtot
definition source: WEB: http://en.wikipedia.org/wiki/Line_chart
alternative term: line chart
editor preferred term: line graph
has curation status: IAO_0000122

assigning a centrally registered identifier
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has participant
  some values from: CRID symbol
subclass of: Restriction
  on property: has participant
  some values from: CRID registry
example of usage: A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned.
term editor: Person:Alan Ruttenberg
term editor: Person:Bjoern Peters
term editor: Person:Melanie Courtot
definition: a planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity
has curation status: IAO_0000120

associating information with a CRID in the CRID registry
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: CRID symbol
subclass of: Restriction
  on property: has participant
  some values from: CRID registry
subclass of: Restriction
  on property: has_specified_input
  some values from: information content entity
definition: A planned process in which a CRID registry associates an information content entity with a CRID symbol
term editor: PERSON:Alan Ruttenberg
has curation status: IAO_0000120

obsolete_establishing a CRID registry
type: Class
subclass of: ObsoleteClass
definition: a planned process with the objective to establish a system that allows to refer to specific entities of a certain kind and store information about them, by establishing a CRID registry and plan specifications for the process of 1) assigning a CRID and 2) looking up a CRID.
editor note: MC, 20101124: deprecated following discussion at IAO call 20101124. Term was deemed not necessary - no use case for now.
has obsolescence reason: IAO_0000103

CRID symbol
type: Class
subclass of: symbol
definition: A symbol that is part_of a CRID and that is sufficient to look up a record from the CRID's registry.
editor note: IAO call, 20101124: 12345 is not a CRID symbol. To be a CRID symbol you need to have some information about the registry within which the CRID is recorded.
definition source: Original proposal from Bjoern, discussions at IAO calls
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bill Hogan
term editor: PERSON: Bjoern Peters
term editor: PERSON: Melanie Courtot
example of usage: PMID:12345, 12345 in a database column which has header "pubmedID"

CRID
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: has part
  some values from: CRID symbol
alternative term: Centrally Registered IDentifier
editor note: Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation.
definition: An information content entity that consists of a CRID symbol and additional information about which CRID registry it belongs.
example of usage: Entries in a Column of which the header is "Pubmed ID"
editor note: Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered.
definition source: Original proposal from Bjoern, discussions at IAO calls
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bill Hogan
term editor: PERSON: Bjoern Peters
term editor: PERSON: Melanie Courtot
example of usage: PMID:12345
example of usage: The following URL: "http://www.ncbi.nlm.nih.gov/pubmed/19918065"
example of usage: The following sentence contains a CRID: "The article with Pubmed ID: 19918065".

CRID registry
type: Class
subclass of: data set
definition: A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process.
editor note: IAO call, 20101124: PubMed registry is an instance of CRID registry
definition source: Original proposal from Bjoern, discussions at IAO calls
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bill Hogan
term editor: PERSON: Bjoern Peters
term editor: PERSON: Melanie Courtot
has curation status: IAO_0000123

looking up a CRID
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: CRID symbol
subclass of: Restriction
  on property: has participant
  some values from: CRID registry
definition: A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bill Hogan
term editor: PERSON: Bjoern Peters
term editor: PERSON: Melanie Courtot
has curation status: IAO_0000120

time stamped measurement datum
type: Class
subclass of: measurement datum
subclass of: Class
  intersection of: Restriction
    on property: has time stamp
    some values from: time measurement datum
  intersection of: Restriction
    on property: has measurement datum
    some values from: measurement datum
has curation status: IAO_0000123

time sampled measurement data set
type: Class
subclass of: data set
subclass of: Restriction
  on property: has part
  some values from: time stamped measurement datum
definition: A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time.
term editor: Alan Ruttenberg
alternative term: experimental time series
example of usage: pmid:20604925 - time-lapse live cell microscopy
has curation status: IAO_0000120

written name
type: Class
subclass of: textual entity
example of usage: "Bill Clinton"
example of usage: "The Eiffel Tower"
example of usage: "United States of America"
definition: A textual entity that denotes a particular in reality.
term editor: PERSON: Bill Hogan
curator note: The qualifier "written" is to set it apart from spoken names. Also, note the restrictions to particulars. We are not naming universals. We could however, be naming, attributive collections which are particulars, so "All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT" would be a name.
definition source: http://code.google.com/p/information-artifact-ontology/issues/detail
editor preferred term: written name
has curation status: IAO_0000125

software method
type: Class
subclass of: software
definition: A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task.
term editor: PERSON: Melanie Courtot
term editor: PERSON: Michel Dumontier
definition source: http://code.google.com/p/information-artifact-ontology/issues/detail
has curation status: IAO_0000123

software module
type: Class
subclass of: software
definition: A software module is software composed of a collection of software methods.
term editor: PERSON: Melanei Courtot
term editor: PERSON: Michel Dumontier
definition source: http://code.google.com/p/information-artifact-ontology/issues/detail
has curation status: IAO_0000123

software library
type: Class
subclass of: software
definition: A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application.
term editor: PERSON: Melanie Courtot
term editor: PERSON: Michel Dumontier
definition source: http://code.google.com/p/information-artifact-ontology/issues/detail
has curation status: IAO_0000123

software application
type: Class
subclass of: software
definition: A software application is software that can be directly executed by some processing unit.
term editor: PERSON: Melanie Courtot
term editor: PERSON: Michel Dumontier
definition source: http://code.google.com/p/information-artifact-ontology/issues/detail
has curation status: IAO_0000123

software script
type: Class
subclass of: software
definition: A software script is software whose instructions can be executed using a software interpreter.
term editor: PERSON: Melanie Courtot
term editor: PERSON: Michel Dumontier
definition source: http://code.google.com/p/information-artifact-ontology/issues/detail
has curation status: IAO_0000123

Cricetinae
type: Class
subclass of: Cricetidae
editor preferred term: Cricetinae
imported from: ncbitaxon.owl

Phodopus
type: Class
subclass of: Cricetinae
editor preferred term: Phodopus
imported from: ncbitaxon.owl

Phodopus sungorus
type: Class
subclass of: Phodopus
editor preferred term: Phodopus sungorus
imported from: ncbitaxon.owl

Muridae
type: Class
subclass of: Muroidea
editor preferred term: Muridae
imported from: ncbitaxon.owl

Mus
type: Class
subclass of: Murinae
editor preferred term: Mus
imported from: ncbitaxon.owl

Mus musculus
type: Class
subclass of: Mus
editor preferred term: Mus musculus
imported from: ncbitaxon.owl

Rattus
type: Class
subclass of: Murinae
editor preferred term: Rattus
imported from: ncbitaxon.owl

Rattus norvegicus
type: Class
subclass of: Rattus
editor preferred term: Rattus norvegicus
imported from: ncbitaxon.owl

Viruses
type: Class
subclass of: OBI_0100026
editor preferred term: Viruses
imported from: ncbitaxon.owl

Asteroideae
type: Class
subclass of: Asteraceae
editor preferred term: Asteroideae
imported from: ncbitaxon.owl

Heliantheae
type: Class
subclass of: Asteroideae
editor preferred term: Heliantheae
imported from: ncbitaxon.owl

Mutisieae
type: Class
subclass of: Mutisioideae
editor preferred term: Mutisieae
imported from: ncbitaxon.owl

Obtectomera
type: Class
subclass of: Ditrysia
editor preferred term: Obtectomera
imported from: ncbitaxon.owl

Rhodobacter
type: Class
subclass of: Rhodobacteraceae
editor preferred term: Rhodobacter
imported from: ncbitaxon.owl

canis group
type: Class
subclass of: Ehrlichia
editor preferred term: canis group
imported from: ncbitaxon.owl

phagocytophilum group
type: Class
subclass of: Anaplasma
editor preferred term: phagocytophilum group
imported from: ncbitaxon.owl

Rhodobacter sphaeroides
type: Class
subclass of: Rhodobacter
editor preferred term: Rhodobacter sphaeroides
imported from: ncbitaxon.owl

mitosporic Filobasidiales
type: Class
subclass of: Filobasidiales
editor preferred term: mitosporic Filobasidiales
imported from: ncbitaxon.owl

Thlaspi caerulescens
type: Class
subclass of: Thlaspi
editor preferred term: Thlaspi caerulescens
imported from: ncbitaxon.owl

Cryptococcus [NCBITaxon:107441]
type: Class
subclass of: mitosporic Filobasidiales
editor preferred term: Cryptococcus [NCBITaxon:107441]
imported from: ncbitaxon.owl

Parvoviridae
type: Class
subclass of: ssDNA viruses
editor preferred term: Parvoviridae
imported from: ncbitaxon.owl

Dependovirus
type: Class
subclass of: Parvovirinae
editor preferred term: Dependovirus
imported from: ncbitaxon.owl

Adeno-associated virus - 2
type: Class
subclass of: Dependovirus
editor preferred term: Adeno-associated virus - 2
imported from: ncbitaxon.owl

Rhodospirillum
type: Class
subclass of: Rhodospirillaceae
editor preferred term: Rhodospirillum
imported from: ncbitaxon.owl

Rhodospirillum rubrum
type: Class
subclass of: Rhodospirillum
editor preferred term: Rhodospirillum rubrum
imported from: ncbitaxon.owl

Chloroflexaceae
type: Class
subclass of: Chloroflexales
editor preferred term: Chloroflexaceae
imported from: ncbitaxon.owl

Nectriaceae
type: Class
subclass of: Hypocreales
editor preferred term: Nectriaceae
imported from: ncbitaxon.owl

Chloroflexus
type: Class
subclass of: Chloroflexaceae
editor preferred term: Chloroflexus
imported from: ncbitaxon.owl

Chloroflexus aurantiacus
type: Class
subclass of: Chloroflexus
editor preferred term: Chloroflexus aurantiacus
imported from: ncbitaxon.owl

Coronaviridae
type: Class
subclass of: Nidovirales
editor preferred term: Coronaviridae
imported from: ncbitaxon.owl

Coronavirus
type: Class
subclass of: Coronaviridae
editor preferred term: Coronavirus
imported from: ncbitaxon.owl

Penaeoidea
type: Class
subclass of: Dendrobranchiata
editor preferred term: Penaeoidea
imported from: ncbitaxon.owl

pseudomallei group
type: Class
subclass of: Burkholderia
editor preferred term: pseudomallei group
imported from: ncbitaxon.owl

Cyanobacteria
type: Class
subclass of: Bacteria
editor preferred term: Cyanobacteria
imported from: ncbitaxon.owl

Chroococcales
type: Class
subclass of: Cyanobacteria
editor preferred term: Chroococcales
imported from: ncbitaxon.owl

Synechococcus
type: Class
subclass of: Chroococcales
editor preferred term: Synechococcus
imported from: ncbitaxon.owl

Polytrichopsida
type: Class
subclass of: Moss Superclass V
editor preferred term: Polytrichopsida
imported from: ncbitaxon.owl

Populus tremula
type: Class
subclass of: Populus
editor preferred term: Populus tremula
imported from: ncbitaxon.owl

Synechocystis
type: Class
subclass of: Chroococcales
editor preferred term: Synechocystis
imported from: ncbitaxon.owl

spotted fever group
type: Class
subclass of: Rickettsia
editor preferred term: spotted fever group
imported from: ncbitaxon.owl

typhus group
type: Class
subclass of: Rickettsia
editor preferred term: typhus group
imported from: ncbitaxon.owl

Synechocystis sp.
type: Class
subclass of: Synechocystis
editor preferred term: Synechocystis sp.
imported from: ncbitaxon.owl

Saccharomyces kudriavzevii
type: Class
subclass of: Saccharomyces
editor preferred term: Saccharomyces kudriavzevii
imported from: ncbitaxon.owl

Saccharomyces mikatae
type: Class
subclass of: Saccharomyces
editor preferred term: Saccharomyces mikatae
imported from: ncbitaxon.owl

Funariidae
type: Class
subclass of: Bryopsida
editor preferred term: Funariidae
imported from: ncbitaxon.owl

Synechocystis sp. PCC 6803
type: Class
subclass of: Synechocystis
editor preferred term: Synechocystis sp. PCC 6803
imported from: ncbitaxon.owl

Oscillatoriales
type: Class
subclass of: Cyanobacteria
editor preferred term: Oscillatoriales
imported from: ncbitaxon.owl

Nostocales
type: Class
subclass of: Cyanobacteria
editor preferred term: Nostocales
imported from: ncbitaxon.owl

Nostocaceae
type: Class
subclass of: Nostocales
editor preferred term: Nostocaceae
imported from: ncbitaxon.owl

Anabaena
type: Class
subclass of: Nostocaceae
editor preferred term: Anabaena
imported from: ncbitaxon.owl

Anabaena variabilis
type: Class
subclass of: Anabaena
editor preferred term: Anabaena variabilis
imported from: ncbitaxon.owl

Teleostomi
type: Class
subclass of: Gnathostomata
editor preferred term: Teleostomi
imported from: ncbitaxon.owl

Euteleostomi
type: Class
subclass of: Teleostomi
editor preferred term: Euteleostomi
imported from: ncbitaxon.owl

Nostoc
type: Class
subclass of: Nostocaceae
editor preferred term: Nostoc
imported from: ncbitaxon.owl

Sphingobacteria
type: Class
subclass of: Bacteroidetes
editor preferred term: Sphingobacteria
imported from: ncbitaxon.owl

mitosporic Saccharomycetales
type: Class
subclass of: Saccharomycetales
editor preferred term: mitosporic Saccharomycetales
imported from: ncbitaxon.owl

Populus tomentosa
type: Class
subclass of: Populus
editor preferred term: Populus tomentosa
imported from: ncbitaxon.owl

Brucellaceae
type: Class
subclass of: Rhizobiales
editor preferred term: Brucellaceae
imported from: ncbitaxon.owl

Sulfolobaceae
type: Class
subclass of: Sulfolobales
editor preferred term: Sulfolobaceae
imported from: ncbitaxon.owl

Deinococcales
type: Class
subclass of: Deinococci
editor preferred term: Deinococcales
imported from: ncbitaxon.owl

Coxiellaceae
type: Class
subclass of: Legionellales
editor preferred term: Coxiellaceae
imported from: ncbitaxon.owl

Legionellales
type: Class
subclass of: Gammaproteobacteria
editor preferred term: Legionellales
imported from: ncbitaxon.owl

Burkholderiaceae
type: Class
subclass of: Burkholderiales
editor preferred term: Burkholderiaceae
imported from: ncbitaxon.owl

unclassified Burkholderiales
type: Class
subclass of: Burkholderiales
editor preferred term: unclassified Burkholderiales
imported from: ncbitaxon.owl

Thermoanaerobacter tengcongensis
type: Class
subclass of: Thermoanaerobacter
editor preferred term: Thermoanaerobacter tengcongensis
imported from: ncbitaxon.owl

Chromadorea
type: Class
subclass of: Nematoda
editor preferred term: Chromadorea
imported from: ncbitaxon.owl

Bombyciformes
type: Class
subclass of: Bombycoidea
editor preferred term: Bombyciformes
imported from: ncbitaxon.owl

Acidithiobacillus
type: Class
subclass of: Acidithiobacillaceae
editor preferred term: Acidithiobacillus
imported from: ncbitaxon.owl

Trichodesmium
type: Class
subclass of: Oscillatoriales
editor preferred term: Trichodesmium
imported from: ncbitaxon.owl

Trichodesmium erythraeum
type: Class
subclass of: Trichodesmium
editor preferred term: Trichodesmium erythraeum
imported from: ncbitaxon.owl

Paracoccidioides brasiliensis
type: Class
subclass of: Paracoccidioides
editor preferred term: Paracoccidioides brasiliensis
imported from: ncbitaxon.owl

Proteobacteria
type: Class
subclass of: Bacteria
editor preferred term: Proteobacteria
imported from: ncbitaxon.owl

Neoteleostei
type: Class
subclass of: Neognathi
editor preferred term: Neoteleostei
imported from: ncbitaxon.owl

Eurypterygii
type: Class
subclass of: Neoteleostei
editor preferred term: Eurypterygii
imported from: ncbitaxon.owl

Ctenosquamata
type: Class
subclass of: Eurypterygii
editor preferred term: Ctenosquamata
imported from: ncbitaxon.owl

Acanthomorpha
type: Class
subclass of: Ctenosquamata
editor preferred term: Acanthomorpha
imported from: ncbitaxon.owl

Euacanthomorpha
type: Class
subclass of: Acanthomorpha
editor preferred term: Euacanthomorpha
imported from: ncbitaxon.owl

Holacanthopterygii
type: Class
subclass of: Euacanthomorpha
editor preferred term: Holacanthopterygii
imported from: ncbitaxon.owl

Gammaproteobacteria
type: Class
subclass of: Proteobacteria
editor preferred term: Gammaproteobacteria
imported from: ncbitaxon.owl

Firmicutes
type: Class
subclass of: Bacteria
editor preferred term: Firmicutes
imported from: ncbitaxon.owl

Leuconostoc
type: Class
subclass of: Leuconostocaceae
editor preferred term: Leuconostoc
imported from: ncbitaxon.owl

Leuconostoc mesenteroides
type: Class
subclass of: Leuconostoc
editor preferred term: Leuconostoc mesenteroides
imported from: ncbitaxon.owl

Oenococcus oeni
type: Class
subclass of: Oenococcus
editor preferred term: Oenococcus oeni
imported from: ncbitaxon.owl

Pediococcus
type: Class
subclass of: Lactobacillaceae
editor preferred term: Pediococcus
imported from: ncbitaxon.owl

Pediococcus pentosaceus
type: Class
subclass of: Pediococcus
editor preferred term: Pediococcus pentosaceus
imported from: ncbitaxon.owl

Staphylococcus
type: Class
subclass of: Staphylococcaceae
editor preferred term: Staphylococcus
imported from: ncbitaxon.owl

Staphylococcus aureus
type: Class
subclass of: Staphylococcus
editor preferred term: Staphylococcus aureus
imported from: ncbitaxon.owl

Polytrichum juniperinum
type: Class
subclass of: Polytrichum
editor preferred term: Polytrichum juniperinum
imported from: ncbitaxon.owl

Deinococcus-Thermus
type: Class
subclass of: Bacteria
editor preferred term: Deinococcus-Thermus
imported from: ncbitaxon.owl

Deinococcus
type: Class
subclass of: Deinococcaceae
editor preferred term: Deinococcus
imported from: ncbitaxon.owl

Deinococcus radiodurans
type: Class
subclass of: Deinococcus
editor preferred term: Deinococcus radiodurans
imported from: ncbitaxon.owl

Euacanthopterygii
type: Class
subclass of: Acanthopterygii
editor preferred term: Euacanthopterygii
imported from: ncbitaxon.owl

Streptococcaceae
type: Class
subclass of: Lactobacillales
editor preferred term: Streptococcaceae
imported from: ncbitaxon.owl

Streptococcus
type: Class
subclass of: Streptococcaceae
editor preferred term: Streptococcus
imported from: ncbitaxon.owl

Streptococcus gordonii
type: Class
subclass of: Streptococcus
editor preferred term: Streptococcus gordonii
imported from: ncbitaxon.owl

Streptococcus suis
type: Class
subclass of: Streptococcus
editor preferred term: Streptococcus suis
imported from: ncbitaxon.owl

Streptococcus mutans
type: Class
subclass of: Streptococcus
editor preferred term: Streptococcus mutans
imported from: ncbitaxon.owl

Streptococcus agalactiae
type: Class
subclass of: Streptococcus
editor preferred term: Streptococcus agalactiae
imported from: ncbitaxon.owl

Streptophytina
type: Class
subclass of: Streptophyta
editor preferred term: Streptophytina
imported from: ncbitaxon.owl

Streptococcus pneumoniae
type: Class
subclass of: Streptococcus
editor preferred term: Streptococcus pneumoniae
imported from: ncbitaxon.owl

Magnetospirillum
type: Class
subclass of: Rhodospirillaceae
editor preferred term: Magnetospirillum
imported from: ncbitaxon.owl

Streptococcus pyogenes
type: Class
subclass of: Streptococcus
editor preferred term: Streptococcus pyogenes
imported from: ncbitaxon.owl

Thlaspi
type: Class
subclass of: Brassicaceae
editor preferred term: Thlaspi
imported from: ncbitaxon.owl

Burkholderia mallei
type: Class
subclass of: Burkholderia
editor preferred term: Burkholderia mallei
imported from: ncbitaxon.owl

Penaeus
type: Class
subclass of: Penaeidae
editor preferred term: Penaeus
imported from: ncbitaxon.owl

Coffea
type: Class
subclass of: Coffeeae
editor preferred term: Coffea
imported from: ncbitaxon.owl

Coffea arabica
type: Class
subclass of: Coffea
editor preferred term: Coffea arabica
imported from: ncbitaxon.owl

Burkholderia fungorum
type: Class
subclass of: Burkholderia
editor preferred term: Burkholderia fungorum
imported from: ncbitaxon.owl

Enterococcus
type: Class
subclass of: Enterococcaceae
editor preferred term: Enterococcus
imported from: ncbitaxon.owl

Enterococcus faecalis
type: Class
subclass of: Enterococcus
editor preferred term: Enterococcus faecalis
imported from: ncbitaxon.owl

Enterococcus faecium
type: Class
subclass of: Enterococcus
editor preferred term: Enterococcus faecium
imported from: ncbitaxon.owl

Gerbera
type: Class
subclass of: Mutisieae
editor preferred term: Gerbera
imported from: ncbitaxon.owl

Xanthomonadales
type: Class
subclass of: Gammaproteobacteria
editor preferred term: Xanthomonadales
imported from: ncbitaxon.owl

Pseudomonadaceae
type: Class
subclass of: Pseudomonadales
editor preferred term: Pseudomonadaceae
imported from: ncbitaxon.owl

Alteromonadales
type: Class
subclass of: Gammaproteobacteria
editor preferred term: Alteromonadales
imported from: ncbitaxon.owl

Vibrionales
type: Class
subclass of: Gammaproteobacteria
editor preferred term: Vibrionales
imported from: ncbitaxon.owl

Pasteurellales
type: Class
subclass of: Gammaproteobacteria
editor preferred term: Pasteurellales
imported from: ncbitaxon.owl

Lactococcus
type: Class
subclass of: Streptococcaceae
editor preferred term: Lactococcus
imported from: ncbitaxon.owl

Lactococcus lactis
type: Class
subclass of: Lactococcus
editor preferred term: Lactococcus lactis
imported from: ncbitaxon.owl

Spirochaetales
type: Class
subclass of: Spirochaetes (class)
editor preferred term: Spirochaetales
imported from: ncbitaxon.owl

Pseudomonas aeruginosa group
type: Class
subclass of: Pseudomonas
editor preferred term: Pseudomonas aeruginosa group
imported from: ncbitaxon.owl

Pseudomonas fluorescens group
type: Class
subclass of: Pseudomonas
editor preferred term: Pseudomonas fluorescens group
imported from: ncbitaxon.owl

Pseudomonas putida group
type: Class
subclass of: Pseudomonas
editor preferred term: Pseudomonas putida group
imported from: ncbitaxon.owl

Spirochaetaceae
type: Class
subclass of: Spirochaetales
editor preferred term: Spirochaetaceae
imported from: ncbitaxon.owl

Borrelia
type: Class
subclass of: Spirochaetaceae
editor preferred term: Borrelia
imported from: ncbitaxon.owl

Pteridaceae
type: Class
subclass of: Filicales
editor preferred term: Pteridaceae
imported from: ncbitaxon.owl

Bacillales
type: Class
subclass of: Bacilli
editor preferred term: Bacillales
imported from: ncbitaxon.owl

Bacillus
type: Class
subclass of: Bacillaceae
editor preferred term: Bacillus
imported from: ncbitaxon.owl

Borrelia burgdorferi
type: Class
subclass of: Borrelia burgdorferi group
editor preferred term: Borrelia burgdorferi
imported from: ncbitaxon.owl

Bacillus anthracis
type: Class
subclass of: Bacillus cereus group
editor preferred term: Bacillus anthracis
imported from: ncbitaxon.owl

Pinus [NCBITaxon:139271]
type: Class
subclass of: Pinus
editor preferred term: Pinus [NCBITaxon:139271]
imported from: ncbitaxon.owl

Bacillus cereus
type: Class
subclass of: Bacillus cereus group
editor preferred term: Bacillus cereus
imported from: ncbitaxon.owl

Bacillus subtilis
type: Class
subclass of: Bacillus
editor preferred term: Bacillus subtilis
imported from: ncbitaxon.owl

Mycetozoa
type: Class
subclass of: Eukaryota
editor preferred term: Mycetozoa
imported from: ncbitaxon.owl

Methanothermobacter
type: Class
subclass of: Methanobacteriaceae
editor preferred term: Methanothermobacter
imported from: ncbitaxon.owl

Methanothermobacter thermautotrophicus
type: Class
subclass of: Methanothermobacter
editor preferred term: Methanothermobacter thermautotrophicus
imported from: ncbitaxon.owl

Ehrhartoideae
type: Class
subclass of: BEP clade
editor preferred term: Ehrhartoideae
imported from: ncbitaxon.owl

Pooideae
type: Class
subclass of: BEP clade
editor preferred term: Pooideae
imported from: ncbitaxon.owl

Panicoideae
type: Class
subclass of: PACCAD clade
editor preferred term: Panicoideae
imported from: ncbitaxon.owl

PACCAD clade
type: Class
subclass of: Poaceae
editor preferred term: PACCAD clade
imported from: ncbitaxon.owl

Oryzeae
type: Class
subclass of: Ehrhartoideae
editor preferred term: Oryzeae
imported from: ncbitaxon.owl

Poeae
type: Class
subclass of: Pooideae
editor preferred term: Poeae
imported from: ncbitaxon.owl

Triticeae
type: Class
subclass of: Pooideae
editor preferred term: Triticeae
imported from: ncbitaxon.owl

Andropogoneae
type: Class
subclass of: Panicoideae
editor preferred term: Andropogoneae
imported from: ncbitaxon.owl

Saccharomycotina
type: Class
subclass of: Ascomycota
editor preferred term: Saccharomycotina
imported from: ncbitaxon.owl

Pezizomycotina
type: Class
subclass of: Ascomycota
editor preferred term: Pezizomycotina
imported from: ncbitaxon.owl

Dothideomycetes et Chaetothyriomycetes incertae sedis
type: Class
subclass of: Pezizomycotina
editor preferred term: Dothideomycetes et Chaetothyriomycetes incertae sedis
imported from: ncbitaxon.owl

Eurotiomycetes
type: Class
subclass of: Pezizomycotina
editor preferred term: Eurotiomycetes
imported from: ncbitaxon.owl

Sordariomycetes
type: Class
subclass of: Pezizomycotina
editor preferred term: Sordariomycetes
imported from: ncbitaxon.owl

Sordariomycetes incertae sedis
type: Class
subclass of: Sordariomycetes
editor preferred term: Sordariomycetes incertae sedis
imported from: ncbitaxon.owl

Schizosaccharomycetes
type: Class
subclass of: Ascomycota
editor preferred term: Schizosaccharomycetes
imported from: ncbitaxon.owl

Magnaporthe
type: Class
subclass of: Magnaporthaceae
editor preferred term: Magnaporthe
imported from: ncbitaxon.owl

Magnaporthe grisea
type: Class
subclass of: Magnaporthe
editor preferred term: Magnaporthe grisea
imported from: ncbitaxon.owl

Clostridium
type: Class
subclass of: Clostridiaceae
editor preferred term: Clostridium
imported from: ncbitaxon.owl

Clostridium acetobutylicum
type: Class
subclass of: Clostridium
editor preferred term: Clostridium acetobutylicum
imported from: ncbitaxon.owl

Clostridium botulinum
type: Class
subclass of: Clostridium
editor preferred term: Clostridium botulinum
imported from: ncbitaxon.owl

Clostridium sporogenes
type: Class
subclass of: Clostridium
editor preferred term: Clostridium sporogenes
imported from: ncbitaxon.owl

Clostridium thermocellum
type: Class
subclass of: Clostridium
editor preferred term: Clostridium thermocellum
imported from: ncbitaxon.owl

Moorella thermoacetica
type: Class
subclass of: Moorella
editor preferred term: Moorella thermoacetica
imported from: ncbitaxon.owl

Tremellomycetidae
type: Class
subclass of: Heterobasidiomycetes
editor preferred term: Tremellomycetidae
imported from: ncbitaxon.owl

Homobasidiomycetes
type: Class
subclass of: Hymenomycetes
editor preferred term: Homobasidiomycetes
imported from: ncbitaxon.owl

Caulobacter vibrioides
type: Class
subclass of: Caulobacter
editor preferred term: Caulobacter vibrioides
imported from: ncbitaxon.owl

Plantaginaceae
type: Class
subclass of: Lamiales
editor preferred term: Plantaginaceae
imported from: ncbitaxon.owl

Group 2 species
type: Class
subclass of: Coronavirus
editor preferred term: Group 2 species
imported from: ncbitaxon.owl

Treponema
type: Class
subclass of: Spirochaetaceae
editor preferred term: Treponema
imported from: ncbitaxon.owl

Lactobacillus
type: Class
subclass of: Lactobacillaceae
editor preferred term: Lactobacillus
imported from: ncbitaxon.owl

Treponema denticola
type: Class
subclass of: Treponema
editor preferred term: Treponema denticola
imported from: ncbitaxon.owl

Citrus aurantiifolia
type: Class
subclass of: Citrus
editor preferred term: Citrus aurantiifolia
imported from: ncbitaxon.owl

Lactobacillus gasseri
type: Class
subclass of: Lactobacillus
editor preferred term: Lactobacillus gasseri
imported from: ncbitaxon.owl

Lactobacillus sakei
type: Class
subclass of: Lactobacillus
editor preferred term: Lactobacillus sakei
imported from: ncbitaxon.owl

Treponema pallidum
type: Class
subclass of: Treponema
editor preferred term: Treponema pallidum
imported from: ncbitaxon.owl

Lactobacillus salivarius
type: Class
subclass of: Lactobacillus
editor preferred term: Lactobacillus salivarius
imported from: ncbitaxon.owl

Listeria
type: Class
subclass of: Listeriaceae
editor preferred term: Listeria
imported from: ncbitaxon.owl

Phaseoleae
type: Class
subclass of: Papilionoideae
editor preferred term: Phaseoleae
imported from: ncbitaxon.owl

Trifolieae
type: Class
subclass of: Papilionoideae
editor preferred term: Trifolieae
imported from: ncbitaxon.owl

Vicieae
type: Class
subclass of: Papilionoideae
editor preferred term: Vicieae
imported from: ncbitaxon.owl

Loteae
type: Class
subclass of: Papilionoideae
editor preferred term: Loteae
imported from: ncbitaxon.owl

Listeria monocytogenes
type: Class
subclass of: Listeria
editor preferred term: Listeria monocytogenes
imported from: ncbitaxon.owl

Listeria innocua
type: Class
subclass of: Listeria
editor preferred term: Listeria innocua
imported from: ncbitaxon.owl

Corynebacteriaceae
type: Class
subclass of: Corynebacterineae
editor preferred term: Corynebacteriaceae
imported from: ncbitaxon.owl

Actinomyces
type: Class
subclass of: Actinomycetaceae
editor preferred term: Actinomyces
imported from: ncbitaxon.owl

Actinomyces naeslundii
type: Class
subclass of: Actinomyces
editor preferred term: Actinomyces naeslundii
imported from: ncbitaxon.owl

Novosphingobium
type: Class
subclass of: Sphingomonadaceae
editor preferred term: Novosphingobium
imported from: ncbitaxon.owl

Heterobasidiomycetes
type: Class
subclass of: Hymenomycetes
editor preferred term: Heterobasidiomycetes
imported from: ncbitaxon.owl

Bifidobacterium
type: Class
subclass of: Bifidobacteriaceae
editor preferred term: Bifidobacterium
imported from: ncbitaxon.owl

Ixoroideae
type: Class
subclass of: Rubiaceae
editor preferred term: Ixoroideae
imported from: ncbitaxon.owl

Coffeeae
type: Class
subclass of: Ixoroideae
editor preferred term: Coffeeae
imported from: ncbitaxon.owl

Corynebacterium
type: Class
subclass of: Corynebacteriaceae
editor preferred term: Corynebacterium
imported from: ncbitaxon.owl

Rosoideae
type: Class
subclass of: Rosaceae
editor preferred term: Rosoideae
imported from: ncbitaxon.owl

Corynebacterium glutamicum
type: Class
subclass of: Corynebacterium
editor preferred term: Corynebacterium glutamicum
imported from: ncbitaxon.owl

Passeroidea
type: Class
subclass of: Passeriformes
editor preferred term: Passeroidea
imported from: ncbitaxon.owl

Thermoanaerobacter
type: Class
subclass of: Thermoanaerobacteriaceae
editor preferred term: Thermoanaerobacter
imported from: ncbitaxon.owl

Actinobacteria (class)
type: Class
subclass of: Actinobacteria
editor preferred term: Actinobacteria (class)
imported from: ncbitaxon.owl

Mycobacteriaceae
type: Class
subclass of: Corynebacterineae
editor preferred term: Mycobacteriaceae
imported from: ncbitaxon.owl

Mycobacterium
type: Class
subclass of: Mycobacteriaceae
editor preferred term: Mycobacterium
imported from: ncbitaxon.owl

Mycobacterium leprae
type: Class
subclass of: Mycobacterium
editor preferred term: Mycobacterium leprae
imported from: ncbitaxon.owl

Mycobacterium tuberculosis
type: Class
subclass of: Mycobacterium tuberculosis complex
editor preferred term: Mycobacterium tuberculosis
imported from: ncbitaxon.owl

Gerbera hybrid cultivar
type: Class
subclass of: Gerbera
editor preferred term: Gerbera hybrid cultivar
imported from: ncbitaxon.owl

Deinococcaceae
type: Class
subclass of: Deinococcales
editor preferred term: Deinococcaceae
imported from: ncbitaxon.owl

Enterogona
type: Class
subclass of: Ascidiacea
editor preferred term: Enterogona
imported from: ncbitaxon.owl

Thermoprotei
type: Class
subclass of: Crenarchaeota
editor preferred term: Thermoprotei
imported from: ncbitaxon.owl

Methanobacteria
type: Class
subclass of: Euryarchaeota
editor preferred term: Methanobacteria
imported from: ncbitaxon.owl

Halobacteria
type: Class
subclass of: Euryarchaeota
editor preferred term: Halobacteria
imported from: ncbitaxon.owl

Thermoplasmata
type: Class
subclass of: Euryarchaeota
editor preferred term: Thermoplasmata
imported from: ncbitaxon.owl

Thermococci
type: Class
subclass of: Euryarchaeota
editor preferred term: Thermococci
imported from: ncbitaxon.owl

Archaeoglobi
type: Class
subclass of: Euryarchaeota
editor preferred term: Archaeoglobi
imported from: ncbitaxon.owl

Psathyrellaceae
type: Class
subclass of: Agaricales
editor preferred term: Psathyrellaceae
imported from: ncbitaxon.owl

Coprinopsis
type: Class
subclass of: Psathyrellaceae
editor preferred term: Coprinopsis
imported from: ncbitaxon.owl

Drosophiliti
type: Class
subclass of: Drosophilina
editor preferred term: Drosophiliti
imported from: ncbitaxon.owl

Entomoplasmatales
type: Class
subclass of: Mollicutes
editor preferred term: Entomoplasmatales
imported from: ncbitaxon.owl

Actinopteri
type: Class
subclass of: Actinopterygii
editor preferred term: Actinopteri
imported from: ncbitaxon.owl

Elopocephala
type: Class
subclass of: Teleostei
editor preferred term: Elopocephala
imported from: ncbitaxon.owl

Clupeocephala
type: Class
subclass of: Elopocephala
editor preferred term: Clupeocephala
imported from: ncbitaxon.owl

Otophysi
type: Class
subclass of: Ostariophysi
editor preferred term: Otophysi
imported from: ncbitaxon.owl

Cypriniphysi
type: Class
subclass of: Otophysi
editor preferred term: Cypriniphysi
imported from: ncbitaxon.owl

Otocephala
type: Class
subclass of: Clupeocephala
editor preferred term: Otocephala
imported from: ncbitaxon.owl

Clostridia
type: Class
subclass of: Firmicutes
editor preferred term: Clostridia
imported from: ncbitaxon.owl

Clostridiales
type: Class
subclass of: Clostridia
editor preferred term: Clostridiales
imported from: ncbitaxon.owl

Peptococcaceae
type: Class
subclass of: Clostridiales
editor preferred term: Peptococcaceae
imported from: ncbitaxon.owl

Thermoanaerobacteriaceae
type: Class
subclass of: Thermoanaerobacteriales
editor preferred term: Thermoanaerobacteriaceae
imported from: ncbitaxon.owl

Bacillaceae
type: Class
subclass of: Bacillales
editor preferred term: Bacillaceae
imported from: ncbitaxon.owl

Listeriaceae
type: Class
subclass of: Bacillales
editor preferred term: Listeriaceae
imported from: ncbitaxon.owl

Alicyclobacillaceae
type: Class
subclass of: Bacillales
editor preferred term: Alicyclobacillaceae
imported from: ncbitaxon.owl

Lactobacillales
type: Class
subclass of: Bacilli
editor preferred term: Lactobacillales
imported from: ncbitaxon.owl

Neognathi
type: Class
subclass of: Euteleostei
editor preferred term: Neognathi
imported from: ncbitaxon.owl

Salmonoidei
type: Class
subclass of: Salmoniformes
editor preferred term: Salmonoidei
imported from: ncbitaxon.owl

Anurophorinae
type: Class
subclass of: Isotomidae
editor preferred term: Anurophorinae
imported from: ncbitaxon.owl

Cryptopygus
type: Class
subclass of: Anurophorinae
editor preferred term: Cryptopygus
imported from: ncbitaxon.owl

Cryptopygus antarcticus
type: Class
subclass of: Cryptopygus
editor preferred term: Cryptopygus antarcticus
imported from: ncbitaxon.owl

Aquificae (class)
type: Class
subclass of: Aquificae
editor preferred term: Aquificae (class)
imported from: ncbitaxon.owl

Magnetospirillum magnetotacticum
type: Class
subclass of: Magnetospirillum
editor preferred term: Magnetospirillum magnetotacticum
imported from: ncbitaxon.owl

Streptomyces
type: Class
subclass of: Streptomycetaceae
editor preferred term: Streptomyces
imported from: ncbitaxon.owl

Thermotogae (class)
type: Class
subclass of: Thermotogae
editor preferred term: Thermotogae (class)
imported from: ncbitaxon.owl

Thermotogaceae
type: Class
subclass of: Thermotogales
editor preferred term: Thermotogaceae
imported from: ncbitaxon.owl

Deinococci
type: Class
subclass of: Deinococcus-Thermus
editor preferred term: Deinococci
imported from: ncbitaxon.owl

Orbiliomycetes
type: Class
subclass of: Pezizomycotina
editor preferred term: Orbiliomycetes
imported from: ncbitaxon.owl

Orbiliales
type: Class
subclass of: Orbiliomycetes
editor preferred term: Orbiliales
imported from: ncbitaxon.owl

Zinnia
type: Class
subclass of: Heliantheae
editor preferred term: Zinnia
imported from: ncbitaxon.owl

Streptomyces coelicolor
type: Class
subclass of: Streptomyces
editor preferred term: Streptomyces coelicolor
imported from: ncbitaxon.owl

Lepidium
type: Class
subclass of: Brassicaceae
editor preferred term: Lepidium
imported from: ncbitaxon.owl

Campylobacter
type: Class
subclass of: Campylobacteraceae
editor preferred term: Campylobacter
imported from: ncbitaxon.owl

Desulfovibrionaceae
type: Class
subclass of: Desulfovibrionales
editor preferred term: Desulfovibrionaceae
imported from: ncbitaxon.owl

Pleuronichthys
type: Class
subclass of: Pleuronectidae
editor preferred term: Pleuronichthys
imported from: ncbitaxon.owl

Pleuronichthys verticalis
type: Class
subclass of: Pleuronichthys
editor preferred term: Pleuronichthys verticalis
imported from: ncbitaxon.owl

Corynebacterium glutamicum ATCC 13032
type: Class
subclass of: Corynebacterium glutamicum
editor preferred term: Corynebacterium glutamicum ATCC 13032
imported from: ncbitaxon.owl

Campylobacter jejuni
type: Class
subclass of: Campylobacter
editor preferred term: Campylobacter jejuni
imported from: ncbitaxon.owl

Pancrustacea
type: Class
subclass of: Mandibulata
editor preferred term: Pancrustacea
imported from: ncbitaxon.owl

Mandibulata
type: Class
subclass of: Arthropoda
editor preferred term: Mandibulata
imported from: ncbitaxon.owl

Bacteria
type: Class
subclass of: OBI_0100026
editor preferred term: Bacteria
imported from: ncbitaxon.owl

Sphingobacteriales
type: Class
subclass of: Sphingobacteria
editor preferred term: Sphingobacteriales
imported from: ncbitaxon.owl

Aquificae
type: Class
subclass of: Bacteria
editor preferred term: Aquificae
imported from: ncbitaxon.owl

Chloroflexi
type: Class
subclass of: Bacteria
editor preferred term: Chloroflexi
imported from: ncbitaxon.owl

Thermotogae
type: Class
subclass of: Bacteria
editor preferred term: Thermotogae
imported from: ncbitaxon.owl

Actinobacteria
type: Class
subclass of: Bacteria
editor preferred term: Actinobacteria
imported from: ncbitaxon.owl

Thermobifida fusca
type: Class
subclass of: Thermobifida
editor preferred term: Thermobifida fusca
imported from: ncbitaxon.owl

Fusobacteria (class)
type: Class
subclass of: Fusobacteria
editor preferred term: Fusobacteria (class)
imported from: ncbitaxon.owl

Fusobacterales
type: Class
subclass of: Fusobacteria (class)
editor preferred term: Fusobacterales
imported from: ncbitaxon.owl

Fusobacteriaceae
type: Class
subclass of: Fusobacterales
editor preferred term: Fusobacteriaceae
imported from: ncbitaxon.owl

Spirochaetes
type: Class
subclass of: Bacteria
editor preferred term: Spirochaetes
imported from: ncbitaxon.owl

Spirochaetes (class)
type: Class
subclass of: Spirochaetes
editor preferred term: Spirochaetes (class)
imported from: ncbitaxon.owl

Actinomycetales
type: Class
subclass of: Actinobacteridae
editor preferred term: Actinomycetales
imported from: ncbitaxon.owl

Chlamydiae
type: Class
subclass of: Chlamydiae/Verrucomicrobia group
editor preferred term: Chlamydiae
imported from: ncbitaxon.owl

Chlamydiae (class)
type: Class
subclass of: Chlamydiae
editor preferred term: Chlamydiae (class)
imported from: ncbitaxon.owl

Rhodospirillales
type: Class
subclass of: Alphaproteobacteria
editor preferred term: Rhodospirillales
imported from: ncbitaxon.owl

Rhodobacterales
type: Class
subclass of: Alphaproteobacteria
editor preferred term: Rhodobacterales
imported from: ncbitaxon.owl

Sphingomonadales
type: Class
subclass of: Alphaproteobacteria
editor preferred term: Sphingomonadales
imported from: ncbitaxon.owl

Caulobacterales
type: Class
subclass of: Alphaproteobacteria
editor preferred term: Caulobacterales
imported from: ncbitaxon.owl

Herminiimonas arsenicoxydans
type: Class
subclass of: Herminiimonas
editor preferred term: Herminiimonas arsenicoxydans
imported from: ncbitaxon.owl

Actinomycetaceae
type: Class
subclass of: Actinomycineae
editor preferred term: Actinomycetaceae
imported from: ncbitaxon.owl

Streptomycetaceae
type: Class
subclass of: Streptomycineae
editor preferred term: Streptomycetaceae
imported from: ncbitaxon.owl

Methylophilales
type: Class
subclass of: Betaproteobacteria
editor preferred term: Methylophilales
imported from: ncbitaxon.owl

Neisseriales
type: Class
subclass of: Betaproteobacteria
editor preferred term: Neisseriales
imported from: ncbitaxon.owl

Rhodocyclales
type: Class
subclass of: Betaproteobacteria
editor preferred term: Rhodocyclales
imported from: ncbitaxon.owl

Homo/Pan/Gorilla group
type: Class
subclass of: Hominidae
editor preferred term: Homo/Pan/Gorilla group
imported from: ncbitaxon.owl

Mycoplasmatales
type: Class
subclass of: Mollicutes
editor preferred term: Mycoplasmatales
imported from: ncbitaxon.owl

Pasteuria nishizawae
type: Class
subclass of: Pasteuria
editor preferred term: Pasteuria nishizawae
imported from: ncbitaxon.owl

Helicobacter
type: Class
subclass of: Helicobacteraceae
editor preferred term: Helicobacter
imported from: ncbitaxon.owl

Mycoplasmataceae
type: Class
subclass of: Mycoplasmatales
editor preferred term: Mycoplasmataceae
imported from: ncbitaxon.owl

Mycoplasma
type: Class
subclass of: Mycoplasmataceae
editor preferred term: Mycoplasma
imported from: ncbitaxon.owl

Mycoplasma genitalium
type: Class
subclass of: Mycoplasma
editor preferred term: Mycoplasma genitalium
imported from: ncbitaxon.owl

Helicobacter pylori
type: Class
subclass of: Helicobacter
editor preferred term: Helicobacter pylori
imported from: ncbitaxon.owl

Streptococcus mutans UA159
type: Class
subclass of: Streptococcus mutans
editor preferred term: Streptococcus mutans UA159
imported from: ncbitaxon.owl

Mycoplasma pneumoniae
type: Class
subclass of: Mycoplasma
editor preferred term: Mycoplasma pneumoniae
imported from: ncbitaxon.owl

Mycoplasma pulmonis
type: Class
subclass of: Mycoplasma
editor preferred term: Mycoplasma pulmonis
imported from: ncbitaxon.owl

Ureaplasma
type: Class
subclass of: Mycoplasmataceae
editor preferred term: Ureaplasma
imported from: ncbitaxon.owl

Ureaplasma urealyticum
type: Class
subclass of: Ureaplasma
editor preferred term: Ureaplasma urealyticum
imported from: ncbitaxon.owl

Desulfovibrionales
type: Class
subclass of: Deltaproteobacteria
editor preferred term: Desulfovibrionales
imported from: ncbitaxon.owl

Geobacteraceae
type: Class
subclass of: Desulfuromonadales
editor preferred term: Geobacteraceae
imported from: ncbitaxon.owl

Campylobacterales
type: Class
subclass of: Epsilonproteobacteria
editor preferred term: Campylobacterales
imported from: ncbitaxon.owl

Mesoplasma florum
type: Class
subclass of: Mesoplasma
editor preferred term: Mesoplasma florum
imported from: ncbitaxon.owl

Archaea
type: Class
subclass of: OBI_0100026
editor preferred term: Archaea
imported from: ncbitaxon.owl

Methanobacteriales
type: Class
subclass of: Methanobacteria
editor preferred term: Methanobacteriales
imported from: ncbitaxon.owl

Methanobacteriaceae
type: Class
subclass of: Methanobacteriales
editor preferred term: Methanobacteriaceae
imported from: ncbitaxon.owl

Sylvia communis
type: Class
subclass of: Sylvia
editor preferred term: Sylvia communis
imported from: ncbitaxon.owl

Lymnaeoidea
type: Class
subclass of: Basommatophora
editor preferred term: Lymnaeoidea
imported from: ncbitaxon.owl

Antirrhineae
type: Class
subclass of: Plantaginaceae
editor preferred term: Antirrhineae
imported from: ncbitaxon.owl

Bifidobacterium longum
type: Class
subclass of: Bifidobacterium
editor preferred term: Bifidobacterium longum
imported from: ncbitaxon.owl

Mutisioideae
type: Class
subclass of: Asteraceae
editor preferred term: Mutisioideae
imported from: ncbitaxon.owl

Methanosarcinaceae
type: Class
subclass of: Methanosarcinales
editor preferred term: Methanosarcinaceae
imported from: ncbitaxon.owl

Methanosarcina
type: Class
subclass of: Methanosarcinaceae
editor preferred term: Methanosarcina
imported from: ncbitaxon.owl

Methanosarcina barkeri
type: Class
subclass of: Methanosarcina
editor preferred term: Methanosarcina barkeri
imported from: ncbitaxon.owl

Methanosarcina mazei
type: Class
subclass of: Methanosarcina
editor preferred term: Methanosarcina mazei
imported from: ncbitaxon.owl

Methanococcoides
type: Class
subclass of: Methanosarcinaceae
editor preferred term: Methanococcoides
imported from: ncbitaxon.owl

Hypocreomycetidae
type: Class
subclass of: Sordariomycetes
editor preferred term: Hypocreomycetidae
imported from: ncbitaxon.owl

Sordariomycetidae
type: Class
subclass of: Sordariomycetes
editor preferred term: Sordariomycetidae
imported from: ncbitaxon.owl

Archaeoglobales
type: Class
subclass of: Archaeoglobi
editor preferred term: Archaeoglobales
imported from: ncbitaxon.owl

Archaeoglobaceae
type: Class
subclass of: Archaeoglobales
editor preferred term: Archaeoglobaceae
imported from: ncbitaxon.owl

Archaeoglobus
type: Class
subclass of: Archaeoglobaceae
editor preferred term: Archaeoglobus
imported from: ncbitaxon.owl

Archaeoglobus fulgidus
type: Class
subclass of: Archaeoglobus
editor preferred term: Archaeoglobus fulgidus
imported from: ncbitaxon.owl

Halobacteriales
type: Class
subclass of: Halobacteria
editor preferred term: Halobacteriales
imported from: ncbitaxon.owl

Halobacteriaceae
type: Class
subclass of: Halobacteriales
editor preferred term: Halobacteriaceae
imported from: ncbitaxon.owl

Halobacterium
type: Class
subclass of: Halobacteriaceae
editor preferred term: Halobacterium
imported from: ncbitaxon.owl

Halobacterium salinarum
type: Class
subclass of: Halobacterium
editor preferred term: Halobacterium salinarum
imported from: ncbitaxon.owl

Halobacterium sp.
type: Class
subclass of: Halobacterium
editor preferred term: Halobacterium sp.
imported from: ncbitaxon.owl

Burkholderiales Genera incertae sedis
type: Class
subclass of: unclassified Burkholderiales
editor preferred term: Burkholderiales Genera incertae sedis
imported from: ncbitaxon.owl

Haloferax volcanii
type: Class
subclass of: Haloferax
editor preferred term: Haloferax volcanii
imported from: ncbitaxon.owl

Methanomicrobia
type: Class
subclass of: Euryarchaeota
editor preferred term: Methanomicrobia
imported from: ncbitaxon.owl

Acidithiobacillales
type: Class
subclass of: Gammaproteobacteria
editor preferred term: Acidithiobacillales
imported from: ncbitaxon.owl

Acidithiobacillaceae
type: Class
subclass of: Acidithiobacillales
editor preferred term: Acidithiobacillaceae
imported from: ncbitaxon.owl

Haloferax
type: Class
subclass of: Halobacteriaceae
editor preferred term: Haloferax
imported from: ncbitaxon.owl

Thermococcales
type: Class
subclass of: Thermococci
editor preferred term: Thermococcales
imported from: ncbitaxon.owl

Thermococcaceae
type: Class
subclass of: Thermococcales
editor preferred term: Thermococcaceae
imported from: ncbitaxon.owl

Pyrococcus
type: Class
subclass of: Thermococcaceae
editor preferred term: Pyrococcus
imported from: ncbitaxon.owl

Thermoproteales
type: Class
subclass of: Thermoprotei
editor preferred term: Thermoproteales
imported from: ncbitaxon.owl

Thermoproteaceae
type: Class
subclass of: Thermoproteales
editor preferred term: Thermoproteaceae
imported from: ncbitaxon.owl

Thermoproteus
type: Class
subclass of: Thermoproteaceae
editor preferred term: Thermoproteus
imported from: ncbitaxon.owl

Thermoproteus tenax
type: Class
subclass of: Thermoproteus
editor preferred term: Thermoproteus tenax
imported from: ncbitaxon.owl

Rhizobium/Agrobacterium group
type: Class
subclass of: Rhizobiaceae
editor preferred term: Rhizobium/Agrobacterium group
imported from: ncbitaxon.owl

Sinorhizobium/Ensifer group
type: Class
subclass of: Rhizobiaceae
editor preferred term: Sinorhizobium/Ensifer group
imported from: ncbitaxon.owl

Paxilineae
type: Class
subclass of: Boletales
editor preferred term: Paxilineae
imported from: ncbitaxon.owl

SARS coronavirus
type: Class
subclass of: Group 2 species
editor preferred term: SARS coronavirus
imported from: ncbitaxon.owl

Sulfolobales
type: Class
subclass of: Thermoprotei
editor preferred term: Sulfolobales
imported from: ncbitaxon.owl

Sulfolobus
type: Class
subclass of: Sulfolobaceae
editor preferred term: Sulfolobus
imported from: ncbitaxon.owl

Sulfolobus acidocaldarius
type: Class
subclass of: Sulfolobus
editor preferred term: Sulfolobus acidocaldarius
imported from: ncbitaxon.owl

Sulfolobus solfataricus
type: Class
subclass of: Sulfolobus
editor preferred term: Sulfolobus solfataricus
imported from: ncbitaxon.owl

Thermoplasmatales
type: Class
subclass of: Thermoplasmata
editor preferred term: Thermoplasmatales
imported from: ncbitaxon.owl

Thermoplasma
type: Class
subclass of: Thermoplasmataceae
editor preferred term: Thermoplasma
imported from: ncbitaxon.owl

Thermoplasma acidophilum
type: Class
subclass of: Thermoplasma
editor preferred term: Thermoplasma acidophilum
imported from: ncbitaxon.owl

Rubus
type: Class
subclass of: Rosoideae
editor preferred term: Rubus
imported from: ncbitaxon.owl

magnoliids
type: Class
subclass of: Magnoliophyta
editor preferred term: magnoliids
imported from: ncbitaxon.owl

Thermotoga
type: Class
subclass of: Thermotogaceae
editor preferred term: Thermotoga
imported from: ncbitaxon.owl

Thermotoga maritima
type: Class
subclass of: Thermotoga
editor preferred term: Thermotoga maritima
imported from: ncbitaxon.owl

Brucella
type: Class
subclass of: Brucellaceae
editor preferred term: Brucella
imported from: ncbitaxon.owl

Brucella abortus
type: Class
subclass of: Brucella
editor preferred term: Brucella abortus
imported from: ncbitaxon.owl

Rutaceae
type: Class
subclass of: Sapindales
editor preferred term: Rutaceae
imported from: ncbitaxon.owl

Xylella
type: Class
subclass of: Xanthomonadaceae
editor preferred term: Xylella
imported from: ncbitaxon.owl

Xylella fastidiosa
type: Class
subclass of: Xylella
editor preferred term: Xylella fastidiosa
imported from: ncbitaxon.owl

Saliceae
type: Class
subclass of: Salicaceae
editor preferred term: Saliceae
imported from: ncbitaxon.owl

Moniliformopses
type: Class
subclass of: Euphyllophyta
editor preferred term: Moniliformopses
imported from: ncbitaxon.owl

Thermotogales
type: Class
subclass of: Thermotogae (class)
editor preferred term: Thermotogales
imported from: ncbitaxon.owl

Rubiaceae
type: Class
subclass of: Gentianales
editor preferred term: Rubiaceae
imported from: ncbitaxon.owl

Rubrobacterineae
type: Class
subclass of: Rubrobacterales
editor preferred term: Rubrobacterineae
imported from: ncbitaxon.owl

Dechloromonas aromatica
type: Class
subclass of: Dechloromonas
editor preferred term: Dechloromonas aromatica
imported from: ncbitaxon.owl

Francisella
type: Class
subclass of: Francisellaceae
editor preferred term: Francisella
imported from: ncbitaxon.owl

Xenopus [NCBITaxon:262014]
type: Class
subclass of: Xenopus
editor preferred term: Xenopus [NCBITaxon:262014]
imported from: ncbitaxon.owl

Francisella tularensis
type: Class
subclass of: Francisella
editor preferred term: Francisella tularensis
imported from: ncbitaxon.owl

Crocosphaera
type: Class
subclass of: Chroococcales
editor preferred term: Crocosphaera
imported from: ncbitaxon.owl

Crocosphaera watsonii
type: Class
subclass of: Crocosphaera
editor preferred term: Crocosphaera watsonii
imported from: ncbitaxon.owl

Francisella tularensis subsp. novicida
type: Class
subclass of: Francisella tularensis
editor preferred term: Francisella tularensis subsp. novicida
imported from: ncbitaxon.owl

Rickettsia sibirica subgroup
type: Class
subclass of: spotted fever group
editor preferred term: Rickettsia sibirica subgroup
imported from: ncbitaxon.owl

Citrus
type: Class
subclass of: Rutaceae
editor preferred term: Citrus
imported from: ncbitaxon.owl

Citrus sinensis
type: Class
subclass of: Citrus
editor preferred term: Citrus sinensis
imported from: ncbitaxon.owl

Aquifex
type: Class
subclass of: Aquificaceae
editor preferred term: Aquifex
imported from: ncbitaxon.owl

Nostoc punctiforme
type: Class
subclass of: Nostoc
editor preferred term: Nostoc punctiforme
imported from: ncbitaxon.owl

Saccharomyces paradoxus
type: Class
subclass of: Saccharomyces
editor preferred term: Saccharomyces paradoxus
imported from: ncbitaxon.owl

Saccharomyces pastorianus
type: Class
subclass of: Saccharomyces
editor preferred term: Saccharomyces pastorianus
imported from: ncbitaxon.owl

Eukaryota
type: Class
subclass of: OBI_0100026
editor preferred term: Eukaryota
imported from: ncbitaxon.owl

Bovinae
type: Class
subclass of: Bovidae
editor preferred term: Bovinae
imported from: ncbitaxon.owl

Coregonus
type: Class
subclass of: Salmonidae
editor preferred term: Coregonus
imported from: ncbitaxon.owl

Rubrivivax
type: Class
subclass of: Burkholderiales Genera incertae sedis
editor preferred term: Rubrivivax
imported from: ncbitaxon.owl

Rubrivivax gelatinosus
type: Class
subclass of: Rubrivivax
editor preferred term: Rubrivivax gelatinosus
imported from: ncbitaxon.owl

Ralstonia syzygii
type: Class
subclass of: Ralstonia
editor preferred term: Ralstonia syzygii
imported from: ncbitaxon.owl

Sinorhizobium
type: Class
subclass of: Sinorhizobium/Ensifer group
editor preferred term: Sinorhizobium
imported from: ncbitaxon.owl

Alphaproteobacteria
type: Class
subclass of: Proteobacteria
editor preferred term: Alphaproteobacteria
imported from: ncbitaxon.owl

Betaproteobacteria
type: Class
subclass of: Proteobacteria
editor preferred term: Betaproteobacteria
imported from: ncbitaxon.owl

Deltaproteobacteria
type: Class
subclass of: delta/epsilon subdivisions
editor preferred term: Deltaproteobacteria
imported from: ncbitaxon.owl

Geobacter
type: Class
subclass of: Geobacteraceae
editor preferred term: Geobacter
imported from: ncbitaxon.owl

Geobacter metallireducens
type: Class
subclass of: Geobacter
editor preferred term: Geobacter metallireducens
imported from: ncbitaxon.owl

Staphylococcus aureus subsp. aureus MSSA476
type: Class
subclass of: Staphylococcus aureus subsp. aureus
editor preferred term: Staphylococcus aureus subsp. aureus MSSA476
imported from: ncbitaxon.owl

Burkholderia pseudomallei
type: Class
subclass of: pseudomallei group
editor preferred term: Burkholderia pseudomallei
imported from: ncbitaxon.owl

Trichocomaceae
type: Class
subclass of: Eurotiales
editor preferred term: Trichocomaceae
imported from: ncbitaxon.owl

Pseudomonas
type: Class
subclass of: Pseudomonadaceae
editor preferred term: Pseudomonas
imported from: ncbitaxon.owl

Pseudomonas aeruginosa
type: Class
subclass of: Pseudomonas aeruginosa group
editor preferred term: Pseudomonas aeruginosa
imported from: ncbitaxon.owl

Phaeophyceae
type: Class
subclass of: stramenopiles
editor preferred term: Phaeophyceae
imported from: ncbitaxon.owl

Ectocarpales
type: Class
subclass of: Phaeophyceae
editor preferred term: Ectocarpales
imported from: ncbitaxon.owl

Ectocarpaceae
type: Class
subclass of: Ectocarpales
editor preferred term: Ectocarpaceae
imported from: ncbitaxon.owl

Ectocarpus
type: Class
subclass of: Ectocarpaceae
editor preferred term: Ectocarpus
imported from: ncbitaxon.owl

Ectocarpus siliculosus
type: Class
subclass of: Ectocarpus
editor preferred term: Ectocarpus siliculosus
imported from: ncbitaxon.owl

Crenarchaeota
type: Class
subclass of: Archaea
editor preferred term: Crenarchaeota
imported from: ncbitaxon.owl

Euryarchaeota
type: Class
subclass of: Archaea
editor preferred term: Euryarchaeota
imported from: ncbitaxon.owl

Salmonella enterica
type: Class
subclass of: Salmonella
editor preferred term: Salmonella enterica
imported from: ncbitaxon.owl

Burkholderia cepacia
type: Class
subclass of: Burkholderia cepacia complex
editor preferred term: Burkholderia cepacia
imported from: ncbitaxon.owl

ssDNA viruses
type: Class
subclass of: Viruses
editor preferred term: ssDNA viruses
imported from: ncbitaxon.owl

Cryptococcus gattii
type: Class
subclass of: Cryptococcus [NCBITaxon:107441]
editor preferred term: Cryptococcus gattii
imported from: ncbitaxon.owl

Methanococcoides burtonii
type: Class
subclass of: Methanococcoides
editor preferred term: Methanococcoides burtonii
imported from: ncbitaxon.owl

Pseudomonas fluorescens
type: Class
subclass of: Pseudomonas fluorescens group
editor preferred term: Pseudomonas fluorescens
imported from: ncbitaxon.owl

Veillonella
type: Class
subclass of: Acidaminococcaceae
editor preferred term: Veillonella
imported from: ncbitaxon.owl

Veillonella parvula
type: Class
subclass of: Veillonella
editor preferred term: Veillonella parvula
imported from: ncbitaxon.owl

Epsilonproteobacteria
type: Class
subclass of: delta/epsilon subdivisions
editor preferred term: Epsilonproteobacteria
imported from: ncbitaxon.owl

Ceratopteris
type: Class
subclass of: Pteridaceae
editor preferred term: Ceratopteris
imported from: ncbitaxon.owl

Ceratopteris thalictroides
type: Class
subclass of: Ceratopteris
editor preferred term: Ceratopteris thalictroides
imported from: ncbitaxon.owl

Vitis vinifera
type: Class
subclass of: Vitis
editor preferred term: Vitis vinifera
imported from: ncbitaxon.owl

Hypocrea
type: Class
subclass of: Hypocreaceae
editor preferred term: Hypocrea
imported from: ncbitaxon.owl

Collembola
type: Class
subclass of: Ellipura
editor preferred term: Collembola
imported from: ncbitaxon.owl

Lachancea
type: Class
subclass of: Saccharomycetaceae
editor preferred term: Lachancea
imported from: ncbitaxon.owl

Pseudomonas putida
type: Class
subclass of: Pseudomonas putida group
editor preferred term: Pseudomonas putida
imported from: ncbitaxon.owl

Mesobatrachia
type: Class
subclass of: Anura
editor preferred term: Mesobatrachia
imported from: ncbitaxon.owl

Pipoidea
type: Class
subclass of: Mesobatrachia
editor preferred term: Pipoidea
imported from: ncbitaxon.owl

Herminiimonas
type: Class
subclass of: Oxalobacteraceae
editor preferred term: Herminiimonas
imported from: ncbitaxon.owl

Chlorophyta
type: Class
subclass of: Viridiplantae
editor preferred term: Chlorophyta
imported from: ncbitaxon.owl

Chlamydomonadales
type: Class
subclass of: Chlorophyceae
editor preferred term: Chlamydomonadales
imported from: ncbitaxon.owl

Ralstonia solanacearum
type: Class
subclass of: Ralstonia
editor preferred term: Ralstonia solanacearum
imported from: ncbitaxon.owl

Chlamydomonadaceae
type: Class
subclass of: Chlamydomonadales
editor preferred term: Chlamydomonadaceae
imported from: ncbitaxon.owl

Chlamydomonas
type: Class
subclass of: Chlamydomonadaceae
editor preferred term: Chlamydomonas
imported from: ncbitaxon.owl

Chlamydomonas reinhardtii
type: Class
subclass of: Chlamydomonas
editor preferred term: Chlamydomonas reinhardtii
imported from: ncbitaxon.owl

Cyprinoidea
type: Class
subclass of: Cypriniformes
editor preferred term: Cyprinoidea
imported from: ncbitaxon.owl

Pleuronectoidei
type: Class
subclass of: Pleuronectiformes
editor preferred term: Pleuronectoidei
imported from: ncbitaxon.owl

Tetraodontiformes
type: Class
subclass of: Percomorpha
editor preferred term: Tetraodontiformes
imported from: ncbitaxon.owl

Tetraodontoidei
type: Class
subclass of: Tetraodontiformes
editor preferred term: Tetraodontoidei
imported from: ncbitaxon.owl

Tetraodontidae
type: Class
subclass of: Tetradontoidea
editor preferred term: Tetraodontidae
imported from: ncbitaxon.owl

Takifugu
type: Class
subclass of: Tetraodontidae
editor preferred term: Takifugu
imported from: ncbitaxon.owl

Takifugu rubripes
type: Class
subclass of: Takifugu
editor preferred term: Takifugu rubripes
imported from: ncbitaxon.owl

Schistosomatoidea
type: Class
subclass of: Strigeidida
editor preferred term: Schistosomatoidea
imported from: ncbitaxon.owl

Schistosomatidae
type: Class
subclass of: Schistosomatoidea
editor preferred term: Schistosomatidae
imported from: ncbitaxon.owl

Laurasiatheria
type: Class
subclass of: Eutheria
editor preferred term: Laurasiatheria
imported from: ncbitaxon.owl

Euarchontoglires
type: Class
subclass of: Eutheria
editor preferred term: Euarchontoglires
imported from: ncbitaxon.owl

Glires
type: Class
subclass of: Euarchontoglires
editor preferred term: Glires
imported from: ncbitaxon.owl

Simiiformes
type: Class
subclass of: Haplorrhini
editor preferred term: Simiiformes
imported from: ncbitaxon.owl

Cercopithecoidea
type: Class
subclass of: Catarrhini
editor preferred term: Cercopithecoidea
imported from: ncbitaxon.owl

Hominoidea
type: Class
subclass of: Catarrhini
editor preferred term: Hominoidea
imported from: ncbitaxon.owl

Chlorophyceae
type: Class
subclass of: Chlorophyta
editor preferred term: Chlorophyceae
imported from: ncbitaxon.owl

Saccharophagus
type: Class
subclass of: Alteromonadaceae
editor preferred term: Saccharophagus
imported from: ncbitaxon.owl

Embryophyta
type: Class
subclass of: Streptophytina
editor preferred term: Embryophyta
imported from: ncbitaxon.owl

Bifidobacteriaceae
type: Class
subclass of: Bifidobacteriales
editor preferred term: Bifidobacteriaceae
imported from: ncbitaxon.owl

Mollicutes
type: Class
subclass of: Firmicutes
editor preferred term: Mollicutes
imported from: ncbitaxon.owl

Acidaminococcaceae
type: Class
subclass of: Clostridiales
editor preferred term: Acidaminococcaceae
imported from: ncbitaxon.owl

Clostridiaceae
type: Class
subclass of: Clostridiales
editor preferred term: Clostridiaceae
imported from: ncbitaxon.owl

Rhodobacteraceae
type: Class
subclass of: Rhodobacterales
editor preferred term: Rhodobacteraceae
imported from: ncbitaxon.owl

Burkholderia
type: Class
subclass of: Burkholderiaceae
editor preferred term: Burkholderia
imported from: ncbitaxon.owl

Methylophilaceae
type: Class
subclass of: Methylophilales
editor preferred term: Methylophilaceae
imported from: ncbitaxon.owl

Thiomonas
type: Class
subclass of: Burkholderiales Genera incertae sedis
editor preferred term: Thiomonas
imported from: ncbitaxon.owl

Xanthomonadaceae
type: Class
subclass of: Xanthomonadales
editor preferred term: Xanthomonadaceae
imported from: ncbitaxon.owl

Synechococcus elongatus
type: Class
subclass of: Synechococcus
editor preferred term: Synechococcus elongatus
imported from: ncbitaxon.owl

Chloroflexi (class)
type: Class
subclass of: Chloroflexi
editor preferred term: Chloroflexi (class)
imported from: ncbitaxon.owl

Chloroflexales
type: Class
subclass of: Chloroflexi (class)
editor preferred term: Chloroflexales
imported from: ncbitaxon.owl

Fusobacteria
type: Class
subclass of: Bacteria
editor preferred term: Fusobacteria
imported from: ncbitaxon.owl

Aquificales
type: Class
subclass of: Aquificae (class)
editor preferred term: Aquificales
imported from: ncbitaxon.owl

Bryophyta
type: Class
subclass of: Embryophyta
editor preferred term: Bryophyta
imported from: ncbitaxon.owl

Polytrichales
type: Class
subclass of: Polytrichopsida
editor preferred term: Polytrichales
imported from: ncbitaxon.owl

Polytrichaceae
type: Class
subclass of: Polytrichales
editor preferred term: Polytrichaceae
imported from: ncbitaxon.owl

Polytrichum
type: Class
subclass of: Polytrichaceae
editor preferred term: Polytrichum
imported from: ncbitaxon.owl

Bryopsida
type: Class
subclass of: Moss Superclass V
editor preferred term: Bryopsida
imported from: ncbitaxon.owl

Funariales
type: Class
subclass of: Funariidae
editor preferred term: Funariales
imported from: ncbitaxon.owl

Funariaceae
type: Class
subclass of: Funariales
editor preferred term: Funariaceae
imported from: ncbitaxon.owl

Physcomitrella
type: Class
subclass of: Funariaceae
editor preferred term: Physcomitrella
imported from: ncbitaxon.owl

Physcomitrella patens
type: Class
subclass of: Physcomitrella
editor preferred term: Physcomitrella patens
imported from: ncbitaxon.owl

Buchnera
type: Class
subclass of: Enterobacteriaceae
editor preferred term: Buchnera
imported from: ncbitaxon.owl

Rubus idaeus
type: Class
subclass of: Rubus
editor preferred term: Rubus idaeus
imported from: ncbitaxon.owl

Sophophora
type: Class
subclass of: Drosophila
editor preferred term: Sophophora
imported from: ncbitaxon.owl

melanogaster group
type: Class
subclass of: Sophophora
editor preferred term: melanogaster group
imported from: ncbitaxon.owl

melanogaster subgroup
type: Class
subclass of: melanogaster group
editor preferred term: melanogaster subgroup
imported from: ncbitaxon.owl

obscura group
type: Class
subclass of: Sophophora
editor preferred term: obscura group
imported from: ncbitaxon.owl

pseudoobscura subgroup
type: Class
subclass of: obscura group
editor preferred term: pseudoobscura subgroup
imported from: ncbitaxon.owl

Lycopodiophyta
type: Class
subclass of: Tracheophyta
editor preferred term: Lycopodiophyta
imported from: ncbitaxon.owl

Isoetopsida
type: Class
subclass of: Lycopodiophyta
editor preferred term: Isoetopsida
imported from: ncbitaxon.owl

Selaginellales
type: Class
subclass of: Isoetopsida
editor preferred term: Selaginellales
imported from: ncbitaxon.owl

Teleostei
type: Class
subclass of: Neopterygii
editor preferred term: Teleostei
imported from: ncbitaxon.owl

Euteleostei
type: Class
subclass of: Clupeocephala
editor preferred term: Euteleostei
imported from: ncbitaxon.owl

Selaginellaceae
type: Class
subclass of: Selaginellales
editor preferred term: Selaginellaceae
imported from: ncbitaxon.owl

Acanthopterygii
type: Class
subclass of: Holacanthopterygii
editor preferred term: Acanthopterygii
imported from: ncbitaxon.owl

Selaginella
type: Class
subclass of: Selaginellaceae
editor preferred term: Selaginella
imported from: ncbitaxon.owl

Percomorpha
type: Class
subclass of: Euacanthopterygii
editor preferred term: Percomorpha
imported from: ncbitaxon.owl

Tetradontoidea
type: Class
subclass of: Tetraodontoidei
editor preferred term: Tetradontoidea
imported from: ncbitaxon.owl

Paracanthopterygii
type: Class
subclass of: Holacanthopterygii
editor preferred term: Paracanthopterygii
imported from: ncbitaxon.owl

Ostariophysi
type: Class
subclass of: Otocephala
editor preferred term: Ostariophysi
imported from: ncbitaxon.owl

Tetrapoda
type: Class
subclass of: Sarcopterygii
editor preferred term: Tetrapoda
imported from: ncbitaxon.owl

Amniota
type: Class
subclass of: Tetrapoda
editor preferred term: Amniota
imported from: ncbitaxon.owl

Theria
type: Class
subclass of: Mammalia
editor preferred term: Theria
imported from: ncbitaxon.owl

Sauria
type: Class
subclass of: Sauropsida
editor preferred term: Sauria
imported from: ncbitaxon.owl

Filicophyta
type: Class
subclass of: Moniliformopses
editor preferred term: Filicophyta
imported from: ncbitaxon.owl

Filicales
type: Class
subclass of: Filicopsida
editor preferred term: Filicales
imported from: ncbitaxon.owl

Ralstonia pickettii
type: Class
subclass of: Ralstonia
editor preferred term: Ralstonia pickettii
imported from: ncbitaxon.owl

Filicopsida
type: Class
subclass of: Filicophyta
editor preferred term: Filicopsida
imported from: ncbitaxon.owl

Bartonella grahamii
type: Class
subclass of: Bartonella
editor preferred term: Bartonella grahamii
imported from: ncbitaxon.owl

Dictyosteliida
type: Class
subclass of: Mycetozoa
editor preferred term: Dictyosteliida
imported from: ncbitaxon.owl

Viridiplantae
type: Class
subclass of: Eukaryota
editor preferred term: Viridiplantae
imported from: ncbitaxon.owl

Coniferophyta
type: Class
subclass of: Spermatophyta
editor preferred term: Coniferophyta
imported from: ncbitaxon.owl

Lepidium sativum
type: Class
subclass of: Lepidium
editor preferred term: Lepidium sativum
imported from: ncbitaxon.owl

Coniferales
type: Class
subclass of: Coniferopsida
editor preferred term: Coniferales
imported from: ncbitaxon.owl

Fungi/Metazoa group
type: Class
subclass of: Eukaryota
editor preferred term: Fungi/Metazoa group
imported from: ncbitaxon.owl

Eremothecium gossypii
type: Class
subclass of: Eremothecium
editor preferred term: Eremothecium gossypii
imported from: ncbitaxon.owl

Eremothecium
type: Class
subclass of: Saccharomycetaceae
editor preferred term: Eremothecium
imported from: ncbitaxon.owl

Aspergillus terreus
type: Class
subclass of: Aspergillus
editor preferred term: Aspergillus terreus
imported from: ncbitaxon.owl

Pinaceae
type: Class
subclass of: Coniferales
editor preferred term: Pinaceae
imported from: ncbitaxon.owl

Onygenales
type: Class
subclass of: Eurotiomycetes
editor preferred term: Onygenales
imported from: ncbitaxon.owl

Metazoa
type: Class
subclass of: Fungi/Metazoa group
editor preferred term: Metazoa
imported from: ncbitaxon.owl

Bilateria
type: Class
subclass of: Eumetazoa
editor preferred term: Bilateria
imported from: ncbitaxon.owl

Acoelomata
type: Class
subclass of: Bilateria
editor preferred term: Acoelomata
imported from: ncbitaxon.owl

Pseudocoelomata
type: Class
subclass of: Bilateria
editor preferred term: Pseudocoelomata
imported from: ncbitaxon.owl

Picea
type: Class
subclass of: Pinaceae
editor preferred term: Picea
imported from: ncbitaxon.owl

Tylenchina
type: Class
subclass of: Tylenchida
editor preferred term: Tylenchina
imported from: ncbitaxon.owl

Tylenchoidea
type: Class
subclass of: Tylenchina
editor preferred term: Tylenchoidea
imported from: ncbitaxon.owl

Heteroderinae
type: Class
subclass of: Heteroderidae
editor preferred term: Heteroderinae
imported from: ncbitaxon.owl

Picea glauca
type: Class
subclass of: Picea
editor preferred term: Picea glauca
imported from: ncbitaxon.owl

Coelomata
type: Class
subclass of: Bilateria
editor preferred term: Coelomata
imported from: ncbitaxon.owl

Protostomia
type: Class
subclass of: Coelomata
editor preferred term: Protostomia
imported from: ncbitaxon.owl

Neoptera
type: Class
subclass of: Pterygota
editor preferred term: Neoptera
imported from: ncbitaxon.owl

Pinus
type: Class
subclass of: Pinaceae
editor preferred term: Pinus
imported from: ncbitaxon.owl

Endopterygota
type: Class
subclass of: Neoptera
editor preferred term: Endopterygota
imported from: ncbitaxon.owl

Pinus radiata
type: Class
subclass of: Pinus [NCBITaxon:139271]
editor preferred term: Pinus radiata
imported from: ncbitaxon.owl

Deuterostomia
type: Class
subclass of: Coelomata
editor preferred term: Deuterostomia
imported from: ncbitaxon.owl

Sciurognathi
type: Class
subclass of: Rodentia
editor preferred term: Sciurognathi
imported from: ncbitaxon.owl

Carnivora
type: Class
subclass of: Laurasiatheria
editor preferred term: Carnivora
imported from: ncbitaxon.owl

Alveolata
type: Class
subclass of: Eukaryota
editor preferred term: Alveolata
imported from: ncbitaxon.owl

stramenopiles
type: Class
subclass of: Eukaryota
editor preferred term: stramenopiles
imported from: ncbitaxon.owl

Euglenozoa
type: Class
subclass of: Eukaryota
editor preferred term: Euglenozoa
imported from: ncbitaxon.owl

Cricetidae
type: Class
subclass of: Muroidea
editor preferred term: Cricetidae
imported from: ncbitaxon.owl

Muroidea
type: Class
subclass of: Sciurognathi
editor preferred term: Muroidea
imported from: ncbitaxon.owl

Xanthomonas
type: Class
subclass of: Xanthomonadaceae
editor preferred term: Xanthomonas
imported from: ncbitaxon.owl

Felinae
type: Class
subclass of: Felidae
editor preferred term: Felinae
imported from: ncbitaxon.owl

Xanthomonas campestris
type: Class
subclass of: Xanthomonas
editor preferred term: Xanthomonas campestris
imported from: ncbitaxon.owl

Streptomyces avermitilis
type: Class
subclass of: Streptomyces
editor preferred term: Streptomyces avermitilis
imported from: ncbitaxon.owl

Entomoplasmataceae
type: Class
subclass of: Entomoplasmatales
editor preferred term: Entomoplasmataceae
imported from: ncbitaxon.owl

Lactobacillaceae
type: Class
subclass of: Lactobacillales
editor preferred term: Lactobacillaceae
imported from: ncbitaxon.owl

Magnoliophyta
type: Class
subclass of: Spermatophyta
editor preferred term: Magnoliophyta
imported from: ncbitaxon.owl

Rickettsieae
type: Class
subclass of: Rickettsiaceae
editor preferred term: Rickettsieae
imported from: ncbitaxon.owl

Xanthomonas campestris pv. campestris
type: Class
subclass of: Xanthomonas campestris
editor preferred term: Xanthomonas campestris pv. campestris
imported from: ncbitaxon.owl

Magnoliales
type: Class
subclass of: magnoliids
editor preferred term: Magnoliales
imported from: ncbitaxon.owl

Magnoliaceae
type: Class
subclass of: Magnoliales
editor preferred term: Magnoliaceae
imported from: ncbitaxon.owl

Francisellaceae
type: Class
subclass of: Thiotrichales
editor preferred term: Francisellaceae
imported from: ncbitaxon.owl

Liriodendron
type: Class
subclass of: Magnoliaceae
editor preferred term: Liriodendron
imported from: ncbitaxon.owl

Liriodendron tulipifera
type: Class
subclass of: Liriodendron
editor preferred term: Liriodendron tulipifera
imported from: ncbitaxon.owl

Zinnia elegans
type: Class
subclass of: Zinnia
editor preferred term: Zinnia elegans
imported from: ncbitaxon.owl

Lotus japonicus
type: Class
subclass of: Lotus
editor preferred term: Lotus japonicus
imported from: ncbitaxon.owl

Schizosaccharomycetales
type: Class
subclass of: Schizosaccharomycetes
editor preferred term: Schizosaccharomycetales
imported from: ncbitaxon.owl

mitosporic Trichocomaceae
type: Class
subclass of: Trichocomaceae
editor preferred term: mitosporic Trichocomaceae
imported from: ncbitaxon.owl

mitosporic Onygenales
type: Class
subclass of: Onygenales
editor preferred term: mitosporic Onygenales
imported from: ncbitaxon.owl

Strongyloides ratti
type: Class
subclass of: Strongyloides
editor preferred term: Strongyloides ratti
imported from: ncbitaxon.owl

Heterodera
type: Class
subclass of: Heteroderinae
editor preferred term: Heterodera
imported from: ncbitaxon.owl

Apoidea
type: Class
subclass of: Aculeata
editor preferred term: Apoidea
imported from: ncbitaxon.owl

Cannabaceae
type: Class
subclass of: Rosales
editor preferred term: Cannabaceae
imported from: ncbitaxon.owl

Cannabis
type: Class
subclass of: Cannabaceae
editor preferred term: Cannabis
imported from: ncbitaxon.owl

Cannabis sativa
type: Class
subclass of: Cannabis
editor preferred term: Cannabis sativa
imported from: ncbitaxon.owl

Fagales
type: Class
subclass of: eurosids I
editor preferred term: Fagales
imported from: ncbitaxon.owl

Betula
type: Class
subclass of: Betulaceae
editor preferred term: Betula
imported from: ncbitaxon.owl

Betula pendula
type: Class
subclass of: Betula
editor preferred term: Betula pendula
imported from: ncbitaxon.owl

Cryptosporidiidae
type: Class
subclass of: Eimeriorina
editor preferred term: Cryptosporidiidae
imported from: ncbitaxon.owl

Azotobacter group
type: Class
subclass of: Pseudomonadaceae
editor preferred term: Azotobacter group
imported from: ncbitaxon.owl

Betulaceae
type: Class
subclass of: Fagales
editor preferred term: Betulaceae
imported from: ncbitaxon.owl

Azotobacter
type: Class
subclass of: Azotobacter group
editor preferred term: Azotobacter
imported from: ncbitaxon.owl

ssRNA positive-strand viruses, no DNA stage
type: Class
subclass of: Viruses
editor preferred term: ssRNA positive-strand viruses, no DNA stage
imported from: ncbitaxon.owl

Azotobacter vinelandii
type: Class
subclass of: Azotobacter
editor preferred term: Azotobacter vinelandii
imported from: ncbitaxon.owl

Streptophyta
type: Class
subclass of: Viridiplantae
editor preferred term: Streptophyta
imported from: ncbitaxon.owl

Suina
type: Class
subclass of: Cetartiodactyla
editor preferred term: Suina
imported from: ncbitaxon.owl

Pecora
type: Class
subclass of: Ruminantia
editor preferred term: Pecora
imported from: ncbitaxon.owl

Equus subg. Equus
type: Class
subclass of: Equus
editor preferred term: Equus subg. Equus
imported from: ncbitaxon.owl

Rhizobiales
type: Class
subclass of: Alphaproteobacteria
editor preferred term: Rhizobiales
imported from: ncbitaxon.owl

Agrobacterium
type: Class
subclass of: Rhizobium/Agrobacterium group
editor preferred term: Agrobacterium
imported from: ncbitaxon.owl

Rickettsia sibirica
type: Class
subclass of: Rickettsia sibirica subgroup
editor preferred term: Rickettsia sibirica
imported from: ncbitaxon.owl

Agrobacterium tumefaciens
type: Class
subclass of: Agrobacterium
editor preferred term: Agrobacterium tumefaciens
imported from: ncbitaxon.owl

BEP clade
type: Class
subclass of: Poaceae
editor preferred term: BEP clade
imported from: ncbitaxon.owl

Vitaceae
type: Class
subclass of: Vitales
editor preferred term: Vitaceae
imported from: ncbitaxon.owl

Vitis
type: Class
subclass of: Vitaceae
editor preferred term: Vitis
imported from: ncbitaxon.owl

Isotomidae
type: Class
subclass of: Entomobryoidea
editor preferred term: Isotomidae
imported from: ncbitaxon.owl

Sylviidae
type: Class
subclass of: Passeriformes
editor preferred term: Sylviidae
imported from: ncbitaxon.owl

Malpighiales
type: Class
subclass of: eurosids I
editor preferred term: Malpighiales
imported from: ncbitaxon.owl

Neosartorya
type: Class
subclass of: Trichocomaceae
editor preferred term: Neosartorya
imported from: ncbitaxon.owl

Neosartorya fischeri
type: Class
subclass of: Neosartorya fischeri group
editor preferred term: Neosartorya fischeri
imported from: ncbitaxon.owl

Desulfitobacterium
type: Class
subclass of: Peptococcaceae
editor preferred term: Desulfitobacterium
imported from: ncbitaxon.owl

Salicaceae
type: Class
subclass of: Malpighiales
editor preferred term: Salicaceae
imported from: ncbitaxon.owl

Populus
type: Class
subclass of: Saliceae
editor preferred term: Populus
imported from: ncbitaxon.owl

Populus trichocarpa
type: Class
subclass of: Populus
editor preferred term: Populus trichocarpa
imported from: ncbitaxon.owl

Populus trichocarpa x Populus deltoides
type: Class
subclass of: Populus
editor preferred term: Populus trichocarpa x Populus deltoides
imported from: ncbitaxon.owl

Populus deltoides
type: Class
subclass of: Populus
editor preferred term: Populus deltoides
imported from: ncbitaxon.owl

Brassicales
type: Class
subclass of: eurosids II
editor preferred term: Brassicales
imported from: ncbitaxon.owl

Brassicaceae
type: Class
subclass of: Brassicales
editor preferred term: Brassicaceae
imported from: ncbitaxon.owl

Arabidopsis
type: Class
subclass of: Brassicaceae
editor preferred term: Arabidopsis
imported from: ncbitaxon.owl

Arabidopsis thaliana
type: Class
subclass of: Arabidopsis
editor preferred term: Arabidopsis thaliana
imported from: ncbitaxon.owl

Brassica
type: Class
subclass of: Brassicaceae
editor preferred term: Brassica
imported from: ncbitaxon.owl

Brassica juncea
type: Class
subclass of: Brassica
editor preferred term: Brassica juncea
imported from: ncbitaxon.owl

Brassica napus
type: Class
subclass of: Brassica
editor preferred term: Brassica napus
imported from: ncbitaxon.owl

Brassica rapa
type: Class
subclass of: Brassica
editor preferred term: Brassica rapa
imported from: ncbitaxon.owl

Rosales
type: Class
subclass of: eurosids I
editor preferred term: Rosales
imported from: ncbitaxon.owl

Rosaceae
type: Class
subclass of: Rosales
editor preferred term: Rosaceae
imported from: ncbitaxon.owl

Aedes/Ochlerotatus group
type: Class
subclass of: Culicini
editor preferred term: Aedes/Ochlerotatus group
imported from: ncbitaxon.owl

Ditrysia
type: Class
subclass of: Heteroneura
editor preferred term: Ditrysia
imported from: ncbitaxon.owl

Bombycoidea
type: Class
subclass of: Obtectomera
editor preferred term: Bombycoidea
imported from: ncbitaxon.owl

Noctuoidea
type: Class
subclass of: Obtectomera
editor preferred term: Noctuoidea
imported from: ncbitaxon.owl

Estrildidae
type: Class
subclass of: Passeroidea
editor preferred term: Estrildidae
imported from: ncbitaxon.owl

Viannia
type: Class
subclass of: Leishmania
editor preferred term: Viannia
imported from: ncbitaxon.owl

Leishmania braziliensis species complex
type: Class
subclass of: Viannia
editor preferred term: Leishmania braziliensis species complex
imported from: ncbitaxon.owl

Haplorrhini
type: Class
subclass of: Primates
editor preferred term: Haplorrhini
imported from: ncbitaxon.owl

Rhizobium
type: Class
subclass of: Rhizobium/Agrobacterium group
editor preferred term: Rhizobium
imported from: ncbitaxon.owl

Feliformia
type: Class
subclass of: Carnivora
editor preferred term: Feliformia
imported from: ncbitaxon.owl

Caniformia
type: Class
subclass of: Carnivora
editor preferred term: Caniformia
imported from: ncbitaxon.owl

Fabaceae
type: Class
subclass of: Fabales
editor preferred term: Fabaceae
imported from: ncbitaxon.owl

Mesorhizobium loti
type: Class
subclass of: Mesorhizobium
editor preferred term: Mesorhizobium loti
imported from: ncbitaxon.owl

Papilionoideae
type: Class
subclass of: Fabaceae
editor preferred term: Papilionoideae
imported from: ncbitaxon.owl

Sinorhizobium meliloti
type: Class
subclass of: Sinorhizobium
editor preferred term: Sinorhizobium meliloti
imported from: ncbitaxon.owl

Bartonella henselae
type: Class
subclass of: Bartonella
editor preferred term: Bartonella henselae
imported from: ncbitaxon.owl

Rhizobium leguminosarum
type: Class
subclass of: Rhizobium
editor preferred term: Rhizobium leguminosarum
imported from: ncbitaxon.owl

Glycine
type: Class
subclass of: Phaseoleae
editor preferred term: Glycine
imported from: ncbitaxon.owl

Glycine max
type: Class
subclass of: Glycine
editor preferred term: Glycine max
imported from: ncbitaxon.owl

Leishmania [NCBITaxon:38568]
type: Class
subclass of: Leishmania
editor preferred term: Leishmania [NCBITaxon:38568]
imported from: ncbitaxon.owl

Leishmania infantum species complex
type: Class
subclass of: Leishmania [NCBITaxon:38568]
editor preferred term: Leishmania infantum species complex
imported from: ncbitaxon.owl

Leishmania donovani species complex
type: Class
subclass of: Leishmania [NCBITaxon:38568]
editor preferred term: Leishmania donovani species complex
imported from: ncbitaxon.owl

Leishmania major species complex
type: Class
subclass of: Leishmania [NCBITaxon:38568]
editor preferred term: Leishmania major species complex
imported from: ncbitaxon.owl

Leishmania mexicana species complex
type: Class
subclass of: Leishmania [NCBITaxon:38568]
editor preferred term: Leishmania mexicana species complex
imported from: ncbitaxon.owl

Diprotodontia
type: Class
subclass of: Metatheria
editor preferred term: Diprotodontia
imported from: ncbitaxon.owl

Lotus
type: Class
subclass of: Loteae
editor preferred term: Lotus
imported from: ncbitaxon.owl

Medicago
type: Class
subclass of: Trifolieae
editor preferred term: Medicago
imported from: ncbitaxon.owl

Medicago sativa
type: Class
subclass of: Medicago
editor preferred term: Medicago sativa
imported from: ncbitaxon.owl

Medicago truncatula
type: Class
subclass of: Medicago
editor preferred term: Medicago truncatula
imported from: ncbitaxon.owl

Poales
type: Class
subclass of: commelinids
editor preferred term: Poales
imported from: ncbitaxon.owl

Pisum
type: Class
subclass of: Vicieae
editor preferred term: Pisum
imported from: ncbitaxon.owl

Pisum sativum
type: Class
subclass of: Pisum
editor preferred term: Pisum sativum
imported from: ncbitaxon.owl

Paracoccidioides
type: Class
subclass of: mitosporic Onygenales
editor preferred term: Paracoccidioides
imported from: ncbitaxon.owl

Trifolium
type: Class
subclass of: Trifolieae
editor preferred term: Trifolium
imported from: ncbitaxon.owl

Trifolium repens
type: Class
subclass of: Trifolium
editor preferred term: Trifolium repens
imported from: ncbitaxon.owl

Murinae
type: Class
subclass of: Muridae
editor preferred term: Murinae
imported from: ncbitaxon.owl

Cyprininae
type: Class
subclass of: Cyprinidae
editor preferred term: Cyprininae
imported from: ncbitaxon.owl

Rasborinae
type: Class
subclass of: Cyprinidae
editor preferred term: Rasborinae
imported from: ncbitaxon.owl

Trypanozoon
type: Class
subclass of: Trypanosoma
editor preferred term: Trypanozoon
imported from: ncbitaxon.owl

Oryza sativa (indica cultivar-group)
type: Class
subclass of: Oryza sativa
editor preferred term: Oryza sativa (indica cultivar-group)
imported from: ncbitaxon.owl

Oryza sativa (japonica cultivar-group)
type: Class
subclass of: Oryza sativa
editor preferred term: Oryza sativa (japonica cultivar-group)
imported from: ncbitaxon.owl

Linaceae
type: Class
subclass of: Malpighiales
editor preferred term: Linaceae
imported from: ncbitaxon.owl

Linum
type: Class
subclass of: Linaceae
editor preferred term: Linum
imported from: ncbitaxon.owl

Linum usitatissimum
type: Class
subclass of: Linum
editor preferred term: Linum usitatissimum
imported from: ncbitaxon.owl

Thraupini
type: Class
subclass of: Emberizinae
editor preferred term: Thraupini
imported from: ncbitaxon.owl

Parvovirinae
type: Class
subclass of: Parvoviridae
editor preferred term: Parvovirinae
imported from: ncbitaxon.owl

Estrildinae
type: Class
subclass of: Estrildidae
editor preferred term: Estrildinae
imported from: ncbitaxon.owl

Vitales
type: Class
subclass of: core eudicotyledons
editor preferred term: Vitales
imported from: ncbitaxon.owl

Methylobacillus
type: Class
subclass of: Methylophilaceae
editor preferred term: Methylobacillus
imported from: ncbitaxon.owl

Moss Superclass V
type: Class
subclass of: Bryophyta
editor preferred term: Moss Superclass V
imported from: ncbitaxon.owl

Methylobacillus flagellatus
type: Class
subclass of: Methylobacillus
editor preferred term: Methylobacillus flagellatus
imported from: ncbitaxon.owl

Gentianales
type: Class
subclass of: lamiids
editor preferred term: Gentianales
imported from: ncbitaxon.owl

Mammalia
type: Class
subclass of: Amniota
editor preferred term: Mammalia
imported from: ncbitaxon.owl

Solanales
type: Class
subclass of: lamiids
editor preferred term: Solanales
imported from: ncbitaxon.owl

Solanaceae
type: Class
subclass of: Solanales
editor preferred term: Solanaceae
imported from: ncbitaxon.owl

Capsicum
type: Class
subclass of: Capsiceae
editor preferred term: Capsicum
imported from: ncbitaxon.owl

Capsicum annuum
type: Class
subclass of: Capsicum
editor preferred term: Capsicum annuum
imported from: ncbitaxon.owl

Solanum lycopersicum
type: Class
subclass of: Lycopersicon
editor preferred term: Solanum lycopersicum
imported from: ncbitaxon.owl

Nicotiana
type: Class
subclass of: Nicotianeae
editor preferred term: Nicotiana
imported from: ncbitaxon.owl

Nicotiana benthamiana
type: Class
subclass of: Nicotiana
editor preferred term: Nicotiana benthamiana
imported from: ncbitaxon.owl

Neosartorya fennelliae
type: Class
subclass of: Neosartorya
editor preferred term: Neosartorya fennelliae
imported from: ncbitaxon.owl

Solanum
type: Class
subclass of: Solaneae
editor preferred term: Solanum
imported from: ncbitaxon.owl

Solanum tuberosum
type: Class
subclass of: Solanum
editor preferred term: Solanum tuberosum
imported from: ncbitaxon.owl

Glossata
type: Class
subclass of: Lepidoptera
editor preferred term: Glossata
imported from: ncbitaxon.owl

Neolepidoptera
type: Class
subclass of: Glossata
editor preferred term: Neolepidoptera
imported from: ncbitaxon.owl

Heteroneura
type: Class
subclass of: Neolepidoptera
editor preferred term: Heteroneura
imported from: ncbitaxon.owl

Mycosphaerella
type: Class
subclass of: Mycosphaerellaceae
editor preferred term: Mycosphaerella
imported from: ncbitaxon.owl

Rhodospirillaceae
type: Class
subclass of: Rhodospirillales
editor preferred term: Rhodospirillaceae
imported from: ncbitaxon.owl

Sphingomonadaceae
type: Class
subclass of: Sphingomonadales
editor preferred term: Sphingomonadaceae
imported from: ncbitaxon.owl

Lamiales
type: Class
subclass of: lamiids
editor preferred term: Lamiales
imported from: ncbitaxon.owl

Antirrhinum
type: Class
subclass of: Antirrhineae
editor preferred term: Antirrhinum
imported from: ncbitaxon.owl

Antirrhinum majus
type: Class
subclass of: Antirrhinum
editor preferred term: Antirrhinum majus
imported from: ncbitaxon.owl

Neopterygii
type: Class
subclass of: Actinopteri
editor preferred term: Neopterygii
imported from: ncbitaxon.owl

Batrachia
type: Class
subclass of: Amphibia
editor preferred term: Batrachia
imported from: ncbitaxon.owl

Protacanthopterygii
type: Class
subclass of: Euteleostei
editor preferred term: Protacanthopterygii
imported from: ncbitaxon.owl

Plasmodium (Vinckeia)
type: Class
subclass of: Plasmodium
editor preferred term: Plasmodium (Vinckeia)
imported from: ncbitaxon.owl

Plasmodium (Laverania)
type: Class
subclass of: Plasmodium
editor preferred term: Plasmodium (Laverania)
imported from: ncbitaxon.owl

Culicoidea
type: Class
subclass of: Culicimorpha
editor preferred term: Culicoidea
imported from: ncbitaxon.owl

Sapindales
type: Class
subclass of: eurosids II
editor preferred term: Sapindales
imported from: ncbitaxon.owl

Asterales
type: Class
subclass of: campanulids
editor preferred term: Asterales
imported from: ncbitaxon.owl

Asteraceae
type: Class
subclass of: Asterales
editor preferred term: Asteraceae
imported from: ncbitaxon.owl

Rubrobacter
type: Class
subclass of: Rubrobacteraceae
editor preferred term: Rubrobacter
imported from: ncbitaxon.owl

Aconoidasida
type: Class
subclass of: Apicomplexa
editor preferred term: Aconoidasida
imported from: ncbitaxon.owl

Eimeriorina
type: Class
subclass of: Eucoccidiorida
editor preferred term: Eimeriorina
imported from: ncbitaxon.owl

Candida dubliniensis
type: Class
subclass of: Candida
editor preferred term: Candida dubliniensis
imported from: ncbitaxon.owl

Solanoideae
type: Class
subclass of: Solanaceae
editor preferred term: Solanoideae
imported from: ncbitaxon.owl

Nicotianoideae
type: Class
subclass of: Solanaceae
editor preferred term: Nicotianoideae
imported from: ncbitaxon.owl

Nicotianeae
type: Class
subclass of: Nicotianoideae
editor preferred term: Nicotianeae
imported from: ncbitaxon.owl

Capsiceae
type: Class
subclass of: Solanoideae
editor preferred term: Capsiceae
imported from: ncbitaxon.owl

Solaneae
type: Class
subclass of: Solanoideae
editor preferred term: Solaneae
imported from: ncbitaxon.owl

Thiomonas sp. 3As
type: Class
subclass of: Thiomonas
editor preferred term: Thiomonas sp. 3As
imported from: ncbitaxon.owl

Moorella group
type: Class
subclass of: Thermoanaerobacteriaceae
editor preferred term: Moorella group
imported from: ncbitaxon.owl

Trichoderma reesei QM6a
type: Class
subclass of: Hypocrea jecorina
editor preferred term: Trichoderma reesei QM6a
imported from: ncbitaxon.owl

Sylvia
type: Class
subclass of: Sylviidae
editor preferred term: Sylvia
imported from: ncbitaxon.owl

Dinosauria
type: Class
subclass of: Archosauria
editor preferred term: Dinosauria
imported from: ncbitaxon.owl

Saurischia
type: Class
subclass of: Dinosauria
editor preferred term: Saurischia
imported from: ncbitaxon.owl

Theropoda
type: Class
subclass of: Saurischia
editor preferred term: Theropoda
imported from: ncbitaxon.owl

Coelurosauria
type: Class
subclass of: Theropoda
editor preferred term: Coelurosauria
imported from: ncbitaxon.owl

Muscomorpha
type: Class
subclass of: Brachycera
editor preferred term: Muscomorpha
imported from: ncbitaxon.owl

Schizophora
type: Class
subclass of: Muscomorpha
editor preferred term: Schizophora
imported from: ncbitaxon.owl

Acalyptratae
type: Class
subclass of: Schizophora
editor preferred term: Acalyptratae
imported from: ncbitaxon.owl

Ephydroidea
type: Class
subclass of: Acalyptratae
editor preferred term: Ephydroidea
imported from: ncbitaxon.owl

Culicimorpha
type: Class
subclass of: Nematocera
editor preferred term: Culicimorpha
imported from: ncbitaxon.owl

Anophelinae
type: Class
subclass of: Culicidae
editor preferred term: Anophelinae
imported from: ncbitaxon.owl

Culicinae
type: Class
subclass of: Culicidae
editor preferred term: Culicinae
imported from: ncbitaxon.owl

Drosophilinae
type: Class
subclass of: Drosophilidae
editor preferred term: Drosophilinae
imported from: ncbitaxon.owl

Cyanothece
type: Class
subclass of: Chroococcales
editor preferred term: Cyanothece
imported from: ncbitaxon.owl

Cyanothece sp. ATCC 51142
type: Class
subclass of: Cyanothece
editor preferred term: Cyanothece sp. ATCC 51142
imported from: ncbitaxon.owl

Moorella
type: Class
subclass of: Moorella group
editor preferred term: Moorella
imported from: ncbitaxon.owl

Liliopsida
type: Class
subclass of: Magnoliophyta
editor preferred term: Liliopsida
imported from: ncbitaxon.owl

Cellia
type: Class
subclass of: Anopheles
editor preferred term: Cellia
imported from: ncbitaxon.owl

