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Pierre Grenon and Barry Smith: "SNAP and SPAN: Towards Geospatial Dynamics"
Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester
Allyson Lister
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/
An ontology for the annotation of biomedical and functional genomics experiments.
Barry Smith
Bill Bug
Bjoern Peters
Carlo Torniai
Chris Mungall
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
Alan Ruttenberg
Chris Stoeckert
Chris Taylor
Cristian Cocos
Daniel Rubin
Daniel Schober
Dawn Field
Dirk Derom
Elisabetta Manduchi
Eric Deutsch
Frank Gibson
Gilberto Fragoso
Helen C. Causton
Helen Parkinson
Holger Stenzhorn
James Malone
Jay Greenbaum
Jeffrey Grethe
Jennifer Fostel
Jessica Turner
Jie Zheng
Joe White
John Westbrook
Kevin Clancy
Larisa Soldatova
Lawrence Hunter
Liju Fan
Luisa Montecchi
Matthew Pocock
Melanie Courtot
Melissa Haendel
Mervi Heiskanen
Monnie McGee
Norman Morrison
OWL-DL
Ontology for Biomedical Investigation
Philip Lord
Philippe Rocca-Serra
Pierre Grenon
Richard Bruskiewich
Richard Scheuermann
Robert Stevens
Ryan R. Brinkman
Stefan Wiemann
Susanna-Assunta Sansone
Tanya Gray
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.
Tina Hernandez-Boussard
Trish Whetzel
Yongqun He
free, no license required.
Description
An account of the content of the resource.
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
Person:Alan Ruttenberg
Use on obsolete terms, relating the term to another term that can be used as a substitute
Contributor
An entity responsible for making contributions to the content of the resource.
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
An administrative note of use for a curator but of no use for a user
PERSON:Alan Ruttenberg
OBO foundry unique label
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 .
An alternative name for a class or property which is unique across the OBO Foundry.
GROUP:OBO Foundry <http://obofoundry.org/>
PERSON:Bjoern Peters
PERSON:Chris Mungall
PERSON:Melanie Courtot
has obsolescence reason
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.
Creator
An entity primarily responsible for making the content of the resource.
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
The topic of the content of the resource.
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.
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
An alternative term used by the Functional Genomics Data (FGED) Society.
Resource Identifier
An unambiguous reference to the resource within a given context.
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
A date associated with an event in the life cycle of the resource.
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
Typically, a Title will be a name by which the resource is formally known.
A name given to the resource.
Relation
Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system.
A reference to a related resource.
adjacent to
x adjacent to y if and only if x and y share a boundary
expand expression to
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
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)"
has_specified_input
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.
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.
PERSON: Alan Ruttenberg
see is_input_of example_of_usage
definition
PERSON:Daniel Schober
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
editor note
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.
in branch
An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.
has ID prefix
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.
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
PERSON:Bill Bug
Language
A language of the intellectual content of the resource.
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
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
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
Resource Type
The nature or genre of the content of the resource.
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
part_of antisymmetric property xsd:true
use boolean value xsd:true to indicate that the property is an antisymmetric property
first order logic expression
has_specified_output
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
20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
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
expand assertion to
A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
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)"
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
Source
A reference to a resource from which the present resource is derived.
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
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
example of usage
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
example
Publisher
An entity responsible for making the resource available
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
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.
The extent or scope of the content of the resource.
In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')
relates an class defined in an ontology, to the type of it's denotator
is denotator type
Relating an ontology used to record id policy to the ontology namespace whose policy it manages
has ID range allocated to
Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300]
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
For external terms/classes, the ontology from which the term was imported
has ID digit count
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
The physical or digital manifestation of the resource.
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
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.