Pyretophorus
type: Class
subclass of: Cellia
editor preferred term: Pyretophorus
imported from: ncbitaxon.owl

gambiae species complex
type: Class
subclass of: Pyretophorus
editor preferred term: gambiae species complex
imported from: ncbitaxon.owl

Dictyostelium discoideum
type: Class
subclass of: Dictyostelium
editor preferred term: Dictyostelium discoideum
imported from: ncbitaxon.owl

Poaceae
type: Class
subclass of: Poales
editor preferred term: Poaceae
imported from: ncbitaxon.owl

Hordeum
type: Class
subclass of: Triticeae
editor preferred term: Hordeum
imported from: ncbitaxon.owl

Hordeum vulgare
type: Class
subclass of: Hordeum
editor preferred term: Hordeum vulgare
imported from: ncbitaxon.owl

Lolium
type: Class
subclass of: Poeae
editor preferred term: Lolium
imported from: ncbitaxon.owl

Lolium perenne
type: Class
subclass of: Lolium
editor preferred term: Lolium perenne
imported from: ncbitaxon.owl

Oryza
type: Class
subclass of: Oryzeae
editor preferred term: Oryza
imported from: ncbitaxon.owl

Oryza sativa
type: Class
subclass of: Oryza
editor preferred term: Oryza sativa
imported from: ncbitaxon.owl

Triticum
type: Class
subclass of: Triticeae
editor preferred term: Triticum
imported from: ncbitaxon.owl

Triticum aestivum
type: Class
subclass of: Triticum
editor preferred term: Triticum aestivum
imported from: ncbitaxon.owl

Triticum turgidum subsp. durum
type: Class
subclass of: Triticum turgidum
editor preferred term: Triticum turgidum subsp. durum
imported from: ncbitaxon.owl

Triticum turgidum
type: Class
subclass of: Triticum
editor preferred term: Triticum turgidum
imported from: ncbitaxon.owl

Zea
type: Class
subclass of: Andropogoneae
editor preferred term: Zea
imported from: ncbitaxon.owl

Zea mays
type: Class
subclass of: Zea
editor preferred term: Zea mays
imported from: ncbitaxon.owl

Festuca
type: Class
subclass of: Poeae
editor preferred term: Festuca
imported from: ncbitaxon.owl

Festuca arundinacea
type: Class
subclass of: Festuca
editor preferred term: Festuca arundinacea
imported from: ncbitaxon.owl

Staphylococcus aureus subsp. aureus
type: Class
subclass of: Staphylococcus aureus
editor preferred term: Staphylococcus aureus subsp. aureus
imported from: ncbitaxon.owl

Mesoplasma
type: Class
subclass of: Entomoplasmataceae
editor preferred term: Mesoplasma
imported from: ncbitaxon.owl

Oenococcus
type: Class
subclass of: Leuconostocaceae
editor preferred term: Oenococcus
imported from: ncbitaxon.owl

Thermoplasmataceae
type: Class
subclass of: Thermoplasmatales
editor preferred term: Thermoplasmataceae
imported from: ncbitaxon.owl

Moraxellaceae
type: Class
subclass of: Pseudomonadales
editor preferred term: Moraxellaceae
imported from: ncbitaxon.owl

Drosophilini
type: Class
subclass of: Drosophilinae
editor preferred term: Drosophilini
imported from: ncbitaxon.owl

Drosophilina
type: Class
subclass of: Drosophilini
editor preferred term: Drosophilina
imported from: ncbitaxon.owl

Acinetobacter
type: Class
subclass of: Moraxellaceae
editor preferred term: Acinetobacter
imported from: ncbitaxon.owl

Acinetobacter baumannii
type: Class
subclass of: Acinetobacter
editor preferred term: Acinetobacter baumannii
imported from: ncbitaxon.owl

Orbiliaceae
type: Class
subclass of: Orbiliales
editor preferred term: Orbiliaceae
imported from: ncbitaxon.owl

Tetraodon
type: Class
subclass of: Tetraodontidae
editor preferred term: Tetraodon
imported from: ncbitaxon.owl

commelinids
type: Class
subclass of: Liliopsida
editor preferred term: commelinids
imported from: ncbitaxon.owl

Fungi
type: Class
subclass of: Fungi/Metazoa group
editor preferred term: Fungi
imported from: ncbitaxon.owl

Schizotrypanum
type: Class
subclass of: Trypanosoma
editor preferred term: Schizotrypanum
imported from: ncbitaxon.owl

Agrotis
type: Class
subclass of: Noctuinae
editor preferred term: Agrotis
imported from: ncbitaxon.owl

Agrotis segetum
type: Class
subclass of: Agrotis
editor preferred term: Agrotis segetum
imported from: ncbitaxon.owl

Neisseriaceae
type: Class
subclass of: Neisseriales
editor preferred term: Neisseriaceae
imported from: ncbitaxon.owl

Neisseria
type: Class
subclass of: Neisseriaceae
editor preferred term: Neisseria
imported from: ncbitaxon.owl

Neisseria gonorrhoeae
type: Class
subclass of: Neisseria
editor preferred term: Neisseria gonorrhoeae
imported from: ncbitaxon.owl

Neisseria meningitidis
type: Class
subclass of: Neisseria
editor preferred term: Neisseria meningitidis
imported from: ncbitaxon.owl

Ralstonia
type: Class
subclass of: Burkholderiaceae
editor preferred term: Ralstonia
imported from: ncbitaxon.owl

Geospiza
type: Class
subclass of: Thraupini
editor preferred term: Geospiza
imported from: ncbitaxon.owl

Geospiza conirostris
type: Class
subclass of: Geospiza
editor preferred term: Geospiza conirostris
imported from: ncbitaxon.owl

Geospiza fortis
type: Class
subclass of: Geospiza
editor preferred term: Geospiza fortis
imported from: ncbitaxon.owl

Geospiza magnirostris
type: Class
subclass of: Geospiza
editor preferred term: Geospiza magnirostris
imported from: ncbitaxon.owl

Geospiza scandens
type: Class
subclass of: Geospiza
editor preferred term: Geospiza scandens
imported from: ncbitaxon.owl

Ascomycota
type: Class
subclass of: Fungi
editor preferred term: Ascomycota
imported from: ncbitaxon.owl

Saccharomycetes
type: Class
subclass of: Saccharomycotina
editor preferred term: Saccharomycetes
imported from: ncbitaxon.owl

Saccharomycetales
type: Class
subclass of: Saccharomycetes
editor preferred term: Saccharomycetales
imported from: ncbitaxon.owl

Saccharomycetaceae
type: Class
subclass of: Saccharomycetales
editor preferred term: Saccharomycetaceae
imported from: ncbitaxon.owl

Novosphingobium aromaticivorans
type: Class
subclass of: Novosphingobium
editor preferred term: Novosphingobium aromaticivorans
imported from: ncbitaxon.owl

Schizosaccharomycetaceae
type: Class
subclass of: Schizosaccharomycetales
editor preferred term: Schizosaccharomycetaceae
imported from: ncbitaxon.owl

Schizosaccharomyces
type: Class
subclass of: Schizosaccharomycetaceae
editor preferred term: Schizosaccharomyces
imported from: ncbitaxon.owl

Schizosaccharomyces pombe
type: Class
subclass of: Schizosaccharomyces
editor preferred term: Schizosaccharomyces pombe
imported from: ncbitaxon.owl

Kluyveromyces
type: Class
subclass of: Saccharomycetaceae
editor preferred term: Kluyveromyces
imported from: ncbitaxon.owl

Kluyveromyces waltii
type: Class
subclass of: Kluyveromyces
editor preferred term: Kluyveromyces waltii
imported from: ncbitaxon.owl

Pichia
type: Class
subclass of: Saccharomycetaceae
editor preferred term: Pichia
imported from: ncbitaxon.owl

Pichia pastoris
type: Class
subclass of: Pichia
editor preferred term: Pichia pastoris
imported from: ncbitaxon.owl

Lycopersicon
type: Class
subclass of: Solanum
editor preferred term: Lycopersicon
imported from: ncbitaxon.owl

Saccharomyces
type: Class
subclass of: Saccharomycetaceae
editor preferred term: Saccharomyces
imported from: ncbitaxon.owl

Saccharomyces bayanus
type: Class
subclass of: Saccharomyces
editor preferred term: Saccharomyces bayanus
imported from: ncbitaxon.owl

Rubrobacter xylanophilus
type: Class
subclass of: Rubrobacter
editor preferred term: Rubrobacter xylanophilus
imported from: ncbitaxon.owl

Saccharomyces cerevisiae
type: Class
subclass of: Saccharomyces
editor preferred term: Saccharomyces cerevisiae
imported from: ncbitaxon.owl

Desulfitobacterium hafniense
type: Class
subclass of: Desulfitobacterium
editor preferred term: Desulfitobacterium hafniense
imported from: ncbitaxon.owl

Lachancea kluyveri
type: Class
subclass of: Lachancea
editor preferred term: Lachancea kluyveri
imported from: ncbitaxon.owl

Thermoplasma volcanium
type: Class
subclass of: Thermoplasma
editor preferred term: Thermoplasma volcanium
imported from: ncbitaxon.owl

Eurotiales
type: Class
subclass of: Eurotiomycetes
editor preferred term: Eurotiales
imported from: ncbitaxon.owl

Aspergillus
type: Class
subclass of: mitosporic Trichocomaceae
editor preferred term: Aspergillus
imported from: ncbitaxon.owl

Insecta
type: Class
subclass of: Hexapoda
editor preferred term: Insecta
imported from: ncbitaxon.owl

Aspergillus clavatus
type: Class
subclass of: Aspergillus
editor preferred term: Aspergillus clavatus
imported from: ncbitaxon.owl

Alcaligenaceae
type: Class
subclass of: Burkholderiales
editor preferred term: Alcaligenaceae
imported from: ncbitaxon.owl

Aspergillus niger
type: Class
subclass of: Aspergillus
editor preferred term: Aspergillus niger
imported from: ncbitaxon.owl

Aspergillus fumigatus
type: Class
subclass of: Aspergillus
editor preferred term: Aspergillus fumigatus
imported from: ncbitaxon.owl

Heterodera glycines
type: Class
subclass of: Heterodera
editor preferred term: Heterodera glycines
imported from: ncbitaxon.owl

Hypocreales
type: Class
subclass of: Hypocreomycetidae
editor preferred term: Hypocreales
imported from: ncbitaxon.owl

Gibberella
type: Class
subclass of: Nectriaceae
editor preferred term: Gibberella
imported from: ncbitaxon.owl

Hypocreaceae
type: Class
subclass of: Hypocreales
editor preferred term: Hypocreaceae
imported from: ncbitaxon.owl

Chlamydiae/Verrucomicrobia group
type: Class
subclass of: Bacteria
editor preferred term: Chlamydiae/Verrucomicrobia group
imported from: ncbitaxon.owl

Chlamydiales
type: Class
subclass of: Chlamydiae (class)
editor preferred term: Chlamydiales
imported from: ncbitaxon.owl

Sordariales
type: Class
subclass of: Sordariomycetidae
editor preferred term: Sordariales
imported from: ncbitaxon.owl

Neurospora
type: Class
subclass of: Sordariaceae
editor preferred term: Neurospora
imported from: ncbitaxon.owl

Neurospora crassa
type: Class
subclass of: Neurospora
editor preferred term: Neurospora crassa
imported from: ncbitaxon.owl

Hypocrea jecorina
type: Class
subclass of: Hypocrea
editor preferred term: Hypocrea jecorina
imported from: ncbitaxon.owl

Sordaria
type: Class
subclass of: Sordariaceae
editor preferred term: Sordaria
imported from: ncbitaxon.owl

Sordaria macrospora
type: Class
subclass of: Sordaria
editor preferred term: Sordaria macrospora
imported from: ncbitaxon.owl

Sordariaceae
type: Class
subclass of: Sordariales
editor preferred term: Sordariaceae
imported from: ncbitaxon.owl

Ciona savignyi
type: Class
subclass of: Ciona
editor preferred term: Ciona savignyi
imported from: ncbitaxon.owl

Bordetella
type: Class
subclass of: Alcaligenaceae
editor preferred term: Bordetella
imported from: ncbitaxon.owl

Bordetella bronchiseptica
type: Class
subclass of: Bordetella
editor preferred term: Bordetella bronchiseptica
imported from: ncbitaxon.owl

Bordetella pertussis
type: Class
subclass of: Bordetella
editor preferred term: Bordetella pertussis
imported from: ncbitaxon.owl

Basidiomycota
type: Class
subclass of: Fungi
editor preferred term: Basidiomycota
imported from: ncbitaxon.owl

Festuca rubra
type: Class
subclass of: Festuca
editor preferred term: Festuca rubra
imported from: ncbitaxon.owl

Ustilaginomycetes
type: Class
subclass of: Basidiomycota
editor preferred term: Ustilaginomycetes
imported from: ncbitaxon.owl

Ustilaginales
type: Class
subclass of: Ustilaginomycetidae
editor preferred term: Ustilaginales
imported from: ncbitaxon.owl

Ustilaginaceae
type: Class
subclass of: Ustilaginales
editor preferred term: Ustilaginaceae
imported from: ncbitaxon.owl

Ustilago
type: Class
subclass of: Ustilaginaceae
editor preferred term: Ustilago
imported from: ncbitaxon.owl

Ustilago maydis
type: Class
subclass of: Ustilago
editor preferred term: Ustilago maydis
imported from: ncbitaxon.owl

Leymus
type: Class
subclass of: Triticeae
editor preferred term: Leymus
imported from: ncbitaxon.owl

Hymenomycetes
type: Class
subclass of: Basidiomycota
editor preferred term: Hymenomycetes
imported from: ncbitaxon.owl

Aphyllophorales
type: Class
subclass of: Homobasidiomycetes
editor preferred term: Aphyllophorales
imported from: ncbitaxon.owl

Corticiaceae
type: Class
subclass of: Aphyllophorales
editor preferred term: Corticiaceae
imported from: ncbitaxon.owl

Phanerochaete
type: Class
subclass of: Corticiaceae
editor preferred term: Phanerochaete
imported from: ncbitaxon.owl

Phanerochaete chrysosporium
type: Class
subclass of: Phanerochaete
editor preferred term: Phanerochaete chrysosporium
imported from: ncbitaxon.owl

Agaricales
type: Class
subclass of: Homobasidiomycetes
editor preferred term: Agaricales
imported from: ncbitaxon.owl

Xanthomonas axonopodis
type: Class
subclass of: Xanthomonas
editor preferred term: Xanthomonas axonopodis
imported from: ncbitaxon.owl

Coprinopsis cinerea
type: Class
subclass of: Coprinopsis
editor preferred term: Coprinopsis cinerea
imported from: ncbitaxon.owl

Stegomyia
type: Class
subclass of: Aedes
editor preferred term: Stegomyia
imported from: ncbitaxon.owl

Culicini
type: Class
subclass of: Culicinae
editor preferred term: Culicini
imported from: ncbitaxon.owl

Paxillaceae
type: Class
subclass of: Paxilineae
editor preferred term: Paxillaceae
imported from: ncbitaxon.owl

Paxillus
type: Class
subclass of: Paxillaceae
editor preferred term: Paxillus
imported from: ncbitaxon.owl

Pyrococcus horikoshii
type: Class
subclass of: Pyrococcus
editor preferred term: Pyrococcus horikoshii
imported from: ncbitaxon.owl

mitosporic Orbiliaceae
type: Class
subclass of: Orbiliaceae
editor preferred term: mitosporic Orbiliaceae
imported from: ncbitaxon.owl

Monacrosporium
type: Class
subclass of: mitosporic Orbiliaceae
editor preferred term: Monacrosporium
imported from: ncbitaxon.owl

Zymomonas
type: Class
subclass of: Sphingomonadaceae
editor preferred term: Zymomonas
imported from: ncbitaxon.owl

Zymomonas mobilis
type: Class
subclass of: Zymomonas
editor preferred term: Zymomonas mobilis
imported from: ncbitaxon.owl

Enterobacteriaceae
type: Class
subclass of: Enterobacteriales
editor preferred term: Enterobacteriaceae
imported from: ncbitaxon.owl

Mycosphaerella graminicola
type: Class
subclass of: Mycosphaerella
editor preferred term: Mycosphaerella graminicola
imported from: ncbitaxon.owl

Candida
type: Class
subclass of: mitosporic Saccharomycetales
editor preferred term: Candida
imported from: ncbitaxon.owl

Candida albicans
type: Class
subclass of: Candida
editor preferred term: Candida albicans
imported from: ncbitaxon.owl

Candida glabrata
type: Class
subclass of: Candida
editor preferred term: Candida glabrata
imported from: ncbitaxon.owl

Pinus resinosa
type: Class
subclass of: Pinus [NCBITaxon:139271]
editor preferred term: Pinus resinosa
imported from: ncbitaxon.owl

Gibberella zeae
type: Class
subclass of: Gibberella
editor preferred term: Gibberella zeae
imported from: ncbitaxon.owl

Panagrolaimoidea
type: Class
subclass of: Rhabditida
editor preferred term: Panagrolaimoidea
imported from: ncbitaxon.owl

Rhabditoidea
type: Class
subclass of: Rhabditida
editor preferred term: Rhabditoidea
imported from: ncbitaxon.owl

Peloderinae
type: Class
subclass of: Rhabditidae
editor preferred term: Peloderinae
imported from: ncbitaxon.owl

Escherichia
type: Class
subclass of: Enterobacteriaceae
editor preferred term: Escherichia
imported from: ncbitaxon.owl

Escherichia coli
type: Class
subclass of: Escherichia
editor preferred term: Escherichia coli
imported from: ncbitaxon.owl

Agrotis ipsilon
type: Class
subclass of: Agrotis
editor preferred term: Agrotis ipsilon
imported from: ncbitaxon.owl

Kinetoplastida
type: Class
subclass of: Euglenozoa
editor preferred term: Kinetoplastida
imported from: ncbitaxon.owl

Trypanosomatidae
type: Class
subclass of: Kinetoplastida
editor preferred term: Trypanosomatidae
imported from: ncbitaxon.owl

Leishmania
type: Class
subclass of: Trypanosomatidae
editor preferred term: Leishmania
imported from: ncbitaxon.owl

Leishmania braziliensis
type: Class
subclass of: Leishmania braziliensis species complex
editor preferred term: Leishmania braziliensis
imported from: ncbitaxon.owl

Leishmania donovani
type: Class
subclass of: Leishmania donovani species complex
editor preferred term: Leishmania donovani
imported from: ncbitaxon.owl

Leishmania major
type: Class
subclass of: Leishmania major species complex
editor preferred term: Leishmania major
imported from: ncbitaxon.owl

Leishmania mexicana
type: Class
subclass of: Leishmania mexicana species complex
editor preferred term: Leishmania mexicana
imported from: ncbitaxon.owl

Leishmania infantum
type: Class
subclass of: Leishmania infantum species complex
editor preferred term: Leishmania infantum
imported from: ncbitaxon.owl

Trypanosoma
type: Class
subclass of: Trypanosomatidae
editor preferred term: Trypanosoma
imported from: ncbitaxon.owl

Trypanosoma brucei
type: Class
subclass of: Trypanozoon
editor preferred term: Trypanosoma brucei
imported from: ncbitaxon.owl

Trypanosoma cruzi
type: Class
subclass of: Schizotrypanum
editor preferred term: Trypanosoma cruzi
imported from: ncbitaxon.owl

Dictyostelium
type: Class
subclass of: Dictyosteliida
editor preferred term: Dictyostelium
imported from: ncbitaxon.owl

Apicomplexa
type: Class
subclass of: Alveolata
editor preferred term: Apicomplexa
imported from: ncbitaxon.owl

Coccidia
type: Class
subclass of: Apicomplexa
editor preferred term: Coccidia
imported from: ncbitaxon.owl

Burkholderia thailandensis
type: Class
subclass of: pseudomallei group
editor preferred term: Burkholderia thailandensis
imported from: ncbitaxon.owl

Coniferopsida
type: Class
subclass of: Coniferophyta
editor preferred term: Coniferopsida
imported from: ncbitaxon.owl

Tracheophyta
type: Class
subclass of: Embryophyta
editor preferred term: Tracheophyta
imported from: ncbitaxon.owl

Spermatophyta
type: Class
subclass of: Euphyllophyta
editor preferred term: Spermatophyta
imported from: ncbitaxon.owl

Cryptosporidium
type: Class
subclass of: Cryptosporidiidae
editor preferred term: Cryptosporidium
imported from: ncbitaxon.owl

Cryptosporidium parvum
type: Class
subclass of: Cryptosporidium
editor preferred term: Cryptosporidium parvum
imported from: ncbitaxon.owl

Haemosporida
type: Class
subclass of: Aconoidasida
editor preferred term: Haemosporida
imported from: ncbitaxon.owl

Plasmodium
type: Class
subclass of: Haemosporida
editor preferred term: Plasmodium
imported from: ncbitaxon.owl

Plasmodium berghei
type: Class
subclass of: Plasmodium (Vinckeia)
editor preferred term: Plasmodium berghei
imported from: ncbitaxon.owl

Plasmodium falciparum
type: Class
subclass of: Plasmodium (Laverania)
editor preferred term: Plasmodium falciparum
imported from: ncbitaxon.owl

Salmonella
type: Class
subclass of: Enterobacteriaceae
editor preferred term: Salmonella
imported from: ncbitaxon.owl

Salmonella enteritidis
type: Class
subclass of: Salmonella
editor preferred term: Salmonella enteritidis
imported from: ncbitaxon.owl

Taeniopygia
type: Class
subclass of: Estrildinae
editor preferred term: Taeniopygia
imported from: ncbitaxon.owl

Taeniopygia guttata
type: Class
subclass of: Taeniopygia
editor preferred term: Taeniopygia guttata
imported from: ncbitaxon.owl

Coregonus clupeaformis
type: Class
subclass of: Coregonus
editor preferred term: Coregonus clupeaformis
imported from: ncbitaxon.owl

Salmonella typhi
type: Class
subclass of: Salmonella
editor preferred term: Salmonella typhi
imported from: ncbitaxon.owl

Salmonella typhimurium
type: Class
subclass of: Salmonella
editor preferred term: Salmonella typhimurium
imported from: ncbitaxon.owl

Eumetazoa
type: Class
subclass of: Metazoa
editor preferred term: Eumetazoa
imported from: ncbitaxon.owl

Neosartorya fischeri group
type: Class
subclass of: Neosartorya
editor preferred term: Neosartorya fischeri group
imported from: ncbitaxon.owl

Platyhelminthes
type: Class
subclass of: Acoelomata
editor preferred term: Platyhelminthes
imported from: ncbitaxon.owl

Trematoda
type: Class
subclass of: Platyhelminthes
editor preferred term: Trematoda
imported from: ncbitaxon.owl

Digenea
type: Class
subclass of: Trematoda
editor preferred term: Digenea
imported from: ncbitaxon.owl

Strigeidida
type: Class
subclass of: Digenea
editor preferred term: Strigeidida
imported from: ncbitaxon.owl

Schistosoma
type: Class
subclass of: Schistosomatidae
editor preferred term: Schistosoma
imported from: ncbitaxon.owl

Schistosoma japonicum
type: Class
subclass of: Schistosoma
editor preferred term: Schistosoma japonicum
imported from: ncbitaxon.owl

Schistosoma mansoni
type: Class
subclass of: Schistosoma
editor preferred term: Schistosoma mansoni
imported from: ncbitaxon.owl

Emberizinae
type: Class
subclass of: Fringillidae
editor preferred term: Emberizinae
imported from: ncbitaxon.owl

Nematoda
type: Class
subclass of: Pseudocoelomata
editor preferred term: Nematoda
imported from: ncbitaxon.owl

Rhabditida
type: Class
subclass of: Chromadorea
editor preferred term: Rhabditida
imported from: ncbitaxon.owl

Caenorhabditis
type: Class
subclass of: Peloderinae
editor preferred term: Caenorhabditis
imported from: ncbitaxon.owl

Caenorhabditis briggsae
type: Class
subclass of: Caenorhabditis
editor preferred term: Caenorhabditis briggsae
imported from: ncbitaxon.owl

Caenorhabditis elegans
type: Class
subclass of: Caenorhabditis
editor preferred term: Caenorhabditis elegans
imported from: ncbitaxon.owl

Rhabditidae
type: Class
subclass of: Rhabditoidea
editor preferred term: Rhabditidae
imported from: ncbitaxon.owl

Strongyloididae
type: Class
subclass of: Panagrolaimoidea
editor preferred term: Strongyloididae
imported from: ncbitaxon.owl

Strongyloides
type: Class
subclass of: Strongyloididae
editor preferred term: Strongyloides
imported from: ncbitaxon.owl

Spirurida
type: Class
subclass of: Chromadorea
editor preferred term: Spirurida
imported from: ncbitaxon.owl

Brugia
type: Class
subclass of: Onchocercidae
editor preferred term: Brugia
imported from: ncbitaxon.owl

Brugia malayi
type: Class
subclass of: Brugia
editor preferred term: Brugia malayi
imported from: ncbitaxon.owl

Yersinia
type: Class
subclass of: Enterobacteriaceae
editor preferred term: Yersinia
imported from: ncbitaxon.owl

Ustilaginomycetidae
type: Class
subclass of: Ustilaginomycetes
editor preferred term: Ustilaginomycetidae
imported from: ncbitaxon.owl

Filarioidea
type: Class
subclass of: Spirurida
editor preferred term: Filarioidea
imported from: ncbitaxon.owl

Onchocercidae
type: Class
subclass of: Filarioidea
editor preferred term: Onchocercidae
imported from: ncbitaxon.owl

Tylenchida
type: Class
subclass of: Chromadorea
editor preferred term: Tylenchida
imported from: ncbitaxon.owl

Heteroderidae
type: Class
subclass of: Tylenchoidea
editor preferred term: Heteroderidae
imported from: ncbitaxon.owl

Yersinia pestis
type: Class
subclass of: Yersinia
editor preferred term: Yersinia pestis
imported from: ncbitaxon.owl

Aquifex aeolicus
type: Class
subclass of: Aquifex
editor preferred term: Aquifex aeolicus
imported from: ncbitaxon.owl

Vibrionaceae
type: Class
subclass of: Vibrionales
editor preferred term: Vibrionaceae
imported from: ncbitaxon.owl

Mollusca
type: Class
subclass of: Protostomia
editor preferred term: Mollusca
imported from: ncbitaxon.owl

Gastropoda
type: Class
subclass of: Mollusca
editor preferred term: Gastropoda
imported from: ncbitaxon.owl

Buchnera sp.
type: Class
subclass of: Buchnera
editor preferred term: Buchnera sp.
imported from: ncbitaxon.owl

Borrelia burgdorferi group
type: Class
subclass of: Borrelia
editor preferred term: Borrelia burgdorferi group
imported from: ncbitaxon.owl

Aquificaceae
type: Class
subclass of: Aquificales
editor preferred term: Aquificaceae
imported from: ncbitaxon.owl

Pulmonata
type: Class
subclass of: Gastropoda
editor preferred term: Pulmonata
imported from: ncbitaxon.owl

Basommatophora
type: Class
subclass of: Pulmonata
editor preferred term: Basommatophora
imported from: ncbitaxon.owl

Planorbidae
type: Class
subclass of: Lymnaeoidea
editor preferred term: Planorbidae
imported from: ncbitaxon.owl

Biomphalaria
type: Class
subclass of: Planorbidae
editor preferred term: Biomphalaria
imported from: ncbitaxon.owl

Biomphalaria glabrata
type: Class
subclass of: Biomphalaria
editor preferred term: Biomphalaria glabrata
imported from: ncbitaxon.owl

Photobacterium
type: Class
subclass of: Vibrionaceae
editor preferred term: Photobacterium
imported from: ncbitaxon.owl

Vibrio
type: Class
subclass of: Vibrionaceae
editor preferred term: Vibrio
imported from: ncbitaxon.owl

Arthropoda
type: Class
subclass of: Panarthropoda
editor preferred term: Arthropoda
imported from: ncbitaxon.owl

Crustacea
type: Class
subclass of: Pancrustacea
editor preferred term: Crustacea
imported from: ncbitaxon.owl

Vibrio cholerae
type: Class
subclass of: Vibrio
editor preferred term: Vibrio cholerae
imported from: ncbitaxon.owl

Malacostraca
type: Class
subclass of: Crustacea
editor preferred term: Malacostraca
imported from: ncbitaxon.owl

Eucarida
type: Class
subclass of: Eumalacostraca
editor preferred term: Eucarida
imported from: ncbitaxon.owl

Decapoda
type: Class
subclass of: Eucarida
editor preferred term: Decapoda
imported from: ncbitaxon.owl

Dendrobranchiata
type: Class
subclass of: Decapoda
editor preferred term: Dendrobranchiata
imported from: ncbitaxon.owl

Penaeidae
type: Class
subclass of: Penaeoidea
editor preferred term: Penaeidae
imported from: ncbitaxon.owl

Penaeus monodon
type: Class
subclass of: Penaeus
editor preferred term: Penaeus monodon
imported from: ncbitaxon.owl

Mesorhizobium
type: Class
subclass of: Phyllobacteriaceae
editor preferred term: Mesorhizobium
imported from: ncbitaxon.owl

Thermoanaerobacteriales
type: Class
subclass of: Clostridia
editor preferred term: Thermoanaerobacteriales
imported from: ncbitaxon.owl

Bacteroidetes/Chlorobi group
type: Class
subclass of: Bacteria
editor preferred term: Bacteroidetes/Chlorobi group
imported from: ncbitaxon.owl

delta/epsilon subdivisions
type: Class
subclass of: Proteobacteria
editor preferred term: delta/epsilon subdivisions
imported from: ncbitaxon.owl

Boletales
type: Class
subclass of: Homobasidiomycetes
editor preferred term: Boletales
imported from: ncbitaxon.owl

Phyllobacteriaceae
type: Class
subclass of: Rhizobiales
editor preferred term: Phyllobacteriaceae
imported from: ncbitaxon.owl

Desulfuromonadales
type: Class
subclass of: Deltaproteobacteria
editor preferred term: Desulfuromonadales
imported from: ncbitaxon.owl

Hexapoda
type: Class
subclass of: Pancrustacea
editor preferred term: Hexapoda
imported from: ncbitaxon.owl

Lepidoptera
type: Class
subclass of: Amphiesmenoptera
editor preferred term: Lepidoptera
imported from: ncbitaxon.owl

Bombycidae
type: Class
subclass of: Bombyciformes
editor preferred term: Bombycidae
imported from: ncbitaxon.owl

Bombyx
type: Class
subclass of: Bombycidae
editor preferred term: Bombyx
imported from: ncbitaxon.owl

Bombyx mori
type: Class
subclass of: Bombyx
editor preferred term: Bombyx mori
imported from: ncbitaxon.owl

Apinae
type: Class
subclass of: Apidae
editor preferred term: Apinae
imported from: ncbitaxon.owl

Noctuidae
type: Class
subclass of: Noctuoidea
editor preferred term: Noctuidae
imported from: ncbitaxon.owl

Paxillus involutus
type: Class
subclass of: Paxillus
editor preferred term: Paxillus involutus
imported from: ncbitaxon.owl

Pasteurellaceae
type: Class
subclass of: Pasteurellales
editor preferred term: Pasteurellaceae
imported from: ncbitaxon.owl

eudicotyledons
type: Class
subclass of: Magnoliophyta
editor preferred term: eudicotyledons
imported from: ncbitaxon.owl

asterids
type: Class
subclass of: core eudicotyledons
editor preferred term: asterids
imported from: ncbitaxon.owl

rosids
type: Class
subclass of: core eudicotyledons
editor preferred term: rosids
imported from: ncbitaxon.owl

Actinobacillus
type: Class
subclass of: Pasteurellaceae
editor preferred term: Actinobacillus
imported from: ncbitaxon.owl

Diptera
type: Class
subclass of: Endopterygota
editor preferred term: Diptera
imported from: ncbitaxon.owl

Nematocera
type: Class
subclass of: Diptera
editor preferred term: Nematocera
imported from: ncbitaxon.owl

Actinobacillus pleuropneumoniae
type: Class
subclass of: Actinobacillus
editor preferred term: Actinobacillus pleuropneumoniae
imported from: ncbitaxon.owl

Culicidae
type: Class
subclass of: Culicoidea
editor preferred term: Culicidae
imported from: ncbitaxon.owl

Aedes
type: Class
subclass of: Aedes/Ochlerotatus group
editor preferred term: Aedes
imported from: ncbitaxon.owl

Aedes aegypti
type: Class
subclass of: Stegomyia
editor preferred term: Aedes aegypti
imported from: ncbitaxon.owl

Anopheles
type: Class
subclass of: Anophelinae
editor preferred term: Anopheles
imported from: ncbitaxon.owl

Anopheles gambiae
type: Class
subclass of: gambiae species complex
editor preferred term: Anopheles gambiae
imported from: ncbitaxon.owl

Fabales
type: Class
subclass of: eurosids I
editor preferred term: Fabales
imported from: ncbitaxon.owl

Brachycera
type: Class
subclass of: Diptera
editor preferred term: Brachycera
imported from: ncbitaxon.owl

Eumalacostraca
type: Class
subclass of: Malacostraca
editor preferred term: Eumalacostraca
imported from: ncbitaxon.owl

Drosophilidae
type: Class
subclass of: Ephydroidea
editor preferred term: Drosophilidae
imported from: ncbitaxon.owl

Drosophila
type: Class
subclass of: Drosophiliti
editor preferred term: Drosophila
imported from: ncbitaxon.owl

Drosophila erecta
type: Class
subclass of: melanogaster subgroup
editor preferred term: Drosophila erecta
imported from: ncbitaxon.owl

Drosophila mauritiana
type: Class
subclass of: melanogaster subgroup
editor preferred term: Drosophila mauritiana
imported from: ncbitaxon.owl

Drosophila melanogaster
type: Class
subclass of: melanogaster subgroup
editor preferred term: Drosophila melanogaster
imported from: ncbitaxon.owl

Thiotrichales
type: Class
subclass of: Gammaproteobacteria
editor preferred term: Thiotrichales
imported from: ncbitaxon.owl

Pseudomonadales
type: Class
subclass of: Gammaproteobacteria
editor preferred term: Pseudomonadales
imported from: ncbitaxon.owl

Alteromonadaceae
type: Class
subclass of: Alteromonadales
editor preferred term: Alteromonadaceae
imported from: ncbitaxon.owl

Helicobacteraceae
type: Class
subclass of: Campylobacterales
editor preferred term: Helicobacteraceae
imported from: ncbitaxon.owl

Campylobacteraceae
type: Class
subclass of: Campylobacterales
editor preferred term: Campylobacteraceae
imported from: ncbitaxon.owl

Drosophila orena
type: Class
subclass of: melanogaster subgroup
editor preferred term: Drosophila orena
imported from: ncbitaxon.owl

Drosophila pseudoobscura
type: Class
subclass of: pseudoobscura subgroup
editor preferred term: Drosophila pseudoobscura
imported from: ncbitaxon.owl

Drosophila sechellia
type: Class
subclass of: melanogaster subgroup
editor preferred term: Drosophila sechellia
imported from: ncbitaxon.owl

Haemophilus
type: Class
subclass of: Pasteurellaceae
editor preferred term: Haemophilus
imported from: ncbitaxon.owl

Drosophila simulans
type: Class
subclass of: melanogaster subgroup
editor preferred term: Drosophila simulans
imported from: ncbitaxon.owl

Drosophila teissieri
type: Class
subclass of: melanogaster subgroup
editor preferred term: Drosophila teissieri
imported from: ncbitaxon.owl

Drosophila yakuba
type: Class
subclass of: melanogaster subgroup
editor preferred term: Drosophila yakuba
imported from: ncbitaxon.owl

Haemophilus influenzae
type: Class
subclass of: Haemophilus
editor preferred term: Haemophilus influenzae
imported from: ncbitaxon.owl

Dechloromonas
type: Class
subclass of: Rhodocyclaceae
editor preferred term: Dechloromonas
imported from: ncbitaxon.owl

Hymenoptera
type: Class
subclass of: Endopterygota
editor preferred term: Hymenoptera
imported from: ncbitaxon.owl

Apocrita
type: Class
subclass of: Hymenoptera
editor preferred term: Apocrita
imported from: ncbitaxon.owl

Photobacterium profundum
type: Class
subclass of: Photobacterium
editor preferred term: Photobacterium profundum
imported from: ncbitaxon.owl

Aculeata
type: Class
subclass of: Apocrita
editor preferred term: Aculeata
imported from: ncbitaxon.owl

Monacrosporium haptotylum
type: Class
subclass of: Monacrosporium
editor preferred term: Monacrosporium haptotylum
imported from: ncbitaxon.owl

Pasteurella
type: Class
subclass of: Pasteurellaceae
editor preferred term: Pasteurella
imported from: ncbitaxon.owl

Apidae
type: Class
subclass of: Apoidea
editor preferred term: Apidae
imported from: ncbitaxon.owl

Apis
type: Class
subclass of: Apini
editor preferred term: Apis
imported from: ncbitaxon.owl

Apis mellifera
type: Class
subclass of: Apis
editor preferred term: Apis mellifera
imported from: ncbitaxon.owl

Pasteurella multocida
type: Class
subclass of: Pasteurella
editor preferred term: Pasteurella multocida
imported from: ncbitaxon.owl

Pterygota
type: Class
subclass of: Dicondylia
editor preferred term: Pterygota
imported from: ncbitaxon.owl

Ferroplasma
type: Class
subclass of: Ferroplasmaceae
editor preferred term: Ferroplasma
imported from: ncbitaxon.owl

Caulobacter
type: Class
subclass of: Caulobacteraceae
editor preferred term: Caulobacter
imported from: ncbitaxon.owl

Oxalobacteraceae
type: Class
subclass of: Burkholderiales
editor preferred term: Oxalobacteraceae
imported from: ncbitaxon.owl

Populus euphratica
type: Class
subclass of: Populus
editor preferred term: Populus euphratica
imported from: ncbitaxon.owl

Eucoccidiorida
type: Class
subclass of: Coccidia
editor preferred term: Eucoccidiorida
imported from: ncbitaxon.owl

Rhodocyclaceae
type: Class
subclass of: Rhodocyclales
editor preferred term: Rhodocyclaceae
imported from: ncbitaxon.owl

Rickettsiales
type: Class
subclass of: Alphaproteobacteria
editor preferred term: Rickettsiales
imported from: ncbitaxon.owl

Anaplasma
type: Class
subclass of: Anaplasmataceae
editor preferred term: Anaplasma
imported from: ncbitaxon.owl

Nidovirales
type: Class
subclass of: ssRNA positive-strand viruses, no DNA stage
editor preferred term: Nidovirales
imported from: ncbitaxon.owl

Caulobacteraceae
type: Class
subclass of: Caulobacterales
editor preferred term: Caulobacteraceae
imported from: ncbitaxon.owl

Chordata
type: Class
subclass of: Deuterostomia
editor preferred term: Chordata
imported from: ncbitaxon.owl

Urochordata
type: Class
subclass of: Chordata
editor preferred term: Urochordata
imported from: ncbitaxon.owl

Ascidiacea
type: Class
subclass of: Urochordata
editor preferred term: Ascidiacea
imported from: ncbitaxon.owl

Phlebobranchia
type: Class
subclass of: Enterogona
editor preferred term: Phlebobranchia
imported from: ncbitaxon.owl

Cionidae
type: Class
subclass of: Phlebobranchia
editor preferred term: Cionidae
imported from: ncbitaxon.owl

Ciona
type: Class
subclass of: Cionidae
editor preferred term: Ciona
imported from: ncbitaxon.owl

Ciona intestinalis
type: Class
subclass of: Ciona
editor preferred term: Ciona intestinalis
imported from: ncbitaxon.owl

Bartonellaceae
type: Class
subclass of: Rhizobiales
editor preferred term: Bartonellaceae
imported from: ncbitaxon.owl

Stolidobranchia
type: Class
subclass of: Ascidiacea
editor preferred term: Stolidobranchia
imported from: ncbitaxon.owl

Pyuridae
type: Class
subclass of: Stolidobranchia
editor preferred term: Pyuridae
imported from: ncbitaxon.owl

Bartonella
type: Class
subclass of: Bartonellaceae
editor preferred term: Bartonella
imported from: ncbitaxon.owl

Herdmania
type: Class
subclass of: Pyuridae
editor preferred term: Herdmania
imported from: ncbitaxon.owl

Herdmania momus
type: Class
subclass of: Herdmania
editor preferred term: Herdmania momus
imported from: ncbitaxon.owl

Vertebrata
type: Class
subclass of: Craniata
editor preferred term: Vertebrata
imported from: ncbitaxon.owl

Rickettsiaceae
type: Class
subclass of: Rickettsiales
editor preferred term: Rickettsiaceae
imported from: ncbitaxon.owl

Coxiella
type: Class
subclass of: Coxiellaceae
editor preferred term: Coxiella
imported from: ncbitaxon.owl

Mycobacterium tuberculosis complex
type: Class
subclass of: Mycobacterium
editor preferred term: Mycobacterium tuberculosis complex
imported from: ncbitaxon.owl

Coxiella burnetii
type: Class
subclass of: Coxiella
editor preferred term: Coxiella burnetii
imported from: ncbitaxon.owl

Gnathostomata
type: Class
subclass of: Vertebrata
editor preferred term: Gnathostomata
imported from: ncbitaxon.owl

Rickettsia
type: Class
subclass of: Rickettsieae
editor preferred term: Rickettsia
imported from: ncbitaxon.owl

Rickettsia conorii
type: Class
subclass of: spotted fever group
editor preferred term: Rickettsia conorii
imported from: ncbitaxon.owl

Rickettsia prowazekii
type: Class
subclass of: typhus group
editor preferred term: Rickettsia prowazekii
imported from: ncbitaxon.owl

Rickettsia rickettsii
type: Class
subclass of: spotted fever group
editor preferred term: Rickettsia rickettsii
imported from: ncbitaxon.owl

Euphyllophyta
type: Class
subclass of: Tracheophyta
editor preferred term: Euphyllophyta
imported from: ncbitaxon.owl

Actinopterygii
type: Class
subclass of: Euteleostomi
editor preferred term: Actinopterygii
imported from: ncbitaxon.owl

Cypriniformes
type: Class
subclass of: Cypriniphysi
editor preferred term: Cypriniformes
imported from: ncbitaxon.owl

Cyprinidae
type: Class
subclass of: Cyprinoidea
editor preferred term: Cyprinidae
imported from: ncbitaxon.owl

Danio
type: Class
subclass of: Rasborinae
editor preferred term: Danio
imported from: ncbitaxon.owl

Danio rerio
type: Class
subclass of: Danio
editor preferred term: Danio rerio
imported from: ncbitaxon.owl

Cyprinus
type: Class
subclass of: Cyprininae
editor preferred term: Cyprinus
imported from: ncbitaxon.owl

Cyprinus carpio
type: Class
subclass of: Cyprinus
editor preferred term: Cyprinus carpio
imported from: ncbitaxon.owl

Arthropleona
type: Class
subclass of: Collembola
editor preferred term: Arthropleona
imported from: ncbitaxon.owl

Entomobryoidea
type: Class
subclass of: Arthropleona
editor preferred term: Entomobryoidea
imported from: ncbitaxon.owl

Ellipura
type: Class
subclass of: Hexapoda
editor preferred term: Ellipura
imported from: ncbitaxon.owl

Salmoniformes
type: Class
subclass of: Protacanthopterygii
editor preferred term: Salmoniformes
imported from: ncbitaxon.owl

Salmonidae
type: Class
subclass of: Salmonoidei
editor preferred term: Salmonidae
imported from: ncbitaxon.owl

Oncorhynchus
type: Class
subclass of: Salmonidae
editor preferred term: Oncorhynchus
imported from: ncbitaxon.owl

Oncorhynchus mykiss
type: Class
subclass of: Oncorhynchus
editor preferred term: Oncorhynchus mykiss
imported from: ncbitaxon.owl

Salmo
type: Class
subclass of: Salmonidae
editor preferred term: Salmo
imported from: ncbitaxon.owl

Bartonella quintana
type: Class
subclass of: Bartonella
editor preferred term: Bartonella quintana
imported from: ncbitaxon.owl

Salmo salar
type: Class
subclass of: Salmo
editor preferred term: Salmo salar
imported from: ncbitaxon.owl

Salmo trutta
type: Class
subclass of: Salmo
editor preferred term: Salmo trutta
imported from: ncbitaxon.owl

Gadiformes
type: Class
subclass of: Paracanthopterygii
editor preferred term: Gadiformes
imported from: ncbitaxon.owl

Gadidae
type: Class
subclass of: Gadiformes
editor preferred term: Gadidae
imported from: ncbitaxon.owl

Gadus
type: Class
subclass of: Gadidae
editor preferred term: Gadus
imported from: ncbitaxon.owl

Gadus morhua
type: Class
subclass of: Gadus
editor preferred term: Gadus morhua
imported from: ncbitaxon.owl

Burkholderiales
type: Class
subclass of: Betaproteobacteria
editor preferred term: Burkholderiales
imported from: ncbitaxon.owl

Populus tremula x Populus alba
type: Class
subclass of: Populus
editor preferred term: Populus tremula x Populus alba
imported from: ncbitaxon.owl

Chlamydiaceae
type: Class
subclass of: Chlamydiales
editor preferred term: Chlamydiaceae
imported from: ncbitaxon.owl

Chlamydia
type: Class
subclass of: Chlamydiaceae
editor preferred term: Chlamydia
imported from: ncbitaxon.owl

Magnaporthaceae
type: Class
subclass of: Sordariomycetes incertae sedis
editor preferred term: Magnaporthaceae
imported from: ncbitaxon.owl

Perciformes
type: Class
subclass of: Percomorpha
editor preferred term: Perciformes
imported from: ncbitaxon.owl

Percoidei
type: Class
subclass of: Perciformes
editor preferred term: Percoidei
imported from: ncbitaxon.owl

Chlamydia trachomatis
type: Class
subclass of: Chlamydia
editor preferred term: Chlamydia trachomatis
imported from: ncbitaxon.owl

Sparidae
type: Class
subclass of: Percoidei
editor preferred term: Sparidae
imported from: ncbitaxon.owl

Sparus
type: Class
subclass of: Sparidae
editor preferred term: Sparus
imported from: ncbitaxon.owl

Sparus aurata
type: Class
subclass of: Sparus
editor preferred term: Sparus aurata
imported from: ncbitaxon.owl

Leuconostocaceae
type: Class
subclass of: Lactobacillales
editor preferred term: Leuconostocaceae
imported from: ncbitaxon.owl

Enterococcaceae
type: Class
subclass of: Lactobacillales
editor preferred term: Enterococcaceae
imported from: ncbitaxon.owl

Rhizobiaceae
type: Class
subclass of: Rhizobiales
editor preferred term: Rhizobiaceae
imported from: ncbitaxon.owl

Pleuronectiformes
type: Class
subclass of: Percomorpha
editor preferred term: Pleuronectiformes
imported from: ncbitaxon.owl

Pleuronectidae
type: Class
subclass of: Pleuronectoidei
editor preferred term: Pleuronectidae
imported from: ncbitaxon.owl

Platichthys
type: Class
subclass of: Pleuronectidae
editor preferred term: Platichthys
imported from: ncbitaxon.owl

Platichthys flesus
type: Class
subclass of: Platichthys
editor preferred term: Platichthys flesus
imported from: ncbitaxon.owl

Sarcopterygii
type: Class
subclass of: Euteleostomi
editor preferred term: Sarcopterygii
imported from: ncbitaxon.owl

Amphibia
type: Class
subclass of: Tetrapoda
editor preferred term: Amphibia
imported from: ncbitaxon.owl

Apini
type: Class
subclass of: Apinae
editor preferred term: Apini
imported from: ncbitaxon.owl

Anura
type: Class
subclass of: Batrachia
editor preferred term: Anura
imported from: ncbitaxon.owl

Pipidae
type: Class
subclass of: Pipoidea
editor preferred term: Pipidae
imported from: ncbitaxon.owl

Xenopus
type: Class
subclass of: Xenopodinae
editor preferred term: Xenopus
imported from: ncbitaxon.owl

Xenopus laevis
type: Class
subclass of: Xenopus [NCBITaxon:262014]
editor preferred term: Xenopus laevis
imported from: ncbitaxon.owl

Chlamydophila
type: Class
subclass of: Chlamydiaceae
editor preferred term: Chlamydophila
imported from: ncbitaxon.owl

Chlamydophila pneumoniae
type: Class
subclass of: Chlamydophila
editor preferred term: Chlamydophila pneumoniae
imported from: ncbitaxon.owl

Xenopodinae
type: Class
subclass of: Pipidae
editor preferred term: Xenopodinae
imported from: ncbitaxon.owl

Silurana
type: Class
subclass of: Xenopus
editor preferred term: Silurana
imported from: ncbitaxon.owl

Xenopus tropicalis
type: Class
subclass of: Silurana
editor preferred term: Xenopus tropicalis
imported from: ncbitaxon.owl

Nocardiopsaceae
type: Class
subclass of: Streptosporangineae
editor preferred term: Nocardiopsaceae
imported from: ncbitaxon.owl

Thermobifida
type: Class
subclass of: Nocardiopsaceae
editor preferred term: Thermobifida
imported from: ncbitaxon.owl

Sauropsida
type: Class
subclass of: Amniota
editor preferred term: Sauropsida
imported from: ncbitaxon.owl

Fusobacterium
type: Class
subclass of: Fusobacteriaceae
editor preferred term: Fusobacterium
imported from: ncbitaxon.owl

Archosauria
type: Class
subclass of: Sauria
editor preferred term: Archosauria
imported from: ncbitaxon.owl

Rubrobacteridae
type: Class
subclass of: Actinobacteria (class)
editor preferred term: Rubrobacteridae
imported from: ncbitaxon.owl

Rubrobacterales
type: Class
subclass of: Rubrobacteridae
editor preferred term: Rubrobacterales
imported from: ncbitaxon.owl

Rubrobacteraceae
type: Class
subclass of: Rubrobacterineae
editor preferred term: Rubrobacteraceae
imported from: ncbitaxon.owl

Actinobacteridae
type: Class
subclass of: Actinobacteria (class)
editor preferred term: Actinobacteridae
imported from: ncbitaxon.owl

Bifidobacteriales
type: Class
subclass of: Actinobacteridae
editor preferred term: Bifidobacteriales
imported from: ncbitaxon.owl

Actinomycineae
type: Class
subclass of: Actinomycetales
editor preferred term: Actinomycineae
imported from: ncbitaxon.owl

Corynebacterineae
type: Class
subclass of: Actinomycetales
editor preferred term: Corynebacterineae
imported from: ncbitaxon.owl

Streptomycineae
type: Class
subclass of: Actinomycetales
editor preferred term: Streptomycineae
imported from: ncbitaxon.owl

Streptosporangineae
type: Class
subclass of: Actinomycetales
editor preferred term: Streptosporangineae
imported from: ncbitaxon.owl

Fusobacterium nucleatum
type: Class
subclass of: Fusobacterium
editor preferred term: Fusobacterium nucleatum
imported from: ncbitaxon.owl

Dicondylia
type: Class
subclass of: Insecta
editor preferred term: Dicondylia
imported from: ncbitaxon.owl

Amphiesmenoptera
type: Class
subclass of: Endopterygota
editor preferred term: Amphiesmenoptera
imported from: ncbitaxon.owl

Citrus clementina
type: Class
subclass of: Citrus
editor preferred term: Citrus clementina
imported from: ncbitaxon.owl

Triticum turgidum subsp. dicoccoides
type: Class
subclass of: Triticum turgidum
editor preferred term: Triticum turgidum subsp. dicoccoides
imported from: ncbitaxon.owl

Paxillus filamentosus
type: Class
subclass of: Paxillus
editor preferred term: Paxillus filamentosus
imported from: ncbitaxon.owl

Pasteuria
type: Class
subclass of: Alicyclobacillaceae
editor preferred term: Pasteuria
imported from: ncbitaxon.owl

Leymus cinereus
type: Class
subclass of: Leymus
editor preferred term: Leymus cinereus
imported from: ncbitaxon.owl

Leymus triticoides
type: Class
subclass of: Leymus
editor preferred term: Leymus triticoides
imported from: ncbitaxon.owl

Saccharophagus degradans
type: Class
subclass of: Saccharophagus
editor preferred term: Saccharophagus degradans
imported from: ncbitaxon.owl

Bacillus cereus group
type: Class
subclass of: Bacillus
editor preferred term: Bacillus cereus group
imported from: ncbitaxon.owl

Bacillus halodurans
type: Class
subclass of: Bacillus
editor preferred term: Bacillus halodurans
imported from: ncbitaxon.owl

Geospiza difficilis
type: Class
subclass of: Geospiza
editor preferred term: Geospiza difficilis
imported from: ncbitaxon.owl

Desulfovibrio
type: Class
subclass of: Desulfovibrionaceae
editor preferred term: Desulfovibrio
imported from: ncbitaxon.owl

Desulfovibrio desulfuricans
type: Class
subclass of: Desulfovibrio
editor preferred term: Desulfovibrio desulfuricans
imported from: ncbitaxon.owl

Aves
type: Class
subclass of: Coelurosauria
editor preferred term: Aves
imported from: ncbitaxon.owl

Burkholderia cepacia complex
type: Class
subclass of: Burkholderia
editor preferred term: Burkholderia cepacia complex
imported from: ncbitaxon.owl

Neognathae
type: Class
subclass of: Aves
editor preferred term: Neognathae
imported from: ncbitaxon.owl

Panarthropoda
type: Class
subclass of: Protostomia
editor preferred term: Panarthropoda
imported from: ncbitaxon.owl

Flexibacteraceae
type: Class
subclass of: Sphingobacteriales
editor preferred term: Flexibacteraceae
imported from: ncbitaxon.owl

Craniata
type: Class
subclass of: Chordata
editor preferred term: Craniata
imported from: ncbitaxon.owl

Galliformes
type: Class
subclass of: Neognathae
editor preferred term: Galliformes
imported from: ncbitaxon.owl

Phasianidae
type: Class
subclass of: Galliformes
editor preferred term: Phasianidae
imported from: ncbitaxon.owl

Ferroplasmaceae
type: Class
subclass of: Thermoplasmatales
editor preferred term: Ferroplasmaceae
imported from: ncbitaxon.owl

Gallus
type: Class
subclass of: Phasianinae
editor preferred term: Gallus
imported from: ncbitaxon.owl

Gallus gallus
type: Class
subclass of: Gallus
editor preferred term: Gallus gallus
imported from: ncbitaxon.owl

Phasianinae
type: Class
subclass of: Phasianidae
editor preferred term: Phasianinae
imported from: ncbitaxon.owl

Filobasidiales
type: Class
subclass of: Tremellomycetidae
editor preferred term: Filobasidiales
imported from: ncbitaxon.owl

Staphylococcaceae
type: Class
subclass of: Bacillales
editor preferred term: Staphylococcaceae
imported from: ncbitaxon.owl

Bacilli
type: Class
subclass of: Firmicutes
editor preferred term: Bacilli
imported from: ncbitaxon.owl

Passeriformes
type: Class
subclass of: Neognathae
editor preferred term: Passeriformes
imported from: ncbitaxon.owl

Fringillidae
type: Class
subclass of: Passeroidea
editor preferred term: Fringillidae
imported from: ncbitaxon.owl

Enterobacteriales
type: Class
subclass of: Gammaproteobacteria
editor preferred term: Enterobacteriales
imported from: ncbitaxon.owl

Cetartiodactyla
type: Class
subclass of: Laurasiatheria
editor preferred term: Cetartiodactyla
imported from: ncbitaxon.owl

core eudicotyledons
type: Class
subclass of: eudicotyledons
editor preferred term: core eudicotyledons
imported from: ncbitaxon.owl

eurosids I
type: Class
subclass of: rosids
editor preferred term: eurosids I
imported from: ncbitaxon.owl

eurosids II
type: Class
subclass of: rosids
editor preferred term: eurosids II
imported from: ncbitaxon.owl

campanulids
type: Class
subclass of: asterids
editor preferred term: campanulids
imported from: ncbitaxon.owl

lamiids
type: Class
subclass of: asterids
editor preferred term: lamiids
imported from: ncbitaxon.owl

Acidithiobacillus ferrooxidans
type: Class
subclass of: Acidithiobacillus
editor preferred term: Acidithiobacillus ferrooxidans
imported from: ncbitaxon.owl

Bartonella koehlerae
type: Class
subclass of: Bartonella
editor preferred term: Bartonella koehlerae
imported from: ncbitaxon.owl

Metatheria
type: Class
subclass of: Theria
editor preferred term: Metatheria
imported from: ncbitaxon.owl

Xanthomonas axonopodis pv. citri
type: Class
subclass of: Xanthomonas axonopodis
editor preferred term: Xanthomonas axonopodis pv. citri
imported from: ncbitaxon.owl

Macropodidae
type: Class
subclass of: Diprotodontia
editor preferred term: Macropodidae
imported from: ncbitaxon.owl

Macropus
type: Class
subclass of: Macropodidae
editor preferred term: Macropus
imported from: ncbitaxon.owl

Mycosphaerellaceae
type: Class
subclass of: Dothideomycetes et Chaetothyriomycetes incertae sedis
editor preferred term: Mycosphaerellaceae
imported from: ncbitaxon.owl

Macropus eugenii
type: Class
subclass of: Macropus
editor preferred term: Macropus eugenii
imported from: ncbitaxon.owl

Eutheria
type: Class
subclass of: Theria
editor preferred term: Eutheria
imported from: ncbitaxon.owl

Anaplasmataceae
type: Class
subclass of: Rickettsiales
editor preferred term: Anaplasmataceae
imported from: ncbitaxon.owl

Ehrlichia
type: Class
subclass of: Anaplasmataceae
editor preferred term: Ehrlichia
imported from: ncbitaxon.owl

Ehrlichia canis
type: Class
subclass of: canis group
editor preferred term: Ehrlichia canis
imported from: ncbitaxon.owl

Primates
type: Class
subclass of: Euarchontoglires
editor preferred term: Primates
imported from: ncbitaxon.owl

Methanosarcinales
type: Class
subclass of: Methanomicrobia
editor preferred term: Methanosarcinales
imported from: ncbitaxon.owl

Platyrrhini
type: Class
subclass of: Simiiformes
editor preferred term: Platyrrhini
imported from: ncbitaxon.owl

Anaplasma phagocytophilum
type: Class
subclass of: phagocytophilum group
editor preferred term: Anaplasma phagocytophilum
imported from: ncbitaxon.owl

Callitrichinae
type: Class
subclass of: Cebidae
editor preferred term: Callitrichinae
imported from: ncbitaxon.owl

Callithrix
type: Class
subclass of: Callitrichinae
editor preferred term: Callithrix
imported from: ncbitaxon.owl

Callithrix jacchus
type: Class
subclass of: Callithrix
editor preferred term: Callithrix jacchus
imported from: ncbitaxon.owl

Cebidae
type: Class
subclass of: Platyrrhini
editor preferred term: Cebidae
imported from: ncbitaxon.owl

Noctuinae
type: Class
subclass of: Noctuidae
editor preferred term: Noctuinae
imported from: ncbitaxon.owl

Catarrhini
type: Class
subclass of: Simiiformes
editor preferred term: Catarrhini
imported from: ncbitaxon.owl

Cercopithecidae
type: Class
subclass of: Cercopithecoidea
editor preferred term: Cercopithecidae
imported from: ncbitaxon.owl

Cercopithecinae
type: Class
subclass of: Cercopithecidae
editor preferred term: Cercopithecinae
imported from: ncbitaxon.owl

Macaca
type: Class
subclass of: Cercopithecinae
editor preferred term: Macaca
imported from: ncbitaxon.owl

Macaca fascicularis
type: Class
subclass of: Macaca
editor preferred term: Macaca fascicularis
imported from: ncbitaxon.owl

Macaca fuscata
type: Class
subclass of: Macaca
editor preferred term: Macaca fuscata
imported from: ncbitaxon.owl

Macaca mulatta
type: Class
subclass of: Macaca
editor preferred term: Macaca mulatta
imported from: ncbitaxon.owl

Pan
type: Class
subclass of: Homo/Pan/Gorilla group
editor preferred term: Pan
imported from: ncbitaxon.owl

Pan troglodytes
type: Class
subclass of: Pan
editor preferred term: Pan troglodytes
imported from: ncbitaxon.owl

Pongo
type: Class
subclass of: Hominidae
editor preferred term: Pongo
imported from: ncbitaxon.owl

Pongo pygmaeus
type: Class
subclass of: Pongo
editor preferred term: Pongo pygmaeus
imported from: ncbitaxon.owl

Hominidae
type: Class
subclass of: Hominoidea
editor preferred term: Hominidae
imported from: ncbitaxon.owl

Homo
type: Class
subclass of: Homo/Pan/Gorilla group
editor preferred term: Homo
imported from: ncbitaxon.owl

Homo sapiens
type: Class
subclass of: Homo
alternative term: human being
editor preferred term: Homo sapiens
imported from: ncbitaxon.owl

Canidae
type: Class
subclass of: Caniformia
editor preferred term: Canidae
imported from: ncbitaxon.owl

Canis
type: Class
subclass of: Canidae
editor preferred term: Canis
imported from: ncbitaxon.owl

Canis familiaris
type: Class
subclass of: Canis
editor preferred term: Canis familiaris
imported from: ncbitaxon.owl

Vulpes
type: Class
subclass of: Canidae
editor preferred term: Vulpes
imported from: ncbitaxon.owl

Vulpes vulpes
type: Class
subclass of: Vulpes
editor preferred term: Vulpes vulpes
imported from: ncbitaxon.owl

Felidae
type: Class
subclass of: Feliformia
editor preferred term: Felidae
imported from: ncbitaxon.owl

Felis
type: Class
subclass of: Felinae
editor preferred term: Felis
imported from: ncbitaxon.owl

Felis catus
type: Class
subclass of: Felis
editor preferred term: Felis catus
imported from: ncbitaxon.owl

Ferroplasma acidarmanus
type: Class
subclass of: Ferroplasma
editor preferred term: Ferroplasma acidarmanus
imported from: ncbitaxon.owl

Bacteroidetes
type: Class
subclass of: Bacteroidetes/Chlorobi group
editor preferred term: Bacteroidetes
imported from: ncbitaxon.owl

Cytophaga
type: Class
subclass of: Flexibacteraceae
editor preferred term: Cytophaga
imported from: ncbitaxon.owl

Perissodactyla
type: Class
subclass of: Laurasiatheria
editor preferred term: Perissodactyla
imported from: ncbitaxon.owl

Equidae
type: Class
subclass of: Perissodactyla
editor preferred term: Equidae
imported from: ncbitaxon.owl

Equus
type: Class
subclass of: Equidae
editor preferred term: Equus
imported from: ncbitaxon.owl

Equus caballus
type: Class
subclass of: Equus subg. Equus
editor preferred term: Equus caballus
imported from: ncbitaxon.owl

Suidae
type: Class
subclass of: Suina
editor preferred term: Suidae
imported from: ncbitaxon.owl

Sus
type: Class
subclass of: Suidae
editor preferred term: Sus
imported from: ncbitaxon.owl

Sus scrofa
type: Class
subclass of: Sus
editor preferred term: Sus scrofa
imported from: ncbitaxon.owl

Ruminantia
type: Class
subclass of: Cetartiodactyla
editor preferred term: Ruminantia
imported from: ncbitaxon.owl

Cytophaga hutchinsonii
type: Class
subclass of: Cytophaga
editor preferred term: Cytophaga hutchinsonii
imported from: ncbitaxon.owl

Festuca brevipila
type: Class
subclass of: Festuca
editor preferred term: Festuca brevipila
imported from: ncbitaxon.owl

Festuca rubra subsp. fallax
type: Class
subclass of: Festuca rubra
editor preferred term: Festuca rubra subsp. fallax
imported from: ncbitaxon.owl

Festuca rubra subsp. littoralis
type: Class
subclass of: Festuca rubra
editor preferred term: Festuca rubra subsp. littoralis
imported from: ncbitaxon.owl

Bovidae
type: Class
subclass of: Pecora
editor preferred term: Bovidae
imported from: ncbitaxon.owl

Bos
type: Class
subclass of: Bovinae
editor preferred term: Bos
imported from: ncbitaxon.owl

Bos taurus
type: Class
subclass of: Bos
editor preferred term: Bos taurus
imported from: ncbitaxon.owl

Bos indicus
type: Class
subclass of: Bos
editor preferred term: Bos indicus
imported from: ncbitaxon.owl

Ovis
type: Class
subclass of: Caprinae
editor preferred term: Ovis
imported from: ncbitaxon.owl

Ovis aries
type: Class
subclass of: Ovis
editor preferred term: Ovis aries
imported from: ncbitaxon.owl

Caprinae
type: Class
subclass of: Bovidae
editor preferred term: Caprinae
imported from: ncbitaxon.owl

Tetraodon nigroviridis
type: Class
subclass of: Tetraodon
editor preferred term: Tetraodon nigroviridis
imported from: ncbitaxon.owl

Rodentia
type: Class
subclass of: Glires
editor preferred term: Rodentia
imported from: ncbitaxon.owl

role of being consumer safety officer
type: Class
subclass of: role of regulator of consumables and medical devices
disjoint with: notified body role
term editor: Person:Helen Parkinson
editor preferred term: role of being consumer safety officer
definition: the role of a human being that is realized by enforcing regulations to ensure consumer safety
example of usage: Consumer safety officer; Consumer Safety Officer Positions at FDA http://69.20.19.211/jobs/cso.htm
term editor: Jennifer Fostel
definition source: OBI, CDISC
example of usage: Person charged with serving as CSO, FDA official who coordinates the review
has curation status: IAO_0000120

fluorescent reporter intensity
type: Class
subclass of: measurement datum
disjoint with: ratio of collected to emitted light
disjoint with: measured expression level
disjoint with: number of particles in subset
disjoint with: number of lost events electronic
disjoint with: parameter threshold
disjoint with: number of lost events computer
disjoint with: survival rate
disjoint with: spike train datum
disjoint with: categorical measurement datum
disjoint with: dose
disjoint with: obsolete_general scalar measurement datum
disjoint with: 3D structural organization datum
definition source: group:OBI
definition: A measurement datum that represents the output of a scanner measuring the intensity value for each fluorescent reporter.
curator note: From the DT branch: This term and definition were originally submitted by the community to our branch, but we thought they best fit DENRIE. However we see several issues with this. First of all the name 'probe' might not be used in OBI. Instead we have a 'reporter' role. Also, albeit the term 'probe intensity' is often used in communities such as the microarray one, the name 'probe' is ambiguous (some use it to refer to what's on the array, some use it to refer to what's hybed to the array). Furthermore, this concept could possibly be encompassed by combining different OBI terms, such as the roles of analyte, detector and reporter (you need something hybed to a probe on the array to get an intensity) and maybe a more general term for 'measuring intensities'. We need to find the right balance between what is consistent with OBI and combinations of its terms and what is user-friendly. Finally, note that 'intensity' is already in the OBI .owl file and is also in PATO. Why didn't OBI import it from PATO? This might be a problem.
editor preferred term: fluorescent reporter intensity
term editor: person:Chris Stoeckert
has curation status: IAO_0000125

planned process
type: Class
equivalent class: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: Class
      intersection of: plan specification
      intersection of: Restriction
        on property: has part
        some values from: objective specification
subclass of: process
editor note: 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
curator note: 6/11/9: Edited at workshop. Used to include: is initiated by an agent
term editor: Bjoern Peters
example of usage: Injecting mice with a vaccine in order to test its efficacy
editor note: We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
definition source: branch derived
definition: A processual entity that realizes a plan which is the concretization of a plan specification.
curator note: This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
editor preferred term: planned process
has curation status: IAO_0000122

regulator role
type: Class
subclass of: regulatory role
disjoint with: regulation-assigned role
alternative term: regulator
editor preferred term: regulator role
example of usage: Fact sheet - Regulating the companies The role of the regulator. Ofwat is the economic regulator of the water and sewerage industry in England and Wales. http://www.ofwat.gov.uk/aptrix/ofwat/publish.nsf/Content/roleofregulator_factsheet170805
definition source: OBI
term editor: Person:Jennifer Fostel
definition: a regulatory role involved with making and/or enforcing relevant legislation and governmental orders
has curation status: IAO_0000120

biological feature identification objective
type: Class
subclass of: objective specification
disjoint with: methodology testing objective
disjoint with: assay objective
disjoint with: material transformation objective
disjoint with: specimen creation objective
disjoint with: material maintenance objective
disjoint with: training objective
disjoint with: service provision objective
disjoint with: assay validation objective
disjoint with: selective organism creation objective
disjoint with: OBI_0200166
definition: Biological_feature_identification_objective is an objective role carried out by the proposition defining the aim of a study designed to examine or characterize a particular biological feature.
term editor: Jennifer Fostel
editor preferred term: biological feature identification objective
has curation status: IAO_0000123

regulation-assigned role
type: Class
subclass of: regulatory role
example of usage: Approval letter
term editor: Person: Jennifer Fostel
definition: Regulation-assigned role is a regulatory role defined by legislation or governmental orders
editor preferred term: regulation-assigned role
has curation status: IAO_0000123

regulatory role
type: Class
subclass of: role
disjoint with: reference substance role
disjoint with: centrifuge pellet role
disjoint with: supernatant role
disjoint with: drug role
disjoint with: evaluant role
disjoint with: reagent role
disjoint with: detector reagent role
disjoint with: patient role
disjoint with: study subject role
disjoint with: specimen role
disjoint with: label role
disjoint with: study group role
disjoint with: nutrient role
disjoint with: antigen role
disjoint with: analyte role
disjoint with: material to be added role
disjoint with: cloning insert role
disjoint with: target of material addition role
disjoint with: manufacturer role
disjoint with: pathogen role
disjoint with: host role
disjoint with: test substance role
disjoint with: complementary nucleotide probe role
disjoint with: service consumer role
disjoint with: service provider role
disjoint with: accessed material role
disjoint with: OBI_0302731
disjoint with: OBI_0302732
disjoint with: OBI_0302733
disjoint with: OBI_1110082
disjoint with: OBI_1110083
disjoint with: OBI_1110086
disjoint with: OBI_1110087
disjoint with: OBI_1110091
disjoint with: OBI_1110092
disjoint with: OBI_1110120
term editor: GROUP: Role branch
definition source: OBI, CDISC
example of usage: Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008
definition: a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body.
curator note: govt agents responsible for creating regulations; proxies for enforcing regulations. CDISC definition: regulatory authorities. Bodies having the power to regulate. NOTE: In the ICH GCP guideline the term includes the authorities that review submitted clinical data and those that conduct inspections. These bodies are sometimes referred to as competent
editor preferred term: regulatory role
has curation status: IAO_0000120

material supplier role
type: Class
subclass of: service provider role
example of usage: Jackson Labs is an organization which provide mice as experimental material
editor note: Supplier role is a special kind of service, e.g. biobank
alternative term: material provider role
editor preferred term: material supplier role
alternative term: supplier
term editor: PERSON:Jennifer Fostel
definition: a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation.
has curation status: IAO_0000120

contract research organization role
type: Class
subclass of: worker role
alternative term: contract research organization
editor preferred term: contract research organization role
term editor: Person: Jennifer Fostel
definition: a worker role of carrying out the study according to the protocol document or study plan delivered by the PI, under the control of the study director. This role cannot make decisions about the study execution
has curation status: IAO_0000123

list-mode data file
type: Class
subclass of: information content entity
disjoint with: eMedical record
disjoint with: electronic case report tabulation
disjoint with: eSource document
disjoint with: electronic case report form
disjoint with: analytical cytology data file
disjoint with: fluorescence compensation matrix
disjoint with: record of missing knowledge
disjoint with: sequence feature annotation
disjoint with: OBI_0302838
disjoint with: OBI_0302840
definition source: group:Flow Cytometry community
definition: A list-mode data file is a binary digital entity where events are stored sequentially, parameter by parameter.
example of usage: An example of a list-mode data file is a file following list-mode Flow Cytometry Standard (FCS) format. Since FCS files can be in histogram mode or list-mode we have to specify which data format specifically. List-mode format in the overwhelming (even universal) option used.
editor note: One example of usage is in the context of flow cytometry, however is not restricted to this community and is more widely used, e.g. by imaging people.
editor preferred term: list-mode data file
term editor: person:Chris Stoeckert
has curation status: IAO_0000125

classified data set
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: class prediction data transformation
subclass of: data set
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
editor preferred term: classified data set
alternative term: data set with assigned class labels
definition: A data set that is produced as the output of a class prediction data transformation and consists of a data set with assigned class labels.
has curation status: IAO_0000125

reference substance role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: material entity
disjoint with: centrifuge pellet role
disjoint with: supernatant role
disjoint with: drug role
disjoint with: evaluant role
disjoint with: reagent role
disjoint with: detector reagent role
disjoint with: patient role
disjoint with: study subject role
disjoint with: specimen role
disjoint with: label role
disjoint with: study group role
disjoint with: nutrient role
disjoint with: antigen role
disjoint with: analyte role
disjoint with: material to be added role
disjoint with: cloning insert role
disjoint with: target of material addition role
disjoint with: manufacturer role
disjoint with: pathogen role
disjoint with: host role
disjoint with: test substance role
disjoint with: complementary nucleotide probe role
disjoint with: service consumer role
disjoint with: service provider role
disjoint with: accessed material role
disjoint with: OBI_0302731
disjoint with: OBI_0302732
disjoint with: OBI_0302733
disjoint with: OBI_1110082
disjoint with: OBI_1110083
disjoint with: OBI_1110086
disjoint with: OBI_1110087
disjoint with: OBI_1110091
disjoint with: OBI_1110092
disjoint with: OBI_1110120
alternative term: reference substance
editor preferred term: reference substance role
example of usage: Calibration standard, positive control substance, vehicle Good Laboratory Practices: Questions and Answers - Test Control and Reference Substance Characterization http://www.epa.gov/enforcement/monitoring/programs/fifra/glpqanda-character.html
definition source: OBI
term editor: Person:Jennifer Fostel
definition: a role inhering in a material entity that is realized when characteristics or responses elicited by the substance are used for comparison or reference.
has curation status: IAO_0000120

cytological stain role
type: Class
subclass of: dye role
disjoint with: pH indicator dye role
disjoint with: vital dye role
term editor: Person:Helen Parkinson
definition: a role of a stain that is realized when the stain is used to colour cells and or cellular components for the purposes of visualization
alternative term: cytological stain
editor preferred term: cytological stain role
example of usage: haemotoxylin is a general purpose nuclear stain extracted from the wood of the logwood tree WEB: http://en.wikipedia.org/wiki/Haematoxylin
term editor: Person:Jennifer Fostel
has curation status: IAO_0000120

centrifuge pellet role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: material entity
subclass of: Restriction
  on property: is realized by
  all values from: OBI_0302886
disjoint with: supernatant role
disjoint with: drug role
disjoint with: evaluant role
disjoint with: reagent role
disjoint with: detector reagent role
disjoint with: patient role
disjoint with: study subject role
disjoint with: specimen role
disjoint with: label role
disjoint with: study group role
disjoint with: nutrient role
disjoint with: antigen role
disjoint with: analyte role
disjoint with: material to be added role
disjoint with: cloning insert role
disjoint with: target of material addition role
disjoint with: manufacturer role
disjoint with: pathogen role
disjoint with: host role
disjoint with: test substance role
disjoint with: complementary nucleotide probe role
disjoint with: service consumer role
disjoint with: service provider role
disjoint with: accessed material role
disjoint with: OBI_0302731
disjoint with: OBI_0302732
disjoint with: OBI_0302733
disjoint with: OBI_1110082
disjoint with: OBI_1110083
disjoint with: OBI_1110086
disjoint with: OBI_1110087
disjoint with: OBI_1110091
disjoint with: OBI_1110092
disjoint with: OBI_1110120
curator note: 9Mar09 after discussion with process branch changed definition to include use of centrifuge;
example of usage: Definition of pellet :the material concentrated at the bottom of a centrifuge tube after centrifugation. http://www.everythingbio.com/glos/definition.php?word=pellet
term editor: GROUP: Role branch
definition source: OBI
editor preferred term: centrifuge pellet role
definition: pellet role is a role which inheres in a material entity and is realized by a material separation process using gravitational force generated by a centrifuge in which the material bearing the pellet role is the heavier or heaviest component of the output material..
has curation status: IAO_0000125

clinical research coordinator role
type: Class
subclass of: worker role
alternative term: clinical research coordinator
editor preferred term: clinical research coordinator role
term editor: Person:Jennifer Fostel
definition: a worker role comprised of handling the administrative duties of a trial or study.
has curation status: IAO_0000123

supernatant role
type: Class
subclass of: role
subclass of: Restriction
  on property: is realized by
  all values from: OBI_0600014
subclass of: Restriction
  on property: inheres in
  some values from: material entity
disjoint with: drug role
disjoint with: evaluant role
disjoint with: reagent role
disjoint with: detector reagent role
disjoint with: patient role
disjoint with: study subject role
disjoint with: specimen role
disjoint with: label role
disjoint with: study group role
disjoint with: nutrient role
disjoint with: antigen role
disjoint with: analyte role
disjoint with: material to be added role
disjoint with: cloning insert role
disjoint with: target of material addition role
disjoint with: manufacturer role
disjoint with: pathogen role
disjoint with: host role
disjoint with: test substance role
disjoint with: complementary nucleotide probe role
disjoint with: service consumer role
disjoint with: service provider role
disjoint with: accessed material role
disjoint with: OBI_0302731
disjoint with: OBI_0302732
disjoint with: OBI_0302733
disjoint with: OBI_1110082
disjoint with: OBI_1110083
disjoint with: OBI_1110086
disjoint with: OBI_1110087
disjoint with: OBI_1110091
disjoint with: OBI_1110092
disjoint with: OBI_1110120
term editor: GROUP: Role branch
definition source: OBI
example of usage: Precipitation is the formation of a solid in a solution during a chemical reaction. When the reaction occurs, the solid formed is called the precipitate, and the liquid remaining above the solid is called the supernate. Wikipedia
editor preferred term: supernatant role
definition: supernatant role is a role which inheres in a material entity and is realized by a material separation process using gravitational force in which the material bearing the supernatant role is the liquid component of the output material.
has curation status: IAO_0000120

chromatography column
type: Class
subclass of: material separation device
subclass of: Restriction
  on property: has function
  some values from: Class
    intersection of: material separation function
    intersection of: Restriction
      on property: is realized by
      all values from: OBI_0600046
disjoint with: pump valve switch
disjoint with: chromatography device
disjoint with: mass spectrometer
disjoint with: liquid chromatography mass spectrometry platform
disjoint with: microarray platform
disjoint with: gamma counter
disjoint with: incubator
disjoint with: supernatant collection system harvesting frame
disjoint with: filter paper
disjoint with: microtiter plate
disjoint with: mass analyzer
disjoint with: ion source
disjoint with: ion detector
disjoint with: isoelectric focusing device
disjoint with: thermostatic circulator
disjoint with: blot module
disjoint with: gel dryer
disjoint with: syringe
disjoint with: needle
disjoint with: column chromatography detector
disjoint with: NMR sample holder
disjoint with: chromatography instrument
disjoint with: rapid resolution column
disjoint with: NMR tube washing system
disjoint with: NMR console
disjoint with: variable wavelength detector
disjoint with: multiple wavelength detector
disjoint with: NMR probe
disjoint with: NMR magnet
disjoint with: magic angle spinning rotor
disjoint with: Bruker SampleRail system
disjoint with: evaporative light scattering detector
disjoint with: autosampler
disjoint with: fluorescene detector
disjoint with: electrical conductivity detector
disjoint with: NMR instrument
disjoint with: refractive index detector
disjoint with: pulsed amperometric detector
disjoint with: glucometer
disjoint with: micro electrode
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus

drug role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: molecular entity
disjoint with: evaluant role
disjoint with: reagent role
disjoint with: detector reagent role
disjoint with: patient role
disjoint with: study subject role
disjoint with: specimen role
disjoint with: label role
disjoint with: study group role
disjoint with: nutrient role
disjoint with: antigen role
disjoint with: analyte role
disjoint with: material to be added role
disjoint with: cloning insert role
disjoint with: target of material addition role
disjoint with: manufacturer role
disjoint with: pathogen role
disjoint with: host role
disjoint with: test substance role
disjoint with: complementary nucleotide probe role
disjoint with: service consumer role
disjoint with: service provider role
disjoint with: accessed material role
disjoint with: OBI_0302731
disjoint with: OBI_0302732
disjoint with: OBI_0302733
disjoint with: OBI_1110082
disjoint with: OBI_1110083
disjoint with: OBI_1110086
disjoint with: OBI_1110087
disjoint with: OBI_1110091
disjoint with: OBI_1110092
disjoint with: OBI_1110120
alternative term: drug
example of usage: http://www.answers.com/topic/drug 1. A substance used in the diagnosis, treatment, or prevention of a disease or as a component of a medication. 2. Such a substance as recognized or defined by the U.S. Food, Drug, and Cosmetic Act.
definition source: OBI, CDISC
term editor: Role Branch
definition: a role borne by a molecular entity and is realized in a process of absorption by an organism alters, or effects (or is assumed to effect) a function(s) which inhere in an organism
editor preferred term: drug role
has curation status: IAO_0000120

pump valve switch
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
disjoint with: chromatography device
disjoint with: mass spectrometer
disjoint with: liquid chromatography mass spectrometry platform
disjoint with: microarray platform
disjoint with: gamma counter
disjoint with: incubator
disjoint with: supernatant collection system harvesting frame
disjoint with: filter paper
disjoint with: microtiter plate
disjoint with: mass analyzer
disjoint with: ion source
disjoint with: ion detector
disjoint with: isoelectric focusing device
disjoint with: thermostatic circulator
disjoint with: blot module
disjoint with: gel dryer
disjoint with: syringe
disjoint with: needle
disjoint with: column chromatography detector
disjoint with: NMR sample holder
disjoint with: chromatography instrument
disjoint with: rapid resolution column
disjoint with: NMR tube washing system
disjoint with: NMR console
disjoint with: variable wavelength detector
disjoint with: multiple wavelength detector
disjoint with: NMR probe
disjoint with: NMR magnet
disjoint with: magic angle spinning rotor
disjoint with: Bruker SampleRail system
disjoint with: evaporative light scattering detector
disjoint with: autosampler
disjoint with: fluorescene detector
disjoint with: electrical conductivity detector
disjoint with: NMR instrument
disjoint with: refractive index detector
disjoint with: pulsed amperometric detector
disjoint with: glucometer
disjoint with: micro electrode
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus

xenotransplantation
type: Class
subclass of: transplantation
disjoint with: allotransplantation
disjoint with: autotransplantation
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
definition: is the transplantation of living cells, tissues or \norgans from one species to another such as from pigs to humans
editor preferred term: xenotransplantation
has curation status: IAO_0000125

physical document
type: Class
subclass of: processed material
definition source: GROUP: OBI
term editor: PERSON: Bjoern Peters
definition: A physical document is an object serving as a record of information by means of symbolic marks.
example of usage: a book is a physical document
editor preferred term: physical document
has curation status: IAO_0000120

waiting
type: Class
subclass of: OBI_0600009
disjoint with: OBI_0600011
curator note: BP: I have doubts about the utility of this.
definition source: OBI branch derived
term editor: PERSON:Alan Ruttenberg
curator note: We need a better handling/modeling of time (January 2008)
definition: not actively doing anything to a material for a duration of time.
editor preferred term: waiting
has curation status: IAO_0000125

processed material
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: material processing
subclass of: material entity
example of usage: Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
definition: Is a material entity that is created or changed during material processing.
term editor: PERSON: Alan Ruttenberg
editor preferred term: processed material
has curation status: IAO_0000122

chromatography device
type: Class
subclass of: measurement device
subclass of: material separation device
subclass of: container
subclass of: environmental control device
subclass of: Restriction
  on property: has function
  some values from: environment control function
disjoint with: mass spectrometer
disjoint with: liquid chromatography mass spectrometry platform
disjoint with: microarray platform
disjoint with: gamma counter
disjoint with: incubator
disjoint with: supernatant collection system harvesting frame
disjoint with: filter paper
disjoint with: microtiter plate
disjoint with: mass analyzer
disjoint with: ion source
disjoint with: ion detector
disjoint with: isoelectric focusing device
disjoint with: thermostatic circulator
disjoint with: blot module
disjoint with: gel dryer
disjoint with: syringe
disjoint with: needle
disjoint with: column chromatography detector
disjoint with: NMR sample holder
disjoint with: chromatography instrument
disjoint with: rapid resolution column
disjoint with: NMR tube washing system
disjoint with: NMR console
disjoint with: variable wavelength detector
disjoint with: multiple wavelength detector
disjoint with: NMR probe
disjoint with: NMR magnet
disjoint with: magic angle spinning rotor
disjoint with: Bruker SampleRail system
disjoint with: evaporative light scattering detector
disjoint with: autosampler
disjoint with: fluorescene detector
disjoint with: electrical conductivity detector
disjoint with: NMR instrument
disjoint with: refractive index detector
disjoint with: pulsed amperometric detector
disjoint with: glucometer
disjoint with: micro electrode
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system

mass spectrometer
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has_supplier
  some values from: Class
    union of: Homo sapiens
    union of: organization
disjoint with: liquid chromatography mass spectrometry platform
disjoint with: microarray platform
disjoint with: gamma counter
disjoint with: incubator
disjoint with: supernatant collection system harvesting frame
disjoint with: filter paper
disjoint with: microtiter plate
disjoint with: mass analyzer
disjoint with: ion source
disjoint with: ion detector
disjoint with: isoelectric focusing device
disjoint with: thermostatic circulator
disjoint with: blot module
disjoint with: gel dryer
disjoint with: syringe
disjoint with: needle
disjoint with: column chromatography detector
disjoint with: NMR sample holder
disjoint with: chromatography instrument
disjoint with: rapid resolution column
disjoint with: NMR tube washing system
disjoint with: NMR console
disjoint with: variable wavelength detector
disjoint with: multiple wavelength detector
disjoint with: NMR probe
disjoint with: NMR magnet
disjoint with: magic angle spinning rotor
disjoint with: Bruker SampleRail system
disjoint with: evaporative light scattering detector
disjoint with: autosampler
disjoint with: fluorescene detector
disjoint with: electrical conductivity detector
disjoint with: NMR instrument
disjoint with: refractive index detector
disjoint with: pulsed amperometric detector
disjoint with: glucometer
disjoint with: micro electrode
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device

obsolete_platform
type: Class
subclass of: ObsoleteClass
definition source: OBI Instrument branch
term editor: OBI Instrument branch
curator note: suggested for deprecation https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178
deprecated: true
definition: A platform is an object_aggregate that is the set of instruments and software needed to perform a process. definition_source: OBI.
editor preferred term: platform
curator note: rem1: We decided at the Philly workshop that consumables do not include reagents. FG: we could actully add a relation to platform which would be "has_part some instrument" DS: Sounds fine to me, with the restriction that I would assume a min. cardinality of 2 to be applicable for this crossproduct, so at least 2 instruments make it a platform... at least one is not enough AR:has_part is transitive, and transitive properties can't have cardinality constraints in OWL-DL. We can always put this particular constraint in the owl-full file. We need to make this a defined class when the class software is in the ontology
has obsolescence reason: IAO_0000103
has curation status: IAO_0000123

liquid chromatography mass spectrometry platform
type: Class
subclass of: measurement device
subclass of: material separation device
subclass of: Restriction
  on property: has function
  some values from: measure function
disjoint with: microarray platform
disjoint with: gamma counter
disjoint with: incubator
disjoint with: supernatant collection system harvesting frame
disjoint with: filter paper
disjoint with: microtiter plate
disjoint with: mass analyzer
disjoint with: ion source
disjoint with: ion detector
disjoint with: isoelectric focusing device
disjoint with: thermostatic circulator
disjoint with: blot module
disjoint with: gel dryer
disjoint with: syringe
disjoint with: needle
disjoint with: column chromatography detector
disjoint with: NMR sample holder
disjoint with: chromatography instrument
disjoint with: rapid resolution column
disjoint with: NMR tube washing system
disjoint with: NMR console
disjoint with: variable wavelength detector
disjoint with: multiple wavelength detector
disjoint with: NMR probe
disjoint with: NMR magnet
disjoint with: magic angle spinning rotor
disjoint with: Bruker SampleRail system
disjoint with: evaporative light scattering detector
disjoint with: autosampler
disjoint with: fluorescene detector
disjoint with: electrical conductivity detector
disjoint with: NMR instrument
disjoint with: refractive index detector
disjoint with: pulsed amperometric detector
disjoint with: glucometer
disjoint with: micro electrode
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device

microarray platform
type: Class
subclass of: environmental control device
subclass of: Restriction
  on property: has function
  some values from: environment control function
disjoint with: gamma counter
disjoint with: incubator
disjoint with: supernatant collection system harvesting frame
disjoint with: filter paper
disjoint with: microtiter plate
disjoint with: mass analyzer
disjoint with: ion source
disjoint with: ion detector
disjoint with: isoelectric focusing device
disjoint with: thermostatic circulator
disjoint with: blot module
disjoint with: gel dryer
disjoint with: syringe
disjoint with: needle
disjoint with: column chromatography detector
disjoint with: NMR sample holder
disjoint with: chromatography instrument
disjoint with: rapid resolution column
disjoint with: NMR tube washing system
disjoint with: NMR console
disjoint with: variable wavelength detector
disjoint with: multiple wavelength detector
disjoint with: NMR probe
disjoint with: NMR magnet
disjoint with: magic angle spinning rotor
disjoint with: Bruker SampleRail system
disjoint with: evaporative light scattering detector
disjoint with: autosampler
disjoint with: fluorescene detector
disjoint with: electrical conductivity detector
disjoint with: NMR instrument
disjoint with: refractive index detector
disjoint with: pulsed amperometric detector
disjoint with: glucometer
disjoint with: micro electrode
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester

ratio of collected to emitted light
type: Class
subclass of: measurement datum
disjoint with: measured expression level
disjoint with: number of particles in subset
disjoint with: number of lost events electronic
disjoint with: parameter threshold
disjoint with: number of lost events computer
disjoint with: survival rate
disjoint with: spike train datum
disjoint with: categorical measurement datum
disjoint with: dose
disjoint with: obsolete_general scalar measurement datum
disjoint with: 3D structural organization datum
definition source: Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
example of usage: 10%
definition: A measurement datum measuring the amount of light collected s compared to the total amount of emitted light in the detector component of a flow cytometer instrument. The datum has a qualitative role
term editor: person:Chris Stoeckert
term editor: person:Kevin Clancy
editor preferred term: ratio of collected to emitted light
has curation status: IAO_0000120

software optimization objective
type: Class
subclass of: software testing objective
term editor: Jennifer Fostel
definition: Software_optimization is a software_testing_objective role describing a study designed to identify the best software or parameters of the software.
editor preferred term: software optimization objective
has curation status: IAO_0000123

notified body role
type: Class
subclass of: role of regulator of consumables and medical devices
alternative term: notified body
editor preferred term: notified body role
editor note: Notified Body (NB). A private institution charged by the Competent Authority with verifying compliance of medical devices (not drugs) with the applicable Essential Requirements stated in the Medical Device Directive. This process, called Conformity Assessment, has EU-wide validity once completed by the NB.
definition: Notified body is regulator of consumables and medical devices charged by the Competent Authority with verifying compliance of medical devices (not drugs) with the applicable Essential Requirements stated in the Medical Device Directive
definition source: OBI, CDISC
term editor: Person: Jennifer Fostel
example of usage: The role of notified bodies presentation: http://ec.europa.eu/enterprise/electr_equipment/emc/revision/notified_bodies.pdf
has curation status: IAO_0000120

allotransplantation
type: Class
subclass of: transplantation
disjoint with: autotransplantation
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
editor preferred term: allotransplantation
definition: is the transplantation of organs between members of the same species.
has curation status: IAO_0000125

gamma counter
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
disjoint with: incubator
disjoint with: supernatant collection system harvesting frame
disjoint with: filter paper
disjoint with: microtiter plate
disjoint with: mass analyzer
disjoint with: ion source
disjoint with: ion detector
disjoint with: isoelectric focusing device
disjoint with: thermostatic circulator
disjoint with: blot module
disjoint with: gel dryer
disjoint with: syringe
disjoint with: needle
disjoint with: column chromatography detector
disjoint with: NMR sample holder
disjoint with: chromatography instrument
disjoint with: rapid resolution column
disjoint with: NMR tube washing system
disjoint with: NMR console
disjoint with: variable wavelength detector
disjoint with: multiple wavelength detector
disjoint with: NMR probe
disjoint with: NMR magnet
disjoint with: magic angle spinning rotor
disjoint with: Bruker SampleRail system
disjoint with: evaporative light scattering detector
disjoint with: autosampler
disjoint with: fluorescene detector
disjoint with: electrical conductivity detector
disjoint with: NMR instrument
disjoint with: refractive index detector
disjoint with: pulsed amperometric detector
disjoint with: glucometer
disjoint with: micro electrode
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener

trial monitor role
type: Class
subclass of: responsible party role
alternative term: trial monitor
editor preferred term: trial monitor role
curator note: CDISC definition: Person employed by the sponsor or CRO who is responsible for determining that a trial is being conducted in accordance with the protocol and GCP guidance. NOTE: A monitor's duties may include, but are not limited to, helping to plan and initiate a trial, assessing the conduct of trials, and assisting in data analysis, interpretation and extrapolation. Clinical Research Associate: Primary representative of the sponsor; monitors progress of investigator sites participating in a clinical study.
term editor: Person:Jennifer Fostel
definition: a responsible party involved in planning, overseeing the conduct of a study or study component, and interpreting data from a study
has curation status: IAO_0000123

positive reference substance role
type: Class
subclass of: reference substance role
subclass of: Restriction
  on property: is realized by
  all values from: assay
disjoint with: calibration substance role
disjoint with: negative reference substance role
disjoint with: nucleic acid template role
disjoint with: spike-in quality control role
disjoint with: dye swap quality control role
definition: a reference role in which the characteristics or responses elicited by the substance playing the reference substance role are used to establish a "100%" response
alternative term: positive reference substance
editor preferred term: positive reference substance role
example of usage: MMS mutagen
term editor: Person: Jennifer Fostel
has curation status: IAO_0000123

polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether
type: Class
subclass of: molecular entity
disjoint with: fucoidan
example of usage: PMID: 30799. J Histochem Cytochem. 1978 Sep;26(9):696-712. Acid lipase: a histochemical and biochemical study using triton X100-naphtyl palmitate micelles.
term editor: Philippe Rocca-Serra
definition source: adapted from Wikipedia before possible import from CHEBI
editor preferred term: polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether
definition: triton X100 is a chemical entity which belongs to the group of The pluronics which are triblock copolymers of ethylene oxide and propylene oxide. Triton x-100 is_used_as detergent due to its non-ionic surfactant properties
has curation status: IAO_0000123

investigation
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has part
  some values from: documenting
subclass of: Restriction
  on property: has part
  some values from: study design execution
subclass of: Restriction
  on property: has_specified_output
  some values from: conclusion textual entity
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: planning
    intersection of: Restriction
      on property: has_specified_output
      some values from: OBI_0500000
curator note: Could add specific objective specification
example of usage: Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation
term editor: Bjoern Peters
definition source: OBI branch derived
definition: a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
editor preferred term: investigation
has curation status: IAO_0000122

evaluant role
type: Class
subclass of: role
subclass of: Restriction
  on property: is realized by
  all values from: assay
disjoint with: reagent role
disjoint with: detector reagent role
disjoint with: patient role
disjoint with: study subject role
disjoint with: specimen role
disjoint with: label role
disjoint with: study group role
disjoint with: nutrient role
disjoint with: antigen role
disjoint with: analyte role
disjoint with: material to be added role
disjoint with: cloning insert role
disjoint with: target of material addition role
disjoint with: manufacturer role
disjoint with: pathogen role
disjoint with: host role
disjoint with: test substance role
disjoint with: complementary nucleotide probe role
disjoint with: service consumer role
disjoint with: service provider role
disjoint with: accessed material role
disjoint with: OBI_0302731
disjoint with: OBI_0302732
disjoint with: OBI_0302733
disjoint with: OBI_1110082
disjoint with: OBI_1110083
disjoint with: OBI_1110086
disjoint with: OBI_1110087
disjoint with: OBI_1110091
disjoint with: OBI_1110092
disjoint with: OBI_1110120
curator note: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
term editor: GROUP: Role Branch
definition source: OBI
editor note: Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is)
example of usage: When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role.
definition: a role that inheres in an entity that is realized in an assay in which data is generated about the bearer of the evaluant role
editor preferred term: evaluant role
editor note: examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected")
has curation status: IAO_0000120

reporting party role
type: Class
subclass of: investigation agent role
editor note: MO:submitter mapped to this term. So, alternative term 'submitter' was added.
example of usage: Person who prepares microarray data in MAGE-TAB format and submits to a database, such as ArrayExpress.
alternative term: reporting party
editor preferred term: reporting party role
alternative term: submitter
term editor: Jennifer Fostel
definition source: OBI
example of usage: The first section has been pre-designated as the 'Reporting Party' section and should be filled with the Reporting Party's personal information. http://www.mercedsheriff.com/SelfReporting.htm
definition: a study personnel role played by a party who reports the outcome of a study component
has curation status: IAO_0000120

assay
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: has role
      some values from: evaluant role
subclass of: Restriction
  on property: realizes
  some values from: evaluant role
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: information content entity
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: continuant
        intersection of: Restriction
disjoint with: planning
disjoint with: OBI_0200000
example of usage: Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
definition: A planned process with the objective to produce information about some evaluant
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
editor preferred term: assay
alternative term: measuring
alternative term: scientific observation
has curation status: IAO_0000122

quantitative confidence value
type: Class
subclass of: data item
disjoint with: dose response curve
disjoint with: OBI_0001404
definition source: group:OBI
definition: A data item which is used to indicate the degree of uncertainty about a measurement.
term editor: person:Chris Stoeckert
editor preferred term: quantitative confidence value
has curation status: IAO_0000125

sample preparation for assay
type: Class
subclass of: material processing
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
definition: A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI.
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
editor preferred term: sample preparation for assay
alternative term: study
has curation status: IAO_0000125

diagnosis textual entity
type: Class
subclass of: textual entity
term editor: Jennifer Fostel
definition: diagnosis is an assessment of a disease or injury, its likely prognosis and treatment.
editor preferred term: diagnosis textual entity
has curation status: IAO_0000123

unplanned occurrence effecting an investigation
type: Class
subclass of: process
definition source: OBI
term editor: PERSON: Bjoern Peters
editor preferred term: unplanned occurrence effecting an investigation
example of usage: Earthquake that destroys the lab, an outside investigator discovering an adverse effect of the reagants used
definition: a process which is external in origin to the investigation that has an impact on the outcome.
has curation status: IAO_0000120

eMedical record
type: Class
subclass of: information content entity
disjoint with: electronic case report tabulation
disjoint with: eSource document
disjoint with: electronic case report form
disjoint with: analytical cytology data file
disjoint with: fluorescence compensation matrix
disjoint with: record of missing knowledge
disjoint with: sequence feature annotation
disjoint with: OBI_0302838
disjoint with: OBI_0302840
definition source: article-without-pmid-or-doi:CDISCglossary
definition: An eMedical record is a digital document derived from a computer system used primarily for patient care in a clinical setting. Not required to be compliant with requirements of 21 CFR Part 11.
editor preferred term: eMedical record
term editor: person:Jennifer Fostel
has curation status: IAO_0000125

culture medium
type: Class
subclass of: processed material
definition: a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.
editor note: changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178 Modification made by JZ.
editor preferred term: culture medium
example of usage: A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008
definition source: OBI
term editor: Person: Jennifer Fostel, Jie Zheng
has curation status: IAO_0000120

electronic case report tabulation
type: Class
subclass of: information content entity
disjoint with: eSource document
disjoint with: electronic case report form
disjoint with: analytical cytology data file
disjoint with: fluorescence compensation matrix
disjoint with: record of missing knowledge
disjoint with: sequence feature annotation
disjoint with: OBI_0302838
disjoint with: OBI_0302840
definition source: CDISC glossary
definition: An electronic case report tabulation is a digital document containing tabular data about multiple trial participants which is part of a clinical regulatory submission. An eCRT has the property that it can be audited and compliant with requirements of 21 CFR Part 11 and has format suited to review by regulators.
editor preferred term: electronic case report tabulation
term editor: person:Jennifer Fostel
has curation status: IAO_0000120

polystyrene tube
type: Class
subclass of: test tube
disjoint with: NMR sample tube
disjoint with: anticoagulant-containing test tube
disjoint with: OBI_0400020
disjoint with: OBI_0400091
term editor: PERSON: Chris Stoeckert
definition source: PERSON: Chris Stoeckert
example of usage: Polystyrene tubes can be used to contain tissue culture cells during centrifgation
definition: a polystyrene tube is a test tube made of polystyrene
editor preferred term: polystyrene tube
has curation status: IAO_0000122

reagent role
type: Class
subclass of: role
disjoint with: detector reagent role
disjoint with: patient role
disjoint with: study subject role
disjoint with: specimen role
disjoint with: label role
disjoint with: study group role
disjoint with: nutrient role
disjoint with: antigen role
disjoint with: analyte role
disjoint with: material to be added role
disjoint with: cloning insert role
disjoint with: target of material addition role
disjoint with: manufacturer role
disjoint with: pathogen role
disjoint with: host role
disjoint with: test substance role
disjoint with: complementary nucleotide probe role
disjoint with: service consumer role
disjoint with: service provider role
disjoint with: accessed material role
disjoint with: OBI_0302731
disjoint with: OBI_0302732
disjoint with: OBI_0302733
disjoint with: OBI_1110082
disjoint with: OBI_1110083
disjoint with: OBI_1110086
disjoint with: OBI_1110087
disjoint with: OBI_1110091
disjoint with: OBI_1110092
disjoint with: OBI_1110120
curator note: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
alternative term: reagent
editor preferred term: reagent role
definition source: www.answers.com/topic/reagent; November 2008
example of usage: Buffer, dye, a catalyst, a solvating agent.
term editor: GROUP: Role Branch
definition: a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances
has curation status: IAO_0000120

role of regulator of chemical manufacturer
type: Class
subclass of: regulator role
disjoint with: role of Institutional Review Board
disjoint with: role of regulator of consumables and medical devices
alternative term: regulator of chemical manufacture
editor preferred term: role of regulator of chemical manufacturer
example of usage: EPA; John Mollison is the registrar of chemical products in Tasmania, the body that administers the Act that regulates chemical use in that State. http://www.abc.net.au/rn/science/earth/stories/s1160346.htm
definition source: OBI
term editor: Person: Jennifer Fostel
definition: a regulator involved with making and enforcing legislation and governmental orders relevant to chemical manufacture
has curation status: IAO_0000120

detector reagent role
type: Class
subclass of: role
disjoint with: patient role
disjoint with: study subject role
disjoint with: specimen role
disjoint with: label role
disjoint with: study group role
disjoint with: nutrient role
disjoint with: antigen role
disjoint with: analyte role
disjoint with: material to be added role
disjoint with: cloning insert role
disjoint with: target of material addition role
disjoint with: manufacturer role
disjoint with: pathogen role
disjoint with: host role
disjoint with: test substance role
disjoint with: complementary nucleotide probe role
disjoint with: service consumer role
disjoint with: service provider role
disjoint with: accessed material role
disjoint with: OBI_0302731
disjoint with: OBI_0302732
disjoint with: OBI_0302733
disjoint with: OBI_1110082
disjoint with: OBI_1110083
disjoint with: OBI_1110086
disjoint with: OBI_1110087
disjoint with: OBI_1110091
disjoint with: OBI_1110092
disjoint with: OBI_1110120
editor note: 19feb2009. not clear we need this term. originally if came from microarrays -- the probes on the array are termed detectors in some instances
definition source: One that detects, especially a mechanical, electrical, or chemical device that automatically identifies and records or registers a stimulus, such as an environmental change in pressure or temperature, an electric signal, or radiation from a radioactive material. http://www.answers.com/topic/detector 19feb2009
definition: a role which inheres in a molecular entity and is realized by the process of recording or registering a stimulus.
editor preferred term: detector reagent role
has curation status: IAO_0000123

role of certified IRB professional
type: Class
subclass of: regulation-assigned role
disjoint with: role of impartial witness
disjoint with: role of legally acceptable representative
term editor: Person:Helen Parkinson
definition source: WEB: http://en.wikipedia.org/wiki/Certified_IRB_Professional
definition: a role of which inheres in a Homo sapiens and realized during administration and oversight of the daily activities of Institutional Review Boards (IRBs) in the USA
alternative term: certified IRB professional
editor preferred term: role of certified IRB professional
example of usage: CIP= Certified IRB Professional; http://acronyms.thefreedictionary.com/Certified+IRB+Professional
term editor: Person:Jennifer Fostel
has curation status: IAO_0000120

patient role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: Homo sapiens
disjoint with: study subject role
disjoint with: specimen role
disjoint with: label role
disjoint with: study group role
disjoint with: nutrient role
disjoint with: antigen role
disjoint with: analyte role
disjoint with: material to be added role
disjoint with: cloning insert role
disjoint with: target of material addition role
disjoint with: manufacturer role
disjoint with: pathogen role
disjoint with: host role
disjoint with: test substance role
disjoint with: complementary nucleotide probe role
disjoint with: service consumer role
disjoint with: service provider role
disjoint with: accessed material role
disjoint with: OBI_0302731
disjoint with: OBI_0302732
disjoint with: OBI_0302733
disjoint with: OBI_1110082
disjoint with: OBI_1110083
disjoint with: OBI_1110086
disjoint with: OBI_1110087
disjoint with: OBI_1110091
disjoint with: OBI_1110092
disjoint with: OBI_1110120
alternative term: patient
editor preferred term: patient role
curator note: CDISC definition: patient. Person under a physician's care for a particular disease or condition. NOTE: A subject in a clinical trial is not necessarily a patient, but a patient in a clinical trial is a subject. See also subject, trial subject, healthy volunteer. Often used interchangeably
term editor: GROUP:Role Branch
definition source: OBI, CDISC
example of usage: a hospitalized person; a person with controlled diabetes; the patient's role http://www.fertilityjourney.com/testingAndDiagnosis/theRightDoctor/thePatientsRole/index.asp?C=55245395146924652778
definition: a role which inheres in a person and is realized by the process of being under the care of a physician or health care provider
has curation status: IAO_0000120

material processing
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: processed material
subclass of: Restriction
  on property: has_specified_output
  all values from: material entity
subclass of: Restriction
  on property: has_specified_input
  all values from: material entity
example of usage: A cell lysis, production of a cloning vector, creating a buffer.
term editor: PERSON: Frank Gibson
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Melanie Courtot
term editor: PERSON: Philippe Rocca Serra
editor preferred term: material processing
definition: A planned process which results in physical changes in a specified input material
definition source: OBI branch derived
term editor: PERSON: Bjoern Peters
alternative term: material transformation
has curation status: IAO_0000122

protocol testing objective
type: Class
subclass of: methodology testing objective
disjoint with: hardware testing objective
disjoint with: software testing objective
term editor: Jennifer Fostel
definition: Protocol_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different protocols.
editor preferred term: protocol testing objective
has curation status: IAO_0000123

study subject role
type: Class
subclass of: role
subclass of: Restriction
  on property: concretizes
  some values from: Class
    union of: intervention design
    union of: OBI_0300311
subclass of: Restriction
  on property: is realized by
  all values from: study design execution
disjoint with: specimen role
disjoint with: label role
disjoint with: study group role
disjoint with: nutrient role
disjoint with: antigen role
disjoint with: analyte role
disjoint with: material to be added role
disjoint with: cloning insert role
disjoint with: target of material addition role
disjoint with: manufacturer role
disjoint with: pathogen role
disjoint with: host role
disjoint with: test substance role
disjoint with: complementary nucleotide probe role
disjoint with: service consumer role
disjoint with: service provider role
disjoint with: accessed material role
disjoint with: OBI_0302731
disjoint with: OBI_0302732
disjoint with: OBI_0302733
disjoint with: OBI_1110082
disjoint with: OBI_1110083
disjoint with: OBI_1110086
disjoint with: OBI_1110087
disjoint with: OBI_1110091
disjoint with: OBI_1110092
disjoint with: OBI_1110120
example of usage: Human subjects in a clinical trial, rats in a toxicogenomics study, tissue cutlures subjected to drug tests, fish observed in an ecotoxicology study. Parasite example people infected, then extract parasite which are then tested = observation study of the parasite 1 study in which we observe people and 1 study in which subject is parasite is one way to split this. the true definition will come from the study design specification.
definition source: OBI
definition: study subject role inheres in an entity and realized through the execution of a study design in which the entity participates by being that which the results are about.
term editor: GROUP: Role Branch
editor preferred term: study subject role
has curation status: IAO_0000122

obsolete_role of being first subject treated
type: Class
subclass of: ObsoleteClass
definition source: OBI
deprecated: true
editor preferred term: First subject treated
definition: First subject treated role is a study subject role borne by the subject realized in the application of the process specified in intervention study design with no previous study subject realizing the role prior in the study
example of usage: Rat 1A; first enrolled patient to receive treatment
term editor: Role Branch
editor note: first subject treated. First subject who receives the test article or placebo in a clinical trial.
has obsolescence reason: IAO_0000103
has curation status: IAO_0000120

measured expression level
type: Class
subclass of: measurement datum
disjoint with: number of particles in subset
disjoint with: number of lost events electronic
disjoint with: parameter threshold
disjoint with: number of lost events computer
disjoint with: survival rate
disjoint with: spike train datum
disjoint with: categorical measurement datum
disjoint with: dose
disjoint with: obsolete_general scalar measurement datum
disjoint with: 3D structural organization datum
definition source: OBI Data Transformation branch
definition: A measurement datum that is the outcome of the quantification of an assay for the activity of a gene, or the number of RNA transcripts.
example of usage: Examples are quantified data from an expression microarray experiment, PCR measurements, etc.
editor preferred term: measured expression level
term editor: person:Chris Stoeckert
has curation status: IAO_0000120

responsible party role
type: Class
subclass of: investigation agent role
alternative term: responsible party
editor preferred term: responsible party role
definition source: OBI
term editor: Person: Jennifer Fostel
definition: a study personnel role played by a party who is accountable for the execution of a study component and can make decisions about the conduct of the study
example of usage: he THERAPIST has the ability to print a separate statement for the patient and each responsible party. http://www.beaverlog.com/therapist/ez_support/billing/responsible_party_statements.htm
has curation status: IAO_0000120

principal investigator role
type: Class
subclass of: responsible party role
alternative term: principal investigator
editor preferred term: principal investigator role
curator note: CDISC definition: A person responsible for the conduct of the clinical trial at a trial site. If a trial is conducted by a team of individuals at a trial site, the investigator is the responsible leader of the team and may be called the principal investigator. 2. The individual principal investigator. 2. The individual under whose immediate direction the test article is administered or dispensed to, or used involving, a subject, or, in the event of an investigation conducted by a team of individuals, is See also sponsor-investigator.; Leiter der klinischen Prufung.Under the German Drug Law, the physician who is head of the clinical investigation (CDISC): coordinating investigator (CDISC) (also study coordinator, MUSC); sponsor-investigator. An individual who both initiates and conducts, alone or with others, a clinical trial, and under whose immediate direction the investigational product is administered to, dispensed to, or used by a subject.NOTE: The term does not include any person other than an individual, hence not a corporation, agency (CDISC)
term editor: Person: Jennifer Fostel
definition: a responsible party role played by a person responsible for the overall conduct of a study
has curation status: IAO_0000123

transplantation
type: Class
subclass of: material processing
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
definition: a protocol application to replace an organ or tissue of an organism
editor preferred term: transplantation
has curation status: IAO_0000125

biological vector role
type: Class
subclass of: material to be added role
curator note: 6/12/2009 Alan made this a material to be added role, because it was, and because this speeded up reasoning
editor note: Feb 20, 2009. The material transmitted can be genetic information (as in cloning vector) or a pathogen (as in a disease vector)
term editor: GROUP: Role Branch
definition source: OBI and Wikipedia
definition: a biological vector role is a material to be added role that is realized by the process of transmitting material to the organism that is the target of the transmission.
editor preferred term: biological vector role
example of usage: 1983 Sci. Amer. Jan. 58/2 Plasmids are routinely used as vectors for introducing foreign DNA into bacteria.
example of usage: Some epidemiological aspects and vector role of tick infestation on layers in the Faisalabad district (Pakistan). http://journals.cambridge.org/action/displayAbstract;jsessionid=0373164489D00868AEEF2C556EB4FD29.tomcat1?fromPage=online&aid=624280
has curation status: IAO_0000120

pH indicator dye role
type: Class
subclass of: dye role
disjoint with: vital dye role
term editor: Person:Helen Parkinson
example of usage: bromophenol blue has a pH indicator dye role
alternative term: pH indicator dye
editor preferred term: pH indicator dye role
definition: the role of a dye that is realized when the dye is used in an experiment to measure the pH in a material entity
term editor: Person: Jennifer Fostel
example of usage: phenol red in RPMI; pH=4 indicator dye (also carries reference role)
has curation status: IAO_0000120

specimen role
type: Class
subclass of: role
subclass of: Restriction
  on property: is realized by
  all values from: investigation
subclass of: Restriction
  on property: inheres in
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection
disjoint with: label role
disjoint with: study group role
disjoint with: nutrient role
disjoint with: antigen role
disjoint with: analyte role
disjoint with: material to be added role
disjoint with: cloning insert role
disjoint with: target of material addition role
disjoint with: manufacturer role
disjoint with: pathogen role
disjoint with: host role
disjoint with: test substance role
disjoint with: complementary nucleotide probe role
disjoint with: service consumer role
disjoint with: service provider role
disjoint with: accessed material role
disjoint with: OBI_0302731
disjoint with: OBI_0302732
disjoint with: OBI_0302733
disjoint with: OBI_1110082
disjoint with: OBI_1110083
disjoint with: OBI_1110086
disjoint with: OBI_1110087
disjoint with: OBI_1110091
disjoint with: OBI_1110092
disjoint with: OBI_1110120
editor note: 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role.
term editor: GROUP: Role Branch
editor note: Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
definition source: OBI
example of usage: liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.
editor preferred term: specimen role
definition: a role borne by a material entity that is gained during a specimen creation process and that can be realized by use of the specimen in an investigation
editor note: blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen.
editor note: parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject.
has curation status: IAO_0000122

sequence feature identification objective
type: Class
subclass of: biological feature identification objective
disjoint with: molecular feature identification objective
disjoint with: cellular feature identification objective
disjoint with: organism feature identification objective
term editor: Jennifer Fostel
definition: Sequence_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features exhibited at the level of a macromolecular sequence, e.g. nucleic acid, protein, polysaccharide.
editor preferred term: sequence feature identification objective
has curation status: IAO_0000123

intervention design
type: Class
equivalent class: Class
  intersection of: OBI_0500000
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: independent variable specification
      intersection of: Restriction
        on property: is about
        some values from: study intervention
subclass of: OBI_0500000
definition: An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays.
definition source: OBI branch derived
example of usage: PMID: 18208636.Br J Nutr. 2008 Jan 22;:1-11.Effect of vitamin D supplementation on bone and vitamin D status among Pakistani immigrants in Denmark: a randomised double-blinded placebo-controlled intervention study.
term editor: Philppe Rocca-Serra
editor preferred term: intervention design
has curation status: IAO_0000125

worker role
type: Class
subclass of: investigation agent role
editor note: "executes the study plan" includes the suppliers and manufacturers of reagents and other materials used in the study
alternative term: worker
editor preferred term: worker role
definition source: OBI
term editor: Person:Jennifer Fostel
example of usage: Public sector workers in states that run their own OSHA programs are covered by those states. http://www.osha.gov/as/opa/worker/index.html
definition: a personnel role played by a party who executes a component of the study plan; this can occur before, during, after or outside the study timeline
has curation status: IAO_0000120