Information about rights held in and over the resource.
is part of
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
part of
part_of
domain of part of
has part
has_part
inheres in
inheres_in
is bearer of
bearer of
bearer_of
is realized by
realized by
realized_by
realizes
participates in
participates_in
has participant
has_participant
is concretization of
concretization of
concretization_of
concretizes
is immediately preceded by
immediately preceded by
immediately_preceded_by
immediately precedes
immediately_precedes
is preceded by
preceded by
preceded_by
precedes
is course of
course of
course_of
has course
has_course
occurs in
occurs_in
has site of
has_site_of
begins to exist during
begins_to_exist_during
ceases to exist during
ceases_to_exist_during
s depends on
s_depends_on
has granular part
has_granular_part
has granular process part
has_granular_process_part
is granular part of
granular part of
granular_part_of
is granular part of process
granular part of process
granular_part_of_process
is aggregate of
aggregate of
aggregate_of
is fiat part of
fiat part of
fiat_part_of
has participant beginning to exist
has_participant_beginning_to_exist
has participant ceasing to exist
has_participant_ceasing_to_exist
is function of
function of
function_of
is quality of
quality of
quality_of
is role of
role of
role_of
is located in
located in
located_in
is located at
located at
located_at
g depends on
g_depends_on
has function
has_function
has quality
has_quality
has role
has_role
has measurement unit label
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
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
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
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.
see http://code.google.com/p/information-artifact-ontology/issues/detail?id=25&q=denote
is about
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.
This document is about information artifacts and their representations
is_about is a (currently) primitive relation that relates an information artifact to an entity.
person:Alan Ruttenberg
mentions
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)
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
An information artifact IA mentions an entity E exactly when it has a component/part that denotes E
PERSON: Jonathan Rees
Person: Alan Ruttenberg
denotes
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
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.
Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
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
is quality measurement of
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
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.
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.
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.
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.
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
has coordinate unit label
relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point
is duration of
relates a process to a time-measurement-datum that represents the duration of the process
is quality measured as
2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship
inverse of the relation of is quality measurement of
is quality specification of
Person:Bjoern Peters
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.
quality is specified as
inverse of the relation of is quality specification of
has time stamp
relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken
has measurement datum
relates a time stamped measurement datum to the measurement datum that was measured
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
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.
obsolete_is_concretization_of
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.
replaced by: http://purl.obolibrary.org/obo/BFO_0000059
is_specified_input_of
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
obsolete_is_concretized_as
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.
replaced by: http://purl.obolibrary.org/obo/BFO_0000058
obsolete_has_quality
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]
replaced by: http://purl.obolibrary.org/obo/BFO_0000086
obsolete_is_realized_by
Relation between a realizable and a process. Reciprocal relation of realizes [GOC:cjm]
replaced by http://purl.obolibrary.org/obo/BFO_0000054: 'is realized by'
obsoleted_has_specified_output_information
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.
is_manufactured_by
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.
has_make
has_manufacturer
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)
obsolete_has_function
Relation between an independent continuant and a function.
replaced by: http://purl.obolibrary.org/obo/BFO_0000085
obsoleted_is_reagent_in
Relationship between a substance and a protocol application in which it participates, where the substance has a ReagentRole
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
obsolete_realizes
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: 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.
replaced by http://purl.obolibrary.org/obo/BFO_0000055: 'realizes'
obsoleted_utilizes_reagent
Relationship between a protocol application and a substance that has role reagent that participates in the protocol application
see example_of_usage for is_reagent_in
obsoleted_is_device_for
Relationship between a device and a protocol application in which it participates
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
is_specified_output_of
obsoleted_utilizes_device
Relationship between protocol application and an intrument in which it participates
see example_of_usage for is_device_for
is_proxy_for
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)
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.
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
obsoleted_has_specified_input_information
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.
obsolete_has_role
A relation between a continuant C and a role R. The reciprocal relation of role_of.
replaced by: http://purl.obolibrary.org/obo/BFO_0000087
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
A cell sorting process achieves the objective specification 'material separation objective'
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.
modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
A relation between a data set and the process in which it participates and was produced. Inverse of outputs_specified_data relation.
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
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.
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
Is the inverse relation of has_specfied_input_information
is grain of
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
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.
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.
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.
definition needs clean up to indicate directionality
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
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
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.
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.
A relationship between two material entitites that each have disposition to form a complex with the other.
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
has organization member
Relating an organization to a legal person or organization.
See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_id=177891&atid=886178
The production of IFN-gamma by effector T cells is a process result of T cell stimulation through the TCR
is a relationship between a process and a preceding occurrent that directly caused the later one to occur
derives from
A is spatially_disjoint_from B if and only if they have no parts in common
surrounded by
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
temporal relation
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
starts
starts with
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.
Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
has measurement value
has x coordinate value
has z coordinate value
has y coordinate value
has_feature_value
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.
entity
continuant
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.
a heart
a person
a symphony orchestra
endurant
the color of a tomato
the disposition of blood to coagulate
the lawn and atmosphere in front of our building
the mass of a cloud
occurrent
An entity that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants.
a surgical operation as processual context for a nosocomical infection
perdurant
the life of an organism
the most interesting part of Van Gogh's life
the spatiotemporal context occupied by a process of cellular meiosis
the spatiotemporal region occupied by the development of a cancer tumor
independent continuant
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
a chair
a leg
an organism
substantial entity
the bottom right portion of a human torso
dependent continuant
A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities.
spatial region
A continuant that is neither bearer of quality entities nor inheres in any other entities.
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.
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].
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.
parts of the sum total of all space in the universe
the sum total of all space in the universe
process
A processual entity that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities.
the process of cell-division
the process of sleeping
temporal region
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].
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.
An occurrent that is part of time.
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].
the duration of a surgical procedure
the moment of death
the time it takes to run a marathon
two dimensional region
A spatial region with two dimensions.
the surface of a cube-shaped part of space
the surface of a rectilinear planar figure-shaped part of space
the surface of a sphere-shaped part of space
disposition
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.
the disposition of a patient with a weakened immune system to contract disease
the disposition of a vase to brake if dropped
the disposition of metal to conduct electricity
the disposition of vegetables to decay when not refrigerated
realizable entity
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.
If a realizable entity [snap:RealizableEntity] inheres in a continuant [snap:Continuant], this does not imply that it is actually realized.
the function of the reproductive organs
the role of being a doctor
zero dimensional region
A spatial region with no dimensions.
a point
quality
A specifically dependent continuant that is exhibited if it inheres in an entity or entities at all (a categorical property).
the ambient temperature of air
the circumference of a waist
the mass of a piece of gold
the shape of a nose
the weight of a chimpanzee
specifically dependent continuant
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.
mode
property
the disposition of fish to decay
the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc.
the liquidity of blood
the smell of mozzarella
trope
temporal instant
A connected temporal region comprising a single moment of time.
right now
the moment at which a child is born
the moment at which a finger is detached in an industrial accident
connected temporal region
A temporal region every point of which is mediately or immediately connected with every other point of which.
the 1970s years
the time from the beginning to the end of a heart attack
the time taken up by cellular meiosis
role
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.
the role of a biological grandfather as legal guardian in the context of a system of laws
the role of a chemical compound in an experiment
the role of a patient relative as defined by a hospital administrative form
the role of a person as a surgeon
the role of a student in a university
the role of a woman as a legal mother in the context of system of laws
the role of ingested matter in digestion
object boundary
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.
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.
substance boundary
the outer surface of a cell or cell wall
the surface of the earth
the surface of the interior of the stomach
the surface of the skin
one dimensional region
A spatial region with one dimension.
an edge of a cube-shaped part of space
the part of space that is a line stretching from one end of absolute space to the other
three dimensional region
A spatial region with three dimensions.
a cube-shaped part of space
a sphere-shaped part of space
site
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.
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).