Bernoulli trial
type: Class
subclass of: assay
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
editor preferred term: Bernoulli trial
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
definition: is an assay where the output data is a datum with one of two values denoted success and failure.
has curation status: IAO_0000125

gene list
type: Class
subclass of: data set
disjoint with: cluster
definition source: group:OBI
definition: A data set of the names or identifiers of genes that are the outcome of an analysis or have been put together for the purpose of an analysis.
example of usage: Gene lists may arise from analysis to determine differentially expressed genes, may be collected from the literature for involvement in a particular process or pathway (e.g., inflammation), or may be the input for gene set enrichment analysis.
editor preferred term: gene list
curator note: kind of report. (alan) need to be careful to distinguish from output of a data transformation or calculation. A gene list is a report when it is published as such? Relates to question of whether report is a whole, or whether it can be a part of some other narrative object.
term editor: person:Chris Stoeckert
has curation status: IAO_0000125

number of particles in subset
type: Class
subclass of: measurement datum
disjoint with: number of lost events electronic
disjoint with: parameter threshold
disjoint with: number of lost events computer
disjoint with: survival rate
disjoint with: spike train datum
disjoint with: categorical measurement datum
disjoint with: dose
disjoint with: obsolete_general scalar measurement datum
disjoint with: 3D structural organization datum
definition source: Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
example of usage: 500, 200, 0
definition: A measurement datum measuring the number of subjects in a defined subset in a flow cytometer instrument. The datum has a qualitative role
editor preferred term: number of particles in subset
term editor: person:Kevin Clancy
has curation status: IAO_0000120

number of lost events electronic
type: Class
subclass of: measurement datum
disjoint with: parameter threshold
disjoint with: number of lost events computer
disjoint with: survival rate
disjoint with: spike train datum
disjoint with: categorical measurement datum
disjoint with: dose
disjoint with: obsolete_general scalar measurement datum
disjoint with: 3D structural organization datum
definition source: Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
example of usage: 74, 0, 14 events lost due to data acquisition electronic coincidence.
definition: A measurement datum measuring the number of analysis events lost due to errors in data acquisition electronic coincidence in a flow cytometer instrument. The datum has a qualitative role.
editor preferred term: number of lost events electronic
term editor: person:Kevin Clancy
has curation status: IAO_0000120

calibration substance role
type: Class
subclass of: reference substance role
subclass of: Restriction
  on property: is realized by
  all values from: calibration
disjoint with: negative reference substance role
disjoint with: nucleic acid template role
disjoint with: spike-in quality control role
disjoint with: dye swap quality control role
definition: A reference substance role that is realized when characteristics or responses elicited by the bearer are used to ensure an instrument is within protocol specification of accuracy or performance
term editor: Jennifer Fostel
editor preferred term: calibration substance role
example of usage: pH buffer used to calibrate a pH meter bears a calibration substance role
has curation status: IAO_0000122

molecular feature identification objective
type: Class
subclass of: biological feature identification objective
disjoint with: cellular feature identification objective
disjoint with: organism feature identification objective
term editor: Jennifer Fostel
definition: Molecular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features of a biological system, e.g. expression profiling, copy number of molecular components, epigenetic modifications.
editor preferred term: molecular feature identification objective
has curation status: IAO_0000123

hardware testing objective
type: Class
subclass of: methodology testing objective
disjoint with: software testing objective
definition: Hardware_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different hardware, e.g. scanner.
term editor: Jennifer Fostel
editor preferred term: hardware testing objective
has curation status: IAO_0000123

incubator
type: Class
subclass of: environmental control device
subclass of: Restriction
  on property: has function
  some values from: environment control function
disjoint with: supernatant collection system harvesting frame
disjoint with: filter paper
disjoint with: microtiter plate
disjoint with: mass analyzer
disjoint with: ion source
disjoint with: ion detector
disjoint with: isoelectric focusing device
disjoint with: thermostatic circulator
disjoint with: blot module
disjoint with: gel dryer
disjoint with: syringe
disjoint with: needle
disjoint with: column chromatography detector
disjoint with: NMR sample holder
disjoint with: chromatography instrument
disjoint with: rapid resolution column
disjoint with: NMR tube washing system
disjoint with: NMR console
disjoint with: variable wavelength detector
disjoint with: multiple wavelength detector
disjoint with: NMR probe
disjoint with: NMR magnet
disjoint with: magic angle spinning rotor
disjoint with: Bruker SampleRail system
disjoint with: evaporative light scattering detector
disjoint with: autosampler
disjoint with: fluorescene detector
disjoint with: electrical conductivity detector
disjoint with: NMR instrument
disjoint with: refractive index detector
disjoint with: pulsed amperometric detector
disjoint with: glucometer
disjoint with: micro electrode
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker

label role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: material entity
disjoint with: study group role
disjoint with: nutrient role
disjoint with: antigen role
disjoint with: analyte role
disjoint with: material to be added role
disjoint with: cloning insert role
disjoint with: target of material addition role
disjoint with: manufacturer role
disjoint with: pathogen role
disjoint with: host role
disjoint with: test substance role
disjoint with: complementary nucleotide probe role
disjoint with: service consumer role
disjoint with: service provider role
disjoint with: accessed material role
disjoint with: OBI_0302731
disjoint with: OBI_0302732
disjoint with: OBI_0302733
disjoint with: OBI_1110082
disjoint with: OBI_1110083
disjoint with: OBI_1110086
disjoint with: OBI_1110087
disjoint with: OBI_1110091
disjoint with: OBI_1110092
disjoint with: OBI_1110120
definition source: OBI
alternative term: label
definition: Label role is a role which inheres in a material entity and which is realized in a detection of label assay
editor note: Nucleotides synthesized with the incorporation of biotin were used to synthesize cDNA, which was then detected by adding fluorochrome-conjugated anti-biotin antibody. the fluorochrome bears label role, the antibody bears detector role, the biotin bears reporter role. may need to change the terms following discussion
term editor: Role Branch
editor preferred term: label role
editor note: need to add a restriction that the material entity has the disposition / quality that permits it to be detected, and one way to say this (BP) is that the entity is such that an assay exists that detects the presence of the material entity
editor note: we need to sort out probe, detector and reporter. See https://sourceforge.net/tracker/index.php?func=detail&aid=1866458&group_id=177891&atid=886178
has curation status: IAO_0000120

baseline participant role
type: Class
subclass of: reference subject role
disjoint with: crossover population role
disjoint with: biological replicate role
disjoint with: technical replicate role
definition: a reference participant role which is realized by making the reference to qualities at the start of the study or intervention
alternative term: baseline participant
editor preferred term: baseline participant role
term editor: Person: Jennifer Fostel
example of usage: Subject at time = 0; subject before a stress test.
has curation status: IAO_0000123

role of independent data monitoring committee
type: Class
subclass of: trial monitor role
alternative term: independent data monitoring committee
editor preferred term: role of independent data monitoring committee
term editor: Person: Jennifer Fostel
definition: a trial monitor role charged recommending whether to continue, modify, or end the trial
has curation status: IAO_0000120

pathologist role
type: Class
subclass of: worker role
alternative term: Pathologist
editor preferred term: pathologist role
term editor: Person:Jennifer Fostel
definition: a worker role of being responsible for making the histopathology diagnoses associated with data from a study; this activity occurs outside the study timeline
has curation status: IAO_0000123

supernatant collection system harvesting frame
type: Class
subclass of: container
subclass of: Restriction
  on property: has function
  some values from: contain function
disjoint with: filter paper
disjoint with: microtiter plate
disjoint with: mass analyzer
disjoint with: ion source
disjoint with: ion detector
disjoint with: isoelectric focusing device
disjoint with: thermostatic circulator
disjoint with: blot module
disjoint with: gel dryer
disjoint with: syringe
disjoint with: needle
disjoint with: column chromatography detector
disjoint with: NMR sample holder
disjoint with: chromatography instrument
disjoint with: rapid resolution column
disjoint with: NMR tube washing system
disjoint with: NMR console
disjoint with: variable wavelength detector
disjoint with: multiple wavelength detector
disjoint with: NMR probe
disjoint with: NMR magnet
disjoint with: magic angle spinning rotor
disjoint with: Bruker SampleRail system
disjoint with: evaporative light scattering detector
disjoint with: autosampler
disjoint with: fluorescene detector
disjoint with: electrical conductivity detector
disjoint with: NMR instrument
disjoint with: refractive index detector
disjoint with: pulsed amperometric detector
disjoint with: glucometer
disjoint with: micro electrode
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer

filter paper
type: Class
subclass of: material separation device
subclass of: Restriction
  on property: has function
  some values from: filter function
disjoint with: microtiter plate
disjoint with: mass analyzer
disjoint with: ion source
disjoint with: ion detector
disjoint with: isoelectric focusing device
disjoint with: thermostatic circulator
disjoint with: blot module
disjoint with: gel dryer
disjoint with: syringe
disjoint with: needle
disjoint with: column chromatography detector
disjoint with: NMR sample holder
disjoint with: chromatography instrument
disjoint with: rapid resolution column
disjoint with: NMR tube washing system
disjoint with: NMR console
disjoint with: variable wavelength detector
disjoint with: multiple wavelength detector
disjoint with: NMR probe
disjoint with: NMR magnet
disjoint with: magic angle spinning rotor
disjoint with: Bruker SampleRail system
disjoint with: evaporative light scattering detector
disjoint with: autosampler
disjoint with: fluorescene detector
disjoint with: electrical conductivity detector
disjoint with: NMR instrument
disjoint with: refractive index detector
disjoint with: pulsed amperometric detector
disjoint with: glucometer
disjoint with: micro electrode
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine

cell co-culturing
type: Class
subclass of: material processing
subclass of: Restriction
  on property: has_specified_output
  some values from: OBI_0100060
subclass of: Class
  intersection of: Restriction
    on property: has_specified_input
    some values from: cell
  intersection of: Restriction
    on property: has_specified_input
    min cardinality: 2
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: Restriction
  on property: has_specified_input
  some values from: culture medium
definition: A material combination in which cell cultures of two or more different types are are combined and allowed to culture as one.
example of usage: Culturing cytotoxic T-lymphocytes together with target cells in order to study lysis of the target cells. See chromium_release_assay
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
editor preferred term: cell co-culturing
has curation status: IAO_0000125

role of Institutional Review Board
type: Class
subclass of: regulator role
disjoint with: role of regulator of consumables and medical devices
example of usage: Animal protocol review board
alternative term: Internal Review Board
term editor: Person:Helen Parkinson
editor preferred term: role of Institutional Review Board
definition: the role of a organization that is realized by members reviewing study designs for their agreement with regulations
example of usage: An institutional review board/independent ethics committee (IRB/IEC) (also known as ethical review board) is a group that has been formally designated to approve, monitor, and review biomedical and behavioral research involving humans with the alleged aim to protect the rights and welfare of the subjects. Wikipedia March 2008
curator note: CDISC definition: institutional review board; independent ethics committee (IEC). An independent body (a review board or a committee, institutional, regional, national, or supranational) constituted of medical/scientific professionals and non-scientific members, whose responsibility it is to ensure the protection of the rights, safety and well-being of human subjects involved in a trial.
definition source: OBI, CDISC
term editor: Person:Jennifer Fostel
has curation status: IAO_0000120

eSource document
type: Class
subclass of: information content entity
disjoint with: electronic case report form
disjoint with: analytical cytology data file
disjoint with: fluorescence compensation matrix
disjoint with: record of missing knowledge
disjoint with: sequence feature annotation
disjoint with: OBI_0302838
disjoint with: OBI_0302840
definition source: article-without-pmid-or-doi:CDISCglossary
definition: an eSource document is a digital document consisting of a logical collection of Source data and other eSource documents that can be presented in an ordered way and capture the time of completion, change, and any signatures
editor preferred term: eSource document
term editor: person:Jennifer Fostel
has curation status: IAO_0000125

crossover population role
type: Class
subclass of: reference subject role
disjoint with: biological replicate role
disjoint with: technical replicate role
definition: a role realized when a participant serves as reference to itself
alternative term: crossover population
editor preferred term: crossover population role
term editor: Person: Jennifer Fostel
has curation status: IAO_0000123

complete nutrient role
type: Class
subclass of: nutrient role
definition: A nutrient role that inheres in a material entity and is realized in the use of that material entity by an organism to provide all needed nourishment.
alternative term: complete nutrient
editor preferred term: complete nutrient role
term editor: Person: Jennifer Fostel
example of usage: Rat chow; RPMI medium + serum; use example: CNS17 (Complete Nutrient System) Grow 3-2-4, http://www.kalyx.com/store/proddetail.cfm/ItemID/552307/CategoryID/12000/SubCatID/2755/file.htm
has curation status: IAO_0000123

radiolabel role
type: Class
subclass of: label role
subclass of: Restriction
  on property: is realized by
  all values from: radioactivity detection
disjoint with: dye role
term editor: Jennifer Fostel
alternative term: radiolabel
editor preferred term: radiolabel role
definition: radiolabel role is a role which inheres in a material entity which is realized by the process of radioactivity detection
has curation status: IAO_0000120

cDNA library
type: Class
subclass of: recombinant vector
subclass of: Restriction
  on property: has grain
  some values from: recombinant vector
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0600064
disjoint with: population
disjoint with: organization
disjoint with: eluate
disjoint with: polyacrylamide gel
disjoint with: agarose gel
disjoint with: scattered molecular aggregate
disjoint with: urine specimen
disjoint with: blood specimen
disjoint with: whole organism preparation
disjoint with: capsule shell
disjoint with: guar gum
disjoint with: cloacal specimen
disjoint with: nasopharyngeal aspirate specimen
disjoint with: nasal swab specimen
disjoint with: device
disjoint with: growth environment
disjoint with: OBI_0001468
disjoint with: OBI_0001485
disjoint with: OBI_0100014
disjoint with: OBI_0100016
disjoint with: OBI_0100017
disjoint with: OBI_0100055
disjoint with: OBI_0100058
disjoint with: OBI_0100060
disjoint with: OBI_0100067
disjoint with: OBI_0100086
disjoint with: OBI_1000023
disjoint with: OBI_1000024
disjoint with: OBI_1000029
disjoint with: OBI_1000036
disjoint with: OBI_1000042
definition source: GROUP: PSI
definition: Mixed population of cDNAs (complementaryDNA) made from mRNA from a defined source, usually a specific cell type. This term should be associated only to nucleic acid interactors not to their proteins product. For instance in 2h screening use living cells (MI:0349) as sample process. ALT DEF (PRS):: a cDNA library is a collection of host cells, typically E.Coli cells but not exclusively. modified by transfer of plasmid DNA molecule used as vector containing a fragment or totality of cDNA molecule (the insert) . cDNA library may have an array of role and applications.
term editor: PERSON: Luisa Montecchi
term editor: PERSON: Philippe Rocca-Serra
example of usage: PMID:6110205. collection of cDNA derived from mouse splenocytes.
curator note: PRS: 22022008. class moved under population, modification of definition and replacement of biomaterials in previous definition with 'material' addition of has_role restriction
editor preferred term: cDNA library
has curation status: IAO_0000123

electronic case report form
type: Class
subclass of: information content entity
disjoint with: analytical cytology data file
disjoint with: fluorescence compensation matrix
disjoint with: record of missing knowledge
disjoint with: sequence feature annotation
disjoint with: OBI_0302838
disjoint with: OBI_0302840
definition source: CDISC glossary
definition: An electronic case report form is a digital document used to record all of the protocol required information to be reported for each trial subject. An eCRF has the property that it can be audited and compliant with requirements of 21 CFR Part 11.
editor preferred term: electronic case report form
term editor: person:Jennifer Fostel
has curation status: IAO_0000120

placebo role
type: Class
subclass of: negative reference substance role
definition: a negative reference substance is a reference role in which the substance playing the reference substance role is physically similar in appearance to the test substance
alternative term: placebo
editor preferred term: placebo role
curator note: CDISC definition placebo. A pharmaceutical preparation that does not contain the investigational agent. In blinded studies, it is generally prepared to be physically indistinguishable from the preparation containing the investigational product.
term editor: Person:Jennifer Fostel
example of usage: Pill consisting of inert materials
has curation status: IAO_0000120

autotransplantation
type: Class
subclass of: transplantation
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
editor preferred term: autotransplantation
definition: is the transplantation of tissue from one part of \nthe body to another in the same individual. )
has curation status: IAO_0000125

parameter threshold
type: Class
subclass of: measurement datum
disjoint with: number of lost events computer
disjoint with: survival rate
disjoint with: spike train datum
disjoint with: categorical measurement datum
disjoint with: dose
disjoint with: obsolete_general scalar measurement datum
disjoint with: 3D structural organization datum
definition source: Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
example of usage: 0.01, 0.03
definition: A measurement datum measuring the minimal signal that must be detected to generate an electrical event, as compared to the maximal detected signal in a flow cytometer instrument. The datum has a qualitative role
editor preferred term: parameter threshold
term editor: person:Kevin Clancy
has curation status: IAO_0000120

study group role
type: Class
subclass of: role
disjoint with: nutrient role
disjoint with: antigen role
disjoint with: analyte role
disjoint with: material to be added role
disjoint with: cloning insert role
disjoint with: target of material addition role
disjoint with: manufacturer role
disjoint with: pathogen role
disjoint with: host role
disjoint with: test substance role
disjoint with: complementary nucleotide probe role
disjoint with: service consumer role
disjoint with: service provider role
disjoint with: accessed material role
disjoint with: OBI_0302731
disjoint with: OBI_0302732
disjoint with: OBI_0302733
disjoint with: OBI_1110082
disjoint with: OBI_1110083
disjoint with: OBI_1110086
disjoint with: OBI_1110087
disjoint with: OBI_1110091
disjoint with: OBI_1110092
disjoint with: OBI_1110120
example of usage: The group of randomized participants that are assigned to a treatment arm of the trial
alternative term: study group population
editor preferred term: study group role
term editor: Jennifer Fostel
definition: a study population role where the bearer is a population of material entities and the role is realized in the implementation of a study design wherein the entities bearing the study population role are observed or subjected to intervention according to the study design and are biological replicates, i.e. they receive the same treatment under the protocol
has curation status: IAO_0000123

p-value
type: Class
subclass of: quantitative confidence value
disjoint with: standard error
disjoint with: FWER adjusted p-value
disjoint with: OBI_0001442
editor note: May be outside the scope of OBI long term, is needed so is retained
example of usage: PMID:19696660 in contrast to the in-vivo data AT-III increased significantly from 113.5% at baseline to 117% after 4 days (n = 10, P-value= 0.02; Table 2).
definition source: WEB: http://en.wikipedia.org/wiki/P-value
definition: A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.
term editor: PERSON:Chris Stoeckert
editor preferred term: p-value
has curation status: IAO_0000121

population
type: Class
subclass of: material entity
disjoint with: organization
disjoint with: eluate
disjoint with: polyacrylamide gel
disjoint with: agarose gel
disjoint with: scattered molecular aggregate
disjoint with: urine specimen
disjoint with: blood specimen
disjoint with: whole organism preparation
disjoint with: capsule shell
disjoint with: guar gum
disjoint with: cloacal specimen
disjoint with: nasopharyngeal aspirate specimen
disjoint with: nasal swab specimen
disjoint with: device
disjoint with: growth environment
disjoint with: OBI_0001468
disjoint with: OBI_0001485
disjoint with: OBI_0100014
disjoint with: OBI_0100016
disjoint with: OBI_0100017
disjoint with: OBI_0100055
disjoint with: OBI_0100058
disjoint with: OBI_0100060
disjoint with: OBI_0100067
disjoint with: OBI_0100086
disjoint with: OBI_1000023
disjoint with: OBI_1000024
disjoint with: OBI_1000029
disjoint with: OBI_1000036
disjoint with: OBI_1000042
term editor: PERSON: Philippe Rocca-Serra
example of usage: PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population.
definition: a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area
definition source: adapted from Oxford English Dictionnary
editor preferred term: population
curator note: rem1: collection somehow always involve a selection process
has curation status: IAO_0000125

nuclear magnetic resonance assay
type: Class
subclass of: OBI_0600045
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: 3D structural organization datum
term editor: PlanAndPlannedProcess Branch
definition: an assay used to identify the chemical structure of a compound or biological macromolecule using an NMR instrument.
editor preferred term: nuclear magnetic resonance assay
definition source: www.nature.com/nrd/journal/v2/n5/glossary/nrd1086_glossary.html OBI branch derived
has curation status: IAO_0000120

imaging assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has_specified_output
  some values from: image
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
definition: An imaging assay is an assay to produce a picture of an entity. definition_source: OBI.
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
editor preferred term: imaging assay
has curation status: IAO_0000125

protocol optimization objective
type: Class
subclass of: protocol testing objective
term editor: Jennifer Fostel
definition: Protocol_optimization is a protocol_testing_objective role describing a study designed to identify the best protocol. This may be carried out by comparing different protocols or by modifying the parameters used within a single protocol.
editor preferred term: protocol optimization objective
has curation status: IAO_0000123

role of pathology review board
type: Class
subclass of: worker role
alternative term: pathology review board
editor preferred term: role of pathology review board
term editor: Person: Jennifer Fostel
definition: a worker role comprised of providing a confirmed and consensus diagnosis for histopathology results obtained during the investigation
has curation status: IAO_0000123

microtiter plate
type: Class
subclass of: container
subclass of: Restriction
  on property: has function
  some values from: contain function
disjoint with: mass analyzer
disjoint with: ion source
disjoint with: ion detector
disjoint with: isoelectric focusing device
disjoint with: thermostatic circulator
disjoint with: blot module
disjoint with: gel dryer
disjoint with: syringe
disjoint with: needle
disjoint with: column chromatography detector
disjoint with: NMR sample holder
disjoint with: chromatography instrument
disjoint with: rapid resolution column
disjoint with: NMR tube washing system
disjoint with: NMR console
disjoint with: variable wavelength detector
disjoint with: multiple wavelength detector
disjoint with: NMR probe
disjoint with: NMR magnet
disjoint with: magic angle spinning rotor
disjoint with: Bruker SampleRail system
disjoint with: evaporative light scattering detector
disjoint with: autosampler
disjoint with: fluorescene detector
disjoint with: electrical conductivity detector
disjoint with: NMR instrument
disjoint with: refractive index detector
disjoint with: pulsed amperometric detector
disjoint with: glucometer
disjoint with: micro electrode
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner

role of impartial witness
type: Class
subclass of: regulation-assigned role
disjoint with: role of legally acceptable representative
term editor: Person: Helen Parkinson
definition: a role which inheres in a Homo sapiens and is realized during a clinical trial - the impartial witness is independent of the trial and cannot be unfairly influenced by people involved with the trial
alternative term: impartial witness
editor preferred term: role of impartial witness
example of usage: According to GCP , an impartial witness should be present for an illiterate subject. PharmPK Discussion, http://www.boomer.org/pkin/PK06/PK2006253.html
term editor: Person: Jennifer Fostel
editor note: impartial witness. A person, who is independent of the trial, who cannot be unfairly influenced by people involved with the trial, who attends the informed consent process if the subject or the subject's legally acceptable representative cannot read, and who
has curation status: IAO_0000123

biological replicate role
type: Class
subclass of: reference subject role
disjoint with: technical replicate role
definition: a reference participant role realized by equivalent treatment of participants
alternative term: biological replicate
editor preferred term: biological replicate role
example of usage: A member of a dose-time group; a patient in a given arm of a trial
definition source: OBI
term editor: Person:Jennifer Fostel
has curation status: IAO_0000120

radioactivity detection
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: Restriction
subclass of: assay
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
definition: An assay in which a material's radioactivity is measured.
example of usage: Measurment of the radioactivity of a supernatant, as in chromium_release_assay.
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
editor preferred term: radioactivity detection
has curation status: IAO_0000125

investigation agent role
type: Class
equivalent class: Class
  intersection of: role
  intersection of: Restriction
    on property: inheres in
    some values from: Class
      intersection of: Class
        union of: Homo sapiens
        union of: organization
      intersection of: Restriction
        on property: is bearer of
        some values from: Restriction
subclass of: role
curator note: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
editor note: Implementing a study means carrying out or performing the study and providing reagents or other materials used in the study and other tasks without which the study would not happen.
editor preferred term: investigation agent role
alternative term: investigator
term editor: GROUP: Role Branch
definition: Investigation agent role is a role borne by a person or organization which is realized in a process that is part of an investigation in which an objective is achieved. These processes include: planning, overseeing, funding, reviewing.
definition source: OBI
example of usage: The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress.
has curation status: IAO_0000122

nutrient role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: material entity
disjoint with: antigen role
disjoint with: analyte role
disjoint with: material to be added role
disjoint with: cloning insert role
disjoint with: target of material addition role
disjoint with: manufacturer role
disjoint with: pathogen role
disjoint with: host role
disjoint with: test substance role
disjoint with: complementary nucleotide probe role
disjoint with: service consumer role
disjoint with: service provider role
disjoint with: accessed material role
disjoint with: OBI_0302731
disjoint with: OBI_0302732
disjoint with: OBI_0302733
disjoint with: OBI_1110082
disjoint with: OBI_1110083
disjoint with: OBI_1110086
disjoint with: OBI_1110087
disjoint with: OBI_1110091
disjoint with: OBI_1110092
disjoint with: OBI_1110120
curator note: 19 Feb 2009; old def: A nutrient role is a role played by a substance used in an organism's metabolism which is taken in from the environment and provides nourishment.
alternative term: nutrient
editor preferred term: nutrient role
term editor: GROUP: Role branch
example of usage: Luria broth; vitamin A; A nutrient is a substance used in an organism's metabolism which must be taken in from the environment. Wikipedia.
definition source: Wikipedia, feb 29, 2008
definition: a role that inheres in a material entity and is realized in the use of that material entity by an organism when it is used in that organism's metabolism and provides nourishment.
has curation status: IAO_0000120

obsolete_dropout role
type: Class
subclass of: ObsoleteClass
definition source: OBI
editor note: Will be modelled as defined material, ouput of some 'dropout or withdrawal process' instead of role
deprecated: true
editor preferred term: Dropout
definition: Dropout is a study subject role borne by an entity realized by a process of leaving the study earlier than the protocol specified and where the bearer of the dropout role had been borne study subject role prior to bearing dropout role.
example of usage: Escaped rat; human who moved to another city. Rat which escapes part way through a study; a human study participant who moved to another city before the study was completed (and stopped participating in the study)
term editor: Role Branch
has obsolescence reason: IAO_0000103
has curation status: IAO_0000120

health care provider role
type: Class
subclass of: worker role
alternative term: health care provider
editor preferred term: health care provider role
term editor: Person:Jennifer Fostel
definition: a worker role of providing medical care either within or outside the study timeline
has curation status: IAO_0000120

methodology testing objective
type: Class
subclass of: objective specification
disjoint with: assay objective
disjoint with: material transformation objective
disjoint with: specimen creation objective
disjoint with: material maintenance objective
disjoint with: training objective
disjoint with: service provision objective
disjoint with: assay validation objective
disjoint with: selective organism creation objective
disjoint with: OBI_0200166
term editor: Jennifer Fostel
definition: Methodology_testing_objective is an objective role carried out by a proposition defining the aim of the study is to examine the effect of using different methodologies.
editor preferred term: methodology testing objective
has curation status: IAO_0000123

analytical cytology data file
type: Class
subclass of: information content entity
disjoint with: fluorescence compensation matrix
disjoint with: record of missing knowledge
disjoint with: sequence feature annotation
disjoint with: OBI_0302838
disjoint with: OBI_0302840
definition source: group:Flow Cytometry community
definition: A digital entity intended to capture data in analytical cytology domain.
example of usage: FCS file, ACS file, foo.fcs, foo.asc
editor preferred term: analytical cytology data file
term editor: person:Chris Stoeckert
has curation status: IAO_0000125

proxy respondent role
type: Class
subclass of: worker role
alternative term: proxy respondent
editor preferred term: proxy respondent role
term editor: Jennifer Fostel
definition: Proxy respondent is a worker role of describing patient's symptoms or condition to medical personnel
has curation status: IAO_0000120

fluorescence compensation matrix
type: Class
subclass of: information content entity
disjoint with: record of missing knowledge
disjoint with: sequence feature annotation
disjoint with: OBI_0302838
disjoint with: OBI_0302840
definition source: group:Flow Cytometry community
example of usage: ((1.053096, -0.22476), (-0.24877, 1.053096))
definition: A fluorescence compensation matrix is a square matrix which is used as the left multiplier of the vector of fluorescence values while performing digital fluorescence compensation. Also, fluorescence compensation matrix is the inverse of the fluorescence spillover matrix.
editor preferred term: fluorescence compensation matrix
term editor: person:Chris Stoeckert
has curation status: IAO_0000125

negative reference substance role
type: Class
subclass of: reference substance role
subclass of: Restriction
  on property: is realized by
  all values from: assay
disjoint with: nucleic acid template role
disjoint with: spike-in quality control role
disjoint with: dye swap quality control role
definition: a reference role in which the characteristics or responses elicited by the substance playing the reference substance role are used to establish a "no effect" response
alternative term: negative reference substance
editor preferred term: negative reference substance role
term editor: Person: Jennifer Fostel
example of usage: Saline solution
has curation status: IAO_0000123

role of legally acceptable representative
type: Class
subclass of: regulation-assigned role
term editor: Person:Helen Parkinson
definition: a role which inheres in a human or organization who are able subject to applicable law to consent, on behalf of a prospective subject, to the subject`s participation in as clinical trial.
alternative term: legally acceptable representative
editor preferred term: role of legally acceptable representative
definition source: OBI, CDISC
example of usage: Parent of minor patient; Definition of legally acceptable representative An individual or juridicial or other body authorized under applicable law to consent, on behalf of a prospective subject, to the subject`s participation in the clinical trial. http://www.geneed.com/website/catalog/glossary_search.php?id=2134&search_term=legally%20acceptable%20representative&select=TRUE
term editor: Person: Jennifer Fostel
editor note: legally acceptable representative. An individual or juridical or other body authorized under applicable law to consent, on behalf of a prospective subject, to the subject's participation in the clinical trial. [ICH, E6 Glossary]
has curation status: IAO_0000120

investigation results report
type: Class
subclass of: report
disjoint with: OBI_1110300
definition source: group:OBI
definition: An investigation report is a report on the results of an investigation.
editor preferred term: investigation results report
term editor: person:Chris Stoeckert
has curation status: IAO_0000125

cellular feature identification objective
type: Class
subclass of: biological feature identification objective
disjoint with: organism feature identification objective
definition: Cellular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the cellular level, e.g. stage of cell cycle, stage of differentiation.
term editor: Jennifer Fostel
editor preferred term: cellular feature identification objective
has curation status: IAO_0000123

reference subject role
type: Class
subclass of: study subject role
subclass of: Restriction
  on property: inheres in
  some values from: Class
    union of: OBI_0100026
    union of: OBI_0100051
disjoint with: to be treated with active ingredient role
disjoint with: to be treated with placebo role
alternative term: reference participant
editor preferred term: reference subject role
term editor: Jennifer Fostel
definition source: OBI
example of usage: Saline treated rat; one of three identically-treated subjects
definition: a reference subject role which inheres in an organism or entity of organismal origin so that the characteristics or responses of the participant playing the reference participant role are used for comparison or reference
has curation status: IAO_0000120

vital dye role
type: Class
subclass of: dye role
editor note: 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893048&group_id=177891&atid=886178
term editor: Person: Helen Parkinson
definition: The role of a dye that is realized when used in an experiment to stain live cells
example of usage: typtan blue has a vital dye
alternative term: vital dye
editor preferred term: vital dye role
term editor: Person: Jennifer Fostel
has curation status: IAO_0000120

obsolete_blinded medication role
type: Class
subclass of: ObsoleteClass
example of usage: 115 patients received ipilimumab and blinded medication
definition: Is a role which inheres in a material entity which is manufactured to be similar in appearance to a test material entity in e.g. a clinical trial to prevent participants from detecting which is the active and inactive substance
term editor: Person:Helen Parkinson
editor note: Will be modelled using a blinding process and specified output blinded medication instead
deprecated: true
editor preferred term: Blinded medication
example of usage: Inert pill shaped like aspirin tablet
term editor: Jennifer Fostel
has obsolescence reason: IAO_0000103
has curation status: IAO_0000120

sub-investigator role
type: Class
subclass of: worker role
alternative term: sub-investigator
editor preferred term: sub-investigator role
curator note: CDISC definition: Sub-investigator. Any member of the clinical trial team designated and supervised by the investigator at a trial site to perform critical trial-related procedures and/or to make important trial-related decisions (e.g., associates, residents, research fellows) [ICH] See associates, residents, research fellows
term editor: Person: Jennifer Fostel
definition: a worker role authorized to make study-related decisions and carry out tasks related to the study; this role occurs during the study timeline
has curation status: IAO_0000123

data encoding
type: Class
subclass of: documenting
disjoint with: OBI_0302914
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
curator note: We (protocol application branch) placed this term because it kept getting bounced from data transformation and DENRIE
definition: a documenting process to encode an information entity into a digital document
editor preferred term: data encoding
example of usage: storage of measurement results from an assay into a text file, such as
has curation status: IAO_0000120

enzymatic cleavage
type: Class
subclass of: material processing
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: Restriction
  on property: has_specified_input
  some values from: OBI_0100051
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: function
    intersection of: Restriction
      on property: inheres in
      some values from: enzyme
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
example of usage: Polymorphism R62W results in resistance of CD23 to enzymatic cleavage in cultured cells. Genes Immun. 2007 Apr;8(3):215-23. Epub 2007 Feb 15. PMID: 17301828
editor preferred term: enzymatic cleavage
definition: enzymatic cleavage is a protocol application to digest the fraction of input material that is susceptible to that enzyme
has curation status: IAO_0000125

hardware optimization objective
type: Class
subclass of: hardware testing objective
definition: Hardware_optimization is a hardware_testing_objective describing a study designed to identify the best hardware.
term editor: Jennifer Fostel
editor preferred term: hardware optimization objective
has curation status: IAO_0000123

obsolete_defined_material
type: Class
subclass of: ObsoleteClass
definition source: OBI Biomaterial derived
term editor: Susanna Sansone
editor note: false
deprecated: true
definition: Place holder class, Utility class to gather the defined classes
editor preferred term: _defined_material
has curation status: IAO_0000121
has obsolescence reason: IAO_0000226

trial statistician role
type: Class
subclass of: worker role
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0500001
  intersection of: Restriction
    on property: is realized by
    all values from: investigation
alternative term: trial statistician
editor preferred term: trial statistician role
curator note: CDISC definition: trial statistician. A statistician who has a combination of education/training and experience sufficient to implement the principles in the ICH E9 guidance and who is responsible for the statistical aspects of the trial. [ICH E9]
term editor: Person:Jennifer Fostel
definition: a worker role that analyzes data obtained during a trial or study; this role occurs after the trial or study is completed or terminated.
has curation status: IAO_0000123

standard error
type: Class
subclass of: quantitative confidence value
disjoint with: FWER adjusted p-value
disjoint with: OBI_0001442
definition source: group:OBI
definition: A quantitative confidence value which is the standard deviations of the sample in a frequency distribution, obtained by dividing the standard deviation by the total number of cases in the frequency distribution.
term editor: person:Chris Stoeckert
curator note: see P-Value
editor preferred term: standard error
has curation status: IAO_0000125

antigen role
type: Class
subclass of: role
subclass of: Restriction
  on property: is realized by
  all values from: immune response
disjoint with: analyte role
disjoint with: material to be added role
disjoint with: cloning insert role
disjoint with: target of material addition role
disjoint with: manufacturer role
disjoint with: pathogen role
disjoint with: host role
disjoint with: test substance role
disjoint with: complementary nucleotide probe role
disjoint with: service consumer role
disjoint with: service provider role
disjoint with: accessed material role
disjoint with: OBI_0302731
disjoint with: OBI_0302732
disjoint with: OBI_0302733
disjoint with: OBI_1110082
disjoint with: OBI_1110083
disjoint with: OBI_1110086
disjoint with: OBI_1110087
disjoint with: OBI_1110091
disjoint with: OBI_1110092
disjoint with: OBI_1110120
curator note: 9Mar09 waiting for discussion with immunology terms
editor note: An antigen is a substance that prompts the generation of antibodies and can cause an immune response. Wikipedia http://en.wikipedia.org/wiki/Antigen. In the strict sense, immunogens are those substances that elicit a response from the immune system, whereas antigens are defined as substances that bind to specific antibodies. Not all antigens produce an immunogenic response, but all immunogens are antigens
definition source: OBI
editor preferred term: antigen role
definition: Antigen is a role played by material which when introduced into an immune-competent organism causes an immune response
term editor: Role Branch
has curation status: IAO_0000123

software testing objective
type: Class
subclass of: methodology testing objective
term editor: Jennifer Fostel
definition: Software_testing_objective is a hardware_optimization role describing a study designed to examine the effects of using different software or software parameters, e.g. data processing software.
editor preferred term: software testing objective
has curation status: IAO_0000123

sponsor role
type: Class
subclass of: responsible party role
alternative term: sponsor
curator note: CDISC definition: sponsor. 1. An individual, company, institution, or organization that takes responsibility for the initiation, management, and/or financing of a clinical trial. 2. A corporation or agency whose employees conduct the investigation is considered a sponsor; employees are considered investigators
term editor: Person: Jennifer Fostel
definition: a responsible party role involved with any of the following activities: initiating, managing and funding a study
editor preferred term: sponsor role
has curation status: IAO_0000120

organization
type: Class
subclass of: material entity
disjoint with: eluate
disjoint with: polyacrylamide gel
disjoint with: agarose gel
disjoint with: scattered molecular aggregate
disjoint with: urine specimen
disjoint with: blood specimen
disjoint with: whole organism preparation
disjoint with: capsule shell
disjoint with: guar gum
disjoint with: cloacal specimen
disjoint with: nasopharyngeal aspirate specimen
disjoint with: nasal swab specimen
disjoint with: device
disjoint with: growth environment
disjoint with: OBI_0001468
disjoint with: OBI_0001485
disjoint with: OBI_0100014
disjoint with: OBI_0100016
disjoint with: OBI_0100017
disjoint with: OBI_0100055
disjoint with: OBI_0100058
disjoint with: OBI_0100060
disjoint with: OBI_0100067
disjoint with: OBI_0100086
disjoint with: OBI_1000023
disjoint with: OBI_1000024
disjoint with: OBI_1000029
disjoint with: OBI_1000036
disjoint with: OBI_1000042
definition source: GROUP: OBI
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Philippe Rocca-Serra
term editor: PERSON: Susanna Sansone
definition: An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
editor note: BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now.
example of usage: PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
editor preferred term: organization
has curation status: IAO_0000122

feed role
type: Class
subclass of: complete nutrient role
definition: a role that inheres in a material entity and is realized in the use of that material entity by lab animal to provide all needed nourishment.
alternative term: feed
editor preferred term: feed role
definition source: OBI
term editor: Person: Jennifer Fostel
example of usage: Purina rat chow; cited use: Control; F = feed (rat chow); W = water; F. g. = feed-ginger concentrate. www.academicjournals.org/AJB/PDF/pdf2007/19Sep/Egwurugwu%20et%20al.pdf - Feb 29, 2008
has curation status: IAO_0000120

technical replicate role
type: Class
subclass of: reference subject role
alternative term: technical replicate
editor preferred term: technical replicate role
definition: technical replicate role is realized when two portions from one evaluant are used in replicate runs of an assay
example of usage: Aliquots of a tissue subjected to parallel assays
term editor: Person: Jennifer Fostel
has curation status: IAO_0000123

dye role
type: Class
subclass of: label role
definition source: A substance used to color materials www.answers.com/topic/dye 19feb09
definition: Label role is a reagent role which inheres in a material entity and which is realized in the process of dyeing or imparting color to a target material
alternative term: dye
term editor: Jennifer Fostel
editor preferred term: dye role
has curation status: IAO_0000120

cluster
type: Class
subclass of: data set
definition source: group:OBI
definition: A data set which is a subset of data that are a similar to each other in some way.
example of usage: Cluster of the lymphocytes population.
editor preferred term: cluster
term editor: person:Allyson
term editor: person:Chris Stoeckert
has curation status: IAO_0000125

cohort role
type: Class
subclass of: biological replicate role
definition source: WEB:http://www.sceoc.com/glossaryofterms/ # a group of individuals having a statistical factor (as age or class membership) in common in a demographic study, such as a cohort of students.
definition source: WEB:http://www.thebody.org/content/treat/art2612.html # a group of individuals in a study who share a demographic, clinical, or other statistical characteristic (eg, age, study site).
definition source: WEB:http://www.uhhospitals.org/tabid/591/Default.aspx # A cohort is a group of people with a common characteristic that is studied over a period of time as part of a scientific or medical investigation.
editor preferred term: cohort role
example of usage: In statistics and demography, a cohort is a group of subjects - most often humans from a given population - defined by experiencing an event (typically birth) in a particular time span. Wikipedia "cohort", Feb 29 2008
term editor: Jennifer Fostel
definition: a cohort role is a biological replicate role played by a group of study participants who share a common characteristic of interest to the study.
has curation status: IAO_0000123

artificially induced nucleic acid hybridization
type: Class
subclass of: material processing
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
definition: Is a material transformation in which strands of nucleic acids that are (somewhat) complementary form a double-stranded molecule. Has input at least two single stranded molecules of nucleic acid molecules.
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
editor preferred term: artificially induced nucleic acid hybridization
example of usage: www.ornl.gov/sci/techresources/Human_Genome/publicat/97pr/09gloss.html, http://www.accessexcellence.org/RC/VL/GG/nucleic.html, http://omrf.ouhsc.edu/~frank/HYBNOTES.html. http://en.wikipedia.org/wiki/Nucleic_acid_hybridization,http://www.pnas.org/cgi/reprint/46/8/1044.pdf
has curation status: IAO_0000125

DNA extraction
type: Class
subclass of: OBI_0666667
subclass of: Restriction
  on property: has_specified_output
  some values from: deoxyribonucleic acids
disjoint with: OBI_0666666
definition: A DNA extraction is a nucleic acid extraction where the desired output material is DNA.
editor preferred term: DNA extraction
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
has curation status: IAO_0000123

plan
type: Class
subclass of: realizable entity
example of usage: The plan of researcher X to perform an experiment according to a protocol.
editor note: This class is included to make clear how the plan specification, the plan, and the planned process relate. OBI will however only subclass and work under the 'plan specification', and 'planned process' class, as we want to avoid to get deep into discussions of 'intend' etc.
definition: A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process.
term editor: AR, BP, JM, MC, PRS
definition source: branch derived
editor preferred term: plan
has curation status: IAO_0000125

obsolete_sample population
type: Class
subclass of: ObsoleteClass
editor note: 03/21/2010: BP, obsoleting this term, as it is duplicated by 'material sample'. Use that instead term instead, which now also has 'sample population' as an alternative label.
definition source: GROUP: OBI Biomaterial Branch
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Philippe Rocca-Serra
deprecated: true
definition: A sample population is an object aggregate that is selected from the population, e.g. the fish in the net that were sampled from the lake, the people that responded to the call for volunteers.
example of usage: Patterns of benzylpiperazine/trifluoromethylphenylpiperazine party pill use and adverse effects in a population sample in New Zealand. Drug Alcohol Rev. 2008 Mar 31:1-7. PMID: 18608458
alternative term: recruited population
editor preferred term: sample population
has curation status: IAO_0000120
has obsolescence reason: IAO_0000227

organism feature identification objective
type: Class
subclass of: biological feature identification objective
term editor: Jennifer Fostel
definition: Organism_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the level of the organism, e.g. height, weight, stage of development, stage of life cycle.
editor preferred term: organism feature identification objective
has curation status: IAO_0000123

number of lost events computer
type: Class
subclass of: measurement datum
disjoint with: survival rate
disjoint with: spike train datum
disjoint with: categorical measurement datum
disjoint with: dose
disjoint with: obsolete_general scalar measurement datum
disjoint with: 3D structural organization datum
definition source: Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
example of usage: 0, 125, 787 events lost due to computer busy.
definition: A measurement datum recording the number of measurement events lost due to overloading of the analysis chip in a flow cytometer instrument. The datum has a qualitative role
editor preferred term: number of lost events computer
term editor: person:Kevin Clancy
has curation status: IAO_0000120

protocol
type: Class
subclass of: plan specification
subclass of: Restriction
  on property: has part
  some values from: objective specification
disjoint with: OBI_0500000
definition source: OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
example of usage: PMID: 18388943.Nat Protoc. 2008;3(4):612-8.Protocol for the induction of arthritis in C57BL/6 mice.
term editor: PlanAndPlannedProcess Branch
definition: a protocol is a plan specification which has sufficient level of detail and quantitative information to communicate it between domain experts, so that different domain experts will reliably be able to independently reproduce the process.
editor preferred term: protocol
has curation status: IAO_0000122

role of regulator of consumables and medical devices
type: Class
subclass of: regulator role
alternative term: drug regulatoy authority
editor preferred term: role of regulator of consumables and medical devices
example of usage: FDA, EMEA; http://www.fda.gov/; The International Conference of Drug Regulatory Authorities (ICDRAs) provide drug regulatory authorities of WHO Member States with a forum to meet and discuss ways to strengthen collaboration.http://www.who.int/medicines/areas/quality_safety/regulation_legislation/icdra/en/index.html
definition source: OBI, CDISC
term editor: Person: Jennifer Fostel
definition: a regulator involved with making and enforcing legislation and governmental orders relevant to the development, testing, manufacture and use of food, drugs and medical devices
has curation status: IAO_0000120

adding a material entity into a target
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: adding material objective
subclass of: material combination
subclass of: Restriction
  on property: realizes
  some values from: target of material addition role
subclass of: Restriction
  on property: realizes
  some values from: material to be added role
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: is located in
      some values from: Class
        intersection of: material entity
        intersection of: Restriction
    intersection of: Restriction
      on property: has role
      some values from: material to be added role
term editor: BP
editor note: Class was renamed from 'administering substance', as this is commonly used only for additions into organisms.
example of usage: Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water.
editor preferred term: adding a material entity into a target
definition source: branch derived
definition: is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'.
has curation status: IAO_0000122

analyte role
type: Class
subclass of: role
subclass of: Restriction
  on property: is realized by
  all values from: analyte assay
disjoint with: material to be added role
disjoint with: cloning insert role
disjoint with: target of material addition role
disjoint with: manufacturer role
disjoint with: pathogen role
disjoint with: host role
disjoint with: test substance role
disjoint with: complementary nucleotide probe role
disjoint with: service consumer role
disjoint with: service provider role
disjoint with: accessed material role
disjoint with: OBI_0302731
disjoint with: OBI_0302732
disjoint with: OBI_0302733
disjoint with: OBI_1110082
disjoint with: OBI_1110083
disjoint with: OBI_1110086
disjoint with: OBI_1110087
disjoint with: OBI_1110091
disjoint with: OBI_1110092
disjoint with: OBI_1110120
curator note: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
term editor: GROUP: Role Branch
example of usage: Glucose in blood (measured in an assay to determine the concentration of glucose).
definition source: OBI
editor preferred term: analyte role
editor note: interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role
editor note: pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested.
editor note: qualities such as weight, color are not assayed but measured, so they do not fall into this category.
definition: Analyte role is a role borne by a molecular entity and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role
has curation status: IAO_0000122

disease stage
type: Class
subclass of: biological_process
subclass of: Restriction
  on property: is part of
  some values from: OGMS_0000022
disjoint with: OBI_0001588
disjoint with: OBI_0302901
disjoint with: OBI_1110061
disjoint with: OBI_1110111
disjoint with: OBI_1110122
term editor: PERSON: Bjoern peters
editor preferred term: disease stage
example of usage: Stage II breast cancer, The timepoint of recovery from a disease
definition: a part of an occurrence of a disease process which is associated with position in the normal progression of the disease
has curation status: IAO_0000123

intraperitoneal injection
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: realizes
    some values from: material to be added role
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: inheres in
        some values from: syringe
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: target of material addition role
      intersection of: Restriction
        on property: is role of
        some values from: UBERON_0002358
subclass of: injection
subclass of: intraperitoneal administration
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: adding material objective
term editor: BP
editor preferred term: intraperitoneal injection
definition: is the injection of a material entity (bearing the administered substance role) into the peritoneum (bearing the target role) of an organism using a syringe
has curation status: IAO_0000123

precipitate
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0600034
definition source: GROUP: OBI Biomaterial Branch
term editor: PERSON: Philippe Rocca-Serra
example of usage: Physicochemical properties and antibacterial activity of the precipitate of vancomycin and ceftazidime: implications in the management of endophthalmitis. Retina. 2008 Feb;28(2):320-5. PMID: 18301038
definition: a precipitate is a material entity which is output of a precipitation process
editor preferred term: precipitate
alternative term: precipited material
has curation status: IAO_0000120

protein-protein interaction detection
type: Class
subclass of: assay
editor note: 20091101, Bjoern Peters: This class may be overly broad. Lot's of assays would seem to classify under it, and I have the feeling that the intend would be to limit this to determining protein-protein interactions as they occur within an organism, rather than e.g. peptide:MHC binding assays.
definition: An assay with the objective to determine interactions between proteins, such as protein-protein binding.
editor preferred term: protein-protein interaction detection
has curation status: IAO_0000123

transcription factor binding site identification
type: Class
subclass of: binding assay
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: gene expression
        intersection of: sequence-specific DNA binding
definition source: OBI
term editor: Philippe Rocca-Serra
editor preferred term: transcription factor binding site identification
example of usage: Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms. Funct Integr Genomics. 2007 Oct;7(4):335-45. Epub 2007 Jul 19. PMID: 17638031
definition: a planned process with objective to find DNA region specifically recognized by proteins that function as transcription factors
has curation status: IAO_0000120

obsolete_enrollment
type: Class
subclass of: ObsoleteClass
editor note: merged with 'enrollment of human subjects
deprecated: true
term editor: Bjoern Peters
example of usage: Enrollment of patients in a study. Short-term outcome of neuropsychiatric events in systemic lupus erythematosus upon enrollment into an international inception cohort study. Arthritis Rheum. 2008 May 15;59(5):721-9. PMID: 18438902
definition source: IEDB
editor preferred term: enrollment
definition: enrollment is a process of identifying a set of objects for further use in an investigation based on a set of criteria or rules
has curation status: IAO_0000125
has obsolescence reason: IAO_0000227

adverse event trigger
type: Class
subclass of: conditional specification
definition source: OBI branch derived
term editor: PERSON:Alan Ruttenberg
editor preferred term: adverse event trigger
definition: revisit?
has curation status: IAO_0000125

eluate
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0302905
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: molecular entity
    intersection of: Restriction
      on property: has role
      some values from: OBI_0302732
disjoint with: polyacrylamide gel
disjoint with: agarose gel
disjoint with: scattered molecular aggregate
disjoint with: urine specimen
disjoint with: blood specimen
disjoint with: whole organism preparation
disjoint with: capsule shell
disjoint with: guar gum
disjoint with: cloacal specimen
disjoint with: nasopharyngeal aspirate specimen
disjoint with: nasal swab specimen
disjoint with: device
disjoint with: growth environment
disjoint with: OBI_0001468
disjoint with: OBI_0001485
disjoint with: OBI_0100014
disjoint with: OBI_0100016
disjoint with: OBI_0100017
disjoint with: OBI_0100055
disjoint with: OBI_0100058
disjoint with: OBI_0100060
disjoint with: OBI_0100067
disjoint with: OBI_0100086
disjoint with: OBI_1000023
disjoint with: OBI_1000024
disjoint with: OBI_1000029
disjoint with: OBI_1000036
disjoint with: OBI_1000042
definition source: OBI Bionaterial
term editor: PERSON: Philippe Rocca-Serra
example of usage: Raman spectroscopic detection of haemoproteins in the eluate from high-performance liquid chromatography. J Chromatogr. 1983 Jan 7;254:285-8. PMID: 6298263
definition: a eluate is a material entity which results from an elution, e.g. from a chromatography column. it has as part a material entity with role mobile phase
editor preferred term: eluate
alternative term: eluted material
editor note: need to add restriction to indicate: has_part some (material entity has_role mobile phase) need to add mobile phase as role
has curation status: IAO_0000120

material to be added role
type: Class
subclass of: role
subclass of: Restriction
  on property: is realized by
  all values from: adding a material entity into a target
disjoint with: cloning insert role
disjoint with: target of material addition role
disjoint with: manufacturer role
disjoint with: pathogen role
disjoint with: host role
disjoint with: test substance role
disjoint with: complementary nucleotide probe role
disjoint with: service consumer role
disjoint with: service provider role
disjoint with: accessed material role
disjoint with: OBI_0302731
disjoint with: OBI_0302732
disjoint with: OBI_0302733
disjoint with: OBI_1110082
disjoint with: OBI_1110083
disjoint with: OBI_1110086
disjoint with: OBI_1110087
disjoint with: OBI_1110091
disjoint with: OBI_1110092
disjoint with: OBI_1110120
curator note: 9 March 09 from discussion with PA branch
definition source: OBI
term editor: Role Branch
example of usage: drug added to a buffer contained in a tube; substance injected into an animal;
editor preferred term: material to be added role
definition: material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process
has curation status: IAO_0000120

obsolete_peritoneum
type: Class
subclass of: ObsoleteClass
editor preferred term: peritoneum
deprecated: true
editor note: BP: should be imported in the future, but I need it now to demonstrate how to define intraperitoneal injection
definition: is the serous membrane that forms the lining of the abdominal cavity
has curation status: IAO_0000002
has obsolescence reason: IAO_0000228

interpreting data
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: conclusion textual entity
definition source: Bjoern Peters
example of usage: Identifiying and removing outliers from data by eye. Examining data to and deriving a new hypothesis.
term editor: PERSON: Bjoern Peters
term editor: PERSON: Jennifer Fostel
editor preferred term: interpreting data
definition: the process of evaluating the data gathered in an investigation in the context of literature knowledge with the objective to generate more general conclusions or to identify what additional data is necessary to draw conclusions
has curation status: IAO_0000120

planning
type: Class
subclass of: process
subclass of: Class
  intersection of: process
  intersection of: Restriction
    on property: has participant
    some values from: plan specification
editor note: 7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'.
term editor: Bjoern Peters
definition source: Bjoern Peters
definition source: PPPB branch
editor preferred term: planning
example of usage: the process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment.
definition: a process of creating or modifying a plan.
has curation status: IAO_0000122

obsolete_documenting
type: Class
subclass of: ObsoleteClass
editor note: 6/11/9: Edited at workshop. Should go into IAO. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape
term editor: Bjoern Peters
term replaced by: IAO_0000572
example of usage: Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
editor preferred term: obsolete_documenting
deprecated: true
definition source: wikipedia http://en.wikipedia.org/wiki/Documenting
has obsolescence reason: IAO_0000103
has curation status: IAO_0000125
has obsolescence reason: IAO_0000228

histological sample preparation
type: Class
subclass of: material processing
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: Restriction
  on property: has_specified_input
  some values from: OBI_0100066
subclass of: Restriction
  on property: has participant
  some values from: OBI_0400168
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: specimen creation objective
definition source: OBI branch derived
term editor: PERSON:Bjoern Peters
editor preferred term: histological sample preparation
definition: histological sample preparation is the preparation of an input tissue via slicing and labeling to make tissue microstructure of interest visible in a future histology assay
has curation status: IAO_0000125

inductive reasoning
type: Class
subclass of: interpreting data
disjoint with: OBI_0001546
disjoint with: OBI_0001575
term editor: Bjoern Peters
editor preferred term: inductive reasoning
definition source: wikipedia: http://en.wikipedia.org/wiki/Inductive_reasoning
example of usage: Based on the observation that all lung cancer patients treated with aspirin in our clinical trial survived longer than the control group, we conclude by inductive reasining that aspirin has a therapeutic effect on lung cancer.
definition: a interpreting data that is used to ascribe properties or relations to types based on an observation instance (i.e., on a number of observations or experiences); or to formulate laws based on limited observations of recurring phenomenal patterns.
has curation status: IAO_0000120

mass analyzer
type: Class
subclass of: measurement device
subclass of: material separation device
subclass of: Restriction
  on property: has function
  some values from: measure function
disjoint with: ion source
disjoint with: ion detector
disjoint with: isoelectric focusing device
disjoint with: thermostatic circulator
disjoint with: blot module
disjoint with: gel dryer
disjoint with: syringe
disjoint with: needle
disjoint with: column chromatography detector
disjoint with: NMR sample holder
disjoint with: chromatography instrument
disjoint with: rapid resolution column
disjoint with: NMR tube washing system
disjoint with: NMR console
disjoint with: variable wavelength detector
disjoint with: multiple wavelength detector
disjoint with: NMR probe
disjoint with: NMR magnet
disjoint with: magic angle spinning rotor
disjoint with: Bruker SampleRail system
disjoint with: evaporative light scattering detector
disjoint with: autosampler
disjoint with: fluorescene detector
disjoint with: electrical conductivity detector
disjoint with: NMR instrument
disjoint with: refractive index detector
disjoint with: pulsed amperometric detector
disjoint with: glucometer
disjoint with: micro electrode
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner

hypothesis driven investigation
type: Class
subclass of: investigation
disjoint with: hypothesis generating investigation
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
editor preferred term: hypothesis driven investigation
definition: is an investigation with the goal to test one or more hypothesis
has curation status: IAO_0000125

hypothesis generating investigation
type: Class
subclass of: investigation
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
editor preferred term: hypothesis generating investigation
definition: is an investigation in which data is generated and analyzed with the purpose of generating new hypothesis
has curation status: IAO_0000125

ion source
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: ionization function
disjoint with: ion detector
disjoint with: isoelectric focusing device
disjoint with: thermostatic circulator
disjoint with: blot module
disjoint with: gel dryer
disjoint with: syringe
disjoint with: needle
disjoint with: column chromatography detector
disjoint with: NMR sample holder
disjoint with: chromatography instrument
disjoint with: rapid resolution column
disjoint with: NMR tube washing system
disjoint with: NMR console
disjoint with: variable wavelength detector
disjoint with: multiple wavelength detector
disjoint with: NMR probe
disjoint with: NMR magnet
disjoint with: magic angle spinning rotor
disjoint with: Bruker SampleRail system
disjoint with: evaporative light scattering detector
disjoint with: autosampler
disjoint with: fluorescene detector
disjoint with: electrical conductivity detector
disjoint with: NMR instrument
disjoint with: refractive index detector
disjoint with: pulsed amperometric detector
disjoint with: glucometer
disjoint with: micro electrode
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station

ion detector
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
disjoint with: isoelectric focusing device
disjoint with: thermostatic circulator
disjoint with: blot module
disjoint with: gel dryer
disjoint with: syringe
disjoint with: needle
disjoint with: column chromatography detector
disjoint with: NMR sample holder
disjoint with: chromatography instrument
disjoint with: rapid resolution column
disjoint with: NMR tube washing system
disjoint with: NMR console
disjoint with: variable wavelength detector
disjoint with: multiple wavelength detector
disjoint with: NMR probe
disjoint with: NMR magnet
disjoint with: magic angle spinning rotor
disjoint with: Bruker SampleRail system
disjoint with: evaporative light scattering detector
disjoint with: autosampler
disjoint with: fluorescene detector
disjoint with: electrical conductivity detector
disjoint with: NMR instrument
disjoint with: refractive index detector
disjoint with: pulsed amperometric detector
disjoint with: glucometer
disjoint with: micro electrode
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer

metabolite profiling
type: Class
subclass of: assay
subclass of: Restriction
  on property: has_specified_output
  some values from: measurement datum
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: has_specified_input
  some values from: OBI_0100051
definition source: OBI
term editor: Philippe Rocca-Serra
alternative term: metabolite assay
editor preferred term: metabolite profiling
example of usage: Metabolite profiling of human colon carcinoma - deregulation of TCA cycle and amino acid turnover. Mol Cancer. 2008 Sep 18;7(1):72. PMID: 18799019
definition: metabolite profiling is a process which aims at detecting and identifying chemical entities resulting from biochemical and cellular metabolism
has curation status: IAO_0000120

light emission function
type: Class
subclass of: excitation function
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
definition: A light emission function is an excitation function to excite a material to a specific excitation state that it emits light.
editor preferred term: light emission function
has curation status: IAO_0000122

record function
type: Class
subclass of: function
disjoint with: magnify function
disjoint with: contain function
disjoint with: heat function
disjoint with: material separation function
disjoint with: excitation function
disjoint with: freeze function
disjoint with: synthesizing function
disjoint with: perturb function
disjoint with: mechanical function
disjoint with: transfer function
disjoint with: ionization function
disjoint with: cool function
disjoint with: connection function
disjoint with: energy supply function
disjoint with: information processor function
disjoint with: solid support function
disjoint with: environment control function
disjoint with: measure function
disjoint with: consume data function
disjoint with: material combination function
disjoint with: sterilization function
disjoint with: reagent application function
disjoint with: specimen fixation function
disjoint with: current amplification function
disjoint with: stabilization function
disjoint with: OBI_0005246
disjoint with: OBI_1110016
disjoint with: OBI_1110085
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
definition: A record function is a function that registers or collects information in a particular format on a particular recording medium. For example on paper or a digital representation
editor preferred term: record function
has curation status: IAO_0000122

magnify function
type: Class
subclass of: function
disjoint with: contain function
disjoint with: heat function
disjoint with: material separation function
disjoint with: excitation function
disjoint with: freeze function
disjoint with: synthesizing function
disjoint with: perturb function
disjoint with: mechanical function
disjoint with: transfer function
disjoint with: ionization function
disjoint with: cool function
disjoint with: connection function
disjoint with: energy supply function
disjoint with: information processor function
disjoint with: solid support function
disjoint with: environment control function
disjoint with: measure function
disjoint with: consume data function
disjoint with: material combination function
disjoint with: sterilization function
disjoint with: reagent application function
disjoint with: specimen fixation function
disjoint with: current amplification function
disjoint with: stabilization function
disjoint with: OBI_0005246
disjoint with: OBI_1110016
disjoint with: OBI_1110085
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
definition: A magnify function is a function to increase the size of a transmitted object image through the precise arrangement of energy diffraction elements along an imaging path.
editor preferred term: magnify function
has curation status: IAO_0000122

contain function
type: Class
subclass of: function
disjoint with: heat function
disjoint with: material separation function
disjoint with: excitation function
disjoint with: freeze function
disjoint with: synthesizing function
disjoint with: perturb function
disjoint with: mechanical function
disjoint with: transfer function
disjoint with: ionization function
disjoint with: cool function
disjoint with: connection function
disjoint with: energy supply function
disjoint with: information processor function
disjoint with: solid support function
disjoint with: environment control function
disjoint with: measure function
disjoint with: consume data function
disjoint with: material combination function
disjoint with: sterilization function
disjoint with: reagent application function
disjoint with: specimen fixation function
disjoint with: current amplification function
disjoint with: stabilization function
disjoint with: OBI_0005246
disjoint with: OBI_1110016
disjoint with: OBI_1110085
example of usage: A syringe, a beaker
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
definition: A contain function is a function to constrain a material entities location in space
editor preferred term: contain function
has curation status: IAO_0000122

heat function
type: Class
subclass of: function
disjoint with: material separation function
disjoint with: excitation function
disjoint with: freeze function
disjoint with: synthesizing function
disjoint with: perturb function
disjoint with: mechanical function
disjoint with: transfer function
disjoint with: ionization function
disjoint with: cool function
disjoint with: connection function
disjoint with: energy supply function
disjoint with: information processor function
disjoint with: solid support function
disjoint with: environment control function
disjoint with: measure function
disjoint with: consume data function
disjoint with: material combination function
disjoint with: sterilization function
disjoint with: reagent application function
disjoint with: specimen fixation function
disjoint with: current amplification function
disjoint with: stabilization function
disjoint with: OBI_0005246
disjoint with: OBI_1110016
disjoint with: OBI_1110085
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
definition: A heat function is a function that increases the internal kinetic energy of a material
editor preferred term: heat function
has curation status: IAO_0000122

material separation function
type: Class
subclass of: function
disjoint with: excitation function
disjoint with: freeze function
disjoint with: synthesizing function
disjoint with: perturb function
disjoint with: mechanical function
disjoint with: transfer function
disjoint with: ionization function
disjoint with: cool function
disjoint with: connection function
disjoint with: energy supply function
disjoint with: information processor function
disjoint with: solid support function
disjoint with: environment control function
disjoint with: measure function
disjoint with: consume data function
disjoint with: material combination function
disjoint with: sterilization function
disjoint with: reagent application function
disjoint with: specimen fixation function
disjoint with: current amplification function
disjoint with: stabilization function
disjoint with: OBI_0005246
disjoint with: OBI_1110016
disjoint with: OBI_1110085
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
definition: A material separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality.
editor preferred term: material separation function
has curation status: IAO_0000122

ionize process
type: Class
subclass of: material processing
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: Restriction
  on property: has participant
  some values from: continuant
subclass of: Restriction
  on property: realizes
  some values from: ionization function
editor note: 2009-11-10. Tracker: http://en.wikipedia.org/wiki/Ionize
example of usage: Electrospray ionization in mass spectrometry
term editor: Person:Bjoern Peters
definition: a physical process of converting an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions. This excludes chemical processes of dissociation.
editor preferred term: ionize process
has curation status: IAO_0000123

excitation function
type: Class
subclass of: function
disjoint with: freeze function
disjoint with: synthesizing function
disjoint with: perturb function
disjoint with: mechanical function
disjoint with: transfer function
disjoint with: ionization function
disjoint with: cool function
disjoint with: connection function
disjoint with: energy supply function
disjoint with: information processor function
disjoint with: solid support function
disjoint with: environment control function
disjoint with: measure function
disjoint with: consume data function
disjoint with: material combination function
disjoint with: sterilization function
disjoint with: reagent application function
disjoint with: specimen fixation function
disjoint with: current amplification function
disjoint with: stabilization function
disjoint with: OBI_0005246
disjoint with: OBI_1110016
disjoint with: OBI_1110085
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
definition: A excitation function is a function to inject energy by bombarding a material with energetic particles (e.g., photons) thereby imbuing internal material components such as electrons with additional energy. These internal, 'excited' particles may lead to the rupturing of covalent chemical bonds or may quickly relax back to there unexcited state with an exponential time course thereby locally emitting energy in the form of photons.
editor preferred term: excitation function
has curation status: IAO_0000122

freeze function
type: Class
subclass of: function
disjoint with: synthesizing function
disjoint with: perturb function
disjoint with: mechanical function
disjoint with: transfer function
disjoint with: ionization function
disjoint with: cool function
disjoint with: connection function
disjoint with: energy supply function
disjoint with: information processor function
disjoint with: solid support function
disjoint with: environment control function
disjoint with: measure function
disjoint with: consume data function
disjoint with: material combination function
disjoint with: sterilization function
disjoint with: reagent application function
disjoint with: specimen fixation function
disjoint with: current amplification function
disjoint with: stabilization function
disjoint with: OBI_0005246
disjoint with: OBI_1110016
disjoint with: OBI_1110085
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
definition: A freeze function is a function to decrease the internal kinetic energy of a material below the freezing point of that type of material.
editor preferred term: freeze function
has curation status: IAO_0000122

synthesizing function
type: Class
subclass of: function
disjoint with: perturb function
disjoint with: mechanical function
disjoint with: transfer function
disjoint with: ionization function
disjoint with: cool function
disjoint with: connection function
disjoint with: energy supply function
disjoint with: information processor function
disjoint with: solid support function
disjoint with: environment control function
disjoint with: measure function
disjoint with: consume data function
disjoint with: material combination function
disjoint with: sterilization function
disjoint with: reagent application function
disjoint with: specimen fixation function
disjoint with: current amplification function
disjoint with: stabilization function
disjoint with: OBI_0005246
disjoint with: OBI_1110016
disjoint with: OBI_1110085
definition: A synthesizing function is a function to assemble new output materials from distinct input materials. The output materials typically consist of chemically distinct monomeric objects or object aggregate polymers.
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
editor preferred term: synthesizing function
has curation status: IAO_0000122

perturb function
type: Class
subclass of: function
disjoint with: mechanical function
disjoint with: transfer function
disjoint with: ionization function
disjoint with: cool function
disjoint with: connection function
disjoint with: energy supply function
disjoint with: information processor function
disjoint with: solid support function
disjoint with: environment control function
disjoint with: measure function
disjoint with: consume data function
disjoint with: material combination function
disjoint with: sterilization function
disjoint with: reagent application function
disjoint with: specimen fixation function
disjoint with: current amplification function
disjoint with: stabilization function
disjoint with: OBI_0005246
disjoint with: OBI_1110016
disjoint with: OBI_1110085
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
definition: A perturb function is a function that disrupts the normal function of a system induced through either internal or external means. External means of perturbation include: (1) displacement fields in the physical sense - e.g., temperature change, osmotic shock, pressure change; (2) application of small molecules such as drugs or toxins to perturb the function of specific pathways or application of surfactants to perturb the normal function of plasma membrane. Internal means of perturbation include: (1) manipulation of gene function via gene knockout or transcript knockdown via RNAi; (2) directed genetic mutation leading to minimal aa alterations that interfere with peptide function.
definition source: http://en.wikipedia.org/wiki/Perturbation_biology
editor preferred term: perturb function
has curation status: IAO_0000122

filter function
type: Class
subclass of: material separation function
disjoint with: sort function
term editor: Frank Gibson
definition: A filter function is a function to prevent the flow of certain entities based on a quality or qualities of the entity while allowing entities which have different qualities to pass through
editor preferred term: filter function
has curation status: IAO_0000122

mechanical function
type: Class
subclass of: function
disjoint with: transfer function
disjoint with: ionization function
disjoint with: cool function
disjoint with: connection function
disjoint with: energy supply function
disjoint with: information processor function
disjoint with: solid support function
disjoint with: environment control function
disjoint with: measure function
disjoint with: consume data function
disjoint with: material combination function
disjoint with: sterilization function
disjoint with: reagent application function
disjoint with: specimen fixation function
disjoint with: current amplification function
disjoint with: stabilization function
disjoint with: OBI_0005246
disjoint with: OBI_1110016
disjoint with: OBI_1110085
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
definition: A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force).
definition source: http://en.wikipedia.org/wiki/Mechanical_work
editor preferred term: mechanical function
has curation status: IAO_0000122

gas filter function
type: Class
subclass of: filter function
disjoint with: liquid filter function
term editor: Frank Gibson
definition: A gas filter function is a filter function which prevents the flow of solid objects, defined by specific qualities, in a gas-solid mixture
editor preferred term: gas filter function
has curation status: IAO_0000122

liquid filter function
type: Class
subclass of: filter function
term editor: Frank Gibson
definition: A liquid filter function is a filter function which prevents the flow of solid objects, defined by specific qualities, in a liquid-solid mixture
editor preferred term: liquid filter function
has curation status: IAO_0000122

transfer function
type: Class
subclass of: function
disjoint with: ionization function
disjoint with: cool function
disjoint with: connection function
disjoint with: energy supply function
disjoint with: information processor function
disjoint with: solid support function
disjoint with: environment control function
disjoint with: measure function
disjoint with: consume data function
disjoint with: material combination function
disjoint with: sterilization function
disjoint with: reagent application function
disjoint with: specimen fixation function
disjoint with: current amplification function
disjoint with: stabilization function
disjoint with: OBI_0005246
disjoint with: OBI_1110016
disjoint with: OBI_1110085
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
definition: A transfer function is a function to displace a material from one location to another.
editor preferred term: transfer function
has curation status: IAO_0000122

electricity supply function
type: Class
subclass of: energy supply function
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
example of usage: the function of supplying current during a neuroscience experiment.
definition: An electricity supply function is an energy supply function to transfer electricity from one source to another, typically a consumer of the electricity or as a stimulus during a neuroscience experiment.
editor preferred term: electricity supply function
alternative term: power supply
has curation status: IAO_0000122

ionization function
type: Class
subclass of: function
disjoint with: cool function
disjoint with: connection function
disjoint with: energy supply function
disjoint with: information processor function
disjoint with: solid support function
disjoint with: environment control function
disjoint with: measure function
disjoint with: consume data function
disjoint with: material combination function
disjoint with: sterilization function
disjoint with: reagent application function
disjoint with: specimen fixation function
disjoint with: current amplification function
disjoint with: stabilization function
disjoint with: OBI_0005246
disjoint with: OBI_1110016
disjoint with: OBI_1110085
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
example of usage: The ion source in amass spectrometer
definition: An ionization function is a function to physically convert an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions.
definition source: http://en.wikipedia.org/wiki/Ionization
editor preferred term: ionization function
has curation status: IAO_0000122

cool function
type: Class
subclass of: function
disjoint with: connection function
disjoint with: energy supply function
disjoint with: information processor function
disjoint with: solid support function
disjoint with: environment control function
disjoint with: measure function
disjoint with: consume data function
disjoint with: material combination function
disjoint with: sterilization function
disjoint with: reagent application function
disjoint with: specimen fixation function
disjoint with: current amplification function
disjoint with: stabilization function
disjoint with: OBI_0005246
disjoint with: OBI_1110016
disjoint with: OBI_1110085
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
definition: A cool function is a function to decrease the internal kinetic energy of a material below the initial kinetic energy of that type of material.
editor preferred term: cool function
has curation status: IAO_0000122

connection function
type: Class
subclass of: function
disjoint with: energy supply function
disjoint with: information processor function
disjoint with: solid support function
disjoint with: environment control function
disjoint with: measure function
disjoint with: consume data function
disjoint with: material combination function
disjoint with: sterilization function
disjoint with: reagent application function
disjoint with: specimen fixation function
disjoint with: current amplification function
disjoint with: stabilization function
disjoint with: OBI_0005246
disjoint with: OBI_1110016
disjoint with: OBI_1110085
example of usage: An electricity cable
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
definition: A connection function is a function to couple two or more flow channels so that material or signals can be transported from one set of channels to another.
editor preferred term: connection function
has curation status: IAO_0000122

isoelectric focusing device
type: Class
subclass of: container
subclass of: environmental control device
subclass of: Restriction
  on property: has function
  some values from: contain function
disjoint with: thermostatic circulator
disjoint with: blot module
disjoint with: gel dryer
disjoint with: syringe
disjoint with: needle
disjoint with: column chromatography detector
disjoint with: NMR sample holder
disjoint with: chromatography instrument
disjoint with: rapid resolution column
disjoint with: NMR tube washing system
disjoint with: NMR console
disjoint with: variable wavelength detector
disjoint with: multiple wavelength detector
disjoint with: NMR probe
disjoint with: NMR magnet
disjoint with: magic angle spinning rotor
disjoint with: Bruker SampleRail system
disjoint with: evaporative light scattering detector
disjoint with: autosampler
disjoint with: fluorescene detector
disjoint with: electrical conductivity detector
disjoint with: NMR instrument
disjoint with: refractive index detector
disjoint with: pulsed amperometric detector
disjoint with: glucometer
disjoint with: micro electrode
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer

thermostatic circulator
type: Class
subclass of: container
subclass of: environmental control device
subclass of: Restriction
  on property: has function
  some values from: contain function
disjoint with: blot module
disjoint with: gel dryer
disjoint with: syringe
disjoint with: needle
disjoint with: column chromatography detector
disjoint with: NMR sample holder
disjoint with: chromatography instrument
disjoint with: rapid resolution column
disjoint with: NMR tube washing system
disjoint with: NMR console
disjoint with: variable wavelength detector
disjoint with: multiple wavelength detector
disjoint with: NMR probe
disjoint with: NMR magnet
disjoint with: magic angle spinning rotor
disjoint with: Bruker SampleRail system
disjoint with: evaporative light scattering detector
disjoint with: autosampler
disjoint with: fluorescene detector
disjoint with: electrical conductivity detector
disjoint with: NMR instrument
disjoint with: refractive index detector
disjoint with: pulsed amperometric detector
disjoint with: glucometer
disjoint with: micro electrode
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader

energy supply function
type: Class
subclass of: function
disjoint with: information processor function
disjoint with: solid support function
disjoint with: environment control function
disjoint with: measure function
disjoint with: consume data function
disjoint with: material combination function
disjoint with: sterilization function
disjoint with: reagent application function
disjoint with: specimen fixation function
disjoint with: current amplification function
disjoint with: stabilization function
disjoint with: OBI_0005246
disjoint with: OBI_1110016
disjoint with: OBI_1110085
term editor: Frank Gibson
definition: An energy supply function is a function to supply or transfer energy from an energy source to a consumer of the energy
editor preferred term: energy supply function
has curation status: IAO_0000122

information processor function
type: Class
subclass of: function
subclass of: Restriction
  on property: has part
  some values from: consume data function
subclass of: Restriction
  on property: has part
  some values from: measure function
disjoint with: solid support function
disjoint with: environment control function
disjoint with: measure function
disjoint with: consume data function
disjoint with: material combination function
disjoint with: sterilization function
disjoint with: reagent application function
disjoint with: specimen fixation function
disjoint with: current amplification function
disjoint with: stabilization function
disjoint with: OBI_0005246
disjoint with: OBI_1110016
disjoint with: OBI_1110085
term editor: Frank Gibson
definition: An information processor function is a function that converts information from one form to another, by a lossless process or an extraction process.
alternative term: data processor function
editor preferred term: information processor function
has curation status: IAO_0000122

signal conversion function
type: Class
subclass of: information processor function
disjoint with: display function
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
alternative term: transduction function
definition: A signal conversion function is an information processor function which transforms a signal into another type of signal. For example an analog-to-digital_converter, Ac/Ac converter, a synapse converts electrical action potentials into an intermediate chemical signal. The post synapse converts it back into an electric one passed on to the axon.
editor preferred term: signal conversion function
has curation status: IAO_0000122

blot module
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: transfer function
disjoint with: gel dryer
disjoint with: syringe
disjoint with: needle
disjoint with: column chromatography detector
disjoint with: NMR sample holder
disjoint with: chromatography instrument
disjoint with: rapid resolution column
disjoint with: NMR tube washing system
disjoint with: NMR console
disjoint with: variable wavelength detector
disjoint with: multiple wavelength detector
disjoint with: NMR probe
disjoint with: NMR magnet
disjoint with: magic angle spinning rotor
disjoint with: Bruker SampleRail system
disjoint with: evaporative light scattering detector
disjoint with: autosampler
disjoint with: fluorescene detector
disjoint with: electrical conductivity detector
disjoint with: NMR instrument
disjoint with: refractive index detector
disjoint with: pulsed amperometric detector
disjoint with: glucometer
disjoint with: micro electrode
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave

signal amplification function
type: Class
subclass of: signal conversion function
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
definition: A signal amplification function is a signal conversion function to inject energy into an input signal so as to produce an output signal with increased differential magnitude while also seeking to minimize increases in the signal to noise ratio. For example, to produce a 0.1 KW output signal from a 1 mW RMS input signal.
editor preferred term: signal amplification function
has curation status: IAO_0000122

image acquisition function
type: Class
subclass of: measure function
subclass of: Restriction
  on property: is realized by
  all values from: image acquisition
subclass of: Restriction
  on property: inheres in
  some values from: image acquisition device
term editor: Frank Gibson
definition: An image acquisition function is a function to acquire an image of a material
editor preferred term: image acquisition function
has curation status: IAO_0000122

image acquisition device
type: Class
equivalent class: Class
  intersection of: device
  intersection of: Restriction
    on property: has function
    some values from: image acquisition function
subclass of: measurement device
term editor: Frank Gibson
definition source: sep:00096
definition: An image acquisition device is a device which captures a digitized image of an object
editor preferred term: image acquisition device
has curation status: IAO_0000123

solid support function
type: Class
subclass of: function
disjoint with: environment control function
disjoint with: measure function
disjoint with: consume data function
disjoint with: material combination function
disjoint with: sterilization function
disjoint with: reagent application function
disjoint with: specimen fixation function
disjoint with: current amplification function
disjoint with: stabilization function
disjoint with: OBI_0005246
disjoint with: OBI_1110016
disjoint with: OBI_1110085
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
example of usage: Taped, glued, pinned, dried or molecularly bonded to a solid support
editor preferred term: solid support function
definition: A solid support function is a function of a device on which an entity is kept in a defined position and prevented in its movement
has curation status: IAO_0000122

display function
type: Class
subclass of: information processor function
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
definition: A display function is a function to present information by translating that information through some lookup process into visual form.
editor preferred term: display function
has curation status: IAO_0000122

environment control function
type: Class
subclass of: function
disjoint with: measure function
disjoint with: consume data function
disjoint with: material combination function
disjoint with: sterilization function
disjoint with: reagent application function
disjoint with: specimen fixation function
disjoint with: current amplification function
disjoint with: stabilization function
disjoint with: OBI_0005246
disjoint with: OBI_1110016
disjoint with: OBI_1110085
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
definition: An environmental control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature.
editor preferred term: environment control function
has curation status: IAO_0000122

sort function
type: Class
subclass of: material separation function
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
definition: A sort function is a function to distinguish material components based on some associated physical quality or entity and to partition the separate components into distinct fractions according to a defined order.
editor preferred term: sort function
has curation status: IAO_0000122

gel dryer
type: Class
subclass of: container
subclass of: environmental control device
subclass of: Restriction
  on property: has function
  some values from: contain function
disjoint with: syringe
disjoint with: needle
disjoint with: column chromatography detector
disjoint with: NMR sample holder
disjoint with: chromatography instrument
disjoint with: rapid resolution column
disjoint with: NMR tube washing system
disjoint with: NMR console
disjoint with: variable wavelength detector
disjoint with: multiple wavelength detector
disjoint with: NMR probe
disjoint with: NMR magnet
disjoint with: magic angle spinning rotor
disjoint with: Bruker SampleRail system
disjoint with: evaporative light scattering detector
disjoint with: autosampler
disjoint with: fluorescene detector
disjoint with: electrical conductivity detector
disjoint with: NMR instrument
disjoint with: refractive index detector
disjoint with: pulsed amperometric detector
disjoint with: glucometer
disjoint with: micro electrode
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave

primer role
type: Class
subclass of: complementary nucleotide probe role
subclass of: Restriction
  on property: is realized by
  all values from: polymerase chain reaction
definition source: (cell and molecular biology) A short strand of RNA that is synthesized along single-stranded DNA during replication, initiating DNA polymerase-catalyzed synthesis of the complementary strand. http://www.answers.com/topic/rna-primer
definition: a complementary nucleotide probe role which inheres in nucleic acid molecular entity and is realized by the use of the entity bearing the role to initiate chain elongation.
editor preferred term: primer role
has curation status: IAO_0000123

PCR product
type: Class
equivalent class: Class
  intersection of: double-stranded DNA
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: polymerase chain reaction
subclass of: double-stranded DNA
subclass of: amplified DNA
term editor: GROUP: OBI BIomaterial Branch
definition source: GROUP: OBI BIomaterial Branch
example of usage: PCR products are the results of amplifcation process. Detection of a PCR products is used to detect DNA and RNA.
editor preferred term: PCR product
editor note: We are using PCR and not the written out words, as this is the most common used.
definition: is double stranded DNA that is the specified output of a polymerase chain reaction
has curation status: IAO_0000122

viral RNA extraction
type: Class
subclass of: OBI_0666666
subclass of: Restriction
  on property: has_specified_input
  some values from: Viruses
disjoint with: polyA RNA extraction
disjoint with: organellar RNA extraction
disjoint with: total RNA extraction
disjoint with: cytoplasmic RNA extraction
disjoint with: nuclear RNA extraction
term editor: Person:Bjoern Peters
example of usage: The AccuPrepTM Viral RNA Extraction Kit is designed for the rapid and convenient extraction of viral RNA from cell-free samples as serum, plasma, CSF, urine, etc - http://www.biokits.com/moreinfos.html?id=2703
definition: The extraction of RNA from an input material that specifically isolates viral RNA
editor preferred term: viral RNA extraction
has curation status: IAO_0000123

nucleic acid template role
type: Class
subclass of: reference substance role
subclass of: Restriction
  on property: is realized by
  all values from: polymerase chain reaction
subclass of: Restriction
  on property: inheres in
  some values from: nucleic acid
disjoint with: spike-in quality control role
disjoint with: dye swap quality control role
example of usage: a model or standard for making comparisons; wordnet.princeton.edu/perl/webwn 19 feb 2009
definition: a reference substance role which inheres in nucleic acid material entity and is realized in the process of using the nucleic acid bearing the template role as a reference during synthesis of a reverse copy.
editor preferred term: nucleic acid template role
has curation status: IAO_0000123

recombinant plasmid
type: Class
equivalent class: Class
  intersection of: plasmid
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: OBI_0600064
subclass of: plasmid
subclass of: recombinant vector
definition source: GROUP: OBI Biomaterial Branch
term editor: PERSON: Bjoern Peters
term editor: PERSON: Kevin Clancy
term editor: PERSON: Melanie Courtot
definition: a plasmid in which extraneous DNA has been inserted.
editor preferred term: recombinant plasmid
has curation status: IAO_0000120

cloning vector role
type: Class
subclass of: biological vector role
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: nucleic acid
  intersection of: Restriction
    on property: is realized by
    all values from: OBI_0600064
term editor: PERSON: Helen Parkinson
editor preferred term: cloning vector role
example of usage: pBluescript plays the role of a cloning vector
definition: a vector role played by a small, self-replicating DNA or RNA molecule - usually a plasmid or chromosome - and realized in a process whereby foreign DNA or RNA is inserted into the vector during the process of cloning.
has curation status: IAO_0000123

cell cycle synchronization
type: Class
subclass of: material processing
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: Restriction
  on property: has_specified_output
  some values from: OBI_0100060
subclass of: Restriction
  on property: has_specified_input
  some values from: OBI_0100060
definition source: Bjoern Peters and Nicole Washington
term editor: OBI PA
editor preferred term: cell cycle synchronization
example of usage: Elimination of serum from the culture medium for about 24 hours results in the accumulation of cells at G1 phase. This effect of nutritional deprivation can be restored by their addition by which time the cell synchrony occurs.
definition: a process with the objective to obtain a cell culture in which all cells are in the same stage of the cell cycle
has curation status: IAO_0000120

polymerase chain reaction
type: Class
subclass of: OBI_0600058
subclass of: Restriction
  on property: has_specified_input
  some values from: deoxyribonucleic acids
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: synthesizing function
    intersection of: Restriction
      on property: inheres in
      some values from: DNA polymerase complex
subclass of: Restriction
  on property: has_specified_output
  some values from: PCR product
disjoint with: reverse transcribed polymerase chain reaction
disjoint with: OBI_0001494
disjoint with: OBI_0600049
disjoint with: OBI_0600057
term editor: OBI Plan
definition source: adapted from wikipedai
editor preferred term: polymerase chain reaction
example of usage: Opisthorchis viverrini: Detection by polymerase chain reaction (PCR) in human stool samples. Exp Parasitol. 2008 Sep 9. PMID: 18805413
alternative term: PCR
definition: PCR is the process in which a DNA polymerase is used to amplify a piece of DNA by in vitro enzymatic replication. As PCR progresses, the DNA thus generated is itself used as a template for replication. This sets in motion a chain reaction in which the DNA template is exponentially amplified.
has curation status: IAO_0000123

cloning insert role
type: Class
subclass of: role
disjoint with: target of material addition role
disjoint with: manufacturer role
disjoint with: pathogen role
disjoint with: host role
disjoint with: test substance role
disjoint with: complementary nucleotide probe role
disjoint with: service consumer role
disjoint with: service provider role
disjoint with: accessed material role
disjoint with: OBI_0302731
disjoint with: OBI_0302732
disjoint with: OBI_0302733
disjoint with: OBI_1110082
disjoint with: OBI_1110083
disjoint with: OBI_1110086
disjoint with: OBI_1110087
disjoint with: OBI_1110091
disjoint with: OBI_1110092
disjoint with: OBI_1110120
editor note: Feb 20, 2009. from Wikipedia: cloning of any DNA fragment essentially involves four steps: DNA fragmentation with restriction endonucleases, ligation of DNA fragments to a vector, transfection, and screening/selection. There are multiple processes involved, it is not just "cloning process"
term editor: GROUP: Role branch
definition source: OBII and Wikipedia
editor preferred term: cloning insert role
definition: cloning insert role is a role which inheres in DNA or RNA and is realized by the process of being inserted into a cloning vector in a cloning process.
has curation status: IAO_0000121

measuring glucose concentration in blood serum
type: Class
subclass of: analyte assay
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: evaluant role
    intersection of: Restriction
      on property: is role of
      some values from: OBI_0100017
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: analyte role
    intersection of: Restriction
      on property: is role of
      some values from: glucose
definition: An assay that determines the concentration of glucose molecules in a blood serum sample
term editor: Person:Bjoern Peters
editor preferred term: measuring glucose concentration in blood serum
has curation status: IAO_0000123

reverse transcriptase
type: Class
equivalent class: Class
  intersection of: enzyme
  intersection of: Restriction
    on property: has function
    some values from: RNA-directed DNA polymerase activity
subclass of: enzyme
definition source: group:OBI
term editor: person:Melanie Courtot
definition: enzyme and has_function some GO:0003964 (RNA-directed DNA polymerase activity)
editor preferred term: reverse transcriptase
has curation status: IAO_0000125

obsolete_trypsinized material
type: Class
subclass of: ObsoleteClass
definition: A material entity that has undergone a process of digestion with trypsin
example of usage: A trypsinized suspension of cells
term editor: Person:Bjoern Peters
editor note: decided to be deprecated on Aug 2, 2010 dev call
editor preferred term: obsolete_trypsinized material
deprecated: true
curator note: Test Class: to evaluate OBI design pattern
has curation status: IAO_0000002
has obsolescence reason: IAO_0000103

syringe
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: transfer function
disjoint with: needle
disjoint with: column chromatography detector
disjoint with: NMR sample holder
disjoint with: chromatography instrument
disjoint with: rapid resolution column
disjoint with: NMR tube washing system
disjoint with: NMR console
disjoint with: variable wavelength detector
disjoint with: multiple wavelength detector
disjoint with: NMR probe
disjoint with: NMR magnet
disjoint with: magic angle spinning rotor
disjoint with: Bruker SampleRail system
disjoint with: evaporative light scattering detector
disjoint with: autosampler
disjoint with: fluorescene detector
disjoint with: electrical conductivity detector
disjoint with: NMR instrument
disjoint with: refractive index detector
disjoint with: pulsed amperometric detector
disjoint with: glucometer
disjoint with: micro electrode
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument

extract
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0302884
definition source: GROUP: OBI Biomatrial Branch
term editor: PERSON: Philippe Rocca-Serra
example of usage: Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923
definition: an extract is a material entity which results from an extraction process
editor preferred term: extract
alternative term: extracted material
has curation status: IAO_0000120

transcription profiling assay
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: transcription profiling identification objective
subclass of: analyte assay
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measured expression level
    intersection of: Restriction
      on property: is about
      some values from: gene expression
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: gene expression
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: analyte role
    intersection of: Restriction
      on property: is role of
      some values from: ribonucleic acids
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: OBI_0100051
    intersection of: Restriction
      on property: has part
      some values from: ribonucleic acids
definition source: OBI
term editor: Philippe Rocca-Serra
editor preferred term: transcription profiling assay
definition: An assay which aims to provide information about gene expression and transcription activity using ribonucleic acids collected from a material entity using a range of techniques and instrument such as DNA sequencers, DNA microarrays, Northern Blot
example of usage: Whole genome transcription profiling of Anaplasma phagocytophilum in human and tick host cells by tiling array analysis. BMC Genomics. 2008 Jul 31;9:364. PMID: 18671858
alternative term: gene expression profiling
has curation status: IAO_0000120

averaging objective
type: Class
subclass of: OBI_0200166
disjoint with: fuzzy clustering objective
disjoint with: statistical hypothesis test objective
disjoint with: decision tree induction objective
disjoint with: pattern matching objective
disjoint with: OBI_0200005
disjoint with: OBI_0200031
disjoint with: OBI_0200078
disjoint with: OBI_0200081
disjoint with: OBI_0200083
disjoint with: OBI_0200091
disjoint with: OBI_0200157
disjoint with: OBI_0200167
disjoint with: OBI_0200168
disjoint with: OBI_0200172
disjoint with: OBI_0200174
disjoint with: OBI_0200177
disjoint with: OBI_0200178
disjoint with: OBI_0200179
disjoint with: OBI_0200180
disjoint with: OBI_0200183
disjoint with: OBI_0200189
disjoint with: OBI_0200196
disjoint with: OBI_0200197
term editor: Elisabetta Manduchi
definition source: PERSON: Elisabetta Manduchi
example of usage: A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment.
definition: An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation.
term editor: James Malone
editor preferred term: averaging objective
has curation status: IAO_0000122

injection
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: realizes
    some values from: material to be added role
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: inheres in
        some values from: syringe
subclass of: adding a material entity into a target
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: adding material objective
definition source: OBI Biomaterial
term editor: Philippe Rocca-Serra
editor preferred term: injection
example of usage: Multiple Small-Dose Injections Can Reduce the Passage of Sclerosant Foam into Deep Veins During Foam Sclerotherapy for Varicose Veins. Eur J Vasc Endovasc Surg. 2008 Oct 13. PMID: 18922712
definition: injection is process which aims at introducing a compound or a mixture into a material entity (either biological entity or instrument) by relying on devices such as syringe or injector connection, attached or forced into a vascular system (veins of an organism or tubes of a machine) or in a tissue.
has curation status: IAO_0000120

enzyme
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Class
    union of: ribonucleic acids
    union of: protein complex
    union of: PR_000000001
    union of: Restriction
      on property: has part
      some values from: ribonucleic acids
    union of: Restriction
      on property: has part
      some values from: protein complex
    union of: Restriction
      on property: has part
      some values from: PR_000000001
  intersection of: Restriction
    on property: has function
    some values from: catalytic activity
subclass of: material entity
definition source: GROUP:OBI
editor note: MC: known issue: enzyme doesn't classify under material entity for now as it isn't stated that anything that has_part some material entity is a material entity. If we add as equivalent classes to material entity has_part some material entity and part_of some material entity (each one in his own necessary and sufficient block) Pellet in P3 doesn't classify any more.
term editor: person: Melanie Courtot
definition: (protein or rna) or has_part (protein or rna) and has_function some GO:0003824 (catalytic activity)
editor preferred term: enzyme
has curation status: IAO_0000125

intraperitoneal administration
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: realizes
    some values from: material to be added role
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: target of material addition role
      intersection of: Restriction
        on property: is role of
        some values from: UBERON_0002358
subclass of: OBI_0600007
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: adding material objective
term editor: Person:Bjoern Peters
example of usage: Rats were injected intraperitoneally with either rrIL-6 (250 ng/0.5 ml) or equal-volume sterile saline twice within an interval of 24 h
definition: The administration of a substance into the peritoneum of an organism
editor preferred term: intraperitoneal administration
has curation status: IAO_0000123

plasmid
type: Class
equivalent class: Class
  intersection of: double-stranded DNA
  intersection of: Restriction
    on property: has function
    some values from: Restriction
      on property: is realized by
      all values from: gene expression
  intersection of: Restriction
    on property: has quality
    some values from: SO_0000988
subclass of: double-stranded DNA
definition source: group:OBI
term editor: person:Melanie Courtot
editor preferred term: plasmid
definition: plasmid = DNA and has_quality circular and has_function (is_realized_as some gene expression) GO:0010467
has curation status: IAO_0000125

injection into organ section
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: realizes
    some values from: material to be added role
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: inheres in
        some values from: syringe
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: target of material addition role
      intersection of: Restriction
        on property: is role of
        some values from: OBI_0100066
subclass of: injection
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: adding material objective
definition: A process in which an input substance is injected into a organ section.
term editor: Person:Bjoern Peters
example of usage: Staining a specimen of human lung tissue with hematoxylin and eosin in order as a preparative step in histology
editor preferred term: injection into organ section
has curation status: IAO_0000123

polyacrylamide gel
type: Class
subclass of: processed material
subclass of: Restriction
  on property: has part
  some values from: acrylamide
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0302890
disjoint with: agarose gel
disjoint with: scattered molecular aggregate
disjoint with: urine specimen
disjoint with: blood specimen
disjoint with: whole organism preparation
disjoint with: capsule shell
disjoint with: guar gum
disjoint with: cloacal specimen
disjoint with: nasopharyngeal aspirate specimen
disjoint with: nasal swab specimen
disjoint with: device
disjoint with: growth environment
disjoint with: OBI_0001468
disjoint with: OBI_0001485
disjoint with: OBI_0100014
disjoint with: OBI_0100016
disjoint with: OBI_0100017
disjoint with: OBI_0100055
disjoint with: OBI_0100058
disjoint with: OBI_0100060
disjoint with: OBI_0100067
disjoint with: OBI_0100086
disjoint with: OBI_1000023
disjoint with: OBI_1000024
disjoint with: OBI_1000029
disjoint with: OBI_1000036
disjoint with: OBI_1000042
definition source: GROUP: OBI Biomaterial Branch
term editor: PERSON: Jie Zheng
term editor: PERSON: Philippe Rocca-Serra
example of usage: Assessing CMT cell line stability by two dimensional polyacrylamide gel electrophoresis and mass spectrometry based proteome analysis. J Proteomics. 2008 Jul 21;71(2):160-7. PMID: 18617143
definition: a material entity resulting from the polymerization of acrylamide with TEMED in some buffer solution
editor preferred term: polyacrylamide gel
has curation status: IAO_0000120

DNA sequence feature detection
type: Class
subclass of: assay
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: sequence feature identification objective
subclass of: Restriction
  on property: has_specified_input
  some values from: deoxyribonucleic acids
subclass of: Restriction
  on property: has_specified_output
  some values from: measurement datum
definition: An assay with the objective to determine a sequence feature of DNA
editor preferred term: DNA sequence feature detection
definition source: OBI
term editor: Person:Bjoern Peters
term editor: Philippe Rocca-Serra
example of usage: genotyping using an Affymetrix chip
editor note: should be a defined class where interpretation of data generated by assay qualifies a DNA sequence
has curation status: IAO_0000123

adding material objective
type: Class
subclass of: material combination objective
term editor: BP
editor preferred term: adding material objective
example of usage: creating a mouse infected with LCM virus
definition: is the specification of an objective to add a material into a target material. The adding is asymmetric in the sense that the target material largely retains its identity
has curation status: IAO_0000122

genotyping assay
type: Class
equivalent class: Restriction
  on property: has_specified_output
  some values from: genotype information
subclass of: analyte assay
subclass of: Restriction
  on property: has_specified_output
  some values from: genotype information
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: analyte role
    intersection of: Restriction
      on property: is role of
      some values from: deoxyribonucleic acids
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: OBI_0100051
    intersection of: Restriction
      on property: has part
      some values from: deoxyribonucleic acids
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: sequence feature identification objective
definition source: OBI Biomaterial
term editor: Philippe Rocca-Serra
editor preferred term: genotyping assay
example of usage: High-throughput genotyping of oncogenic human papilloma viruses with MALDI-TOF mass spectrometry. Clin Chem. 2008 Jan;54(1):86-92. Epub 2007 Nov 2.PMID: 17981923
definition: an assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions.
alternative term: genotype profiling, SNP genotyping
has curation status: IAO_0000120

needle
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: transfer function
disjoint with: column chromatography detector
disjoint with: NMR sample holder
disjoint with: chromatography instrument
disjoint with: rapid resolution column
disjoint with: NMR tube washing system
disjoint with: NMR console
disjoint with: variable wavelength detector
disjoint with: multiple wavelength detector
disjoint with: NMR probe
disjoint with: NMR magnet
disjoint with: magic angle spinning rotor
disjoint with: Bruker SampleRail system
disjoint with: evaporative light scattering detector
disjoint with: autosampler
disjoint with: fluorescene detector
disjoint with: electrical conductivity detector
disjoint with: NMR instrument
disjoint with: refractive index detector
disjoint with: pulsed amperometric detector
disjoint with: glucometer
disjoint with: micro electrode
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold

analyte measurement objective
type: Class
subclass of: assay objective
term editor: PERSON: Bjoern Peters
definition source: PPPB branch
example of usage: The objective to measure the concentration of glucose in a blood sample
editor preferred term: analyte measurement objective
definition: is an assay objective to determine the presence or concentration of an analyte in the evaluant
has curation status: IAO_0000122

DNA sequence variation detection
type: Class
subclass of: assay
subclass of: Restriction
  on property: has_specified_output
  some values from: measurement datum
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: sequence feature identification objective
subclass of: Restriction
  on property: has_specified_input
  some values from: deoxyribonucleic acids
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
editor preferred term: DNA sequence variation detection
definition source: OBI Biomaterial
term editor: Philippe Rocca-Serra
example of usage: Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform. Nucleic Acids Res. 2006;34(18):e121. PMID: 17000641
definition: DNA sequence variation detection is a process which aims at finding changes (expansion, amplification, deletion, mutation) in sequence of DNA molecule.
has curation status: IAO_0000122

agarose gel
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0302890
disjoint with: scattered molecular aggregate
disjoint with: urine specimen
disjoint with: blood specimen
disjoint with: whole organism preparation
disjoint with: capsule shell
disjoint with: guar gum
disjoint with: cloacal specimen
disjoint with: nasopharyngeal aspirate specimen
disjoint with: nasal swab specimen
disjoint with: device
disjoint with: growth environment
disjoint with: OBI_0001468
disjoint with: OBI_0001485
disjoint with: OBI_0100014
disjoint with: OBI_0100016
disjoint with: OBI_0100017
disjoint with: OBI_0100055
disjoint with: OBI_0100058
disjoint with: OBI_0100060
disjoint with: OBI_0100067
disjoint with: OBI_0100086
disjoint with: OBI_1000023
disjoint with: OBI_1000024
disjoint with: OBI_1000029
disjoint with: OBI_1000036
disjoint with: OBI_1000042
definition source: GROUP: OBI Biomaterial Branch
term editor: PERSON: Philippe Rocca-Serra
example of usage: Performance comparison of capillary and agarose gel electrophoresis for the identification and characterization of monoclonal immunoglobulins. Am J Clin Pathol. 2008 Mar;129(3):451-8. PMID: 18285269
definition: a material entity resulting from the polymerization of agarose after heating agarose suspended in some buffer solution
editor preferred term: agarose gel
has curation status: IAO_0000120

assay objective
type: Class
subclass of: objective specification
disjoint with: material transformation objective
disjoint with: specimen creation objective
disjoint with: material maintenance objective
disjoint with: training objective
disjoint with: service provision objective
disjoint with: assay validation objective
disjoint with: selective organism creation objective
disjoint with: OBI_0200166
definition source: PPPB branch
term editor: PPPB branch
editor preferred term: assay objective
example of usage: the objective to determine the weight of a mouse.
definition: is the specification of an objective to determine a specified type of information about an evaluated entity (independent continuant bearing evaluant role)
has curation status: IAO_0000122

obsolete_heart
type: Class
subclass of: ObsoleteClass
example of usage: Alan Ruttenberg's heart
term editor: Person:Bjoern Peters
definition: The heart is a muscular organ found in all vertebrates that is responsible for pumping blood throughout the blood vessels by repeated, rhythmic contractions
definition source: http://en.wikipedia.org/wiki/Heart
deprecated: true
editor note: unused class. decided to be deprecated on Aug 2, 2010 dev call. Will be imported when need.
editor note: MC: should be imported
editor preferred term: heart
has curation status: IAO_0000002
has obsolescence reason: IAO_0000230

analyte assay
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: is role of
        some values from: material entity
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: analyte role
      intersection of: Restriction
        on property: is role of
        some values from: scattered molecular aggregate
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: analyte measurement objective
subclass of: assay
subclass of: Restriction
  on property: has_specified_output
  some values from: measurement datum
definition source: PERSON:Bjoern Peters PERSON:Helen Parkinson PERSON:Philippe Rocca-Serra PERSON:Alan Ruttenberg GROUP:OBI Planned process branch
term editor: PERSON:Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Alan Ruttenberg
editor preferred term: analyte assay
editor note: logical def modified to remove expression below, as some analyte assays report below the level of detection, and therefore not a scalar measurement datum, replaced by measurement datum and ('has measurement unit label' some 'measurement unit label') and ('is quality measurement of' some 'molecular concentration'))
definition: An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant.
editor note: Note: is_realization of some analyte role isn't always true, for example when there is none of the analyte in the evaluant. For the moment we are writing it this way, but when the information ontology is further worked out this will be replaced with a condition discussing the measurement.
example of usage: example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output
has curation status: IAO_0000122

target of material addition role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: material entity
subclass of: Restriction
  on property: is realized by
  all values from: adding a material entity into a target
disjoint with: manufacturer role
disjoint with: pathogen role
disjoint with: host role
disjoint with: test substance role
disjoint with: complementary nucleotide probe role
disjoint with: service consumer role
disjoint with: service provider role
disjoint with: accessed material role
disjoint with: OBI_0302731
disjoint with: OBI_0302732
disjoint with: OBI_0302733
disjoint with: OBI_1110082
disjoint with: OBI_1110083
disjoint with: OBI_1110086
disjoint with: OBI_1110087
disjoint with: OBI_1110091
disjoint with: OBI_1110092
disjoint with: OBI_1110120
editor note: From Branch discussion with BP, AR, MC -- there is a need for the recipient to interact with the administered material. for example, a tooth receiving a filling was not considered to be a target role.
term editor: GROUP: Role Branch
definition source: OBI
example of usage: peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application.
editor preferred term: target of material addition role
definition: target of material addition role is a role realized by an entity into which a material is added in a material addition process
has curation status: IAO_0000120

mass measurement assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: evaluant role
    intersection of: Restriction
      on property: is role of
      some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: mass measurement datum
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: has role
      some values from: evaluant role
term editor: Helen Parkinson
definition source: OBI
comment: Philippe Rocca-Serra
example of usage: The patients was weighed and mass was determined to be 47 kilograms
editor preferred term: mass measurement assay
definition: a process to determine the mass of an evaluant
has curation status: IAO_0000120

obsolete_identification
type: Class
subclass of: ObsoleteClass
editor note: Alan Ruttenberg 2010/11/22: After OBI call. A specific identification objective should be used instead, as necessary
term editor: Philippe Rocca-Serra
editor note: See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3302925&group_id=177891&atid=886178
editor preferred term: identification
deprecated: true
example of usage: DNA cleavage assay for the identification of topoisomerase I inhibitors. Nat Protoc. 2008;3(11):1736-50. PMID: 18927559
definition: a process by which the identity (what a thing is) of a material entity is established within a certain confidence interval
has obsolescence reason: IAO_0000103
has curation status: IAO_0000124

intra cellular electrophysiology recording
type: Class
subclass of: assay
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: ion-channel activity
definition: An intracellular electrophysiology recording is a process where the recording location of the electrode is intracellular
term editor: PERSON: Frank Gibson
definition source: PERSON: Frank Gibson
editor preferred term: intra cellular electrophysiology recording
has curation status: IAO_0000123

packed column
type: Class
subclass of: chromatography column
disjoint with: organic acid column
disjoint with: protein column
disjoint with: normal phase column
disjoint with: capillary column
disjoint with: reversed phase column
disjoint with: chromatofocusing column
disjoint with: trap column
disjoint with: affinity column
disjoint with: ion exchange column
disjoint with: spin column
disjoint with: high temperature column
disjoint with: plunger column
disjoint with: liquid chromatography column
disjoint with: open tubular column
disjoint with: glass column
disjoint with: size exclusion column
disjoint with: custom made column
disjoint with: gel permeation column
disjoint with: carbon nanotube column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01218
definition: A packed column is a chromatography column where the particles of the solid stationary phase or the support coated with a liquid stationary phase may fill the whole inside volume of the tube.
term editor: PERSON:Daniel Schober
definition source: WEB:<http:www.iupac.org/publications/pac/1993/pdf/6504x0819.pdf>
editor preferred term: packed column
has curation status: IAO_0000120

obsolete_defined_output
type: Class
subclass of: ObsoleteClass
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: James Malone
term editor: PERSON: Melanie Courtot
editor preferred term: _defined_output
deprecated: true
definition: This is only a placeholder for defined classes, as are its siblings _defined_material and _defined protocol application. Its children should be defined classes constructed as output of a process.
example of usage: example of subclass: normalized data set - A normalized data set is a data set that is produced as the output of a normalization data transformation.
has curation status: IAO_0000121
has obsolescence reason: IAO_0000226

regulatory agency
type: Class
equivalent class: Class
  intersection of: organization
  intersection of: Restriction
    on property: has role
    some values from: regulator role
subclass of: organization
term editor: GROUP: OBI Biomaterial Branch
example of usage: The US Environmental Protection Agency
definition source: WEB: en.wikipedia.org/wiki/Regulator
definition: A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government.
editor preferred term: regulatory agency
has curation status: IAO_0000122

normalized data set
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: OBI_0200169
subclass of: data set
term editor: PERSON: James Malone
term editor: PERSON: Melanie Courtot
editor preferred term: normalized data set
definition: A data set that is produced as the output of a normalization data transformation.
has curation status: IAO_0000125

measure function
type: Class
subclass of: function
subclass of: Restriction
  on property: is realized by
  all values from: Restriction
    on property: has_specified_output
    some values from: data item
subclass of: Restriction
  on property: is function of
  some values from: processed material
disjoint with: consume data function
disjoint with: material combination function
disjoint with: sterilization function
disjoint with: reagent application function
disjoint with: specimen fixation function
disjoint with: current amplification function
disjoint with: stabilization function
disjoint with: OBI_0005246
disjoint with: OBI_1110016
disjoint with: OBI_1110085
example of usage: A glucometer measures blood glucose concentration, the glucometer has a measure function.
term editor: PERSON: Daniel Schober
term editor: PERSON: Helen Parkinson
term editor: PERSON: Melanie Courtot
term editor: PERSON:Frank Gibson
definition: Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference.
editor preferred term: measure function
has curation status: IAO_0000122

extracellular electrophysiology recording
type: Class
subclass of: assay
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: ion-channel activity
definition: An extracellular electrophysiology recording is process where the recording location of the electrode is extracellular and data
definition source: PERSON: Frank Gibson
term editor: PERSON: Frank Gibson, Helen Parkinson
example of usage: The recording of a spike train in the caudate nucleus of a monkey where the electrodes are extra cellular, i.e. not in the neuron
editor preferred term: extracellular electrophysiology recording
has curation status: IAO_0000120

consume data function
type: Class
subclass of: function
subclass of: Restriction
  on property: is function of
  some values from: material entity
disjoint with: material combination function
disjoint with: sterilization function
disjoint with: reagent application function
disjoint with: specimen fixation function
disjoint with: current amplification function
disjoint with: stabilization function
disjoint with: OBI_0005246
disjoint with: OBI_1110016
disjoint with: OBI_1110085
term editor: PERSON: Daniel Schober
term editor: PERSON: Frank Gibson
term editor: PERSON: Melanie Courtot
definition: Process data function is a function that is borne by in a material entity by virtue of its structure. When realized the material entity consumes data.
editor preferred term: consume data function
has curation status: IAO_0000122

material transformation objective
type: Class
subclass of: objective specification
disjoint with: specimen creation objective
disjoint with: material maintenance objective
disjoint with: training objective
disjoint with: service provision objective
disjoint with: assay validation objective
disjoint with: selective organism creation objective
disjoint with: OBI_0200166
definition source: GROUP: OBI PlanAndPlannedProcess Branch
term editor: PERSON: Bjoern Peters
term editor: PERSON: Frank Gibson
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Melanie Courtot
term editor: PERSON: Philippe Rocca-Serra
example of usage: The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.
editor preferred term: material transformation objective
definition: an objective specifiction that creates an specific output object from input materials.
alternative term: artifact creation objective
has curation status: IAO_0000122

manufacturing
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: manufacturing objective
subclass of: material processing
subclass of: Restriction
  on property: has_specified_output
  some values from: processed material
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
definition source: GROUP: OBI PlanAndPlannedProcess Branch
editor note: Manufacturing implies reproducibility and responsibility AR
term editor: PERSON: Bjoern Peters
term editor: PERSON: Frank Gibson
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Melanie Courtot
term editor: PERSON: Philippe Rocca-Serra
editor preferred term: manufacturing
definition: Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process
editor note: This includes a single scientist making a processed material for personal use.
has curation status: IAO_0000122

manufacturing objective
type: Class
subclass of: material transformation objective
disjoint with: material combination objective
disjoint with: device creation objective
disjoint with: genetic transformation objective
definition source: GROUP: OBI PlanAndPlannedProcess Branch
term editor: PERSON: Bjoern Peters
term editor: PERSON: Frank Gibson
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Melanie Courtot
term editor: PERSON: Philippe Rocca-Serra
editor preferred term: manufacturing objective
definition: is the objective to manufacture a material of a certain function (device)
has curation status: IAO_0000122

column chromatography detector
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
disjoint with: NMR sample holder
disjoint with: chromatography instrument
disjoint with: rapid resolution column
disjoint with: NMR tube washing system
disjoint with: NMR console
disjoint with: variable wavelength detector
disjoint with: multiple wavelength detector
disjoint with: NMR probe
disjoint with: NMR magnet
disjoint with: magic angle spinning rotor
disjoint with: Bruker SampleRail system
disjoint with: evaporative light scattering detector
disjoint with: autosampler
disjoint with: fluorescene detector
disjoint with: electrical conductivity detector
disjoint with: NMR instrument
disjoint with: refractive index detector
disjoint with: pulsed amperometric detector
disjoint with: glucometer
disjoint with: micro electrode
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette

Bruker autosampler
type: Class
subclass of: autosampler
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400209
definition: A Bruker autosampler is an autosampler made by Bruker.
editor preferred term: Bruker autosampler
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
has curation status: IAO_0000120

organic acid column
type: Class
subclass of: chromatography column
disjoint with: protein column
disjoint with: normal phase column
disjoint with: capillary column
disjoint with: reversed phase column
disjoint with: chromatofocusing column
disjoint with: trap column
disjoint with: affinity column
disjoint with: ion exchange column
disjoint with: spin column
disjoint with: high temperature column
disjoint with: plunger column
disjoint with: liquid chromatography column
disjoint with: open tubular column
disjoint with: glass column
disjoint with: size exclusion column
disjoint with: custom made column
disjoint with: gel permeation column
disjoint with: carbon nanotube column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01099
definition: An organic acid column is a chromatography column which enables (reversed-phase) separation of hydrophilic aliphatic and aromatic organic acids with UV detection. Organic acid columns allow retention of polar and apolar organic acids and are hydrolysis resistant.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: organic acid column
has curation status: IAO_0000120

thermal conductivity detector
type: Class
subclass of: gas chromatography detector
disjoint with: nitrogen phosphorous detector
disjoint with: photoionization detector
disjoint with: electron capture detector
disjoint with: flame ionization detector
disjoint with: mass selective detector
disjoint with: flame photometric detector
disjoint with: ozone-induced chemiluminescence detector
disjoint with: fluorine-induced chemiluminescence detector
disjoint with: atomic emission detector
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01084
term editor: PERSON:Daniel Schober
alternative term: TCD, hot wire detector
definition: The most commonly used detector in preparative GC is the thermal conductivity detector (hot wire detector). Even this detector, however, is often too sensitive and has too high a flow impedance. Under such circumstances, the procedure mentioned above must be employed. The eluent from the preparative column is split and a small portion diverted through the detector (sometimes with further dilution with carrier gas to reduce sensitivity).
definition source: WEB:<http://www.chromatography-online.org/Preparative/Apparatus/Detectors/rs27.html>
editor preferred term: thermal conductivity detector
has curation status: IAO_0000120

Bruker US 2 NMR magnet
type: Class
subclass of: Bruker NMR magnet
disjoint with: Bruker UltraShield Plus NMR magnet
disjoint with: Bruker UltraShield NMR magnet
disjoint with: Bruker Ultrastabilized NMR magnet
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400189
definition: An actively-shielded superconducting magnet from Bruker that combines Bruker BioSpin's advanced, proprietary UltraShield active shielding and UltraStabilized sub-cooling technologies. This shielded and stabilized (US2) magnet system delivers high sensitivity and spectral dispersion.
editor preferred term: Bruker US 2 NMR magnet
curator note: NMR instrument
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.bruker-biospin.com/nmr_magnets_950us2.html>
has curation status: IAO_0000120

protein column
type: Class
subclass of: chromatography column
disjoint with: normal phase column
disjoint with: capillary column
disjoint with: reversed phase column
disjoint with: chromatofocusing column
disjoint with: trap column
disjoint with: affinity column
disjoint with: ion exchange column
disjoint with: spin column
disjoint with: high temperature column
disjoint with: plunger column
disjoint with: liquid chromatography column
disjoint with: open tubular column
disjoint with: glass column
disjoint with: size exclusion column
disjoint with: custom made column
disjoint with: gel permeation column
disjoint with: carbon nanotube column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01238
definition: A protein column is a chromatography column used for the separation of complex protein mixtures. Protein columns enable sample desalting, followed by chromatographic separation or fractionation of complex protein samples, e.g. immunodepleted serum or plasma proteins.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: protein column
curator note: refactor as defined class
has curation status: IAO_0000120

solvent mixer
type: Class
subclass of: chromatography instrument
disjoint with: chromatography detector
disjoint with: liquid chromatography autosampler
disjoint with: fraction collector
disjoint with: column cartridger
disjoint with: chromatography pump system
disjoint with: column heater
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01072
definition: A liquid chromatography device that mixes different solvents, e.g. under high pressure and in differrent volumes ranging from 5 ml to 5 L capacity. Powerful magnetic mixers provide vigorous agitation required for high pressure reaction chemistry.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
curator note: check on definition !
editor preferred term: solvent mixer
has curation status: IAO_0000120

mass spectrometry assay
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has_specified_input
    some values from: mass spectrometer
subclass of: assay
example of usage: Identification of Human Pituitary Growth Hormone Variants by Mass Spectrometry. Kohler M, Thomas A, Püschel K, Schänzer W, Thevis M. J Proteome Res. 2009 Jan 5. PMID: 19123788
definition source: PRIDE: PRIDE:0000027
term editor: Philippe Rocca-Serra
definition: This is a measuring method consisting of turning elements in a sample into ions, isolating them according to the ratio between the mass and charge numbers and detecting it electrically.
alternative term: mass spectrometry
editor preferred term: mass spectrometry assay
has curation status: IAO_0000123

study design execution
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: realizes
    some values from: Restriction
      on property: concretizes
      some values from: OBI_0500000
  intersection of: Restriction
    on property: has_specified_output
    some values from: data item
subclass of: planned process
curator note: 6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation.
definition: a planned process that realizes the concretization of a study design
definition source: branch derived
example of usage: injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design.
editor note: removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired.
editor preferred term: study design execution
has curation status: IAO_0000122

Bruker NMR Case sample changer
type: Class
subclass of: Bruker autosampler
disjoint with: Bruker B-ACS system
disjoint with: Bruker BEST NMR system
disjoint with: Bruker SampleJet system
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400203
editor preferred term: Bruker NMR Case sample changer
curator note: NMR instrument
term editor: PERSON:Daniel Schober
definition: The NMR Case is an economical NMR sample changer for laboratories with modest automation needs. It expands the maximum number of samples your spectrometer can process during unattended operation to 24. The NMR Case consists of multiple components. The NMR Case exchange module installed atop your cryostat. The two front legs are adjustable, making the NMR Case compatible with many different cryostats.
definition source: WEB:<http://www.bruker-biospin.com/automation.html>
has curation status: IAO_0000120

nano pump system
type: Class
subclass of: chromatography pump system
disjoint with: vacuum degasser
disjoint with: capillary pump system
disjoint with: isocratic pump system
disjoint with: flash pump system
disjoint with: gradient pump system
disjoint with: quaternary pump system
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01052
definition: A pump system optimized for nano flow chromatography.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: nano pump system
has curation status: IAO_0000120

Bruker AutoClean system
type: Class
subclass of: NMR tube washing system
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400205
editor preferred term: Bruker AutoClean system
definition: NMR tubes are often used once and discarded, creating needless waste. With the Bruker BioSpin Autoclean system you can now recycle 5mm, 3mm, or 5mm/3mm step-down (Wilmad 520-1B) NMR tubes. AutoClean NMR Tube Washing System is a simple way to recoup the substantial investment your organization makes in quality NMR tubes, and cut back on needless waste material.
term editor: PERSON:Daniel Schober
editor note: washing system/NMR tube washing system, XPS: device has function washing
has curation status: IAO_0000120

manual injection system
type: Class
subclass of: sample injection system
disjoint with: splitless GC injector
disjoint with: auto injector
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01064
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
definition: The traditional hardware system that allows a human to inject a sample into an inlet by hand, using a syringe.
editor preferred term: manual injection system
has curation status: IAO_0000120

Varian GEMINI spectrometer
type: Class
subclass of: Varian NMR instrument
disjoint with: Varian VXR spectrometer
disjoint with: Varian UNITY INOVA spectrometer
disjoint with: Varian UNITY spectrometer
disjoint with: Varian MERCURY spectrometer
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400239
definition: An older Varian Broadband NMR spectrometer.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR instrument
term editor: PERSON:Daniel Schober
editor preferred term: Varian GEMINI spectrometer
has curation status: IAO_0000120

column connector
type: Class
subclass of: chromatography device
disjoint with: sample inlet
disjoint with: sample injection system
disjoint with: column jacket
disjoint with: liquid chromatography valve
disjoint with: column cartridge
disjoint with: gas chromatography equipment
disjoint with: column compartment
disjoint with: needle assembly
disjoint with: transfer line
disjoint with: column adapter
disjoint with: chromatography consumable
disjoint with: column frit
disjoint with: chart recorder
disjoint with: guard column
disjoint with: chromatography splitter
disjoint with: liquid chromatography instrument
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01236
definition: A device that connects two or more columns together in a functional way with leak-tight connection, low dead volume, low thermal mass and high inertness.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
curator note: chromatography device
editor preferred term: column connector
has curation status: IAO_0000120

solid NMR probe
type: Class
subclass of: NMR probe
disjoint with: direct detection NMR probe
disjoint with: flow probe
disjoint with: JEOL NMR probe
disjoint with: imaging NMR probe
disjoint with: liquid NMR probe
disjoint with: Bruker NMR probe
disjoint with: indirect detection probe
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400243
definition: An NMR probe that is designed to hold a solid sample.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR device
term editor: PERSON:Daniel Schober
editor preferred term: solid NMR probe
has curation status: IAO_0000120

Bruker high resolution probe
type: Class
subclass of: Bruker NMR probe
disjoint with: Bruker CryoProbe
disjoint with: Bruker 1mm MicroProbe
disjoint with: Bruker micro imaging probe
disjoint with: Bruker solid magic angle spinning probe
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400223
definition: BRUKER BIOSPIN's experienced Research & Development group not only delivers top-performance probes for the more common experiments, but also a wealth of special probes for almost any application. For high resolution (HR) NMR we offer probes with a variety of important characteristics and features.
editor preferred term: Bruker high resolution probe
definition source: GROUP:<http://msi-ontology.sourceforge.net>
alternative term: HR Probe
curator note: NMR probe
term editor: PERSON:Daniel Schober
has curation status: IAO_0000120

chromatography detector
type: Class
subclass of: chromatography instrument
disjoint with: liquid chromatography autosampler
disjoint with: fraction collector
disjoint with: column cartridger
disjoint with: chromatography pump system
disjoint with: column heater
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01012
definition: A chromatography detector is a device that locates in the dimensions of space and time, the positions of the components of a mixture that has been subjected to a chromatographic process and thus permits the senses to appreciate the nature of the separation. Defining characteristics are Dynamic Range, Response Index or Linearity, Linear Dynamic range, Detector Response, Detector Noise Level, Detector Sensitivity or Minimum Detectable Concentration, Total System Dispersion, Sensor Dimensions, Detector Time Constant, Pressure Sensitivity, Flow Sensitivity, Operating Temperature Range.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.chromatography-online.org/GC-Detectors/Classification/rs1.html>
editor preferred term: chromatography detector
has curation status: IAO_0000120

normal phase column
type: Class
subclass of: chromatography column
disjoint with: capillary column
disjoint with: reversed phase column
disjoint with: chromatofocusing column
disjoint with: trap column
disjoint with: affinity column
disjoint with: ion exchange column
disjoint with: spin column
disjoint with: high temperature column
disjoint with: plunger column
disjoint with: liquid chromatography column
disjoint with: open tubular column
disjoint with: glass column
disjoint with: size exclusion column
disjoint with: custom made column
disjoint with: gel permeation column
disjoint with: carbon nanotube column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01097
definition: A normal phase column is a chromatography column in which the stationary phase is more polar than the mobile phase. Its counterpart is the reversed phase column.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: normal phase column
has curation status: IAO_0000120

APOLLO console
type: Class
subclass of: tecmag NMR console
disjoint with: DISCOVERY console
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400249
editor preferred term: APOLLO console
curator note: NMR instrument/NMR console
term editor: PERSON:Daniel Schober
definition: The APOLLO is a compact, modular, multiple-DSP, Windows XP Professional-based console that can be equipped with up to 8 DDS-based RF transmitter channels configurable from 2 kHz to 3.5 GHz. Each transmitter channel produces a nominal 1V output and has the most agile frequency, phase and amplitude control of any system on the market. An array of additional options are available including multiple RF transmitters, linear high-power RF amplifiers, digital receiver arrays, low noise figure preamplifiers, a gradient control system, shim unit, MAS spin-speed controller, variable temperature unit, digital lock system and probe/coil interface. With its numerous options, the Apollo can be configured for any NMR, NQR or MRI application.
definition source: WEB:<http://www.tecmag.com/apollo.htm>
has curation status: IAO_0000120

NMR sample holder
type: Class
subclass of: device
disjoint with: chromatography instrument
disjoint with: rapid resolution column
disjoint with: NMR tube washing system
disjoint with: NMR console
disjoint with: variable wavelength detector
disjoint with: multiple wavelength detector
disjoint with: NMR probe
disjoint with: NMR magnet
disjoint with: magic angle spinning rotor
disjoint with: Bruker SampleRail system
disjoint with: evaporative light scattering detector
disjoint with: autosampler
disjoint with: fluorescene detector
disjoint with: electrical conductivity detector
disjoint with: NMR instrument
disjoint with: refractive index detector
disjoint with: pulsed amperometric detector
disjoint with: glucometer
disjoint with: micro electrode
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester

chromatography instrument
type: Class
subclass of: material separation device
subclass of: Restriction
  on property: has function
  some values from: material separation function
disjoint with: rapid resolution column
disjoint with: NMR tube washing system
disjoint with: NMR console
disjoint with: variable wavelength detector
disjoint with: multiple wavelength detector
disjoint with: NMR probe
disjoint with: NMR magnet
disjoint with: magic angle spinning rotor
disjoint with: Bruker SampleRail system
disjoint with: evaporative light scattering detector
disjoint with: autosampler
disjoint with: fluorescene detector
disjoint with: electrical conductivity detector
disjoint with: NMR instrument
disjoint with: refractive index detector
disjoint with: pulsed amperometric detector
disjoint with: glucometer
disjoint with: micro electrode
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer

continuous wave NMR instrument
type: Class
subclass of: NMR instrument
disjoint with: fourier transformation NMR instrument
disjoint with: tecmag NMR instrument
disjoint with: Bruker NMR instrument
disjoint with: JEOL NMR instrument
disjoint with: Varian NMR instrument
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400283
definition: Continuous wave NMR spectrometers are similar to optical spectrometers, but the sample is held in a strong magnetic field, where the frequency of the source is slowly scanned (in some instruments, the source frequency is held constant, and the field is scanned).
curator note: NMR instrument
term editor: PERSON:Daniel Schober
definition source: WEB:<http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm>
editor preferred term: continuous wave NMR instrument
has curation status: IAO_0000120

fourier transformation NMR instrument
type: Class
subclass of: NMR instrument
disjoint with: tecmag NMR instrument
disjoint with: Bruker NMR instrument
disjoint with: JEOL NMR instrument
disjoint with: Varian NMR instrument
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400284
definition source: GROUP:<http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm>
definition: In fourier transformation NMR, all frequencies in a spectrum are irradiated simultaneously with a radio frequency pulse. Following the pulse, the nuclei return to thermal equilibrium. A time domain emission signal is recorded by the instrument as the nuclei relax. A frequency domain spectrum is obtained by Fourier transformation.
curator note: NMR instrument
term editor: PERSON:Daniel Schober
editor preferred term: fourier transformation NMR instrument
has curation status: IAO_0000120

nitrogen phosphorous detector
type: Class
subclass of: gas chromatography detector
disjoint with: photoionization detector
disjoint with: electron capture detector
disjoint with: flame ionization detector
disjoint with: mass selective detector
disjoint with: flame photometric detector
disjoint with: ozone-induced chemiluminescence detector
disjoint with: fluorine-induced chemiluminescence detector
disjoint with: atomic emission detector
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01089
term editor: PERSON:Daniel Schober
definition: The nitrogen phosphorus detector (NPD) (sometimes called the thermionic detector) is a very sensitive, specific detector the design of which, is based on the FID. Physically the sensor appears to be very similar to the FID but, in fact, operates on an entirely different principle. The nitrogen phosphorous detector (sometimes called the thermionic detector) is a very sensitive but specific detector that responds almost exclusively to nitrogen and phosphorous compounds. It is based on the flame ionization detector but differs in that it contains a rubidium or cesium silicate (glass) bead situated in a heater coil, a little distance from the hydrogen flame. If the detector is to respond to both nitrogen and phosphorous then the hydrogen flow should be minimal so that the gas does not ignite at the jet. If the detector is to respond to phosphorous only, a large flow of hydrogen is used which is burnt at the jet. The heated bead emits electrons by thermionic emission. These electrons are collected under a potential of a few volts by an appropriately placed anode, and provides a background current. When a solute containing nitrogen or phosphorous is eluted from the column, the partially combusted nitrogen and phosphorous materials are adsorbed on the surface of the bead. The adsorbed material reduces the work function of the surface and, as consequence, the emission of electrons is increased which raises the current collected at the electrode. The sensitivity of the detector to phosphorous is about 10-12 gram per ml and for nitrogen about 10-11 gram per ml at a signal to nose ratio of 2. The alkali bead as a finite life and needs regular replacement.
definition source: WEB:<http://www.chromatography-online.org/topics/nitrogen/phosphorus/detector.html>
editor preferred term: nitrogen phosphorous detector
has curation status: IAO_0000120

cation exchange column
type: Class
subclass of: ion exchange column
disjoint with: anion exchange column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01096
definition: A cation exchange column is a chromatography column that is used in cation exchange chromatography.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: cation exchange column
has curation status: IAO_0000120

direct detection NMR probe
type: Class
subclass of: NMR probe
disjoint with: flow probe
disjoint with: JEOL NMR probe
disjoint with: imaging NMR probe
disjoint with: liquid NMR probe
disjoint with: Bruker NMR probe
disjoint with: indirect detection probe
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400280
definition: An NMR probe designed to allow the direct detection of acquisition nuclei.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR device
term editor: PERSON:Daniel Schober
editor preferred term: direct detection NMR probe
has curation status: IAO_0000120

Bruker B-ACS system
type: Class
subclass of: Bruker autosampler
disjoint with: Bruker BEST NMR system
disjoint with: Bruker SampleJet system
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400210
editor preferred term: Bruker B-ACS system
curator note: NMR instrument
term editor: PERSON:Daniel Schober
definition: The Bruker Automatic Sample Changer (B-ACS 60/120), used in conjunction with Bruker DISNMR, UXNMR or XWIN-NMR software, provides dialog-guided facilities which allow the user to easily and effectively perform automatic (continuous) experiments. Features include a 60 or 120 sample capacity, random accessing of samples, positive sample identification with the optional bar code reader, and temperature control of individual samples with the optional sample heater unit.
definition source: WEB:<http://www.bruker-biospin.com/automation.html>
has curation status: IAO_0000120

rapid resolution column
type: Class
subclass of: material separation device
subclass of: Restriction
  on property: has function
  some values from: material separation function
disjoint with: NMR tube washing system
disjoint with: NMR console
disjoint with: variable wavelength detector
disjoint with: multiple wavelength detector
disjoint with: NMR probe
disjoint with: NMR magnet
disjoint with: magic angle spinning rotor
disjoint with: Bruker SampleRail system
disjoint with: evaporative light scattering detector
disjoint with: autosampler
disjoint with: fluorescene detector
disjoint with: electrical conductivity detector
disjoint with: NMR instrument
disjoint with: refractive index detector
disjoint with: pulsed amperometric detector
disjoint with: glucometer
disjoint with: micro electrode
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument

liquid chromatography autosampler
type: Class
subclass of: chromatography instrument
disjoint with: fraction collector
disjoint with: column cartridger
disjoint with: chromatography pump system
disjoint with: column heater
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01061
definition: Designed to perform capillary LC with injection of sample volumes ranging from nL to L.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: liquid chromatography autosampler
has curation status: IAO_0000120

vacuum degasser
type: Class
subclass of: chromatography pump system
disjoint with: capillary pump system
disjoint with: isocratic pump system
disjoint with: flash pump system
disjoint with: gradient pump system
disjoint with: quaternary pump system
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01053
definition: A degassing system used for degassing solvents in liquid chromatography. Dissolved gasses, usually nitrogen and oxygen from the air, tend to be evolved in the mobile phase as the pressure is reduced when the mobile phase leaves the liquid chromatography column and enters the detector. Gasses in the mobile phase in the detector can produce completely unacceptable noise and, thus, must be removed. The dissolved gasses were originally removed under vacuum but, unfortunately, are soon replaced if the solvent is left in contact with air at atmospheric pressure. For this reason degassing is now usually carried out by bubbling helium through the mobile phase reservoirs. Secondly, vacuum is used in the thermionic detector. This consists of a device, very similar in design to the thermionic valve which is attached to a vacuum and a small quantity of the eluent from a gas chromatography column allowed to bleed through it. Helium is used as the carrier gas. The presence of solute vapor causes the thermionic current to fall. This type of detector tends to become contaminated rather readily.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.chromatography-online.org/topics/vacuum.html>
editor preferred term: vacuum degasser
has curation status: IAO_0000120

capillary column
type: Class
subclass of: chromatography column
disjoint with: reversed phase column
disjoint with: chromatofocusing column
disjoint with: trap column
disjoint with: affinity column
disjoint with: ion exchange column
disjoint with: spin column
disjoint with: high temperature column
disjoint with: plunger column
disjoint with: liquid chromatography column
disjoint with: open tubular column
disjoint with: glass column
disjoint with: size exclusion column
disjoint with: custom made column
disjoint with: gel permeation column
disjoint with: carbon nanotube column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01066
definition: A capillary column is a thin tube with a small inner diameter, usually around 0.5 mm.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: capillary column
has curation status: IAO_0000120

sample inlet
type: Class
subclass of: chromatography device
disjoint with: sample injection system
disjoint with: column jacket
disjoint with: liquid chromatography valve
disjoint with: column cartridge
disjoint with: gas chromatography equipment
disjoint with: column compartment
disjoint with: needle assembly
disjoint with: transfer line
disjoint with: column adapter
disjoint with: chromatography consumable
disjoint with: column frit
disjoint with: chart recorder
disjoint with: guard column
disjoint with: chromatography splitter
disjoint with: liquid chromatography instrument
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01044
term editor: PERSON:Daniel Schober
definition: The column inlet (or injector) provides the means to introduce a sample into a continuous flow of carrier gas. The inlet is a piece of hardware attached to the column head.
definition source: WEB:<http://en.wikipedia.org/wiki/Gas_chromatography#Inlets>
curator note: chromatography device
editor preferred term: sample inlet
has curation status: IAO_0000120

NMR tube washing system
type: Class
subclass of: device
disjoint with: NMR console
disjoint with: variable wavelength detector
disjoint with: multiple wavelength detector
disjoint with: NMR probe
disjoint with: NMR magnet
disjoint with: magic angle spinning rotor
disjoint with: Bruker SampleRail system
disjoint with: evaporative light scattering detector
disjoint with: autosampler
disjoint with: fluorescene detector
disjoint with: electrical conductivity detector
disjoint with: NMR instrument
disjoint with: refractive index detector
disjoint with: pulsed amperometric detector
disjoint with: glucometer
disjoint with: micro electrode
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller

NMR console
type: Class
subclass of: device
disjoint with: variable wavelength detector
disjoint with: multiple wavelength detector
disjoint with: NMR probe
disjoint with: NMR magnet
disjoint with: magic angle spinning rotor
disjoint with: Bruker SampleRail system
disjoint with: evaporative light scattering detector
disjoint with: autosampler
disjoint with: fluorescene detector
disjoint with: electrical conductivity detector
disjoint with: NMR instrument
disjoint with: refractive index detector
disjoint with: pulsed amperometric detector
disjoint with: glucometer
disjoint with: micro electrode
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system

dual loop autosampler
type: Class
subclass of: liquid chromatography autosampler
disjoint with: preparative autosampler
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01063
definition: A dual loop autosampler is an autosampler that is designed for handling both analytical (10 mL/min flow rate) to preparative scale sample purification (100 mL/min flow rate).
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.chem.agilent.com/scripts/pds.asp?lpage=17149>
editor preferred term: dual loop autosampler
has curation status: IAO_0000120

variable wavelength detector
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
disjoint with: multiple wavelength detector
disjoint with: NMR probe
disjoint with: NMR magnet
disjoint with: magic angle spinning rotor
disjoint with: Bruker SampleRail system
disjoint with: evaporative light scattering detector
disjoint with: autosampler
disjoint with: fluorescene detector
disjoint with: electrical conductivity detector
disjoint with: NMR instrument
disjoint with: refractive index detector
disjoint with: pulsed amperometric detector
disjoint with: glucometer
disjoint with: micro electrode
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette

Bruker LC-NMR platform
type: Class
subclass of: Bruker NMR instrument
disjoint with: Bruker AMX series NMR instrument
disjoint with: Bruker AC series NMR instrument
disjoint with: Bruker Capillary LC-NMR platform
disjoint with: AVANCE II spectrometer
disjoint with: Bruker LC-NMR/MS platform
disjoint with: Bruker SPE-NMR platform
disjoint with: Bruker Metabolic Profiler
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400276
curator note: hyphenated NMR instrument platform
editor preferred term: Bruker LC-NMR platform
curator note: NMR instrument
term editor: PERSON:Daniel Schober
definition: The LC-NMR/MS setup was first introduced by Bruker BioSpin in 1999. An LC-NMR system including a Bruker Peak Sampling Unit (BPSU-36) was coupled with a Bruker Daltonics esquire series ion trap mass spectrometer via a Bruker NMR-MS interface (BNMI). Since October 2004 the Bruker Daltonics microTOF-LC time-of-flight mass spectrometer can also be integrated in an LC-NMR setup.
definition source: WEB:<http://www.bruker-biospin.com/hyphenation_lcnmr_ms.html>
has curation status: IAO_0000120

sample injection system
type: Class
subclass of: chromatography device
disjoint with: column jacket
disjoint with: liquid chromatography valve
disjoint with: column cartridge
disjoint with: gas chromatography equipment
disjoint with: column compartment
disjoint with: needle assembly
disjoint with: transfer line
disjoint with: column adapter
disjoint with: chromatography consumable
disjoint with: column frit
disjoint with: chart recorder
disjoint with: guard column
disjoint with: chromatography splitter
disjoint with: liquid chromatography instrument
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01057
definition: An automated chromatography system that injects the sample into the chromatography columns in order to increase speed and minimize human involvement in the purification process for better reproducibility.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
curator note: chromatography device
editor preferred term: sample injection system
has curation status: IAO_0000120

multiple wavelength detector
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
disjoint with: NMR probe
disjoint with: NMR magnet
disjoint with: magic angle spinning rotor
disjoint with: Bruker SampleRail system
disjoint with: evaporative light scattering detector
disjoint with: autosampler
disjoint with: fluorescene detector
disjoint with: electrical conductivity detector
disjoint with: NMR instrument
disjoint with: refractive index detector
disjoint with: pulsed amperometric detector
disjoint with: glucometer
disjoint with: micro electrode
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device

photoionization detector
type: Class
subclass of: gas chromatography detector
disjoint with: electron capture detector
disjoint with: flame ionization detector
disjoint with: mass selective detector
disjoint with: flame photometric detector
disjoint with: ozone-induced chemiluminescence detector
disjoint with: fluorine-induced chemiluminescence detector
disjoint with: atomic emission detector
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01090
term editor: PERSON:Daniel Schober
alternative term: PID
definition: The selective determination of aromatic hydrocarbons or organo-heteroatom species is the job of the photoionization detector (PID). This device uses ultraviolet light as a means of ionizing an analyte exiting from a GC column. The ions produced by this process are collected by electrodes. The current generated is therefore a measure of the analyte concentration. f the amount of ionization is reproducible for a given compound, pressure, and light source then the current collected at the PID's reaction cell electrodes is reproducibly proportional to the amount of that compound entering the cell. The reason why the compounds that are routinely analyzed are either aromatic hydrocarbons or heteroatom containing compounds (like organosulfur or organophosphorus species) is because these species have ionization potentials (IP) that are within reach of commercially available UV lamps. The available lamp energies range from 8.3 to 11.7 ev, that is, lambda max ranging from 150 nm to 106 nm. Although most PIDs have only one lamp, lamps in the PID are exchanged depending on the compound selectivity required in the analysis.
definition source: WEB:<http://www.chemistry.adelaide.edu.au/external/soc-rel/content/pid.htm>
editor preferred term: photoionization detector
has curation status: IAO_0000120

gas generator
type: Class
subclass of: gas chromatography equipment
disjoint with: gas chromatography oven
disjoint with: gas purifier
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01033
definition: An instrument that generates gases for use with the gas chromatograph. Previously gas was obtained from gas tanks or gas cylinders. However, over the past decade the use of gas generators have become more popular as it avoids having gases at high pressure in the laboratory which is perceived by some as potentially dangerous. In addition, the use of a hydrogen generator avoids the use of a cylinder of hydrogen at high pressure which is also perceived by some as a serious fire hazard despite the fact that they have been used in laboratories, quite safely for nearly a century.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.chromatography-online.org/GC/Gas-Supplies/Pure-Air-Generators./rs5.html>
curator note: gas chromatography equipment
editor preferred term: gas generator
has curation status: IAO_0000120

column jacket
type: Class
subclass of: chromatography device
disjoint with: liquid chromatography valve
disjoint with: column cartridge
disjoint with: gas chromatography equipment
disjoint with: column compartment
disjoint with: needle assembly
disjoint with: transfer line
disjoint with: column adapter
disjoint with: chromatography consumable
disjoint with: column frit
disjoint with: chart recorder
disjoint with: guard column
disjoint with: chromatography splitter
disjoint with: liquid chromatography instrument
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01276
definition: A column jacket is a piece of column chromatography equipment that covers a column in order to ensure thermoisolation and create a controllable thermostatic microenvironment.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
curator note: chromatography device
editor preferred term: column jacket
has curation status: IAO_0000120

electron capture detector
type: Class
subclass of: gas chromatography detector
disjoint with: flame ionization detector
disjoint with: mass selective detector
disjoint with: flame photometric detector
disjoint with: ozone-induced chemiluminescence detector
disjoint with: fluorine-induced chemiluminescence detector
disjoint with: atomic emission detector
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01085
alternative term: ECD
term editor: PERSON:Daniel Schober
definition: The electron capture detector is a GC detector that uses a radioactive Beta emitter (electrons) to ionize some of the carrier gas and produce a current between a biased pair of electrodes. When organic molecules that contain electronegative functional groups, such as halogens, phosphorous, and nitro groups pass by the detector, they capture some of the electrons and reduce the current measured between the electrodes.
definition source: WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html>
editor preferred term: electron capture detector
has curation status: IAO_0000120

reversed phase column
type: Class
subclass of: chromatography column
disjoint with: chromatofocusing column
disjoint with: trap column
disjoint with: affinity column
disjoint with: ion exchange column
disjoint with: spin column
disjoint with: high temperature column
disjoint with: plunger column
disjoint with: liquid chromatography column
disjoint with: open tubular column
disjoint with: glass column
disjoint with: size exclusion column
disjoint with: custom made column
disjoint with: gel permeation column
disjoint with: carbon nanotube column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01106
definition: A reversed phase column is a chromatography column in which the mobile phase is more polar than the stationary phase. Its counterpart is the normal phase column.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: reversed phase column
has curation status: IAO_0000120

injector lubricant
type: Class
subclass of: chromatography consumable
disjoint with: vial
disjoint with: piston-seal
disjoint with: chromatography detector filter
disjoint with: detector lamp
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01118
definition: A lubricant used in liquid chromatography that eases sample injector penetration.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: injector lubricant
has curation status: IAO_0000120

isolation of cell population
type: Class
subclass of: OBI_0600014
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: separation into different composition objective
subclass of: Restriction
  on property: has_specified_output
  some values from: OBI_0100060
subclass of: Restriction
  on property: has_specified_input
  some values from: OBI_0100060
term editor: Person: Bjoern Peters
definition: a process in which a population of cells with certain characteristics is isolated from a larger population
editor preferred term: isolation of cell population
example of usage: removing CD4+ cells from PBMCs using magnetic beads.
has curation status: IAO_0000123

DISCOVERY console
type: Class
subclass of: tecmag NMR console
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400247
editor preferred term: DISCOVERY console
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR instrument/NMR console
term editor: PERSON:Daniel Schober
definition: The Discovery console is a Windows XP Professional-based, integrated console designed especially for Solid-State NMR. The console includes everything needed to interface to any magnet and solids probe - from computer to cables to duplexing network.
has curation status: IAO_0000120

Bruker AMX series NMR instrument
type: Class
subclass of: Bruker NMR instrument
disjoint with: Bruker AC series NMR instrument
disjoint with: Bruker Capillary LC-NMR platform
disjoint with: AVANCE II spectrometer
disjoint with: Bruker LC-NMR/MS platform
disjoint with: Bruker SPE-NMR platform
disjoint with: Bruker Metabolic Profiler
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400240
definition: A series of older Bruker NMR magnets, now out of production. The Bruker AMX500 has proven an extremely reliable workhorse, with excellent lineshape yielding superior water suppression even without gradients. The Oxford 11.7 Tesla 5.2 cm bore magnet rests on a TMC vibration damping table. Homogeneity is controlled by a BSN-18 and BSN-2 with 19 shim controls. In addition to the 5 mm triple resonance probe, the AMX is equipped with a 10mm broadband observe probe.
editor preferred term: Bruker AMX series NMR instrument
curator note: NMR instrument
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.tufts.edu/med/biochemistry/NMR/amx500.html>
has curation status: IAO_0000120

chromatofocusing column
type: Class
subclass of: chromatography column
disjoint with: trap column
disjoint with: affinity column
disjoint with: ion exchange column
disjoint with: spin column
disjoint with: high temperature column
disjoint with: plunger column
disjoint with: liquid chromatography column
disjoint with: open tubular column
disjoint with: glass column
disjoint with: size exclusion column
disjoint with: custom made column
disjoint with: gel permeation column
disjoint with: carbon nanotube column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01209
definition: A chromatofocusing column is a chromatography column in which a resin is equilibrated at one pH and eluted at a second pH. The use of a weak ion-exchange resin causes a pH gradient to be formed at the solvent front owing to the buffering action of the resin. This pH gradient in turn leads to an ordering of proteins by isoelectric point. Molecules of charge sign opposite the resin bind; those of charge sign like the resin do not bind.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.bioprocessintl.com/default.asp?page=glossary&TopicID=1>
editor preferred term: chromatofocusing column
has curation status: IAO_0000120

NMR probe
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
disjoint with: NMR magnet
disjoint with: magic angle spinning rotor
disjoint with: Bruker SampleRail system
disjoint with: evaporative light scattering detector
disjoint with: autosampler
disjoint with: fluorescene detector
disjoint with: electrical conductivity detector
disjoint with: NMR instrument
disjoint with: refractive index detector
disjoint with: pulsed amperometric detector
disjoint with: glucometer
disjoint with: micro electrode
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven

NMR magnet
type: Class
subclass of: device
disjoint with: magic angle spinning rotor
disjoint with: Bruker SampleRail system
disjoint with: evaporative light scattering detector
disjoint with: autosampler
disjoint with: fluorescene detector
disjoint with: electrical conductivity detector
disjoint with: NMR instrument
disjoint with: refractive index detector
disjoint with: pulsed amperometric detector
disjoint with: glucometer
disjoint with: micro electrode
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer

trap column
type: Class
subclass of: chromatography column
disjoint with: affinity column
disjoint with: ion exchange column
disjoint with: spin column
disjoint with: high temperature column
disjoint with: plunger column
disjoint with: liquid chromatography column
disjoint with: open tubular column
disjoint with: glass column
disjoint with: size exclusion column
disjoint with: custom made column
disjoint with: gel permeation column
disjoint with: carbon nanotube column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01261
definition: A trap column is a chromatography column which is used prior to a, e.g. mass spectrometry, separation to clean up or concentrate controlled amounts of samples prior to elution to a detector.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: trap column
has curation status: IAO_0000120

flow probe
type: Class
subclass of: NMR probe
disjoint with: JEOL NMR probe
disjoint with: imaging NMR probe
disjoint with: liquid NMR probe
disjoint with: Bruker NMR probe
disjoint with: indirect detection probe
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400131
definition: An NMR probe that allows the automatized flow-through of a sample. The sample is aspirated via a syringe pump into the Flow probe, the NMR spectrum is acquired and when the experiment is complete, the sample is returned to back to an external source (well plate) or flushed to waste. Sometimes pulsed field gradients (PFG) can be established in flow probes.
curator note: NMR device
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.varianinc.com/cgi-bin/nav?products/NMR/accessory/auto_samplers/vast/index&cid=HFIH>
editor preferred term: flow probe
has curation status: IAO_0000120

clinical chemistry assay
type: Class
subclass of: analyte assay
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: analyte role
    intersection of: Restriction
      on property: is role of
      some values from: scattered molecular aggregate
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: analyte measurement objective
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: evaluant role
    intersection of: Restriction
      on property: is role of
      some values from: material entity
editor note: 3/26/09: There needs to be a restriction set that specifies which type of evaluants are used in the assay, somewhere along the lines of 'sample derived of bodily fluid'
example of usage: Influence of hydroxyethyl starch (6% HES 130/0.4) administration on hematology and clinical chemistry parameters. Mueller T, Schimetta W, Dieplinger B, Loeffler P, Rehm M, Kreimeier U, Poelz W, Haltmayer M. Clin Chem Lab Med. 2008;46(4):558-62. PMID: 18605936
term editor: Person: Philippe Rocca-Serra
definition: a process which uses analytical methods to produce measurements and data on the concentration of a chemical parameters (analytes) present in a bodily fluid collected from an organism.
definition source: adapted from Wikipedia
alternative term: chemical pathology
editor preferred term: clinical chemistry assay
alternative term: detection of analyte in blood sample
has curation status: IAO_0000120

flame ionization detector
type: Class
subclass of: gas chromatography detector
disjoint with: mass selective detector
disjoint with: flame photometric detector
disjoint with: ozone-induced chemiluminescence detector
disjoint with: fluorine-induced chemiluminescence detector
disjoint with: atomic emission detector
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01197
definition: A flame ionization detector is a GC detector that consist of a hydrogen/air flame and a collector plate which are normally heated independently of the chromatographic oven. Heating is necessary in order to prevent condensation of water generated by the flame and also to prevent any hold-up of solutes as they pass from the column to the flame. There is an electrode above the flame to collect the ions formed at a hydrogen/air flame. The number of ions hitting the collector is measured and a signal is generated. Flame ionization detectors are most widely used and generally applicable for gas chromatography and hence is used for routine and general purpose analysis. It is easy to use but destructive of the sample.
alternative term: FID
term editor: PERSON:Daniel Schober
definition source: WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html>
editor preferred term: flame ionization detector
has curation status: IAO_0000120

vial
type: Class
subclass of: chromatography consumable
disjoint with: piston-seal
disjoint with: chromatography detector filter
disjoint with: detector lamp
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01117
definition: A vial is a cylindrical container often made from glass tubing.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: vial
has curation status: IAO_0000120

magic angle spinning rotor
type: Class
subclass of: device
subclass of: Restriction
  on property: is part of
  some values from: NMR instrument
disjoint with: Bruker SampleRail system
disjoint with: evaporative light scattering detector
disjoint with: autosampler
disjoint with: fluorescene detector
disjoint with: electrical conductivity detector
disjoint with: NMR instrument
disjoint with: refractive index detector
disjoint with: pulsed amperometric detector
disjoint with: glucometer
disjoint with: micro electrode
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument

Varian VXR spectrometer
type: Class
subclass of: Varian NMR instrument
disjoint with: Varian UNITY INOVA spectrometer
disjoint with: Varian UNITY spectrometer
disjoint with: Varian MERCURY spectrometer
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400238
definition: A Varian NMR spectrometer.
curator note: NMR instrument
term editor: PERSON:Daniel Schober
editor preferred term: Varian VXR spectrometer
definition source: WEB:<http://www.scs.uiuc.edu/NMR/instruments/vxr500.php>
has curation status: IAO_0000120

splitless GC injector
type: Class
subclass of: sample injection system
disjoint with: auto injector
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01060
definition: Injected sample enters column immediately (while split valve to split vent is closed). Here a sample is introduced into a heated small chamber via a syringe through a septum - the heat facilitates volatilization of the sample and sample matrix. The carrier gas then either sweeps the entirety (splitless mode) or a portion (split mode) of the sample into the column. In split mode, a part of the sample/carrier gas mixture in the injection chamber is exhausted through the split vent.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://en.wikipedia.org/wiki/Gas_chromatography>
editor preferred term: splitless GC injector
has curation status: IAO_0000120

preparative autosampler
type: Class
subclass of: liquid chromatography autosampler
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01062
definition: For preparative LC with injection of sample volumes ranging from L to mL ranges.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: preparative autosampler
has curation status: IAO_0000120

flow high resolution probe
type: Class
subclass of: Bruker high resolution probe
disjoint with: high resolution magic angle spin probe
disjoint with: high resolution probe with automatic tuning and matching
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400195
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition: Hyphenated analytical techniques combining mass spectrometry and chromatography are well-established laboratory tools. The combination of chromatography and NMR has also made its way into the analytical laboratory. Further developments even combine all three techniques into an LC-NMR/NMR-MS system. The use of solid phase extraction provides an efficient interface between chromatography and NMR with demands for special type of flow probes.
curator note: NMR probe
term editor: PERSON:Daniel Schober
alternative term: flow HR-probe
editor preferred term: flow high resolution probe
has curation status: IAO_0000120

liquid chromatography valve
type: Class
subclass of: chromatography device
disjoint with: column cartridge
disjoint with: gas chromatography equipment
disjoint with: column compartment
disjoint with: needle assembly
disjoint with: transfer line
disjoint with: column adapter
disjoint with: chromatography consumable
disjoint with: column frit
disjoint with: chart recorder
disjoint with: guard column
disjoint with: chromatography splitter
disjoint with: liquid chromatography instrument
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01110
definition: A sample valve that must be able to sustain pressures up to 10,000 p.s.i., although it is most likely to operate on a continuous basis, at pressures of 3,000 p.s.i. or less. The higher the operating pressure the tighter the valve seating surfaces must be forced together to eliminate any leak. It follows that any abrasive material, however fine, that passes into the valve can cause the valve seating to become scored each time it is rotated which will ultimately lead to leaks. This will cause the sample size to vary between samples and eventually affect the accuracy of the analysis. It follows that any solid material must be carefully removed from any sample before filling the valve. The sample volume of an internal loop valve is situated in the connecting slot of the valve rotor and can be used only for relatively small sample volumes. Internal sample loop valves provide samples with volumes ranging from 0.1 ml to about 0.5 ml. Valve operation is shown in figure 6. The left-hand side diagram shows the load position. The sample occupies the rotor slot and has been filled by passing the sample from an appropriate syringe through the rotor slot to waste. While loading the sample, the mobile phase supply is passed through the valve directly to the column. To place the sample onto the column, the valve is then rotated and the valve slot containing the sample is now placed between the solvent supply and the column. As a result, the sample is passed into the column by the flow of solvent.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.chromatography-online.org/EC-Dispersion/HPLC-Sample-Valves/rs16.html>
curator note: chromatography device
editor preferred term: liquid chromatography valve
has curation status: IAO_0000120

JEOL NMR probe
type: Class
subclass of: NMR probe
disjoint with: imaging NMR probe
disjoint with: liquid NMR probe
disjoint with: Bruker NMR probe
disjoint with: indirect detection probe
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400232
definition: An NMR probe that is manufactured by JEOL.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
editor preferred term: JEOL NMR probe
curator note: NMR device
term editor: PERSON:Daniel Schober
has curation status: IAO_0000120

Bruker UltraShield Plus NMR magnet
type: Class
subclass of: Bruker NMR magnet
disjoint with: Bruker UltraShield NMR magnet
disjoint with: Bruker Ultrastabilized NMR magnet
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400190
definition: An NMR magnet of which Brukers claims it is the latest and most advanced self-shielding NMR magnet technology ever developed. These magnets are the ultimate advancement in high performance, actively-shielded NMR solutions. They offer unprecedented shielding performance whilst ensuring no compromise in system homogeneity, stability or cryogenic specifications.
editor preferred term: Bruker UltraShield Plus NMR magnet
curator note: NMR instrument
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.bruker-biospin.com/nmr_magnets_usplus.html>
has curation status: IAO_0000120

Bruker CryoProbe
type: Class
subclass of: Bruker NMR probe
disjoint with: Bruker 1mm MicroProbe
disjoint with: Bruker micro imaging probe
disjoint with: Bruker solid magic angle spinning probe
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400191
editor preferred term: Bruker CryoProbe
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR probe
term editor: PERSON:Daniel Schober
definition: The Bruker BioSpin CryoProbe is a high-performance cryogenically cooled probe developed for high-resolution applications. It has improved signal/noise (S/N) ratios obtained by reducing the operating temperature of the coil and the pre-amplifier. As a result, the efficiency of the coil is improved and the noise of the coil and the pre-amplifier are reduced.The dramatic increase in the S/N ratio by a factor of 3-4, as compared to conventional probes, leads to a possible reduction in experiment time of up to 16 or a reduction in required sample concentration by a factor of up to 4. The CryoProbes possess key characteristics for NMR analysis:\n Significant S/N gains (with moderately salty samples also)\n Short pulse widths\n Short ring down times\n Linear behavior in power response\n Gradient capability\n CryoProbes are available as Triple Resonance, Dual, Selective X Detection, MicroImaging, and Quad Nucleus Probes configurations at 400 MHz and higher\n All high resolution probes have a lock circuit\n All high resolution probes have Z-gradient.
has curation status: IAO_0000120

column cartridge
type: Class
subclass of: chromatography device
disjoint with: gas chromatography equipment
disjoint with: column compartment
disjoint with: needle assembly
disjoint with: transfer line
disjoint with: column adapter
disjoint with: chromatography consumable
disjoint with: column frit
disjoint with: chart recorder
disjoint with: guard column
disjoint with: chromatography splitter
disjoint with: liquid chromatography instrument
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01055
definition: A device that binds the chromatography column and additional connector elements and / or valves or syringes into one physical unity for further processing.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
curator note: chromatography device, check on definition !
editor preferred term: column cartridge
has curation status: IAO_0000120

affinity column
type: Class
subclass of: chromatography column
disjoint with: ion exchange column
disjoint with: spin column
disjoint with: high temperature column
disjoint with: plunger column
disjoint with: liquid chromatography column
disjoint with: open tubular column
disjoint with: glass column
disjoint with: size exclusion column
disjoint with: custom made column
disjoint with: gel permeation column
disjoint with: carbon nanotube column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01094
definition: An affinity column is a chromatography column that is used in affinity chromatography. Differences in the affinity of molecules to be separated to a stationary phase are used for discriminate retention.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: affinity column
has curation status: IAO_0000120

tecmag NMR instrument
type: Class
subclass of: NMR instrument
disjoint with: Bruker NMR instrument
disjoint with: JEOL NMR instrument
disjoint with: Varian NMR instrument
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400250
definition: An NMR instrument that is manufactured by tecmag.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR instrument
term editor: PERSON:Daniel Schober
editor preferred term: tecmag NMR instrument
has curation status: IAO_0000120

gel filtration column
type: Class
subclass of: size exclusion column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01104
definition: A Gel filtration column is a chromatography column for size-exclusion chromatography, in which the stationary phase is a gel. The main application of gel filtration chromatography is the fractionation of proteins and other water-soluble polymers.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: gel filtration column
has curation status: IAO_0000120

fraction collector
type: Class
subclass of: chromatography instrument
disjoint with: column cartridger
disjoint with: chromatography pump system
disjoint with: column heater
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01073
definition: A fraction detector is a device that allows regular or specified samples to be taken from a column eluate and stored in a retrievable form. The storage vessels are usually small sample tubes or vials that are oriented in a rotating disk or in a moving belt, there movement usually being controlled by a microprocessor. On receiving a signal from the microprocessor, the next vial is placed under the column outlet and the eluate collected until receiving another signal from the computer. Once the properties of the chromatogram that describes the separation has been ascertained, then the collection program can be defined. The fractions can be collected on a basis of time either at regular intervals or a specific times to collect specific peaks. Alternatively the fractions can be collected by monitoring the detector output and when a peak starts to elute the fraction collector is activated and the peak collected in a specific vial. When the peak returns to base line the column eluate is then directed to waste until the next peak starts eluting. Fraction collectors are in common use with most liquid chromatographs. They are used to collect samples for further purification, subsequent examination by spectroscopic techniques or for biological or organoleptic testing.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.chromatography-online.org/topics/fraction/collector.html>
editor preferred term: fraction collector
has curation status: IAO_0000120

copy number variation profiling
type: Class
subclass of: assay
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: OBI_0001404
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
alternative term: CNV analysis
term editor: Philippe Rocca-Serra
example of usage: Profiling of copy number variations (CNVs) in healthy individuals from three ethnic groups using a human genome 32 K BAC-clone-based array. de Ståhl TD, Sandgren J, Piotrowski A, Nord H, Andersson R, Menzel U, Bogdan A, Thuresson AC, Poplawski A, von Tell D, Hansson CM, Elshafie AI, Elghazali G, Imreh S, Nordenskjöld M, Upadhyaya M, Komorowski J, Bruder CE, Dumanski JP. Hum Mutat. 2008 Mar;29(3):398-408. PMID: 18058796
editor preferred term: copy number variation profiling
definition: copy number variation profiling is a process which aims to provide information about lost or amplified genomic regions of DNA by comparing genomic DNA originated from tissues from same or different individuals using specific techniques such as CGH, array CGH, SNP genotyping.
has curation status: IAO_0000120

in-line filter
type: Class
subclass of: chromatography detector filter
disjoint with: syringe filter
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01123
definition: A solvent filter that sits between the pump and the injection valve that prevents dust particles, general debris and, to some extent, bacteria from entering the chromatography system. Contaminants can interfere with the low-pressure gradient former or the pump and particles entering valves may interfere with the proper function. The result could cause an increased baseline noise, non-repeatable gradient forming, unreliable flow rate or other interferences. Solvent in-line filters are low-pressure filters and will allow a high flow rate due to a large surface area and large porosity.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.appliedporous.com/frits-chromatography.htm>
editor preferred term: in-line filter
has curation status: IAO_0000120

imaging NMR probe
type: Class
subclass of: NMR probe
disjoint with: liquid NMR probe
disjoint with: Bruker NMR probe
disjoint with: indirect detection probe
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400244
definition: An NMR probe that is designed for generating pictures from sample states via NMR imaging.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR device
term editor: PERSON:Daniel Schober
editor preferred term: imaging NMR probe
has curation status: IAO_0000120

isolation of adherent cells
type: Class
subclass of: isolation of cell population
subclass of: Restriction
  on property: has_specified_output
  some values from: OBI_0100060
subclass of: Restriction
  on property: has_specified_input
  some values from: OBI_0100060
disjoint with: isolation of PBMCs
definition: a material separation process in which cells that stick to the container in which they are grown as a cell culture are separated from those in the liquid component of the culture. The output of this process are adherent cells.
editor preferred term: isolation of adherent cells
has curation status: IAO_0000123

Bruker AC series NMR instrument
type: Class
subclass of: Bruker NMR instrument
disjoint with: Bruker Capillary LC-NMR platform
disjoint with: AVANCE II spectrometer
disjoint with: Bruker LC-NMR/MS platform
disjoint with: Bruker SPE-NMR platform
disjoint with: Bruker Metabolic Profiler
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400241
definition: A series of older Bruker NMR magnets, now out of production.
editor preferred term: Bruker AC series NMR instrument
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR instrument
term editor: PERSON:Daniel Schober
has curation status: IAO_0000120

gas chromatography equipment
type: Class
subclass of: chromatography device
disjoint with: column compartment
disjoint with: needle assembly
disjoint with: transfer line
disjoint with: column adapter
disjoint with: chromatography consumable
disjoint with: column frit
disjoint with: chart recorder
disjoint with: guard column
disjoint with: chromatography splitter
disjoint with: liquid chromatography instrument
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01030
definition: Any device used in a gas chromatography experiment.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: gas chromatography equipment
curator note: will become defined class/xps
has curation status: IAO_0000120

syringe filter
type: Class
subclass of: chromatography detector filter
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01122
definition: A small membrane filter of defined pore size, that filters samples from a syringe.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: syringe filter
has curation status: IAO_0000120

Bruker SampleRail system
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: transfer function
disjoint with: evaporative light scattering detector
disjoint with: autosampler
disjoint with: fluorescene detector
disjoint with: electrical conductivity detector
disjoint with: NMR instrument
disjoint with: refractive index detector
disjoint with: pulsed amperometric detector
disjoint with: glucometer
disjoint with: micro electrode
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance

column compartment
type: Class
subclass of: chromatography device
disjoint with: needle assembly
disjoint with: transfer line
disjoint with: column adapter
disjoint with: chromatography consumable
disjoint with: column frit
disjoint with: chart recorder
disjoint with: guard column
disjoint with: chromatography splitter
disjoint with: liquid chromatography instrument
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01068
definition: For chromatography analyses, the ability to maintain a stable column environment regardless of ambient temperature fluctuations is critical for maintaining retention time precision. In order to ensure such stable conditions at different chromatography steps a column compartment can be installed that ensures e.g. stable temperature of the column in a given step.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: column compartment
has curation status: IAO_0000120

capillary pump system
type: Class
subclass of: chromatography pump system
disjoint with: isocratic pump system
disjoint with: flash pump system
disjoint with: gradient pump system
disjoint with: quaternary pump system
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01051
definition: A pump system optimized for capillary chromatography.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: capillary pump system
has curation status: IAO_0000120

evaporative light scattering detector
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
disjoint with: autosampler
disjoint with: fluorescene detector
disjoint with: electrical conductivity detector
disjoint with: NMR instrument
disjoint with: refractive index detector
disjoint with: pulsed amperometric detector
disjoint with: glucometer
disjoint with: micro electrode
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument

isolation of PBMCs
type: Class
subclass of: isolation of cell population
subclass of: Restriction
  on property: has_specified_output
  some values from: OBI_0100060
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: separation into different composition objective
subclass of: Restriction
  on property: has_specified_input
  some values from: UBERON_0000178
term editor: PERSON: bjoern peters
definition: a process in which cells with a single nucleus are isolated from a blood sample
example of usage: cells are extracted from whole blood using ficoll, a hydrophilic polysaccharide that separates layers of blood, with monocytes and lymphocytes forming a buffy coat under a layer of plasma. This buffy coat contains the PBMCs.
editor preferred term: isolation of PBMCs
definition source: wiki http://en.wikipedia.org/wiki/PBMC
has curation status: IAO_0000120

column cartridger
type: Class
subclass of: chromatography instrument
disjoint with: chromatography pump system
disjoint with: column heater
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01054
definition: A chromatography device where the column cartridge is inserted into and stabilised.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
curator note: check on definition !
editor preferred term: column cartridger
has curation status: IAO_0000120

nitrogen generator
type: Class
subclass of: gas generator
disjoint with: hydrogen generator
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01034
definition: A gas generator that generates nitrogen gas.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: nitrogen generator
has curation status: IAO_0000120

needle assembly
type: Class
subclass of: chromatography device
disjoint with: transfer line
disjoint with: column adapter
disjoint with: chromatography consumable
disjoint with: column frit
disjoint with: chart recorder
disjoint with: guard column
disjoint with: chromatography splitter
disjoint with: liquid chromatography instrument
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01065
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
definition: The needle assembly attached to the autosampler, comprises the injector needle that feeds a sample or carrier gas into the inlet
curator note: chromatography device, check on definition !
editor preferred term: needle assembly
has curation status: IAO_0000120

reverse transcribed polymerase chain reaction
type: Class
subclass of: OBI_0600058
subclass of: Restriction
  on property: has_specified_input
  some values from: ribonucleic acids
subclass of: Restriction
  on property: has_specified_output
  some values from: PCR product
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: polymerase chain reaction
    intersection of: Restriction
      on property: is immediately preceded by
      some values from: OBI_0600028
disjoint with: OBI_0001494
disjoint with: OBI_0600049
disjoint with: OBI_0600057
editor note: 3/21/10, BP:Modified definition to clarify that this is not the assay, but the material transformation
example of usage: Harmonisation of multi-centre real-time reverse-transcribed PCR results of a candidate prognostic marker in breast cancer: an EU-FP6 supported study of members of the EORTC - PathoBiology Group. Span PN, Sieuwerts AM, Heuvel JJ, Spyratos F, Duffy MJ, Eppenberger-Castori S, Vacher S, O'Brien K, McKiernan E, Pierce A, Vuaroqueaux V, Foekens JA, Sweep FC, Martens JW. Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094
term editor: Philippe Rocca-Serra
alternative term: RT-PCR
definition: reverse transcribe pcr is a process which allow amplification of cDNA during a pcr reaction while the cDNA results from a retrotranscription of messenger RNA isolated from a material entity.
editor preferred term: reverse transcribed polymerase chain reaction
alternative term: reverse transcription polymerase chain reaction
has curation status: IAO_0000123

Bruker Capillary LC-NMR platform
type: Class
subclass of: Bruker NMR instrument
disjoint with: AVANCE II spectrometer
disjoint with: Bruker LC-NMR/MS platform
disjoint with: Bruker SPE-NMR platform
disjoint with: Bruker Metabolic Profiler
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400279
curator note: hyphenated NMR instrument platform
editor preferred term: Bruker Capillary LC-NMR platform
definition: Capillary LC-NMR is a hyphenated technique coupling capillary liquid chromatography and NMR, which increases sensitivity dramatically through the use of miniaturization of the chromatographic techniques and NMR detection volume. LC-NMR hyphenated systems separate a mixture into its pure components and couple the output to NMR for automatic sample analysis. The ever increasing need to measure lower sample amounts and lower level impurities demands the highest NMR sensitivity. Traditional LC-NMR systems with relatively large peak volumes are not optimized for such low levels of detection. Bruker BioSpin, together with Waters and Protasis has developed a Capillary LC-NMR system. The latest capillary LC attributes and highest capillary flow probe sensitivity combine with state of the art NMR systems technology. Greater mass sensitivity and faster spectral analysis with smaller sample volumes is possible. This system is ideal for analysis of metabolites and impurities associated with the drug development process.
curator note: NMR instrument
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.bruker-biospin.com/hyphenation_caplcnmr.html>
has curation status: IAO_0000120

gas chromatography oven
type: Class
subclass of: gas chromatography equipment
disjoint with: gas purifier
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01039
definition: A gas chromatography oven is an oven with a heated connection between the GC and the MS instrument in a GCMS-analysis, that keeps compounds in the gas phase as they leave the GC oven.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
curator note: gas chromatography equipment
editor preferred term: gas chromatography oven
has curation status: IAO_0000120

autosampler
type: Class
subclass of: device
disjoint with: fluorescene detector
disjoint with: electrical conductivity detector
disjoint with: NMR instrument
disjoint with: refractive index detector
disjoint with: pulsed amperometric detector
disjoint with: glucometer
disjoint with: micro electrode
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer

isocratic pump system
type: Class
subclass of: chromatography pump system
disjoint with: flash pump system
disjoint with: gradient pump system
disjoint with: quaternary pump system
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01049
definition: A pump system optimized for isocratic chromatography.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.buchi.com/Isocratic-Pump-System.253.0.html>
editor preferred term: isocratic pump system
has curation status: IAO_0000120

flash pump system
type: Class
subclass of: chromatography pump system
disjoint with: gradient pump system
disjoint with: quaternary pump system
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01048
definition: Any pump system used in flash column chromatography to push the solvent through the column. Better flow rates can be achieved by using a pump or by using compressed gas (e.g. air, nitrogen, or argon) to push the solvent through the column (flash column chromatography).
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: flash pump system
has curation status: IAO_0000120

Varian UNITY INOVA spectrometer
type: Class
subclass of: Varian NMR instrument
disjoint with: Varian UNITY spectrometer
disjoint with: Varian MERCURY spectrometer
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400236
curator note: NMR instrument
term editor: PERSON:Daniel Schober
definition: The UNITY INOVA is also the easiest spectrometer to use and is also the choice of those interested in using advanced NMR techniques in their own research, but without becoming, or hiring, an NMR expert. A complete set of turnkey operating environments is available for the UNITY INOVA covering the structure and dynamics of biological macromolecules, small molecules, solids, and imaging. These packages put the combined NMR expertise of the entire Varian NMR community at your fingertips.
editor preferred term: Varian UNITY INOVA spectrometer
definition source: WEB:<http://www.varianinc.com/cgi-bin/nav?products/NMR/spectromet/inova/index&cid=HFIH>
has curation status: IAO_0000120

liquid NMR probe
type: Class
subclass of: NMR probe
disjoint with: Bruker NMR probe
disjoint with: indirect detection probe
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400242
definition: An NMR probe that is designed to hold a liquid sample.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR device
term editor: PERSON:Daniel Schober
editor preferred term: liquid NMR probe
has curation status: IAO_0000120

ion exchange column
type: Class
subclass of: chromatography column
disjoint with: spin column
disjoint with: high temperature column
disjoint with: plunger column
disjoint with: liquid chromatography column
disjoint with: open tubular column
disjoint with: glass column
disjoint with: size exclusion column
disjoint with: custom made column
disjoint with: gel permeation column
disjoint with: carbon nanotube column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01105
definition: An ion exchange column is a chromatography column that is used in ion exchange chromatography and anion or cation exchange resins to enable separation.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: ion exchange column
has curation status: IAO_0000120

Bruker NMR probe
type: Class
subclass of: NMR probe
disjoint with: indirect detection probe
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400231
definition: An NMR probe that is manufactured by Bruker.
editor preferred term: Bruker NMR probe
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR device, TODO: May need no definition.
term editor: PERSON:Daniel Schober
has curation status: IAO_0000120

anion trap column
type: Class
subclass of: trap column
disjoint with: cation trap column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01277
definition: An anion trap column is a trap column and ion-exchange column which contains cationic anion-exchange resins.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: anion trap column
has curation status: IAO_0000120

fluorescene detector
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
disjoint with: electrical conductivity detector
disjoint with: NMR instrument
disjoint with: refractive index detector
disjoint with: pulsed amperometric detector
disjoint with: glucometer
disjoint with: micro electrode
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source

tecmag EAGLE probe
type: Class
subclass of: solid NMR probe
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400248
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR probe
term editor: PERSON:Daniel Schober
definition: The Eagle is a 4 mm 1H/X solid-state MAS probe with a top spinning speed of 18 kHz. Its simple design is robust, reliable and easy to spin. Configurations are available for 200 to 600 MHz wide bore magnets on Tecmag, Bruker, Chemagnetics, JEOL and Varian spectrometers.
editor preferred term: tecmag EAGLE probe
has curation status: IAO_0000120

electrical conductivity detector
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
disjoint with: NMR instrument
disjoint with: refractive index detector
disjoint with: pulsed amperometric detector
disjoint with: glucometer
disjoint with: micro electrode
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007

NMR instrument
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
disjoint with: refractive index detector
disjoint with: pulsed amperometric detector
disjoint with: glucometer
disjoint with: micro electrode
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008

Bruker UltraShield NMR magnet
type: Class
subclass of: Bruker NMR magnet
disjoint with: Bruker Ultrastabilized NMR magnet
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400187
definition: An NMR magnet manufactured by Bruker that ensures field homogeneity without amplified effects from vibrations or thermal changes. This magnet technology uses active shielding and optimizes coil design.
editor preferred term: Bruker UltraShield NMR magnet
curator note: NMR instrument
term editor: PERSON:Daniel Schober
has curation status: IAO_0000120

piston-seal
type: Class
subclass of: chromatography consumable
disjoint with: chromatography detector filter
disjoint with: detector lamp
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01116
term editor: PERSON:Daniel Schober
definition: The seal made by a piston in a diaphragm pump. The unique property of the reciprocating diaphragm pump is that the actuating piston does not come into direct contact with the mobile phase and thus, the demands on the piston-cylinder seal are not so great. The diaphragm has a relatively high surface area and thus, the movement of the diaphragm is relatively small and consequently the pump can be operated at a fairly high frequency. High frequency pumping results in a very significant reduction in pulse amplitude and, in addition, high frequency pulses are more readily damped by the column system. Nevertheless, it must be emphasized that diaphragm pumps are not pulseless.
definition source: WEB:<http://www.chromatography-online.org/HPLC/Basic-HPLC/Pump/Diaphragm/rs15.html>
editor preferred term: piston-seal
has curation status: IAO_0000120

mass selective detector
type: Class
subclass of: gas chromatography detector
disjoint with: flame photometric detector
disjoint with: ozone-induced chemiluminescence detector
disjoint with: fluorine-induced chemiluminescence detector
disjoint with: atomic emission detector
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01198
definition: A mass selective detector is a GC detector that uses mass spectrometry. It is based upon the ionization of solute molecules in the ion source and the separation of the ions generated on the basis of their mass/charge ratio by an analyzer unit. This may be a magnetic sector analyzer, a quadruple mass filter, or an ion trap. Ions are detected by a dynode electron multiplier.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html>
editor preferred term: mass selective detector
alternative term: mass spectrometry detector
has curation status: IAO_0000120

spin column
type: Class
subclass of: chromatography column
disjoint with: high temperature column
disjoint with: plunger column
disjoint with: liquid chromatography column
disjoint with: open tubular column
disjoint with: glass column
disjoint with: size exclusion column
disjoint with: custom made column
disjoint with: gel permeation column
disjoint with: carbon nanotube column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01232
definition: A spin column is a chromatography column which is suitable for putting it into a centrifuge. A spin column enforces separation through increased G-forces while spinning the column in a centrifuge. It is often used in DNA gel extraction kits.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: spin column
has curation status: IAO_0000120

manufacturer role
type: Class
subclass of: role
subclass of: Restriction
  on property: is realized by
  all values from: manufacturing
subclass of: Restriction
  on property: inheres in
  some values from: Class
    union of: Homo sapiens
    union of: organization
disjoint with: pathogen role
disjoint with: host role
disjoint with: test substance role
disjoint with: complementary nucleotide probe role
disjoint with: service consumer role
disjoint with: service provider role
disjoint with: accessed material role
disjoint with: OBI_0302731
disjoint with: OBI_0302732
disjoint with: OBI_0302733
disjoint with: OBI_1110082
disjoint with: OBI_1110083
disjoint with: OBI_1110086
disjoint with: OBI_1110087
disjoint with: OBI_1110091
disjoint with: OBI_1110092
disjoint with: OBI_1110120
term editor: GROUP: Role Branch
definition: Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process.
definition source: OBI
example of usage: With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role.
editor preferred term: manufacturer role
has curation status: IAO_0000123

transfer line
type: Class
subclass of: chromatography device
disjoint with: column adapter
disjoint with: chromatography consumable
disjoint with: column frit
disjoint with: chart recorder
disjoint with: guard column
disjoint with: chromatography splitter
disjoint with: liquid chromatography instrument
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01235
definition: A combination of devices that are used in connection with a sampling head for transferring components of an applied sample to the analyzing part of a chromatography system.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.freepatentsonline.com/5702671.html>
curator note: chromatography device
editor preferred term: transfer line
has curation status: IAO_0000120

gradient pump system
type: Class
subclass of: chromatography pump system
disjoint with: quaternary pump system
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01050
definition: A pump system optimized for gradient chromatography.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.buchi.com/Gradient-Pump-System.531.0.html>
editor preferred term: gradient pump system
has curation status: IAO_0000120

high temperature column
type: Class
subclass of: chromatography column
disjoint with: plunger column
disjoint with: liquid chromatography column
disjoint with: open tubular column
disjoint with: glass column
disjoint with: size exclusion column
disjoint with: custom made column
disjoint with: gel permeation column
disjoint with: carbon nanotube column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01233
definition: A high temperature column is a chromatography column which is suitable for and withstands very high temperatures in chromatography ovens.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: high temperature column
has curation status: IAO_0000120

Bruker Ultrastabilized NMR magnet
type: Class
subclass of: Bruker NMR magnet
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400188
definition: An NMR magnet manufactured by Bruker for Ultra-High Field NMR, available from 750 MHz to 900 MHz, which provides reliable operation at reduced temperature and ambient pressure via being rigidly mounted and stabilized.
editor preferred term: Bruker Ultrastabilized NMR magnet
curator note: NMR instrument
term editor: PERSON:Daniel Schober
has curation status: IAO_0000120

scattered molecular aggregate
type: Class
subclass of: material entity
subclass of: Restriction
  on property: has grain
  all values from: molecular entity
subclass of: Restriction
  on property: has grain
  some values from: molecular entity
disjoint with: urine specimen
disjoint with: blood specimen
disjoint with: whole organism preparation
disjoint with: capsule shell
disjoint with: guar gum
disjoint with: cloacal specimen
disjoint with: nasopharyngeal aspirate specimen
disjoint with: nasal swab specimen
disjoint with: device
disjoint with: growth environment
disjoint with: OBI_0001468
disjoint with: OBI_0001485
disjoint with: OBI_0100014
disjoint with: OBI_0100016
disjoint with: OBI_0100017
disjoint with: OBI_0100055
disjoint with: OBI_0100058
disjoint with: OBI_0100060
disjoint with: OBI_0100067
disjoint with: OBI_0100086
disjoint with: OBI_1000023
disjoint with: OBI_1000024
disjoint with: OBI_1000029
disjoint with: OBI_1000036
disjoint with: OBI_1000042
editor preferred term: scattered molecular aggregate
example of usage: the sodium and chloride ions in a glass of salt water
definition: A scattered molecular aggregate is a material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates
alternative term: Collective
definition source: Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
term editor: PERSON: Alan Ruttenberg
has curation status: IAO_0000123

obsolete_molecular concentration
type: Class
subclass of: ObsoleteClass
definition: A concentration is a relational quality that inheres in a material entity towards molecular scattered aggregate that is part of it by virtue of some ratio of masses of the two or the counts of the grains of the two or volume occupied by the larger material entity.
definition source: Discussion in Karslruhe, Oct 2008, with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg.
editor note: JZ: Can we replace the term by PATO: http://purl.obolibrary.org/obo/PATO_0000033 If not, we will wait the term available in PATO. Although specified that obsolete reason is 'term imported', the term has not imported yet. Will keep tracking this term until import the replaced term. Term depracted since the object property 'towards' used in the axioms is not avaliable in BFO2.
term editor: PERSON: Alan Ruttenberg
editor note: This term represent a quality of molecular concentration. If there is need for some other sort of concentration - e.g. ratio of counts of cells, another term is needed. OBI uses a standard unit for representing concentration qualities but this still needs to be decided on. A relation needs to be defined that relates the quality instance to the representation of its quantitative value in the chosen units. See http://en.wikipedia.org/wiki/Concentration Measurements of concentration may be in any appropriate unit. Note that precise concentrations are virtually never known. Finally, note that there is no such thing as a concentration of 0. A concentration is a *relational* quality and so can't exist unless both entities it inheres in exist. However one map make concentration measurements that turn out not to be about concentrations qualities, if it happens that the scattered molecular aggregate doesn't actually exist.
editor note: logical definition in OBI: 'quality of related physical entities' ('inheres in' some material_entity) and (towards some 'scattered molecular aggregate')
editor preferred term: molecular concentration
example of usage: the phosphate concentration should be 0.1M
deprecated: true
has curation status: IAO_0000123
has obsolescence reason: IAO_0000228

NMR sample tube
type: Class
subclass of: test tube
subclass of: Restriction
  on property: is part of
  some values from: NMR instrument
disjoint with: anticoagulant-containing test tube
disjoint with: OBI_0400020
disjoint with: OBI_0400091
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400132
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR device
editor preferred term: NMR sample tube
term editor: PERSON:Daniel Schober
definition: The sample-tube holds the NMR sample and sits in the nmr probe. It is usually a glass tube of 5-20mm diameter.
has curation status: IAO_0000120

Varian UNITY spectrometer
type: Class
subclass of: Varian NMR instrument
disjoint with: Varian MERCURY spectrometer
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400237
curator note: NMR instrument
term editor: PERSON:Daniel Schober
definition: The predecessor series of the Varian UNITY INOVA spectrometer.
editor preferred term: Varian UNITY spectrometer
definition source: WEB:<http://www.scs.uiuc.edu/NMR/instruments/u400.php>
has curation status: IAO_0000120

AVANCE II spectrometer
type: Class
subclass of: Bruker NMR instrument
disjoint with: Bruker LC-NMR/MS platform
disjoint with: Bruker SPE-NMR platform
disjoint with: Bruker Metabolic Profiler
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400197
definition: A spectrometer suitable for metabolomics and in vivo NMR studies but structural analysis of small molecules and low molecular weight proteins can also be performed. To accomplish these studies there are six probe-heads available. A successor, the AVANCE III came out recently.
editor preferred term: AVANCE II spectrometer
curator note: NMR instrument
term editor: PERSON:Daniel Schober
definition source: WEB:<http://cermax.itqb.unl.pt/mambo/en/index.php?option=com_content&task=view&id=36&Itemid=93>
has curation status: IAO_0000120

y-column connector
type: Class
subclass of: column connector
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01237
definition: A column connector that connects one column on one side with two columns at the other side, hence building a Y shaped structure.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: y-column connector
has curation status: IAO_0000120

Bruker LC-NMR/MS platform
type: Class
subclass of: Bruker NMR instrument
disjoint with: Bruker SPE-NMR platform
disjoint with: Bruker Metabolic Profiler
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400277
curator note: hyphenated NMR instrument platform
editor preferred term: Bruker LC-NMR/MS platform
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition: Includes the connection to a high-resolution TOF-LC-MS system.
curator note: NMR instrument
term editor: PERSON:Daniel Schober
has curation status: IAO_0000120

refractive index detector
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
disjoint with: pulsed amperometric detector
disjoint with: glucometer
disjoint with: micro electrode
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019

anion exchange column
type: Class
subclass of: ion exchange column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01095
definition: An anion exchange column is a chromatography column that is used in anion exchange chromatography and which enables the separation of anion mixtures.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: anion exchange column
has curation status: IAO_0000120

plunger column
type: Class
subclass of: chromatography column
disjoint with: liquid chromatography column
disjoint with: open tubular column
disjoint with: glass column
disjoint with: size exclusion column
disjoint with: custom made column
disjoint with: gel permeation column
disjoint with: carbon nanotube column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01108
definition: A plunger column is a chromatography column with adjustable heigth control. By means of an adjustable endpiece (plunger) the user can adjust the column length without disturbing the packed bed. Plunger columns can equalize volume changes and thus avoids dead volumes within the column.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: plunger column
has curation status: IAO_0000120

flame photometric detector
type: Class
subclass of: gas chromatography detector
disjoint with: ozone-induced chemiluminescence detector
disjoint with: fluorine-induced chemiluminescence detector
disjoint with: atomic emission detector
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01091
alternative term: FPD
term editor: PERSON:Daniel Schober
definition: The determination of sulfur or phosphorus containing compounds is the job of the flame photometric detector (FPD). This device uses the chemiluminescent reactions of these compounds in a hydrogen/air flame as a source of analytical information that is relatively specific for substances containing these two kinds of atoms. The emitting species for sulfur compounds is excited S2. The lambda max for emission of excited S2 is approximately 394 nm. The emitter for phosphorus compounds in the flame is excited HPO (lambda max = doublet 510-526 nm). In order to selectively detect one or the other family of compounds as it elutes from the GC column, an interference filter is used between the flame and the photomultiplier tube (PMT) to isolate the appropriate emission band. The drawback here being that the filter must be exchanged between chromatographic runs if the other family of compounds is to be detected.
definition source: WEB:<http://www.shsu.edu/~chemistry/FPD/FPD.html>
editor preferred term: flame photometric detector
has curation status: IAO_0000120

chromatography pump system
type: Class
subclass of: chromatography instrument
disjoint with: column heater
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01046
definition: Better flow rates can be achieved by using a pump or by using compressed gas (e.g. air, nitrogen, or argon) to push the solvent through the column (flash column chromatography).
term editor: PERSON:Daniel Schober
definition source: WEB:<http://en.wikipedia.org/wiki/Column_chromatography>
editor preferred term: chromatography pump system
has curation status: IAO_0000120

Bruker 1mm MicroProbe
type: Class
subclass of: Bruker NMR probe
disjoint with: Bruker micro imaging probe
disjoint with: Bruker solid magic angle spinning probe
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400194
editor preferred term: Bruker 1mm MicroProbe
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR probe
definition: Over the past few years there has been a significantly growing demand for miniaturization in all areas ofmodern research and development. Evoked by many exciting applications, there is a need for analytical methods which require less amounts of sample. Bruker BioSpin meets this challenge with a revolutionary NMR probe design: The 1mm MicroProbe. It operates with disposable 1mm capillary sample tubes and the sample volume of 5 microliters enables the use of lowest amounts of sample to run all high resolution NMR experiments with outstanding sensitivity and up to 16 times faster measurements. Due to the TXI-type probe design, the z-gradient coil and the automatic matching and tuning accessory, the 1mm MicroProbe can be used for a wide variety of NMR experiments. The key advantages of this probe include:\n up to 4 times higher mass sensitivity than 5mm conventional probes (with respect to the same sample amount)\n excellent solvent suppression properties\n virtually no salt effect\n discrete samples in tubes that can be sealed and stored\n automation accessory for sample preparation and handling available.
term editor: PERSON:Daniel Schober
has curation status: IAO_0000120

Bruker BEST NMR system
type: Class
subclass of: Bruker autosampler
disjoint with: Bruker SampleJet system
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400206
editor preferred term: Bruker BEST NMR system
alternative term: Bruker Efficient Sample Transfer NMR
curator note: NMR instrument
term editor: PERSON:Daniel Schober
definition: The introduction of biological screening and combinatorial chemistry for chemical synthesis has also introduced new requirements for NMR automation, e.g., the use of well plates for sample input, increased demands on throughput, and the need for quick and simple interpretation of the acquired NMR data.
definition source: WEB:<http://www.bruker-biospin.com/automation.html>
has curation status: IAO_0000120

chromatography detector filter
type: Class
subclass of: chromatography consumable
disjoint with: detector lamp
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01121
definition: An optical filter that is used to obtain monochromatic light of a defined wavelength from detector lamps.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: chromatography detector filter
has curation status: IAO_0000120

cation trap column
type: Class
subclass of: trap column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01278
definition: A cation trap column is a trap column and ion-exchange column which contains anionic cation-exchange resins.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: cation trap column
has curation status: IAO_0000120

column adapter
type: Class
subclass of: chromatography device
disjoint with: chromatography consumable
disjoint with: column frit
disjoint with: chart recorder
disjoint with: guard column
disjoint with: chromatography splitter
disjoint with: liquid chromatography instrument
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01113
definition: An Adapter that enabled the connection of a column to additional devices.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
curator note: chromatography device
editor preferred term: column adapter
has curation status: IAO_0000120

pulsed amperometric detector
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
disjoint with: glucometer
disjoint with: micro electrode
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032