Maria's nostril or her intestines for a variety of bacteria
a particular room in a particular hospital
generically dependent continuant
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.
a certain PDF file that exists in different and in several hard drives
scattered temporal region
A temporal region every point of which is not mediately or immediately connected with every other point of which.
the time occupied by the individual games of the World Cup
the time occupied by the individual liaisons in a romantic affair
function
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.
the digestive function of the stomach to nutriate the body
the function of a birth canal to enable transport
the function of a computer program to compute mathematical equations
the function of a hammer to drive in nails
the function of a judge in a court of law
the function of an automobile to provide transportation
the function of reproduction in the transmission of genetic material
process boundary
A processual entity that is the fiat or bona fide instantaneous temporal process boundary.
birth
death
the detaching of a finger in an industrial accident
the final separation of two cells at the end of cell-division
the forming of a synapse
the incision at the beginning of a surgery
the onset of REM sleep
temporal interval
A connected temporal region lasting for more than a single moment of time.
any continuous temporal duration during which a process occurs
material entity
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
Examples: collection of random bacteria, a chair, dorsal surface of the body
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.
portion of organism substance
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.
portion of tissue
Anatomical structure, that consists of similar cells and intercellular matrix, aggregated according to genetically determined spatial relationships. [database_cross_reference: CARO:MAH]
multi-tissue structure
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.
epithelium
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.
gross anatomical part
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.
water
An inorganic hydroxy compound that has formula H2O.
biotin
A biotin that has formula C10H16N2O3S.
peptide
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.
deoxyribonucleic acids
High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
hydrogensulfite
A sulfur oxoanion that has formula HO3S.
glucose
5'-adenylyl sulfate
An acyl sulfate that has formula C10H14N5O10PS.
molecular entity
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
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
N-ethyl-N-nitrosourea
proton
Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u.
luciferin
A low-molecular-mass compound present in bioluminescent organisms that emits light when oxidized in presence of enzyme luciferase.
sodium chloride
An inorganic chloride salt that has formula ClNa.
lead(0)
An elemental lead that has formula Pb.
acrylamide
An acrylamide that has formula C3H5NO.
hydroxyl
A reactive oxygen specy that has formula HO.
ruthenium
An iron group element that has formula Ru.
fluorescein
A xanthene dye that has formula C20H12O5.
gadodiamide hydrate
gadoteridol
phenolsulfonphthalein
rhodium
A cobalt group element that has formula Rh.
gadolinium
A lanthanoid that has formula Gd.
terbium
A lanthanoid that has formula Tb.
nucleic acid
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.
ribonucleic acids
Naturally occurring polyribonucleotides.
amino acids
Carboxylic acids containing one or more amino groups.
macromolecule
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.
polymer
gadolinium molecular entities
gadodiamide
A gadolinium coordination entity that has formula C16H26GdN5O8.
sodium phosphates
phosphorus-32
The radioactive isotope of phosphorus with relative atomic mass 31.973907 and half-life of 14.26 days.
phosphorus-33
The radioactive isotope of phosphorus with relative atomic mass 32.971725, half-life of 25.34 days and nuclear spin (1)/2.
Cy3 dye
Cy5 dye
digoxigenin
A 12beta-hydroxy steroid that has formula C23H34O5.
ethylenediaminetetraacetic acid
A tetracarboxylic acid that has formula C10H16N2O8.
double-stranded DNA
chromium-51
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.
Alexa Fluor 532
An organosulfonic acid that has formula C34H33N3O11S2.
Alexa Fluor 546
An organic heteropentacyclic compound that has formula C44H45Cl3N4NaO14S3.
Alexa Fluor 555
A fluorescent dye of absorption wavelength 555 nm and emission wavelength 565 nm, derived from a 3,6-diaminoxanthene-4,5-disulfate.
tritiated thymidine
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.
Dimethyl sulfate
Diethylpyrocarbonate
1,1-dihydroxy-3-ethoxy-2-butanone
A butanone derivative having two hydroxy substituents at the 1-position and an ethoxy substituent at the 3-position.
N-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimide
A carbodiimide having cyclcohexyl and 2-(4-morpholinyl)ethyl as the two N-substituents.