Bruker NMR instrument
type: Class
subclass of: NMR instrument
disjoint with: JEOL NMR instrument
disjoint with: Varian NMR instrument
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400198
definition: An NMR instrument that is manufactured by Bruker.
editor preferred term: Bruker NMR instrument
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR instrument
term editor: PERSON:Daniel Schober
has curation status: IAO_0000120

Bruker NMR magnet
type: Class
subclass of: NMR magnet
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400186
definition: An NMR magnet that is manufactured by Bruker.
editor preferred term: Bruker NMR magnet
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR instrument
term editor: PERSON:Daniel Schober
has curation status: IAO_0000120

ozone-induced chemiluminescence detector
type: Class
subclass of: gas chromatography detector
disjoint with: fluorine-induced chemiluminescence detector
disjoint with: atomic emission detector
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01088
definition: Although there are many direct ozone chemiluminescent reactions with various gaseous molecules, the incorporation of a conversion step to convert various non-chemiluminescent analytes to a species capable of reacting with ozone to produce chemiluminescence broadens the horizon of this technique tremendously. The conversion of nearly all nitrogen- and sulfur-containing compounds to their respective chemiluminescent species for universal nitrogen and sulfur detection has made nitrogen/sulfur chemiluminescence detection the most widely used analytical methods based upon ozone-induced chemiluminescence. In addition to non-chromatographic applications, nitrogen/sulfur chemiluminescence detection has been adapted to various chromatographic techniques from gas chromatography to liquid and supercritical fluid chromatography as specialized element-specific detectors. The characteristics of these detectors are evaluated and compared to other element-selective detection techniques. The unique features of the chemiluminescence detectors have made them powerful tools in many diverse fields of analytical chemistry.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://sangerhinxtongbr.library.ingentaconnect.com/content/els/00219673/1999/00000842/00000001/art00177>
editor preferred term: ozone-induced chemiluminescence detector
has curation status: IAO_0000120

tecmag NMR console
type: Class
subclass of: NMR console
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400246
definition: An NMR console manufactured by tecmac.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR instrument
term editor: PERSON:Daniel Schober
editor preferred term: tecmag NMR console
has curation status: IAO_0000120

JEOL NMR instrument
type: Class
subclass of: NMR instrument
disjoint with: Varian NMR instrument
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400226
definition: An NMR instrument that is manufactured by JEOL.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
editor preferred term: JEOL NMR instrument
curator note: NMR instrument
term editor: PERSON:Daniel Schober
has curation status: IAO_0000120

chromatography consumable
type: Class
subclass of: chromatography device
disjoint with: column frit
disjoint with: chart recorder
disjoint with: guard column
disjoint with: chromatography splitter
disjoint with: liquid chromatography instrument
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01115
definition: A chromatography consumable is a consumable that is used in a chromatography experiment.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: chromatography consumable
curator note: chromatography device
has curation status: IAO_0000120

column frit
type: Class
subclass of: chromatography device
disjoint with: chart recorder
disjoint with: guard column
disjoint with: chromatography splitter
disjoint with: liquid chromatography instrument
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01070
definition: A part of the column content that separates column packing compartments. In radial columns the packing is supported between two cylindrical frits and the gap between represents the bed height or column length. The outer frit is the column inlet and consequently the sample initially has a large area of stationary phase with which to interact. Frits are porous metal products to prevent unwanted particles from entering the chromatography system. These particles may come from the sample, the solvent or debris generated by the chromatography system itself. Such particles entering the system may lead to clogging of capillaries, interference with the chromatography by changing chromatographic parameters or disturbance of the detector function. Characteristics of a frit, besides the diameter and the thickness, is the porosity (pore distribution, density).
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.chromatography-online.org/topics/radial/columns.html>
curator note: chromatography device
editor preferred term: column frit
has curation status: IAO_0000120

liquid chromatography column
type: Class
subclass of: chromatography column
disjoint with: open tubular column
disjoint with: glass column
disjoint with: size exclusion column
disjoint with: custom made column
disjoint with: gel permeation column
disjoint with: carbon nanotube column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01227
definition: A liquid chromatography column is a chromatography column that is used in liquid chromatography, i.e. a column that is provided with a liquid sample mix.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: liquid chromatography column
has curation status: IAO_0000120

detector lamp
type: Class
subclass of: chromatography consumable
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01119
definition: A lamp used in a chromatography detector that excites sample molecules at certain frequencies / emission wavelengths, e.g. Mercury Vapor Lamp (253.7 nm), Zinc Vapor Lamp (2123.9 nm and 307.6 nm), Cadmium Vapor Lamp (228.8, 326.1,340.3, and 346.6 nm). To obtain monochromatic light an appropriate light filter would be needed.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.chromatography-online.org/HPLC/UV-Detectors/Fixed-Wavelength/rs23.html>
editor preferred term: detector lamp
has curation status: IAO_0000120

chart recorder
type: Class
subclass of: chromatography device
disjoint with: guard column
disjoint with: chromatography splitter
disjoint with: liquid chromatography instrument
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01069
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
definition: The chart recorder is a device that transduces signal-intensities into a graphical peak output: As the separated components of the gas sample emerge into the detector, the change in voltage in the detecting bridge circuit causes a representative peak to be drawn on a chart recorder. The position of the peak along the time axis of the chart measures the component's retention time, which identifies the component. This is directly related to carrier gas flow rate, temperature and column packing and dimensions. The area under each peak is proportional to the concentration of the component of the sample. The area of the peaks inscribed on the chart recorder can be determined by multiplying the height of the peak in mm, by the width of the peak in mm at 1/2 the peak height. The calibration curves for use with the chart recorder are therefore peak area plotted against concentration.
editor preferred term: chart recorder
curator note: chromatography device
has curation status: IAO_0000120

open tubular column
type: Class
subclass of: chromatography column
disjoint with: glass column
disjoint with: size exclusion column
disjoint with: custom made column
disjoint with: gel permeation column
disjoint with: carbon nanotube column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01219
definition: An open tubular column is a chromatography column in which the particles of the solid stationary phase or the support coated with a liquid stationary phase are concentrated on or along the inside tube wall leaving an open, unrestricted path for the mobile phase in the middle part of the tube.
term editor: PERSON:Daniel Schober
definition source: WEB:<http:www.iupac.org/publications/pac/1993/pdf/6504x0819.pdf>
editor preferred term: open tubular column
has curation status: IAO_0000120

high resolution magic angle spin probe
type: Class
subclass of: Bruker high resolution probe
disjoint with: high resolution probe with automatic tuning and matching
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400192
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR probe
term editor: PERSON:Daniel Schober
definition: Samples that are neither solid nor liquid, being of biological, chemical, or pharmaceutical interest, reveal highly resolved spectra when magic angle spinning is applied. The correct solution is a gradient, such that the field varies along the spinner axis. This so-called Magic Angle Gradient is employed in Brukers high resolution Magic Angle Spinning (hr-MAS) probes, and is implemented in such a way that it is compatible with the stator and does not interfere with the sample eject or insert. Bruker BioSpin has developed a series of dedicated probes for standard bore magnets to accommodate the rapidly expanding field of hr-MAS. These probes are available in double (e.g. 1H and 13C) and triple resonance (e.g. 1H, 13C, 15N) modes and come equipped with a deuterium lock channel. The probes have automatic sample ejection and insertion capability, with the availability of an optional sample changer, enabling fully automated sample runs. Probes can be equipped with an optional B0 gradient, directed along the magic angle, so that gradient spectroscopy can be done used.
alternative term: high resolution MAS, hr-MAS
editor preferred term: high resolution magic angle spin probe
has curation status: IAO_0000120

hydrogen generator
type: Class
subclass of: gas generator
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01035
definition: A gas generator that generates hydrogen gas.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: hydrogen generator
has curation status: IAO_0000120

glass column
type: Class
subclass of: chromatography column
disjoint with: size exclusion column
disjoint with: custom made column
disjoint with: gel permeation column
disjoint with: carbon nanotube column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01101
definition: A glass column is a chromatography column made out of glass that is usually used for larger scale and preparative liquid chromatography separations.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: glass column
has curation status: IAO_0000120

auto injector
type: Class
subclass of: sample injection system
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01058
definition: A gas chromatography device that can auto-inject a small number of samples an inlet.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: auto injector
has curation status: IAO_0000120

Varian NMR instrument
type: Class
subclass of: NMR instrument
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400234
definition: An NMR instrument that is manufactured by Varian.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR instrument
term editor: PERSON:Daniel Schober
editor preferred term: Varian NMR instrument
has curation status: IAO_0000120

Bruker MATCH tube holder system
type: Class
subclass of: NMR sample holder
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400211
editor preferred term: Bruker MATCH tube holder system
alternative term: Bruker Multiple Adjustable Tube Clamp Holder
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR instrument
term editor: PERSON:Daniel Schober
definition: The Bruker Multiple Adjustable Tube Clamp Holder MATCH system is a holder for 100 mm long NMR sample tubes with diameters ranging from micro tubes up to 5 mm NMR tubes. The MATCH insert fits into a standard 10 mm Bruker spinner and is suitable for all non-spinning applications.\n The MATCH system provides an easy and cost efficient means of optimizing the signal-to-noise ratio of each sample. By matching the NMR tube diameter to the size of the sample, most of the sample can be placed in the active column of the NMR coil. This leads to an enhanced signal detection compared to diluting the same sample quantity in a larger tube.
has curation status: IAO_0000120

Bruker SPE-NMR platform
type: Class
subclass of: Bruker NMR instrument
disjoint with: Bruker Metabolic Profiler
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400278
curator note: hyphenated NMR instrument platform
definition: A Solid Phase Extraction (SPE) system provides an interface between liquid chromatography (LC) and NMR. For the process of LC-SPE NMR a chromatographic separation is done and the peaks of interest are trapped on an individual SPE cartridge after the column. The peak selection is done either by UV detection or by evaluation of the on-line registered MS or MSn spectra.
editor preferred term: Bruker SPE-NMR platform
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR instrument
term editor: PERSON:Daniel Schober
has curation status: IAO_0000120

guard column
type: Class
subclass of: chromatography device
disjoint with: chromatography splitter
disjoint with: liquid chromatography instrument
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01111
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition: Guard columns are installed between the injection valve and the analytical or preparative column and here will remove contaminants and prolong the lifetime of the columns.
term editor: PERSON:Daniel Schober
curator note: chromatography device
editor preferred term: guard column
has curation status: IAO_0000120

protein expression profiling
type: Class
subclass of: assay
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
definition source: OBI branch derived
term editor: Phlippe Rocca-Serra
example of usage: Protein Expression Profiling During Chick Retinal Maturation: A Proteomics-based approach. Finnegan S, Robson JL, Wylie M, Healy A, Stitt AW, Curry WJ. Proteome Sci. 2008 Dec 10;6(1):34.PMID: 19077203
definition: a planned process which aims to provide information about protein expression and translation activity using protein extracts collected from a material entity using a range of techniques and instrument such as Mass spectrometers, Gel electrophoresis, Western Blots, Protein microarrays
editor preferred term: protein expression profiling
alternative term: proteomic analysis
has curation status: IAO_0000120

high resolution probe with automatic tuning and matching
type: Class
subclass of: Bruker high resolution probe
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400224
definition source: GROUP:<http://msi-ontology.sourceforge.net>
alternative term: High Resolution Probes with Automatic Tuning and Matching, HR_probe_with_ATM
curator note: NMR probe
term editor: PERSON:Daniel Schober
definition: The Automatic Tuning and Matching (ATM) option for AVANCE spectrometers is available for double resonance probes in fixed-frequency and broadband tunable configurations with either direct or indirect detection. Thus, for multinuclear operation, as often required for applications in inorganic chemistry, ATM facilitates the accurate setting of 90 degree pulse widths on both observe and decoupling channels for each chosen nucleus and each individual sample - even with full automation. Triple resonance probes in fixed-frequency configurations, as typically used for inverse detection with high-field systems.
editor preferred term: high resolution probe with automatic tuning and matching
has curation status: IAO_0000120

fluorine-induced chemiluminescence detector
type: Class
subclass of: gas chromatography detector
disjoint with: atomic emission detector
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01087
definition: A gas chromatographic detection system based on the low pressure, gas phase chemiluminescence of the reaction mixture of molecular fluorine with organo-sulfur, -selenium, and -tellurium compounds separated from (gas phase) headspace samples. This detector was originally developed in the research group of John Birks at the University of Colorado, USA and was manufactured and sold by Sievers Instruments (Boulder Colorado, USA). This system can be divided up into three parts: the chromatograph, transfer line, and reaction cell; PMT and photon counting electronics; and the molecular fluorine generator.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.shsu.edu/~chm_tgc/publications/JPP/chasteen.htm>
editor preferred term: fluorine-induced chemiluminescence detector
has curation status: IAO_0000120

size exclusion column
type: Class
subclass of: chromatography column
disjoint with: custom made column
disjoint with: gel permeation column
disjoint with: carbon nanotube column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01100
definition: A size exclusion column is a chromatography column as used in size exclusion chromatography and which enables the separation of mixtures according to differrences in molecular size.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: size exclusion column
has curation status: IAO_0000120

chromatography splitter
type: Class
subclass of: chromatography device
disjoint with: liquid chromatography instrument
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01041
definition: An adjustable restriction that is placed in the waste outlet to allow the necessary pressure to develop at the column inlet to force a flow (q ml/min) through the column. If the flow of mobile phase is Q ml/min then the waste flow will be (Q-q) ml/min. by adjusting the waste flow, the proportion of the sample entering the capillary column can be varied over a wide range of values and the necessary minimum permissible volume for the particular column in use can be selected for analysis. Unfortunately, the fraction taken in this way may not be representative of the original sample. This is due to the individual solutes in the mixture having different diffusivities and, thus, they distribute themselves across the sampling tube in an irregular manner. In general, the components with higher diffusivities (e.g., those solutes of lower molecular weight) will diffuse away from the bulk sample more quickly than those having lower diffusivities.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.chromatography-online.org/EC-Dispersion/GC-Capillary-Columns/rs13.html>
curator note: chromatography device
editor preferred term: chromatography splitter
has curation status: IAO_0000120

Bruker micro imaging probe
type: Class
subclass of: Bruker NMR probe
disjoint with: Bruker solid magic angle spinning probe
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400225
editor preferred term: Bruker micro imaging probe
definition: For medical, biological and material sciences research, avance imaging systems provide optimal object handling and performance with a variety of samples types. Two classes of imaging probes are available: in vivo probes for handling and sustaining live objects such as animals and plants, and conventional imaging probes for materials samples.
curator note: NMR probe
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.bruker-biospin.com/probes_microimaging.html>
has curation status: IAO_0000120

custom made column
type: Class
subclass of: chromatography column
disjoint with: gel permeation column
disjoint with: carbon nanotube column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01234
definition: A custom made column ia a chromatography column which is specifically tailored according to the needs of the separation as requested by a scientist or working group.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: custom made column
has curation status: IAO_0000120

gel permeation column
type: Class
subclass of: chromatography column
disjoint with: carbon nanotube column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01103
definition: A gel permeation column is a chromatography column which is used in gel permeation chromatography and which employs as the stationary phase a swollen gel made by polymerizing and cross-linking styrene in the presence of a diluent which is a nonsolvent for the styrene polymer. The polymer to be analyzed is introduced at the top of the column and then is elutriated with a solvent. The polymer molecules diffuse through the gel at rates depending on their molecular size.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://composite.about.com/od/glossaries/l/bldef_g2419.htm>
editor preferred term: gel permeation column
has curation status: IAO_0000120

NMR spectroscopy
type: Class
subclass of: assay
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
example of usage: Metabolic profiling studies on the toxicological effects of realgar in rats by (1)H NMR spectroscopy. Wei L, Liao P, Wu H, Li X, Pei F, Li W, Wu Y. Toxicol Appl Pharmacol. 2008 Nov 25. PMID: 19073202
editor preferred term: NMR spectroscopy
definition: NMR spectroscopy is a process which exploits the magnetic properties of certain nuclei (those with a spin) to resonate when placed in particular magnetic field conditions. Instruments recording NMR spectrum and sets of analysis can be used to deduce identity of chemical as well as composition of complex chemical mixtures.
alternative term: Nuclear magnetic resonance spectroscopy
term editor: Philippe Rocca-Serra
definition source: adapted from Wikipedia
has curation status: IAO_0000123

Bruker SampleJet system
type: Class
subclass of: Bruker autosampler
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400208
definition: Bruker BioSpin introduces the SampleJet, a robot for NMR tube automation. The SampleJet has been consciously designed to meet the growing customer demand for simplicity, versatility and higher throughput in NMR sample tube automation.\n The SampleJet utilizes the modern-day industry standard for sample arrangements-the 96 well plate array. Therefore, the samples may be handled by standard lab automation devices before or after the NMR measurement.
editor preferred term: Bruker SampleJet system
curator note: NMR instrument
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.bruker-biospin.com/automation.html>
has curation status: IAO_0000120

JEOL ECX NMR spectrometer
type: Class
subclass of: JEOL NMR instrument
disjoint with: JEOL ECA NMR spectrometer
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400227
editor preferred term: JEOL ECX NMR spectrometer
curator note: NMR instrument
term editor: PERSON:Daniel Schober
definition: The ECX series of NMR spectrometers is designed for any laboratory needing an easy-to-use, reliable, routine NMR system. The ECX NMR series is available from 300 to 500 MHz. The console is designed around a modular, digital NMR electronics chassis controlled by an intelligent acquisition computer. For unprecedented flexibility, the JEOL NMR system offers a Windows XP, Mac OSX or LINUX. Both the workstation and spectrometer may be connected to a standard network, allowing seamless remote operation anywhere in the world.
definition source: WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/ECX/tabid/145/Default.aspx>
has curation status: IAO_0000120

DNA sequencing
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has_specified_input
    some values from: Class
      intersection of: deoxyribonucleic acids
      intersection of: Restriction
        on property: has role
        some values from: evaluant role
  intersection of: Restriction
    on property: has_specified_output
    some values from: OBI_0001573
subclass of: OBI_0600047
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
editor preferred term: DNA sequencing
definition: DNA sequencing is a sequencing process which uses deoxyribonucleic acid as input and results in a the creation of DNA sequence information artifact using a DNA sequencer instrument.
example of usage: Genomic deletions of OFD1 account for 23% of oral-facial-digital type 1 syndrome after negative DNA sequencing. Thauvin-Robinet C, Franco B, Saugier-Veber P, Aral B, Gigot N, Donzel A, Van Maldergem L, Bieth E, Layet V, Mathieu M, Teebi A, Lespinasse J, Callier P, Mugneret F, Masurel-Paulet A, Gautier E, Huet F, Teyssier JR, Tosi M, Frébourg T, Faivre L. Hum Mutat. 2008 Nov 19. PMID: 19023858
definition source: OBI Branch derived
term editor: Philippe Rocca-Serra
has curation status: IAO_0000123

quaternary pump system
type: Class
subclass of: chromatography pump system
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01047
definition: A pump system that pump and mix up to four different solvents in parallel.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: quaternary pump system
has curation status: IAO_0000120

carbon nanotube column
type: Class
subclass of: chromatography column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01107
definition: Carbon nanotubes (CNTs) are known to have high thermal and mechanical stability and have the potential to be high-performance separation media that utilize the nanoscale interactions. CNT can be applied in long capillary tubes for the development of gas chromatography columns. A film of CNTs can be deposited by chemical vapor deposition (CVD) to form the stationary phase in the open tubular format. Altering the CVD conditions can vary the thickness and the morphology of the CNT film, which opens the possibility of selectivity tuning. The ability to fabricate long tubes coated with CNTs can be readily employed in other gas- and liquid-phase separations as well.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://pubs.acs.org/cgi-bin/abstract.cgi/ancham/2005/77/i21/abs/ac050812j.html>
editor preferred term: carbon nanotube column
has curation status: IAO_0000120

Bruker solid magic angle spinning probe
type: Class
subclass of: Bruker NMR probe
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400193
editor preferred term: Bruker solid magic angle spinning probe
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition: Magic angle spinning, nowadays a routine technique for solids NMR, still offers the capability of innovation. The high mechanical performance of MAS probes in conjunction with efficient rf pulse techniques open new exciting fields in solids NMR of biological samples and in the field of quadrupolar nuclei.
curator note: NMR probe
term editor: PERSON:Daniel Schober
alternative term: solid MAS probe
has curation status: IAO_0000120

hematology
type: Class
subclass of: assay
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: information content entity
    intersection of: Restriction
      on property: is about
      some values from: hemopoiesis
example of usage: Co-associations between insulin sensitivity and measures of liver function, subclinical inflammation, and hematology. Godsland IF, Johnston DG. Metabolism. 2008 Sep;57(9):1190-7. PMID: 18702943
definition source: OBI branch derived
term editor: Philippe Rocca-Serra
alternative term: blood analysis, haematology
editor preferred term: hematology
definition: hematology is a process studying blood and blood producing organs relying on a variety of techniques and instruments
has curation status: IAO_0000123

Varian MERCURY spectrometer
type: Class
subclass of: Varian NMR instrument
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400235
definition: MERCURYplus spectrometers provide superior control, stability, and performance for high-productivity environments. Surface-mount electronics enable a small footprint without compromising data quality. Modular design allows flexible configuration. Direct digital synthesis, linear amplifiers, and other innovative RF and digital technologies enable push-button operation.
curator note: NMR instrument
term editor: PERSON:Daniel Schober
editor preferred term: Varian MERCURY spectrometer
has curation status: IAO_0000120

Bruker Metabolic Profiler
type: Class
subclass of: Bruker NMR instrument
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400199
curator note: hyphenated NMR instrument platform
definition: An NMR platform for conducting metabonomics studies, traditional metabolism studies, and analysis of complex mixtures, featuring an Avance NMR spectrometer and a microTOF from Bruker Daltonics. By combining the structural resolving power of NMR with mass accuracy of the microTOF Bruker offers a complete system for metabolic research. The Metabolic Profiler provides a simple, easy to use and inexpensive base-system to acquire the spectroscopic data, needed to do basic metabolic profiling including metabonomic statistical analysis.
editor preferred term: Bruker Metabolic Profiler
curator note: NMR instrument
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.bruker-biospin.com/metabolicprofiler.html>
has curation status: IAO_0000120

column heater
type: Class
subclass of: chromatography instrument
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01040
term editor: PERSON:Daniel Schober
definition: The glass liner can be fitted with a separate heater and the volatilization temperature can, thus, be controlled. This flash heater system is available in most chromatographs. By using a syringe with a long needle, the tip can be made to penetrate past the liner and discharge its contents directly into the column packing. This procedure is called 'on-column injection' and, as it reduces peak dispersion on injection and thus, provides higher column efficiencies, is often the preferred procedure.
definition source: WEB:<http://www.chromatography-online.org/GC/Injection-Devices/Open-Tubular-Column/rs15.html>
editor preferred term: column heater
has curation status: IAO_0000120

DNA methylation profiling assay
type: Class
equivalent class: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: information content entity
    intersection of: Restriction
      on property: is about
      some values from: regulation of DNA methylation
subclass of: analyte assay
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: epigenetic modification identification objective
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: analyte role
    intersection of: Restriction
      on property: is role of
      some values from: deoxyribonucleic acids
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: OBI_0100051
    intersection of: Restriction
      on property: has part
      some values from: deoxyribonucleic acids
editor preferred term: DNA methylation profiling assay
example of usage: Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion. Reinders J, Delucinge Vivier C, Theiler G, Chollet D, Descombes P, Paszkowski J. Genome Res. 2008 Mar;18(3):469-76. Epub 2008 Jan 24. PMID: 18218979
definition source: OBI branch derived
term editor: Philippe Rocca-Serra
definition: an assay which aims to provide information about state of methylation of DNA molecules using genomic DNA collected from a material entity using a range of techniques and instrument such as DNA sequencers and often relying on treatment with bisulfites to ensure cytosine conversion.
has curation status: IAO_0000122

JEOL CapNMR probe
type: Class
subclass of: JEOL NMR probe
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400233
editor preferred term: JEOL CapNMR probe
curator note: NMR probe
term editor: PERSON:Daniel Schober
definition: The JEOL ECA and ECX NMR spectrometers now support the MRM/Protasis CapNMR Probe for well plate-based and microvial-based NMR analysis. The CapNMR probe is available at proton frequencies ranging from 300 MHz to 800 MHz in both indirect configurations (e.g. 1H{13C} and 1H {31P}) and also in triple resonance configurations (e.g. 1H{13C, 15N}, 1H{31P, 15N}). Both employ a high-strength z-directed field gradient. The flowprobes come with the choice of two flowcell volumes: a 5 µl flowcell with an NMR active volume of 2.5 µl, and a 10 µl flowcell with an NMR active volume of 5 µl. The fluidic connections are 75 µm i.d. and 1/32 o.d. FEP Teflon with hastelloy unions for exceptional solvent compatibility.
definition source: WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/CapNMRProbe/tabid/396/Default.aspx>
has curation status: IAO_0000120

acquisition computer
type: Class
subclass of: OBI_0400107
subclass of: Restriction
  on property: has function
  some values from: information processor function
disjoint with: computer cluster
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400013
definition: A Computer used for NMR, can be divided into central processing unit (CPU), consisting of instruction, interpretation and arithmetic unit plus fast access memory, and peripheral devices such as bulk data storage and input and output devices (including, via the interface, the spectrometer). Under software control, the computer controls the RF pulses and gradients necessary to acquire data, and process the data to produce spectra or images. Note that devices such as the spectrometer may themselves incorporate small computers.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR instrument
term editor: PERSON:Daniel Schober
editor preferred term: acquisition computer
has curation status: IAO_0000120

gas chromatography detector
type: Class
subclass of: chromatography detector
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01083
definition: A gas chromatography detector is a chromatography detector that locates in the dimensions of space and time, the positions of the components of a mixture that has been subjected to a gas chromatographic process and thus permits the senses to appreciate the nature of the separation. There is no LC detector that has an equivalent performance to the flame ionization detector (FID) used in GC. In general, LC detectors have sensitivities of two to three orders of magnitude less than their GC counterparts and linear dynamic ranges one to two orders of magnitude lower. Only highly specific LC detectors have sensitivities that can approach those of GC detectors.
alternative term: FID
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.chromatography-online.org/GC-Detectors/Classification/rs1.html>
curator note: chromatography detector, defined class/xps
editor preferred term: gas chromatography detector
has curation status: IAO_0000120

gas purifier
type: Class
subclass of: gas chromatography equipment
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01036
definition: Gas purifiers are instruments used for the removal of gas impurities like hydrocarbons, oxygen, and moisture from carrier gas and fuel gases for GC or GC-MS systems.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.sigmaaldrich.com/Area_of_Interest/Analytical__Chromatography/Gas_Chromatography/Accessories/SGT_Gas_Purifier.html>
curator note: gas chromatography equipment
editor preferred term: gas purifier
has curation status: IAO_0000120

material separation objective
type: Class
equivalent class: Class
  union of: portioning objective
  union of: separation into different composition objective
subclass of: material transformation objective
definition source: PPPB branch
term editor: PPPB branch
example of usage: The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood.
definition: is an objective to transform a material entity into spatially separated components.
editor preferred term: material separation objective
has curation status: IAO_0000122

indirect detection probe
type: Class
subclass of: NMR probe
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400281
definition: An NMR probe designed to allow the indirect detection of acquisition nuclei.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR device
term editor: PERSON:Daniel Schober
editor preferred term: indirect detection probe
has curation status: IAO_0000120

JEOL ECA NMR spectrometer
type: Class
subclass of: JEOL NMR instrument
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400228
editor preferred term: JEOL ECA NMR spectrometer
curator note: NMR instrument
term editor: PERSON:Daniel Schober
definition: The ECA series of NMR spectrometers is a high performance, research grade NMR system configurable to a wide range off applications. The ECA NMR is available from 300 to 930 MHz field strengths and is 1GHz ready. The system is designed around a modular, digital NMR electronics chassis controlled from a UNIX or Windows workstation and acquisition system. Both the workstation and spectrometer may be connected to a standard network, allowing seamless remote operation anywhere in the world.
definition source: WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/ECA/tabid/146/Default.aspx>
has curation status: IAO_0000120

atomic emission detector
type: Class
subclass of: gas chromatography detector
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01086
alternative term: AED
definition: Instead of measuring simple gas phase (carbon containing) ions created in a flame as with the flame ionization detector, or the change in background current because of electronegative element capture of thermal electrons as with the electron capture detector, the AED has a much wider applicability because it is based on the detection of atomic emissions. The strength of the AED lies in the detector's ability to simultaneously determine the atomic emissions of many of the elements in analytes that elute from a GC capillary column (called eluants or solutes in some books). As eluants come off the capillary column they are fed into a microwave powered plasma (or discharge) cavity where the compounds are destroyed and their atoms are excited by the energy of the plasma. The light that is emitted by the excited particles is separated into individual lines via a photodiode array. The associated computer then sorts out the individual emission lines and can produce chromatograms made up of peaks from eluants that contain only a specific element.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://elchem.kaist.ac.kr/vt/chem-ed/sep/gc/detector/aed.htmt>
editor preferred term: atomic emission detector
has curation status: IAO_0000120

clustered data set
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: OBI_0200175
subclass of: data set
example of usage: A clustered data set is the output of a K means clustering data transformation
curator note: AR thinks could be a data item instead
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
editor preferred term: clustered data set
alternative term: data set with assigned discovered class labels
definition: A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels.
has curation status: IAO_0000125

data set of features
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: OBI_0200184
subclass of: data set
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
editor preferred term: data set of features
definition: A data set that is produced as the output of a descriptive statistical calculation data transformation and consists of producing a data set that represents one or more features of interest about the input data set.
has curation status: IAO_0000125

differential expression analysis data transformation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: OBI_0200031
subclass of: OBI_0200000
definition: A differential expression analysis data transformation is a data transformation that has objective differential expression analysis and that consists of
term editor: James Malone
term editor: Melanie Courtot
term editor: Monnie McGee
definition source: WEB:
editor preferred term: differential expression analysis data transformation
has curation status: IAO_0000122

urine specimen
type: Class
subclass of: OBI_0001479
subclass of: Restriction
  on property: has role
  some values from: specimen role
subclass of: Restriction
  on property: derives from
  some values from: UBERON_0001088
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0600005
disjoint with: blood specimen
disjoint with: whole organism preparation
disjoint with: capsule shell
disjoint with: guar gum
disjoint with: cloacal specimen
disjoint with: nasopharyngeal aspirate specimen
disjoint with: nasal swab specimen
disjoint with: device
disjoint with: growth environment
disjoint with: OBI_0001468
disjoint with: OBI_0001485
disjoint with: OBI_0100014
disjoint with: OBI_0100016
disjoint with: OBI_0100017
disjoint with: OBI_0100055
disjoint with: OBI_0100058
disjoint with: OBI_0100060
disjoint with: OBI_0100067
disjoint with: OBI_0100086
disjoint with: OBI_1000023
disjoint with: OBI_1000024
disjoint with: OBI_1000029
disjoint with: OBI_1000036
disjoint with: OBI_1000042
editor note: 4/10/2011BP: It seems to me that the editor notes refer to a previous version, and are no longer relevant.
editor note: This could be instead a kind of collection of secreted stuff. Among secreted stuff there is passive, and active. urine is secreted, passiv. lavage is secreted, active
definition: a portion of urine collected from an organism
editor note: are we happy calling collection of urine a material separation?
editor preferred term: urine specimen
has curation status: IAO_0000120

material combination
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material combination objective
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: material entity
example of usage: Mixing two fluids. Adding salt into water. Injecting a mouse with PBS.
term editor: bp
definition source: bp
editor note: created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes.
definition: is a material processing with the objective to combine two or more material entities as input into a single material entity as output.
editor preferred term: material combination
has curation status: IAO_0000122

fuzzy clustering objective
type: Class
subclass of: OBI_0200166
disjoint with: statistical hypothesis test objective
disjoint with: decision tree induction objective
disjoint with: pattern matching objective
disjoint with: OBI_0200005
disjoint with: OBI_0200031
disjoint with: OBI_0200078
disjoint with: OBI_0200081
disjoint with: OBI_0200083
disjoint with: OBI_0200091
disjoint with: OBI_0200157
disjoint with: OBI_0200167
disjoint with: OBI_0200168
disjoint with: OBI_0200172
disjoint with: OBI_0200174
disjoint with: OBI_0200177
disjoint with: OBI_0200178
disjoint with: OBI_0200179
disjoint with: OBI_0200180
disjoint with: OBI_0200183
disjoint with: OBI_0200189
disjoint with: OBI_0200196
disjoint with: OBI_0200197
definition source: PERSON: James Malone
definition source: PERSON: Ryan Brinkman
definition: A fuzzy clustering objective is a data transformation objective where the aim is to assign input objects (typically vectors of attributes) a probability that a point belongs to a class, where the number of class and their specifications are not known a priori.
term editor: James Malone
editor preferred term: fuzzy clustering objective
has curation status: IAO_0000122

device setting
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: processed material
example of usage: Examples, 300V for 4 hours, 200mvolts, 37degrees.A knob set a 300 V is the device setting, the protocol stating to set the instrument to 300V is a device setting specification
term editor: PERSON: Frank Gibson
definition: a quality inheres_in some device and is concretization of some (device_setting_specification and is_about a quality of the device
editor preferred term: device setting
has curation status: IAO_0000123

blood specimen
type: Class
subclass of: OBI_0001479
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0600005
subclass of: Restriction
  on property: has role
  some values from: specimen role
subclass of: Restriction
  on property: derives from
  some values from: UBERON_0000178
disjoint with: whole organism preparation
disjoint with: capsule shell
disjoint with: guar gum
disjoint with: cloacal specimen
disjoint with: nasopharyngeal aspirate specimen
disjoint with: nasal swab specimen
disjoint with: device
disjoint with: growth environment
disjoint with: OBI_0001468
disjoint with: OBI_0001485
disjoint with: OBI_0100014
disjoint with: OBI_0100016
disjoint with: OBI_0100017
disjoint with: OBI_0100055
disjoint with: OBI_0100058
disjoint with: OBI_0100060
disjoint with: OBI_0100067
disjoint with: OBI_0100086
disjoint with: OBI_1000023
disjoint with: OBI_1000024
disjoint with: OBI_1000029
disjoint with: OBI_1000036
disjoint with: OBI_1000042
definition source: Bjoern Peters
term editor: Bjoern Peters
definition: a material entity derived from a portion of blood collected from an organism
example of usage: blood drawn from a human for glucose assay
editor preferred term: blood specimen
has curation status: IAO_0000122

data set of predicted values according to fitted curve
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: OBI_0200072
subclass of: data set
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
editor preferred term: data set of predicted values according to fitted curve
definition: A data set which is the output of a curve fitting data transformation in which the aim is to find a curve which matches a series of data points and possibly other constraints.
has curation status: IAO_0000125

data representational model
type: Class
subclass of: directive information entity
disjoint with: independent variable specification
disjoint with: dependent variable specification
disjoint with: controlled variable specification
disjoint with: dose specification
curator note: 2009-02-28: work on this term has been finalized during the OBI workshop winter 2009
definition: Data representational model is an information content entity of the relationships between data items. A data representational model is encoded in a data format specification such as for cytoscape or biopax.
definition source: GROUP: OBI
term editor: Melanie Courtot
editor preferred term: data representational model
alternative term: data structure
alternative term: data structure specification
example of usage: gene regulatory graph model
example of usage: phylogenetic tree
example of usage: protein interaction network
has curation status: IAO_0000120

specimen collection
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: has_specified_output
    some values from: OBI_0100051
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: specimen creation objective
subclass of: planned process
curator note: 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
curator note: 6/9/09: used at workshop
term editor: Bjoern Peters
editor note: Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
definition: a planned process with the objective of obtaining specimen.
editor preferred term: specimen creation
has curation status: IAO_0000123

background corrected data set
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: background correction data transformation
subclass of: data set
term editor: PERSON: James Malone
term editor: PERSON: Melanie Courtot
editor preferred term: background corrected data set
definition: A data set that is produced as the output of a background correction data transformation.
has curation status: IAO_0000125

ELISA
type: Class
subclass of: analyte assay
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: analyte measurement objective
subclass of: Restriction
  on property: realizes
  some values from: analyte role
example of usage: 1) Detection of IL-2 (analyte) in a cell supernatant (evaluant), using plate bound anti IL-2 antibodies, and a reporter enzyme linked reporter antibody. 2) Measurement of IgG antibody (analyte) titer in a serum sample (evaluant) using plate bound antigen and a reporter anti-IgG antibody.
editor preferred term: ELISA
definition: ELISA is an assay where an enzyme linked antibody is used to detect a plate bound material in a liquid (the evaluant) utilizing a chemiluminescent reaction. The detected signal is proxy for the concentration of an analyte in the evaluant.
alternative term: Enzyme-Linked ImmunoSorbent Assay
term editor: IEDB
definition source: IEDB
editor note: It is possible to add further restrictions, such as utilizing a plate as part of the assay.
has curation status: IAO_0000122

error corrected data set
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: error correction data transformation
subclass of: data set
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
editor preferred term: error corrected data set
definition: A data set that is produced as the output of an error correction data transformation and consists of producing a data set which has had erroneous contributions from the input to the data transformation removed (corrected for).
has curation status: IAO_0000125

class prediction data transformation
type: Class
equivalent class: Class
  union of: Restriction
    on property: has_specified_output
    some values from: classified data set
  union of: Restriction
    on property: achieves_planned_objective
    some values from: OBI_0200179
subclass of: OBI_0200000
term editor: James Malone
alternative term: supervised classification data transformation
definition: A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction.
definition source: PERSON: James Malone
editor preferred term: class prediction data transformation
has curation status: IAO_0000122

BrdU incorporation assay
type: Class
subclass of: cell proliferation assay
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: label role
    intersection of: Restriction
      on property: inheres in
      some values from: 5-bromo-2-deoxyuridine
definition: A BrdU incorporation assay is an assay to detect actively replicating cells. BrdU is incorporated into the newly synthesized DNA of replicating cells (during the S phase of the cell cycle), substituting for thymidine during DNA replication. Antibodies specific for BrdU can then be used to detect the incorporated chemical, thus indicating cells that were actively replicating their DNA.
editor preferred term: BrdU incorporation assay
term editor: IEDB
example of usage: The measurement of T cell proliferation as a response to a viral peptide by culturing T cells stimulated with APCs and peptide in the presence of BrdU.
definition source: wiki http://en.wikipedia.org/wiki/BrdU
has curation status: IAO_0000120

intracellular cytokine staining assay
type: Class
equivalent class: Class
  intersection of: intracellular material detection by flow cytometry assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: cytokine production
subclass of: intracellular material detection by flow cytometry assay
alternative term: ICCS
alternative term: ICS
term editor: IEDB
definition source: IEDB
example of usage: Permeabilizing T cells and staining them with fluorescent labeled anti-IFN-gamma antibodies
definition: The measurement of cytokines within the cytoplasm of a cell by permeabilizing the cell membrane to allow entry of specific antibodies, and counting the stained cells using a flow cytometer.
editor preferred term: intracellular cytokine staining assay
has curation status: IAO_0000120

background correction data transformation
type: Class
equivalent class: Class
  union of: Restriction
    on property: has_specified_output
    some values from: background corrected data set
  union of: Restriction
    on property: achieves_planned_objective
    some values from: OBI_0200173
subclass of: OBI_0200000
term editor: James Malone
definition: A background correction data transformation (sometimes called supervised classification) is a data transformation that has the objective background correction.
definition source: PERSON: James Malone
editor preferred term: background correction data transformation
has curation status: IAO_0000122

MHC multimer staining assay
type: Class
subclass of: flow cytometry assay
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: has_specified_input
  some values from: OBI_0100060
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: function
    intersection of: Restriction
      on property: inheres in
      some values from: OBI_0400044
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: function
    intersection of: Restriction
      on property: inheres in
      some values from: fluorescently labeled MHC multimer
curator note: 2/26/09 RESOLVE: Need to add a restriction for the 'MHC multimer' as a reagent used
definition: An MHC multimer assay is an assay that detects T cells capable of binding the MHC:ligand complexes present in the multimer. The multimer is fluorescently labelled. The T cells bound to multimers are counted in a flow cytometer
definition source: IEDB
term editor: IEDB
editor preferred term: MHC multimer staining assay
alternative term: MHC tetramer assay
example of usage: Measuring T cells that are specific for the SYFPEITHI peptide when presented by the murine MHC molecule H-2 Kd by staining them with a tetramer of peptide loaded MHC complexes.
has curation status: IAO_0000120

error correction data transformation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: OBI_0200186
subclass of: OBI_0200000
definition source: EDITORS
term editor: Monnie McGee
definition: An error correction data transformation is a data transformation that has the objective of error correction, where the aim is to remove (correct for) erroneous contributions from the input to the data transformation.
term editor: James Malone
editor preferred term: error correction data transformation
has curation status: IAO_0000122

tritiated thymidine incorporation assay
type: Class
subclass of: cell proliferation assay
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: label role
    intersection of: Restriction
      on property: inheres in
      some values from: tritiated thymidine
editor note: 2/26/09: RESOLVE: need to replace 'molecular entities' in the logical definition with 'tritiated thymidine'
definition: A tritiated thymidine incorporation assay is an assay to detect actively replicating cells. Tritiated thymidine is incorporated into the newly synthesized DNA of replicating cells (during the S phase of the cell cycle). The radioactivity of tritiated thymidine can then be detected thus indicating cells that were actively replicating their DNA.
term editor: IEDB
definition source: IEDB
example of usage: The measurement of T cell proliferation as a response to a viral peptide by culturing T cells stimulated with APCs and peptide in the presence of tritiated thymidine, and using a scintillation counter to detect the radioactivity.
editor preferred term: tritiated thymidine incorporation assay
has curation status: IAO_0000125

sample from organism
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has role
    some values from: material sample role
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: OBI_0600005
subclass of: material sample
subclass of: OBI_0001479
subclass of: Restriction
  on property: derives from
  some values from: gross anatomical part
editor note: 5/29: This is a helper class for now
definition: a material obtained from an organism in order to be a representative of the whole
editor preferred term: sample from organism
editor note: we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about.
has curation status: IAO_0000002

statistical hypothesis test
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: statistical hypothesis test objective
subclass of: OBI_0200000
term editor: James Malone
definition: A statistical hypothesis test data transformation is a data transformation that has objective statistical hypothesis test.
definition source: PERSON: James Malone
editor preferred term: statistical hypothesis test
has curation status: IAO_0000120

center value
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: OBI_0200181
subclass of: data item
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
editor preferred term: center value
alternative term: median
definition: A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data.
has curation status: IAO_0000125

statistical hypothesis test objective
type: Class
subclass of: OBI_0200166
disjoint with: decision tree induction objective
disjoint with: pattern matching objective
disjoint with: OBI_0200005
disjoint with: OBI_0200031
disjoint with: OBI_0200078
disjoint with: OBI_0200081
disjoint with: OBI_0200083
disjoint with: OBI_0200091
disjoint with: OBI_0200157
disjoint with: OBI_0200167
disjoint with: OBI_0200168
disjoint with: OBI_0200172
disjoint with: OBI_0200174
disjoint with: OBI_0200177
disjoint with: OBI_0200178
disjoint with: OBI_0200179
disjoint with: OBI_0200180
disjoint with: OBI_0200183
disjoint with: OBI_0200189
disjoint with: OBI_0200196
disjoint with: OBI_0200197
term editor: Person:Helen Parkinson
definition source: WEB: http://en.wikipedia.org/wiki/Statistical_hypothesis_testing
alternative term: hypothesis test objective
definition: is a data transformation objective where the aim is to estimate statistical significance with the aim of proving or disproving a hypothesis by means of some data transformation
term editor: James Malone
editor preferred term: statistical hypothesis test objective
has curation status: IAO_0000123

reduced dimension data set
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: OBI_0200182
subclass of: data set
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
editor preferred term: reduced dimension data set
definition: A data set that is produced as the output of a data vector reduction data transformation and consists of producing a data set which has fewer vectors than the input data set.
has curation status: IAO_0000125

portioning objective
type: Class
subclass of: material separation objective
disjoint with: separation into different composition objective
example of usage: The objective to obtain multiple aliquots of an enzyme preparation.
definition: is the objective to separate material into multiple portions, each of which contains a similar composition of the input material.
editor preferred term: portioning objective
has curation status: IAO_0000123

average value
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: OBI_0200170
subclass of: data item
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
alternative term: arithmetic mean
editor preferred term: average value
definition: A data item that is produced as the output of an averaging data transformation and represents the average value of the input data.
has curation status: IAO_0000125

whole organism preparation
type: Class
subclass of: OBI_0100051
subclass of: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: specimen role
subclass of: Restriction
  on property: derives from
  some values from: OBI_0100026
subclass of: Restriction
  on property: is_specified_output_of
  some values from: specimen collection
disjoint with: capsule shell
disjoint with: guar gum
disjoint with: cloacal specimen
disjoint with: nasopharyngeal aspirate specimen
disjoint with: nasal swab specimen
disjoint with: device
disjoint with: growth environment
disjoint with: OBI_0001468
disjoint with: OBI_0001485
disjoint with: OBI_0100014
disjoint with: OBI_0100016
disjoint with: OBI_0100017
disjoint with: OBI_0100055
disjoint with: OBI_0100058
disjoint with: OBI_0100060
disjoint with: OBI_0100067
disjoint with: OBI_0100086
disjoint with: OBI_1000023
disjoint with: OBI_1000024
disjoint with: OBI_1000029
disjoint with: OBI_1000036
disjoint with: OBI_1000042
definition: A material entity which is the output of a process in which one or more whole organisms are prepared in a way to make it easier to study them, and in which the great majority of organismal parts are maintained
editor note: does this include injecting a dye to a patient to be able to visualize parts of his brain? If not, we should state that the components of the organism are substantially re-arranged.
example of usage: putting a mouse in the blender. Not: putting a mouse on a scale
editor preferred term: whole organism preparation
has curation status: IAO_0000123

separation into different composition objective
type: Class
subclass of: material separation objective
example of usage: The objective to obtain cells contained in a sample of blood.
editor note: We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives
definition: is the objective to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities)
editor preferred term: separation into different composition objective
has curation status: IAO_0000120

obsolete_study result
type: Class
subclass of: ObsoleteClass
curator note: 2009-02-28: work on this term has been finalized during the OBI workshop winter 2009
definition source: GROUP: OBI
definition: Study result is an information content entity that is a specified data output of a study.
editor preferred term: study result
deprecated: true
has curation status: IAO_0000120
has obsolescence reason: IAO_0000230

specimen creation objective
type: Class
subclass of: objective specification
disjoint with: material maintenance objective
disjoint with: training objective
disjoint with: service provision objective
disjoint with: assay validation objective
disjoint with: selective organism creation objective
disjoint with: OBI_0200166
definition: A specimen creation objective is to obtain a material entity for potential use as an input during an investigation
term editor: Bjoern Peters
definition source: Bjoern Peters
example of usage: The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
editor preferred term: specimen creation objective
has curation status: IAO_0000123

creating a mixture of molecules in solution
type: Class
subclass of: material combination
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: Restriction
  on property: has_specified_output
  some values from: OBI_0302729
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material combination objective
term editor: Bjoern Peters
definition source: PERSON: Helen Parkinson
example of usage: The production of PBS
editor preferred term: creating a mixture of molecules in solution
definition: is a process with the objective to prepare a liquid solution of one or more chemicals at desired concentrations.
has curation status: IAO_0000120

material combination objective
type: Class
subclass of: material transformation objective
disjoint with: device creation objective
disjoint with: genetic transformation objective
term editor: PPPB branch
definition source: bp
definition: is an objective to obtain an output material that contains several input materials.
editor preferred term: material combination objective
has curation status: IAO_0000122

nucleotide overhang cloning
type: Class
subclass of: OBI_0600064
disjoint with: recombination enzyme based cloning
disjoint with: restriction enzyme based cloning
disjoint with: recombinant BAC cloning
disjoint with: recombinant phage cloning
disjoint with: recombinant YAC cloning
disjoint with: OBI_0600048
disjoint with: OBI_0600063
example of usage: Cloning vectors are commercially available and supplied in linearized form with 3' dT overhangs
term editor: Helen Parkinson
definition: Nucleotide overhang cloning is the process of inserting nucleic acid into a vector using nucleotide overhangs used to prevent self ligation
editor preferred term: nucleotide overhang cloning
has curation status: IAO_0000120

rodent care protocol
type: Class
subclass of: animal care protocol
definition: A rodent care protocol is an animal protocol in which the animals being taken care of are rodents.
term editor: Bjoern Peters
definition source: Bjoern Peters
example of usage: Keeping mice in the UCSD animals facility at 20 - 25 degrees celsius, in cages of 4 animals each and providing food twice daily.
editor preferred term: rodent care protocol
has curation status: IAO_0000123

454 Genome Sequence 20
type: Class
subclass of: OBI_0400103
subclass of: Restriction
  on property: is_manufactured_by
  has value: OBI_0000758
disjoint with: ABI 377 automated sequencer
disjoint with: AB SOLiD System
disjoint with: 454 Genome Sequencer FLX
disjoint with: Illumina Genome Analyzer II
disjoint with: Li-Cor 4300 DNA Analysis System
disjoint with: HeliScope Single Molecule Sequencer
editor preferred term: 454 Genome Sequence 20
alternative term: GS 20
example of usage: PMID: 18946007.Pyrosequencing analysis of the oral microflora of healthy adults. Keijser BJ, Zaura E, Huse SM, van der Vossen JM, Schuren FH, Montijn RC, ten Cate JM, Crielaard W. J Dent Res. 2008 Nov;87(11):1016-20.
term editor: Philippe Rocca-Serra
definition: is a DNA sequencer which is manufactured by 454 Life Science Corporation and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information.
has curation status: IAO_0000120

immunoprecipitation
type: Class
subclass of: OBI_0600014
subclass of: Restriction
  on property: has_specified_input
  some values from: immunoglobulin complex, circulating
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material separation objective
definition source: OBI plan and planned process branch
example of usage: PMID: 19419533. Arabidopsis RNA immunoprecipitation. Terzi LC, Simpson GG. Plant J. 2009 Jul;59(1):163-8.
term editor: Philippe Rocca-Serra
editor preferred term: immunoprecipitation
definition: is a process which realizes a material separation objective by relying on antibodies to specifically binding to material entity
has curation status: IAO_0000123

ABI 377 automated sequencer
type: Class
subclass of: OBI_0400103
subclass of: Restriction
  on property: is_manufactured_by
  has value: OBI_0000776
disjoint with: AB SOLiD System
disjoint with: 454 Genome Sequencer FLX
disjoint with: Illumina Genome Analyzer II
disjoint with: Li-Cor 4300 DNA Analysis System
disjoint with: HeliScope Single Molecule Sequencer
editor preferred term: ABI 377 automated sequencer
definition source: Applied Biosystems
term editor: Philippe Rocca-Serra
definition: is a DNA sequencer which is manufactured by Applied Biosystems corporation (formerly Perkin-Elmer). It allows automated chain termination DNA sequencing. It has part polyacrylamide gel electrophoresis system and a laser -based detection system to detect fluorescence intensity emitted by the dyes attached to the dideoxyterminator nucleotides or to the primers.
has curation status: IAO_0000120

recombination enzyme based cloning
type: Class
subclass of: OBI_0600064
disjoint with: restriction enzyme based cloning
disjoint with: recombinant BAC cloning
disjoint with: recombinant phage cloning
disjoint with: recombinant YAC cloning
disjoint with: OBI_0600048
disjoint with: OBI_0600063
definition: a recombination enzyme based cloning is a recombinant vector cloning process that uses complementary nucleotide sequences in both the insert genetic material and the cloning vector with a recombination enzyme to directly create a recombinant vector
editor preferred term: recombination enzyme based cloning
has curation status: IAO_0000123

MeDIP-SEQ assay
type: Class
subclass of: DNA methylation profiling assay
subclass of: OBI_0001700
subclass of: OBI_0600047
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: sequence data
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: primary structure of DNA macromolecule
        intersection of: Restriction
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: has part
    some values from: library preparation
subclass of: Restriction
  on property: has part
  some values from: immunoprecipitation
subclass of: Restriction
  on property: has part
  some values from: Class
    union of: Helicos sequencing
    union of: SOLiD sequencing
    union of: Solexa sequencing
    union of: pyrosequencing
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: deoxyribonucleic acids
    intersection of: Restriction
      on property: has role
      some values from: evaluant role
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: sequence data
    intersection of: Restriction
      on property: is about
      some values from: regulation of DNA methylation
editor preferred term: MeDIP-SEQ assay
alternative term: Methylated DNA immunoprecipitation sequencing assay
example of usage: PMID: 18612301. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gräf S, Johnson N, Herrero J, Tomazou EM, Thorne NP, Bäckdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavaré S, Beck S. Nat Biotechnol. 2008 Jul;26(7):779-85.
term editor: Philippe Rocca-Serra
definition source: adapted from wikipedia
definition: is an assay which aims at identifying methylated sites in genomic DNA and determining methylation pattern that affect gene transcription by relying on immunoprecipitation of methylated genomic DNA, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods.
has curation status: IAO_0000120

animal feeding
type: Class
subclass of: planned process
subclass of: Restriction
  on property: realizes
  some values from: feed role
subclass of: Restriction
  on property: has_specified_input
  some values from: OBI_0100026
subclass of: Restriction
  on property: has_specified_output
  some values from: OBI_0100026
term editor: Bjoern Peters
editor note: In an investigation, this will typically be part of an animal care process
editor preferred term: animal feeding
definition: animal feeding is a process in which animals are provided with food
definition source: branch derived
example of usage: giving crickets to a snake.
has curation status: IAO_0000123

chain termination sequencing
type: Class
subclass of: DNA sequencing by synthesis
subclass of: Restriction
  on property: has_specified_input
  some values from: PCR product
subclass of: Restriction
  on property: has participant
  some values from: Class
    union of: ABI 377 automated sequencer
    union of: Li-Cor 4300 DNA Analysis System
disjoint with: Helicos sequencing
disjoint with: Solexa sequencing
disjoint with: pyrosequencing
example of usage: PMID: 271968. DNA sequencing with chain-terminating inhibitors. Sanger F, Nicklen S, Coulson AR. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463-7.
term editor: Philippe Rocca-Serra
alternative term: Sanger sequencing
definition source: adapted from wikipedia
editor preferred term: chain termination sequencing
alternative term: dye terminator sequencing
definition: is a DNA sequencing which rely on the use of dideoxynucleotides used in 4 distinct sequencing reaction on the same DNA sample. The dideoxynucleotides, once incorporated in the complementary DNA strand being synthesized by the DNA polymerase prevent any further chain elongation. The newly generated sequences are resolved on a polyacrylamide gel using electrophoresis and labels (either fluorochrome or radioactivity) are used to determine the nucleotide present at a given position
has curation status: IAO_0000120

AB SOLiD System
type: Class
subclass of: OBI_0400103
subclass of: Restriction
  on property: is_manufactured_by
  has value: OBI_0000776
disjoint with: 454 Genome Sequencer FLX
disjoint with: Illumina Genome Analyzer II
disjoint with: Li-Cor 4300 DNA Analysis System
disjoint with: HeliScope Single Molecule Sequencer
editor preferred term: AB SOLiD System
definition source: Applied Biosystems
example of usage: PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR. Methods. 2009 Jul;48(3):249-57.
term editor: Philippe Rocca-Serra
definition: is a DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation
has curation status: IAO_0000120

Helicos sequencing
type: Class
subclass of: DNA sequencing by synthesis
subclass of: Restriction
  on property: has participant
  some values from: HeliScope Single Molecule Sequencer
subclass of: Restriction
  on property: is immediately preceded by
  some values from: OBI_0302902
disjoint with: Solexa sequencing
disjoint with: pyrosequencing
editor preferred term: Helicos sequencing
example of usage: PMID: 18388294. Single-molecule DNA sequencing of a viral genome. Harris TD, Buzby PR, Babcock H, Beer E, Bowers J, Braslavsky I, Causey M, Colonell J, Dimeo J, Efcavitch JW, Giladi E, Gill J, Healy J, Jarosz M, Lapen D, Moulton K, Quake SR, Steinmann K, Thayer E, Tyurina A, Ward R, Weiss H, Xie Z. Science. 2008 Apr 4;320(5872):106-9.
term editor: Philippe Rocca-Serra
definition source: adapted from wikipedia
definition: is a DNA sequencing which allows sequence identification of billions of DNA molecules immobilized to a surface by using DNA polymerase and fluorescently labeled nucleotides added one at a time. The sequencing process does not requires amplification step and is typically able to produce reads of 25 base pair length.
alternative term: true single molecule sequencing
has curation status: IAO_0000120

obsolete_DNA ligase
type: Class
subclass of: ObsoleteClass
editor note: 5/22 Need to explore if there are GO / other classes exist that capture this. We need it now for cloning experiments
definition: A DNA ligase is an enzyme that covalently joins two compatible pieces of DNA through the cleavage of an ATP molecule
editor preferred term: DNA ligase
term editor: Kevin Clancy, Bjoern Peters
alternative term: ligase
editor note: replaced by imported PRO: DNA ligase
deprecated: true
has curation status: IAO_0000123
has obsolescence reason: IAO_0000228

survival assessment
type: Class
subclass of: assay
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: survival rate
    intersection of: Restriction
      on property: is about
      some values from: OBI_0100026
subclass of: Restriction
  on property: has_specified_input
  some values from: OBI_0100026
editor note: Need to point out more specifically that survival / death is measured.
definition: Survival assessment is an assay that measures the occurrence of death events in one or more organisms that are monitored over time
editor preferred term: survival assessment
has curation status: IAO_0000123

support vector machine
type: Class
subclass of: class prediction data transformation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: OBI_0200179
disjoint with: self-organizing map
disjoint with: peak matching
disjoint with: k-nearest neighbors
disjoint with: Student's t-test
disjoint with: CART
disjoint with: Likelihood-ratio test
disjoint with: performing a diagnosis
disjoint with: feature extraction
disjoint with: OBI_0001477
disjoint with: OBI_0200002
disjoint with: OBI_0200003
disjoint with: OBI_0200004
disjoint with: OBI_0200006
disjoint with: OBI_0200007
disjoint with: OBI_0200008
disjoint with: OBI_0200011
disjoint with: OBI_0200014
disjoint with: OBI_0200016
disjoint with: OBI_0200017
disjoint with: OBI_0200021
disjoint with: OBI_0200022
disjoint with: OBI_0200025
disjoint with: OBI_0200026
disjoint with: OBI_0200027
disjoint with: OBI_0200028
disjoint with: OBI_0200029
disjoint with: OBI_0200030
disjoint with: OBI_0200033
disjoint with: OBI_0200034
disjoint with: OBI_0200035
disjoint with: OBI_0200036
disjoint with: OBI_0200037
disjoint with: OBI_0200041
disjoint with: OBI_0200042
disjoint with: OBI_0200049
disjoint with: OBI_0200050
disjoint with: OBI_0200052
disjoint with: OBI_0200056
disjoint with: OBI_0200057
disjoint with: OBI_0200058
disjoint with: OBI_0200059
disjoint with: OBI_0200060
disjoint with: OBI_0200061
disjoint with: OBI_0200062
disjoint with: OBI_0200063
disjoint with: OBI_0200064
disjoint with: OBI_0200066
disjoint with: OBI_0200071
disjoint with: OBI_0200077
disjoint with: OBI_0200079
disjoint with: OBI_0200080
disjoint with: OBI_0200082
disjoint with: OBI_0200088
disjoint with: OBI_0200092
disjoint with: OBI_0200093
disjoint with: OBI_0200094
disjoint with: OBI_0200095
disjoint with: OBI_0200097
disjoint with: OBI_0200098
disjoint with: OBI_0200102
disjoint with: OBI_0200106
disjoint with: OBI_0200108
disjoint with: OBI_0200109
disjoint with: OBI_0200110
disjoint with: OBI_0200113
disjoint with: OBI_0200116
disjoint with: OBI_0200117
disjoint with: OBI_0200118
disjoint with: OBI_0200119
disjoint with: OBI_0200120
disjoint with: OBI_0200121
disjoint with: OBI_0200122
disjoint with: OBI_0200123
disjoint with: OBI_0200124
disjoint with: OBI_0200125
disjoint with: OBI_0200140
disjoint with: OBI_0200149

self-organizing map
type: Class
subclass of: OBI_0200175
subclass of: Class
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      union of: clustered data set
      union of: topologically preserved clustered data set
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: OBI_0200178
disjoint with: peak matching
disjoint with: k-nearest neighbors
disjoint with: Student's t-test
disjoint with: CART
disjoint with: Likelihood-ratio test
disjoint with: performing a diagnosis
disjoint with: feature extraction
disjoint with: OBI_0001477
disjoint with: OBI_0200002
disjoint with: OBI_0200003
disjoint with: OBI_0200004
disjoint with: OBI_0200006
disjoint with: OBI_0200007
disjoint with: OBI_0200008
disjoint with: OBI_0200011
disjoint with: OBI_0200014
disjoint with: OBI_0200016
disjoint with: OBI_0200017
disjoint with: OBI_0200021
disjoint with: OBI_0200022
disjoint with: OBI_0200025
disjoint with: OBI_0200026
disjoint with: OBI_0200027
disjoint with: OBI_0200028
disjoint with: OBI_0200029
disjoint with: OBI_0200030
disjoint with: OBI_0200033
disjoint with: OBI_0200034
disjoint with: OBI_0200035
disjoint with: OBI_0200036
disjoint with: OBI_0200037
disjoint with: OBI_0200041
disjoint with: OBI_0200042
disjoint with: OBI_0200049
disjoint with: OBI_0200050
disjoint with: OBI_0200052
disjoint with: OBI_0200056
disjoint with: OBI_0200057
disjoint with: OBI_0200058
disjoint with: OBI_0200059
disjoint with: OBI_0200060
disjoint with: OBI_0200061
disjoint with: OBI_0200062
disjoint with: OBI_0200063
disjoint with: OBI_0200064
disjoint with: OBI_0200066
disjoint with: OBI_0200071
disjoint with: OBI_0200077
disjoint with: OBI_0200079
disjoint with: OBI_0200080
disjoint with: OBI_0200082
disjoint with: OBI_0200088
disjoint with: OBI_0200092
disjoint with: OBI_0200093
disjoint with: OBI_0200094
disjoint with: OBI_0200095
disjoint with: OBI_0200097
disjoint with: OBI_0200098
disjoint with: OBI_0200102
disjoint with: OBI_0200106
disjoint with: OBI_0200108
disjoint with: OBI_0200109
disjoint with: OBI_0200110
disjoint with: OBI_0200113
disjoint with: OBI_0200116
disjoint with: OBI_0200117
disjoint with: OBI_0200118
disjoint with: OBI_0200119
disjoint with: OBI_0200120
disjoint with: OBI_0200121
disjoint with: OBI_0200122
disjoint with: OBI_0200123
disjoint with: OBI_0200124
disjoint with: OBI_0200125
disjoint with: OBI_0200140
disjoint with: OBI_0200149
disjoint with: OBI_0200150

454 Genome Sequencer FLX
type: Class
subclass of: OBI_0400103
subclass of: Restriction
  on property: is_manufactured_by
  has value: OBI_0000758
disjoint with: Illumina Genome Analyzer II
disjoint with: Li-Cor 4300 DNA Analysis System
disjoint with: HeliScope Single Molecule Sequencer
alternative term: 454 GS FLX
editor preferred term: 454 Genome Sequencer FLX
alternative term: GS-FLX
example of usage: PMID: 18616967. The Genome Sequencer FLX System--longer reads, more applications, straight forward bioinformatics and more complete data sets. Droege M, Hill B. J Biotechnol. 2008 Aug 31;136(1-2):3-10.
term editor: Philippe Rocca-Serra
definition source: adapted from https://www.roche-applied-science.com/servlet/RCProductDisplay?langId=-1&storeId=10202&productId=3.8.8.1.1.3&catalogId=10202&krypto=mgV8a0Sdps6%2BCXU8IoddmzNEyGgjde9j8MOFCiMzRsduELeenAlVZ%2FE1QR%2BxLpzNlqMZPLRHqaI%3D&ddkey=https:RCProductDisplay
definition: is a DNA sequencer which is manufactured by 454 Life Science Corporation and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information.
has curation status: IAO_0000120

Illumina Genome Analyzer II
type: Class
subclass of: OBI_0400103
subclass of: Restriction
  on property: is_manufactured_by
  has value: OBI_0000759
disjoint with: Li-Cor 4300 DNA Analysis System
disjoint with: HeliScope Single Molecule Sequencer
definition source: Illumina Corporation
editor preferred term: Illumina Genome Analyzer II
example of usage: PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR.Methods. 2009 Jul;48(3):249-57.
term editor: Philippe Rocca-Serra
definition: is a DNA sequence which is manufactured by Illumina (Solexa) corporation. it support sequencing of single or paired end clone libraries relying on sequencing by synthesis technology
has curation status: IAO_0000120

decision tree induction objective
type: Class
subclass of: OBI_0200166
disjoint with: pattern matching objective
disjoint with: OBI_0200005
disjoint with: OBI_0200031
disjoint with: OBI_0200078
disjoint with: OBI_0200081
disjoint with: OBI_0200083
disjoint with: OBI_0200091
disjoint with: OBI_0200157
disjoint with: OBI_0200167
disjoint with: OBI_0200168
disjoint with: OBI_0200172
disjoint with: OBI_0200174
disjoint with: OBI_0200177
disjoint with: OBI_0200178
disjoint with: OBI_0200179
disjoint with: OBI_0200180
disjoint with: OBI_0200183
disjoint with: OBI_0200189
disjoint with: OBI_0200196
disjoint with: OBI_0200197
definition: A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made.
term editor: James Malone
editor preferred term: decision tree induction objective
has curation status: IAO_0000123

Edman degradation
type: Class
subclass of: OBI_0600047
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: information content entity
    intersection of: Restriction
      on property: is about
      some values from: SO_0000104
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: peptide
    union of: PR_000000001
subclass of: Restriction
  on property: has_specified_input
  some values from: molecular entity
editor preferred term: Edman degradation
example of usage: PMID 4773306. Niall HD (1973). "Automated Edman degradation: the protein sequenator". Meth. Enzymol. 27: 942-1010
definition source: adapted from Wikipedia (http://en.wikipedia.org/wiki/Edman_degradation)
definition: is a process which produces a sequence from an input peptide or protein. In this process, the amino-terminal (N-terminal) residue is labeled and cleaved from the peptide without disrupting the peptide bonds between other amino acid residues.
has curation status: IAO_0000120

SOLiD sequencing
type: Class
subclass of: DNA sequencing by ligation
subclass of: Restriction
  on property: has_specified_input
  some values from: PR_000023089
subclass of: Restriction
  on property: has participant
  some values from: AB SOLiD System
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: paired-end library
    union of: single fragment library
subclass of: Restriction
  on property: is immediately preceded by
  some values from: Class
    intersection of: OBI_0302902
    intersection of: Restriction
      on property: is immediately preceded by
      some values from: OBI_0600048
example of usage: PMID: 19119315. High-resolution analysis of the 5'-end transcriptome using a next generation DNA sequencer. Hashimoto S, Qu W, Ahsan B, Ogoshi K, Sasaki A, Nakatani Y, Lee Y, Ogawa M, Ametani A, Suzuki Y, Sugano S, Lee CC, Nutter RC, Morishita S, Matsushima K. PLoS One. 2009;4(1):e4108.
term editor: Philippe Rocca-Serra
editor preferred term: SOLiD sequencing
definition source: adapted from Wikipedia and Applied Biosystems web site
definition: is a DNA sequencing which allows sequence identification by relying on the following steps: 1. Primers hybridize to the P1 adapter sequence within the library template. 2. A set of four fluorescently labeled di-base probes compete for ligation to the sequencing primer. Specificity of the di-base probe is achieved by interrogating every 1st and 2nd base in each ligation reaction. 3. Multiple cycles of ligation, detection and cleavage are performed with the number of cycles determining the eventual read length. 4. Following a series of ligation cycles, the extension product is removed and the template is reset with a primer complementary to the n-1 position for a second round of ligation cycles
has curation status: IAO_0000120

decision tree building data transformation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: decision tree induction objective
subclass of: OBI_0200000
term editor: James Malone
definition: A decision tree building data transformation is a data transformation that has objective decision tree induction.
definition source: PERSON: James Malone
editor preferred term: decision tree building data transformation
has curation status: IAO_0000120

laboratory animal care
type: Class
equivalent class: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: animal care protocol
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: OBI_0100026
    intersection of: Restriction
      on property: is located in
      some values from: site
definition: a process that realizes an animal care protocol that specifies how animals are kept and maintained
editor preferred term: laboratory animal care
has curation status: IAO_0000123

yeast artificial chromosome vector
type: Class
subclass of: double-stranded DNA
subclass of: cloning vector
subclass of: Restriction
  on property: has role
  some values from: cloning vector role
term editor: Kevin Clancy, Bjoern Peters
alternative term: YAC
definition: a double-stranded DNA that was engineered to contain a yeast origin of replication, encodes for a selectable gene product, contains a cloning site, and has yeast telomerase sequences
editor note: this should be a child of 'chromosome' if we import that from another source
editor preferred term: yeast artificial chromosome vector
has curation status: IAO_0000123

Li-Cor 4300 DNA Analysis System
type: Class
subclass of: OBI_0400103
subclass of: Restriction
  on property: is_manufactured_by
  has value: OBI_0000769
disjoint with: HeliScope Single Molecule Sequencer
editor preferred term: Li-Cor 4300 DNA Analysis System
definition source: OBI and Li-Cor
term editor: Philippe Rocca-Serra
definition: is a DNA sequencer which is manufactured by Li-Cor corporation and enable automated chain termination based DNA sequencing
has curation status: IAO_0000120

library preparation
type: Class
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: deoxyribonucleic acids
    union of: double-stranded DNA
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    union of: cDNA library
    union of: paired-end library
    union of: single fragment library
    union of: OBI_1000029
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
example of usage: PMID: 19570239. Construction and analysis of cotton (Gossypium arboreum L.) drought-related cDNA library. Zhang L, Li FG, Liu CL, Zhang CJ, Zhang XY. BMC Res Notes. 2009 Jul 2;2:120.
term editor: Philippe Rocca-Serra
definition: is a process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors.
alternative term: library construction
editor preferred term: library preparation
has curation status: IAO_0000120

pathogen challenge
type: Class
subclass of: OBI_0600007
subclass of: Restriction
  on property: realizes
  some values from: host role
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: material to be added role
    intersection of: Restriction
      on property: is role of
      some values from: Class
        intersection of: OBI_0100026
        intersection of: Restriction
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: target of material addition role
    intersection of: Restriction
      on property: is role of
      some values from: Class
        intersection of: OBI_0100026
        intersection of: Restriction
definition: A pathogen challenge is the administration of a live pathogenic organism to a host
editor preferred term: pathogen challenge
has curation status: IAO_0000123

GenePattern software
type: Class
subclass of: software
editor preferred term: GenePattern software
term editor: James Malone
term editor: Person:Helen Parkinson
definition source: WEB: http://www.broadinstitute.org/cancer/software/genepattern/
definition: a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks.
has curation status: IAO_0000120

graph of vertices
type: Class
subclass of: graph
definition: A construct that consists of many nodes connected with edges. The edges represent a relationship between the objects represented by the nodes. A graph can be equivalently represented as a matrix.
term editor: Bjoern Peters
term editor: Chris Stoeckert
example of usage: For example, if the nodes are cities, then the edges may have numerical values that correspond to the distances between the cities.
term editor: James Malone
definition source: WEB: http://mitpress.mit.edu/books/FLAOH/cbnhtml/glossary-G.html
editor preferred term: graph of vertices
has curation status: IAO_0000123

animal care protocol
type: Class
subclass of: protocol
definition: An animal care protocol is a protocol which specifies the environment in which animals are being kept in captivity for research purposes
definition source: Bjoern Peters
term editor: Bjoern Peters
example of usage: Keeping mice in the UCSD animals facility at 20 - 25 degrees celsius, in cages of 4 animals each and providing food twice daily.
editor preferred term: animal care protocol
has curation status: IAO_0000123

ChIP-seq assay
type: Class
subclass of: analyte assay
subclass of: OBI_0001700
subclass of: OBI_0600047
subclass of: Restriction
  on property: has participant
  some values from: OBI_0400103
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: OBI_0001398
subclass of: Restriction
  on property: has part
  some values from: DNA sequencing
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: analyte role
    intersection of: Restriction
      on property: is role of
      some values from: deoxyribonucleic acids
subclass of: Restriction
  on property: has part
  some values from: immunoprecipitation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: epigenetic modification identification objective
subclass of: Restriction
  on property: has part
  some values from: library preparation
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: primary structure of DNA macromolecule
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: information content entity
    intersection of: Restriction
      on property: is about
      some values from: Class
        union of: chromatin remodeling
        union of: regulation of molecular function, epigenetic
        union of: sequence-specific DNA binding
        union of: transcription factor binding site
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: OBI_0100051
    intersection of: Class
      intersection of: Restriction
        on property: has part
        some values from: deoxyribonucleic acids
      intersection of: Restriction
        on property: has part
        some values from: protein complex
editor preferred term: ChIP-seq assay
example of usage: PMID: 19275939 ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT. Methods. 2009 Jul;48(3):240-8. Epub 2009 Mar 9.
term editor: Philippe Rocca-Serra
definition source: adapted from Wikipedia
definition: an assay which aims at identifying protein binding sites in genomic DNA and determining how protein may regulate gene transcription by relying on immunoprecipitation of DNA bound protein, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods.
alternative term: chromatin immunoprecipitation sequencing assay
curator note: made some modification based on the discussion on 2011/4/4 obi dev call, using DNA sequencing instead of union of some specific DNA sequencing processes
has curation status: IAO_0000122

HeliScope Single Molecule Sequencer
type: Class
subclass of: OBI_0400103
subclass of: Restriction
  on property: is_manufactured_by
  has value: OBI_0000757
editor preferred term: HeliScope Single Molecule Sequencer
term editor: Philippe Rocca-Serra
definition: is a DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry
has curation status: IAO_0000120

pathogen role
type: Class
subclass of: role
subclass of: Restriction
  on property: is realized by
  all values from: OGMS_0000022
subclass of: Restriction
  on property: inheres in
  some values from: OBI_0100026
disjoint with: host role
disjoint with: test substance role
disjoint with: complementary nucleotide probe role
disjoint with: service consumer role
disjoint with: service provider role
disjoint with: accessed material role
disjoint with: OBI_0302731
disjoint with: OBI_0302732
disjoint with: OBI_0302733
disjoint with: OBI_1110082
disjoint with: OBI_1110083
disjoint with: OBI_1110086
disjoint with: OBI_1110087
disjoint with: OBI_1110091
disjoint with: OBI_1110092
disjoint with: OBI_1110120
curator note: 6 April 2009: from the Vaccine Community
term editor: GROUP: Role Branch
definition source: OBI
example of usage: Pathogen: An agent of disease. A disease producer. The term pathogen most commonly is used to refer to infectious organisms. These include bacteria (such as staph), viruses (such as HIV), and fungi (such as yeast). Less commonly, pathogen refers to a noninfectious agent of disease such as a chemical. http://www.medterms.com/script/main/art.asp?articlekey=6383
editor preferred term: pathogen role
definition: pathogen role is a role which inheres in an organism and realized in the process of disease course in the organism bearing host role caused by the organism bearing pathogen role
has curation status: IAO_0000120

vaccine preparation
type: Class
subclass of: material processing
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
definition source: OBI
example of usage: The production of B. pertussis vaccine.
editor preferred term: vaccine preparation
definition: vaccine preparation is a planned process with specified output a vaccine
has curation status: IAO_0000120

immunologic adjuvant role
type: Class
subclass of: OBI_1110092
subclass of: Restriction
  on property: is realized by
  all values from: immune response
editor note: 11Feb09:Vaccine Ontology Definition: Adjuvant boosts immune response of a vaccine or antigen in the host. the role 'adjuvant role' inheres in some 'material entity' and is realized by some 'immune response assay'.
example of usage: Adjuvants are pharmacological or immunological agents that modify the effect of other agents (e.g., drugs, vaccines) while having few if any direct effects when given by themselves. http://en.wikipedia.org/wiki/Adjuvant
term editor: GROUP: Role branch
curator note: Renamed from adjuvent role, to be a more specific useage for immunology, tracker https://sourceforge.net/tracker/?func=detail&atid=886178&aid=2887909&group_id=177891
definition: The role a material entity plays when it is co-administered with an immunogen in order to enhance the immune response to the immunogen.
definition source: Vaccine Ontology, Wikipedia, OBI
editor preferred term: immunologic adjuvant role
has curation status: IAO_0000120

glucose tolerance test
type: Class
subclass of: assay
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: biological feature identification objective
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: OBI_0500020
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: OBI_0200000
    intersection of: Restriction
      on property: has_specified_input
      some values from: measurement datum
    intersection of: Restriction
      on property: has_specified_output
      some values from: graph
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: measuring glucose concentration in blood serum
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: dependent variable specification
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: independent variable specification
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: information content entity
    intersection of: Restriction
      on property: is_proxy_for
      some values from: Insulin resistance
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: OBI_0600007
    intersection of: Restriction
      on property: has_specified_input
      some values from: glucose
definition source: NuGO OBI plan branch
example of usage: PMID: 19527607 Using the 100-g Oral Glucose Tolerance Test to Predict Fetal and Maternal Outcomes in Women with Gestational Diabetes Mellitus. Lin CH, Wen SF, Wu YH, Huang MJ. Chang Gung Med J. 2009 May-Jun;32(3):283-9.
term editor: Philippe Rocca-Serra
editor preferred term: glucose tolerance test
definition: is a process in which following administration of a bolus a glucose in-vivo, glucose clearance from blood plasma is monitored over time by repeated glucose measurement in blood serum. the output of a process is a measure which can be used to evaluate the severity of insulin resistance or the efficiency of glucose clearance.
has curation status: IAO_0000122

paired-end library
type: Class
subclass of: processed material
example of usage: PMID: 19339662. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 2009 Apr;19(4):521-32. Fullwood MJ, Wei CL, Liu ET, Ruan Y.
term editor: Philippe Rocca-Serra
definition source: adapted from information provided by Solid web site
definition: is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs
alternative term: mate-paired library
editor preferred term: paired-end library
alternative term: paired-end tag (PET) library
has curation status: IAO_0000123

DNA sequencing by ligation
type: Class
subclass of: DNA sequencing
subclass of: Restriction
  on property: has_specified_input
  some values from: PR_000023089
editor preferred term: DNA sequencing by ligation
editor note: PERSON: Philippe Rocca-Serra
example of usage: PMID: 19546169. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two base encoding. McKernan KJ, Peckham HE, Costa G, McLaughlin S, Tsung E, Fu Y, Clouser C, Dunkan C, Ichikawa J, Lee C, Zhang Z, Sheridan A, Fu H, Ranade S, Dimilanta E, Sokolsky T, Zhang L, Hendrickson C, Li B, Kotler L, Stuart J, Malek J, Manning J, Antipova A, Perez D, Moore M, Hayashibara K, Lyons M, Beaudoin R, Coleman B, Laptewicz M, Sanicandro A, Rhodes M, De La Vega F, Gottimukkala RK, Hyland F, Reese M, Yang S, Bafna V, Bashir A, Macbride A, Aklan C, Kidd JM, Eichler EE, Blanchard AP. Genome Res. 2009 Jun 22.
definition: is a DNA sequencing which relies on DNA ligase activity to perform chain extension during the sequencing reaction step.
has curation status: IAO_0000123

Solexa sequencing
type: Class
subclass of: DNA sequencing by synthesis
subclass of: Restriction
  on property: is immediately preceded by
  some values from: Class
    intersection of: OBI_0302902
    intersection of: Restriction
      on property: is immediately preceded by
      some values from: OBI_0600048
subclass of: Restriction
  on property: has participant
  some values from: Illumina Genome Analyzer II
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: paired-end library
    union of: single fragment library
disjoint with: pyrosequencing
example of usage: PMID: 18987734 Accurate whole human genome sequencing using reversible terminator chemistry. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, Boutell JM, Bryant J, Carter RJ, Keira Cheetham R, Cox AJ, Ellis DJ, Flatbush MR, Gormley NA, Humphray SJ, Irving LJ, Karbelashvili MS, Kirk SM, Li H, Liu X, Maisinger KS, Murray LJ, Obradovic B, Ost T, Parkinson ML, Pratt MR, Rasolonjatovo IM, Reed MT, Rigatti R, Rodighiero C, Ross MT, Sabot A, Sankar SV, Scally A, Schroth GP, Smith ME, Smith VP, Spiridou A, Torrance PE, Tzonev SS, Vermaas EH, Walter K, Wu X, Zhang L, Alam MD, Anastasi C, Aniebo IC, Bailey DM, Bancarz IR, Banerjee S, Barbour SG, Baybayan PA, Benoit VA, Benson KF, Bevis C, Black PJ, Boodhun A, Brennan JS, Bridgham JA, Brown RC, Brown AA, Buermann DH, Bundu AA, Burrows JC, Carter NP, Castillo N, Chiara E Catenazzi M, Chang S, Neil Cooley R, Crake NR, Dada OO, Diakoumakos KD, Dominguez-Fernandez B, Earnshaw DJ, Egbujor UC, Elmore DW, Etchin SS, Ewan MR, Fedurco M, Fraser LJ, Fuentes Fajardo KV, Scott Furey W, George D, Gietzen KJ, Goddard CP, Golda GS, Granieri PA, Green DE, Gustafson DL, Hansen NF, Harnish K, Haudenschild CD, Heyer NI, Hims MM, Ho JT, Horgan AM, Hoschler K, Hurwitz S, Ivanov DV, Johnson MQ, James T, Huw Jones TA, Kang GD, Kerelska TH, Kersey AD, Khrebtukova I, Kindwall AP, Kingsbury Z, Kokko-Gonzales PI, Kumar A, Laurent MA, Lawley CT, Lee SE, Lee X, Liao AK, Loch JA, Lok M, Luo S, Mammen RM, Martin JW, McCauley PG, McNitt P, Mehta P, Moon KW, Mullens JW, Newington T, Ning Z, Ling Ng B, Novo SM, O'Neill MJ, Osborne MA, Osnowski A, Ostadan O, Paraschos LL, Pickering L, Pike AC, Pike AC, Chris Pinkard D, Pliskin DP, Podhasky J, Quijano VJ, Raczy C, Rae VH, Rawlings SR, Chiva Rodriguez A, Roe PM, Rogers J, Rogert Bacigalupo MC, Romanov N, Romieu A, Roth RK, Rourke NJ, Ruediger ST, Rusman E, Sanches-Kuiper RM, Schenker MR, Seoane JM, Shaw RJ, Shiver MK, Short SW, Sizto NL, Sluis JP,…
term editor: Philippe Rocca-Serra
editor preferred term: Solexa sequencing
definition source: adapted from Wikipedia and Illumina / Solexa web site (SS_DNAsequencing.pdf document available on july 2009)
definition: is a DNA sequencing which allows sequence identification by relying on use of DNA polymerase and reversible terminator. The methods requires immobilization of genomic DNA fragment onto a surface and a specific clonal amplification step known as bridge PCR. Reliance on reversible terminator allow cycles of DNA chain extension by DNA polymerase and imaging without the need of electrophoretic separation of newly synthesized DNA fragment as with Sanger sequencing.
alternative term: reversible terminator sequencing
has curation status: IAO_0000120

host role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: OBI_0100026
disjoint with: test substance role
disjoint with: complementary nucleotide probe role
disjoint with: service consumer role
disjoint with: service provider role
disjoint with: accessed material role
disjoint with: OBI_0302731
disjoint with: OBI_0302732
disjoint with: OBI_0302733
disjoint with: OBI_1110082
disjoint with: OBI_1110083
disjoint with: OBI_1110086
disjoint with: OBI_1110087
disjoint with: OBI_1110091
disjoint with: OBI_1110092
disjoint with: OBI_1110120
definition source: 30 Mar09 submitted by vaccine community
editor note: 30Mar09 virus reproducing inside a cell; bacteria causing a disease, host can be harmed or not. we want to avoid a cat sitting on my lap and an animal care technician; these are not examples or hosts; dental cares = on tooth, but part of outer layer of tooth, so covered by "within" in the definition
term editor: GROUP: Role Branch
example of usage: In biology, a host is an organism that harbors a virus or parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter. http://en.wikipedia.org/wiki/Host_(biology) 30 March 09
definition source: OBI
editor preferred term: host role
definition: host role is a role played by an organism and realized by providing nourishment, shelter or a means of reproduction to another organism within the organism playing the host role
definition source: http://en.wikipedia.org/wiki/Host_(biology)
has curation status: IAO_0000120

peak matching
type: Class
subclass of: OBI_0200000
disjoint with: k-nearest neighbors
disjoint with: Student's t-test
disjoint with: CART
disjoint with: Likelihood-ratio test
disjoint with: performing a diagnosis
disjoint with: feature extraction
disjoint with: OBI_0001477
disjoint with: OBI_0200002
disjoint with: OBI_0200003
disjoint with: OBI_0200004
disjoint with: OBI_0200006
disjoint with: OBI_0200007
disjoint with: OBI_0200008
disjoint with: OBI_0200011
disjoint with: OBI_0200014
disjoint with: OBI_0200016
disjoint with: OBI_0200017
disjoint with: OBI_0200021
disjoint with: OBI_0200022
disjoint with: OBI_0200025
disjoint with: OBI_0200026
disjoint with: OBI_0200027
disjoint with: OBI_0200028
disjoint with: OBI_0200029
disjoint with: OBI_0200030
disjoint with: OBI_0200033
disjoint with: OBI_0200034
disjoint with: OBI_0200035
disjoint with: OBI_0200036
disjoint with: OBI_0200037
disjoint with: OBI_0200041
disjoint with: OBI_0200042
disjoint with: OBI_0200049
disjoint with: OBI_0200050
disjoint with: OBI_0200052
disjoint with: OBI_0200056
disjoint with: OBI_0200057
disjoint with: OBI_0200058
disjoint with: OBI_0200059
disjoint with: OBI_0200060
disjoint with: OBI_0200061
disjoint with: OBI_0200062
disjoint with: OBI_0200063
disjoint with: OBI_0200064
disjoint with: OBI_0200066
disjoint with: OBI_0200071
disjoint with: OBI_0200077
disjoint with: OBI_0200079
disjoint with: OBI_0200080
disjoint with: OBI_0200082
disjoint with: OBI_0200088
disjoint with: OBI_0200092
disjoint with: OBI_0200093
disjoint with: OBI_0200094
disjoint with: OBI_0200095
disjoint with: OBI_0200097
disjoint with: OBI_0200098
disjoint with: OBI_0200102
disjoint with: OBI_0200106
disjoint with: OBI_0200108
disjoint with: OBI_0200109
disjoint with: OBI_0200110
disjoint with: OBI_0200113
disjoint with: OBI_0200116
disjoint with: OBI_0200117
disjoint with: OBI_0200118
disjoint with: OBI_0200119
disjoint with: OBI_0200120
disjoint with: OBI_0200121
disjoint with: OBI_0200122
disjoint with: OBI_0200123
disjoint with: OBI_0200124
disjoint with: OBI_0200125
disjoint with: OBI_0200140
disjoint with: OBI_0200149
disjoint with: OBI_0200150
disjoint with: OBI_0200156

k-nearest neighbors
type: Class
subclass of: OBI_0200171
subclass of: OBI_0200175
subclass of: Class
  intersection of: Restriction
    on property: has_specified_output
    some values from: clustered data set
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: OBI_0200178
disjoint with: Student's t-test
disjoint with: CART
disjoint with: Likelihood-ratio test
disjoint with: performing a diagnosis
disjoint with: feature extraction
disjoint with: OBI_0001477
disjoint with: OBI_0200002
disjoint with: OBI_0200003
disjoint with: OBI_0200004
disjoint with: OBI_0200006
disjoint with: OBI_0200007
disjoint with: OBI_0200008
disjoint with: OBI_0200011
disjoint with: OBI_0200014
disjoint with: OBI_0200016
disjoint with: OBI_0200017
disjoint with: OBI_0200021
disjoint with: OBI_0200022
disjoint with: OBI_0200025
disjoint with: OBI_0200026
disjoint with: OBI_0200027
disjoint with: OBI_0200028
disjoint with: OBI_0200029
disjoint with: OBI_0200030
disjoint with: OBI_0200033
disjoint with: OBI_0200034
disjoint with: OBI_0200035
disjoint with: OBI_0200036
disjoint with: OBI_0200037
disjoint with: OBI_0200041
disjoint with: OBI_0200042
disjoint with: OBI_0200049
disjoint with: OBI_0200050
disjoint with: OBI_0200052
disjoint with: OBI_0200056
disjoint with: OBI_0200057
disjoint with: OBI_0200058
disjoint with: OBI_0200059
disjoint with: OBI_0200060
disjoint with: OBI_0200061
disjoint with: OBI_0200062
disjoint with: OBI_0200063
disjoint with: OBI_0200064
disjoint with: OBI_0200066
disjoint with: OBI_0200071
disjoint with: OBI_0200077
disjoint with: OBI_0200079
disjoint with: OBI_0200080
disjoint with: OBI_0200082
disjoint with: OBI_0200088
disjoint with: OBI_0200092
disjoint with: OBI_0200093
disjoint with: OBI_0200094
disjoint with: OBI_0200095
disjoint with: OBI_0200097
disjoint with: OBI_0200098
disjoint with: OBI_0200102
disjoint with: OBI_0200106
disjoint with: OBI_0200108
disjoint with: OBI_0200109
disjoint with: OBI_0200110
disjoint with: OBI_0200113
disjoint with: OBI_0200116
disjoint with: OBI_0200117
disjoint with: OBI_0200118
disjoint with: OBI_0200119
disjoint with: OBI_0200120
disjoint with: OBI_0200121
disjoint with: OBI_0200122
disjoint with: OBI_0200123
disjoint with: OBI_0200124
disjoint with: OBI_0200125
disjoint with: OBI_0200140
disjoint with: OBI_0200149
disjoint with: OBI_0200150
disjoint with: OBI_0200156

rodent care
type: Class
subclass of: laboratory animal care
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: rodent care protocol
subclass of: Restriction
  on property: has_specified_input
  some values from: Rodentia
subclass of: Restriction
  on property: has_specified_output
  some values from: Rodentia
subclass of: Restriction
  on property: has part
  some values from: animal feeding
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: contain function
    intersection of: Restriction
      on property: inheres in
      some values from: OBI_0400171
definition source: PPPB branch
term editor: PPPB branch
example of usage: keeping animal
editor preferred term: rodent care
definition: rodent care is the process by which rodents are being provided with a controlled living environment while kept in captivity for the purpose of research.
has curation status: IAO_0000123

cloning plasmid
type: Class
equivalent class: Class
  intersection of: plasmid
  intersection of: Restriction
    on property: has role
    some values from: cloning vector role
subclass of: plasmid
subclass of: cloning vector
definition: A cloning plasmid is a plasmid that was engineered to contain a bacterial origin of replication, encodes for a selectable gene product and contains a cloning site.
editor note: Note: 'cloning vector role' is really a function. Should be dealt with globally
editor preferred term: cloning plasmid
has curation status: IAO_0000123

pyrosequencing
type: Class
subclass of: DNA sequencing by synthesis
subclass of: Restriction
  on property: has participant
  some values from: Class
    union of: 454 Genome Sequence 20
    union of: 454 Genome Sequencer FLX
term editor: Philippe Rocca-Serra
example of usage: Pyrosequencing sheds light on DNA sequencing. PMID: 1115661. Ronaghi M. Genome Res. 2001 Jan;11(1):3-11. Review.
definition source: Wikipedia (http://en.wikipedia.org/wiki/Pyrosequencing) and Roche 454 life science web site
definition: is a DNA sequencing which allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step. The template DNA is immobilized, and solutions of A, C, G, and T nucleotides are added and removed after the reaction, sequentially. Light is produced only when the nucleotide solution complements the first unpaired base of the template. The sequence of solutions which produce chemiluminescent signals allows the determination of the sequence of the template. ssDNA template is hybridized to a sequencing primer and incubated with the enzymes DNA polymerase, ATP sulfurylase, luciferase and apyrase, and with the substrates adenosine 5-prime phosphosulfate (APS) and luciferin.
editor preferred term: pyrosequencing
has curation status: IAO_0000120

recombinant vector
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: OBI_0600064
subclass of: processed material
definition: A recombinant vector is created by a recombinant vector cloning process, and contains nucleic acids that can be amplified. It retains functions of the original cloning vector.
editor preferred term: recombinant vector
has curation status: IAO_0000123

restriction enzyme
type: Class
subclass of: enzyme
subclass of: PR_000000001
subclass of: Restriction
  on property: has function
  some values from: catalytic activity
disjoint with: OBI_1110132
curator note: 5/22 Need to explore if there are GO / other classes exist that capture this. We need it now for cloning experiments
term editor: Kevin Clancy, Bjoern Peters
example of usage: The enzyme EcoR1 cuts DNA at the canonical cleavage site CAATTG
definition: an enzyme that has a specific target cleavage sites within nucleic acids
editor preferred term: restriction enzyme
has curation status: IAO_0000123

DNA sequencing by synthesis
type: Class
subclass of: DNA sequencing
subclass of: Restriction
  on property: has_specified_input
  some values from: DNA polymerase complex
editor preferred term: DNA sequencing by synthesis
term editor: PERSON: Philippe Rocca-Serra
example of usage: PMID: 18263613. A new class of cleavable fluorescent nucleotides: synthesis and optimization as reversible terminators for DNA sequencing by synthesis. Turcatti G, Romieu A, Fedurco M, Tairi AP. Nucleic Acids Res. 2008 Mar;36(4):e25.
definition: is a DNA sequencing which relies on DNA polymerase activity to perform chain extension during the sequencing reaction step.
has curation status: IAO_0000123

NTP-2000
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: manufacturing
subclass of: Restriction
  on property: has role
  some values from: feed role
term editor: Jennifer Fostel, Bjoern Peters
editor preferred term: NTP-2000
definition: a material consisting of 14.5% protein, 8.5% fat and 9.5% fiber produced to feed rodents
has curation status: IAO_0000123

single fragment library
type: Class
subclass of: processed material
term editor: Philippe Rocca-Serra
alternative term: fragment library
definition: is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs
editor preferred term: single fragment library
has curation status: IAO_0000123

cloning vector
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: cloning vector role
subclass of: processed material
subclass of: OBI_1110108
subclass of: Restriction
  on property: is_specified_output_of
  some values from: material processing
definition: A cloning vector is an engineered material that is used as an input material for a recombinant vector cloning process to carry inserted nucleic acids. It contains an origin of replication for a specific destination host organism, encodes for a selectable gene product and contains a cloning site.
editor preferred term: cloning vector
has curation status: IAO_0000123

restriction enzyme based cloning
type: Class
subclass of: OBI_0600064
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: cloning vector role
    intersection of: Restriction
      on property: is role of
      some values from: nucleic acid restriction enzyme digest
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: cloning insert role
    intersection of: Restriction
      on property: is role of
      some values from: nucleic acid restriction enzyme digest
subclass of: Restriction
  on property: has part
  some values from: OBI_0302892
disjoint with: recombinant BAC cloning
disjoint with: recombinant phage cloning
disjoint with: recombinant YAC cloning
disjoint with: OBI_0600048
disjoint with: OBI_0600063
term editor: Kevin Clancy, Bjoern Peters
editor preferred term: restriction enzyme based cloning
definition: restriction enzyme based cloning is a recombinant vector cloning process that has as an input genetic material that was cleaved with restriction enzymes, and a cloning vector that was cleaved with complementary restriction enzymes. It uses ligase to chemically join the input genetic material and the cloning vector to create a recombinant vector.
has curation status: IAO_0000123

Student's t-test
type: Class
subclass of: statistical hypothesis test
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
disjoint with: CART
disjoint with: Likelihood-ratio test
disjoint with: performing a diagnosis
disjoint with: feature extraction
disjoint with: OBI_0001477
disjoint with: OBI_0200002
disjoint with: OBI_0200003
disjoint with: OBI_0200004
disjoint with: OBI_0200006
disjoint with: OBI_0200007
disjoint with: OBI_0200008
disjoint with: OBI_0200011
disjoint with: OBI_0200014
disjoint with: OBI_0200016
disjoint with: OBI_0200017
disjoint with: OBI_0200021
disjoint with: OBI_0200022
disjoint with: OBI_0200025
disjoint with: OBI_0200026
disjoint with: OBI_0200027
disjoint with: OBI_0200028
disjoint with: OBI_0200029
disjoint with: OBI_0200030
disjoint with: OBI_0200033
disjoint with: OBI_0200034
disjoint with: OBI_0200035
disjoint with: OBI_0200036
disjoint with: OBI_0200037
disjoint with: OBI_0200041
disjoint with: OBI_0200042
disjoint with: OBI_0200049
disjoint with: OBI_0200050
disjoint with: OBI_0200052
disjoint with: OBI_0200056
disjoint with: OBI_0200057
disjoint with: OBI_0200058
disjoint with: OBI_0200059
disjoint with: OBI_0200060
disjoint with: OBI_0200061
disjoint with: OBI_0200062
disjoint with: OBI_0200063
disjoint with: OBI_0200064
disjoint with: OBI_0200066
disjoint with: OBI_0200071
disjoint with: OBI_0200077
disjoint with: OBI_0200079
disjoint with: OBI_0200080
disjoint with: OBI_0200082
disjoint with: OBI_0200088
disjoint with: OBI_0200092
disjoint with: OBI_0200093
disjoint with: OBI_0200094
disjoint with: OBI_0200095
disjoint with: OBI_0200097
disjoint with: OBI_0200098
disjoint with: OBI_0200102
disjoint with: OBI_0200106
disjoint with: OBI_0200108
disjoint with: OBI_0200109
disjoint with: OBI_0200110
disjoint with: OBI_0200113
disjoint with: OBI_0200116
disjoint with: OBI_0200117
disjoint with: OBI_0200118
disjoint with: OBI_0200119
disjoint with: OBI_0200120
disjoint with: OBI_0200121
disjoint with: OBI_0200122
disjoint with: OBI_0200123
disjoint with: OBI_0200124
disjoint with: OBI_0200125
disjoint with: OBI_0200140
disjoint with: OBI_0200149
disjoint with: OBI_0200150
disjoint with: OBI_0200156
disjoint with: OBI_0200160
disjoint with: OBI_0200161

material sample role
type: Class
subclass of: specimen role
editor note: 7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off.
definition: A material sample role is a specimen role borne by a material entity that is the output of a material sampling process.
example of usage: a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
editor preferred term: material sample role
has curation status: IAO_0000125

topologically preserved clustered data set
type: Class
subclass of: clustered data set
definition: A clustered data set in which the topology, i.e. the spatial properties between data points, is preserved from the original input data from which it was derived.
term editor: James Malone
definition source: PERSON: James Malone
example of usage: the output data set generated from a self-organizing map.
editor preferred term: topologically preserved clustered data set
has curation status: IAO_0000125

nucleic acid restriction enzyme digest
type: Class
equivalent class: Class
  intersection of: nucleic acid
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: Class
      intersection of: OBI_0600050
      intersection of: Restriction
        on property: has participant
        some values from: restriction enzyme
      intersection of: Restriction
        on property: has_specified_input
        some values from: nucleic acid
subclass of: nucleic acid
subclass of: processed material
definition: A nucleic acid digest is a material that is the output of a process in which nucleic acids are combined with a restriction enzyme resulting in digested fragments with defined ends based on the enzymes cleavage site
term editor: Kevin Clancy, Bjoern Peters
editor preferred term: nucleic acid restriction enzyme digest
has curation status: IAO_0000123

immune response assay
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: immune response
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: assay objective
subclass of: assay
definition: an assay with the objective to determine information about an immune response
editor preferred term: immune response assay
has curation status: IAO_0000123

material sampling process
type: Class
equivalent class: Class
  intersection of: specimen collection
  intersection of: Restriction
    on property: has_specified_input
    some values from: material entity
  intersection of: Restriction
    on property: has_specified_output
    some values from: material sample
subclass of: specimen collection
definition: A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity
editor preferred term: material sampling process
has curation status: IAO_0000123

material sample
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: material sample role
subclass of: OBI_0100051
definition: A material entity that has the material sample role
term editor: OBI: workshop
example of usage: blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
editor preferred term: material sample
alternative term: sample population
has curation status: IAO_0000123

bisulfite sequencing
type: Class
subclass of: DNA methylation profiling assay
subclass of: OBI_0600047
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: DNA residue methylation
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: deoxyribonucleic acids
    intersection of: Restriction
      on property: has role
      some values from: evaluant role
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: reagent role
    intersection of: Restriction
      on property: inheres in
      some values from: hydrogensulfite
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: sequence data
    intersection of: Restriction
      on property: is about
      some values from: regulation of DNA methylation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
editor note: 8/19/09: Chris says that there may used to be a way of doing bisulfite sequencing comparing lengths of restriction fragments, which implies that it is possible to do without DNA sequencing.
example of usage: PMID: 19581485. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Hodges E, Smith A, Kendall J, Xuan Z, Ravi K, Rooks M, Zhang M, Ye K, Battacharjee A, Brizuela L, McCombie WR, Wigler M, Hannon GJ, Hicks J. Genome Res. 2009 Jul 6.
term editor: Philippe Rocca-Serra
definition source: adapted from Wikipedia
editor preferred term: bisulfite sequencing
definition: is a DNA sequencing which allows to determine the methylation status of genomic DNA using DNA sequencing techniques preceded by a bisulfite based chemical modification of genomic DNA at CpG island location.
has curation status: IAO_0000120