N-methylisatoic anhydride
A 3,1-benzoxazin-1,4-dione having an N-methyl substituent.
Fe-BABE
A tetracarboxylic acid consisting of ethylenediaminetetraacetic acid having a 4-bromoacetamidobenzyl group at the C1-position and (S)-configuration.
EDTA methidiumpropylamide
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.
bromophenol blue
tris
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.
cell
Anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .."
fibroblast
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.
epithelial cell
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.
T cell
A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex.
mast cell
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.
hepatocyte
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.
erythrocyte
A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen.
macrophage
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.
B cell
A lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
dendritic cell
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).
lymphocyte
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.
CD4-positive, alpha-beta T cell
A mature alpha-beta T cell that expresses an alpha-beta T cell receptor and the CD4 coreceptor.
CD8-positive, alpha-beta T cell
A T cell expressing an alpha-beta T cell receptor and the CD8 coreceptor.
basophil
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.
plasma cell
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.
alpha-beta T cell
A T cell that expresses an alpha-beta T cell receptor complex.
CD8-positive, alpha-beta cytotoxic T cell
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.
mature NK T cell
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.
mononuclear cell
A leukocyte with a single non-segmented nucleus in the mature form.
soil
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.
podzol
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.
Material in or on which organisms may live.
geographical location
A reference to a place on the Earth, by its name or by its geographical location.
antibody-dependent cellular cytotoxicity
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.
type IV hypersensitivity
An inflammatory response driven by T cell recognition of processed soluble or cell-associated antigens leading to cytokine release and leukocyte activation.
cytokine production
The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
cell killing
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.
T cell mediated cytotoxicity
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.
adaptive immune response
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).
cytokine production involved in immune response
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.
platelet activating factor production
The synthesis or release of platelet activating factor following a stimulus, resulting in an increase in its intracellular or extracellular levels.
tolerance induction
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.
B cell tolerance induction
A process involving any mechanism for tolerance induction in B cells.
T cell tolerance induction
A process involving any mechanism for tolerance induction in T cells.
hypersensitivity
An inflammatory response to an exogenous environmental antigen or an endogenous antigen initiated by the adaptive immune system.
cytokine production involved in inflammatory response
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.
molecular_function
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.
antigen binding
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.
catalytic activity
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.
RNA-directed DNA polymerase activity
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.
ion-channel activity
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.
cellular_component
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.
chromosome
A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. Source: ISBN:0198547684
glucose metabolic process
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.
chromatin remodeling
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
phagocytosis
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.
immune response
Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
response to DNA damage stimulus
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.
cell cycle
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.
blood coagulation
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.
biological_process
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.
opsonization
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.
cell proliferation
The multiplication or reproduction of cells, resulting in the expansion of a cell population.
fertilization
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).
cellular process
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.
gene expression
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.
vascular endothelial growth factor production
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.
immunoglobulin mediated immune response
An immune response mediated by immunoglobulins, whether cell-bound or in solution.
immunoglobulin complex
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.
B cell receptor complex
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.
antigen processing and presentation
The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex.
protein domain specific binding
Interacting selectively and non-covalently with a specific domain of a protein. Source: GOC:go_curators
actin filament polymerization
Assembly of actin filaments by the addition of actin monomers to a filament. Source: GOC:mah
hemopoiesis
connective tissue growth factor production
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.
chemokine production
The appearance of a chemokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
granulocyte macrophage colony-stimulating factor production
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.
hepatocyte growth factor production
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.
type I interferon production
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.
interferon-beta production
The appearance of interferon-beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interferon-gamma production
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.
interleukin-1 alpha production
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.
interleukin-1 beta production
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.
interleukin-1 production
The appearance of interleukin-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-10 production
The appearance of interleukin-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-11 production
The appearance of interleukin-11 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-12 production
The appearance of interleukin-12 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-13 production
The appearance of interleukin-13 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-14 production
The appearance of interleukin-14 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-15 production
The appearance of interleukin-15 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-16 production
The appearance of interleukin-16 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-17 production
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.
interleukin-18 production
The appearance of interleukin-18 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-19 production
The appearance of interleukin-19 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-2 production
The appearance of interleukin-2 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-20 production
The appearance of interleukin-20 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-21 production
The appearance of interleukin-21 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-22 production
The appearance of interleukin-22 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-23 production
The appearance of interleukin-23 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-24 production
The appearance of interleukin-24 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-25 production
The appearance of interleukin-25 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-26 production
The appearance of interleukin-26 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-27 production
The appearance of interleukin-27 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-3 production
The appearance of interleukin-3 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-4 production
The appearance of interleukin-4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-5 production
The appearance of interleukin-5 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-6 production
The appearance of interleukin-6 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-7 production
The appearance of interleukin-7 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-8 production
The appearance of interleukin-8 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-9 production
The appearance of interleukin-9 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
TRAIL production
The appearance of TRAIL due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
tumor necrosis factor production
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.
lymphotoxin A production
The appearance of lymphotoxin A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
transforming growth factor beta1 production
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.
transforming growth factor beta2 production
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.
transforming growth factor beta3 production
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.
macromolecule localization
Any process in which a macromolecule is transported to, or maintained in, a specific location.Source: GOC:mah
DNA polymerase activity
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.
type III interferon production
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.
chemokine (C-X-C motif) ligand 9 production
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.
helper T cell enhancement of adaptive immune response
Positive regulation of an adaptive immune response mediated via cytokine production by helper T cell.
helper T cell enhancement of T cell mediated immune response
Positive regulation of a T cell mediated immune response mediated via cytokine production by a helper T cell.
helper T cell enhancement of B cell mediated immune response
Positive regulation of a B cell mediated immune response mediated via cytokine production by a helper T cell.
granzyme A production
The appearance of granzyme A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
perforin production
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.
granulysin production
The appearance of granulysin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
regulation of gene expression, epigenetic
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
regulation of molecular function, epigenetic
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
T cell proliferation
The expansion of a T cell population by cell division. Follows T cell activation.
T cell receptor complex
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.
T cell activation
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.
immunoglobulin complex, circulating
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.
DNA polymerase complex
A protein complex that possesses DNA polymerase activity and is involved in template directed synthesis of DNA.
peptide antigen binding
Interacting selectively and non-covalently with an antigen peptide.
MHC protein complex
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.
membrane-bounded organelle
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.
protein complex
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.
cytotoxic T cell degranulation
The regulated exocytosis of secretory granules containing preformed mediators such as perforin and granzymes by a cytotoxic T cell.
sequence-specific DNA binding
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.
regulation of DNA methylation
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
cellular developmental process
A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition.
response to stimulus
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.
chromosome organization
actin polymerization-dependent cell motility
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
transforming growth factor beta production
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.
monocyte chemotactic protein-1 production
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.
chemokine (C-C motif) ligand 4 production
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.
macrophage inflammatory protein-1 gamma production
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.
macrophage inflammatory protein-1 alpha production
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.
chemokine (C-C motif) ligand 5 production
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.
chemokine (C-C motif) ligand 1 production
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.
granulocyte colony-stimulating factor production
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.
IP-10 production
The appearance of IP-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
granzyme B production
The appearance of granzyme B due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
tumor necrosis factor superfamily cytokine production
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.
tumor necrosis factor (ligand) superfamily member 11 production
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.
interleukin-17A production
The appearance of interleukin-17A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-17F production
The appearance of interleukin-17F due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
complement-dependent cytotoxicity
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.
histamine secretion mediated by immunoglobulin
Histamine release triggered by the binding of an antigen to an immunoglobulin bound to the cell surface.
immune complex formation
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.
immunoglobulin-mediated neutralization
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.
Insulin resistance
`Increased resistance` (PATO:0001650) towards `insulin` (PRO:000009054).
conditional specification
OBI branch derived
PlanAndPlannedProcess Branch
a directive information entity that specifies what should happen if the trigger condition is fulfilled
measurement unit label
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.