CART
type: Class
subclass of: decision tree building data transformation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: decision tree induction objective
disjoint with: Likelihood-ratio test
disjoint with: performing a diagnosis
disjoint with: feature extraction
disjoint with: OBI_0001477
disjoint with: OBI_0200002
disjoint with: OBI_0200003
disjoint with: OBI_0200004
disjoint with: OBI_0200006
disjoint with: OBI_0200007
disjoint with: OBI_0200008
disjoint with: OBI_0200011
disjoint with: OBI_0200014
disjoint with: OBI_0200016
disjoint with: OBI_0200017
disjoint with: OBI_0200021
disjoint with: OBI_0200022
disjoint with: OBI_0200025
disjoint with: OBI_0200026
disjoint with: OBI_0200027
disjoint with: OBI_0200028
disjoint with: OBI_0200029
disjoint with: OBI_0200030
disjoint with: OBI_0200033
disjoint with: OBI_0200034
disjoint with: OBI_0200035
disjoint with: OBI_0200036
disjoint with: OBI_0200037
disjoint with: OBI_0200041
disjoint with: OBI_0200042
disjoint with: OBI_0200049
disjoint with: OBI_0200050
disjoint with: OBI_0200052
disjoint with: OBI_0200056
disjoint with: OBI_0200057
disjoint with: OBI_0200058
disjoint with: OBI_0200059
disjoint with: OBI_0200060
disjoint with: OBI_0200061
disjoint with: OBI_0200062
disjoint with: OBI_0200063
disjoint with: OBI_0200064
disjoint with: OBI_0200066
disjoint with: OBI_0200071
disjoint with: OBI_0200077
disjoint with: OBI_0200079
disjoint with: OBI_0200080
disjoint with: OBI_0200082
disjoint with: OBI_0200088
disjoint with: OBI_0200092
disjoint with: OBI_0200093
disjoint with: OBI_0200094
disjoint with: OBI_0200095
disjoint with: OBI_0200097
disjoint with: OBI_0200098
disjoint with: OBI_0200102
disjoint with: OBI_0200106
disjoint with: OBI_0200108
disjoint with: OBI_0200109
disjoint with: OBI_0200110
disjoint with: OBI_0200113
disjoint with: OBI_0200116
disjoint with: OBI_0200117
disjoint with: OBI_0200118
disjoint with: OBI_0200119
disjoint with: OBI_0200120
disjoint with: OBI_0200121
disjoint with: OBI_0200122
disjoint with: OBI_0200123
disjoint with: OBI_0200124
disjoint with: OBI_0200125
disjoint with: OBI_0200140
disjoint with: OBI_0200149
disjoint with: OBI_0200150
disjoint with: OBI_0200156
disjoint with: OBI_0200160
disjoint with: OBI_0200161
disjoint with: OBI_0200162

independent variable specification
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: is part of
  some values from: plan specification
disjoint with: dependent variable specification
disjoint with: controlled variable specification
disjoint with: dose specification
curator note: 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Chris Stoeckert
definition source: Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables
editor preferred term: independent variable specification
editor note: 2/2/2009 Original definition - In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled.
definition: a directive information entity that is part of a study design. Independent variables are entities whose values are selected to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled
has curation status: IAO_0000125

dependent variable specification
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: is part of
  some values from: plan specification
disjoint with: controlled variable specification
disjoint with: dose specification
curator note: 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Chris Stoeckert
definition source: WEB: http://en.wikipedia.org/wiki/Dependent_and_independent_variables
editor preferred term: dependent variable specification
editor note: 2/2/2009 In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled.
definition: dependent variable specification is part of a study design. The dependent variable is the event studied and expected to change when the independent variable varies.
has curation status: IAO_0000125

anticoagulant-containing test tube
type: Class
subclass of: test tube
subclass of: Restriction
  on property: surrounded by
  some values from: Restriction
    on property: has part
    some values from: Restriction
      on property: has grain
      some values from: sodium citrate dihydrate
disjoint with: OBI_0400020
disjoint with: OBI_0400091
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A 'blue top' test tube that contains anticoagulant for storing blood specimens'
term editor: Person:Alan Ruttenberg
editor preferred term: anticoagulant-containing test tube
has curation status: IAO_0000120

controlled variable specification
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: is part of
  some values from: plan specification
disjoint with: dose specification
curator note: 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Chris Stoeckert
definition source: WEB: http://en.wikipedia.org/wiki/Control_variable
editor preferred term: controlled variable specification
editor note: 2/2/2009 Original definition: Controlled variables are also important to identify in experiments. They are the variables that are kept constant to prevent their influence on the effect of the independent variable on the dependent. Every experiment has a controlling variable, and it is necessary to not change it, or the results of the experiment won't be valid
definition: Controlled variable specification is a part of a study design. They are the entities that could vary, but are kept constant to prevent their influence on the effect of the independent variable on the dependent.
has curation status: IAO_0000125

human antithrombin-III (AT-III) in blood assay
type: Class
subclass of: analyte assay
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: analyte role
    intersection of: Restriction
      on property: is role of
      some values from: Class
        intersection of: scattered molecular aggregate
        intersection of: Restriction
subclass of: Class
  intersection of: Restriction
    on property: has_specified_input
    some values from: OBI_0100017
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: scalar measurement datum
      intersection of: Restriction
        on property: is about
        some values from: blood coagulation
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: analyte measurement objective
definition: An assay to measure the amount of antithrombin III in blood.
example of usage: PMID:19696660#The antithrombin-III (AT-III) was determined using a Berichrom(r) Antithrombin-III (A) kit.
term editor: Person:Alan Ruttenberg
definition source: WEB:http://www.muschealth.com/lab/content.aspx?id=150006@2009/08/06
editor preferred term: human antithrombin-III (AT-III) in blood assay
has curation status: IAO_0000122

fluorescently labeled MHC multimer
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is bearer of
  some values from: PATO_0000018
definition: A complex of two or more linked MHC molecules including a fluorescent label that can be loaded with a ligand, and is used in flow cytometry assay to bind to T cell receptors of T cells specific for the ligand
editor preferred term: fluorescently labeled MHC multimer
has curation status: IAO_0000123

survival rate
type: Class
subclass of: measurement datum
disjoint with: spike train datum
disjoint with: categorical measurement datum
disjoint with: dose
disjoint with: obsolete_general scalar measurement datum
disjoint with: 3D structural organization datum
definition: A measurement data that represents the percentage of people or animals in a study or treatment group who are alive for a given period of time after diagnosis or initiation of monitoring.
term editor: Oliver He
definition source: adapted from wikipedia http://en.wikipedia.org/wiki/Survival_rate
editor preferred term: survival rate
has curation status: IAO_0000120

recombinant BAC cloning
type: Class
subclass of: OBI_0600064
disjoint with: recombinant phage cloning
disjoint with: recombinant YAC cloning
disjoint with: OBI_0600048
disjoint with: OBI_0600063
definition: Recombinant BAC cloning is a process with the objective to insert genetic material into an F plasmid based bacterial artificial chromosome for future replication of the inserted material
definition source: http://en.wikipedia.org/wiki/Bacterial_artificial_chromosome
editor preferred term: recombinant BAC cloning
has curation status: IAO_0000123

multiple testing correction objective
type: Class
subclass of: OBI_0200186
definition: A multiple testing correction objectives is a data transformation objective where the aim is to correct for a set of statistical inferences considered simultaneously
example of usage: Application of the Bonferroni correction
definition source: http://en.wikipedia.org/wiki/Multiple_Testing_Correction
alternative term: multiple comparison correction objective
editor preferred term: multiple testing correction objective
has curation status: IAO_0000120

statistical model validation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: OBI_0200188
subclass of: OBI_0200171
definition: A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set.
term editor: Helen Parkinson
example of usage: Using the expression levels of 20 proteins to predict whether a cancer patient will respond to a drug. A practical goal would be to determine which subset of the 20 features should be used to produce the best predictive model. - wikipedia
definition source: http://en.wikipedia.org/wiki/Cross-validation_%28statistics%29
editor preferred term: statistical model validation
has curation status: IAO_0000120

double blind study execution
type: Class
equivalent class: Class
  intersection of: treatment portion of study execution
  intersection of: Restriction
    on property: has part
    all values from: Class
      complement of: Class
        union of: informing investigator of subject study arm
        union of: informing subject of study arm
subclass of: single blind study execution
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A double blind study execution is defined as any study execution in which neither the subjects nor the investigators are informed of which study arm the subjects are part of during the portion of the trial when the subjects are being treated
term editor: Person:Alan Ruttenberg
editor preferred term: double blind study execution
definition source: http://clinicaltrials.gov/ct2/info/glossary#double
has curation status: IAO_0000120

transcription factor binding site
type: Class
subclass of: sequence feature annotation
comment: PLace_holder for sequence ontology term
definition source: SO:0000235
editor preferred term: transcription factor binding site
has curation status: IAO_0000002

glucometer
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
disjoint with: micro electrode
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043

purification objective
type: Class
subclass of: separation into different composition objective
curator note: 10/14/09, BP: This should be linked to the 'purified' 'currently conferred quality
definition source: BP
term editor: PERSON:Bjoern Peters
definition: The objective to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest
alternative term: isolation objective
editor preferred term: purification objective
example of usage: the objective to obtain a pure fraction of a specific peptide when running an HPLC on a crude synthesis of peptides.
has curation status: IAO_0000120

obsolete_primary structure of protein
type: Class
subclass of: ObsoleteClass
term editor: Person:Bjoern Peters
example of usage: SIINFEKL' is the primary structure of a peptide
definition: The primary structure of a protein that is completely defined by the set of its amino acid residue parts and the linear order induced by the peptide bonds that hold them together
editor preferred term: obsolete_primary structure of protein
comment: replaced by SO_0000104 polypeptide
deprecated: true
has obsolescence reason: IAO_0000228

capsule shell
type: Class
subclass of: material entity
disjoint with: guar gum
disjoint with: cloacal specimen
disjoint with: nasopharyngeal aspirate specimen
disjoint with: nasal swab specimen
disjoint with: device
disjoint with: growth environment
disjoint with: OBI_0001468
disjoint with: OBI_0001485
disjoint with: OBI_0100014
disjoint with: OBI_0100016
disjoint with: OBI_0100017
disjoint with: OBI_0100055
disjoint with: OBI_0100058
disjoint with: OBI_0100060
disjoint with: OBI_0100067
disjoint with: OBI_0100086
disjoint with: OBI_1000023
disjoint with: OBI_1000024
disjoint with: OBI_1000029
disjoint with: OBI_1000036
disjoint with: OBI_1000042
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
term editor: Person:Alan Ruttenberg
definition: a small rounded gelatinous container
editor preferred term: capsule shell
definition source: http://www.golovchenko.org/cgi-bin/wnsearch#2n
has curation status: IAO_0000120

recombinant phage cloning
type: Class
subclass of: OBI_0600064
disjoint with: recombinant YAC cloning
disjoint with: OBI_0600048
disjoint with: OBI_0600063
term editor: Helen Parkinson
example of usage: Insert selection by BamHI methyltransferase protection in P1 phage-based cloning
definition: Recombinant phage cloning is the process of using a phage plus some insert nucleic acid for the purposes of amplification of the insert material achieved by phage assembly in vitro.
definition source: http://www.ncbi.nlm.nih.gov/books/bv.fcgi
editor preferred term: recombinant phage cloning
has curation status: IAO_0000120

cross linking
type: Class
subclass of: material processing
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: Restriction
  on property: has_specified_output
  some values from: molecular entity
definition: A process in which bonds are created that link one polymer to another
term editor: PERSON: Chris Stoeckert
editor preferred term: cross linking
example of usage: cross linking can be used as a probe to link proteins together, to check protein protein interactions
definition source: http://en.wikipedia.org/wiki/Cross-link
has curation status: IAO_0000120

spike train datum
type: Class
subclass of: measurement datum
disjoint with: categorical measurement datum
disjoint with: dose
disjoint with: obsolete_general scalar measurement datum
disjoint with: 3D structural organization datum
definition: A measurement datum which represents information about an ordered series of action potentials in an organism's CNS measured over time.
term editor: Helen Parkinson, Alan Ruttenberg
definition source: Jessica Turner, NIF
example of usage: Measurement of temporal regularity of spike train responses in auditory nerve fibers of the green treefrog
editor note: needs more work to see exactly what the data set looks like - HP
editor preferred term: spike train datum
alternative term: spike train measurement
has curation status: IAO_0000120

prothrombin time assay
type: Class
subclass of: assay
subclass of: Class
  intersection of: Restriction
    on property: has_specified_input
    some values from: OBI_0100017
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: scalar measurement datum
      intersection of: Restriction
        on property: is about
        some values from: blood coagulation
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
editor note: 2009/10/18 Alan Ruttenberg. This assay was added during the fucoidan use case exercise but still needs to be fleshed out. Only the AT-III assay has more carefully specified inputs and outputs
example of usage: PMID:19696660#The prothrombin time (PT) was quantitatively determined using RecombiPlasTin (Instrumentation Laboratory Company, Lexington, Massachusetts, USA).
term editor: Person:Alan Ruttenberg
definition: The prothrombin time is an assay most commonly measured using blood plasma. Blood is drawn into a test tube containing liquid citrate, which acts as an anticoagulant by binding the calcium in a sample. The blood is mixed, then centrifuged to separate blood cells from plasma. In newborns, whole blood is used. The plasma is analyzed by a biomedical scientist on an automated instrument at 37 degrees C, which takes a sample of the plasma. An excess of calcium is added (thereby reversing the effects of citrate), which enables the blood to clot again. For an accurate measurement the proportion of blood to citrate needs to be fixed; many laboratories will not perform the assay if the tube is underfilled and contains a relatively high concentration of citrate. If the tube is underfilled or overfilled with blood, the standardized dilution of 1 part anticoagulant to 9 parts whole blood is no longer valid. For the prothrombin time test the appropriate sample is the blue top tube, or sodium citrate tube, which is a liquid anticoagulant. Tissue factor (also known as factor III or thromboplastin) is added, and the time the sample takes to clot is measured optically. Some laboratories use a mechanical measurement, which eliminates interferences from lipemic and icteric samples. The prothrombin ratio is the prothrombin time for a patient, divided by the result for control plasma.
definition source: WEB:http://en.wikipedia.org/wiki/Prothrombin_time@2009/10/06
editor preferred term: prothrombin time assay
has curation status: IAO_0000120

denaturing
type: Class
subclass of: material processing
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: nucleic acid
    union of: PR_000000001
example of usage: Denaturing DNA in alcohol
definition: Is a process in which the tertiary or secondary structure of a polymer is disrupted
editor preferred term: denaturing
definition source: http://en.wikipedia.org/wiki/Denaturation_%28biochemistry%29
has curation status: IAO_0000123

informing investigator of subject study arm
type: Class
subclass of: planned process
subclass of: Class
  intersection of: Restriction
    on property: has participant
    some values from: Restriction
      on property: has role
      some values from: investigation agent role
  intersection of: Restriction
    on property: has_specified_input
    some values from: Restriction
      on property: denotes
      some values from: Restriction
        on property: is bearer of
        some values from: study subject role
editor note: 09/28/2009 Alan Ruttenberg. This and the class informing-subject-of-study-arm are defined in order to solve the question of how to represent single and double blind experiments. To represent the aspect of double blinding pertaining to investigators, we say that the study execution doesn't include any processes of this sort
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A process in which an investigator is made aware of which study arm that a patient is participating in, for example whether they are receiving a placebo or a treatment with an investigational compound.
term editor: Person:Alan Ruttenberg
editor preferred term: informing investigator of subject study arm
has curation status: IAO_0000120

antithrombin-III (AT-III) berichrome assay
type: Class
subclass of: human antithrombin-III (AT-III) in blood assay
subclass of: Class
  intersection of: Restriction
    on property: has participant
    some values from: Berichrom(r) Antithrombin III (A) Kit
  intersection of: Restriction
    on property: has_specified_output
    some values from: scalar measurement datum
  intersection of: Restriction
    on property: has_specified_output
    cardinality: 1
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: An antithrombin-III (AT-III) assay in which exogenous bovine thrombin and heparin are added to test plasma to form a thrombin-heparin-AT complex. The residual thrombin not bound then hydrolyzes the p-nitroalanine substrate to produce a yellow color, which is read at 405 nm. The intensity of color produced is inversely proportional to the AT present. A calibration is done with standard human plasma reagent and results for a given specimen are reported as a percentage relative to the standard
definition source: WEB:http://www.clinchem.org/cgi/content/full/43/9/1783@2009/08/06
editor preferred term: antithrombin-III (AT-III) berichrome assay
editor note: todo Reagents from Berichrom(r) Antithrombin III (A) and standard human plasma
has curation status: IAO_0000120

material maintenance objective
type: Class
subclass of: objective specification
disjoint with: training objective
disjoint with: service provision objective
disjoint with: assay validation objective
disjoint with: selective organism creation objective
disjoint with: OBI_0200166
term editor: PERSON: Bjoern Peters
definition: is the objective to maintain some or all of the qualities of a material over time.
editor preferred term: material maintenance objective
has curation status: IAO_0000123

presentation of stimulus
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: OBI_0100026
    intersection of: Restriction
      on property: has role
      some values from: study subject role
definition source: Helen Parkinson, Jessica Turner, Dirk Derom
term editor: Helen Parkinson, Jessica Turner, Dirk Derom
example of usage: The presentation of a flashing light to a monkey during reward training
definition: a planned process in which an organism is exposed to some stimulus with the intent to invoke an action
editor preferred term: presentation of stimulus
alternative term: stimulation of organism
has curation status: IAO_0000120

spectrolyse heparin antifactor-Xa assay
type: Class
subclass of: assay
subclass of: Class
  intersection of: Restriction
    on property: has_specified_input
    some values from: OBI_0100017
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: scalar measurement datum
      intersection of: Restriction
        on property: is about
        some values from: blood coagulation
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
editor note: 2009/10/18 Alan Ruttenberg. This assay was added during the fucoidan use case exercise but still needs to be fleshed out. Only the AT-III assay has more carefully specified inputs and outputs
definition: A Spectrolyse Heparin (Xa) assay is intended for the quantitative determination of therapeutic Heparin in human plasma. The principle inhibitor of Thrombin, Factor Xa and other coagulation serine proteases in plasma is Antithrombin III. The rate of inhibition, under normal conditions, is slow, but can be increased several thousand-fold by Heparin. This mechanism accounts for the anticoagulant effect of Heparin. Low Molecular Weight Therapeutic Heparin (LMWH) preparations appear to catalyze the reaction between Factor Xa and Antithrombin III more readily than the reaction between Thrombin and Antithrombin III while standard Heparin catalyzes both reactions equally. The Factor Xa inhibition test is the most useful test for assaying the widest variety of therapeutic Heparin preparations. In this method, when both Factor Xa and Antithrombin III are present in excess, the rate of Factor Xa inhibition is directly proportional to the Heparin concentration. The residual Factor Xa activity, measured with a Factor Xa-specific chromogenic substrate, is inversely proportional to the Heparin concentration.
example of usage: PMID:19696660#Antifactor-Xa (anti-Xa) was determined using spectrolyse heparin (Xa) (Trinity Biotech plc, Bray, County Wicklow, Ireland).
term editor: Person:Alan Ruttenberg
definition source: WEB:http://www.kordia.nl/en/product/hemostasis/specialty_kits__reagens/598/spectrolyse_heparin_anti_xa@2009/08/06
editor preferred term: spectrolyse heparin antifactor-Xa assay
has curation status: IAO_0000120

amplified DNA
type: Class
equivalent class: Class
  intersection of: deoxyribonucleic acids
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: OBI_0600058
subclass of: deoxyribonucleic acids
subclass of: processed material
definition source: Alan Ruttenberg
example of usage: Amplied DNA created by PCR
definition: DNA that has been produced in an enzymatic amplification process
term editor: PERSON: Alan Ruttenberg
editor preferred term: amplified DNA
has curation status: IAO_0000122

informed consent process
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has participant
  some values from: Restriction
    on property: has role
    some values from: investigation agent role
editor note: 09/28/2009 Alan Ruttenberg: This is made a subclass of the higher level processual entity in BFO because I don't want to take a stand on whether it is a process aggregate. Analogous to the situation with Material entity.
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A planned process in which subject is informed about key facts such as potential risks of a clinical trial both before deciding whether or not to participate, and throughout the study.
term editor: Person:Alan Ruttenberg
definition source: http://clinicaltrials.gov/ct2/info/glossary#informed
editor preferred term: informed consent process
has curation status: IAO_0000120

primary structure of DNA macromolecule
type: Class
equivalent class: Restriction
  on property: is concretization of
  some values from: Restriction
    on property: inheres in
    some values from: deoxyribonucleic acids
subclass of: SO_0000001
term editor: BP et al
definition: a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues.
editor note: placeholder for SO
editor preferred term: primary structure of DNA macromolecule
has curation status: IAO_0000123

measuring neural activity in the caudate nucleus
type: Class
subclass of: extracellular electrophysiology recording
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0001873
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: measure function
    intersection of: Restriction
      on property: inheres in
      some values from: micro electrode
example of usage: An SU micro-electrode was used to measure neural activity in the form of spike trains in the caudate nucleus of monkeys in response to a flashing light stimulus
term editor: Helen Parkinson
definition source: Jessica Turner, NIF, Dirk Derom, OBI
definition: The process of measuring neural activity in the caudate nucleus
editor preferred term: measuring neural activity in the caudate nucleus
has curation status: IAO_0000120

to be treated with active ingredient role
type: Class
subclass of: study subject role
disjoint with: to be treated with placebo role
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A study subject role which begins to exist when a subject is assigned to be one of those who will receive active ingredient, and is realized in a study execution in which they receive the active ingredient
definition source: PERSON: Helen Parkinson
term editor: Person:Alan Ruttenberg
example of usage: Role of a patient in a group treated with an active substance in a clinical trial
editor preferred term: to be treated with active ingredient role
has curation status: IAO_0000122

guar gum
type: Class
subclass of: material entity
disjoint with: cloacal specimen
disjoint with: nasopharyngeal aspirate specimen
disjoint with: nasal swab specimen
disjoint with: device
disjoint with: growth environment
disjoint with: OBI_0001468
disjoint with: OBI_0001485
disjoint with: OBI_0100014
disjoint with: OBI_0100016
disjoint with: OBI_0100017
disjoint with: OBI_0100055
disjoint with: OBI_0100058
disjoint with: OBI_0100060
disjoint with: OBI_0100067
disjoint with: OBI_0100086
disjoint with: OBI_1000023
disjoint with: OBI_1000024
disjoint with: OBI_1000029
disjoint with: OBI_1000036
disjoint with: OBI_1000042
definition: Guar gum, also called guaran, is a galactomannan. It is primarily the ground endosperm of guar beans. The guar seeds are dehusked, milled and screened to obtain the guar gum.[1] It is typically produced as a free flowing, pale, off-white colored, coarse to fine ground powder.
term editor: Helen Parkinson
editor preferred term: guar gum
definition source: http://en.wikipedia.org/wiki/Guar_gum
has curation status: IAO_0000120

Berichrom(r) Antithrombin III (A) Kit
type: Class
subclass of: processed material
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
editor preferred term: Berichrom(r) Antithrombin III (A) Kit
definition: For the chromogenic determination of antithrombin III. Autoanalyzer method for undiluted samples. For the quantitative chromogenic determination of the functional activity of antithrombin III in plasma on autoanalyzers for the diagnosis of diminished AT III synthesis, increased consumption, and for monitoring substitution therapy. Berichrom(r) Antithrombin III (A) is used for the rapid determination of the physiologically active antithrombin III and permits the diagnosis of congenital and acquired antithrombin III deficiency, a condition frequently associated with an increased risk of thrombosis. Acquired antithrombin III deficiencies frequently occur due to consumption following major operations or due to disseminated intravascular coagulation (DIC) in cases of septicaemia, nephroses, liver parenchymal damage (hepatitis, drug intoxication, alcoholism) and estrogen-containing contraceptives. The test permits early detection of patients at increased risk for thrombosis. Kit contains: 6 x for 5.0 mL Thrombin (bovine), 3 x for 3.0 mL Substrate Reagent, 1 x 30.0 mL Buffer Solution
term editor: Person:Alan Ruttenberg
has curation status: IAO_0000120

micro electrode
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: is_manufactured_by
  some values from: organization
disjoint with: test tube
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045

fucoidan
type: Class
subclass of: molecular entity
definition: Fucoidan is a sulfated polysaccharide (MW: average 20,000) found mainly in various species of brown seaweed such as kombu, limu moui,bladderwrack, wakame, mozuku, and hijiki (variant forms of fucoidan have also been found in animal species, including the sea cucumber).
term editor: Helen Parkinson
editor preferred term: fucoidan
definition source: http://en.wikipedia.org/wiki/Fucoidan
has curation status: IAO_0000120

calibration
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has part
  some values from: assay
subclass of: Restriction
  on property: has_specified_output
  some values from: measurement device
definition: A planned process with the objective to establish the relationship between data produced by a measurement device and physical qualities. This is done by using the measurement device under defined conditions, and either tuning it to adjust the measured output, or record the output and use it as a reference in future measurements.
term editor: GROUP: OBI Philly workshop
definition source: WEB:http://en.wikipedia.org/wiki/calibration
editor preferred term: calibration
example of usage: the process of using pH buffer adjust a pH meter
has curation status: IAO_0000122

anticoagulant tube storage of blood specimen
type: Class
subclass of: OBI_0302893
subclass of: Class
  intersection of: Restriction
    on property: has_specified_input
    some values from: OBI_0100017
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: anticoagulant-containing test tube
      intersection of: Restriction
        on property: surrounded by
        some values from: OBI_0100017
disjoint with: freezing storage
disjoint with: lyophilization storage
disjoint with: paraffin storage
disjoint with: agar stab storage
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
term editor: Person:Alan Ruttenberg
definition: Storage of a blood specimen in a tube with anticoagulant
editor preferred term: anticoagulant tube storage of blood specimen
has curation status: IAO_0000120

activated partial thromboplastin time (aPTT) assay
type: Class
subclass of: assay
subclass of: Class
  intersection of: Restriction
    on property: has_specified_input
    some values from: OBI_0100017
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: scalar measurement datum
      intersection of: Restriction
        on property: is about
        some values from: blood coagulation
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
editor note: 2009/10/18 Alan Ruttenberg. This assay was added during the fucoidan use case exercise but still needs to be fleshed out. Only the AT-III assay has more carefully specified inputs and outputs
definition: An activated partial thromboplastin time (aPTT) assay is a an assay measuring the efficacy of both the 'intrinsic' (now referred to as the contact activation pathway) and the common coagulation pathways. In order to activate the intrinsic pathway, phospholipid, an activator (such as silica, celite, kaolin, ellagic acid), and calcium (to reverse the anticoagulant effect of the oxalate) are mixed into the plasma sample . The time is measured until a thrombus (clot) forms.
example of usage: PMID:19696660#The activated partial thromboplastin time (aPTT) was determined using Dade Actin FSL activated PTT reagent.
term editor: Person:Alan Ruttenberg
definition source: WEB:http://en.wikipedia.org/wiki/Partial_thromboplastin_time@2008/10/06
editor preferred term: activated partial thromboplastin time (aPTT) assay
has curation status: IAO_0000120

filled capsule
type: Class
subclass of: pill
subclass of: Restriction
  on property: has part
  some values from: capsule shell
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A pill in the form of a small rounded gelatinous container with medicine inside.
term editor: Person:Alan Ruttenberg
editor preferred term: filled capsule
definition source: http://www.golovchenko.org/cgi-bin/wnsearch#2n
has curation status: IAO_0000120

single blind study execution
type: Class
equivalent class: Class
  intersection of: treatment portion of study execution
  intersection of: Restriction
    on property: has part
    all values from: Class
      complement of: informing subject of study arm
subclass of: treatment portion of study execution
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A single blind study execution is defined as any study execution in which the subjects are not informed of which study arm they are part of during the portion of the trial when the subjects are being treated
term editor: Person:Alan Ruttenberg
definition source: http://clinicaltrials.gov/ct2/info/glossary#single
editor preferred term: single blind study execution
has curation status: IAO_0000120

thrombin time assay
type: Class
subclass of: assay
subclass of: Class
  intersection of: Restriction
    on property: has_specified_input
    some values from: OBI_0100017
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: scalar measurement datum
      intersection of: Restriction
        on property: is about
        some values from: blood coagulation
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
editor note: 2009/10/18 Alan Ruttenberg. This assay was added during the fucoidan use case exercise but still needs to be fleshed out. Only the AT-III assay has more carefully specified inputs and outputs
definition: A thrombin time assay is on in which after liberating the plasma from whole blood by centrifugation, bovine Thrombin is added to the sample of plasma. The clot is formed and is detected optically or mechanically by a coagulation instrument. The time between the addition of the thrombin and the clot formation is recorded as the thrombin clotting time
example of usage: PMID:19696660#The thrombin time was determined using thromboclotin assay kit.
term editor: Person:Alan Ruttenberg
definition source: WEB:http://en.wikipedia.org/wiki/Thrombin_time@2009/10/06
editor preferred term: thrombin time assay
has curation status: IAO_0000120

recombinant YAC cloning
type: Class
subclass of: OBI_0600064
disjoint with: OBI_0600048
disjoint with: OBI_0600063
term editor: Helen Parkinson
example of usage: Isolation of a YAC clone covering a cluster of nine S100 genes on human chromosome 1q21
definition: Recombinant YAC cloning is a process with the objective to insert genetic material into a yeast artificial chromosome vector for future replication of the inserted material
definition source: http://www.ncbi.nlm.nih.gov/books/bv.fcgi
editor preferred term: recombinant YAC cloning
has curation status: IAO_0000123

to be treated with placebo role
type: Class
subclass of: study subject role
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A study subject role which begins to exist when a subject is assigned to be one of those who will receive a placebo, and realized in a study execution in which they receive the placebo
term editor: Person:Alan Ruttenberg
editor preferred term: to be treated with placebo role
has curation status: IAO_0000120

treatment portion of study execution
type: Class
subclass of: planned process
subclass of: Restriction
  on property: is part of
  some values from: study design execution
editor note: 09/28/2009 Alan Ruttenberg. Needed because we have to have a process to scope blinding over
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A planned process, part of a study design execution, during which the treatment of subjects is ongoing
term editor: Person:Alan Ruttenberg
editor preferred term: treatment portion of study execution
has curation status: IAO_0000120

pill
type: Class
subclass of: processed material
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A dose of medicine or placebo in the form of a small pellet.
term editor: Person:Alan Ruttenberg
definition source: http://www.golovchenko.org/cgi-bin/wnsearch#2n
editor preferred term: pill
has curation status: IAO_0000120

research organization
type: Class
subclass of: organization
disjoint with: hospital
definition: An organization formed with a goal to have its members conduct investigations
term editor: Person:Bjoern Peters
example of usage: The SALK institute is a research organization.
editor preferred term: research organization
has curation status: IAO_0000123

obsolete_primary structure of sequence macromolecule
type: Class
subclass of: ObsoleteClass
editor note: 2010-06-28 Alan Ruttenberg. This term and its children to be replaced by sequence ontology terms once we figure out what the right terms are .
definition: A quality inhering in a molecule that is completely defined by the linear sequence of a set of residues which are connected by directional, linear bonds
term editor: Person:Bjoern Peters
editor note: These are all placeholders and should be replaced by SO terms
editor preferred term: obsolete_primary structure of sequence macromolecule
comment: replaced by SO_0000001 region
curator note: these are not in great shape yet; need to clarify how what a 'sequence macromolecule is' and how it differes from molecules in general (directivity of certain bonds, linear connectivity along that type of bond etc.)
deprecated: true
has obsolescence reason: IAO_0000228

DNA residue methylation
type: Class
subclass of: PATO_0001237
disjoint with: secondary structure of sequence macromolecule
editor preferred term: DNA residue methylation
definition: a quality of a DNA residue that has a methyl group attached to it
has curation status: IAO_0000123

measurement device
type: Class
equivalent class: Class
  intersection of: device
  intersection of: Restriction
    on property: has function
    some values from: measure function
subclass of: device
example of usage: A ruler, a microarray scanner, a Geiger counter.
term editor: GROUP:OBI Philly workshop
definition source: OBI
definition: a processed material created to have the function to measure
editor preferred term: measurement device
has curation status: IAO_0000122

high molecular weight DNA extract
type: Class
subclass of: DNA extract
example of usage: Extraction of chromosomal DNA from mammalian cells by first isolating nucei
definition source: OBI
term editor: PERSON:Chris Stoeckert
definition: The output of an extraction process in which DNA molecules above a molecular weight cutoff are purified in order to exclude DNA from organellas.
editor preferred term: high molecular weight DNA extract
has curation status: IAO_0000120

manufacturer
type: Class
equivalent class: Class
  intersection of: Class
    union of: Homo sapiens
    union of: organization
  intersection of: Restriction
    on property: has role
    some values from: manufacturer role
subclass of: material entity
definition: A person or organization that has a manufacturer role
editor preferred term: manufacturer
has curation status: IAO_0000123

test tube
type: Class
subclass of: container
subclass of: Restriction
  on property: has function
  some values from: contain function
disjoint with: Sysmex CA-6000 Coagulation Analyzer
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065

oral ingestion of pill
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: material to be added role
      intersection of: Restriction
        on property: is role of
        some values from: pill
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: target of material addition role
      intersection of: Restriction
        on property: is role of
        some values from: UBERON_0000165
  intersection of: Restriction
    on property: has_specified_input
    some values from: pill
subclass of: oral administration
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: An adding a material entity to target with the entity is a pill and the target is the mouth
term editor: Person:Alan Ruttenberg
editor preferred term: oral ingestion of pill
has curation status: IAO_0000120

material maintenance
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
subclass of: planned process
definition: a process with that achieves the objective to maintain some or all of the characteristics of an input material over time
editor preferred term: material maintenance
has curation status: IAO_0000123

labeled oligonucleotide
type: Class
subclass of: processed material
editor note: 2010-01-31: Philippe Rocca-Serra placeholder
term editor: Person: Philippe Rocca-Serra
definition: a labeled oligonucleotide is a short nucleic acid which underwent a labeling process resulting in a radioactive isotope such as P32 or P33 added to its backbone for instance by end labeling with polynucleotide kinase which added radiolabeled ATP to the 5' end of oligonucleotide
editor preferred term: labeled oligonucleotide
has curation status: IAO_0000123

unblinding process
type: Class
subclass of: planned process
subclass of: Class
  intersection of: Restriction
    on property: is part of
    some values from: study design execution
  intersection of: Restriction
    on property: is part of
    some values from: informing subject of study arm
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
term editor: Person:Alan Ruttenberg
definition: The part of the study execution in which the subjects are told what study arm they are in and in which the investigators are told which subjects are in which trials
editor preferred term: unblinding process
has curation status: IAO_0000120

subject agrees they understand informed consent document
type: Class
subclass of: planned process
subclass of: Restriction
  on property: is part of
  some values from: informed consent process
editor note: 09/28/2009 Alan Ruttenberg. There's a need for a general process like this in IAO - document and person in, signed document (and associated obligations, rights, out
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A process in which a subject receives an informed consent document and agrees that they have understood it
term editor: Person:Alan Ruttenberg
editor preferred term: subject agrees they understand informed consent document
has curation status: IAO_0000120

informing subject of study arm
type: Class
subclass of: planned process
subclass of: Class
  intersection of: Restriction
    on property: is part of
    some values from: informed consent process
  intersection of: Restriction
    on property: has participant
    some values from: Restriction
      on property: has role
      some values from: study subject role
editor note: 09/28/2009 Alan Ruttenberg. This and the class informing-investigator-of-study-arm are defined in order to solve the question of how to represent single and double blind experiments. To represent the aspect of blinding pertaining to subjects (happens in single and double blinding) we say that that the study execution doesn't include any processes of this sort
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A process in which the subject is made aware of which study arm they are participating in, for example whether they are receiving a placebo or a treatment with an investigational compound.
term editor: Person:Alan Ruttenberg
editor preferred term: informing subject of study arm
has curation status: IAO_0000120

Sysmex CA-6000 Coagulation Analyzer
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: is_manufactured_by
  has value: OBI_0000829
disjoint with: calorimeter
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078

hospital
type: Class
subclass of: organization
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A medical organization at which sick or injured people are given clinical care
term editor: Person:Alan Ruttenberg
term editor: Person:Helen Parkinson
editor preferred term: hospital
definition source: http://www.golovchenko.org/cgi-bin/wnsearch#2n
example of usage: human ethics approval was obtained from the Southern Tasmania Health & Medical Human Research Ethics Committee and the Royal Hobart Hospital Research Ethics Committee [pmid:19696660]
definition source: modified from the wording of the wordnet definition
has curation status: IAO_0000120

primary structure of RNA molecule
type: Class
equivalent class: Restriction
  on property: is concretization of
  some values from: Restriction
    on property: inheres in
    some values from: ribonucleic acids
subclass of: SO_0000001
term editor: Person:Bjoern Peters
definition: The primary structure of an RNA molecule that is completely defined by the set of its nucleic residue parts and the linear order induced by the peptide bonds that hold them together
editor preferred term: primary structure of RNA molecule
has curation status: IAO_0000123

test substance role
type: Class
subclass of: role
disjoint with: complementary nucleotide probe role
disjoint with: service consumer role
disjoint with: service provider role
disjoint with: accessed material role
disjoint with: OBI_0302731
disjoint with: OBI_0302732
disjoint with: OBI_0302733
disjoint with: OBI_1110082
disjoint with: OBI_1110083
disjoint with: OBI_1110086
disjoint with: OBI_1110087
disjoint with: OBI_1110091
disjoint with: OBI_1110092
disjoint with: OBI_1110120
definition: A role born by a material entity and realized in a process where the substance is used as specified as the independent variable for an investigation
definition source: Group:OBI
term editor: Person:Alan Ruttenberg
example of usage: fucoidan bears a test substance role in a study to test safety taking a certain dosage of it orally
editor preferred term: test substance role
has curation status: IAO_0000120

polyA RNA extraction
type: Class
subclass of: OBI_0666666
disjoint with: organellar RNA extraction
disjoint with: total RNA extraction
disjoint with: cytoplasmic RNA extraction
disjoint with: nuclear RNA extraction
definition: A RNA extraction process typically involving the use of poly dT oligomers in which the desired output material is polyA RNA.
term editor: Person: Chris Stoeckert
term editor: Person: Jie Zheng
definition source: UPenn Group
editor preferred term: polyA RNA extraction
has curation status: IAO_0000120

organellar RNA extraction
type: Class
subclass of: OBI_0666666
disjoint with: total RNA extraction
disjoint with: cytoplasmic RNA extraction
disjoint with: nuclear RNA extraction
definition: A RNA extraction process in which the desired output material is RNA in the organelle(s).
term editor: Person: Chris Stoeckert
term editor: Person: Jie Zheng
definition source: UPenn Group
editor preferred term: organellar RNA extraction
has curation status: IAO_0000120

obsolete_diethyl pyrocarbonate
type: Class
subclass of: ObsoleteClass
comment: Replaced by CHEBI_59051 Diethylpyrocarbonate
editor preferred term: obsolete_diethyl pyrocarbonate
deprecated: true
has obsolescence reason: IAO_0000228

record of missing knowledge
type: Class
subclass of: information content entity
disjoint with: sequence feature annotation
disjoint with: OBI_0302838
disjoint with: OBI_0302840
example of usage: A statement in a journal article indicating that the age of a patient at the onset of disease is not known. A statement indicating that the weight of a mouse was not measured.
term editor: Bjoern Peters
editor note: This class should probably end up in IAO. It could be further breaken down to indicate different kinds of lack of knowledge, e.g. inability to determine something vs. no attempt made to determine something vs. no informatino available if it was even attempted to determine something. The design pattern should be generalizable. 'unknown sex' is the first example, and needed immediately.
definition: a information content entity created to indicate that information about something is not available to the person recording it.
editor preferred term: record of missing knowledge
has curation status: IAO_0000120

western blot analysis
type: Class
subclass of: analyte assay
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: evaluant role
    intersection of: Restriction
      on property: inheres in
      some values from: protein extract
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: analyte role
    intersection of: Restriction
      on property: inheres in
      some values from: Class
        intersection of: scattered molecular aggregate
        intersection of: Restriction
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: analyte measurement objective
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: PR_000000001
example of usage: PMID: 6266278. "Western blotting": electrophoretic transfer of proteins from sodium dodecyl sulfate--polyacrylamide gels to unmodified nitrocellulose and radiographic detection with antibody and radioiodinated protein A. Anal Biochem. 1981 Apr;112(2):195-203
definition: a western blot analysis is an assay which allows detection of protein present in a extract resolved on polyacrylamide gel by electrophoresis, transfered to a membrane made of nitrocellulose or polyvinylidene difluoride and immobilized using formaldehyde based cross linking. Specific proteins are probed using specific antibodies. detection is carried by staining with secondary antibody usually linked to biotin or to a reporter enzyme such as alkaline phosphatase or horseradish peroxidase. This means that several secondary antibodies will bind to one primary antibody and enhance the signal. Most commonly, a horseradish peroxidase-linked secondary is used to cleave a chemiluminescent agent, and the reaction product produces luminescence in proportion to the amount of protein. Detection can only be achieved by radio marking antibodies and using Phosphor imagers.
term editor: person: Philippe Rocca-Serra
alternative term: protein immunoblotting
editor preferred term: western blot analysis
definition source: wikipedia
has curation status: IAO_0000120

total RNA extraction
type: Class
subclass of: OBI_0666666
disjoint with: cytoplasmic RNA extraction
disjoint with: nuclear RNA extraction
definition: A RNA extraction process in which total cellular and organelle RNA are extracted.
term editor: Person: Chris Stoeckert
term editor: Person: Jie Zheng
definition source: UPenn Group
editor preferred term: total RNA extraction
has curation status: IAO_0000120

intracellular material detection by flow cytometry assay
type: Class
subclass of: flow cytometry assay
subclass of: Restriction
  on property: has part
  some values from: OBI_0600033
subclass of: Restriction
  on property: has_specified_input
  some values from: OBI_0100060
definition: An assay in which the presence of a material inside a cell is measured by permeabilizing the cell membrane to allow entry of specific antibodies, and counting the stained cells using a flow cytometer.
editor preferred term: intracellular material detection by flow cytometry assay
has curation status: IAO_0000123

complementary nucleotide probe role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: nucleic acid
disjoint with: service consumer role
disjoint with: service provider role
disjoint with: accessed material role
disjoint with: OBI_0302731
disjoint with: OBI_0302732
disjoint with: OBI_0302733
disjoint with: OBI_1110082
disjoint with: OBI_1110083
disjoint with: OBI_1110086
disjoint with: OBI_1110087
disjoint with: OBI_1110091
disjoint with: OBI_1110092
disjoint with: OBI_1110120
example of usage: A primer in a PCR reaction. A probe on an Affymetrix chip.
definition: A role played by a nucleic acid molecule that is used in a planned process for its ability to bind a nucleic acid molecules with complementary nucleotide sequence
term editor: PERSON:Bjoern Peters
editor preferred term: complementary nucleotide probe role
has curation status: IAO_0000120

record of unknown sex
type: Class
subclass of: record of missing knowledge
subclass of: Restriction
  on property: is about
  some values from: PATO_0000047
example of usage: A database record indicating that the tissue sample in a microarray experiment came from an organism for which the biological sex is not known to the person who created the record.
term editor: Bjoern Peters
editor note: I think the statement is still about the instance of the biological sex quality of an organism. It is also about information available to the person making the statement.
definition: a record indicating that the biological sex of an organism is not known.
editor preferred term: record of unknown sex
has curation status: IAO_0000120

cytoplasmic RNA extraction
type: Class
subclass of: OBI_0666666
disjoint with: nuclear RNA extraction
definition: A RNA extraction process in which the desired output material is RNA in the cytoplasm.
term editor: Person: Chris Stoeckert
term editor: Person: Jie Zheng
definition source: UPenn Group
editor preferred term: cytoplasmic RNA extraction
has curation status: IAO_0000120

northern blot analysis
type: Class
subclass of: detection of specific nucleic acids with complementary probes
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: analyte role
    intersection of: Restriction
      on property: inheres in
      some values from: Class
        intersection of: scattered molecular aggregate
        intersection of: Restriction
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: evaluant role
    intersection of: Restriction
      on property: inheres in
      some values from: polyA RNA extract
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: complementary nucleotide probe role
    intersection of: Restriction
      on property: inheres in
      some values from: nucleic acid
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: gene expression
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
editor note: 2010-01-31: Philippe Rocca-Serra: Need to add a restriction taking into account probe and transcript information
example of usage: PMID: 18428227. Analysis of RNA by northern blot hybridization. Brown T, Mackey K. Curr Protoc Hum Genet. 2001 Nov;Appendix 3:Appendix 3K.
term editor: Person: Philippe Rocca-Serra
definition: a northern blot analysis is an assay allowing monitoring presence of gene transcripts by hybridizing labeled RNA or DNA probes against messenger RNAs isolated from tissue or cell cultures, resolved on denaturing agarose gel, transfered by blotting procedure to a nitrocellulose or nylon membrane and immobilized by cross linking or baking to the membrane. Detection of hybridization signals is carried out by immunofluorescence or radioactivity measurements using photographic films or digital imaging devices such as Phosphor Imager
alternative term: northern blot
editor preferred term: northern blot analysis
has curation status: IAO_0000123

Likelihood-ratio test
type: Class
subclass of: OBI_0200000
disjoint with: performing a diagnosis
disjoint with: feature extraction
disjoint with: OBI_0001477
disjoint with: OBI_0200002
disjoint with: OBI_0200003
disjoint with: OBI_0200004
disjoint with: OBI_0200006
disjoint with: OBI_0200007
disjoint with: OBI_0200008
disjoint with: OBI_0200011
disjoint with: OBI_0200014
disjoint with: OBI_0200016
disjoint with: OBI_0200017
disjoint with: OBI_0200021
disjoint with: OBI_0200022
disjoint with: OBI_0200025
disjoint with: OBI_0200026
disjoint with: OBI_0200027
disjoint with: OBI_0200028
disjoint with: OBI_0200029
disjoint with: OBI_0200030
disjoint with: OBI_0200033
disjoint with: OBI_0200034
disjoint with: OBI_0200035
disjoint with: OBI_0200036
disjoint with: OBI_0200037
disjoint with: OBI_0200041
disjoint with: OBI_0200042
disjoint with: OBI_0200049
disjoint with: OBI_0200050
disjoint with: OBI_0200052
disjoint with: OBI_0200056
disjoint with: OBI_0200057
disjoint with: OBI_0200058
disjoint with: OBI_0200059
disjoint with: OBI_0200060
disjoint with: OBI_0200061
disjoint with: OBI_0200062
disjoint with: OBI_0200063
disjoint with: OBI_0200064
disjoint with: OBI_0200066
disjoint with: OBI_0200071
disjoint with: OBI_0200077
disjoint with: OBI_0200079
disjoint with: OBI_0200080
disjoint with: OBI_0200082
disjoint with: OBI_0200088
disjoint with: OBI_0200092
disjoint with: OBI_0200093
disjoint with: OBI_0200094
disjoint with: OBI_0200095
disjoint with: OBI_0200097
disjoint with: OBI_0200098
disjoint with: OBI_0200102
disjoint with: OBI_0200106
disjoint with: OBI_0200108
disjoint with: OBI_0200109
disjoint with: OBI_0200110
disjoint with: OBI_0200113
disjoint with: OBI_0200116
disjoint with: OBI_0200117
disjoint with: OBI_0200118
disjoint with: OBI_0200119
disjoint with: OBI_0200120
disjoint with: OBI_0200121
disjoint with: OBI_0200122
disjoint with: OBI_0200123
disjoint with: OBI_0200124
disjoint with: OBI_0200125
disjoint with: OBI_0200140
disjoint with: OBI_0200149
disjoint with: OBI_0200150
disjoint with: OBI_0200156
disjoint with: OBI_0200160
disjoint with: OBI_0200161
disjoint with: OBI_0200162
disjoint with: OBI_0200164

nuclear RNA extract
type: Class
subclass of: RNA extract
subclass of: Restriction
  on property: is_specified_output_of
  some values from: nuclear RNA extraction
definition: A RNA extract that is the output of an extraction process in which RNA molecules found in the nucleus, including mRNA precursors (pre-mRNA), are extracted.
example of usage: Isolation and purification of nuclear RNA from animal cells using Norgen Bioteck corp. cytoplasmic and nuclear RNA purification kit (http://www.norgenbiotek.com/display-product.php?ID=30)
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition source: UPenn Group
editor preferred term: nuclear RNA extract
has curation status: IAO_0000120

96-well neutralization assay
type: Class
subclass of: serum neutralization of viral infectivity assay
editor preferred term: 96-well neutralization assay
definition: A serum neutralization of viral infectivity assay which done in a 96-well plate.
curator note: MC: 20100217: microneutralization is used by the influenza community, to refer to a nutralizationassay at a smaller scale. However smaller is difficult to define accurately, and we therefore chose a label being more specific.
alternative term: microneutralization assay
term editor: person: Bjoern Peters
term editor: person: Melanie Courtot
has curation status: IAO_0000120

establishing a cancer cell line
type: Class
subclass of: material processing
subclass of: Restriction
  on property: has_specified_output
  some values from: OBI_0100056
subclass of: Restriction
  on property: has_specified_input
  some values from: OBI_0100035
example of usage: Establishment of HeLa immortal cell line
comment: Helen Parkinson
editor preferred term: establishing a cancer cell line
definition: is a planned process in which the objective is to generate a cell line from a natural population of cells which are already immortal
has curation status: IAO_0000123

pattern matching objective
type: Class
subclass of: OBI_0200166
disjoint with: OBI_0200005
disjoint with: OBI_0200031
disjoint with: OBI_0200078
disjoint with: OBI_0200081
disjoint with: OBI_0200083
disjoint with: OBI_0200091
disjoint with: OBI_0200157
disjoint with: OBI_0200167
disjoint with: OBI_0200168
disjoint with: OBI_0200172
disjoint with: OBI_0200174
disjoint with: OBI_0200177
disjoint with: OBI_0200178
disjoint with: OBI_0200179
disjoint with: OBI_0200180
disjoint with: OBI_0200183
disjoint with: OBI_0200189
disjoint with: OBI_0200196
disjoint with: OBI_0200197
definition: A pattern matching objective aims to detect the presence of the constituents of a given pattern. In contrast to pattern recognition, the pattern is rigidly specified. Patterns are typicall sequences or trees.
term editor: Tina Boussard
definition source: http://en.wikipedia.org/wiki/Pattern_matching
editor preferred term: pattern matching objective
has curation status: IAO_0000123

polyA RNA extract
type: Class
subclass of: RNA extract
subclass of: Restriction
  on property: is_specified_output_of
  some values from: polyA RNA extraction
definition: A RNA extract that is the output of an extraction process in which RNA molecules with poly A tail at its 3’ end are purified.
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
example of usage: Preparation of polyA RNA by cellulose-bound oligo-dT (Aviv, H., Leder, P. 1972. Purification of biologically active globin messenger RNA by chromatography on oligothymidylic acid-cellulose. Proc. Nat. Acad. Sci. USA 69, 1408-1412.)
definition source: UPenn Group
editor preferred term: polyA RNA extract
has curation status: IAO_0000120

single-nucleotide-resolution nucleic acid structure mapping assay
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: secondary structure of sequence macromolecule
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: assay objective
subclass of: assay
editor note: 2010-01-31: Philippe Rocca-Serra: OBI needs to review 'structure assay' as currently defined. Need to get feedback from Kevin Clancy.
term editor: Person: Philippe Rocca-Serra
definition source: RNAO
definition: is an assay which aims to provide information about the secondary structure of nucleic acids using chemical or enzymatic probing to establish the extent of base-pairing or solvent accessiblity.
editor preferred term: single-nucleotide-resolution nucleic acid structure mapping assay
has curation status: IAO_0000120

viral hemagglutination assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has part
  some values from: induced hemagglutination
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: Viruses
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: analyte measurement objective
alternative term: HA
alternative term: HI
definition: The viral hemagglutination assay (HA) is a quantification of viruses by hemagglutination.
definition source: WEB: http://en.wikipedia.org/wiki/Hemagglutination_assay
term editor: person: Bjoern Peters
term editor: person: Melanie Courtot
editor preferred term: viral hemagglutination assay
alternative term: viral hemeagglutination assay
has curation status: IAO_0000120

serum neutralization of viral infectivity assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: analyte measurement objective
definition: A quantitative assay where different dilutions of serum are mixed with virus and used to infect cells. At the lower dilutions, antibodies will block infection, but at higher dilutions, there will be too few antibodies to have an effect. The simple process of dilution provides a way to compare the virus- neutralizing abilities of different sera. The neutralization titer is expressed as the reciprocal of the highest dilution at which virus infection is blocked.
curator note: MC, 20100217: I added influenza neutralization assay as alternative term. This should be tagged with a community specific value, eg "influenza ontology" or else.
definition source: WEB: http://www.virology.ws/2009/05/28/influenza-microneutralization-assay/
alternative term: influenza neutralization assay
term editor: person: Bjoern Peters
term editor: person: Melanie Courtot
editor preferred term: serum neutralization of viral infectivity assay
has curation status: IAO_0000120

pre-mortem specimen
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: specimen collection
    intersection of: Restriction
      on property: has_specified_input
      some values from: Class
        intersection of: OBI_0100026
        intersection of: Restriction
subclass of: OBI_0001506
disjoint with: post mortem specimen
term editor: Bjoern Peters
definition: a specimen that was taken from a live organism
example of usage: material obtained through a liver biopsy from a human patient
editor preferred term: pre-mortem specimen
definition source: MO_705 premortem
has curation status: IAO_0000120

detection of specific nucleic acids with complementary probes
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: analyte role
      intersection of: Restriction
        on property: inheres in
        some values from: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: complementary nucleotide probe role
      intersection of: Restriction
        on property: inheres in
        some values from: nucleic acid
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: analyte measurement objective
subclass of: analyte assay
definition: An assay in which a specified input material is examined for the presence or quantity of specified nucleic acid polymers, which are identified based on the use of complementary nucleic acid probes.
example of usage: Primer based PCR assay, Norther blot, Southern Blot, RNAse protection assay
editor preferred term: detection of specific nucleic acids with complementary probes
has curation status: IAO_0000120

viral hemagglutination inhibition assay
type: Class
subclass of: OBI_0001705
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: analyte measurement objective
alternative term: HAI
definition source: WEB: http://www.virology.ws/2009/05/27/influenza-hemagglutination-inhibition-assay/
definition: a highly sensitive procedure for the measurement of soluble antigens in biologic specimens; the amount of hemagglutination reflects the amount of free antibody present after reaction with the specimen and thus varies inversely with amount of antigen in the specimen.
term editor: person: BJoern Peters
term editor: person: Melanie Courtot
editor preferred term: viral hemagglutination inhibition assay
alternative term: viral hemeagglutination inhibition assay
has curation status: IAO_0000120

cytoplasmic RNA extract
type: Class
subclass of: RNA extract
subclass of: Restriction
  on property: is_specified_output_of
  some values from: cytoplasmic RNA extraction
definition: A RNA extract that is the output of a RNA extraction process in which RNA molecules found in the cytoplasm are extracted.
example of usage: Cytoplasmic RNA extraction from mammalian tissues to create cDNA library (Carninci P, Nakamura M, Sato K, Hayashizaki Y, Brownstein MJ. Cytoplasmic RNA extraction from fresh and frozen mammalian tissues. Biotechniques. 2002;33:306–309.)
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition source: UPenn Group
editor preferred term: cytoplasmic RNA extract
has curation status: IAO_0000120

cell line immortalization
type: Class
subclass of: material processing
subclass of: Restriction
  on property: has_specified_output
  some values from: OBI_0100056
term editor: Bjoern Peters
definition source: OBI
example of usage: Production of a cell line for the purposes of experimentation e.g. EBV transformation of PBMs
editor preferred term: cell line immortalization
definition: is the planned process of experimentally creating a cell line which is capable of dividing indefinitely in vitro. Has specified output cell line
has curation status: IAO_0000123

random primed DNA labeling
type: Class
subclass of: OBI_0600038
disjoint with: OBI_0600019
disjoint with: OBI_0600067
definition source: PMID: 6312838. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Feinberg AP, Vogelstein B. Anal Biochem. 1983 Jul 1;132(1):6-13.
example of usage: PMID: 8713846. Random primed 32P-labeling of DNA. Smith DR. Methods Mol Biol. 1996;58:27-9.
term editor: Person: Bjoern Peters Person: Chris Stoeckert
term editor: Person: Philippe Rocca-Serra
definition: a labeling in which random primers are used to uniformly label input DNA
editor note: need to add Klenow subunit of DNA polymerase I under material entity
editor preferred term: random primed DNA labeling
has curation status: IAO_0000120

RNA extract
type: Class
subclass of: nucleic acid extract
subclass of: Restriction
  on property: has grain
  some values from: ribonucleic acids
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0666666
definition source: Group: UPenn Group
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
editor preferred term: RNA extract
definition: an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen.
has curation status: IAO_0000120

cell mediated cell killing assay
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has_specified_input
    some values from: cell
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: cell killing
subclass of: assay
definition: An assay that measures the rate in which a target cell population is killed by effector cells.
term editor: PERSON:Bjoern Peters
editor preferred term: cell mediated cell killing assay
has curation status: IAO_0000120

in vivo cell mediated cell killing assay
type: Class
subclass of: cell mediated cell killing assay
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: cell killing
subclass of: Restriction
  on property: has_specified_input
  some values from: OBI_0100026
definition: An assay that measures the rate in which a target cell population is killed by effector cells within an organism
term editor: PERSON:Bjoern Peters
editor preferred term: in vivo cell mediated cell killing assay
example of usage: injecting CFSE labeled target cells with and without loaded influenza peptide into a mouse, and comparing the recovery rate.
has curation status: IAO_0000120

secondary structure of sequence macromolecule
type: Class
subclass of: PATO_0001237
editor note: 2010-01-31: Philippe Rocca-Serra: This is a placeholder to allow work on 'nucleic acid mapping assay' in collaboration with RNAOntology group. Need to liaise with SO
definition: A quality inhering in a molecule that refers to general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids (DNA/RNA). It does not, however, describe specific atomic positions in three-dimensional space, which are considered to be tertiary structure. Secondary structure was introduced by Kaj Ulrik Linderstrøm-Lang in the 1952 Lane medical lectures at Stanford.
term editor: Person: Philippe Rocca-Serra
definition source: Wikipedia
editor preferred term: secondary structure of sequence macromolecule
has curation status: IAO_0000002

nuclear RNA extraction
type: Class
subclass of: OBI_0666666
definition: A RNA extraction process in which the desired output material is RNA in the nucleus.
term editor: Person: Chris Stoeckert
term editor: Person: Jie Zheng
definition source: UPenn Group
editor preferred term: nuclear RNA extraction
has curation status: IAO_0000120

survival curve
type: Class
subclass of: line graph
subclass of: Restriction
  on property: is about
  some values from: survival rate
definition: A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time.
term editor: PERSON:Chris Stoeckert
term editor: PERSON:James Malone
term editor: PERSON:Melanie Courtot
definition source: WEB: http://www.graphpad.com/www/book/survive.htm
editor preferred term: survival curve
has curation status: IAO_0000122

cell proliferation assay
type: Class
equivalent class: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: cell proliferation
subclass of: assay
subclass of: Restriction
  on property: has_specified_input
  some values from: cell
definition: An assay which measures the rate of proliferation of input cells
example of usage: Measuring the amount of tritiated thymidine incorporated by dividing cells as a proxy for cell proliferation.
editor note: Note that cell proliferation assays can often be a part of another assay. For example, to detect an analyte with a cell culture bioassay.
term editor: PERSON:Bjoern Peters
editor preferred term: cell proliferation assay
has curation status: IAO_0000120

Southern blot analysis
type: Class
subclass of: detection of specific nucleic acids with complementary probes
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: evaluant role
    intersection of: Restriction
      on property: inheres in
      some values from: high molecular weight DNA extract
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: analyte role
    intersection of: Restriction
      on property: inheres in
      some values from: Class
        intersection of: scattered molecular aggregate
        intersection of: Restriction
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: site
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: complementary nucleotide probe role
    intersection of: Restriction
      on property: inheres in
      some values from: nucleic acid
editor note: 2010-01-31: Philippe Rocca-Serra: need extra work on 'labeled probe'
editor note: 2010-01-31: Philippe Rocca-Serra: departure from naming convention as the assay is named after Edwin Southern.
definition source: OBI & Wikipedia
example of usage: PMID: 9452032. Germline mutations detected in the von Hippel-Lindau disease tumor suppressor gene by Southern blot and direct genomic DNA sequencing. Li C, Weber G, Ekman P, Lagercrantz J, Norlen BJ, Akerström G, Nordenskjöld M, Bergerheim US. Hum Mutat. 1998;Suppl 1:S31-3.
term editor: Person: Philippe Rocca-Serra
alternative term: Southern blot
editor preferred term: Southern blot analysis
definition: Southern blot analysis is a an assay used in molecular biology to assert the presence/absence status of a specific DNA sequence in DNA samples. DNA samples to be assayed are first digested by restriction enzymes, fragments are then resolved by gel electrophoresis following by a blotting ensuring transfer to nitrocellulose or nylon membrane. Immobilization of DNA fragments to the membrane is achieved by UV crosslinking and/or baking. Probes raised against the specific sequences are then hybridized to the membrane. Detection of hybridization signals is carried out by immunofluorescence or radioactivity measurements using photographic films or digital imaging devices such as Phosphor Imager.
has curation status: IAO_0000120

real time polymerase chain reaction assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has part
  some values from: polymerase chain reaction
definition: A laboratory technique based on the PCR, which is used to amplify and simultaneously quantify a specific DNA molecule based on the use of complementary probes/primers. It enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample.
alternative term: Q-PCR
definition source: WEB: http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction
alternative term: kinetic polymerase chain reaction
term editor: person: Bjoern Peters
term editor: person: Melanie Courtot
alternative term: qPCR
alternative term: quantitative real time polymerase chain reaction
editor preferred term: real time polymerase chain reaction assay
has curation status: IAO_0000120

protein extract
type: Class
subclass of: extract
subclass of: Restriction
  on property: has part
  some values from: PR_000000001
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0302884
definition source: OBI & wikipedia
example of usage: PMID: 20032479. A bovine whey protein extract stimulates human neutrophils to generate bioactive IL-1Ra through a NF-kappaB- and MAPK-dependent mechanism. Rusu D, Drouin R, Pouliot Y, Gauthier S, Poubelle PE. J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23.
term editor: Person: Philippe Rocca-Serra
definition: a protein extract is the output of an extraction process from tissues or cell cultures resulting in a solution of cellular and/or organellar proteins in buffer solution used to prevent degradation,
editor preferred term: protein extract
has curation status: IAO_0000120

total RNA extract
type: Class
subclass of: RNA extract
subclass of: Restriction
  on property: is_specified_output_of
  some values from: total RNA extraction
definition: A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen.
example of usage: Extraction of total RNA from cells with Qiagen mini RNeasy kit.
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition source: UPenn Group
editor preferred term: total RNA extract
has curation status: IAO_0000120

secondary structure of RNA molecule
type: Class
subclass of: secondary structure of sequence macromolecule
editor note: 2010-01-31: Philippe Rocca-Serra: This is a placeholder to allow work on 'nucleic acid mapping assay' in collaboration with RNAOntology group. Need to liaise with SO
example of usage: PMID: 15630685: Single molecule studies of RNA secondary structure: AFM of TYMV viral RNA.
term editor: Person: Philippe Rocca-Serra
editor preferred term: secondary structure of RNA molecule
has curation status: IAO_0000123

DEPC structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of sequence macromolecule
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: deoxyribonucleic acids
    union of: ribonucleic acids
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: reagent role
    intersection of: Restriction
      on property: inheres in
      some values from: Diethylpyrocarbonate
editor preferred term: DEPC structure mapping assay
example of usage: PMID:2446263. Probing the structure of RNAs in solution. Nucleic Acids Res. 1987 Nov 25;15(22):9109-28.
term editor: Person: Philippe Rocca-Serra
definition source: RNA ontology
definition: is a single-nucleotide-resolution nucleic acid structure mapping assay which uses DEPC as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
has curation status: IAO_0000122

organellar RNA extract
type: Class
subclass of: RNA extract
subclass of: Restriction
  on property: is_specified_output_of
  some values from: organellar RNA extraction
definition: A RNA extract that is the output of an extraction process in which RNA molecules found in an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus, are extracted.
example of usage: Extraction of organellar RNA from plant cells using organellar RNA binding protein.
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition source: UPenn Group
editor preferred term: organellar RNA extract
has curation status: IAO_0000120

post mortem specimen
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: specimen collection
    intersection of: Restriction
      on property: has_specified_input
      some values from: Class
        intersection of: OBI_0100026
        intersection of: Restriction
subclass of: OBI_0001506
term editor: Bjoern Peters
definition: a specimen that was taken from a dead organism
editor preferred term: post mortem specimen
example of usage: the spleen taken from a dead mouse
definition source: MO_416 postmortem
has curation status: IAO_0000120

in vitro cell mediated cell killing assay
type: Class
subclass of: cell mediated cell killing assay
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: cell killing
subclass of: Restriction
  on property: has_specified_input
  some values from: OBI_0100060
definition: An assay that measures the rate in which a target cell population is killed by effector cells in a cell culture.
term editor: PERSON:Bjoern Peters
editor preferred term: in vitro cell mediated cell killing assay
has curation status: IAO_0000120

cell culture analyte detection bioassay
type: Class
subclass of: analyte assay
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: analyte measurement objective
subclass of: Restriction
  on property: has_specified_input
  some values from: OBI_0100062
subclass of: Restriction
  on property: realizes
  some values from: analyte role
subclass of: Restriction
  on property: has part
  some values from: OBI_0600024
definition: An assay in which a reporter cell line is cultured which is affected in its growth characteristics by the presence of a specific analyte. Monitoring the cell line growth is used to detect the analyte in an input material (the evaluant).
example of usage: IEDB curation of Pubmed 12445737: CTLL-2 cells were grown in the presence of hybridoma supernatants and monitoring growth by a 3H-thymidine incorporation (cell proliferation) assay in order to detect IL-2 in the hybridoma supernatant.'
term editor: PERSON:Bjoern Peters
curator note: Tracker request: https://sourceforge.net/tracker/?func=detail&aid=2946262&group_id=177891&atid=886178
editor preferred term: cell culture analyte detection bioassay
has curation status: IAO_0000120

sequence feature annotation
type: Class
subclass of: information content entity
disjoint with: OBI_0302838
disjoint with: OBI_0302840
term editor: Bjoern Peters
definition source: Bjoern Peters
definition: Information about a sequence region
comment: place holder for sequence ontology term
editor preferred term: sequence feature annotation
has curation status: IAO_0000120

induced hemagglutination
type: Class
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: erythrocyte
editor note: MC, 20100217: This term was originally submitted to GO, see discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=2947975&group_id=36855&atid=440764. After discussion it was agreed that this isn't a natural in vivo process and therefore out of scope for GO. Dev call Nov 22, 2010: To reflect this, the term's label has been updated to 'induced hemagglutination'.
definition: The clumping or clustering of red blood cells caused by certain viruses, antibodies, or other substances
definition source: WEB: http://medical-dictionary.thefreedictionary.com/hemagglutination
alternative term: hemeagglutination
editor preferred term: induced hemagglutination
term editor: person: Bjoern Peters
term editor: person: Melanie Courtot
has curation status: IAO_0000120

supplying
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
curator note: 5/31/2012: A supplying process implies that there is an acquisition process. These may need to be tied together, so that modeling either way is reciprocal.
example of usage: Jackson Labs supplies mouse strains.
definition source: Jennifer Fostel
term editor: Jennifer Fostel
definition: The planned process of providing material entities to be used in an investigation.
editor preferred term: supplying
has curation status: IAO_0000120

labeled DNA extract
type: Class
subclass of: labeled nucleic acid extract
subclass of: Restriction
  on property: has grain
  some values from: deoxyribonucleic acids
subclass of: Class
  intersection of: Restriction
    on property: has role
    some values from: specimen role
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: Class
      intersection of: OBI_0600038
      intersection of: Restriction
        on property: has_specified_input
        some values from: DNA extract
definition source: Group: OBI group
term editor: Group: OBI group
editor note: Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. Added duirng Mar 1, 2010 dev call
definition: a labeled specimen that is the output of a labeling process and has grain labeled DNA to be able to detect DNA in future experiments.
editor preferred term: labeled DNA extract
has curation status: IAO_0000120

cloacal specimen
type: Class
subclass of: OBI_0100051
subclass of: Restriction
  on property: has role
  some values from: specimen role
disjoint with: nasopharyngeal aspirate specimen
disjoint with: nasal swab specimen
disjoint with: device
disjoint with: growth environment
disjoint with: OBI_0001468
disjoint with: OBI_0001485
disjoint with: OBI_0100014
disjoint with: OBI_0100016
disjoint with: OBI_0100017
disjoint with: OBI_0100055
disjoint with: OBI_0100058
disjoint with: OBI_0100060
disjoint with: OBI_0100067
disjoint with: OBI_0100086
disjoint with: OBI_1000023
disjoint with: OBI_1000024
disjoint with: OBI_1000029
disjoint with: OBI_1000036
disjoint with: OBI_1000042
definition: A specimen obtained by inserting a swab deeply into the vent of the cloaca of an organism and vigorously swabbing the wall. The swab should be deeply stained with fecal material and is then placed in transport medium.
term editor: PERSON: Melanie Courtot
definition source: WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf
editor preferred term: cloacal specimen
example of usage: type of sample used in the PCIRN influenza network
has curation status: IAO_0000120

radio immuno assay
type: Class
subclass of: radioactivity detection
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: Restriction
        on property: realizes
        some values from: PATO_0001741
definition: An assay in which a radioactive label is used to determine the interaction between an antigen and an antibody. This can be used to detect the presence of an antigen of interest or determine the specificity of an antibody.
definition source: IEDB
term editor: PERSON: Bjoern Peters
alternative term: RIA
example of usage: To evaluate the specificity of antibody binding to 35S-labeled IA-2(256–760) in comparison with 35S-labeled IA-2IC construct, the mutual inhibition activity of different concentrations of unlabeled IA-2IC and/or IA-2(256–760) fragments were tested. The unlabeled fragments were prepared by in vitro transcription and translation as described above but replacing [35S]methionine with unlabeled methionine in the amino acid mixture. Unlabeled recombinant IA-2(256–760) and/or IA-2IC (0.5-, 1-, 2-, and 4-fold the amount of 35S-labeled protein) were added to each tube and incubated overnight at 4°C with patient sera. The following day, after incubation with radiolabeled 35S–IA-2(256–760) or 35S–IA-2IC proteins, samples were processed with the usual radioimmunoprecipitation assay.
editor preferred term: radio immuno assay
has curation status: IAO_0000120

real time reverse-transcription polymerase chain reaction assay
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: real time polymerase chain reaction assay
      intersection of: Restriction
        on property: is immediately preceded by
        some values from: OBI_0600028
  intersection of: Restriction
    on property: is immediately preceded by
    some values from: OBI_0600028
subclass of: assay
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: information content entity
    intersection of: Restriction
      on property: is about
      some values from: gene expression
definition: Is_a PCR real time preceded by a reverse transcription step (reverse transcription step = an RNA strand is reverse transcribed into its DNA complement using the enzyme reverse transcriptase)
term editor: PERSON: Bjoern Peters
term editor: PERSON: Melanie Courtot
alternative term: RRT-PCR
alternative term: RT-rt PCR
alternative term: qRT-PCR
editor preferred term: real time reverse-transcription polymerase chain reaction assay
has curation status: IAO_0000120

X-ray crystallography assay
type: Class
subclass of: OBI_0600045
subclass of: Class
  intersection of: assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: 3D structural organization datum
definition: An assay which used the diffraction of X-ray beams to resolve the 3-dimensional structure of a material entity of interest in a crystal
term editor: PERSON:Bjoern Peters
editor preferred term: X-ray crystallography assay
example of usage: crystallizing an antibody:antigen complex, and recording the diffraction pattern of a synchrotron beam, and assembling the 3d complex structure based on homologous complexes.
has curation status: IAO_0000120

promoter activity detection by reporter gene assay
type: Class
subclass of: binding assay
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: gene expression
        intersection of: sequence-specific DNA binding
example of usage: A T cell hybridoma in which the beta-galactosidase gene (lacZ) was inserted under the control of the IL-2 promoter, is detected by adding the X-gal substrate which when cleaved by lacZ results in detectable blue color.
definition: An assay in which expression of a reporter gene is detected that was inserted under the control of a promoter of interest.
term editor: PERSON:Bjoern Peters
editor preferred term: promoter activity detection by reporter gene assay
has curation status: IAO_0000120

nasopharyngeal aspirate specimen
type: Class
subclass of: OBI_0100051
subclass of: Restriction
  on property: has role
  some values from: specimen role
disjoint with: nasal swab specimen
disjoint with: device
disjoint with: growth environment
disjoint with: OBI_0001468
disjoint with: OBI_0001485
disjoint with: OBI_0100014
disjoint with: OBI_0100016
disjoint with: OBI_0100017
disjoint with: OBI_0100055
disjoint with: OBI_0100058
disjoint with: OBI_0100060
disjoint with: OBI_0100067
disjoint with: OBI_0100086
disjoint with: OBI_1000023
disjoint with: OBI_1000024
disjoint with: OBI_1000029
disjoint with: OBI_1000036
disjoint with: OBI_1000042
definition: A speciemn which derives from nasopharyngeal mucosa after aspiration.
term editor: PERSON: Melanie Courtot
definition source: WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf
editor preferred term: nasopharyngeal aspirate specimen
example of usage: type of sample used in the PCIRN influenza network
has curation status: IAO_0000120

freezing storage
type: Class
subclass of: OBI_0302893
subclass of: Class
  intersection of: Restriction
    on property: has_specified_input
    some values from: Class
      intersection of: material entity
      intersection of: Restriction
        on property: has quality
        all values from: Class
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: material entity
      intersection of: Restriction
        on property: has quality
        some values from: PATO_0001985
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
disjoint with: lyophilization storage
disjoint with: paraffin storage
disjoint with: agar stab storage
editor note: 2010/3/3 Alan Ruttenberg: There is a question of whether we should have a separate objective to "prepare for maintenance"
definition: A process in which a material entity has it's temperature lowered to below the freezing point in order to bring it to a state in which it can be maintained at this lower temperature in order to preserve some of its qualities
example of usage: Freezing a pellet for later assay
definition source: OBI
term editor: Person: Alan Ruttenberg
editor preferred term: freezing storage
definition source: MO_481 frozen_storage
has curation status: IAO_0000120

flow cytometry assay
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: inheres in
        some values from: OBI_0400044
subclass of: assay
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: cell
definition: An assay that uses a flow cytometer to detect fluorescence in individual particles that flow by a laser in solution.
term editor: PERSON:Randi Vita, Bjoern Peters
example of usage: Using a flow cytometer to quantitate the percent of CD3 positive cells in a population by labeling them with a FITC tagged anti-CD3 antibody.
editor preferred term: flow cytometry assay
has curation status: IAO_0000123

nasal swab specimen
type: Class
subclass of: OBI_0100051
subclass of: Restriction
  on property: has role
  some values from: specimen role
disjoint with: device
disjoint with: growth environment
disjoint with: OBI_0001468
disjoint with: OBI_0001485
disjoint with: OBI_0100014
disjoint with: OBI_0100016
disjoint with: OBI_0100017
disjoint with: OBI_0100055
disjoint with: OBI_0100058
disjoint with: OBI_0100060
disjoint with: OBI_0100067
disjoint with: OBI_0100086
disjoint with: OBI_1000023
disjoint with: OBI_1000024
disjoint with: OBI_1000029
disjoint with: OBI_1000036
disjoint with: OBI_1000042
definition: A specimen obtained using a cotton swab on a stick, passed up the nostril to obtain a sample of exudate and epithelial debris for microbiological or cellular examination.
term editor: PERSON: Melanie Courtot
definition source: WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf
editor preferred term: nasal swab specimen
example of usage: type of sample used in the PCIRN influenza network
has curation status: IAO_0000120

Dulbecco's modified Eagle medium
type: Class
subclass of: culture medium
subclass of: Class
  intersection of: Restriction
    on property: has grain
    some values from: glucose
  intersection of: Restriction
    on property: has grain
    some values from: amino acids
definition: A culture medium containing iron, phenol red, amino acids, salts, glucose and vitamins.
alternative term: D-MEM
alternative term: DMEM
editor preferred term: Dulbecco's modified Eagle medium
editor note: Logical definition should contain all components listed in textual definition at some point.
term editor: PERSON:Bjoern Peters
has curation status: IAO_0000123

animal euthanization
type: Class
subclass of: OBI_0600006
subclass of: Restriction
  on property: has_specified_input
  some values from: Vertebrata
disjoint with: OBI_0302894
definition: A process in which is the end of life of animal is brought about in accordance with local regulations on treatment of animal subjects and using a method which causes minimal pain and distress to the animal subject
term editor: Helen Parkinson and Melissa Haendel
definition source: Melissa Haendel
example of usage: Rats were euthanized with CO2
editor preferred term: animal euthanization
alternative term: animal sacrifice
comment: may later be refined with more specific list of organisms
has curation status: IAO_0000120

cytometric bead array assay
type: Class
subclass of: analyte assay
subclass of: Restriction
  on property: realizes
  some values from: analyte role
definition: An assay in which a series of beads coated with antibodies specific for different analytes and marked with discrete fluorescent labels are used to simultaneously capture and quantitate soluble analytes using flow cytometric analysis.
term editor: PERSON:Bjoern Peters
example of usage: Using a Luminex machine to detect IFN-gamma and IL-10 in the supernatant of a cell culture
editor preferred term: cytometric bead array assay
alternative term: multiplexed bead assay, CBA assay
has curation status: IAO_0000120

labeled RNA extract
type: Class
subclass of: labeled nucleic acid extract
subclass of: Restriction
  on property: has grain
  some values from: ribonucleic acids
subclass of: Class
  intersection of: Restriction
    on property: has role
    some values from: specimen role
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: Class
      intersection of: OBI_0600038
      intersection of: Restriction
        on property: has_specified_input
        some values from: RNA extract
term editor: Group: OBI group
definition source: Group: OBI group
editor note: Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. Added duirng Mar 1, 2010 dev call
definition: a labeled specimen that is the output of a labeling process and has grain labeled RNA to be able to detect RNA in future experiments.
editor preferred term: labeled RNA extract
has curation status: IAO_0000120

frozen specimen
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has role
    some values from: specimen role
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: Class
      intersection of: freezing storage
      intersection of: Restriction
        on property: has_specified_input
        some values from: Restriction
subclass of: OBI_0001472
disjoint with: paraffin specimen
disjoint with: lyophilized specimen
disjoint with: fresh specimen
disjoint with: agar stab specimen
definition: A specimen that has been frozen in order to store it.
example of usage: Frozen blood plasma
definition source: MO_610 frozen_sample
term editor: Person:Alan Ruttenberg
editor preferred term: frozen specimen
has curation status: IAO_0000123

surface plasmon resonance assay
type: Class
subclass of: binding constant determination assay
subclass of: Class
  intersection of: binding assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: binding constant
definition: An assay that uses the detection of electromagnetic waves in a surface to detect material entities adsorbed to the surface, which changes the local index of refraction
definition source: IEDB
term editor: PERSON:Bjoern Peters
example of usage: Running a Biacore instrument to measure the affinity, on and off rates of binding of a plate bound antibody to a antigen passing by in flow.
alternative term: SPR assay
editor preferred term: surface plasmon resonance assay
has curation status: IAO_0000120

labeled specimen
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: specimen role
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: Class
      intersection of: OBI_0600038
      intersection of: Restriction
        on property: has_specified_input
        some values from: Restriction
subclass of: processed specimen
definition: A specimen that has been modified in order to be able to detect it in future experiments
term editor: OBI group
editor note: added during call 3/1/2010
editor preferred term: labeled specimen
has curation status: IAO_0000123

infectious agent
type: Class
equivalent class: Restriction
  on property: is bearer of
  some values from: OBI_1110093
subclass of: OBI_0100026
editor preferred term: infectious agent
term editor: IEDB
definition source: IEDB
definition: is a material entity bearing the disposition to infect an organism
has curation status: IAO_0000123

obsolete_ambidexterious handedness
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_ambidexterious handedness
deprecated: true
has obsolescence reason: IAO_0000103

lyophilization storage
type: Class
subclass of: OBI_0302893
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
disjoint with: paraffin storage
disjoint with: agar stab storage
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition: a storage process with input material entity and output freeze dried material for long time storage
comment: can link to freezing-dying equipment, such as freeze-dryer, rotary evaporator, if needed
editor preferred term: lyophilization storage
has curation status: IAO_0000123

material combination function
type: Class
subclass of: function
disjoint with: sterilization function
disjoint with: reagent application function
disjoint with: specimen fixation function
disjoint with: current amplification function
disjoint with: stabilization function
disjoint with: OBI_0005246
disjoint with: OBI_1110016
disjoint with: OBI_1110085
definition: A material separation function is a function that decreases the resolution between two or more material entities.
example of usage: A stirrer has a material combination function
term editor: Helen Parkinson
definition source: OBI
editor preferred term: material combination function
has curation status: IAO_0000120

obsolete_training service provider role
type: Class
subclass of: ObsoleteClass
example of usage: EBI provides training on databases and tools and has a training service provider role
definition source: OBI
term editor: PERSON:Helen Parkinson
definition: a service provider role which is realized by a servicer provider organization performing some training
editor note: obsolete during the San Diego workshop, March 2011 The reason is that we decided to pursue a different modeling approach for services keeping just the 'service consumer' and 'service provider' roles and differentiate just at the level of planned process offered a s service.
editor preferred term: training service provider role
deprecated: true
has obsolescence reason: IAO_0000103
has curation status: IAO_0000123

calorimeter
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
disjoint with: positron emission tomography scanner
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079

study intervention
type: Class
subclass of: planned process
subclass of: Class
  intersection of: Restriction
    on property: has_specified_input
    some values from: OBI_0100051
  intersection of: Restriction
    on property: has_specified_output
    some values from: OBI_0100051
subclass of: Restriction
  on property: is part of
  some values from: Class
    intersection of: study design execution
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: intervention design
definition source: GROUP: OBI
term editor: PERSON: Bjoern Peters
editor preferred term: study intervention
definition: the part of the execution of an intervention design study which is varied between two or more subjects in the study
has curation status: IAO_0000120

material separation device
type: Class
equivalent class: Restriction
  on property: has function
  some values from: material separation function
subclass of: device
definition: A device with a separation function realized in a planed process
example of usage: flow cytometer
editor preferred term: material separation device
has curation status: IAO_0000123

positron emission tomography scanner
type: Class
subclass of: image acquisition device
subclass of: Restriction
  on property: has function
  some values from: image acquisition function
disjoint with: micromanipulator
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080

intramuscular injection
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: realizes
    some values from: material to be added role
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: inheres in
        some values from: syringe
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: target of material addition role
      intersection of: Restriction
        on property: is role of
        some values from: UBERON_0001134
subclass of: injection
subclass of: OBI_0600007
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: adding material objective
editor preferred term: intramuscular injection
definition: is the injection of a material entity (bearing the administered substance role) into the muscle (bearing the target role) of an organism using a syringe
has curation status: IAO_0000123

micromanipulator
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
disjoint with: vibration isolation table
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082

obsolete_material access provider role
type: Class
subclass of: ObsoleteClass
example of usage: A person or organization who provides access to a DNA sequencer.
definition source: OBI
term editor: PERSON:Helen Parkinson
definition: a service provider role which is realized by a servicer provider organization performing access to some material
editor preferred term: material access provider role
editor note: obsolete during the San Diego workshop, March 2011 The reason is that we decided to pursue a different modeling approach for services keeping just the 'service consumer' and 'service provider' roles and differentiate just at the level of planned process offered a s service.
deprecated: true
has obsolescence reason: IAO_0000103
has curation status: IAO_0000123

obsolete_left handedness
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_left handedness
deprecated: true
has obsolescence reason: IAO_0000228

categorical measurement datum
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: has category label
  some values from: categorical label
disjoint with: dose
disjoint with: obsolete_general scalar measurement datum
disjoint with: 3D structural organization datum
definition: A measurement datum that is reported on a categorical scale
term editor: Bjoern Peters
definition source: Bjoern Peters
editor preferred term: categorical measurement datum
alternative term: nominal mesurement datum
has curation status: IAO_0000120

training process
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: training objective
subclass of: planned process
definition: a process that achieves a training objective
example of usage: e.g. a training course run by a vendor on their instrument, a training service on a assay by a core facility
editor preferred term: training process
has curation status: IAO_0000123

optical microscope
type: Class
subclass of: OBI_0400169
disjoint with: electron microscope
disjoint with: confocal microscope
disjoint with: laser capture microdissection microscope
disjoint with: scanning force microscope
disjoint with: digital microscope
definition: A microscope that produces an image of an object by targeting it with an electro-magnetic beam in the visible frequency range
term editor: PERSON:Bjoern Peters
editor preferred term: optical microscope
has curation status: IAO_0000120

service consumer role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: Class
    union of: Homo sapiens
    union of: organization
disjoint with: service provider role
disjoint with: accessed material role
disjoint with: OBI_0302731
disjoint with: OBI_0302732
disjoint with: OBI_0302733
disjoint with: OBI_1110082
disjoint with: OBI_1110083
disjoint with: OBI_1110086
disjoint with: OBI_1110087
disjoint with: OBI_1110091
disjoint with: OBI_1110092
disjoint with: OBI_1110120
example of usage: A biologist who uses a sequencing services fulfills the role of a service consumer
definition source: OBI
term editor: Person:Helen Parkinson
definition: a role which inheres in a person who uses a service
editor preferred term: service consumer role
has curation status: IAO_0000120

intradermal injection
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: realizes
    some values from: material to be added role
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: inheres in
        some values from: syringe
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: target of material addition role
      intersection of: Restriction
        on property: is role of
        some values from: UBERON_0002067
subclass of: injection
subclass of: OBI_0600007
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: adding material objective
term editor: PERSON: Melanie Courtot
editor preferred term: intradermal injection
definition: is the injection of a material entity (bearing the administered substance role) into the dermis (bearing the target role) of an organism using a syringe
has curation status: IAO_0000123

chemical cleavage
type: Class
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: OBI_0100051
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: molecular entity
    intersection of: Restriction
      on property: has role
      some values from: reagent role
term editor: PERSON:Philippe Rocca-Serra
example of usage: PMID: 20171258. Comparative reactivity of mismatched and unpaired bases in relation to their type and surroundings. Chemical cleavage of DNA mismatches in mutation detection analysis.Yakubovskaya MG, Belyakova AA, Gasanova VK, Belitsky GA, Dolinnaya NG. Biochimie. 2010 Feb 18.
definition source: RNA ontology group
editor preferred term: chemical cleavage
definition: chemical cleavage is a protocol application relying on a chemical compound to cause the fragmentation of an input material that is susceptible to that chemical agent
has curation status: IAO_0000120

handedness assay
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: PATO_0002201
subclass of: assay
definition: A handedness assay measures the unequal distribution of fine motor skill between the left and right hands typically in human subjects by means of some questionnaire and scoring procedure.
term editor: Helen Parkinson
example of usage: The Edinburgh handedness assay is a specific method of determing handedness
editor preferred term: handedness assay
alternative term: handedness test
definition source: http://en.wikipedia.org/wiki/Handedness
has curation status: IAO_0000120

vibration isolation table
type: Class
subclass of: environmental control device
subclass of: Restriction
  on property: has function
  some values from: environment control function
disjoint with: oscilloscope
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084

sterilization function
type: Class
subclass of: function
disjoint with: reagent application function
disjoint with: specimen fixation function
disjoint with: current amplification function
disjoint with: stabilization function
disjoint with: OBI_0005246
disjoint with: OBI_1110016
disjoint with: OBI_1110085
definition: a function to remove viable organisms from an input material
editor preferred term: sterilization function
has curation status: IAO_0000123

service provider role
type: Class
subclass of: role
subclass of: Restriction
  on property: is realized by
  all values from: planned process
subclass of: Restriction
  on property: inheres in
  some values from: Class
    union of: Homo sapiens
    union of: organization
disjoint with: accessed material role
disjoint with: OBI_0302731
disjoint with: OBI_0302732
disjoint with: OBI_0302733
disjoint with: OBI_1110082
disjoint with: OBI_1110083
disjoint with: OBI_1110086
disjoint with: OBI_1110087
disjoint with: OBI_1110091
disjoint with: OBI_1110092
disjoint with: OBI_1110120
example of usage: Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer.
term editor: PERSON:Helen Parkinson
definition: is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person
editor preferred term: service provider role
has curation status: IAO_0000123

oscilloscope
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
disjoint with: electrode puller
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086

accessed material role
type: Class
subclass of: role
disjoint with: OBI_0302731
disjoint with: OBI_0302732
disjoint with: OBI_0302733
disjoint with: OBI_1110082
disjoint with: OBI_1110083
disjoint with: OBI_1110086
disjoint with: OBI_1110087
disjoint with: OBI_1110091
disjoint with: OBI_1110092
disjoint with: OBI_1110120
editor note: AR: rent a DNA sequencer for a period of time. two realizations, payment for the service and also when the person who pays for the service uses it
editor preferred term: accessed material role
definition: is realized in a planned process where the bearer participates
example of usage: the role of the DNA sequencer to which someone gets access to a period of time, e.g. by payment, or other mechanism
has curation status: IAO_0000123

paraffin specimen
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has role
    some values from: specimen role
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: Class
      intersection of: paraffin storage
      intersection of: Restriction
        on property: has_specified_input
        some values from: Restriction
subclass of: OBI_0001472
disjoint with: lyophilized specimen
disjoint with: fresh specimen
disjoint with: agar stab specimen
definition source: MO_990 paraffin_sample
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition: a specimen that is output of a paraffin storage process in which specimen is embedded in paraffin
example of usage: liver tissue embedded in paraffin
editor preferred term: paraffin specimen
has curation status: IAO_0000123

compound treatment design
type: Class
equivalent class: Class
  intersection of: OBI_0500000
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: independent variable specification
      intersection of: Restriction
        on property: is about
        some values from: Class
subclass of: intervention design
definition source: MO_555 compound_treatment_design
term editor: PERSON: Bjoern Peters
editor note: This is meant to include all kinds of material administrations, including vaccinations, chemical compounds etc.
definition: an intervention design in which the treatment is the administration of a compound
editor preferred term: compound treatment design
has curation status: IAO_0000120

oral administration
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: realizes
    some values from: material to be added role
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: target of material addition role
      intersection of: Restriction
        on property: is role of
        some values from: UBERON_0000165
subclass of: OBI_0600007
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: adding material objective
term editor: PERSON: Melanie Courtot
definition: The administration of a substance into the mouth of an organism
editor preferred term: oral administration
has curation status: IAO_0000123

processed specimen
type: Class
equivalent class: Class
  intersection of: processed material
  intersection of: OBI_0100051
subclass of: processed material
subclass of: OBI_0100051
definition: A specimen that has been intentionally physically modified.
definition source: Bjoern Peters
term editor: Bjoern Peters
editor preferred term: processed specimen
has curation status: IAO_0000120

subcutaneous injection
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: realizes
    some values from: material to be added role
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: inheres in
        some values from: syringe
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: target of material addition role
      intersection of: Restriction
        on property: is role of
        some values from: UBERON_0002072
subclass of: injection
subclass of: OBI_0600007
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: adding material objective
term editor: PERSON: Melanie Courtot
definition: is the injection of a material entity (bearing the administered substance role) into the hypodermis (bearing the target role) of an organism using a syringe
editor preferred term: subcutaneous injection
has curation status: IAO_0000123

electrode puller
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
disjoint with: vibrotome
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094

obsolete_handedness
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_handedness
deprecated: true
has obsolescence reason: IAO_0000228

self reported handedness assessment
type: Class
subclass of: handedness assay
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: categorical measurement datum
    intersection of: Restriction
      on property: is quality measurement of
      some values from: PATO_0002201
definition: An assay in which a person makes a statement that indicates what handedness he has from a choice of different categories.
editor preferred term: self reported handedness assessment
has curation status: IAO_0000123

vibrotome
type: Class
subclass of: material separation device
subclass of: Restriction
  on property: has function
  some values from: material separation function
disjoint with: computed tomography scanner
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099

reagent application function
type: Class
subclass of: function
disjoint with: specimen fixation function
disjoint with: current amplification function
disjoint with: stabilization function
disjoint with: OBI_0005246
disjoint with: OBI_1110016
disjoint with: OBI_1110085
curator note: 4/10/2011: It is unclear if we need / want this, or what this is supposed to be for. Lots of the functions we have are reagent specific. Will this only confuse people?
definition: A function that is realized when a reagent is automatically added to some research material.
example of usage: An automatic tissue processor automatically applies antibodies and buffers to histological tissue preparations.
definition source: PERSON: Nicole Vasilevsky, Matthew Brush
term editor: PERSON: Nicole Vasilevsky, Matthew Brush
editor preferred term: reagent application function
has curation status: IAO_0000120

addition of molecular tracer function
type: Class
subclass of: reagent application function
definition: A reagent application function that is realized when a molecular tracer, such as an antibody or probe is automatically transferred to a biological specimen.
example of usage: Immunohistochemical labeling of tissue sections by an autostainer staining system.
definition source: PERSON: Nicole Vasilevsky, Matthew Brush
term editor: PERSON: Nicole Vasilevsky, Matthew Brush
editor preferred term: addition of molecular tracer function
has curation status: IAO_0000120

training objective
type: Class
subclass of: objective specification
disjoint with: service provision objective
disjoint with: assay validation objective
disjoint with: selective organism creation objective
disjoint with: OBI_0200166
example of usage: A training objective is fulfilled by e.f. a bioconductor tutorial which instructs the user in the use of a package
definition: An training objective which is fulfilled by the provision of some training
term editor: Helen Parkinson
definition source: OBI
editor preferred term: training objective
has curation status: IAO_0000120

categorical label
type: Class
subclass of: datum label
editor note: 4/10/2011 BP: This is not worded well, and was thrown together quickly to allow this term into the release, as several other terms are depending on it. The example is better than the definition.
definition: A label that is part of a categorical datum and that indicates the category of that datum
term editor: Bjoern Peters
definition source: Bjoern Peters
example of usage: The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels.
editor preferred term: categorical label
has curation status: IAO_0000120

in live cell assay
type: Class
subclass of: assay
definition: An assay in which a measurement is made by observing entities located in a live cell.
editor preferred term: in live cell assay
has curation status: IAO_0000123

lyophilized specimen
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has role
    some values from: specimen role
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: Class
      intersection of: lyophilization storage
      intersection of: Restriction
        on property: has_specified_input
        some values from: Restriction
subclass of: OBI_0001472
disjoint with: fresh specimen
disjoint with: agar stab specimen
definition source: MO_589 freeze_dried_sample
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition: a specimen that is output of a lyophilization storage process in which specimen is lyophilized for storage.
example of usage: freezing dried DNA
editor preferred term: lyophilized specimen
has curation status: IAO_0000123

in live organism assay
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has participant
    some values from: Restriction
      on property: is located in
      some values from: Class
        intersection of: OBI_0100026
        intersection of: Restriction
subclass of: assay
definition: An assay in which a measurement is made by observing entities located in an organism.
example of usage: Measuring the rate in which cells that are pulsed with a peptide are killed inside a mouse by peptide specific cytotoxic T cells.
term editor: PERSON:Bjoern Peters
editor preferred term: in live organism assay
alternative term: in vivo assay
has curation status: IAO_0000120

container
type: Class
equivalent class: Restriction
  on property: has function
  some values from: contain function
subclass of: device
editor note: 03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?)
definition: A device that can be used to restrict the location of material entities over time
term editor: PERSON: Bjoern Peters
editor preferred term: container
has curation status: IAO_0000123

device
type: Class
subclass of: processed material
subclass of: Restriction
  on property: has function
  some values from: function
subclass of: Restriction
  on property: is_specified_output_of
  some values from: material processing
disjoint with: growth environment
disjoint with: OBI_0001468
disjoint with: OBI_0001485
disjoint with: OBI_0100014
disjoint with: OBI_0100016
disjoint with: OBI_0100017
disjoint with: OBI_0100055
disjoint with: OBI_0100058
disjoint with: OBI_0100060
disjoint with: OBI_0100067
disjoint with: OBI_0100086
disjoint with: OBI_1000023
disjoint with: OBI_1000024
disjoint with: OBI_1000029
disjoint with: OBI_1000036
disjoint with: OBI_1000042
definition: A device is a processed material which is designed to perform some function or functions
example of usage: A voltmeter is a measurement device which is intended to perform some measure function.
definition source: OBI Vancouver workshop 2010
term editor: PERSON: Helen Parkinson
editor preferred term: device
editor note: food should not classify as a device - counter example for using manufacturer and not device. macroscopic only
editor note: if we keep this exploratory term we could reinstate the old device class which is obsolete_device. didn't work before as we had manufacturing as part of the definition. device was needed, but couldn't define in Philadelphia. If we decide that in addition to function there are also capabilities for which a device is created we will include these in the definition.
alternative term: instrument
comment: would include reagents
has curation status: IAO_0000123

dose specification
type: Class
subclass of: directive information entity
definition: a directive information entity that describes the dose that will be administered to a target
example of usage: a protocol specifying to administer 1 ml of vaccine to a mouse
editor preferred term: dose specification
has curation status: IAO_0000123

scalar score from composite inputs
type: Class
subclass of: scalar measurement datum
subclass of: Restriction
  on property: has measurement value
  min cardinality: 1
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0200000
alternative term: questionaire score
editor preferred term: scalar score from composite inputs
definition: A measurement datum which is the result of combining multiple datum. For example, a mean or summary score.
editor note: JT: We included this because we wanted to talk about an output from a questionnaire that summarized the answers to the questionnaire, but which was not actually the answer to any single question.
curator note: JZ: can we defined it logically as the output of some data transformation, like aggragate data transformation?
term editor: Person: Jessica Turner
definition source: Person: Jessica Turner
has curation status: IAO_0000120

fresh specimen
type: Class
subclass of: OBI_0001472
disjoint with: agar stab specimen
definition source: MO_730 fresh_sample
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
example of usage: a liver freshly removed from a rat
definition: a specimen that is output of a specimen creation process used for an investigation without storage.
editor preferred term: fresh specimen
has curation status: IAO_0000123

obsolete_electrically powered device
type: Class
subclass of: ObsoleteClass
definition: a processed material created to have a function and which requires electrical power to execute
editor preferred term: obsolete_electrically powered device
deprecated: true
has obsolescence reason: IAO_0000103

sequence data
type: Class
subclass of: measurement datum
subclass of: Class
  intersection of: measurement datum
  intersection of: Restriction
    on property: is about
    some values from: SO_0000001
definition: A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.
definition source: GROUP: OBI
term editor: Person:Chris Stoeckert
example of usage: example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search.
editor preferred term: sequence data
has curation status: IAO_0000120

obsolete_right handedness
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_right handedness
deprecated: true
has obsolescence reason: IAO_0000228

cell-cell binding detection by flow cytometry assay
type: Class
subclass of: flow cytometry assay
definition: An assay which uses a flow cytometer to detect pairs of cells that are interacting by staining them with different fluorescent labels.
term editor: PERSON:Bjoern Peters
example of usage: Staining a B cell with PE and staining a T cell with FITC, incubating them together with a peptide, and counting the number of co-stained conjugates.
editor preferred term: cell-cell binding detection by flow cytometry assay
alternative term: cell:cell conjugate detection assay
has curation status: IAO_0000123

handedness categorical measurement datum
type: Class
subclass of: categorical measurement datum
subclass of: Restriction
  on property: has category label
  some values from: Class
    one of: OBI_0000998
    one of: OBI_0000958
    one of: OBI_0000979
subclass of: Restriction
  on property: is quality measurement of
  some values from: PATO_0002201
definition: A datum used to record the answer to a self assessment of whether a person uses their left hand, right hand primarily or each hand equally
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Jessica Turner
editor preferred term: handedness categorical measurement datum
has curation status: IAO_0000123

paraffin storage
type: Class
subclass of: OBI_0302893
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: gross anatomical part
    union of: OBI_0100026
disjoint with: agar stab storage
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition source: UPenn Group
definition: a storage process with input organism or anatomical entity and paraffin and output material embedded in paraffin for long term storage
comment: need to specify paraffin or wax is one of specified input of the process
editor preferred term: paraffin storage
has curation status: IAO_0000120

in container assay
type: Class
subclass of: assay
definition: an assay in which a measurement is made by observing entities located in a container.
editor preferred term: in container assay
has curation status: IAO_0000123

obsolete_protocol service provider role
type: Class
subclass of: ObsoleteClass
example of usage: DNA sequencing of a sample by a core lab which returns data to the consumer
term editor: PERSON:Helen Parkinson
definition: a service provider role which is realized by a servicer provider organization performing a protocol execution
editor note: obsolete during the San Diego workshop, March 2011 The reason is that we decided to pursue a different modeling approach for services keeping just the 'service consumer' and 'service provider' roles and differentiate just at the level of planned process offered a s service.
editor preferred term: protocol service provider role
deprecated: true
has obsolescence reason: IAO_0000103
has curation status: IAO_0000120

agar stab specimen
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: agar stab storage
    intersection of: Restriction
      on property: has_specified_input
      some values from: Restriction
        on property: has role
        some values from: specimen role
subclass of: OBI_0001472
definition source: MO_971 agar_stab
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition: a specimen that is output of a process that cell culture inoculated into agar for long term storage.
editor preferred term: agar stab specimen
has curation status: IAO_0000123

computed tomography scanner
type: Class
subclass of: image acquisition device
subclass of: Restriction
  on property: has function
  some values from: image acquisition function
disjoint with: Faraday cage
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100

intranasal mucosal administration
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: realizes
    some values from: material to be added role
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: target of material addition role
      intersection of: Restriction
        on property: is role of
        some values from: UBERON_0005022
subclass of: OBI_0600007
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: adding material objective
term editor: PERSON: Melanie Courtot
definition: The administration of a substance into the intranasal mucosis of an organism
editor preferred term: intranasal mucosal administration
has curation status: IAO_0000123

dose
type: Class
subclass of: measurement datum
disjoint with: obsolete_general scalar measurement datum
disjoint with: 3D structural organization datum
definition: A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses.
example of usage: An organism has been injected 1ml of vaccine
editor preferred term: dose
has curation status: IAO_0000123

growth condition intervention design
type: Class
subclass of: intervention design
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: independent variable specification
    intersection of: Restriction
      on property: is about
      some values from: study intervention
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: independent variable specification
    intersection of: Restriction
      on property: is about
      some values from: growth environment
disjoint with: validation by reverse transcription PCR design
disjoint with: validation by real time PCR design
disjoint with: operator variation design
disjoint with: comparative genome hybridization by array design
disjoint with: in vivo design
disjoint with: innate behavior design
disjoint with: cell component comparison design
disjoint with: ex vivo design
disjoint with: normalization testing design
disjoint with: environmental history design
disjoint with: transcription profiling by high thoughput sequencing design
disjoint with: array platform variation design
disjoint with: ChIP-seq design
disjoint with: translational bias design
disjoint with: DNA methylation profiling by array design
disjoint with: in vitro design
disjoint with: RNAi profiling by array design
disjoint with: transcription profiling by array design
disjoint with: disease state design
disjoint with: RNA stability design
disjoint with: species comparison design
disjoint with: transcription profiling by RT-PCR design
disjoint with: microRNA profiling by array design
disjoint with: organism development design
disjoint with: family history design
disjoint with: quality control testing design
disjoint with: clinical history design
disjoint with: OBI_0001358
disjoint with: OBI_0001365
disjoint with: OBI_0001374
disjoint with: OBI_0001377
disjoint with: OBI_0001396
disjoint with: OBI_0001401
disjoint with: OBI_0001403
disjoint with: OBI_0001408
disjoint with: OBI_0001409
disjoint with: OBI_0001410
disjoint with: OBI_0001411
disjoint with: OBI_0001418
disjoint with: OBI_0001422
disjoint with: OBI_0001426
disjoint with: OBI_0001427
disjoint with: OBI_0001429
disjoint with: OBI_0001432
disjoint with: OBI_0001435
disjoint with: OBI_0001440
disjoint with: OBI_0001441
disjoint with: OBI_0001444
disjoint with: OBI_0001448
disjoint with: OBI_0001454
disjoint with: OBI_0001460
disjoint with: OBI_0001464
disjoint with: OBI_0300311
disjoint with: OBI_0500001
disjoint with: OBI_0500005
disjoint with: OBI_0500006
disjoint with: OBI_0500009
disjoint with: OBI_0500010
disjoint with: OBI_0500017
disjoint with: OBI_0500018
disjoint with: OBI_0500019
disjoint with: OBI_0500020
definition: A study design in which the independent variable is the environmental condition in which the specimen is growing
definition source: MO_588 growth_condition_design
term editor: PERSON: Bjoern Peters
editor preferred term: growth condition intervention design
has curation status: IAO_0000120

obsolete_DNA sequencing training service
type: Class
subclass of: ObsoleteClass
editor note: 03/22/2010:workshop: there is a user requirement that not in all cases of the training the trainee gains the skills.
definition: A training process with the objective to provide a trainee with the skill to run DNA sequencing experiments
editor preferred term: DNA sequencing training service
deprecated: true
has obsolescence reason: IAO_0000103
has curation status: IAO_0000123

obsolete_general scalar measurement datum
type: Class
subclass of: ObsoleteClass
disjoint with: 3D structural organization datum
editor note: 4/10/2011 BP: It is unclear to me why we need this, and don't just use the scalar measurement datum.
editor note: See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3302925&group_id=177891&atid=886178
editor preferred term: general scalar measurement datum
deprecated: true
has obsolescence reason: IAO_0000103
has curation status: IAO_0000124

performing a diagnosis
type: Class
subclass of: OBI_0200000
subclass of: Restriction
  on property: has_specified_output
  some values from: diagnosis textual entity
disjoint with: feature extraction
disjoint with: OBI_0001477
disjoint with: OBI_0200002
disjoint with: OBI_0200003
disjoint with: OBI_0200004
disjoint with: OBI_0200006
disjoint with: OBI_0200007
disjoint with: OBI_0200008
disjoint with: OBI_0200011
disjoint with: OBI_0200014
disjoint with: OBI_0200016
disjoint with: OBI_0200017
disjoint with: OBI_0200021
disjoint with: OBI_0200022
disjoint with: OBI_0200025
disjoint with: OBI_0200026
disjoint with: OBI_0200027
disjoint with: OBI_0200028
disjoint with: OBI_0200029
disjoint with: OBI_0200030
disjoint with: OBI_0200033
disjoint with: OBI_0200034
disjoint with: OBI_0200035
disjoint with: OBI_0200036
disjoint with: OBI_0200037
disjoint with: OBI_0200041
disjoint with: OBI_0200042
disjoint with: OBI_0200049
disjoint with: OBI_0200050
disjoint with: OBI_0200052
disjoint with: OBI_0200056
disjoint with: OBI_0200057
disjoint with: OBI_0200058
disjoint with: OBI_0200059
disjoint with: OBI_0200060
disjoint with: OBI_0200061
disjoint with: OBI_0200062
disjoint with: OBI_0200063
disjoint with: OBI_0200064
disjoint with: OBI_0200066
disjoint with: OBI_0200071
disjoint with: OBI_0200077
disjoint with: OBI_0200079
disjoint with: OBI_0200080
disjoint with: OBI_0200082
disjoint with: OBI_0200088
disjoint with: OBI_0200092
disjoint with: OBI_0200093
disjoint with: OBI_0200094
disjoint with: OBI_0200095
disjoint with: OBI_0200097
disjoint with: OBI_0200098
disjoint with: OBI_0200102
disjoint with: OBI_0200106
disjoint with: OBI_0200108
disjoint with: OBI_0200109
disjoint with: OBI_0200110
disjoint with: OBI_0200113
disjoint with: OBI_0200116
disjoint with: OBI_0200117
disjoint with: OBI_0200118
disjoint with: OBI_0200119
disjoint with: OBI_0200120
disjoint with: OBI_0200121
disjoint with: OBI_0200122
disjoint with: OBI_0200123
disjoint with: OBI_0200124
disjoint with: OBI_0200125
disjoint with: OBI_0200140
disjoint with: OBI_0200149
disjoint with: OBI_0200150
disjoint with: OBI_0200156
disjoint with: OBI_0200160
disjoint with: OBI_0200161
disjoint with: OBI_0200162
disjoint with: OBI_0200164
disjoint with: OBI_0200165

PCR instrument
type: Class
subclass of: OBI_0400116
subclass of: Restriction
  on property: has function
  some values from: Restriction
    on property: is realized by
    all values from: polymerase chain reaction
editor note: 03/21/2010: Added because it is unclear if the thermal cycler definition is intentionally broader than PCR instrument. Contacted Melanie and Trish about this. Definitions and use of alternative terms need to be made consistent.
definition: A device that is used to amplify a single or few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence.
editor preferred term: PCR instrument
has curation status: IAO_0000123

electron microscope
type: Class
subclass of: OBI_0400169
disjoint with: confocal microscope
disjoint with: laser capture microdissection microscope
disjoint with: scanning force microscope
disjoint with: digital microscope
definition: A microscope that produces an image of an object by targeting it with an electron beam
editor preferred term: electron microscope
has curation status: IAO_0000123

Edinburgh score
type: Class
subclass of: scalar score from composite inputs
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Edinburgh handedness assay
subclass of: Restriction
  on property: is quality measurement of
  some values from: PATO_0002201
subclass of: Restriction
  on property: has measurement value
  min cardinality: 1
editor preferred term: Edinburgh score
definition source: PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113
term editor: Person: Alan Ruttenberg
term editor: Person:Jessica Turner
definition source: WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html
has curation status: IAO_0000123

DNA sequencing service
type: Class
subclass of: OBI_0001547
subclass of: Restriction
  on property: realizes
  some values from: service consumer role
subclass of: Restriction
  on property: realizes
  some values from: service provider role
subclass of: Restriction
  on property: provides_service_consumer_with
  some values from: DNA sequencing
editor preferred term: DNA sequencing service
editor note: Eagle-i will supply better English definition
definition: is a DNA sequencing process provided as a service - which is the realization of some DNA sequencing in which the service provider role is realized.
has curation status: IAO_0000123

service provision objective
type: Class
subclass of: objective specification
disjoint with: assay validation objective
disjoint with: selective organism creation objective
disjoint with: OBI_0200166
example of usage: A sequencing centre has a service provision objective
definition: An objective which is fulfilled by the provision of some service e.g. a training service
term editor: Helen Parkinson
definition source: OBI
editor preferred term: service provision objective
has curation status: IAO_0000120

intravenous injection
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: realizes
    some values from: material to be added role
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: inheres in
        some values from: syringe
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: target of material addition role
      intersection of: Restriction
        on property: is role of
        some values from: UBERON_0001638
subclass of: injection
subclass of: OBI_0600007
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: adding material objective
term editor: PERSON: Melanie Courtot
editor preferred term: intravenous injection
definition: is the injection of a material entity (bearing the administered substance role) into the vein (bearing the target role) of an organism using a syringe
has curation status: IAO_0000123

administration of material to specimen
type: Class
subclass of: adding a material entity into a target
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: target of material addition role
    intersection of: Restriction
      on property: is role of
      some values from: OBI_0100051
definition source: Bjoern Peters
term editor: Bjoern Peters
example of usage: Staining cells in a tissue slice with a dye.
definition: The directed combination of a material entity with a specimen.
editor preferred term: administration of material to specimen
has curation status: IAO_0000120

device creation objective
type: Class
subclass of: material transformation objective
disjoint with: genetic transformation objective
definition source: OBI
term editor: PERSON: Helen Parkinson
definition: an objective which aims to create a device with a specified function
editor preferred term: device creation objective
has curation status: IAO_0000120

growth environment
type: Class
subclass of: material entity
disjoint with: OBI_0001468
disjoint with: OBI_0001485
disjoint with: OBI_0100014
disjoint with: OBI_0100016
disjoint with: OBI_0100017
disjoint with: OBI_0100055
disjoint with: OBI_0100058
disjoint with: OBI_0100060
disjoint with: OBI_0100067
disjoint with: OBI_0100086
disjoint with: OBI_1000023
disjoint with: OBI_1000024
disjoint with: OBI_1000029
disjoint with: OBI_1000036
disjoint with: OBI_1000042
definition source: OBI group
term editor: PERSON:Richard Scheuermann, Jie Zheng, Bjoern Peters
editor note: Right now this may be incomplete. Should also cover e.g. sound, light as well.
definition: The collection of material entities and their qualities that are located near a live organism, tissue or cell and can influence its growth.
editor preferred term: growth environment
has curation status: IAO_0000120

questionnaire
type: Class
subclass of: document
disjoint with: OBI_0302874
editor note: Need to clarify if this is a document or a directive information entity (or what their connection is))
editor preferred term: questionnaire
definition: A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study.
editor note: JT: It plays a role in collecting data that could be fleshed out more; but I'm thinking it is, in itself, an edited document. JZ: based on textual definition of edited document, it can be defined as N&S. I prefer to leave questionnaire as a document now. We can add more restrictions in the future and use that to determine it is an edited document or not.
definition source: Merriam-Webster
term editor: PERSON: Jessica Turner
has curation status: IAO_0000120

Edinburgh handedness assay
type: Class
subclass of: handedness assay
subclass of: Restriction
  on property: has_specified_output
  some values from: Edinburgh score
subclass of: Restriction
  on property: has_specified_input
  has value: OBI_0001004
editor preferred term: Edinburgh handedness assay
term editor: PERSON:Jessica Turner
term editor: Person:Alan Ruttenberg
definition: The Edinburgh Handedness assay is an assay in which a set of questions = the Edinburgh Handedness inventory - is asked and the answers to these questions are turned into a score, used to assess the dominance of a person's right or left hand in everyday activities. The inventory can be used by an observer assessing the person, or by a person self-reporting hand use. The latter method tends to be less reliable due to a person over-attributing tasks to the dominant hand.
definition source: WEB:http://en.wikipedia.org/wiki/Edinburgh_Handedness_Inventory
has curation status: IAO_0000120

Faraday cage
type: Class
subclass of: environmental control device
subclass of: Restriction
  on property: has function
  some values from: environment control function
disjoint with: angiograph
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101

agar stab storage
type: Class
subclass of: OBI_0302893
subclass of: Restriction
  on property: has_specified_input
  some values from: OBI_0100060
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition source: UPenn Group
definition: a storage process with input cell culture and agar and output agar stab for long time storage
editor preferred term: agar stab storage
comment: need to specify that agar is one of input for this process
has curation status: IAO_0000120

RNASE CL3 structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of RNA molecule
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: catalytic activity
    intersection of: Restriction
      on property: inheres in
      some values from: PR_000025478
subclass of: Restriction
  on property: has_specified_input
  some values from: ribonucleic acids
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
example of usage: PMID:16453415
term editor: Person:Philippe Rocca-Serra
definition source: RNA ontology
editor preferred term: RNASE CL3 structure mapping assay
definition: a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses RNAse CL3 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
alternative term: single nucleotide resolution mapping assay using RNAse CL3
has curation status: IAO_0000122

CMCT structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of sequence macromolecule
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: reagent role
    intersection of: Restriction
      on property: inheres in
      some values from: Diethylpyrocarbonate
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: deoxyribonucleic acids
    union of: ribonucleic acids
editor preferred term: CMCT structure mapping assay
example of usage: PMID:2422386 and PMID:2446263
term editor: Person: Philippe Rocca-Serra
definition source: RNA ontology
definition: a single-nucleotide-resolution nucleic acid structure mapping assay which uses CMCT as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
alternative term: single nucleotide resolution mapping assay using CMCT probe
has curation status: IAO_0000122

image acquisition
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: image
definition: A planned process that captures an image of an object.
term editor: PERSON: Jie Zheng
example of usage: Taking a polaroid picture of a patients skin lesion; Using a digital camera to take a picture of a gel
editor preferred term: image acquisition
has curation status: IAO_0000123

MPE-Fe(II) structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: has_specified_input
  some values from: ribonucleic acids
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: reagent role
    intersection of: Restriction
      on property: inheres in
      some values from: EDTA methidiumpropylamide
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of RNA molecule
editor preferred term: MPE-Fe(II) structure mapping assay
example of usage: PMID:6209709
term editor: Person: Philippe Rocca-Serra
definition source: RNA ontology
definition: a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses Fe-MP as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
alternative term: single nucleotide resolution mapping assay using Fe-MP probe
has curation status: IAO_0000122

obsolete_qualitative binding detection assay
type: Class
subclass of: ObsoleteClass
deprecated: true
definition: A binding assay where the specified output determines if two or more material entities do or do not have the disposition to form a complex above a threshold level of significance. The threshold can be defined through detection limits of the instrument, the use of experimental controls that establish what is considered significant binding, or a predefined cutoff based on what binding is considered significant in a certain context.
term editor: PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum
editor preferred term: obsolete_qualitative binding detection assay
has obsolescence reason: IAO_0000103
has curation status: IAO_0000123

nucleic acid extract
type: Class
subclass of: extract
subclass of: processed specimen
subclass of: Restriction
  on property: has grain
  some values from: nucleic acid
subclass of: Class
  intersection of: Restriction
    on property: has role
    some values from: specimen role
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: OBI_0666667
definition: An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.
term editor: PERSON: Jie Zheng
definition source: UPenn Group
editor preferred term: nucleic acid extract
has curation status: IAO_0000120

ENU structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: deoxyribonucleic acids
    union of: ribonucleic acids
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: reagent role
    intersection of: Restriction
      on property: inheres in
      some values from: N-ethyl-N-nitrosourea
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of sequence macromolecule
editor preferred term: ENU structure mapping assay
example of usage: PMID:7002606 and PMID:2446263
term editor: Person: Philippe Rocca-Serra
definition source: RNA ontology
definition: a single-nucleotide-resolution nucleic acid structure mapping assay which uses ENU as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
alternative term: single nucleotide resolution mapping assay using ENU probe
has curation status: IAO_0000122

RNASE V1 structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
subclass of: Restriction
  on property: has_specified_input
  some values from: ribonucleic acids
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: catalytic activity
    intersection of: Restriction
      on property: inheres in
      some values from: PR_000025477
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of RNA molecule
example of usage: PMID:7031604
term editor: Person:Philippe Rocca-Serra
definition source: RNA ontology
editor preferred term: RNASE V1 structure mapping assay
definition: a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses RNAse V1 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
alternative term: single nucleotide resolution mapping assay using RNAse V1
has curation status: IAO_0000122

kethoxal structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of sequence macromolecule
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: deoxyribonucleic acids
    union of: ribonucleic acids
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: reagent role
    intersection of: Restriction
      on property: inheres in
      some values from: 1,1-dihydroxy-3-ethoxy-2-butanone
term editor: Person: Philippe Rocca-Serra
definition source: RNA ontology
definition: is a single-nucleotide-resolution nucleic acid structure mapping assay which uses kethoxal as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
editor preferred term: kethoxal structure mapping assay
example of usage: single nucleotide resolution mapping assay using Kethoxal probe
has curation status: IAO_0000122

single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
type: Class
equivalent class: Restriction
  on property: realizes
  some values from: Class
    intersection of: catalytic activity
    intersection of: Restriction
      on property: inheres in
      some values from: PR_000000001
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay
term editor: Person: Philippe Rocca-Serra
definition source: RNAO and OBI
definition: a single-nucleotide-resolution nucleic acid structure mapping assay which relies on proteins acting as enzymatic probes in order to produce measurement information which one interpreted provide structural information about the RNA species under study.
editor preferred term: single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
has curation status: IAO_0000122

DMS structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: reagent role
    intersection of: Restriction
      on property: inheres in
      some values from: Dimethyl sulfate
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: deoxyribonucleic acids
    union of: ribonucleic acids
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of sequence macromolecule
editor preferred term: DMS structure mapping assay
example of usage: PMID:6159633 and PMID:2446263
term editor: Person: Philippe Rocca-Serra
definition source: RNA Ontology
definition: a single-nucleotide-resolution nucleic acid structure mapping assay which uses DMS as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
alternative term: single nucleotide resolution mapping assay using DMS probe
has curation status: IAO_0000122

DNASE 1 structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of sequence macromolecule
subclass of: Restriction
  on property: has_specified_input
  some values from: deoxyribonucleic acids
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: catalytic activity
    intersection of: Restriction
      on property: inheres in
      some values from: PR_000006592
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
editor preferred term: DNASE 1 structure mapping assay
alternative term: DNAse footprinting assay
example of usage: PMID:3773731
term editor: Person:Philippe Rocca-Serra
definition source: RNA ontology
definition: a single-nucleotide-resolution deoxyribonucleic acid structure mapping assay which uses DNAse 1 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
alternative term: single nucleotide resolution mapping assay using DNAse I
has curation status: IAO_0000122

single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: reagent role
      intersection of: Restriction
        on property: inheres in
        some values from: Class
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: secondary structure of sequence macromolecule
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay
term editor: Person: Philippe Rocca-Serra
definition source: RNAO and OBI
definition: a single-nucleotide-resolution nucleic acid structure mapping assay which relies on small chemical compounds acting as chemical probes in order to produce measurement information which one interpreted provide structural information about the RNA species under study.
editor preferred term: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
has curation status: IAO_0000122

Rhodium DNA structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of sequence macromolecule
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: deoxyribonucleic acids
    union of: ribonucleic acids
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: reagent role
    intersection of: Restriction
      on property: inheres in
      some values from: rhodium
example of usage: PMID:2843807
term editor: Person:Philippe Rocca-Serra
definition source: RNA ontology
editor preferred term: Rhodium DNA structure mapping assay
definition: a single-nucleotide-resolution nucleic acid structure mapping assay which uses Rhodium as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
alternative term: single nucleotide resolution mapping assay using Rhodium probe
has curation status: IAO_0000122

RNA ADA I RNA structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of RNA molecule
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: catalytic activity
    intersection of: Restriction
      on property: inheres in
      some values from: PR_000003745
subclass of: Restriction
  on property: has_specified_input
  some values from: ribonucleic acids
example of usage: PMID:7527340
term editor: Person: Philippe Rocca-Serra
editor preferred term: RNA ADA I RNA structure mapping assay
definition source: RNA ontology
definition: a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses RNA adenosine deaminase I as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
alternative term: single nucleotide resolution mapping assay using RNA adenosine deaminase I
has curation status: IAO_0000122

Lead structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of sequence macromolecule
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: reagent role
    intersection of: Restriction
      on property: inheres in
      some values from: lead(0)
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: deoxyribonucleic acids
    union of: ribonucleic acids
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
editor preferred term: Lead structure mapping assay
example of usage: PMID:2686708
term editor: Person:Philippe Rocca-Serra
definition source: RNA ontology
definition: a single-nucleotide-resolution nucleic acid structure mapping assay which uses lead as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
alternative term: single nucleotide resolution mapping assay using Lead probe
has curation status: IAO_0000122

RNASE T2 structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
subclass of: Restriction
  on property: has_specified_input
  some values from: ribonucleic acids
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of RNA molecule
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: catalytic activity
    intersection of: Restriction
      on property: inheres in
      some values from: PR_000014060
example of usage: PMID:6207483
term editor: Person:Philippe Rocca-Serra
definition source: RNA ontology
editor preferred term: RNASE T2 structure mapping assay
definition: a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses RNAse T2 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
alternative term: single nucleotide resolution mapping assay using RNAse T2
has curation status: IAO_0000122

gene dosage assay
type: Class
subclass of: assay
definition source: David Osumi Sutherland
term editor: PERSON: Bjoern Peters
definition: an assay of changes in phenotype due to increased or decreased dosage of a single allele of a gene.
editor preferred term: gene dosage assay
has curation status: IAO_0000120

Fe-BABE RNA structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: reagent role
    intersection of: Restriction
      on property: inheres in
      some values from: Fe-BABE
subclass of: Restriction
  on property: has_specified_input
  some values from: ribonucleic acids
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of RNA molecule
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
editor preferred term: Fe-BABE RNA structure mapping assay
example of usage: PMID: 7862644
term editor: Person:Philippe Rocca-Serra
definition source: RNA ontology
definition: a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses Fe-BABE as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
alternative term: single nucleotide resolution mapping assay using Fe-BABE probe
has curation status: IAO_0000122

RNASE U2 structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
subclass of: Restriction
  on property: has_specified_input
  some values from: ribonucleic acids
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of RNA molecule
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: catalytic activity
    intersection of: Restriction
      on property: inheres in
      some values from: PR_000025475
example of usage: PMID:409999
term editor: Person:Philippe Rocca-Serra
definition source: RNA ontology
editor preferred term: RNASE U2 structure mapping assay
definition: a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses RNAase U2 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
alternative term: single nucleotide resolution mapping assay using RNAse U2
has curation status: IAO_0000122

binding constant determination assay
type: Class
equivalent class: Class
  intersection of: binding assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: binding constant
subclass of: binding assay
example of usage: Determination of KD value for an antibody binding a protein using a BIACORE assay.
definition: A binding assay where the specified output is a binding constant
term editor: PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum
editor preferred term: binding constant determination assay
has curation status: IAO_0000123

NMIA RNA structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: has_specified_input
  some values from: ribonucleic acids
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of RNA molecule
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: reagent role
    intersection of: Restriction
      on property: inheres in
      some values from: N-methylisatoic anhydride
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
editor preferred term: NMIA RNA structure mapping assay
example of usage: PMID: 15796531
term editor: Person:Philippe Rocca-Serra
definition source: RNA ontology
alternative term: SHAPE mapping assay
definition: a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses NMIA as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
alternative term: single nucleotide resolution mapping assay using NMIA probe
has curation status: IAO_0000122

Terbium RNA structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: reagent role
    intersection of: Restriction
      on property: inheres in
      some values from: terbium
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of RNA molecule
subclass of: Restriction
  on property: has_specified_input
  some values from: ribonucleic acids
example of usage: PMID:10772868
term editor: Person:Philippe Rocca-Serra
definition source: RNA ontology
editor preferred term: Terbium RNA structure mapping assay
definition: a single-nucleotide-resolution nucleic acid structure mapping assay which uses Terbium as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
alternative term: single nucleotide resolution mapping assay using Terbium probe
has curation status: IAO_0000122

feature extraction
type: Class
subclass of: OBI_0200000
subclass of: Restriction
  on property: has_specified_output
  some values from: data item
disjoint with: OBI_0001477
disjoint with: OBI_0200002
disjoint with: OBI_0200003
disjoint with: OBI_0200004
disjoint with: OBI_0200006
disjoint with: OBI_0200007
disjoint with: OBI_0200008
disjoint with: OBI_0200011
disjoint with: OBI_0200014
disjoint with: OBI_0200016
disjoint with: OBI_0200017
disjoint with: OBI_0200021
disjoint with: OBI_0200022
disjoint with: OBI_0200025
disjoint with: OBI_0200026
disjoint with: OBI_0200027
disjoint with: OBI_0200028
disjoint with: OBI_0200029
disjoint with: OBI_0200030
disjoint with: OBI_0200033
disjoint with: OBI_0200034
disjoint with: OBI_0200035
disjoint with: OBI_0200036
disjoint with: OBI_0200037
disjoint with: OBI_0200041
disjoint with: OBI_0200042
disjoint with: OBI_0200049
disjoint with: OBI_0200050
disjoint with: OBI_0200052
disjoint with: OBI_0200056
disjoint with: OBI_0200057
disjoint with: OBI_0200058
disjoint with: OBI_0200059
disjoint with: OBI_0200060
disjoint with: OBI_0200061
disjoint with: OBI_0200062
disjoint with: OBI_0200063
disjoint with: OBI_0200064
disjoint with: OBI_0200066
disjoint with: OBI_0200071
disjoint with: OBI_0200077
disjoint with: OBI_0200079
disjoint with: OBI_0200080
disjoint with: OBI_0200082
disjoint with: OBI_0200088
disjoint with: OBI_0200092
disjoint with: OBI_0200093
disjoint with: OBI_0200094
disjoint with: OBI_0200095
disjoint with: OBI_0200097
disjoint with: OBI_0200098
disjoint with: OBI_0200102
disjoint with: OBI_0200106
disjoint with: OBI_0200108
disjoint with: OBI_0200109
disjoint with: OBI_0200110
disjoint with: OBI_0200113
disjoint with: OBI_0200116
disjoint with: OBI_0200117
disjoint with: OBI_0200118
disjoint with: OBI_0200119
disjoint with: OBI_0200120
disjoint with: OBI_0200121
disjoint with: OBI_0200122
disjoint with: OBI_0200123
disjoint with: OBI_0200124
disjoint with: OBI_0200125
disjoint with: OBI_0200140
disjoint with: OBI_0200149
disjoint with: OBI_0200150
disjoint with: OBI_0200156
disjoint with: OBI_0200160
disjoint with: OBI_0200161
disjoint with: OBI_0200162
disjoint with: OBI_0200164
disjoint with: OBI_0200165
disjoint with: OBI_0200176

OH-radical structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: reagent role
    intersection of: Restriction
      on property: inheres in
      some values from: hydroxyl
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of sequence macromolecule
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: deoxyribonucleic acids
    union of: ribonucleic acids
alternative term: MOHCA assay
alternative term: OH footprinting assay
editor preferred term: OH-radical structure mapping assay
example of usage: PMID:2501870
term editor: Person:Philippe Rocca-Serra
definition source: RNA ontology
definition: a single-nucleotide-resolution nucleic acid structure mapping assay which uses hydroxyl radical as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
alternative term: single nucleotide resolution mapping assay using OH-radical probe
has curation status: IAO_0000122

RNASE T1 structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: catalytic activity
    intersection of: Restriction
      on property: inheres in
      some values from: PR_000025467
subclass of: Restriction
  on property: has_specified_input
  some values from: ribonucleic acids
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of RNA molecule
example of usage: PMID:114514
term editor: Person:Philippe Rocca-Serra
definition source: RNA ontology
editor preferred term: RNASE T1 structure mapping assay
definition: a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses RNAse T1 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
alternative term: single nucleotide resolution mapping assay using RNAse T1
has curation status: IAO_0000122

array image acquisition
type: Class
subclass of: image acquisition
subclass of: Restriction
  on property: has_specified_output
  some values from: image
subclass of: Restriction
  on property: has_specified_input
  some values from: OBI_0400147
definition: An image acquisition process that generate an image from the array.
definition source: MO_929: image_acquisition
term editor: PERSON: Jie Zheng
editor preferred term: array image acquisition
has curation status: IAO_0000123

light emission device
type: Class
equivalent class: Restriction
  on property: has function
  some values from: light emission function
subclass of: device
example of usage: A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics)
definition source: OBI
term editor: Person:Helen Parkinson
definition: a device which has a function to emit light.
editor preferred term: light emission device
has curation status: IAO_0000120

perturbation device
type: Class
equivalent class: Restriction
  on property: has function
  some values from: perturb function
subclass of: device
example of usage: A homogenizer is a perturbation device.
definition: A perturbation device is a device which is designed to perform a perturb function
term editor: Helen Parkinson
definition source: OBI Vancouver workshop 2010
definition source: PERSON: Helen Parkinson
editor preferred term: perturbation device
has curation status: IAO_0000123

environmental control device
type: Class
equivalent class: Restriction
  on property: has function
  some values from: Class
    union of: heat function
    union of: cool function
    union of: environment control function
subclass of: device
example of usage: A growth chamber is an environmental control device.
definition: An environmental control device is a device which has the function to control some aspect of the environment such as temperature, or humidity.
term editor: Helen Parkinson
definition source: OBI
editor preferred term: environmental control device
has curation status: IAO_0000120

Nuclease S1 structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: has_specified_input
  some values from: ribonucleic acids
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: catalytic activity
    intersection of: Restriction
      on property: inheres in
      some values from: PR_000025471
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of sequence macromolecule
editor preferred term: Nuclease S1 structure mapping assay
example of usage: PMID:363143
term editor: Person: Philippe Rocca-Serra
definition source: RNA ontology
definition: a single-nucleotide-resolution deoxyribonucleic acid structure mapping assay which uses DNAse 1 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
alternative term: single nucleotide resolution mapping assay using Nuclease S1
has curation status: IAO_0000122

specimen fixation function
type: Class
subclass of: function
disjoint with: current amplification function
disjoint with: stabilization function
disjoint with: OBI_0005246
disjoint with: OBI_1110016
disjoint with: OBI_1110085
term editor: EAGLE-I
definition: a function that allows specific identification of individual speciment from one another.
example of usage: e.g the function of a bar code reader used to read slide bar codes
editor preferred term: specimen fixation function
has curation status: IAO_0000123

obsolete_specimen fixation function
type: Class
subclass of: ObsoleteClass
definition: A specimen fixation function is a function that holds or fastens an entity in a fixed position.
term editor: EAGLE-I
comment: duplicate term
editor preferred term: obsolete_specimen fixation function
deprecated: true
has curation status: IAO_0000123
has obsolescence reason: IAO_0000227

Ruthenium structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: reagent role
    intersection of: Restriction
      on property: inheres in
      some values from: ruthenium
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: deoxyribonucleic acids
    union of: ribonucleic acids
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of RNA molecule
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
example of usage: PMID:3016894
term editor: Person:Philippe Rocca-Serra
definition source: RNAOntology
editor preferred term: Ruthenium structure mapping assay
definition: is a single-nucleotide-resolution nucleic acid structure mapping assay which uses Rhutenium as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
has curation status: IAO_0000122

inline probing RNA structure mapping
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: has_specified_input
  some values from: ribonucleic acids
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of RNA molecule
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: reagent role
    intersection of: Restriction
      on property: inheres in
      some values from: ribonucleic acids
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
example of usage: PMID:10573122 and PMID: 18369975
term editor: Person: Philippe Rocca-Serra
definition source: RNA ontology
editor preferred term: inline probing RNA structure mapping
definition: is a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses intromolecular reactivity to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
has curation status: IAO_0000122

current amplification function
type: Class
subclass of: function
disjoint with: stabilization function
disjoint with: OBI_0005246
disjoint with: OBI_1110016
disjoint with: OBI_1110085
definition: A current amplification function is an amplification function that increases the amplitude of a current.
term editor: EAGLE-I
editor preferred term: current amplification function
has curation status: IAO_0000123

stabilization function
type: Class
subclass of: function
disjoint with: OBI_0005246
disjoint with: OBI_1110016
disjoint with: OBI_1110085
definition: A stabilization function is a function that holds or isolates an entity such as an instrument or specimen steadfast or at an unfluctuating level or quantity.
term editor: EAGLE-I
alternative term: isolation function
editor preferred term: stabilization function
has curation status: IAO_0000123

pump function
type: Class
subclass of: transfer function
disjoint with: cell transfer function
term editor: EAGLE-I
definition: a transfer unction where the transfer requires work to move the entity, often against a gradient.
editor preferred term: pump function
has curation status: IAO_0000123

cell transfer function
type: Class
subclass of: transfer function
example of usage: A cell harvester has a cell transfer function.
term editor: EAGLE-I
editor preferred term: cell transfer function
definition: is a transfer function that displaces cells from one place to another
has curation status: IAO_0000123

angiograph
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
disjoint with: capillary blotter
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102

capillary blotter
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: transfer function
disjoint with: bioreactor
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103

bioreactor
type: Class
subclass of: environmental control device
subclass of: Restriction
  on property: has function
  some values from: environment control function
disjoint with: pH meter
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104

pH meter
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
disjoint with: digital camera
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105

digital camera
type: Class
subclass of: image acquisition device
subclass of: Restriction
  on property: has function
  some values from: image acquisition function
disjoint with: chip spotting device
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106

chip spotting device
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: transfer function
disjoint with: electrophoresis system
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107

RNA extraction/purification instrument
type: Class
subclass of: nucleic acid extraction/purification instrument
disjoint with: DNA extraction/purification instrument
definition: A device that is used to isolate and collect RNA for subsequent molecular analysis.
definition source: PERSON: Erik Segerdell
term editor: PERSON: Erik Segerdell
editor preferred term: RNA extraction/purification instrument
has curation status: IAO_0000120

DNA extract
type: Class
subclass of: nucleic acid extract
subclass of: Restriction
  on property: has grain
  some values from: deoxyribonucleic acids
subclass of: Restriction
  on property: is_specified_output_of
  some values from: DNA extraction
editor preferred term: DNA extract
definition source: Group: UPenn group
term editor: Person: Jie Zheng
definition: The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas.
has curation status: IAO_0000120

two-photon laser/detector
type: Class
subclass of: OBI_0400065
disjoint with: OBI_0400009
disjoint with: OBI_0400064
definition: A light source used in fluorescence imaging that allows the imaging of living tissue up to a depth of 1 mm, based on the concept that two photons of low energy can excite a fluorophore in a quantum event, resulting in the emission of a fluorescence photon, typically at a higher energy than either of the two excitatory photons.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Two-photon_excitation_microscopy
editor preferred term: two-photon laser/detector
has curation status: IAO_0000120

electrophoresis system
type: Class
subclass of: material separation device
subclass of: Restriction
  on property: has function
  some values from: material separation function
disjoint with: PET synthesizer
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108

PET synthesizer
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: synthesizing function
disjoint with: microplate reader
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109

spinning-disk confocal microscope
type: Class
subclass of: confocal microscope
subclass of: Restriction
  on property: has function
  some values from: measure function
disjoint with: programmable array microscope
disjoint with: laser scanning confocal microscope
definition: A confocal microscope that uses a Nipkow disk, a mechanical, geometrically operating image scanning device.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Nipkow_disk
editor preferred term: spinning-disk confocal microscope
has curation status: IAO_0000120

DNA synthesizer
type: Class
subclass of: OBI_0400113
definition: An oligonucleotide synthesizer that is used to custom-build DNA molecules to contain a particular sequence of nucleotides.
editor preferred term: DNA synthesizer
term editor: PERSON: Erik Segerdell
definition source: http://www.globalspec.com/LearnMore/Labware_Scientific_Instruments/Clinical_Research_Labware/DNA_Synthesizers
has curation status: IAO_0000120

high performance liquid chromatography instrument
type: Class
subclass of: liquid chromatography instrument
definition: A liquid chromatography instrument that consists of a reservoir of mobile phase, a pump, an injector, a separation column, and a detector. The pump (rather than gravity) provides the higher pressure required to propel the mobile phase and analyte through the densely packed column.
term editor: PERSON: Erik Segerdell
editor preferred term: high performance liquid chromatography instrument
definition source: http://en.wikipedia.org/wiki/High_performance_liquid_chromatography
has curation status: IAO_0000120

microplate reader
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
disjoint with: spot cutter
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110

ELISA microplate reader
type: Class
subclass of: microplate reader
disjoint with: multimode microplate reader
definition: A microplate reader that is used for enzyme-linked immunosorbent assays (ELISA).
editor preferred term: ELISA microplate reader
definition source: PERSON: Erik Segerdell
term editor: PERSON: Erik Segerdell
has curation status: IAO_0000120

spot cutter
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
disjoint with: microwave synthesis system
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112

microwave synthesis system
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: synthesizing function
disjoint with: densitometer
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113

densitometer
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
disjoint with: automatic staining machine
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114

automatic staining machine
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: addition of molecular tracer function
disjoint with: automatic tissue processor
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115

automatic tissue processor
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
disjoint with: perfusion station
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116

stereo microscope
type: Class
subclass of: optical microscope
subclass of: Restriction
  on property: has function
  some values from: measure function
definition: An optical microscope that uses two separate optical paths with two objectives and two eyepieces to provide slightly different viewing angles to the left and right eyes.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Optical_microscope#Stereo_microscope
editor preferred term: stereo microscope
has curation status: IAO_0000120

top loading balance
type: Class
subclass of: balance
disjoint with: mechanical balance
disjoint with: analytical balance
definition: A balance that consists of a metal plate on which to place an object and a digital readout of the measurement of its mass.
definition source: PERSON: Erik Segerdell
term editor: PERSON: Erik Segerdell
editor preferred term: top loading balance
has curation status: IAO_0000120

perfusion station
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: specimen fixation function
disjoint with: SPECT scanner
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117

SPECT scanner
type: Class
subclass of: image acquisition device
subclass of: Restriction
  on property: has function
  some values from: image acquisition function
disjoint with: scintillation counter
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118

array manufacturer role
type: Class
subclass of: manufacturer role
subclass of: Restriction
  on property: is realized by
  all values from: Class
    intersection of: manufacturing
    intersection of: Restriction
      on property: has_specified_output
      some values from: OBI_0400147
definition: a manufacturer role which is played by the person or organization that manufactured the array
definition source: MO_695 array_manufacturer
term editor: PERSON: Chris Stoeckert, Jie Zheng
editor preferred term: array manufacturer role
has curation status: IAO_0000120

scintillation counter
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
disjoint with: cryostat
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119

programmable array microscope
type: Class
subclass of: confocal microscope
subclass of: Restriction
  on property: has function
  some values from: measure function
disjoint with: laser scanning confocal microscope
definition: A confocal microscope that uses a programmable spatial light modulator for generating an arbitrary pattern of conjugate illumination and detection apertures.
term editor: PERSON: Erik Segerdell
definition source: Verveer et al, Journal of Microscopy, vol. 189, pt. 3, pp. 192-8
editor preferred term: programmable array microscope
has curation status: IAO_0000120

cryostat
type: Class
subclass of: container
subclass of: environmental control device
subclass of: Restriction
  on property: has function
  some values from: cool function
disjoint with: microtome knife maker
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119

microtome knife maker
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
disjoint with: cryofixation device
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121

cryofixation device
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: specimen fixation function
disjoint with: incubator shaker
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135

hybridization oven
type: Class
subclass of: incubator
subclass of: container
subclass of: Restriction
  on property: has function
  some values from: mechanical function
subclass of: Restriction
  on property: has function
  some values from: contain function
definition: A device that creates an appropriate environment for nucleic acid hybridization.
definition source: PERSON: Erik Segerdell
term editor: PERSON: Erik Segerdell
editor preferred term: hybridization oven
has curation status: IAO_0000120

incubator shaker
type: Class
subclass of: container
subclass of: environmental control device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
disjoint with: small-animal image acquisition device
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135

small-animal image acquisition device
type: Class
subclass of: image acquisition device
subclass of: Restriction
  on property: has function
  some values from: image acquisition function
disjoint with: infrared image acquisition device
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135
disjoint with: OBI_0400137
disjoint with: OBI_0400140

infrared image acquisition device
type: Class
subclass of: image acquisition device
subclass of: Restriction
  on property: has function
  some values from: measure function
disjoint with: patch clamp device
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135
disjoint with: OBI_0400137
disjoint with: OBI_0400140
disjoint with: OBI_0400142

confocal microscope
type: Class
subclass of: OBI_0400169
subclass of: Restriction
  on property: has function
  some values from: measure function
disjoint with: laser capture microdissection microscope
disjoint with: scanning force microscope
disjoint with: digital microscope
definition: A microscope that is used to increase micrograph contrast and/or reconstruct three-dimensional images by using a spatial pinhole to eliminate out-of-focus light in specimens that are thicker than the focal plane.
term editor: PERSON: Erik Segerdell
editor preferred term: confocal microscope
definition source: http://en.wikipedia.org/wiki/Confocal_microscopy
has curation status: IAO_0000120

patch clamp device
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
disjoint with: gel imaging system
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135
disjoint with: OBI_0400137
disjoint with: OBI_0400140
disjoint with: OBI_0400142
disjoint with: OBI_0400146

gel imaging system
type: Class
subclass of: image acquisition device
subclass of: Restriction
  on property: has function
  some values from: image acquisition function
disjoint with: protein separation apparatus
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135
disjoint with: OBI_0400137
disjoint with: OBI_0400140
disjoint with: OBI_0400142
disjoint with: OBI_0400146
disjoint with: OBI_0400147

protein separation apparatus
type: Class
subclass of: material separation device
subclass of: Restriction
  on property: has function
  some values from: material separation function
disjoint with: vitrification apparatus
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135
disjoint with: OBI_0400137
disjoint with: OBI_0400140
disjoint with: OBI_0400142
disjoint with: OBI_0400146
disjoint with: OBI_0400147
disjoint with: OBI_0400153

multichannel electronic pipette
type: Class
subclass of: multichannel pipette
definition: A multichannel pipette that can be programmed by the user to aspirate a volume of liquid reagent or sample and dispense the aspirated volume or a series of aliquots in successive dispensing operations.
term editor: PERSON: Erik Segerdell
definition source: http://www.faqs.org/patents/app/20090196797
editor preferred term: multichannel electronic pipette
has curation status: IAO_0000120

vitrification apparatus
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
disjoint with: radiography instrument
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135
disjoint with: OBI_0400137
disjoint with: OBI_0400140
disjoint with: OBI_0400142
disjoint with: OBI_0400146
disjoint with: OBI_0400147
disjoint with: OBI_0400153
disjoint with: OBI_0400158

radiography instrument
type: Class
subclass of: image acquisition device
subclass of: Restriction
  on property: has function
  some values from: measure function
disjoint with: radiation measurement device
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135
disjoint with: OBI_0400137
disjoint with: OBI_0400140
disjoint with: OBI_0400142
disjoint with: OBI_0400146
disjoint with: OBI_0400147
disjoint with: OBI_0400153
disjoint with: OBI_0400158
disjoint with: OBI_0400168

radiation measurement device
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
disjoint with: lyophilizer
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135
disjoint with: OBI_0400137
disjoint with: OBI_0400140
disjoint with: OBI_0400142
disjoint with: OBI_0400146
disjoint with: OBI_0400147
disjoint with: OBI_0400153
disjoint with: OBI_0400158
disjoint with: OBI_0400168
disjoint with: OBI_0400169

lyophilizer
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
disjoint with: microhardness tester
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135
disjoint with: OBI_0400137
disjoint with: OBI_0400140
disjoint with: OBI_0400142
disjoint with: OBI_0400146
disjoint with: OBI_0400147
disjoint with: OBI_0400153
disjoint with: OBI_0400158
disjoint with: OBI_0400168
disjoint with: OBI_0400169
disjoint with: OBI_0400170

tandem mass spectrometer
type: Class
subclass of: mass spectrometer
definition: A mass spectrometer in which ions are subjected to two or more sequential stages of analysis (which may be separated spatially or temporally) according to the quotient mass/charge.
term editor: PERSON: Erik Segerdell
definition source: http://goldbook.iupac.org/T06250.html
editor preferred term: tandem mass spectrometer
has curation status: IAO_0000120

microhardness tester
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
disjoint with: microtome knife sharpener
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135
disjoint with: OBI_0400137
disjoint with: OBI_0400140
disjoint with: OBI_0400142
disjoint with: OBI_0400146
disjoint with: OBI_0400147
disjoint with: OBI_0400153
disjoint with: OBI_0400158
disjoint with: OBI_0400168
disjoint with: OBI_0400169
disjoint with: OBI_0400170
disjoint with: OBI_0400171

multimode microplate reader
type: Class
subclass of: microplate reader
definition: A microplate reader that can detect multiple types of absorbance, luminescence or fluorescence.
definition source: PERSON: Erik Segerdell
term editor: PERSON: Erik Segerdell
editor preferred term: multimode microplate reader
has curation status: IAO_0000120

mechanical balance
type: Class
subclass of: balance
disjoint with: analytical balance
definition: A balance that is used to compare the weights of two bodies, to determine the difference in mass (or weight).
term editor: PERSON: Erik Segerdell
definition source: http://www.britannica.com/EBchecked/topic/49765/balance
editor preferred term: mechanical balance
has curation status: IAO_0000120

computer cluster
type: Class
subclass of: OBI_0400107
definition: A group of linked computers, working together closely so that in many respects they form a single computer.
term editor: PERSON: Erik Segerdell
editor preferred term: computer cluster
definition source: http://en.wikipedia.org/wiki/Cluster_(computing)
has curation status: IAO_0000120

microtome knife sharpener
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
disjoint with: plate shaker
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135
disjoint with: OBI_0400137
disjoint with: OBI_0400140
disjoint with: OBI_0400142
disjoint with: OBI_0400146
disjoint with: OBI_0400147
disjoint with: OBI_0400153
disjoint with: OBI_0400158
disjoint with: OBI_0400168
disjoint with: OBI_0400169
disjoint with: OBI_0400170
disjoint with: OBI_0400171
definition: A device that is used to sharpen knives used in microtomy.

plate shaker
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
disjoint with: coagulation analyzer
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135
disjoint with: OBI_0400137
disjoint with: OBI_0400140
disjoint with: OBI_0400142
disjoint with: OBI_0400146
disjoint with: OBI_0400147
disjoint with: OBI_0400153
disjoint with: OBI_0400158
disjoint with: OBI_0400168
disjoint with: OBI_0400169
disjoint with: OBI_0400170
disjoint with: OBI_0400171
definition: A device that provides shaking motion for microplates.
term editor: PERSON: Erik Segerdell

coagulation analyzer
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
disjoint with: ultrasound machine
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135
disjoint with: OBI_0400137
disjoint with: OBI_0400140
disjoint with: OBI_0400142
disjoint with: OBI_0400146
disjoint with: OBI_0400147
disjoint with: OBI_0400153
disjoint with: OBI_0400158
disjoint with: OBI_0400168
disjoint with: OBI_0400169
disjoint with: OBI_0400170
disjoint with: OBI_0400171
definition: A device for automatically analyzing blood coagulation in a clinical laboratory.
term editor: PERSON: Erik Segerdell
definition source: United States Patent 5439646

laser capture microdissection microscope
type: Class
subclass of: OBI_0400169
subclass of: Restriction
  on property: has function
  some values from: measure function
disjoint with: scanning force microscope
disjoint with: digital microscope
definition: A microscope that uses low-energy laser beams and special transfer film to lift single cells from a tissue.
term editor: PERSON: Erik Segerdell
definition source: http://www.answers.com/topic/laser-capture-microdissection-microscope-in-medicine
editor preferred term: laser capture microdissection microscope
has curation status: IAO_0000120

liquid extraction robot
type: Class
subclass of: OBI_0400112
subclass of: Restriction
  on property: has function
  some values from: mechanical function
definition: A liquid handling device that provides automatic liquid extraction.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell
editor preferred term: liquid extraction robot
has curation status: IAO_0000120

ultrasound machine
type: Class
subclass of: image acquisition device
subclass of: Restriction
  on property: has function
  some values from: image acquisition function
disjoint with: immunoblot scanner
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135
disjoint with: OBI_0400137
disjoint with: OBI_0400140
disjoint with: OBI_0400142
disjoint with: OBI_0400146
disjoint with: OBI_0400147
disjoint with: OBI_0400153
disjoint with: OBI_0400158
disjoint with: OBI_0400168
disjoint with: OBI_0400169
disjoint with: OBI_0400170
disjoint with: OBI_0400171
definition: A device that is used to visualize subcutaneous body structures including tendons, muscles, joints, vessels and internal organs.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Sonography
editor preferred term: ultrasound machine

immunoblot scanner
type: Class
subclass of: image acquisition device
subclass of: Restriction
  on property: has function
  some values from: image acquisition function
disjoint with: rocker
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135
disjoint with: OBI_0400137
disjoint with: OBI_0400140
disjoint with: OBI_0400142
disjoint with: OBI_0400146
disjoint with: OBI_0400147
disjoint with: OBI_0400153
disjoint with: OBI_0400158
disjoint with: OBI_0400168
disjoint with: OBI_0400169
disjoint with: OBI_0400170
disjoint with: OBI_0400171
definition: A device that is used for the imaging of immunoblots.
definition source: PERSON: Erik Segerdell
term editor: PERSON: Erik Segerdell
editor preferred term: immunoblot scanner
has curation status: IAO_0000120

microcentrifuge
type: Class
subclass of: OBI_0400106
definition: A type of centrifuge that is designed for small tubes (0.2 ml to 2.0 ml), has a compact design, and has a small footprint.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Laboratory_centrifuge
editor preferred term: microcentrifuge
has curation status: IAO_0000120

electronic repeater pipette
type: Class
subclass of: micropipette
definition: A micropipette that can be programmed by the user to aspirate a volume of liquid reagent or sample and dispense a series of aliquots in successive dispensing operations.
term editor: PERSON: Erik Segerdell
editor preferred term: electronic repeater pipette
definition source: http://www.faqs.org/patents/app/20090196797
has curation status: IAO_0000120

electron paramagnetic resonance spectrometer
type: Class
subclass of: OBI_0400115
disjoint with: OBI_0400063
disjoint with: OBI_0400143
definition: An spectrophotometer that is used to investigate chemical species that have one or more unpaired electrons, such as organic and inorganic free radicals or inorganic complexes possessing a transition metal ion.
term editor: PERSON: Erik Segerdell
editor preferred term: electron paramagnetic resonance spectrometer
definition source: http://en.wikipedia.org/wiki/Electron_paramagnetic_resonance
has curation status: IAO_0000120

rocker
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
disjoint with: tissue embedding station
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135
disjoint with: OBI_0400137
disjoint with: OBI_0400140
disjoint with: OBI_0400142
disjoint with: OBI_0400146
disjoint with: OBI_0400147
disjoint with: OBI_0400153
disjoint with: OBI_0400158
disjoint with: OBI_0400168
disjoint with: OBI_0400169
disjoint with: OBI_0400170
disjoint with: OBI_0400171
definition: A device that provides three-dimensional motion for biomedical applications (e.g., gel trays).
definition source: PERSON: Erik Segerdell
term editor: PERSON: Erik Segerdell
editor preferred term: rocker
has curation status: IAO_0000120

analytical balance
type: Class
subclass of: balance
definition: A balance with weighing pan(s) inside a transparent enclosure that is used to measure mass to a very high degree of precision and accuracy.
term editor: PERSON: Erik Segerdell
editor preferred term: analytical balance
definition source: http://en.wikipedia.org/wiki/Weighing_scale
has curation status: IAO_0000120

scanning force microscope
type: Class
subclass of: OBI_0400169
subclass of: Restriction
  on property: has function
  some values from: measure function
disjoint with: digital microscope
definition: A microscope that forms images of surfaces using a physical probe that scans the specimen.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Scanning_probe_microscopy
editor preferred term: scanning force microscope
has curation status: IAO_0000120

pulsed-field gel electrophoresis system
type: Class
subclass of: gel electrophoresis system
definition: A gel electrophoresis system that is used to separate very large molecules of DNA.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Pulsed_field_gel_electrophoresis
editor preferred term: pulsed-field gel electrophoresis system
has curation status: IAO_0000120

tissue embedding station
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
disjoint with: nucleic acid sequencer
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135
disjoint with: OBI_0400137
disjoint with: OBI_0400140
disjoint with: OBI_0400142
disjoint with: OBI_0400146
disjoint with: OBI_0400147
disjoint with: OBI_0400153
disjoint with: OBI_0400158
disjoint with: OBI_0400168
disjoint with: OBI_0400169
disjoint with: OBI_0400170
disjoint with: OBI_0400171
definition: A device that is used to perform paraffin embedding of tissue specimens.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell
editor preferred term: tissue embedding station
has curation status: IAO_0000120

nucleic acid sequencer
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
disjoint with: bead array reader
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135
disjoint with: OBI_0400137
disjoint with: OBI_0400140
disjoint with: OBI_0400142
disjoint with: OBI_0400146
disjoint with: OBI_0400147
disjoint with: OBI_0400153
disjoint with: OBI_0400158
disjoint with: OBI_0400168
disjoint with: OBI_0400169
disjoint with: OBI_0400170
disjoint with: OBI_0400171
definition: An device that is used to determine the order of nucleotides in nucleic acid sequences.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell
editor preferred term: nucleic acid sequencer
has curation status: IAO_0000120

bead array reader
type: Class
subclass of: image acquisition device
subclass of: Restriction
  on property: has function
  some values from: measure function
subclass of: Restriction
  on property: has function
  some values from: image acquisition function
disjoint with: paraffin oven
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135
disjoint with: OBI_0400137
disjoint with: OBI_0400140
disjoint with: OBI_0400142
disjoint with: OBI_0400146
disjoint with: OBI_0400147
disjoint with: OBI_0400153
disjoint with: OBI_0400158
disjoint with: OBI_0400168
disjoint with: OBI_0400169
disjoint with: OBI_0400170
disjoint with: OBI_0400171
definition: A device that is used to acquire and image bead array data.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell
editor preferred term: bead array reader
has curation status: IAO_0000120

real-time PCR machine
type: Class
subclass of: PCR instrument
definition: An PCR instrument that enables both detection and quantification of one or more specific sequences in a DNA sample.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction
editor preferred term: real-time PCR machine
has curation status: IAO_0000120

paraffin oven
type: Class
subclass of: container
subclass of: environmental control device
subclass of: Restriction
  on property: has function
  some values from: contain function
subclass of: Restriction
  on property: has function
  some values from: heat function
subclass of: Restriction
  on property: has function
  some values from: mechanical function
disjoint with: autoclave
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135
disjoint with: OBI_0400137
disjoint with: OBI_0400140
disjoint with: OBI_0400142
disjoint with: OBI_0400146
disjoint with: OBI_0400147
disjoint with: OBI_0400153
disjoint with: OBI_0400158
disjoint with: OBI_0400168
disjoint with: OBI_0400169
disjoint with: OBI_0400170
disjoint with: OBI_0400171
definition: A device that is used for the warming of paraffin embedding medium.
definition source: PERSON: Erik Segerdell
term editor: PERSON: Erik Segerdell
editor preferred term: paraffin oven
has curation status: IAO_0000120

autoclave
type: Class
subclass of: environmental control device
subclass of: Restriction
  on property: has function
  some values from: sterilization function
subclass of: Restriction
  on property: has function
  some values from: mechanical function
subclass of: Restriction
  on property: has function
  some values from: heat function
disjoint with: microplate washer
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135
disjoint with: OBI_0400137
disjoint with: OBI_0400140
disjoint with: OBI_0400142
disjoint with: OBI_0400146
disjoint with: OBI_0400147
disjoint with: OBI_0400153
disjoint with: OBI_0400158
disjoint with: OBI_0400168
disjoint with: OBI_0400169
disjoint with: OBI_0400170
disjoint with: OBI_0400171
definition: A device that is used to sterilize equipment and supplies by subjecting them to high pressure steam at 121 C or more, typically for 15 to 20 minutes depending on the size of the load and the contents.
definition source: J. Black, Microbiology, Prentice Hall (1993) pg. 334; http://en.wikipedia.org/wiki/Autoclave
term editor: PERSON: Erik Segerdell
editor preferred term: autoclave
has curation status: IAO_0000120

microplate washer
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
disjoint with: nucleic acid extraction/purification instrument
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135
disjoint with: OBI_0400137
disjoint with: OBI_0400140
disjoint with: OBI_0400142
disjoint with: OBI_0400146
disjoint with: OBI_0400147
disjoint with: OBI_0400153
disjoint with: OBI_0400158
disjoint with: OBI_0400168
disjoint with: OBI_0400169
disjoint with: OBI_0400170
disjoint with: OBI_0400171
definition: A device that is used to wash immunoassays in microwell strips and plates with professional accuracy. WHAT IS PROFESSIONAL ACCURACY??
term editor: PERSON: Erik Segerdell
definition source: http://www.articlesnatch.com/Article/Microplate-Readers-And-Washers-For-Laboratories/948037
editor preferred term: microplate washer
has curation status: IAO_0000120

nucleic acid extraction/purification instrument
type: Class
subclass of: material separation device
subclass of: Restriction
  on property: has function
  some values from: material separation function
disjoint with: vacuum manifold
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135
disjoint with: OBI_0400137
disjoint with: OBI_0400140
disjoint with: OBI_0400142
disjoint with: OBI_0400146
disjoint with: OBI_0400147
disjoint with: OBI_0400153
disjoint with: OBI_0400158
disjoint with: OBI_0400168
disjoint with: OBI_0400169
disjoint with: OBI_0400170
disjoint with: OBI_0400171
definition: A device that is used to isolate and collect nucleic acids (DNA or RNA) for subsequent molecular analysis.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell
editor preferred term: nucleic acid extraction/purification instrument
has curation status: IAO_0000120

ELISA microplate washer
type: Class
subclass of: microplate washer
definition: A microplate washer that is used for enzyme-linked immunosorbent assays (ELISA).
editor preferred term: ELISA microplate washer
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell
has curation status: IAO_0000120

vacuum manifold
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
disjoint with: multichannel pipette
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135
disjoint with: OBI_0400137
disjoint with: OBI_0400140
disjoint with: OBI_0400142
disjoint with: OBI_0400146
disjoint with: OBI_0400147
disjoint with: OBI_0400153
disjoint with: OBI_0400158
disjoint with: OBI_0400168
disjoint with: OBI_0400169
disjoint with: OBI_0400170
disjoint with: OBI_0400171
definition: A device that is used for the vacuum-driven processing of multiwell strips or plates, or spin columns. IS THIS AN INSTRUMENT? IS THE DEFINTION CORRECT - TO DISTRIBUTE PRESSURE EVENLY.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell
editor preferred term: vacuum manifold
has curation status: IAO_0000120

DNA extraction/purification instrument
type: Class
subclass of: nucleic acid extraction/purification instrument
definition: A device that is used to isolate and collect DNA for subsequent molecular analysis.
editor preferred term: DNA extraction/purification instrument
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/DNA_extraction
has curation status: IAO_0000120

multichannel pipette
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
subclass of: Restriction
  on property: has function
  some values from: measure function
disjoint with: cell harvester
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135
disjoint with: OBI_0400137
disjoint with: OBI_0400140
disjoint with: OBI_0400142
disjoint with: OBI_0400146
disjoint with: OBI_0400147
disjoint with: OBI_0400153
disjoint with: OBI_0400158
disjoint with: OBI_0400168
disjoint with: OBI_0400169
disjoint with: OBI_0400170
disjoint with: OBI_0400171
definition: A pipetting system that has a plurality of tip fittings and is used for multi-well plate applications.
definition source: PERSON: Erik Segerdell
term editor: PERSON: Erik Segerdell
editor preferred term: multichannel pipette
has curation status: IAO_0000120

cell harvester
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: cell transfer function
disjoint with: diffractometer
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135
disjoint with: OBI_0400137
disjoint with: OBI_0400140
disjoint with: OBI_0400142
disjoint with: OBI_0400146
disjoint with: OBI_0400147
disjoint with: OBI_0400153
disjoint with: OBI_0400158
disjoint with: OBI_0400168
disjoint with: OBI_0400169
disjoint with: OBI_0400170
disjoint with: OBI_0400171
definition: A device that is used to harvest cells from microplates and deposit samples on a filter mat. NOT AN INSTRUMENT?
definition source: PERSON: Erik Segerdell
term editor: PERSON: Erik Segerdell
editor preferred term: cell harvester
has curation status: IAO_0000120

portable fluorometer
type: Class
subclass of: OBI_0400143
definition: A compact fluorometer that can be carried or moved with ease.
definition source: PERSON: Erik Segerdell
term editor: PERSON: Erik Segerdell
editor preferred term: portable fluorometer
has curation status: IAO_0000120

gel electrophoresis system
type: Class
subclass of: electrophoresis system
disjoint with: capillary electrophoresis instrument
disjoint with: agarose gel electrophoresis system
definition: A device that moves charged particles through a medium by using an electric field induced by electrodes.
term editor: PERSON: Erik Segerdell
alternative term: electrophoresis system
editor preferred term: gel electrophoresis system
definition source: http://en.wikipedia.org/wiki/Category:Electrophoresis
has curation status: IAO_0000120

diffractometer
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
disjoint with: microdissection instrument
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135
disjoint with: OBI_0400137
disjoint with: OBI_0400140
disjoint with: OBI_0400142
disjoint with: OBI_0400146
disjoint with: OBI_0400147
disjoint with: OBI_0400153
disjoint with: OBI_0400158
disjoint with: OBI_0400168
disjoint with: OBI_0400169
disjoint with: OBI_0400170
disjoint with: OBI_0400171
definition: A measurement device for analyzing the structure of a material from the scattering pattern produced when a beam of radiation or particles (e.g. X rays or neutrons) interacts with it.
term editor: PERSON: Erik Segerdell
editor preferred term: diffractometer
definition source: http://en.wikipedia.org/wiki/Diffractometer
has curation status: IAO_0000120

microdissection instrument
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
disjoint with: micropipette puller
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135
disjoint with: OBI_0400137
disjoint with: OBI_0400140
disjoint with: OBI_0400142
disjoint with: OBI_0400146
disjoint with: OBI_0400147
disjoint with: OBI_0400153
disjoint with: OBI_0400158
disjoint with: OBI_0400168
disjoint with: OBI_0400169
disjoint with: OBI_0400170
disjoint with: OBI_0400171
definition: A device that is used for the dissection of tissues under magnification.
term editor: PERSON: Erik Segerdell
definition source: http://medical-dictionary.thefreedictionary.com/microdissection
editor preferred term: microdissection instrument
has curation status: IAO_0000120

micropipette puller
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
disjoint with: freeze substitution system
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135
disjoint with: OBI_0400137
disjoint with: OBI_0400140
disjoint with: OBI_0400142
disjoint with: OBI_0400146
disjoint with: OBI_0400147
disjoint with: OBI_0400153
disjoint with: OBI_0400158
disjoint with: OBI_0400168
disjoint with: OBI_0400169
disjoint with: OBI_0400170
disjoint with: OBI_0400171
definition: A device that is used to fabricate glass micropipettes.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Micropipette
editor preferred term: micropipette puller
has curation status: IAO_0000120

laser scanning confocal microscope
type: Class
subclass of: confocal microscope
subclass of: Restriction
  on property: has function
  some values from: measure function
definition: A confocal microscope that obtains high-resolution optical images with depth selectivity, in which a laser beam passes through a light source aperture and then is focused by an objective lens into a small (ideally diffraction limited) focal volume within or on the surface of a specimen.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Confocal_laser_scanning_microscopy
editor preferred term: laser scanning confocal microscope
has curation status: IAO_0000120

digital microscope
type: Class
subclass of: OBI_0400169
subclass of: Restriction
  on property: has function
  some values from: measure function
definition: A microscope that uses optics and a charge-coupled device (CCD) camera to output a digital image to a monitor.
term editor: PERSON: Erik Segerdell
editor preferred term: digital microscope
definition source: http://en.wikipedia.org/wiki/Digital_microscope
has curation status: IAO_0000120

freeze substitution system
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
subclass of: Restriction
  on property: has function
  some values from: freeze function
disjoint with: micropipette
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135
disjoint with: OBI_0400137
disjoint with: OBI_0400140
disjoint with: OBI_0400142
disjoint with: OBI_0400146
disjoint with: OBI_0400147
disjoint with: OBI_0400153
disjoint with: OBI_0400158
disjoint with: OBI_0400168
disjoint with: OBI_0400169
disjoint with: OBI_0400170
disjoint with: OBI_0400171
definition: A device or system for dehydrating and then chemically fixing electron microscopy samples at low temperatures in preparation for various treatments including embedding in resins.
term editor: PERSON: Erik Segerdell
definition source: doi:10.1017/S143192760707866X
editor preferred term: freeze substitution system
has curation status: IAO_0000120

micropipette
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
subclass of: Restriction
  on property: has function
  some values from: mechanical function
disjoint with: voltage clamp device
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135
disjoint with: OBI_0400137
disjoint with: OBI_0400140
disjoint with: OBI_0400142
disjoint with: OBI_0400146
disjoint with: OBI_0400147
disjoint with: OBI_0400153
disjoint with: OBI_0400158
disjoint with: OBI_0400168
disjoint with: OBI_0400169
disjoint with: OBI_0400170
disjoint with: OBI_0400171
definition: A microinjection device that is used to measure very small volumes of liquids.
term editor: PERSON: Erik Segerdell
definition source: http://www.answers.com/topic/micropipette
editor preferred term: micropipette
has curation status: IAO_0000120

voltage clamp device
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
disjoint with: vacuum oven
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135
disjoint with: OBI_0400137
disjoint with: OBI_0400140
disjoint with: OBI_0400142
disjoint with: OBI_0400146
disjoint with: OBI_0400147
disjoint with: OBI_0400153
disjoint with: OBI_0400158
disjoint with: OBI_0400168
disjoint with: OBI_0400169
disjoint with: OBI_0400170
disjoint with: OBI_0400171
definition: A device that is used to measure the ion currents across the membrane of excitable cells, such as neurons, while holding the membrane voltage at a set level.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Voltage_clamp
editor preferred term: voltage clamp device
has curation status: IAO_0000120

vacuum oven
type: Class
subclass of: container
subclass of: environmental control device
subclass of: Restriction
  on property: has function
  some values from: heat function
subclass of: Restriction
  on property: has function
  some values from: contain function
subclass of: Restriction
  on property: has function
  some values from: mechanical function
disjoint with: slide warmer
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135
disjoint with: OBI_0400137
disjoint with: OBI_0400140
disjoint with: OBI_0400142
disjoint with: OBI_0400146
disjoint with: OBI_0400147
disjoint with: OBI_0400153
disjoint with: OBI_0400158
disjoint with: OBI_0400168
disjoint with: OBI_0400169
disjoint with: OBI_0400170
disjoint with: OBI_0400171
definition: A device that heats materials in a vacuum.
definition source: PERSON: Erik Segerdell
term editor: PERSON: Erik Segerdell
editor preferred term: vacuum oven
has curation status: IAO_0000120

slide warmer
type: Class
subclass of: environmental control device
subclass of: Restriction
  on property: has function
  some values from: heat function
disjoint with: denaturing high-performance liquid chromatography instrument
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135
disjoint with: OBI_0400137
disjoint with: OBI_0400140
disjoint with: OBI_0400142
disjoint with: OBI_0400146
disjoint with: OBI_0400147
disjoint with: OBI_0400153
disjoint with: OBI_0400158
disjoint with: OBI_0400168
disjoint with: OBI_0400169
disjoint with: OBI_0400170
disjoint with: OBI_0400171
definition: A device that is used to heat microscope slides.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell
editor preferred term: slide warmer
has curation status: IAO_0000120

capillary electrophoresis instrument
type: Class
subclass of: electrophoresis system
disjoint with: agarose gel electrophoresis system
definition: An electrophoresis system that is used to separate ionic species by their charge and frictional forces and mass.
term editor: PERSON: Erik Segerdell
editor preferred term: capillary electrophoresis instrument
definition source: http://en.wikipedia.org/wiki/Capillary_electrophoresis
has curation status: IAO_0000120

denaturing high-performance liquid chromatography instrument
type: Class
subclass of: material separation device
subclass of: Restriction
  on property: has function
  some values from: material separation function
disjoint with: balance
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135
disjoint with: OBI_0400137
disjoint with: OBI_0400140
disjoint with: OBI_0400142
disjoint with: OBI_0400146
disjoint with: OBI_0400147
disjoint with: OBI_0400153
disjoint with: OBI_0400158
disjoint with: OBI_0400168
disjoint with: OBI_0400169
disjoint with: OBI_0400170
disjoint with: OBI_0400171
definition: A high performance liquid chromatography instrument that employs temperature-dependent separation of DNA containing mismatched base pairs from PCR-amplified DNA fragments for chromatographic mutation analysis.
term editor: PERSON: Erik Segerdell
editor preferred term: denaturing high-performance liquid chromatography instrument
definition source: doi:10.1385/1-59259-850-1:173
has curation status: IAO_0000120

agarose gel electrophoresis system
type: Class
subclass of: electrophoresis system
definition: A gel electrophoresis system that is used to separate DNA or RNA molecules by size, achieved by moving negatively charged nucleic acid molecules through an agarose matrix with an electric field.
term editor: PERSON: Erik Segerdell
editor preferred term: agarose gel electrophoresis system
definition source: http://en.wikipedia.org/wiki/Agarose_gel_electrophoresis
has curation status: IAO_0000120

balance
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
subclass of: Restriction
  on property: has function
  some values from: measure function
disjoint with: surface plasmon resonance instrument
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135
disjoint with: OBI_0400137
disjoint with: OBI_0400140
disjoint with: OBI_0400142
disjoint with: OBI_0400146
disjoint with: OBI_0400147
disjoint with: OBI_0400153
disjoint with: OBI_0400158
disjoint with: OBI_0400168
disjoint with: OBI_0400169
disjoint with: OBI_0400170
disjoint with: OBI_0400171
definition: A measuring instrument that is used to determine the weight or mass of an object.
term editor: PERSON: Erik Segerdell
editor preferred term: balance
definition source: http://en.wikipedia.org/wiki/Weighing_scale
has curation status: IAO_0000120

surface plasmon resonance instrument
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
disjoint with: protein sequencer
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135
disjoint with: OBI_0400137
disjoint with: OBI_0400140
disjoint with: OBI_0400142
disjoint with: OBI_0400146
disjoint with: OBI_0400147
disjoint with: OBI_0400153
disjoint with: OBI_0400158
disjoint with: OBI_0400168
disjoint with: OBI_0400169
disjoint with: OBI_0400170
disjoint with: OBI_0400171
definition: A tool for measuring adsorption of material onto planar metal (typically gold and silver) surfaces or onto the surface of metal nanoparticles.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Surface_plasmon_resonance
editor preferred term: surface plasmon resonance instrument
has curation status: IAO_0000120

protein sequencer
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
disjoint with: X-ray source
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135
disjoint with: OBI_0400137
disjoint with: OBI_0400140
disjoint with: OBI_0400142
disjoint with: OBI_0400146
disjoint with: OBI_0400147
disjoint with: OBI_0400153
disjoint with: OBI_0400158
disjoint with: OBI_0400168
disjoint with: OBI_0400169
disjoint with: OBI_0400170
disjoint with: OBI_0400171
definition: An device that is used to determine the order of amino acids in protein sequences.
definition source: PERSON: Erik Segerdell
term editor: PERSON: Erik Segerdell
editor preferred term: protein sequencer
has curation status: IAO_0000120

X-ray source
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: excitation function
disjoint with: OBI_0400007
disjoint with: OBI_0400008
disjoint with: OBI_0400019
disjoint with: OBI_0400032
disjoint with: OBI_0400043
disjoint with: OBI_0400045
disjoint with: OBI_0400065
disjoint with: OBI_0400078
disjoint with: OBI_0400079
disjoint with: OBI_0400080
disjoint with: OBI_0400082
disjoint with: OBI_0400084
disjoint with: OBI_0400086
disjoint with: OBI_0400094
disjoint with: OBI_0400099
disjoint with: OBI_0400100
disjoint with: OBI_0400101
disjoint with: OBI_0400102
disjoint with: OBI_0400103
disjoint with: OBI_0400104
disjoint with: OBI_0400105
disjoint with: OBI_0400106
disjoint with: OBI_0400107
disjoint with: OBI_0400108
disjoint with: OBI_0400109
disjoint with: OBI_0400110
disjoint with: OBI_0400112
disjoint with: OBI_0400113
disjoint with: OBI_0400114
disjoint with: OBI_0400115
disjoint with: OBI_0400116
disjoint with: OBI_0400117
disjoint with: OBI_0400118
disjoint with: OBI_0400119
disjoint with: OBI_0400120
disjoint with: OBI_0400121
disjoint with: OBI_0400135
disjoint with: OBI_0400137
disjoint with: OBI_0400140
disjoint with: OBI_0400142
disjoint with: OBI_0400146
disjoint with: OBI_0400147
disjoint with: OBI_0400153
disjoint with: OBI_0400158
disjoint with: OBI_0400168
disjoint with: OBI_0400169
disjoint with: OBI_0400170
disjoint with: OBI_0400171
definition: A device that is used to generate X-rays.
term editor: PERSON: Erik Segerdell
editor preferred term: X-ray source
definition source: http://en.wikipedia.org/wiki/X-ray_generator
alternative term: x-ray generator
has curation status: IAO_0000120

liquid chromatography instrument
type: Class
subclass of: chromatography device
definition: A chromatography device that dissolves a mixture in liquid mobile phase to separate the analyte to be measured from other molecules in the mixture and allows it to be isolated
term editor: PERSON: Matthew Brush
definition source: PERSON: Matthew Brush
editor preferred term: liquid chromatography instrument
has curation status: IAO_0000120

spike-in quality control role
type: Class
subclass of: reference substance role
disjoint with: dye swap quality control role
definition source: MO_937 spike_quality_control
term editor: PERSON: Chris Stoeckert, Jie Zheng, Bjoern Peter
definition: a reference substance role that is borne by a material entity with a known amount which is mixed into the evaluant of assays for quality control or data normalization purposes
editor preferred term: spike-in quality control role
has curation status: IAO_0000120

individual organism identifier
type: Class
subclass of: CRID symbol
subclass of: Restriction
  on property: denotes
  all values from: OBI_0100026
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: MO_169 Individual
definition: a CRID symbol used to distinguish one individual organism from another.
editor preferred term: individual organism identifier
has curation status: IAO_0000120

dye swap quality control role
type: Class
subclass of: reference substance role
subclass of: Restriction
  on property: inheres in
  some values from: labeled nucleic acid extract
definition source: MO_524 dye_swap_quality_control
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition: a reference substance role that is borne by a material entity used in a dye swap design experiment for quality control or data normalization purposes
editor preferred term: dye swap quality control role
has curation status: IAO_0000120

labeled nucleic acid extract
type: Class
subclass of: labeled specimen
subclass of: Restriction
  on property: has grain
  some values from: nucleic acid
subclass of: Class
  intersection of: Restriction
    on property: has role
    some values from: specimen role
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: Class
      intersection of: OBI_0600038
      intersection of: Restriction
        on property: has_specified_input
        some values from: nucleic acid extract
definition source: MO_221 labeledExtract
term editor: Person: Jie Zheng
definition: a labeled specimen that is the output of a labeling process and has grain labeled nucleic acid for detection of the nucleic acid in future experiments.
alternative term: labeled extract
editor preferred term: labeled nucleic acid extract
has curation status: IAO_0000120

binding constant
type: Class
equivalent class: Class
  union of: OBI_0001536
  union of: OBI_0001548
  union of: OBI_0001571
  union of: OBI_0001581
  union of: OBI_0001583
  union of: OBI_0001603
  union of: OBI_0001605
subclass of: binding datum
editor note: 10/6/11 BP: The distinction between binding datum and binding constant is based on the later being part of an equation. That should be captured in the logical definition here, and used to make it to a defined class.
definition: A binding datum about the disposition of two or more material entities to form complexes which comes in the form of a scalar and unit that are utilized in equations that model the binding process
term editor: PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum
example of usage: The predicted or measured binding affinity of a peptide to a MHC molecule can be captured in the binding constants "IC50 = 12 nM" or "t 1/2 = 30 minutes".
editor preferred term: binding constant
has curation status: IAO_0000123

binding complex 3D structure determination assay
type: Class
equivalent class: Class
  intersection of: OBI_0600045
  intersection of: Restriction
    on property: has_specified_output
    some values from: 3D structural organization datum
  intersection of: Restriction
    on property: has_specified_output
    some values from: binding datum
subclass of: binding assay
subclass of: OBI_0600045
definition: A 3D structure determination assay in which a complex of 2 or more material enties is characterized which provides information on their mode of binding.
example of usage: Determination of a 3D structure of an antibody binding a protein by X-Ray crystallography, which identifies the specific binding site of the antibody.
editor preferred term: binding complex 3D structure determination assay
has curation status: IAO_0000125

binding assay
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: binding datum
subclass of: assay
subclass of: Restriction
  on property: has_specified_output
  some values from: binding datum
example of usage: Determination of KD value for an antibody binding a protein using a BIACORE assay. Using plate bound antigen in an ELISA to determine if a mixture of serum antibodies bind the antigen. The following are NOT binding assays, as the desired output is not binding data: RNA microarray experiments to determine levels of gene expression. ChIP experiments to determine where in DNA a transcription factor binds. Using an IL-2 antibody on an ELISA plate to determine presence of IL-2 after stimulating a T cell culture.
definition: An assay with the objective to characterize the disposition of two or more material entities to form a complex.
term editor: PERSON:Bjoern Peters, Randi Vita, Jason Greenbaum
editor preferred term: binding assay
has curation status: IAO_0000123

cell culture expansion
type: Class
subclass of: material processing
subclass of: Class
  intersection of: Restriction
    on property: has_specified_input
    some values from: OBI_0100060
  intersection of: Restriction
    on property: has_specified_output
    some values from: OBI_0100060
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
curator note: BP: add it as subclass of 'cell culturing' JZ: No 'cell culturing' in OBI Has term 'cell co-culturing' and 'maintaining cell culture'. Don't think either of it fit. So leave the term under process.
definition source: MO_758 grow
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition: a processual entity that results in the increase of cell numbers
editor preferred term: cell culture expansion
editor note: including grow of yeast and bacteria
has curation status: IAO_0000120

gene knock out
type: Class
subclass of: OBI_0600043
disjoint with: gene knock in
disjoint with: chromosomal substitution
disjoint with: transfection
disjoint with: induced mutation
disjoint with: OBI_0600059
definition source: MO_771 gene_knock_out
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition: a genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods.
editor preferred term: gene knock out
has curation status: IAO_0000120

gene knock in
type: Class
subclass of: OBI_0600043
disjoint with: chromosomal substitution
disjoint with: transfection
disjoint with: induced mutation
disjoint with: OBI_0600059
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: MO_437 gene_knock_in
definition source: WEB: http://en.wikipedia.org/wiki/Gene_Knock-in
definition: a genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a "targeted" insertion.
editor preferred term: gene knock in
has curation status: IAO_0000120

chromosomal substitution
type: Class
subclass of: OBI_0600043
disjoint with: transfection
disjoint with: induced mutation
disjoint with: OBI_0600059
definition: A genetic transformation in which all, or part, of a chromosome from a donor replaces that of the recipient. It does not include chromosome recombination. For single gene insertion, use the term 'gene knock in'.
definition source: MO_995 chromosomal_substitution
term editor: PERSON: Chris Stoeckert, Jie Zheng
editor preferred term: chromosomal substitution
has curation status: IAO_0000120

genetically modified material
type: Class
equivalent class: Class
  union of: OBI_0302859
  union of: Class
    intersection of: cell
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: OBI_0600043
subclass of: processed material
definition source: GROUP: OBI
term editor: PERSON: Jie Zheng
definition: a material entity, organism or cell, that is the output of a genetic transformation process.
editor preferred term: genetically modified material
curator note: term is proposed by BP on Oct 25, 2010 dev call
has curation status: IAO_0000120

transfection
type: Class
subclass of: OBI_0600043
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: Class
      union of: deoxyribonucleic acids
      union of: ribonucleic acids
    intersection of: Restriction
      on property: is bearer of
      some values from: target of material addition role
subclass of: Restriction
  on property: has part
  some values from: OBI_0600033
disjoint with: induced mutation
disjoint with: OBI_0600059
definition source: MO_366 transfection
editor preferred term: transfection
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition: a genetic transformation which relies on the use of physical, electrical and chemical phenomena to introduce DNA or RNA into a cell
has curation status: IAO_0000120

genetic transformation objective
type: Class
subclass of: material transformation objective
curator note: suggested to be added by BP and AR during Oct 25, 2010 dev call
term editor: Person: Jie Zheng
definition source: Person: Jie Zheng
definition: a material transformation objective aims to create genetically modified organism or cell
editor preferred term: genetic transformation objective
has curation status: IAO_0000120

induced mutation
type: Class
subclass of: OBI_0600043
disjoint with: OBI_0600059
definition source: MO_564 induced_mutation
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition: a genetic transformation that the modification of the genetic material (either coding or non-coding) of an organism is caused by mutagenic compounds or irradiation.
editor preferred term: induced mutation
has curation status: IAO_0000120

3D structural organization datum
type: Class
subclass of: measurement datum
editor preferred term: 3D structural organization datum
definition: A measurement datum that describes the structural orientation of a material entity in 3D space.
term editor: PERSON: Jason Greenbaum, Randi Vita, Bjoern Peters
example of usage: The atom coordinates found in a PDB (Protein Data Bank) file, generated by X Ray crystallography or NMR.
has curation status: IAO_0000123

age since planting measurement datum
type: Class
subclass of: age measurement datum
disjoint with: age since hatching measurement datum
disjoint with: age since egg laying measurement datum
disjoint with: age since germination measurement datum
disjoint with: age since eclosion measurement datum
disjoint with: age since sowing measurement datum
disjoint with: age since coitus measurement datum
disjoint with: age since fertilization measurement datum
disjoint with: age since birth measurement datum
definition: An age measurement datum that is the result of the measurement of the age of an organism since planting, the process of placing a plant in media (e.g. soil) to allow it to grow, which excludes sowing.
curator note: Discussed by Jie and Chris, proposed to combine with different kinds of processes as initial time point. Proposed 'age measurement assay' is proceeded by some process. The process can be any kind of process defined in OBI. Think it is more flexible. However, it is hard to model due to lake of temporal predicates on Nov 15, 2010 dev call. Term proposed by Bjoern on Nov 8, 2010 dev call Supported by Alan on Nov 15, 2010 dev call
definition source: MO_495 planting
term editor: PERSON:Chris Stoeckert, Jie Zheng
editor preferred term: age since planting measurement datum
has curation status: IAO_0000120

age since hatching measurement datum
type: Class
subclass of: age measurement datum
disjoint with: age since egg laying measurement datum
disjoint with: age since germination measurement datum
disjoint with: age since eclosion measurement datum
disjoint with: age since sowing measurement datum
disjoint with: age since coitus measurement datum
disjoint with: age since fertilization measurement datum
disjoint with: age since birth measurement datum
definition: An age measurement datum that is the result of the measurement of the age of an organism since hatching, the process of emergence from an egg.
definition source: MO_745 hatching
term editor: PERSON:Chris Stoeckert, Jie Zheng
editor preferred term: age since hatching measurement datum
has curation status: IAO_0000120

age measurement assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has_specified_output
  some values from: age measurement datum
definition: An assay that measures the duration of temporal interval of a process that is part of the life of the bearer, where the initial time point of the measured process is the beginning of some transitional state of the bearer such as birth or when planted.
definition source: OBI group
term editor: PERSON: Alan Ruttenberg
editor note: This assay measures time not developmental stage. we recognize that development takes different time periods under different conditions such as media / temperature. For example, age measurement assay of fly age, the output likes 28 days but not mid-life of age at room temperature.
editor preferred term: age measurement assay
has curation status: IAO_0000120

age since egg laying measurement datum
type: Class
subclass of: age measurement datum
disjoint with: age since germination measurement datum
disjoint with: age since eclosion measurement datum
disjoint with: age since sowing measurement datum
disjoint with: age since coitus measurement datum
disjoint with: age since fertilization measurement datum
disjoint with: age since birth measurement datum
definition: An age measurement datum that is the result of the measurement of the age of an organism since egg laying, the process of the production of egg(s) by an organism.
definition source: MO_767 egg laying
term editor: PERSON:Chris Stoeckert, Jie Zheng
editor preferred term: age since egg laying measurement datum
has curation status: IAO_0000120

assay validation objective
type: Class
subclass of: objective specification
disjoint with: selective organism creation objective
disjoint with: OBI_0200166
definition source: GROUP: Penn Group
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition: an objective specification to check the accuracy or the quality of the results of an assay by comparison with independent results
editor preferred term: assay validation objective
has curation status: IAO_0000120

age since germination measurement datum
type: Class
subclass of: age measurement datum
disjoint with: age since eclosion measurement datum
disjoint with: age since sowing measurement datum
disjoint with: age since coitus measurement datum
disjoint with: age since fertilization measurement datum
disjoint with: age since birth measurement datum
definition: An age measurement datum that is the result of the measurement of the age of an organism since germination, the process consisting of physiological and developmental changes by a seed, spore, pollen grain (microspore), or zygote that occur after release from dormancy, and encompassing events prior to and including the first visible indications of growth.
editor note: Definition of germination comes from GO. However, the term is deprecated from GO now because it is a grouping term without biological significance.
definition source: MO_590 germination
term editor: PERSON:Chris Stoeckert, Jie Zheng
editor preferred term: age since germination measurement datum
has curation status: IAO_0000120

validation by reverse transcription PCR design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: assay validation objective
    intersection of: Restriction
      on property: objective_achieved_by
      some values from: reverse transcription polymerase chain reaction assay
disjoint with: validation by real time PCR design
disjoint with: operator variation design
disjoint with: comparative genome hybridization by array design
disjoint with: in vivo design
disjoint with: innate behavior design
disjoint with: cell component comparison design
disjoint with: ex vivo design
disjoint with: normalization testing design
disjoint with: environmental history design
disjoint with: transcription profiling by high thoughput sequencing design
disjoint with: array platform variation design
disjoint with: ChIP-seq design
disjoint with: translational bias design
disjoint with: DNA methylation profiling by array design
disjoint with: in vitro design
disjoint with: RNAi profiling by array design
disjoint with: transcription profiling by array design
disjoint with: disease state design
disjoint with: RNA stability design
disjoint with: species comparison design
disjoint with: transcription profiling by RT-PCR design
disjoint with: microRNA profiling by array design
disjoint with: organism development design
disjoint with: family history design
disjoint with: quality control testing design
disjoint with: clinical history design
disjoint with: OBI_0001358
disjoint with: OBI_0001365
disjoint with: OBI_0001374
disjoint with: OBI_0001377
disjoint with: OBI_0001396
disjoint with: OBI_0001401
disjoint with: OBI_0001403
disjoint with: OBI_0001408
disjoint with: OBI_0001409
disjoint with: OBI_0001410
disjoint with: OBI_0001411
disjoint with: OBI_0001418
disjoint with: OBI_0001422
disjoint with: OBI_0001426
disjoint with: OBI_0001427
disjoint with: OBI_0001429
disjoint with: OBI_0001432
disjoint with: OBI_0001435
disjoint with: OBI_0001440
disjoint with: OBI_0001441
disjoint with: OBI_0001444
disjoint with: OBI_0001448
disjoint with: OBI_0001454
disjoint with: OBI_0001460
disjoint with: OBI_0001464
disjoint with: OBI_0300311
disjoint with: OBI_0500001
disjoint with: OBI_0500005
disjoint with: OBI_0500006
disjoint with: OBI_0500009
disjoint with: OBI_0500010
disjoint with: OBI_0500017
disjoint with: OBI_0500018
disjoint with: OBI_0500019
disjoint with: OBI_0500020
definition source: MO_986 reverse_transcription_PCR_quality_control
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition: a study design in which checks the accuracy or the quality of the result of an assay by comparing with reverse transcription PCR results
editor preferred term: validation by reverse transcription PCR design
has curation status: IAO_0000120

age since eclosion measurement datum
type: Class
subclass of: age measurement datum
disjoint with: age since sowing measurement datum
disjoint with: age since coitus measurement datum
disjoint with: age since fertilization measurement datum
disjoint with: age since birth measurement datum
definition: An age measurement datum that is the result of the measurement of the age of an organism since eclosion, the process of emergence of an adult insect from its pupa or cocoon.
definition source: MO_876 eclosion
term editor: PERSON:Chris Stoeckert, Jie Zheng
editor preferred term: age since eclosion measurement datum
has curation status: IAO_0000120

age since sowing measurement datum
type: Class
subclass of: age measurement datum
disjoint with: age since coitus measurement datum
disjoint with: age since fertilization measurement datum
disjoint with: age since birth measurement datum
definition: An age measurement datum that is the result of the measurement of the age of an organism since sowing, the process of placing a seed or spore in some media with the intention to invoke germination.
definition source: MO_748 sowing
term editor: PERSON:Chris Stoeckert, Jie Zheng
editor preferred term: age since sowing measurement datum
has curation status: IAO_0000120

age since coitus measurement datum
type: Class
subclass of: age measurement datum
disjoint with: age since fertilization measurement datum
disjoint with: age since birth measurement datum
definition: An age measurement datum that is the result of the measurement of the age of an organism since coitus, the process of copulation that occurs during the process of sexual reproduction.
definition source: MO_783 coitus
term editor: PERSON:Chris Stoeckert, Jie Zheng
editor preferred term: age since coitus measurement datum
has curation status: IAO_0000120

validation by real time PCR design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: assay validation objective
    intersection of: Restriction
      on property: objective_achieved_by
      some values from: real time polymerase chain reaction assay
disjoint with: operator variation design
disjoint with: comparative genome hybridization by array design
disjoint with: in vivo design
disjoint with: innate behavior design
disjoint with: cell component comparison design
disjoint with: ex vivo design
disjoint with: normalization testing design
disjoint with: environmental history design
disjoint with: transcription profiling by high thoughput sequencing design
disjoint with: array platform variation design
disjoint with: ChIP-seq design
disjoint with: translational bias design
disjoint with: DNA methylation profiling by array design
disjoint with: in vitro design
disjoint with: RNAi profiling by array design
disjoint with: transcription profiling by array design
disjoint with: disease state design
disjoint with: RNA stability design
disjoint with: species comparison design
disjoint with: transcription profiling by RT-PCR design
disjoint with: microRNA profiling by array design
disjoint with: organism development design
disjoint with: family history design
disjoint with: quality control testing design
disjoint with: clinical history design
disjoint with: OBI_0001358
disjoint with: OBI_0001365
disjoint with: OBI_0001374
disjoint with: OBI_0001377
disjoint with: OBI_0001396
disjoint with: OBI_0001401
disjoint with: OBI_0001403
disjoint with: OBI_0001408
disjoint with: OBI_0001409
disjoint with: OBI_0001410
disjoint with: OBI_0001411
disjoint with: OBI_0001418
disjoint with: OBI_0001422
disjoint with: OBI_0001426
disjoint with: OBI_0001427
disjoint with: OBI_0001429
disjoint with: OBI_0001432
disjoint with: OBI_0001435
disjoint with: OBI_0001440
disjoint with: OBI_0001441
disjoint with: OBI_0001444
disjoint with: OBI_0001448
disjoint with: OBI_0001454
disjoint with: OBI_0001460
disjoint with: OBI_0001464
disjoint with: OBI_0300311
disjoint with: OBI_0500001
disjoint with: OBI_0500005
disjoint with: OBI_0500006
disjoint with: OBI_0500009
disjoint with: OBI_0500010
disjoint with: OBI_0500017
disjoint with: OBI_0500018
disjoint with: OBI_0500019
disjoint with: OBI_0500020
definition source: MO_434 real_time_PCR_quality_control
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition: a study design in which the accuracy or the quality of the result of an assay is checked by comparing with real time PCR results
editor preferred term: validation by real time PCR design
has curation status: IAO_0000120

age measurement datum
type: Class
subclass of: time measurement datum
subclass of: Restriction
  on property: is_specified_output_of
  some values from: age measurement assay
subclass of: Restriction
  on property: is quality measurement of
  some values from: PATO_0000011
disjoint with: half life datum (t 1/2)
disjoint with: OBI_0001508
definition: A time measurement datum that is the result of measurement of age of an organism
curator note: In MageTab file, we use initialTimePoint (a process) + age (a number expected) + TimeUnit (definied in UO, such as year, hour, day, etc.) Now we use the term label indicating the start time point of measuring the age, (number + TimeUnit) are expected instances of the class
definition source: MO_178 Age
term editor: PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng
curator note: discussed on Nov 15, dev call All subtype will be defined by textual definition now.
editor note: note that we are currently defining subtypes of age measurement datum that specify when the age is relative to, e.g. planting, as we don't have adequate temporal predicates yet. life of bearer doesn't imply organism this assay measures time not developmental stage. we recognize that development can take different time periods under different conditions such as media / temperature age as a quality is dubious; we plan to revisit stages in development are currently handled with controlled vocabulary, such as 2-somite stage
editor preferred term: age measurement datum
has curation status: IAO_0000120

age since fertilization measurement datum
type: Class
subclass of: age measurement datum
disjoint with: age since birth measurement datum
definition: An age measurement datum that is the result of the measurement of the age of an organism since fertilization, the process of the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote.
editor note: Definition of fertilization comes from GO.
definition source: MO_701 fertilization
term editor: PERSON:Chris Stoeckert, Jie Zheng
editor preferred term: age since fertilization measurement datum
has curation status: IAO_0000120

age since birth measurement datum
type: Class
subclass of: age measurement datum
definition: An age measurement datum that is the result of the measurement of the age of an organism since birth, the process of emergence and separation of offspring from the mother.
definition source: MO_710 birth
term editor: PERSON:Chris Stoeckert, Jie Zheng
editor preferred term: age since birth measurement datum
has curation status: IAO_0000120

reverse transcription polymerase chain reaction assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: ribonucleic acids
    intersection of: Restriction
      on property: has role
      some values from: evaluant role
subclass of: Restriction
  on property: has part
  some values from: reverse transcribed polymerase chain reaction
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: information content entity
    intersection of: Restriction
      on property: is about
      some values from: gene expression
definition source: GROUP: Penn Group
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition: an assay that evaluates the concentration of RNA in a sample in which an RNA strand is first reverse transcribed into its DNA complement (complementary DNA, or cDNA) using the enzyme reverse transcriptase, and the resulting cDNA is amplified using traditional or real-time PCR.
editor preferred term: reverse transcription polymerase chain reaction assay
has curation status: IAO_0000120

half life datum (t 1/2)
type: Class
subclass of: time measurement datum
subclass of: Restriction
  on property: has measurement unit label
  some values from: UO_0000003
disjoint with: OBI_0001508
definition source: Bjoern Peters
term editor: Bjoern Peters
definition: The time it takes for 50% of a class of stochastic processes to occur.
editor preferred term: half life datum (t 1/2)
alternative term: t 1/2
has curation status: IAO_0000120

dose response curve
type: Class
subclass of: line graph
disjoint with: OBI_0001404
definition: A data item of paired values, one indicating the dose of a material, the other quantitating a measured effect at that dose. The dosing intervals are chosen so that effect values be interpolated by a plotting a curve.
term editor: Bjoern Peters; Randi Vita
editor preferred term: dose response curve
has curation status: IAO_0000120

service
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: service consumer role
    intersection of: Restriction
      on property: realizes
      some values from: service provider role
subclass of: planned process
subclass of: Restriction
  on property: has part
  some values from: planned process
definition: A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer.
term editor: Carlo; Matt
definition source: OBI workshop San Diego 2011
example of usage: providing a training course for UCSD employees how to run a DNA sequencer; sequencing a DNA sample provided by a service consumer restricted to non-human samples; giving access to tissue samples in a biobank within OHSU; JAX shipping mice from their colony
editor preferred term: service
has curation status: IAO_0000120

passive immunization
type: Class
subclass of: OBI_0600007
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: material to be added role
    intersection of: Restriction
      on property: inheres in
      some values from: OBI_1110022
example of usage: Giving VIG (concentrated antibodies from vaccinated donors) to a patient that is infected with smallpox. Transferring epitope specific T cells from one mouse into another.
term editor: PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum
definition: The injection of immune effector material (antibodies, T cells or B cells) into an organism so that the organisms immune system gains its immune effector function to recognize specific antigens.
alternative term: adoptive transfer
editor preferred term: passive immunization
has curation status: IAO_0000122

selective organism creation objective
type: Class
subclass of: objective specification
disjoint with: OBI_0200166
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: WEB: wikipedia http://en.wikipedia.org/wiki/Cultivar http://en.wikipedia.org/wiki/Ecotype http://en.wikipedia.org/wiki/Strain_%28biology%29
definition: an objective specification to generate a population or type of organism within species that have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms.
editor preferred term: selective organism creation objective
has curation status: IAO_0000120

Individual epitope immunization in vivo
type: Class
subclass of: OBI_1110015
editor note: 3/16/11 BP: This should have as a logical definition the exclusion that the immunogen cannot be something beyond the epitope itself. I don't know if that is possible to do here.
definition: An immunization in which an individual epitope is administered into a host organism.
editor preferred term: Individual epitope immunization in vivo
example of usage: Injection of a peptide T cell epitope into a mouse
term editor: PERSON:Bjoern Peters, Jason Greenbaum, Randi Vita
has curation status: IAO_0000120

RNA sequencing
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has_specified_input
    some values from: Class
      intersection of: ribonucleic acids
      intersection of: Restriction
        on property: has role
        some values from: evaluant role
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: information content entity
      intersection of: Restriction
        on property: is about
        some values from: primary structure of RNA molecule
subclass of: OBI_0600047
editor note: BP 12/21:Created based on a request from Melanie
definition source: Bjoern Peters
term editor: Bjoern Peters
editor preferred term: RNA sequencing
definition: RNA sequencing is a sequencing process which uses ribonucleic acid as input and results in a the creation of RNA sequence information artifact
has curation status: IAO_0000120

efficacy of epitope intervention experiment
type: Class
subclass of: assay
subclass of: Restriction
  on property: has part
  some values from: epitope specific immune intervention
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: OBI_1110001
definition: An experiment that tests if inducing an epitope specific immune response in an organism has an effect, such as the ability to prevent, treat or excarbate diseases in the organism.
term editor: Bjoern Peters
editor preferred term: efficacy of epitope intervention experiment
has curation status: IAO_0000120

epitope protection from infectious challenge experiment
type: Class
subclass of: epitope protection experiment
subclass of: Restriction
  on property: has part
  some values from: pathogen challenge
disjoint with: epitope protection from tumor challenge experiment
disjoint with: epitope protection experiment based on survival
definition: An epitope protection experiment in which the ability of the epitope to protect the host from an infection is assessed.
term editor: Bjoern Peters
editor preferred term: epitope protection from infectious challenge experiment
has curation status: IAO_0000120

half maximal effective concentration (EC50)
type: Class
subclass of: scalar measurement datum
subclass of: Restriction
  on property: has measurement unit label
  some values from: UO_0000051
subclass of: Restriction
  on property: is about
  some values from: dose response curve
disjoint with: half maximal inhibitory concentration (IC50)
disjoint with: OBI_0001554
term editor: Bjoern Peters; Randi Vita
example of usage: Determining the potentency of a drug / antibody / toxicant by measuring a graded dose response curve, and determining the concentration of the compound where 50% of its maximal effect is observed.
editor preferred term: half maximal effective concentration (EC50)
definition: half maximal effective concentration (EC50) is a scalar measurement datum corresponding to the concentration of a compound which induces a response halfway between the baseline and maximum after some specified exposure time.
definition source: wikipedia
has curation status: IAO_0000120

binding datum
type: Class
equivalent class: Class
  intersection of: data item
  intersection of: Restriction
    on property: is about
    some values from: OBI_0001588
subclass of: data item
definition: A data item that states if two or more material entities have the disposition to form a complex, and if so, how strong that disposition is.
term editor: Bjoern Peters; Randi Vita
editor preferred term: binding datum
has curation status: IAO_0000120

negative binding datum
type: Class
subclass of: binding datum
definition: A binding datum that states that there is no significant disposition of two or more entities to form a complex
editor preferred term: negative binding datum
has curation status: IAO_0000123

epitope protection from tumor challenge experiment
type: Class
subclass of: epitope protection experiment
disjoint with: epitope protection experiment based on survival
definition: An epitope protection experiment in which the ability of the epitope to protect the host from developing tumors is assessed.
term editor: Bjoern Peters
editor preferred term: epitope protection from tumor challenge experiment
has curation status: IAO_0000120

epitope protection experiment
type: Class
subclass of: efficacy of epitope intervention experiment
disjoint with: epitope disease exacerbation experiment
disjoint with: epitope treatment experiment
disjoint with: OBI_0001488
term editor: Bjoern Peters
definition: an epitope intervention experiment that tests the efficacy of inducing an immune epitope response to prevent disease in a host.
editor preferred term: epitope protection experiment
has curation status: IAO_0000120

selectively maintained organism
type: Class
equivalent class: Class
  intersection of: OBI_0100026
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: Class
      intersection of: planned process
      intersection of: Restriction
        on property: achieves_planned_objective
        some values from: selective organism creation objective
subclass of: OBI_0100026
definition: An organism that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms
term editor: Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Jie Zheng, Chris Stoeckert
definition source: MO_9 StrainOrLine, MO_71 Ecotype, MO_124 Cultivar
alternative term: cultivar
alternative term: ecotype
alternative term: strain
editor preferred term: selectively maintained organism
has curation status: IAO_0000120

epitope protection from infectious challenge experiment based on pathogen burden
type: Class
subclass of: epitope protection from infectious challenge experiment
subclass of: Restriction
  on property: has part
  some values from: infectious agent detection assay
definition: An epitope protection from infectious challenge experiment in which the readout is a reduction in the presence of pathogens in the host compared to controls.
term editor: Bjoern Peters
editor preferred term: epitope protection from infectious challenge experiment based on pathogen burden
has curation status: IAO_0000120

infectious agent detection assay
type: Class
subclass of: assay
editor note: 2/22/2011, BP: This should probably be an analyte assay, but the logical definition of those is currently restricted to 'scattered molecular aggregates', which excludes using infectious agents as analytes. See below (realizes some ('evaluant role' and (role_of some material_entity))) and (realizes some ('analyte role' and (role_of some 'infectious agent'))) and (achieves_planned_objective some 'analyte measurement objective')
definition: An assay in which the presence or amount of an infectious agent in an input material is detected in an evaluant
term editor: Bjoern Peters, Randi Vita, Jason Greenbaum
example of usage: Culturing a sputum sample on agar medium to detect bacterial growth; Stain slices of liver from a mouse to count presence of infectious centers.
editor preferred term: infectious agent detection assay
has curation status: IAO_0000120

epitope disease exacerbation experiment
type: Class
subclass of: efficacy of epitope intervention experiment
disjoint with: epitope treatment experiment
disjoint with: OBI_0001488
term editor: Bjoern Peters
definition: an epitope intervention experiment that tests the ability of inducing an epitope immune response to increase the severity of an existing disease in the host.
editor preferred term: epitope disease exacerbation experiment
has curation status: IAO_0000120

epitope protection experiment based on survival
type: Class
subclass of: epitope protection experiment
subclass of: Restriction
  on property: has part
  some values from: survival assessment
term editor: Bjoern Peters
definition: an epitope protection experiment that determines the success of the epitope intervention based on increased survival of the host.
editor preferred term: epitope protection experiment based on survival
has curation status: IAO_0000120

epitope treatment experiment
type: Class
subclass of: efficacy of epitope intervention experiment
disjoint with: OBI_0001488
term editor: Bjoern Peters
definition: an epitope intervention experiment that tests the ability of inducing an epitope immune response to treat an existing disease in the host.
editor preferred term: epitope treatment experiment
has curation status: IAO_0000120

half maximal inhibitory concentration (IC50)
type: Class
subclass of: scalar measurement datum
subclass of: Restriction
  on property: has measurement unit label
  some values from: UO_0000051
subclass of: Restriction
  on property: is about
  some values from: dose response curve
disjoint with: OBI_0001554
term editor: Bjoern Peters; Randi Vita
definition: Half maximal inhibitory concentration (IC50) is a scalar measurement datum that measures the effectiveness of a compound to competitively inhibit a given process, and corresponds to the concentration of the compound at which it reaches half of its maximum inhibitory effect.
example of usage: Interpolating that at a dose of IC50=12 nM, half of the binding of a comptetitive ligand is inhibited.
editor preferred term: half maximal inhibitory concentration (IC50)
definition source: wikipedia
has curation status: IAO_0000120

epitope specific immune intervention
type: Class
subclass of: passive immunization
subclass of: Class
  union of: passive immunization
  union of: Individual epitope immunization in vivo
definition: An administration in vivo to either actively or passively immunize an organism in order to induce a response against a specific immune epitope
term editor: Person: Bjoern Peters, Randi Vita, Jason Greenbaum
editor preferred term: epitope specific immune intervention
has curation status: IAO_0000120

epitope specific cytokine production by T cells
type: Class
equivalent class: Class
  intersection of: cytokine production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: cytokine production
definition: A process of cytokine production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific cytokine production by T cells
has curation status: IAO_0000122