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.
A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
Examples of measurement unit labels are liters, inches, weight per volume.
PERSON: Melanie Courtot
objective specification
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."
Answers the question, why did you do this experiment?
OBI Plan and Planned Process/Roles Branch
PERSON: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
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.
purpose of a study; support of hypothesis, discovery of new information
narrative object
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
A narrative object is an information content entity that is a set of propositions.
Examples of narrative objects are reports, journal articles, and patents submission.
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
person:Chris Stoeckert
action specification
OBI Plan and Planned Process branch
Pour the contents of flask 1 into flask 2
a directive information entity that describes an action the bearer will take
datum label
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.
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
GROUP: IAO
software
GROUP: OBI
PERSON: Chris Stoeckert
Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit.
see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178
obsolete2_digital entity
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Superclass was 'digitial quality'
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.
obsolete_digital entity
journal article
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.
a report that is published in a journal
information carrier
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'.
A quality of an information bearer that imparts the information content
The pattern in ink on a page of a paperback novel.
model number
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.
manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers
obsolete2_binary digital entity
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Superclass was 'digital entity'
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.
MS Word document, ZIP file, DICOM file, JPEG file
binary digital entity
digital_entity
a unit of measure is the quality of some material entity compared to which another quality is some multiple of.
programming language
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.
R, Perl, Java
data item
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.
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.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
Data items include counts of things, analyte concentrations, and statistical summaries.
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
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.
data
symbol
20091104, MC: this needs work and will most probably change
a smallish, word-like datum...
numeral
A symbol that denotes a number.
information content entity
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity
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.
integer numeral
a numeral that denotes an integer
scalar measurement datum
10 feet. 3 ml.
2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form
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.
a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
directive information entity
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.
8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
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
time trigger
revisit?
obsolete_study interpretation
2009-03-16: definition was "A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application."
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.
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
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.
dot plot
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.
Dot plot of SSC-H and FSC-H.
person:Allyson Lister
graph
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.
PERSON: Lawrence Hunter
obsolete2_text based digital entity
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digital document'
A text based digital entity is a digital entity that is encoded so that it only contains text characters.
XML file, C++ source code file
text based digital entity
rule
MSI
PRS
a rule is an executable which guides, defines, restricts actions
example to be added
contour plot
Contour plot of SSC-H, FSC-H, and FL1-H.
generically_dependent_continuants
group:Flow Cytometry community
obsolete2_report figure
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
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
Replaced by defined version of figure
report figure
algorithm
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.
PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
software interpreter
A software interpreter is a software application that executes some specified input software.
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
R program, Perl interpreter, Java virtual machine
curation status specification
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
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.
density plot
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.
Density plot of SSC-H and FSC-H.
report
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.
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.
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
Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article.
PERSON:Chris Stoeckert
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)
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
obsolete_report element
2009-03-16: needs some more work (clarify relations).
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.
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).
PERSON: Allyson Lister
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
report element
obsolete2_binary executable
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)
binary executable
person:Jennifer Fostel
source code module
A source code module is a directive information entity that specifies, using a programming language, some algorithm.
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.
obsolete_report table
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
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
report table
data format specification
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"
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
data set
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
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.
Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
image
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.
data about an ontology part
data about an ontology part is a data item about a part of an ontology, for example a term
plan specification
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
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.
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
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.
obsolete2_digital document
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digial entity'
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.
digital document
measurement datum
2/2/2009 is_specified_output of some assay?
A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
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,}.
_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.
version number
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.
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
serial number
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.
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 :-)
lot number
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.
batch number
setting datum
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.
A settings datum is a datum that denotes some configuration of an instrument.
Alan grouped these in placeholder for the moment. Name by analogy to measurement datum.
Need to rework digital entity. Digital quality was suggested by Barry.
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4
conclusion textual entity
2009/10/23 Alan Ruttenberg: We need to work on the definition still
A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers.