ELISPOT assay of epitope specific transforming growth factor-beta production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0600031
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: epitope specific transforming growth factor-beta production by T cells
subclass of: assay of epitope specific transforming growth factor-beta production by T cells
subclass of: OBI_0600031
definition: An ELISPOT assay that measures epitope specific transforming growth factor-beta production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
editor preferred term: ELISPOT assay of epitope specific transforming growth factor-beta production by T cells
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000122

operator variation design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: independent variable specification
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: Homo sapiens
        intersection of: Restriction
disjoint with: comparative genome hybridization by array design
disjoint with: in vivo design
disjoint with: innate behavior design
disjoint with: cell component comparison design
disjoint with: ex vivo design
disjoint with: normalization testing design
disjoint with: environmental history design
disjoint with: transcription profiling by high thoughput sequencing design
disjoint with: array platform variation design
disjoint with: ChIP-seq design
disjoint with: translational bias design
disjoint with: DNA methylation profiling by array design
disjoint with: in vitro design
disjoint with: RNAi profiling by array design
disjoint with: transcription profiling by array design
disjoint with: disease state design
disjoint with: RNA stability design
disjoint with: species comparison design
disjoint with: transcription profiling by RT-PCR design
disjoint with: microRNA profiling by array design
disjoint with: organism development design
disjoint with: family history design
disjoint with: quality control testing design
disjoint with: clinical history design
disjoint with: OBI_0001358
disjoint with: OBI_0001365
disjoint with: OBI_0001374
disjoint with: OBI_0001377
disjoint with: OBI_0001396
disjoint with: OBI_0001401
disjoint with: OBI_0001403
disjoint with: OBI_0001408
disjoint with: OBI_0001409
disjoint with: OBI_0001410
disjoint with: OBI_0001411
disjoint with: OBI_0001418
disjoint with: OBI_0001422
disjoint with: OBI_0001426
disjoint with: OBI_0001427
disjoint with: OBI_0001429
disjoint with: OBI_0001432
disjoint with: OBI_0001435
disjoint with: OBI_0001440
disjoint with: OBI_0001441
disjoint with: OBI_0001444
disjoint with: OBI_0001448
disjoint with: OBI_0001454
disjoint with: OBI_0001460
disjoint with: OBI_0001464
disjoint with: OBI_0300311
disjoint with: OBI_0500001
disjoint with: OBI_0500005
disjoint with: OBI_0500006
disjoint with: OBI_0500009
disjoint with: OBI_0500010
disjoint with: OBI_0500017
disjoint with: OBI_0500018
disjoint with: OBI_0500019
disjoint with: OBI_0500020
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design that assesses the operator performance and relation to data consistency and quality.
definition source: MO_519 operator_variation_design
editor preferred term: operator variation design
has curation status: IAO_0000120

cytometric bead array assay of epitope specific IP-10 production by T cells
type: Class
equivalent class: Class
  intersection of: cytometric bead array assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_0001462
subclass of: cytometric bead array assay
subclass of: assay of epitope specific IP-10 production by T cells
definition: A cytometric bead array assay that measures epitope specific IP-10 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cytometric bead array assay of epitope specific IP-10 production by T cells
has curation status: IAO_0000122

comparative genome hybridization by array design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: molecular feature identification objective
subclass of: Restriction
  on property: is realized by
  all values from: Class
    intersection of: Restriction
      on property: has part
      some values from: OBI_0001393
    intersection of: Restriction
      on property: has participant
      some values from: OBI_0400148
disjoint with: in vivo design
disjoint with: innate behavior design
disjoint with: cell component comparison design
disjoint with: ex vivo design
disjoint with: normalization testing design
disjoint with: environmental history design
disjoint with: transcription profiling by high thoughput sequencing design
disjoint with: array platform variation design
disjoint with: ChIP-seq design
disjoint with: translational bias design
disjoint with: DNA methylation profiling by array design
disjoint with: in vitro design
disjoint with: RNAi profiling by array design
disjoint with: transcription profiling by array design
disjoint with: disease state design
disjoint with: RNA stability design
disjoint with: species comparison design
disjoint with: transcription profiling by RT-PCR design
disjoint with: microRNA profiling by array design
disjoint with: organism development design
disjoint with: family history design
disjoint with: quality control testing design
disjoint with: clinical history design
disjoint with: OBI_0001358
disjoint with: OBI_0001365
disjoint with: OBI_0001374
disjoint with: OBI_0001377
disjoint with: OBI_0001396
disjoint with: OBI_0001401
disjoint with: OBI_0001403
disjoint with: OBI_0001408
disjoint with: OBI_0001409
disjoint with: OBI_0001410
disjoint with: OBI_0001411
disjoint with: OBI_0001418
disjoint with: OBI_0001422
disjoint with: OBI_0001426
disjoint with: OBI_0001427
disjoint with: OBI_0001429
disjoint with: OBI_0001432
disjoint with: OBI_0001435
disjoint with: OBI_0001440
disjoint with: OBI_0001441
disjoint with: OBI_0001444
disjoint with: OBI_0001448
disjoint with: OBI_0001454
disjoint with: OBI_0001460
disjoint with: OBI_0001464
disjoint with: OBI_0300311
disjoint with: OBI_0500001
disjoint with: OBI_0500005
disjoint with: OBI_0500006
disjoint with: OBI_0500009
disjoint with: OBI_0500010
disjoint with: OBI_0500017
disjoint with: OBI_0500018
disjoint with: OBI_0500019
disjoint with: OBI_0500020
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design that detects genomic copy number variations using microarray technology.
definition source: MO_856 comparative_genome_hybridization_design
editor preferred term: comparative genome hybridization by array design
has curation status: IAO_0000120

assay of epitope specific interleukin-27 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: epitope specific interleukin-27 production by T cells
subclass of: OBI_1110129
definition: An assay that measures epitope specific interleukin-27 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: assay of epitope specific interleukin-27 production by T cells
has curation status: IAO_0000122

in vivo design
type: Class
subclass of: OBI_0500000
disjoint with: innate behavior design
disjoint with: cell component comparison design
disjoint with: ex vivo design
disjoint with: normalization testing design
disjoint with: environmental history design
disjoint with: transcription profiling by high thoughput sequencing design
disjoint with: array platform variation design
disjoint with: ChIP-seq design
disjoint with: translational bias design
disjoint with: DNA methylation profiling by array design
disjoint with: in vitro design
disjoint with: RNAi profiling by array design
disjoint with: transcription profiling by array design
disjoint with: disease state design
disjoint with: RNA stability design
disjoint with: species comparison design
disjoint with: transcription profiling by RT-PCR design
disjoint with: microRNA profiling by array design
disjoint with: organism development design
disjoint with: family history design
disjoint with: quality control testing design
disjoint with: clinical history design
disjoint with: OBI_0001358
disjoint with: OBI_0001365
disjoint with: OBI_0001374
disjoint with: OBI_0001377
disjoint with: OBI_0001396
disjoint with: OBI_0001401
disjoint with: OBI_0001403
disjoint with: OBI_0001408
disjoint with: OBI_0001409
disjoint with: OBI_0001410
disjoint with: OBI_0001411
disjoint with: OBI_0001418
disjoint with: OBI_0001422
disjoint with: OBI_0001426
disjoint with: OBI_0001427
disjoint with: OBI_0001429
disjoint with: OBI_0001432
disjoint with: OBI_0001435
disjoint with: OBI_0001440
disjoint with: OBI_0001441
disjoint with: OBI_0001444
disjoint with: OBI_0001448
disjoint with: OBI_0001454
disjoint with: OBI_0001460
disjoint with: OBI_0001464
disjoint with: OBI_0300311
disjoint with: OBI_0500001
disjoint with: OBI_0500005
disjoint with: OBI_0500006
disjoint with: OBI_0500009
disjoint with: OBI_0500010
disjoint with: OBI_0500017
disjoint with: OBI_0500018
disjoint with: OBI_0500019
disjoint with: OBI_0500020
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design that is conducted entirely in a living organism, e.g. a compound treatment in a mouse model.
definition source: MO_454 in_vivo_design
editor preferred term: in vivo design
has curation status: IAO_0000120

genotyping by high throughput sequencing design
type: Class
subclass of: OBI_0001444
subclass of: Restriction
  on property: is realized by
  all values from: Class
    intersection of: Restriction
      on property: has part
      some values from: genotyping by high throughput sequencing assay
    intersection of: Restriction
      on property: has participant
      some values from: OBI_0400103
disjoint with: OBI_0001387
definition source: MO_560 genotyping_design
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using high througput sequencing techniques.
editor preferred term: genotyping by high throughput sequencing design
has curation status: IAO_0000120

epitope specific tolerance induction by T cells
type: Class
equivalent class: Class
  intersection of: tolerance induction
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: tolerance induction
definition: A process of tolerance induction by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific tolerance induction by T cells
has curation status: IAO_0000122

innate behavior design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: organism feature identification objective
disjoint with: cell component comparison design
disjoint with: ex vivo design
disjoint with: normalization testing design
disjoint with: environmental history design
disjoint with: transcription profiling by high thoughput sequencing design
disjoint with: array platform variation design
disjoint with: ChIP-seq design
disjoint with: translational bias design
disjoint with: DNA methylation profiling by array design
disjoint with: in vitro design
disjoint with: RNAi profiling by array design
disjoint with: transcription profiling by array design
disjoint with: disease state design
disjoint with: RNA stability design
disjoint with: species comparison design
disjoint with: transcription profiling by RT-PCR design
disjoint with: microRNA profiling by array design
disjoint with: organism development design
disjoint with: family history design
disjoint with: quality control testing design
disjoint with: clinical history design
disjoint with: OBI_0001358
disjoint with: OBI_0001365
disjoint with: OBI_0001374
disjoint with: OBI_0001377
disjoint with: OBI_0001396
disjoint with: OBI_0001401
disjoint with: OBI_0001403
disjoint with: OBI_0001408
disjoint with: OBI_0001409
disjoint with: OBI_0001410
disjoint with: OBI_0001411
disjoint with: OBI_0001418
disjoint with: OBI_0001422
disjoint with: OBI_0001426
disjoint with: OBI_0001427
disjoint with: OBI_0001429
disjoint with: OBI_0001432
disjoint with: OBI_0001435
disjoint with: OBI_0001440
disjoint with: OBI_0001441
disjoint with: OBI_0001444
disjoint with: OBI_0001448
disjoint with: OBI_0001454
disjoint with: OBI_0001460
disjoint with: OBI_0001464
disjoint with: OBI_0300311
disjoint with: OBI_0500001
disjoint with: OBI_0500005
disjoint with: OBI_0500006
disjoint with: OBI_0500009
disjoint with: OBI_0500010
disjoint with: OBI_0500017
disjoint with: OBI_0500018
disjoint with: OBI_0500019
disjoint with: OBI_0500020
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design in which the innate behavior of the organism is examined, e.g. path finding in bees.
definition source: MO_355 innate_behavior_design
editor preferred term: innate behavior design
has curation status: IAO_0000120

detection of specific nucleic acids with complementary probes of epitope specific transforming growth factor-beta production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acids with complementary probes
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: epitope specific transforming growth factor-beta production by T cells
subclass of: detection of specific nucleic acids with complementary probes
subclass of: assay of epitope specific transforming growth factor-beta production by T cells
definition: A detection of specific nucleic acids with complementary probes that measures epitope specific transforming growth factor-beta production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: detection of specific nucleic acids with complementary probes of epitope specific transforming growth factor-beta production by T cells
has curation status: IAO_0000122

SNP microarray
type: Class
subclass of: OBI_0400148
disjoint with: tiling microarray
definition source: EFO_0002703 SNP array
term editor: Person: Helen Parkinson
definition: a DNA microarray used to detect polymorphisms in DNA samples
editor preferred term: SNP microarray
has curation status: IAO_0000120

cell component comparison design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: independent variable specification
    intersection of: Restriction
      on property: is about
      some values from: cellular_component
subclass of: Restriction
  on property: has part
  some values from: cellular feature identification objective
disjoint with: ex vivo design
disjoint with: normalization testing design
disjoint with: environmental history design
disjoint with: transcription profiling by high thoughput sequencing design
disjoint with: array platform variation design
disjoint with: ChIP-seq design
disjoint with: translational bias design
disjoint with: DNA methylation profiling by array design
disjoint with: in vitro design
disjoint with: RNAi profiling by array design
disjoint with: transcription profiling by array design
disjoint with: disease state design
disjoint with: RNA stability design
disjoint with: species comparison design
disjoint with: transcription profiling by RT-PCR design
disjoint with: microRNA profiling by array design
disjoint with: organism development design
disjoint with: family history design
disjoint with: quality control testing design
disjoint with: clinical history design
disjoint with: OBI_0001358
disjoint with: OBI_0001365
disjoint with: OBI_0001374
disjoint with: OBI_0001377
disjoint with: OBI_0001396
disjoint with: OBI_0001401
disjoint with: OBI_0001403
disjoint with: OBI_0001408
disjoint with: OBI_0001409
disjoint with: OBI_0001410
disjoint with: OBI_0001411
disjoint with: OBI_0001418
disjoint with: OBI_0001422
disjoint with: OBI_0001426
disjoint with: OBI_0001427
disjoint with: OBI_0001429
disjoint with: OBI_0001432
disjoint with: OBI_0001435
disjoint with: OBI_0001440
disjoint with: OBI_0001441
disjoint with: OBI_0001444
disjoint with: OBI_0001448
disjoint with: OBI_0001454
disjoint with: OBI_0001460
disjoint with: OBI_0001464
disjoint with: OBI_0300311
disjoint with: OBI_0500001
disjoint with: OBI_0500005
disjoint with: OBI_0500006
disjoint with: OBI_0500009
disjoint with: OBI_0500010
disjoint with: OBI_0500017
disjoint with: OBI_0500018
disjoint with: OBI_0500019
disjoint with: OBI_0500020
definition: A study design that compares samples from different cell components.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_1019 cell_component_comparison_design
editor preferred term: cell component comparison design
has curation status: IAO_0000120

ELISPOT assay of epitope specific granulocyte macrophage colony-stimulating factor production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0600031
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_1110184
subclass of: assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells
subclass of: OBI_0600031
definition: An ELISPOT assay that measures epitope specific granulocyte macrophage colony-stimulating factor production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
editor preferred term: ELISPOT assay of epitope specific granulocyte macrophage colony-stimulating factor production by T cells
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000122

epitope specific macrophage inflammatory protein-1 alpha production by T cells
type: Class
equivalent class: Class
  intersection of: macrophage inflammatory protein-1 alpha production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: macrophage inflammatory protein-1 alpha production
subclass of: epitope specific cytokine production by T cells
definition: A process of macrophage inflammatory protein-1 alpha production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific macrophage inflammatory protein-1 alpha production by T cells
has curation status: IAO_0000122

epitope specific T cell activation
type: Class
equivalent class: Class
  intersection of: T cell activation
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: T cell activation
definition: A process of T cell activation resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific T cell activation
has curation status: IAO_0000122

assay of epitope specific interleukin-10 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_1110187
subclass of: OBI_1110129
definition: An assay that measures epitope specific interleukin-10 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: assay of epitope specific interleukin-10 production by T cells
has curation status: IAO_0000122

cytometric bead array assay of epitope specific transforming growth factor-beta production by T cells
type: Class
equivalent class: Class
  intersection of: cytometric bead array assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: epitope specific transforming growth factor-beta production by T cells
subclass of: cytometric bead array assay
subclass of: assay of epitope specific transforming growth factor-beta production by T cells
definition: A cytometric bead array assay that measures epitope specific transforming growth factor-beta production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cytometric bead array assay of epitope specific transforming growth factor-beta production by T cells
has curation status: IAO_0000122

ex vivo design
type: Class
subclass of: OBI_0500000
disjoint with: normalization testing design
disjoint with: environmental history design
disjoint with: transcription profiling by high thoughput sequencing design
disjoint with: array platform variation design
disjoint with: ChIP-seq design
disjoint with: translational bias design
disjoint with: DNA methylation profiling by array design
disjoint with: in vitro design
disjoint with: RNAi profiling by array design
disjoint with: transcription profiling by array design
disjoint with: disease state design
disjoint with: RNA stability design
disjoint with: species comparison design
disjoint with: transcription profiling by RT-PCR design
disjoint with: microRNA profiling by array design
disjoint with: organism development design
disjoint with: family history design
disjoint with: quality control testing design
disjoint with: clinical history design
disjoint with: OBI_0001358
disjoint with: OBI_0001365
disjoint with: OBI_0001374
disjoint with: OBI_0001377
disjoint with: OBI_0001396
disjoint with: OBI_0001401
disjoint with: OBI_0001403
disjoint with: OBI_0001408
disjoint with: OBI_0001409
disjoint with: OBI_0001410
disjoint with: OBI_0001411
disjoint with: OBI_0001418
disjoint with: OBI_0001422
disjoint with: OBI_0001426
disjoint with: OBI_0001427
disjoint with: OBI_0001429
disjoint with: OBI_0001432
disjoint with: OBI_0001435
disjoint with: OBI_0001440
disjoint with: OBI_0001441
disjoint with: OBI_0001444
disjoint with: OBI_0001448
disjoint with: OBI_0001454
disjoint with: OBI_0001460
disjoint with: OBI_0001464
disjoint with: OBI_0300311
disjoint with: OBI_0500001
disjoint with: OBI_0500005
disjoint with: OBI_0500006
disjoint with: OBI_0500009
disjoint with: OBI_0500010
disjoint with: OBI_0500017
disjoint with: OBI_0500018
disjoint with: OBI_0500019
disjoint with: OBI_0500020
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design where all or part of an organism is removed and studied in vitro, e.g. part of a mouse is removed and cultured in vitro. A cell culture with an established cell line is an in vitro experiment.
definition source: MO_808 ex_vivo_design
editor preferred term: ex vivo design
has curation status: IAO_0000120

epitope specific type IV hypersensitivity by T cells
type: Class
equivalent class: Class
  intersection of: type IV hypersensitivity
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: type IV hypersensitivity
definition: A process of type IV hypersensitivity by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific type IV hypersensitivity by T cells
has curation status: IAO_0000122

normalization testing design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: independent variable specification
    intersection of: Restriction
      on property: is about
      some values from: OBI_0200169
subclass of: Restriction
  on property: has part
  some values from: software testing objective
disjoint with: environmental history design
disjoint with: transcription profiling by high thoughput sequencing design
disjoint with: array platform variation design
disjoint with: ChIP-seq design
disjoint with: translational bias design
disjoint with: DNA methylation profiling by array design
disjoint with: in vitro design
disjoint with: RNAi profiling by array design
disjoint with: transcription profiling by array design
disjoint with: disease state design
disjoint with: RNA stability design
disjoint with: species comparison design
disjoint with: transcription profiling by RT-PCR design
disjoint with: microRNA profiling by array design
disjoint with: organism development design
disjoint with: family history design
disjoint with: quality control testing design
disjoint with: clinical history design
disjoint with: OBI_0001358
disjoint with: OBI_0001365
disjoint with: OBI_0001374
disjoint with: OBI_0001377
disjoint with: OBI_0001396
disjoint with: OBI_0001401
disjoint with: OBI_0001403
disjoint with: OBI_0001408
disjoint with: OBI_0001409
disjoint with: OBI_0001410
disjoint with: OBI_0001411
disjoint with: OBI_0001418
disjoint with: OBI_0001422
disjoint with: OBI_0001426
disjoint with: OBI_0001427
disjoint with: OBI_0001429
disjoint with: OBI_0001432
disjoint with: OBI_0001435
disjoint with: OBI_0001440
disjoint with: OBI_0001441
disjoint with: OBI_0001444
disjoint with: OBI_0001448
disjoint with: OBI_0001454
disjoint with: OBI_0001460
disjoint with: OBI_0001464
disjoint with: OBI_0300311
disjoint with: OBI_0500001
disjoint with: OBI_0500005
disjoint with: OBI_0500006
disjoint with: OBI_0500009
disjoint with: OBI_0500010
disjoint with: OBI_0500017
disjoint with: OBI_0500018
disjoint with: OBI_0500019
disjoint with: OBI_0500020
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design that tests different normalization procedures.
definition source: MO_729 normalization_testing_design
editor preferred term: normalization testing design
has curation status: IAO_0000120

intracellular staining assay of epitope specific perforin production
type: Class
equivalent class: Class
  intersection of: intracellular material detection by flow cytometry assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_0001502
subclass of: intracellular material detection by flow cytometry assay of epitope specific cytotoxic T cell degranulation
subclass of: OBI_0001497
definition: An intracellular staining assay that measures epitope specific perforin production
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: intracellular staining assay of epitope specific perforin production
has curation status: IAO_0000122

cell culture analyte detection bioassay of epitope specific interleukin-2 production by T cells
type: Class
equivalent class: Class
  intersection of: cell culture analyte detection bioassay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_1110056
subclass of: cell culture analyte detection bioassay
subclass of: OBI_0001445
definition: A cell culture analyte detection bioassay that measures epitope specific interleukin-2 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cell culture analyte detection bioassay of epitope specific interleukin-2 production by T cells
has curation status: IAO_0000122

assay of epitope specific interleukin-22 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_0001399
subclass of: OBI_1110129
definition: An assay that measures epitope specific interleukin-22 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: assay of epitope specific interleukin-22 production by T cells
has curation status: IAO_0000122

assay of epitope specific interleukin-8 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_0001373
subclass of: OBI_1110129
definition: An assay that measures epitope specific interleukin-8 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: assay of epitope specific interleukin-8 production by T cells
has curation status: IAO_0000122

epitope specific chemokine (C-C motif) ligand 1 production by T cells
type: Class
equivalent class: Class
  intersection of: chemokine (C-C motif) ligand 1 production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: chemokine (C-C motif) ligand 1 production
subclass of: epitope specific cytokine production by T cells
definition: A process of chemokine (C-C motif) ligand 1 production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific chemokine (C-C motif) ligand 1 production by T cells
has curation status: IAO_0000122

cell culture analyte detection bioassay of epitope specific interleukin-10 production by T cells
type: Class
equivalent class: Class
  intersection of: cell culture analyte detection bioassay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_1110187
subclass of: cell culture analyte detection bioassay
subclass of: assay of epitope specific interleukin-10 production by T cells
definition: A cell culture analyte detection bioassay that measures epitope specific interleukin-10 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cell culture analyte detection bioassay of epitope specific interleukin-10 production by T cells
has curation status: IAO_0000122

ChIP-chip by SNP array assay
type: Class
subclass of: ChIP-chip assay
subclass of: Restriction
  on property: has participant
  some values from: SNP microarray
disjoint with: OBI_0001419
term editor: Group: ArrayExpress production team
definition: An assay where chromatin immunoprecipitation (ChIP) is used in combination with SNP microarray technology
editor preferred term: ChIP-chip by SNP array assay
definition source: EFO_0002764 ChIP-chip by SNP array
has curation status: IAO_0000120

ELISA of epitope specific RANTES production by T cells
type: Class
equivalent class: Class
  intersection of: ELISA
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_0001366
subclass of: ELISA
subclass of: assay of epitope specific RANTES production by T cells
definition: An ELISA that measures epitope specific RANTES production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
editor preferred term: ELISA of epitope specific RANTES production by T cells
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000122

cytometric bead array assay of epitope specific interleukin-1 beta production by T cells
type: Class
equivalent class: Class
  intersection of: cytometric bead array assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_1110196
subclass of: cytometric bead array assay
subclass of: OBI_0001449
definition: A cytometric bead array assay that measures epitope specific interleukin-1 beta production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cytometric bead array assay of epitope specific interleukin-1 beta production by T cells
has curation status: IAO_0000122

genetic population background information
type: Class
subclass of: OBI_0001404
subclass of: Restriction
  on property: is part of
  some values from: genotype information
disjoint with: genotype information
disjoint with: OBI_0001364
term editor: Group: OBI group
definition source: Group: OBI group
definition: a genetic characteristics information which is a part of genotype information that identifies the population of organisms
editor preferred term: genetic population background information
example of usage: genotype information 'C57BL/6J Hnf1a+/-' in this case, C57BL/6J is the genetic population background information
editor note: proposed and discussed on San Diego OBI workshop, March 2011
has curation status: IAO_0000120

environmental history design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: biological feature identification objective
disjoint with: transcription profiling by high thoughput sequencing design
disjoint with: array platform variation design
disjoint with: ChIP-seq design
disjoint with: translational bias design
disjoint with: DNA methylation profiling by array design
disjoint with: in vitro design
disjoint with: RNAi profiling by array design
disjoint with: transcription profiling by array design
disjoint with: disease state design
disjoint with: RNA stability design
disjoint with: species comparison design
disjoint with: transcription profiling by RT-PCR design
disjoint with: microRNA profiling by array design
disjoint with: organism development design
disjoint with: family history design
disjoint with: quality control testing design
disjoint with: clinical history design
disjoint with: OBI_0001358
disjoint with: OBI_0001365
disjoint with: OBI_0001374
disjoint with: OBI_0001377
disjoint with: OBI_0001396
disjoint with: OBI_0001401
disjoint with: OBI_0001403
disjoint with: OBI_0001408
disjoint with: OBI_0001409
disjoint with: OBI_0001410
disjoint with: OBI_0001411
disjoint with: OBI_0001418
disjoint with: OBI_0001422
disjoint with: OBI_0001426
disjoint with: OBI_0001427
disjoint with: OBI_0001429
disjoint with: OBI_0001432
disjoint with: OBI_0001435
disjoint with: OBI_0001440
disjoint with: OBI_0001441
disjoint with: OBI_0001444
disjoint with: OBI_0001448
disjoint with: OBI_0001454
disjoint with: OBI_0001460
disjoint with: OBI_0001464
disjoint with: OBI_0300311
disjoint with: OBI_0500001
disjoint with: OBI_0500005
disjoint with: OBI_0500006
disjoint with: OBI_0500009
disjoint with: OBI_0500010
disjoint with: OBI_0500017
disjoint with: OBI_0500018
disjoint with: OBI_0500019
disjoint with: OBI_0500020
definition source: MO_698 environmental_history_design
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design in which some aspect of the organism's environmental history is studied, such as exposure to teratogen, radiation, climate etc.
editor preferred term: environmental history design
has curation status: IAO_0000120

ELISPOT assay of epitope specific interleukin-6 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0600031
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_1110203
subclass of: OBI_0001451
subclass of: OBI_0600031
definition: An ELISPOT assay that measures epitope specific interleukin-6 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
editor preferred term: ELISPOT assay of epitope specific interleukin-6 production by T cells
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000122

assay of epitope specific T cell enhancement of B cell mediated immune response
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: epitope specific T cell enhancement of B cell mediated immune response
subclass of: OBI_0001495
definition: An assay that measures epitope specific T cell enhancement of B cell mediated immune response
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: assay of epitope specific T cell enhancement of B cell mediated immune response
has curation status: IAO_0000122

surface plasmon resonance assay of MHC:epitope complex binding to TCR
type: Class
equivalent class: Class
  intersection of: surface plasmon resonance assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_1110057
subclass of: surface plasmon resonance assay
subclass of: OBI_1110124
definition: A surface plasmon resonance assay that measures MHC:epitope complex binding to TCR
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: surface plasmon resonance assay of MHC:epitope complex binding to TCR
has curation status: IAO_0000122

assay of epitope specific interleukin-5 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_1110202
subclass of: OBI_1110129
definition: An assay that measures epitope specific interleukin-5 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: assay of epitope specific interleukin-5 production by T cells
has curation status: IAO_0000122

ELISA of epitope specific transforming growth factor-beta production by T cells
type: Class
equivalent class: Class
  intersection of: ELISA
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: epitope specific transforming growth factor-beta production by T cells
subclass of: ELISA
subclass of: assay of epitope specific transforming growth factor-beta production by T cells
definition: An ELISA that measures epitope specific transforming growth factor-beta production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
editor preferred term: ELISA of epitope specific transforming growth factor-beta production by T cells
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000122

assay of epitope specific RANTES production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_0001366
subclass of: OBI_1110129
definition: An assay that measures epitope specific RANTES production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: assay of epitope specific RANTES production by T cells
has curation status: IAO_0000122

assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_1110184
subclass of: OBI_1110129
definition: An assay that measures epitope specific granulocyte macrophage colony stimulating factor production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells
has curation status: IAO_0000122

epigenetic modification identification objective
type: Class
subclass of: molecular feature identification objective
disjoint with: transcription profiling identification objective
definition: A molecular feature identification objective that aims to detect epigenetic modifications, such as DNA methylation, histone modifications.
term editor: Chris Stoeckert, Jie Zheng
definition source: Person: Chris Stoeckert
editor preferred term: epigenetic modification identification objective
has curation status: IAO_0000120

transcription profiling by tiling array assay
type: Class
subclass of: transcription profiling assay
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: analyte role
    intersection of: Restriction
      on property: is role of
      some values from: ribonucleic acids
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: transcription profiling identification objective
subclass of: Restriction
  on property: has participant
  some values from: tiling microarray
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measured expression level
    intersection of: Restriction
      on property: is about
      some values from: gene expression
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: OBI_0100051
    intersection of: Restriction
      on property: has part
      some values from: ribonucleic acids
term editor: Person: James Malone
definition: An assay in which the transcriptome of a biological sample is analysed using a tiling path array.
definition source: EFO_0002769 transcription profiling by tiling array
editor preferred term: transcription profiling by tiling array assay
has curation status: IAO_0000120

ELISA of epitope specific interleukin-22 production by T cells
type: Class
equivalent class: Class
  intersection of: ELISA
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_0001399
subclass of: ELISA
subclass of: assay of epitope specific interleukin-22 production by T cells
definition: An ELISA that measures epitope specific interleukin-22 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
editor preferred term: ELISA of epitope specific interleukin-22 production by T cells
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000122

assay of epitope specific interleukin-21 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: epitope specific interleukin-21 production by T cells
subclass of: OBI_1110129
definition: An assay that measures epitope specific interleukin-21 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: assay of epitope specific interleukin-21 production by T cells
has curation status: IAO_0000122

ELISA of epitope specific interleukin-9 production by T cells
type: Class
equivalent class: Class
  intersection of: ELISA
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_0001415
subclass of: ELISA
subclass of: assay of epitope specific interleukin-9 production by T cells
definition: An ELISA that measures epitope specific interleukin-9 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
editor preferred term: ELISA of epitope specific interleukin-9 production by T cells
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000122

transcription profiling by high thoughput sequencing design
type: Class
subclass of: OBI_0001430
subclass of: Restriction
  on property: is realized by
  all values from: Class
    intersection of: Restriction
      on property: has part
      some values from: RNA-seq assay
    intersection of: Restriction
      on property: has participant
      some values from: OBI_0400103
subclass of: Restriction
  on property: has part
  some values from: transcription profiling identification objective
disjoint with: array platform variation design
disjoint with: ChIP-seq design
disjoint with: translational bias design
disjoint with: DNA methylation profiling by array design
disjoint with: in vitro design
disjoint with: RNAi profiling by array design
disjoint with: transcription profiling by array design
disjoint with: disease state design
disjoint with: RNA stability design
disjoint with: species comparison design
disjoint with: transcription profiling by RT-PCR design
disjoint with: microRNA profiling by array design
disjoint with: organism development design
disjoint with: family history design
disjoint with: quality control testing design
disjoint with: clinical history design
disjoint with: OBI_0001358
disjoint with: OBI_0001365
disjoint with: OBI_0001374
disjoint with: OBI_0001377
disjoint with: OBI_0001396
disjoint with: OBI_0001401
disjoint with: OBI_0001403
disjoint with: OBI_0001408
disjoint with: OBI_0001409
disjoint with: OBI_0001410
disjoint with: OBI_0001411
disjoint with: OBI_0001418
disjoint with: OBI_0001422
disjoint with: OBI_0001426
disjoint with: OBI_0001427
disjoint with: OBI_0001429
disjoint with: OBI_0001432
disjoint with: OBI_0001435
disjoint with: OBI_0001440
disjoint with: OBI_0001441
disjoint with: OBI_0001444
disjoint with: OBI_0001448
disjoint with: OBI_0001454
disjoint with: OBI_0001460
disjoint with: OBI_0001464
disjoint with: OBI_0300311
disjoint with: OBI_0500001
disjoint with: OBI_0500005
disjoint with: OBI_0500006
disjoint with: OBI_0500009
disjoint with: OBI_0500010
disjoint with: OBI_0500017
disjoint with: OBI_0500018
disjoint with: OBI_0500019
disjoint with: OBI_0500020
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and/or to quantitate transcript abundance
definition source: Group: ArrayExpress production team
editor preferred term: transcription profiling by high thoughput sequencing design
has curation status: IAO_0000120

intracellular cytokine staining assay of epitope specific interleukin-6 production by T cells
type: Class
equivalent class: Class
  intersection of: intracellular cytokine staining assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_1110203
subclass of: intracellular cytokine staining assay
subclass of: OBI_0001451
definition: An intracellular cytokine staining assay that measures epitope specific interleukin-6 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: intracellular cytokine staining assay of epitope specific interleukin-6 production by T cells
has curation status: IAO_0000122

cell culture analyte detection bioassay of epitope specific interleukin-4 production by T cells
type: Class
equivalent class: Class
  intersection of: cell culture analyte detection bioassay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_1110199
subclass of: cell culture analyte detection bioassay
subclass of: OBI_0001450
definition: A cell culture analyte detection bioassay that measures epitope specific interleukin-4 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cell culture analyte detection bioassay of epitope specific interleukin-4 production by T cells
has curation status: IAO_0000122

detection of specific nucleic acids with complementary probes of epitope specific tumor necrosis factor production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acids with complementary probes
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_1110206
subclass of: detection of specific nucleic acids with complementary probes
subclass of: OBI_0001416
definition: A detection of specific nucleic acids with complementary probes that measures epitope specific tumor necrosis factor production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: detection of specific nucleic acids with complementary probes of epitope specific tumor necrosis factor production by T cells
has curation status: IAO_0000122

cytometric bead array assay of epitope specific monocyte chemotactic protein-1 production by T cells
type: Class
equivalent class: Class
  intersection of: cytometric bead array assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_0001386
subclass of: cytometric bead array assay
subclass of: OBI_0001465
definition: A cytometric bead array assay that measures epitope specific monocyte chemotactic protein-1 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cytometric bead array assay of epitope specific monocyte chemotactic protein-1 production by T cells
has curation status: IAO_0000122

ELISA of epitope specific interleukin-23 production by T cells
type: Class
equivalent class: Class
  intersection of: ELISA
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_0001381
subclass of: ELISA
subclass of: OBI_0001363
definition: An ELISA that measures epitope specific interleukin-23 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
editor preferred term: ELISA of epitope specific interleukin-23 production by T cells
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000122

detection of specific nucleic acids with complementary probes of epitope specific perforin production
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acids with complementary probes
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_0001502
subclass of: detection of specific nucleic acids with complementary probes
subclass of: OBI_0001497
definition: A detection of specific nucleic acids with complementary probes that measures epitope specific perforin production
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: detection of specific nucleic acids with complementary probes of epitope specific perforin production
has curation status: IAO_0000122

ELISA of epitope specific tumor necrosis factor superfamily cytokine production by T cells
type: Class
equivalent class: Class
  intersection of: ELISA
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: epitope specific tumor necrosis factor superfamily cytokine production by T cells
subclass of: ELISA
subclass of: OBI_0001400
definition: An ELISA that measures epitope specific tumor necrosis factor superfamily cytokine production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
editor preferred term: ELISA of epitope specific tumor necrosis factor superfamily cytokine production by T cells
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000122

genotyping by high throughput sequencing assay
type: Class
subclass of: genotyping assay
subclass of: OBI_0600047
subclass of: Restriction
  on property: has participant
  some values from: OBI_0400103
disjoint with: genotyping by array assay
term editor: Person: James Malone
definition: An assay in which high througput sequencer is used to detect polymorphisms in DNA samples
definition source: EFO_0002771: genotyping by high throughput sequencing
editor preferred term: genotyping by high throughput sequencing assay
has curation status: IAO_0000120

ChIP-chip assay
type: Class
subclass of: analyte assay
subclass of: OBI_0001700
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: analyte role
    intersection of: Restriction
      on property: is role of
      some values from: deoxyribonucleic acids
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: OBI_0100051
    intersection of: Restriction
      on property: has part
      some values from: deoxyribonucleic acids
    intersection of: Restriction
      on property: has part
      some values from: protein complex
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: OBI_0001398
subclass of: Restriction
  on property: has part
  some values from: immunoprecipitation
subclass of: Restriction
  on property: has participant
  some values from: OBI_0400148
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: information content entity
    intersection of: Restriction
      on property: is about
      some values from: Class
        union of: chromatin remodeling
        union of: regulation of molecular function, epigenetic
        union of: sequence-specific DNA binding
        union of: transcription factor binding site
alternative term: ChIP-on-chip assay
term editor: Person: James Malone
comment: Philippe Rocca-Serra
definition source: WEB: http://en.wikipedia.org/wiki/ChIP-on-chip
definition: an assay that aims to investigate the interactions between protein and DNA relying on chromatin immunoprecipitation ('ChIP') combined with microarray technology ('chip'). Specially, it allows the identification of protein binding sites on a genome-wide basis.
editor preferred term: ChIP-chip assay
has curation status: IAO_0000120

epitope specific T cell tolerance induction
type: Class
equivalent class: Class
  intersection of: T cell tolerance induction
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: T cell tolerance induction
subclass of: epitope specific tolerance induction by T cells
definition: A process of T cell tolerance induction resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific T cell tolerance induction
has curation status: IAO_0000122

intracellular material detection by flow cytometry assay of epitope specific cytotoxic T cell degranulation
type: Class
equivalent class: Class
  intersection of: intracellular material detection by flow cytometry assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: Class
subclass of: intracellular material detection by flow cytometry assay
subclass of: assay of epitope specific cytotoxic T cell degranulation
definition: An intracellular material detection by flow cytometry assay that measures epitope specific cytotoxic T cell degranulation
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: intracellular material detection by flow cytometry assay of epitope specific cytotoxic T cell degranulation
has curation status: IAO_0000122

assay of epitope specific interleukin-13 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_1110191
subclass of: OBI_1110129
definition: An assay that measures epitope specific interleukin-13 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: assay of epitope specific interleukin-13 production by T cells
has curation status: IAO_0000122

array platform variation design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: methodology testing objective
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: independent variable specification
    intersection of: Restriction
      on property: is about
      some values from: microarray platform
disjoint with: ChIP-seq design
disjoint with: translational bias design
disjoint with: DNA methylation profiling by array design
disjoint with: in vitro design
disjoint with: RNAi profiling by array design
disjoint with: transcription profiling by array design
disjoint with: disease state design
disjoint with: RNA stability design
disjoint with: species comparison design
disjoint with: transcription profiling by RT-PCR design
disjoint with: microRNA profiling by array design
disjoint with: organism development design
disjoint with: family history design
disjoint with: quality control testing design
disjoint with: clinical history design
disjoint with: OBI_0001358
disjoint with: OBI_0001365
disjoint with: OBI_0001374
disjoint with: OBI_0001377
disjoint with: OBI_0001396
disjoint with: OBI_0001401
disjoint with: OBI_0001403
disjoint with: OBI_0001408
disjoint with: OBI_0001409
disjoint with: OBI_0001410
disjoint with: OBI_0001411
disjoint with: OBI_0001418
disjoint with: OBI_0001422
disjoint with: OBI_0001426
disjoint with: OBI_0001427
disjoint with: OBI_0001429
disjoint with: OBI_0001432
disjoint with: OBI_0001435
disjoint with: OBI_0001440
disjoint with: OBI_0001441
disjoint with: OBI_0001444
disjoint with: OBI_0001448
disjoint with: OBI_0001454
disjoint with: OBI_0001460
disjoint with: OBI_0001464
disjoint with: OBI_0300311
disjoint with: OBI_0500001
disjoint with: OBI_0500005
disjoint with: OBI_0500006
disjoint with: OBI_0500009
disjoint with: OBI_0500010
disjoint with: OBI_0500017
disjoint with: OBI_0500018
disjoint with: OBI_0500019
disjoint with: OBI_0500020
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design in which the array platform is compared, e.g. Agilent versus Affymetrix.
definition source: MO_899 array_platform_variation_design
editor preferred term: array platform variation design
has curation status: IAO_0000120

assay of epitope specific interleukin-9 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_0001415
subclass of: OBI_1110129
definition: An assay that measures epitope specific interleukin-9 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: assay of epitope specific interleukin-9 production by T cells
has curation status: IAO_0000122

epitope specific interleukin-3 production by T cells
type: Class
equivalent class: Class
  intersection of: interleukin-3 production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: interleukin-3 production
subclass of: epitope specific cytokine production by T cells
definition: A process of interleukin-3 production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific interleukin-3 production by T cells
has curation status: IAO_0000122

detection of specific nucleic acids with complementary probes of epitope specific interleukin-5 production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acids with complementary probes
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_1110202
subclass of: detection of specific nucleic acids with complementary probes
subclass of: assay of epitope specific interleukin-5 production by T cells
definition: A detection of specific nucleic acids with complementary probes that measures epitope specific interleukin-5 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: detection of specific nucleic acids with complementary probes of epitope specific interleukin-5 production by T cells
has curation status: IAO_0000122

epitope specific lymphotoxin A production by T cells
type: Class
equivalent class: Class
  intersection of: lymphotoxin A production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: lymphotoxin A production
subclass of: epitope specific tumor necrosis factor superfamily cytokine production by T cells
definition: A process of lymphotoxin A production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific lymphotoxin A production by T cells
has curation status: IAO_0000122

epitope specific interleukin-1 alpha production by T cells
type: Class
equivalent class: Class
  intersection of: interleukin-1 alpha production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: interleukin-1 alpha production
subclass of: epitope specific cytokine production by T cells
definition: A process of interleukin-1 alpha production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific interleukin-1 alpha production by T cells
has curation status: IAO_0000122

ChIP-seq design
type: Class
subclass of: OBI_0001425
subclass of: Restriction
  on property: is realized by
  all values from: Class
    intersection of: Restriction
      on property: has part
      some values from: ChIP-seq assay
    intersection of: Restriction
      on property: has participant
      some values from: OBI_0400103
subclass of: Restriction
  on property: has part
  some values from: OBI_0001398
subclass of: Restriction
  on property: has part
  some values from: epigenetic modification identification objective
disjoint with: translational bias design
disjoint with: DNA methylation profiling by array design
disjoint with: in vitro design
disjoint with: RNAi profiling by array design
disjoint with: transcription profiling by array design
disjoint with: disease state design
disjoint with: RNA stability design
disjoint with: species comparison design
disjoint with: transcription profiling by RT-PCR design
disjoint with: microRNA profiling by array design
disjoint with: organism development design
disjoint with: family history design
disjoint with: quality control testing design
disjoint with: clinical history design
disjoint with: OBI_0001358
disjoint with: OBI_0001365
disjoint with: OBI_0001374
disjoint with: OBI_0001377
disjoint with: OBI_0001396
disjoint with: OBI_0001401
disjoint with: OBI_0001403
disjoint with: OBI_0001408
disjoint with: OBI_0001409
disjoint with: OBI_0001410
disjoint with: OBI_0001411
disjoint with: OBI_0001418
disjoint with: OBI_0001422
disjoint with: OBI_0001426
disjoint with: OBI_0001427
disjoint with: OBI_0001429
disjoint with: OBI_0001432
disjoint with: OBI_0001435
disjoint with: OBI_0001440
disjoint with: OBI_0001441
disjoint with: OBI_0001444
disjoint with: OBI_0001448
disjoint with: OBI_0001454
disjoint with: OBI_0001460
disjoint with: OBI_0001464
disjoint with: OBI_0300311
disjoint with: OBI_0500001
disjoint with: OBI_0500005
disjoint with: OBI_0500006
disjoint with: OBI_0500009
disjoint with: OBI_0500010
disjoint with: OBI_0500017
disjoint with: OBI_0500018
disjoint with: OBI_0500019
disjoint with: OBI_0500020
definition source: http://en.wikipedia.org/wiki/Chip-Sequencing
definition: A study design which aims to identify protein and DNA interactions using a combination of chromatin immunoprecipitation and high throughput sequencing. Massively parallel sequence analyses are used in conjunction with whole-genome sequence databases to analyze the interaction pattern of any protein with DNA, or the pattern of any epigenetic chromatin modifications.
editor preferred term: ChIP-seq design
term editor: Person: Chris Stoeckert, Jie Zheng
has curation status: IAO_0000120

translational bias design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: biological feature identification objective
disjoint with: DNA methylation profiling by array design
disjoint with: in vitro design
disjoint with: RNAi profiling by array design
disjoint with: transcription profiling by array design
disjoint with: disease state design
disjoint with: RNA stability design
disjoint with: species comparison design
disjoint with: transcription profiling by RT-PCR design
disjoint with: microRNA profiling by array design
disjoint with: organism development design
disjoint with: family history design
disjoint with: quality control testing design
disjoint with: clinical history design
disjoint with: OBI_0001358
disjoint with: OBI_0001365
disjoint with: OBI_0001374
disjoint with: OBI_0001377
disjoint with: OBI_0001396
disjoint with: OBI_0001401
disjoint with: OBI_0001403
disjoint with: OBI_0001408
disjoint with: OBI_0001409
disjoint with: OBI_0001410
disjoint with: OBI_0001411
disjoint with: OBI_0001418
disjoint with: OBI_0001422
disjoint with: OBI_0001426
disjoint with: OBI_0001427
disjoint with: OBI_0001429
disjoint with: OBI_0001432
disjoint with: OBI_0001435
disjoint with: OBI_0001440
disjoint with: OBI_0001441
disjoint with: OBI_0001444
disjoint with: OBI_0001448
disjoint with: OBI_0001454
disjoint with: OBI_0001460
disjoint with: OBI_0001464
disjoint with: OBI_0300311
disjoint with: OBI_0500001
disjoint with: OBI_0500005
disjoint with: OBI_0500006
disjoint with: OBI_0500009
disjoint with: OBI_0500010
disjoint with: OBI_0500017
disjoint with: OBI_0500018
disjoint with: OBI_0500019
disjoint with: OBI_0500020
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design that characterizes the association of transcripts and translation machinery.
definition source: MO_939 translational_bias_design
editor preferred term: translational bias design
has curation status: IAO_0000120

ELISA of epitope specific interleukin-3 production by T cells
type: Class
equivalent class: Class
  intersection of: ELISA
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: epitope specific interleukin-3 production by T cells
subclass of: ELISA
subclass of: OBI_0001406
definition: An ELISA that measures epitope specific interleukin-3 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
editor preferred term: ELISA of epitope specific interleukin-3 production by T cells
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000122

ELISA of epitope specific interleukin-1 alpha production by T cells
type: Class
equivalent class: Class
  intersection of: ELISA
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: epitope specific interleukin-1 alpha production by T cells
subclass of: ELISA
subclass of: OBI_0001388
definition: An ELISA that measures epitope specific interleukin-1 alpha production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
editor preferred term: ELISA of epitope specific interleukin-1 alpha production by T cells
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000122

epitope specific interleukin-27 production by T cells
type: Class
equivalent class: Class
  intersection of: interleukin-27 production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: interleukin-27 production
subclass of: epitope specific cytokine production by T cells
definition: A process of interleukin-27 production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific interleukin-27 production by T cells
has curation status: IAO_0000122

assay of epitope specific helper T cell enhancement of T cell mediated immune response
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_0001420
subclass of: OBI_0001495
definition: An assay that measures epitope specific helper T cell enhancement of T cell mediated immune response
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: assay of epitope specific helper T cell enhancement of T cell mediated immune response
has curation status: IAO_0000122

assay of epitope specific transforming growth factor-beta production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: epitope specific transforming growth factor-beta production by T cells
subclass of: OBI_1110129
definition: An assay that measures epitope specific transforming growth factor-beta production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: assay of epitope specific transforming growth factor-beta production by T cells
has curation status: IAO_0000122

FWER adjusted p-value
type: Class
subclass of: quantitative confidence value
disjoint with: OBI_0001442
editor preferred term: FWER adjusted p-value
definition: A quantitative confidence value resulting from a multiple testing error correction method which adjusts the p-value used as input to control for Type I error in the context of multiple pairwise tests
term editor: PERS:Philippe Rocca-Serra
definition source: adapted from wikipedia (http://en.wikipedia.org/wiki/Familywise_error_rate)
example of usage: http://ugrad.stat.ubc.ca/R/library/LPE/html/mt.rawp2adjp.html
has curation status: IAO_0000122

DNA methylation profiling by high throughput sequencing assay
type: Class
subclass of: DNA methylation profiling assay
subclass of: OBI_0600047
subclass of: Restriction
  on property: has participant
  some values from: OBI_0400103
disjoint with: DNA methylation profiling by array assay
definition source: EFO_0002761 methylation profiling by high throughput sequencing
term editor: Group: ArrayExpress production team, James Malone, Helen Parkinson
comment: Philippe Rocca-Serra
definition: An assay in which the methylation state of DNA is determined and is compared between samples using sequencing based technology
editor preferred term: DNA methylation profiling by high throughput sequencing assay
has curation status: IAO_0000120

epitope specific transforming growth factor-beta production by T cells
type: Class
equivalent class: Class
  intersection of: transforming growth factor beta production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: transforming growth factor beta production
subclass of: epitope specific cytokine production by T cells
definition: A process of transforming growth factor-beta production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific transforming growth factor-beta production by T cells
has curation status: IAO_0000122

detection of specific nucleic acids with complementary probes of epitope specific interleukin-12 production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acids with complementary probes
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_1110190
subclass of: detection of specific nucleic acids with complementary probes
subclass of: OBI_0001391
definition: A detection of specific nucleic acids with complementary probes that measures epitope specific interleukin-12 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: detection of specific nucleic acids with complementary probes of epitope specific interleukin-12 production by T cells
has curation status: IAO_0000122

assay of epitope specific cytotoxic T cell degranulation
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: Class
subclass of: OBI_1110037
definition: An assay that measures epitope specific cytotoxic T cell degranulation
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: assay of epitope specific cytotoxic T cell degranulation
has curation status: IAO_0000122

cell culture analyte detection bioassay of epitope specific transforming growth factor-beta production by T cells
type: Class
equivalent class: Class
  intersection of: cell culture analyte detection bioassay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: epitope specific transforming growth factor-beta production by T cells
subclass of: cell culture analyte detection bioassay
subclass of: assay of epitope specific transforming growth factor-beta production by T cells
definition: A cell culture analyte detection bioassay that measures epitope specific transforming growth factor-beta production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cell culture analyte detection bioassay of epitope specific transforming growth factor-beta production by T cells
has curation status: IAO_0000122

RNA-seq assay
type: Class
subclass of: transcription profiling assay
subclass of: OBI_0600047
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: sequence data
    intersection of: Restriction
      on property: is about
      some values from: gene expression
subclass of: Restriction
  on property: has participant
  some values from: OBI_0400103
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: analyte role
    intersection of: Restriction
      on property: is role of
      some values from: ribonucleic acids
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: transcription profiling identification objective
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: OBI_0100051
    intersection of: Restriction
      on property: has part
      some values from: ribonucleic acids
definition: An assay in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and or to quantitate transcript abundance
definition source: EFO_0002770 transcription profiling by high throughput sequencing
term editor: PERSON: James Malone
editor preferred term: RNA-seq assay
curator note: an assay that uses high-throughput sequencing technologies to sequence cDNA in order to get information about a sample's RNA content. RNA-Seq provides researchers with efficient ways to measure transcriptome data experimentally, allowing them to get information such as how different alleles of a gene are expressed, detect post-transcriptional mutations or identify gene fusions. WEB: http://en.wikipedia.org/wiki/RNA-Seq
alternative term: transcription profiling by high throughput sequencing
has curation status: IAO_0000120

ELISPOT assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0600031
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: epitope specific tumor necrosis factor superfamily cytokine production by T cells
subclass of: OBI_0001400
subclass of: OBI_0600031
definition: An ELISPOT assay that measures epitope specific tumor necrosis factor superfamily cytokine production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
editor preferred term: ELISPOT assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000122

cell culture analyte detection bioassay of epitope specific interleukin-5 production by T cells
type: Class
equivalent class: Class
  intersection of: cell culture analyte detection bioassay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_1110202
subclass of: cell culture analyte detection bioassay
subclass of: assay of epitope specific interleukin-5 production by T cells
definition: A cell culture analyte detection bioassay that measures epitope specific interleukin-5 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cell culture analyte detection bioassay of epitope specific interleukin-5 production by T cells
has curation status: IAO_0000122

genotyping by array assay
type: Class
subclass of: genotyping assay
subclass of: Restriction
  on property: has participant
  some values from: OBI_0400148
term editor: Group: ArrayExpress production team
definition: An assay in which an array is used to detect polymorphisms in DNA samples
definition source: EFO_0002767: genotyping by array
editor preferred term: genotyping by array assay
has curation status: IAO_0000120

epitope specific interleukin-16 production by T cells
type: Class
equivalent class: Class
  intersection of: interleukin-16 production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: interleukin-16 production
subclass of: epitope specific cytokine production by T cells
definition: A process of interleukin-16 production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific interleukin-16 production by T cells
has curation status: IAO_0000122

assay of epitope specific chemokine (C-C motif) ligand 1 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: epitope specific chemokine (C-C motif) ligand 1 production by T cells
subclass of: OBI_1110129
definition: An assay that measures epitope specific chemokine (C-C motif) ligand 1 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: assay of epitope specific chemokine (C-C motif) ligand 1 production by T cells
has curation status: IAO_0000122

detection of specific nucleic acids with complementary probes of epitope specific interleukin-2 production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acids with complementary probes
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_1110056
subclass of: detection of specific nucleic acids with complementary probes
subclass of: OBI_0001445
definition: A detection of specific nucleic acids with complementary probes that measures epitope specific interleukin-2 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: detection of specific nucleic acids with complementary probes of epitope specific interleukin-2 production by T cells
has curation status: IAO_0000122

DNA methylation profiling by array design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: epigenetic modification identification objective
subclass of: Restriction
  on property: is realized by
  all values from: Class
    intersection of: Restriction
      on property: has part
      some values from: DNA methylation profiling by array assay
    intersection of: Restriction
      on property: has participant
      some values from: OBI_0400148
disjoint with: in vitro design
disjoint with: RNAi profiling by array design
disjoint with: transcription profiling by array design
disjoint with: disease state design
disjoint with: RNA stability design
disjoint with: species comparison design
disjoint with: transcription profiling by RT-PCR design
disjoint with: microRNA profiling by array design
disjoint with: organism development design
disjoint with: family history design
disjoint with: quality control testing design
disjoint with: clinical history design
disjoint with: OBI_0001358
disjoint with: OBI_0001365
disjoint with: OBI_0001374
disjoint with: OBI_0001377
disjoint with: OBI_0001396
disjoint with: OBI_0001401
disjoint with: OBI_0001403
disjoint with: OBI_0001408
disjoint with: OBI_0001409
disjoint with: OBI_0001410
disjoint with: OBI_0001411
disjoint with: OBI_0001418
disjoint with: OBI_0001422
disjoint with: OBI_0001426
disjoint with: OBI_0001427
disjoint with: OBI_0001429
disjoint with: OBI_0001432
disjoint with: OBI_0001435
disjoint with: OBI_0001440
disjoint with: OBI_0001441
disjoint with: OBI_0001444
disjoint with: OBI_0001448
disjoint with: OBI_0001454
disjoint with: OBI_0001460
disjoint with: OBI_0001464
disjoint with: OBI_0300311
disjoint with: OBI_0500001
disjoint with: OBI_0500005
disjoint with: OBI_0500006
disjoint with: OBI_0500009
disjoint with: OBI_0500010
disjoint with: OBI_0500017
disjoint with: OBI_0500018
disjoint with: OBI_0500019
disjoint with: OBI_0500020
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design in which the methylation state of DNA is determined and is compared between samples using array technology.
editor preferred term: DNA methylation profiling by array design
definition source: GROUP: ArrayExpress production team
has curation status: IAO_0000120

detection of specific nucleic acids with complementary probes of epitope specific interleukin-22 production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acids with complementary probes
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_0001399
subclass of: detection of specific nucleic acids with complementary probes
subclass of: assay of epitope specific interleukin-22 production by T cells
definition: A detection of specific nucleic acids with complementary probes that measures epitope specific interleukin-22 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: detection of specific nucleic acids with complementary probes of epitope specific interleukin-22 production by T cells
has curation status: IAO_0000122

assay of epitope specific interleukin-16 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: epitope specific interleukin-16 production by T cells
subclass of: OBI_1110129
definition: An assay that measures epitope specific interleukin-16 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: assay of epitope specific interleukin-16 production by T cells
has curation status: IAO_0000122

ELISA of epitope specific IP-10 production by T cells
type: Class
equivalent class: Class
  intersection of: ELISA
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_0001462
subclass of: ELISA
subclass of: assay of epitope specific IP-10 production by T cells
definition: An ELISA that measures epitope specific IP-10 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
editor preferred term: ELISA of epitope specific IP-10 production by T cells
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000122

translation profiling assay
type: Class
subclass of: analyte assay
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: molecular feature identification objective
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: analyte role
    intersection of: Restriction
      on property: is role of
      some values from: ribonucleic acids
definition: An assay in which surface-bound, translationally competent ribosome complexes are used to generate a translation profile for mRNA, which mRNA may be a single molecular species, or a combination of species, including complex mixtures such as those found in the set of mRNAs isolated from a cell or tissue. One or more components of the surface-bound ribosome complex may be labeled at specific positions to permit analysis of multiple or single molecules for determination of ribosomal conformational changes and translation kinetics. Translation profiles are used as the basis for comparison of an mRNA or set of mRNA species. The translation profile can be used to determine such characteristics as kinetics of initiation, kinetic of elongation, identity of the polypeptide product, and the like. Analysis of translation profiles may be used to determine differential gene expression, optimization of mRNA sequences for expression, screening drug candidates for an effect on translation.
definition source: EFO_0001033 translation profiling
term editor: PERSON: James Malone
editor preferred term: translation profiling assay
has curation status: IAO_0000120

ELISA of epitope specific interleukin-15 production by T cells
type: Class
equivalent class: Class
  intersection of: ELISA
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_0001446
subclass of: ELISA
subclass of: assay of epitope specific interleukin-15 production by T cells
definition: An ELISA that measures epitope specific interleukin-15 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
editor preferred term: ELISA of epitope specific interleukin-15 production by T cells
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000122

cytometric bead array assay of epitope specific interleukin-12 production by T cells
type: Class
equivalent class: Class
  intersection of: cytometric bead array assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_1110190
subclass of: cytometric bead array assay
subclass of: OBI_0001391
definition: A cytometric bead array assay that measures epitope specific interleukin-12 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cytometric bead array assay of epitope specific interleukin-12 production by T cells
has curation status: IAO_0000122

in vitro design
type: Class
subclass of: OBI_0500000
disjoint with: RNAi profiling by array design
disjoint with: transcription profiling by array design
disjoint with: disease state design
disjoint with: RNA stability design
disjoint with: species comparison design
disjoint with: transcription profiling by RT-PCR design
disjoint with: microRNA profiling by array design
disjoint with: organism development design
disjoint with: family history design
disjoint with: quality control testing design
disjoint with: clinical history design
disjoint with: OBI_0001358
disjoint with: OBI_0001365
disjoint with: OBI_0001374
disjoint with: OBI_0001377
disjoint with: OBI_0001396
disjoint with: OBI_0001401
disjoint with: OBI_0001403
disjoint with: OBI_0001408
disjoint with: OBI_0001409
disjoint with: OBI_0001410
disjoint with: OBI_0001411
disjoint with: OBI_0001418
disjoint with: OBI_0001422
disjoint with: OBI_0001426
disjoint with: OBI_0001427
disjoint with: OBI_0001429
disjoint with: OBI_0001432
disjoint with: OBI_0001435
disjoint with: OBI_0001440
disjoint with: OBI_0001441
disjoint with: OBI_0001444
disjoint with: OBI_0001448
disjoint with: OBI_0001454
disjoint with: OBI_0001460
disjoint with: OBI_0001464
disjoint with: OBI_0300311
disjoint with: OBI_0500001
disjoint with: OBI_0500005
disjoint with: OBI_0500006
disjoint with: OBI_0500009
disjoint with: OBI_0500010
disjoint with: OBI_0500017
disjoint with: OBI_0500018
disjoint with: OBI_0500019
disjoint with: OBI_0500020
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design that is done in a test tube or a culture dish, e.g. A bacterial invasion assay in an established cell culture.
definition source: MO_347 in_vitro_design
editor preferred term: in vitro design
has curation status: IAO_0000120

RNAi profiling by array design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: molecular feature identification objective
subclass of: Restriction
  on property: is realized by
  all values from: Class
    intersection of: Restriction
      on property: has part
      some values from: RNAi profiling by array assay
    intersection of: Restriction
      on property: has participant
      some values from: OBI_0400148
disjoint with: transcription profiling by array design
disjoint with: disease state design
disjoint with: RNA stability design
disjoint with: species comparison design
disjoint with: transcription profiling by RT-PCR design
disjoint with: microRNA profiling by array design
disjoint with: organism development design
disjoint with: family history design
disjoint with: quality control testing design
disjoint with: clinical history design
disjoint with: OBI_0001358
disjoint with: OBI_0001365
disjoint with: OBI_0001374
disjoint with: OBI_0001377
disjoint with: OBI_0001396
disjoint with: OBI_0001401
disjoint with: OBI_0001403
disjoint with: OBI_0001408
disjoint with: OBI_0001409
disjoint with: OBI_0001410
disjoint with: OBI_0001411
disjoint with: OBI_0001418
disjoint with: OBI_0001422
disjoint with: OBI_0001426
disjoint with: OBI_0001427
disjoint with: OBI_0001429
disjoint with: OBI_0001432
disjoint with: OBI_0001435
disjoint with: OBI_0001440
disjoint with: OBI_0001441
disjoint with: OBI_0001444
disjoint with: OBI_0001448
disjoint with: OBI_0001454
disjoint with: OBI_0001460
disjoint with: OBI_0001464
disjoint with: OBI_0300311
disjoint with: OBI_0500001
disjoint with: OBI_0500005
disjoint with: OBI_0500006
disjoint with: OBI_0500009
disjoint with: OBI_0500010
disjoint with: OBI_0500017
disjoint with: OBI_0500018
disjoint with: OBI_0500019
disjoint with: OBI_0500020
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design in which experiment double stranded RNA is synthesized with a sequence complementary to a gene(s) of interest and introduced into a cell or organism, where it is recognized as exogenous genetic material and activates the RNAi pathway resulting in knockdown of the transcripts and providing a means to study downstream changes in gene expression.
definition source: Group: ArrayExpress production team
editor preferred term: RNAi profiling by array design
has curation status: IAO_0000120

ELISA of epitope specific lymphotoxin A production by T cells
type: Class
equivalent class: Class
  intersection of: ELISA
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: epitope specific lymphotoxin A production by T cells
subclass of: ELISA of epitope specific tumor necrosis factor superfamily cytokine production by T cells
subclass of: assay of epitope specific lymphotoxin A production by T cells
definition: An ELISA that measures epitope specific lymphotoxin A production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
editor preferred term: ELISA of epitope specific lymphotoxin A production by T cells
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000122

cytometric bead array assay of epitope specific interleukin-5 production by T cells
type: Class
equivalent class: Class
  intersection of: cytometric bead array assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_1110202
subclass of: cytometric bead array assay
subclass of: assay of epitope specific interleukin-5 production by T cells
definition: A cytometric bead array assay that measures epitope specific interleukin-5 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cytometric bead array assay of epitope specific interleukin-5 production by T cells
has curation status: IAO_0000122

transcription profiling by array design
type: Class
subclass of: OBI_0001430
subclass of: Restriction
  on property: has part
  some values from: transcription profiling identification objective
subclass of: Restriction
  on property: is realized by
  all values from: Class
    intersection of: Restriction
      on property: has part
      some values from: OBI_0001463
    intersection of: Restriction
      on property: has participant
      some values from: OBI_0400148
disjoint with: disease state design
disjoint with: RNA stability design
disjoint with: species comparison design
disjoint with: transcription profiling by RT-PCR design
disjoint with: microRNA profiling by array design
disjoint with: organism development design
disjoint with: family history design
disjoint with: quality control testing design
disjoint with: clinical history design
disjoint with: OBI_0001358
disjoint with: OBI_0001365
disjoint with: OBI_0001374
disjoint with: OBI_0001377
disjoint with: OBI_0001396
disjoint with: OBI_0001401
disjoint with: OBI_0001403
disjoint with: OBI_0001408
disjoint with: OBI_0001409
disjoint with: OBI_0001410
disjoint with: OBI_0001411
disjoint with: OBI_0001418
disjoint with: OBI_0001422
disjoint with: OBI_0001426
disjoint with: OBI_0001427
disjoint with: OBI_0001429
disjoint with: OBI_0001432
disjoint with: OBI_0001435
disjoint with: OBI_0001440
disjoint with: OBI_0001441
disjoint with: OBI_0001444
disjoint with: OBI_0001448
disjoint with: OBI_0001454
disjoint with: OBI_0001460
disjoint with: OBI_0001464
disjoint with: OBI_0300311
disjoint with: OBI_0500001
disjoint with: OBI_0500005
disjoint with: OBI_0500006
disjoint with: OBI_0500009
disjoint with: OBI_0500010
disjoint with: OBI_0500017
disjoint with: OBI_0500018
disjoint with: OBI_0500019
disjoint with: OBI_0500020
definition source: MO_533 transcript_identification_design
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design that identifies forms and abundance of transcripts in the genome using microarray technology.
editor preferred term: transcription profiling by array design
has curation status: IAO_0000120

detection of specific nucleic acids with complementary probes of epitope specific interleukin-17 production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acids with complementary probes
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_1110193
subclass of: detection of specific nucleic acids with complementary probes
subclass of: assay of epitope specific interleukin-17 production by T cells
definition: A detection of specific nucleic acids with complementary probes that measures epitope specific interleukin-17 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: detection of specific nucleic acids with complementary probes of epitope specific interleukin-17 production by T cells
has curation status: IAO_0000122

assay of epitope specific interleukin-15 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_0001446
subclass of: OBI_1110129
definition: An assay that measures epitope specific interleukin-15 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: assay of epitope specific interleukin-15 production by T cells
has curation status: IAO_0000122

disease state design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: independent variable specification
    intersection of: Restriction
      on property: is about
      some values from: OBI_1110055
subclass of: Restriction
  on property: has part
  some values from: organism feature identification objective
disjoint with: RNA stability design
disjoint with: species comparison design
disjoint with: transcription profiling by RT-PCR design
disjoint with: microRNA profiling by array design
disjoint with: organism development design
disjoint with: family history design
disjoint with: quality control testing design
disjoint with: clinical history design
disjoint with: OBI_0001358
disjoint with: OBI_0001365
disjoint with: OBI_0001374
disjoint with: OBI_0001377
disjoint with: OBI_0001396
disjoint with: OBI_0001401
disjoint with: OBI_0001403
disjoint with: OBI_0001408
disjoint with: OBI_0001409
disjoint with: OBI_0001410
disjoint with: OBI_0001411
disjoint with: OBI_0001418
disjoint with: OBI_0001422
disjoint with: OBI_0001426
disjoint with: OBI_0001427
disjoint with: OBI_0001429
disjoint with: OBI_0001432
disjoint with: OBI_0001435
disjoint with: OBI_0001440
disjoint with: OBI_0001441
disjoint with: OBI_0001444
disjoint with: OBI_0001448
disjoint with: OBI_0001454
disjoint with: OBI_0001460
disjoint with: OBI_0001464
disjoint with: OBI_0300311
disjoint with: OBI_0500001
disjoint with: OBI_0500005
disjoint with: OBI_0500006
disjoint with: OBI_0500009
disjoint with: OBI_0500010
disjoint with: OBI_0500017
disjoint with: OBI_0500018
disjoint with: OBI_0500019
disjoint with: OBI_0500020
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design in which the pathological condition of a part, organ, or system of an organism is studied. The etiology may be from infection, genetic defect, or environmental stress.
definition source: MO_902 disease_state_design
editor preferred term: disease state design
has curation status: IAO_0000120

wild type organism genotype information
type: Class
subclass of: genotype information
example of usage: C57BL/6J wild type
definition source: Group: OBI group
term editor: Group: OBI group
definition: a genotype information about an organism and includes information that there are no known modifications to the genetic background. Generally it is the genotype information of a representative individual from a class of organisms.
editor note: proposed and discussed on San Diego OBI workshop, March 2011
editor preferred term: wild type organism genotype information
has curation status: IAO_0000120

assay of epitope specific interleukin-17 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_1110193
subclass of: OBI_1110129
definition: An assay that measures epitope specific interleukin-17 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: assay of epitope specific interleukin-17 production by T cells
has curation status: IAO_0000122

cytometric bead array assay of epitope specific interleukin-17 production by T cells
type: Class
equivalent class: Class
  intersection of: cytometric bead array assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_1110193
subclass of: cytometric bead array assay
subclass of: assay of epitope specific interleukin-17 production by T cells
definition: A cytometric bead array assay that measures epitope specific interleukin-17 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cytometric bead array assay of epitope specific interleukin-17 production by T cells
has curation status: IAO_0000122

cytometric bead array assay of epitope specific interleukin-10 production by T cells
type: Class
equivalent class: Class
  intersection of: cytometric bead array assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_1110187
subclass of: cytometric bead array assay
subclass of: assay of epitope specific interleukin-10 production by T cells
definition: A cytometric bead array assay that measures epitope specific interleukin-10 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cytometric bead array assay of epitope specific interleukin-10 production by T cells
has curation status: IAO_0000122

detection of specific nucleic acids with complementary probes of epitope specific interleukin-21 production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acids with complementary probes
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: epitope specific interleukin-21 production by T cells
subclass of: detection of specific nucleic acids with complementary probes
subclass of: assay of epitope specific interleukin-21 production by T cells
definition: A detection of specific nucleic acids with complementary probes that measures epitope specific interleukin-21 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: detection of specific nucleic acids with complementary probes of epitope specific interleukin-21 production by T cells
has curation status: IAO_0000122

intracellular cytokine staining assay of epitope specific interleukin-5 production by T cells
type: Class
equivalent class: Class
  intersection of: intracellular cytokine staining assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_1110202
subclass of: intracellular cytokine staining assay
subclass of: assay of epitope specific interleukin-5 production by T cells
definition: An intracellular cytokine staining assay that measures epitope specific interleukin-5 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: intracellular cytokine staining assay of epitope specific interleukin-5 production by T cells
has curation status: IAO_0000122

cytometric bead array assay of epitope specific interleukin-2 production by T cells
type: Class
equivalent class: Class
  intersection of: cytometric bead array assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_1110056
subclass of: cytometric bead array assay
subclass of: OBI_0001445
definition: A cytometric bead array assay that measures epitope specific interleukin-2 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cytometric bead array assay of epitope specific interleukin-2 production by T cells
has curation status: IAO_0000122

cell culture analyte detection bioassay of epitope specific interleukin-16 production by T cells
type: Class
equivalent class: Class
  intersection of: cell culture analyte detection bioassay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: epitope specific interleukin-16 production by T cells
subclass of: cell culture analyte detection bioassay
subclass of: assay of epitope specific interleukin-16 production by T cells
definition: A cell culture analyte detection bioassay that measures epitope specific interleukin-16 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cell culture analyte detection bioassay of epitope specific interleukin-16 production by T cells
has curation status: IAO_0000122

ELISA of epitope specific macrophage inflammatory protein-1 alpha production by T cells
type: Class
equivalent class: Class
  intersection of: ELISA
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: epitope specific macrophage inflammatory protein-1 alpha production by T cells
subclass of: ELISA
subclass of: assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells
definition: An ELISA that measures epitope specific macrophage inflammatory protein-1 alpha production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
editor preferred term: ELISA of epitope specific macrophage inflammatory protein-1 alpha production by T cells
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000122

intracellular cytokine staining assay of epitope specific granulocyte macrophage colony-stimulating factor production by T cells
type: Class
equivalent class: Class
  intersection of: intracellular cytokine staining assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_1110184
subclass of: intracellular cytokine staining assay
subclass of: assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells
definition: An intracellular cytokine staining assay that measures epitope specific granulocyte macrophage colony-stimulating factor production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: intracellular cytokine staining assay of epitope specific granulocyte macrophage colony-stimulating factor production by T cells
has curation status: IAO_0000122

RNAi profiling by array assay
type: Class
subclass of: analyte assay
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: analyte role
    intersection of: Restriction
      on property: is role of
      some values from: ribonucleic acids
subclass of: Restriction
  on property: has participant
  some values from: OBI_0400148
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: molecular feature identification objective
definition: An assay in which double stranded RNA is synthesized with a sequence complementary to a gene(s) of interest and introduced into a cell or organism, where it is recognized as exogenous genetic material and activates the RNAi pathway resulting in knockdown of the transcripts and providing a means to study downstream changes in gene expression.
definition source: EFO_0001030 RNAi profiling by array
term editor: PERSON: James Malone
editor preferred term: RNAi profiling by array assay
has curation status: IAO_0000120

genotype information
type: Class
subclass of: OBI_0001404
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: genetic population background information
  intersection of: Restriction
    on property: has part
    some values from: OBI_0001364
disjoint with: OBI_0001364
example of usage: Genotype information can be: Mus musculus wild type (in this case the genetic population background information is Mus musculus), C57BL/6J Hnf1a+/- (in this case, C57BL/6J is the genetic population background information and Hnf1a+/- is the allele information
term editor: Group: OBI group
definition source: Group: OBI group
definition: a genetic characteristics information that is about the genetic material of an organism and minimally includes information about the genetic background and can in addition contain information about specific alleles, genetic modifications, etc.
editor note: discussed on San Diego OBI workshop, March 2011
editor preferred term: genotype information
has curation status: IAO_0000120

RNA stability design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: molecular feature identification objective
    intersection of: Restriction
      on property: is about
      some values from: ribonucleic acids
disjoint with: species comparison design
disjoint with: transcription profiling by RT-PCR design
disjoint with: microRNA profiling by array design
disjoint with: organism development design
disjoint with: family history design
disjoint with: quality control testing design
disjoint with: clinical history design
disjoint with: OBI_0001358
disjoint with: OBI_0001365
disjoint with: OBI_0001374
disjoint with: OBI_0001377
disjoint with: OBI_0001396
disjoint with: OBI_0001401
disjoint with: OBI_0001403
disjoint with: OBI_0001408
disjoint with: OBI_0001409
disjoint with: OBI_0001410
disjoint with: OBI_0001411
disjoint with: OBI_0001418
disjoint with: OBI_0001422
disjoint with: OBI_0001426
disjoint with: OBI_0001427
disjoint with: OBI_0001429
disjoint with: OBI_0001432
disjoint with: OBI_0001435
disjoint with: OBI_0001440
disjoint with: OBI_0001441
disjoint with: OBI_0001444
disjoint with: OBI_0001448
disjoint with: OBI_0001454
disjoint with: OBI_0001460
disjoint with: OBI_0001464
disjoint with: OBI_0300311
disjoint with: OBI_0500001
disjoint with: OBI_0500005
disjoint with: OBI_0500006
disjoint with: OBI_0500009
disjoint with: OBI_0500010
disjoint with: OBI_0500017
disjoint with: OBI_0500018
disjoint with: OBI_0500019
disjoint with: OBI_0500020
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design that examines the stability and/or decay of RNA transcripts.
definition source: MO_553 RNA_stability_design
editor preferred term: RNA stability design
has curation status: IAO_0000120

tiling microarray
type: Class
subclass of: OBI_0400148
definition source: EFO_0002704: tiling array
term editor: Person: Helen Parkinson
definition: a DNA microarray which has short fragments of nucleic acid immobilized on a substrate. These are designed to cover the whole genome of the target species. Tiling arrays are used to determine genome binding in ChIP assays or to identify transcribed regions.
alternative term: genome tiling array
editor preferred term: tiling microarray
has curation status: IAO_0000120

assay of epitope specific IP-10 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_0001462
subclass of: OBI_1110129
definition: An assay that measures epitope specific IP-10 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: assay of epitope specific IP-10 production by T cells
has curation status: IAO_0000122

intracellular cytokine staining assay of epitope specific interleukin-13 production by T cells
type: Class
equivalent class: Class
  intersection of: intracellular cytokine staining assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_1110191
subclass of: intracellular cytokine staining assay
subclass of: assay of epitope specific interleukin-13 production by T cells
definition: An intracellular cytokine staining assay that measures epitope specific interleukin-13 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: intracellular cytokine staining assay of epitope specific interleukin-13 production by T cells
has curation status: IAO_0000122

species comparison design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: organism feature identification objective
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: independent variable specification
    intersection of: Restriction
      on property: is about
      some values from: OBI_0100026
disjoint with: transcription profiling by RT-PCR design
disjoint with: microRNA profiling by array design
disjoint with: organism development design
disjoint with: family history design
disjoint with: quality control testing design
disjoint with: clinical history design
disjoint with: OBI_0001358
disjoint with: OBI_0001365
disjoint with: OBI_0001374
disjoint with: OBI_0001377
disjoint with: OBI_0001396
disjoint with: OBI_0001401
disjoint with: OBI_0001403
disjoint with: OBI_0001408
disjoint with: OBI_0001409
disjoint with: OBI_0001410
disjoint with: OBI_0001411
disjoint with: OBI_0001418
disjoint with: OBI_0001422
disjoint with: OBI_0001426
disjoint with: OBI_0001427
disjoint with: OBI_0001429
disjoint with: OBI_0001432
disjoint with: OBI_0001435
disjoint with: OBI_0001440
disjoint with: OBI_0001441
disjoint with: OBI_0001444
disjoint with: OBI_0001448
disjoint with: OBI_0001454
disjoint with: OBI_0001460
disjoint with: OBI_0001464
disjoint with: OBI_0300311
disjoint with: OBI_0500001
disjoint with: OBI_0500005
disjoint with: OBI_0500006
disjoint with: OBI_0500009
disjoint with: OBI_0500010
disjoint with: OBI_0500017
disjoint with: OBI_0500018
disjoint with: OBI_0500019
disjoint with: OBI_0500020
definition: A study design that assays differences between distinct species.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_675 species_design
editor preferred term: species comparison design
has curation status: IAO_0000120

X-ray crystallography assay of MHC:epitope complex binding to TCR
type: Class
equivalent class: Class
  intersection of: X-ray crystallography assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_1110057
subclass of: X-ray crystallography assay
subclass of: binding complex 3D structure determination assay
subclass of: OBI_1110124
definition: A X-ray crystallography assay that measures MHC:epitope complex binding to TCR
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: X-ray crystallography assay of MHC:epitope complex binding to TCR
has curation status: IAO_0000122

transcription profiling by RT-PCR design
type: Class
subclass of: OBI_0001430
subclass of: Restriction
  on property: has part
  some values from: transcription profiling identification objective
subclass of: Restriction
  on property: is realized by
  all values from: Class
    intersection of: Restriction
      on property: has part
      some values from: OBI_0001361
    intersection of: Restriction
      on property: has participant
      some values from: PCR instrument
disjoint with: microRNA profiling by array design
disjoint with: organism development design
disjoint with: family history design
disjoint with: quality control testing design
disjoint with: clinical history design
disjoint with: OBI_0001358
disjoint with: OBI_0001365
disjoint with: OBI_0001374
disjoint with: OBI_0001377
disjoint with: OBI_0001396
disjoint with: OBI_0001401
disjoint with: OBI_0001403
disjoint with: OBI_0001408
disjoint with: OBI_0001409
disjoint with: OBI_0001410
disjoint with: OBI_0001411
disjoint with: OBI_0001418
disjoint with: OBI_0001422
disjoint with: OBI_0001426
disjoint with: OBI_0001427
disjoint with: OBI_0001429
disjoint with: OBI_0001432
disjoint with: OBI_0001435
disjoint with: OBI_0001440
disjoint with: OBI_0001441
disjoint with: OBI_0001444
disjoint with: OBI_0001448
disjoint with: OBI_0001454
disjoint with: OBI_0001460
disjoint with: OBI_0001464
disjoint with: OBI_0300311
disjoint with: OBI_0500001
disjoint with: OBI_0500005
disjoint with: OBI_0500006
disjoint with: OBI_0500009
disjoint with: OBI_0500010
disjoint with: OBI_0500017
disjoint with: OBI_0500018
disjoint with: OBI_0500019
disjoint with: OBI_0500020
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design which aims to examine the transcriptome of a biological sample by reverse transcription PCR (RT-PCR).
definition source: Group: ArrayExpress production team
editor preferred term: transcription profiling by RT-PCR design
has curation status: IAO_0000120

epitope specific T cell enhancement of B cell mediated immune response
type: Class
equivalent class: Class
  intersection of: helper T cell enhancement of B cell mediated immune response
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: helper T cell enhancement of B cell mediated immune response
definition: A process of T cell enhancement of B cell mediated immune response resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific T cell enhancement of B cell mediated immune response
has curation status: IAO_0000122

ELISA of epitope specific chemokine (C-C motif) ligand 1 production by T cells
type: Class
equivalent class: Class
  intersection of: ELISA
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: epitope specific chemokine (C-C motif) ligand 1 production by T cells
subclass of: ELISA
subclass of: assay of epitope specific chemokine (C-C motif) ligand 1 production by T cells
definition: An ELISA that measures epitope specific chemokine (C-C motif) ligand 1 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
editor preferred term: ELISA of epitope specific chemokine (C-C motif) ligand 1 production by T cells
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000122

epitope specific interleukin-21 production by T cells
type: Class
equivalent class: Class
  intersection of: interleukin-21 production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: interleukin-21 production
subclass of: epitope specific cytokine production by T cells
definition: A process of interleukin-21 production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific interleukin-21 production by T cells
has curation status: IAO_0000122

cell-cell binding detection by flow cytometry assay of MHC:epitope complex binding to TCR
type: Class
equivalent class: Class
  intersection of: cell-cell binding detection by flow cytometry assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_1110057
subclass of: cell-cell binding detection by flow cytometry assay
subclass of: OBI_1110124
definition: A cell-cell binding detection by flow cytometry assay that measures MHC:epitope complex binding to TCR
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cell-cell binding detection by flow cytometry assay of MHC:epitope complex binding to TCR
has curation status: IAO_0000122

proteomic profiling by array assay
type: Class
subclass of: analyte assay
subclass of: Restriction
  on property: has participant
  some values from: OBI_0400149
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: OBI_0100051
    intersection of: Restriction
      on property: has part
      some values from: PR_000000001
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: analyte role
    intersection of: Restriction
      on property: is role of
      some values from: PR_000000001
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: molecular feature identification objective
term editor: Person: James Malone
definition: An assay that proteins in a sample are detected, quantified or otherwise analysed, e.g. antibody profiling using an array based technology
definition source: EFO_0002765 proteomic profiling by array
editor preferred term: proteomic profiling by array assay
has curation status: IAO_0000120

cell culture analyte detection bioassay of epitope specific interferon-gamma production by T cells
type: Class
equivalent class: Class
  intersection of: cell culture analyte detection bioassay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_1110185
subclass of: cell culture analyte detection bioassay
subclass of: OBI_0001414
definition: A cell culture analyte detection bioassay that measures epitope specific interferon-gamma production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cell culture analyte detection bioassay of epitope specific interferon-gamma production by T cells
has curation status: IAO_0000122

ELISPOT assay of epitope specific granzyme B production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0600031
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_0001371
subclass of: OBI_0001436
subclass of: OBI_0600031
definition: An ELISPOT assay that measures epitope specific granzyme B production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
editor preferred term: ELISPOT assay of epitope specific granzyme B production by T cells
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000122

microRNA profiling by array design
type: Class
subclass of: OBI_0001430
subclass of: Restriction
  on property: is realized by
  all values from: Class
    intersection of: Restriction
      on property: has part
      some values from: microRNA profiling by array assay
    intersection of: Restriction
      on property: has participant
      some values from: OBI_0400148
subclass of: Restriction
  on property: has part
  some values from: transcription profiling identification objective
disjoint with: organism development design
disjoint with: family history design
disjoint with: quality control testing design
disjoint with: clinical history design
disjoint with: OBI_0001358
disjoint with: OBI_0001365
disjoint with: OBI_0001374
disjoint with: OBI_0001377
disjoint with: OBI_0001396
disjoint with: OBI_0001401
disjoint with: OBI_0001403
disjoint with: OBI_0001408
disjoint with: OBI_0001409
disjoint with: OBI_0001410
disjoint with: OBI_0001411
disjoint with: OBI_0001418
disjoint with: OBI_0001422
disjoint with: OBI_0001426
disjoint with: OBI_0001427
disjoint with: OBI_0001429
disjoint with: OBI_0001432
disjoint with: OBI_0001435
disjoint with: OBI_0001440
disjoint with: OBI_0001441
disjoint with: OBI_0001444
disjoint with: OBI_0001448
disjoint with: OBI_0001454
disjoint with: OBI_0001460
disjoint with: OBI_0001464
disjoint with: OBI_0300311
disjoint with: OBI_0500001
disjoint with: OBI_0500005
disjoint with: OBI_0500006
disjoint with: OBI_0500009
disjoint with: OBI_0500010
disjoint with: OBI_0500017
disjoint with: OBI_0500018
disjoint with: OBI_0500019
disjoint with: OBI_0500020
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design in which a microRNA array is used to analyse the microRNA component of the transcriptome.
definition source: Group: ArrayExpress production team
editor preferred term: microRNA profiling by array design
has curation status: IAO_0000120

assay of T cell epitope specific tolerance induction
type: Class
equivalent class: Class
  intersection of: OBI_0001488
  intersection of: Restriction
    on property: has part
    some values from: OBI_0001471
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: epitope specific tolerance induction by T cells
subclass of: OBI_0001484
subclass of: OBI_0001488
subclass of: Restriction
  on property: has part
  some values from: OBI_0001471
definition: An assay that measures epitope specific tolerance induction by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: assay of T cell epitope specific tolerance induction
has curation status: IAO_0000122

detection of specific nucleic acids with complementary probes of epitope specific RANTES production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acids with complementary probes
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_0001366
subclass of: detection of specific nucleic acids with complementary probes
subclass of: assay of epitope specific RANTES production by T cells
definition: A detection of specific nucleic acids with complementary probes that measures epitope specific RANTES production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: detection of specific nucleic acids with complementary probes of epitope specific RANTES production by T cells
has curation status: IAO_0000122

cytometric bead array assay of epitope specific interleukin-4 production by T cells
type: Class
equivalent class: Class
  intersection of: cytometric bead array assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_1110199
subclass of: cytometric bead array assay
subclass of: OBI_0001450
definition: A cytometric bead array assay that measures epitope specific interleukin-4 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cytometric bead array assay of epitope specific interleukin-4 production by T cells
has curation status: IAO_0000122

assay of epitope specific lymphotoxin A production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: epitope specific lymphotoxin A production by T cells
subclass of: OBI_0001400
definition: An assay that measures epitope specific lymphotoxin A production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: assay of epitope specific lymphotoxin A production by T cells
has curation status: IAO_0000122

organism development design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: organism feature identification objective
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: UBERON_0000105
        intersection of: Restriction
disjoint with: family history design
disjoint with: quality control testing design
disjoint with: clinical history design
disjoint with: OBI_0001358
disjoint with: OBI_0001365
disjoint with: OBI_0001374
disjoint with: OBI_0001377
disjoint with: OBI_0001396
disjoint with: OBI_0001401
disjoint with: OBI_0001403
disjoint with: OBI_0001408
disjoint with: OBI_0001409
disjoint with: OBI_0001410
disjoint with: OBI_0001411
disjoint with: OBI_0001418
disjoint with: OBI_0001422
disjoint with: OBI_0001426
disjoint with: OBI_0001427
disjoint with: OBI_0001429
disjoint with: OBI_0001432
disjoint with: OBI_0001435
disjoint with: OBI_0001440
disjoint with: OBI_0001441
disjoint with: OBI_0001444
disjoint with: OBI_0001448
disjoint with: OBI_0001454
disjoint with: OBI_0001460
disjoint with: OBI_0001464
disjoint with: OBI_0300311
disjoint with: OBI_0500001
disjoint with: OBI_0500005
disjoint with: OBI_0500006
disjoint with: OBI_0500009
disjoint with: OBI_0500010
disjoint with: OBI_0500017
disjoint with: OBI_0500018
disjoint with: OBI_0500019
disjoint with: OBI_0500020
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design that assays events associated with development. Development applies to organism(s) acquiring a mature state.
definition source: MO_892 development_or_differentiation_design
editor preferred term: organism development design
has curation status: IAO_0000120

family history design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: organism feature identification objective
disjoint with: quality control testing design
disjoint with: clinical history design
disjoint with: OBI_0001358
disjoint with: OBI_0001365
disjoint with: OBI_0001374
disjoint with: OBI_0001377
disjoint with: OBI_0001396
disjoint with: OBI_0001401
disjoint with: OBI_0001403
disjoint with: OBI_0001408
disjoint with: OBI_0001409
disjoint with: OBI_0001410
disjoint with: OBI_0001411
disjoint with: OBI_0001418
disjoint with: OBI_0001422
disjoint with: OBI_0001426
disjoint with: OBI_0001427
disjoint with: OBI_0001429
disjoint with: OBI_0001432
disjoint with: OBI_0001435
disjoint with: OBI_0001440
disjoint with: OBI_0001441
disjoint with: OBI_0001444
disjoint with: OBI_0001448
disjoint with: OBI_0001454
disjoint with: OBI_0001460
disjoint with: OBI_0001464
disjoint with: OBI_0300311
disjoint with: OBI_0500001
disjoint with: OBI_0500005
disjoint with: OBI_0500006
disjoint with: OBI_0500009
disjoint with: OBI_0500010
disjoint with: OBI_0500017
disjoint with: OBI_0500018
disjoint with: OBI_0500019
disjoint with: OBI_0500020
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design in which the family history such as traits, characteristics, susceptibility to disease is studied.
definition source: MO_544 family_history_design
editor preferred term: family history design
has curation status: IAO_0000120

ELISA of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
type: Class
equivalent class: Class
  intersection of: ELISA
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_0001439
subclass of: ELISA
subclass of: OBI_0001459
definition: An ELISA that measures epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
editor preferred term: ELISA of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000122

transcription profiling identification objective
type: Class
subclass of: molecular feature identification objective
definition: A molecular feature identification objective that aims to characterize the abundance of transcripts
definition source: Group: Penn Group
term editor: Person: Chris Stoeckert, Jie Zheng
editor preferred term: transcription profiling identification objective
has curation status: IAO_0000120

DNA methylation profiling by array assay
type: Class
subclass of: DNA methylation profiling assay
subclass of: Restriction
  on property: has participant
  some values from: OBI_0400148
term editor: Person: James Malone
comment: Philippe Rocca-Serra
definition: An assay in which the methylation state of DNA is determined and is compared between samples using array technology
editor preferred term: DNA methylation profiling by array assay
definition source: EFO_0002759 methylation profiling by array
has curation status: IAO_0000120

assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: epitope specific macrophage inflammatory protein-1 alpha production by T cells
subclass of: OBI_1110129
definition: An assay that measures epitope specific macrophage inflammatory protein-1 alpha production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells
has curation status: IAO_0000122

epitope specific granulocyte colony stimulating factor production by T cells
type: Class
equivalent class: Class
  intersection of: granulocyte colony-stimulating factor production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: granulocyte colony-stimulating factor production
subclass of: epitope specific cytokine production by T cells
definition: A process of granulocyte colony stimulating factor production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific granulocyte colony stimulating factor production by T cells
has curation status: IAO_0000122

microRNA profiling by array assay
type: Class
subclass of: transcription profiling assay
subclass of: Restriction
  on property: has participant
  some values from: OBI_0400148
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: transcription profiling identification objective
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: analyte role
    intersection of: Restriction
      on property: is role of
      some values from: ribonucleic acids
subclass of: Restriction
  on property: has_specified_output
  some values from: measured expression level
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: OBI_0100051
    intersection of: Restriction
      on property: has part
      some values from: ribonucleic acids
definition: An assay in which a microRNA array is used to analyse the microRNA component of the transcriptome.
definition source: EFO_0000753 microRNA profiling by array
term editor: PERSON: James Malone
editor preferred term: microRNA profiling by array assay
has curation status: IAO_0000120

quality control testing design
type: Class
subclass of: OBI_0500000
disjoint with: clinical history design
disjoint with: OBI_0001358
disjoint with: OBI_0001365
disjoint with: OBI_0001374
disjoint with: OBI_0001377
disjoint with: OBI_0001396
disjoint with: OBI_0001401
disjoint with: OBI_0001403
disjoint with: OBI_0001408
disjoint with: OBI_0001409
disjoint with: OBI_0001410
disjoint with: OBI_0001411
disjoint with: OBI_0001418
disjoint with: OBI_0001422
disjoint with: OBI_0001426
disjoint with: OBI_0001427
disjoint with: OBI_0001429
disjoint with: OBI_0001432
disjoint with: OBI_0001435
disjoint with: OBI_0001440
disjoint with: OBI_0001441
disjoint with: OBI_0001444
disjoint with: OBI_0001448
disjoint with: OBI_0001454
disjoint with: OBI_0001460
disjoint with: OBI_0001464
disjoint with: OBI_0300311
disjoint with: OBI_0500001
disjoint with: OBI_0500005
disjoint with: OBI_0500006
disjoint with: OBI_0500009
disjoint with: OBI_0500010
disjoint with: OBI_0500017
disjoint with: OBI_0500018
disjoint with: OBI_0500019
disjoint with: OBI_0500020
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design in which some aspects of the experiment is quality controlled for the purposes of quality assurance.
definition source: MO_981 quality_control_testing_design
editor preferred term: quality control testing design
has curation status: IAO_0000120

clinical history design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: organism feature identification objective
    intersection of: Restriction
      on property: is about
      some values from: OGMS_0000015
disjoint with: OBI_0001358
disjoint with: OBI_0001365
disjoint with: OBI_0001374
disjoint with: OBI_0001377
disjoint with: OBI_0001396
disjoint with: OBI_0001401
disjoint with: OBI_0001403
disjoint with: OBI_0001408
disjoint with: OBI_0001409
disjoint with: OBI_0001410
disjoint with: OBI_0001411
disjoint with: OBI_0001418
disjoint with: OBI_0001422
disjoint with: OBI_0001426
disjoint with: OBI_0001427
disjoint with: OBI_0001429
disjoint with: OBI_0001432
disjoint with: OBI_0001435
disjoint with: OBI_0001440
disjoint with: OBI_0001441
disjoint with: OBI_0001444
disjoint with: OBI_0001448
disjoint with: OBI_0001454
disjoint with: OBI_0001460
disjoint with: OBI_0001464
disjoint with: OBI_0300311
disjoint with: OBI_0500001
disjoint with: OBI_0500005
disjoint with: OBI_0500006
disjoint with: OBI_0500009
disjoint with: OBI_0500010
disjoint with: OBI_0500017
disjoint with: OBI_0500018
disjoint with: OBI_0500019
disjoint with: OBI_0500020
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design that the organism's clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. is studied.
definition source: MO_832 clinical_history_design
editor preferred term: clinical history design
has curation status: IAO_0000120

detection of specific nucleic acids with complementary probes of epitope specific interleukin-4 production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acids with complementary probes
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_1110199
subclass of: detection of specific nucleic acids with complementary probes
subclass of: OBI_0001450
definition: A detection of specific nucleic acids with complementary probes that measures epitope specific interleukin-4 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: detection of specific nucleic acids with complementary probes of epitope specific interleukin-4 production by T cells
has curation status: IAO_0000122

cell culture analyte detection bioassay of epitope specific granulocyte macrophage colony-stimulating factor production by T cells
type: Class
equivalent class: Class
  intersection of: cell culture analyte detection bioassay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_1110184
subclass of: cell culture analyte detection bioassay
subclass of: assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells
definition: A cell culture analyte detection bioassay that measures epitope specific granulocyte macrophage colony-stimulating factor production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cell culture analyte detection bioassay of epitope specific granulocyte macrophage colony-stimulating factor production by T cells
has curation status: IAO_0000122

intracellular cytokine staining assay of epitope specific interleukin-21 production by T cells
type: Class
equivalent class: Class
  intersection of: intracellular cytokine staining assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: epitope specific interleukin-21 production by T cells
subclass of: intracellular cytokine staining assay
subclass of: assay of epitope specific interleukin-21 production by T cells
definition: An intracellular cytokine staining assay that measures epitope specific interleukin-21 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: intracellular cytokine staining assay of epitope specific interleukin-21 production by T cells
has curation status: IAO_0000122

detection of specific nucleic acids with complementary probes of epitope specific monocyte chemotactic protein-1 production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acids with complementary probes
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_0001386
subclass of: detection of specific nucleic acids with complementary probes
subclass of: OBI_0001465
definition: A detection of specific nucleic acids with complementary probes that measures epitope specific monocyte chemotactic protein-1 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: detection of specific nucleic acids with complementary probes of epitope specific monocyte chemotactic protein-1 production by T cells
has curation status: IAO_0000122

ELISA of epitope specific monocyte chemotactic protein-1 production by T cells
type: Class
equivalent class: Class
  intersection of: ELISA
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_0001386
subclass of: ELISA
subclass of: OBI_0001465
definition: An ELISA that measures epitope specific monocyte chemotactic protein-1 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
editor preferred term: ELISA of epitope specific monocyte chemotactic protein-1 production by T cells
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000122

assay of epitope specific chemokine (C-C motif) ligand 4 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_0001362
subclass of: OBI_1110129
definition: An assay that measures epitope specific chemokine (C-C motif) ligand 4 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: assay of epitope specific chemokine (C-C motif) ligand 4 production by T cells
has curation status: IAO_0000122

ELISA of epitope specific interleukin-21 production by T cells
type: Class
equivalent class: Class
  intersection of: ELISA
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: epitope specific interleukin-21 production by T cells
subclass of: ELISA
subclass of: assay of epitope specific interleukin-21 production by T cells
definition: An ELISA that measures epitope specific interleukin-21 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
editor preferred term: ELISA of epitope specific interleukin-21 production by T cells
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000122

assay of epitope specific type IV hypersensitivity by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: epitope specific type IV hypersensitivity by T cells
subclass of: OBI_1110037
definition: An assay that measures epitope specific type IV hypersensitivity by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: assay of epitope specific type IV hypersensitivity by T cells
has curation status: IAO_0000122

cytometric bead array assay of epitope specific interleukin-13 production by T cells
type: Class
equivalent class: Class
  intersection of: cytometric bead array assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_1110191
subclass of: cytometric bead array assay
subclass of: assay of epitope specific interleukin-13 production by T cells
definition: A cytometric bead array assay that measures epitope specific interleukin-13 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cytometric bead array assay of epitope specific interleukin-13 production by T cells
has curation status: IAO_0000122

detection of specific nucleic acids with complementary probes of epitope specific interferon-gamma production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acids with complementary probes
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_1110185
subclass of: detection of specific nucleic acids with complementary probes
subclass of: OBI_0001414
definition: A detection of specific nucleic acids with complementary probes that measures epitope specific interferon-gamma production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: detection of specific nucleic acids with complementary probes of epitope specific interferon-gamma production by T cells
has curation status: IAO_0000122

epitope specific tumor necrosis factor superfamily cytokine production by T cells
type: Class
equivalent class: Class
  intersection of: tumor necrosis factor superfamily cytokine production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: tumor necrosis factor superfamily cytokine production
subclass of: epitope specific cytokine production by T cells
definition: A process of tumor necrosis factor superfamily cytokine production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific tumor necrosis factor superfamily cytokine production by T cells
has curation status: IAO_0000122

allele information
type: Class
subclass of: OBI_0001364
subclass of: Class
  intersection of: Restriction
    on property: is part of
    some values from: genotype information
  intersection of: Restriction
    on property: is about
    some values from: SO_0000001
definition source: MO_58 Allele
term editor: Person: Chris Stoeckert, Jie Zheng
definition: a genetic alteration information that about one of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on sequence. Polymorphisms are included in this definition.
editor preferred term: allele information
editor note: discussed on San Diego OBI workshop, March 2011
example of usage: genotype information 'C57BL/6J Hnf1a+/-' in this case, Hnf1a+/- is the allele information
has curation status: IAO_0000120

cytometric bead array assay of epitope specific tumor necrosis factor production by T cells
type: Class
equivalent class: Class
  intersection of: cytometric bead array assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: OBI_1110206
subclass of: OBI_0001368
subclass of: OBI_0001416
definition: A cytometric bead array assay that measures epitope specific tumor necrosis factor production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cytometric bead array assay of epitope specific tumor necrosis factor production by T cells
has curation status: IAO_0000122

ELISPOT assay of epitope specific interleukin-17 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0600031
subclass of: assay of epitope specific interleukin-17 production by T cells
subclass of: OBI_0600031
definition: An ELISPOT assay that measures epitope specific interleukin-17 production by T cells
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
editor preferred term: ELISPOT assay of epitope specific interleukin-17 production by T cells
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000122