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
material information bearer
An information bearer is a material_entity in which a concretization of an information content entity inheres.
a hard drive, a piece of paper with writing on it, a brain
histogram
A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes.
PERSON:James Malone
heatmap
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.
Venn diagram
A Venn diagram is a report graph showing all hypothetically possible logical relations between a finite collection of sets.
WEB: http://en.wikipedia.org/wiki/Venn_diagram
obsolete_survival curve
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.
WEB: http://www.graphpad.com/www/book/survive.htm
dendrogram
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.
Dendrograms are often used in computational biology to illustrate the clustering of genes.
WEB: http://en.wikipedia.org/wiki/Dendrogram
scatter plot
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.
Comparison of gene expression values in two samples can be displayed in a scatter plot
WEB: http://en.wikipedia.org/wiki/Scatterplot
scattergraph
photograph
A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc.
PERSON:Joanne Luciano
WEB: http://en.wiktionary.org/wiki/photograph
photographic print
A photographic print is a material entity upon which a photograph generically depends.
obsolescence reason specification
The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
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.
textual entity
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.
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.
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.
Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
text
citation
Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183.
a textual entity intended to identify a particular publication
author identification
A textual entity intended to identify a particular author
L. Hunter
institutional identification
A textual entity intended to identify a particular institution
University of Colorado Denver School of Medicine
caption
A textual entity that describes a figure
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.
document title
A textual entity that names a document
Textual characteristics of traditional and Open Access scientific journals are similar
table
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
| T F --+----- T | T F F | F F
table of abbreviations
A table where the constituent texts are abbreviations and their expansions
IAO information artifact ontology OBI ontology of biomedical investiations GO gene ontology
figure
An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
Any picture, diagram or table
diagram
A figure that expresses one or more propositions
A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.
document
A collection of information content entities intended to be understood together as a whole
A journal article, patent application, laboratory notebook, or a book
publication
A document that has been accepted by a publisher
A journal article or book
publication about an investigation
A publication that is about an investigation
Most scientific journal articles
scientific publication
patent
A document that has been accepted by a patent authority
US Patent 6,449,603
document part
An abstract, introduction, method or results section.
an information content entity that is part of a document
abstract
A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes.
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.
introduction to a publication about an investigation
A part of a publication about an investigation that is about the objective specification (why the investigation is being done)
Section labelled 'introduction' of a typical scientific journal article
introduction
methods section
A part of a publication about an investigation that is about the study design of the investigation
The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article.
results section
A part of a publication about an investigation that is about a study design execution
The section labelled 'results' in a typical scientific journal article
discussion section of a publication about an investigation
A part of a publication about an investigation that is about the study interpretation of the investigation
discussion section
references section
A part of a document that has citations as parts
The list of citations found at the end of a scientific publication, grant proposal or patent application, sometimes called "literature cited" or "bibliography"
author list
Lawrence Hunter and Kevin Brettonel Cohen
part of a document that enumerates the authors of the document
institution list
The University of Colorado Denver School of Medicine and the University of Colorado Boulder.
part of a document that has parts that are institution identifications associated with the authors of the document
author contributions section
A part of a publication that is about the specific contributions of each author
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.
acknowledgements section
Part of a publication that is about the contributions of people or institutions other than the authors.
The authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscript
footnote
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.
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.
endnote
supplementary material to a document
appendix
part of a document that is segregated from the rest of the document due to its size
supplementary material
table of contents
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).
table of figures
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).
running title
A shorter version of a document title
copyright section
A document part that describes legal restrictions on making or distributing copies of the document
This work is licensed under a Creative Commons Attribution-Share Alike 3.0 United States License.
cartesian spatial coordinate datum
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
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
one dimensional cartesian spatial coordinate datum
A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region
two dimensional cartesian spatial coordinate datum
A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region
three dimensional cartesian spatial coordinate datum
A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region
length measurement datum
A scalar measurement datum that is the result of measurement of length quality
A denotator type indicates how a term should be interpreted from an ontological perspective.
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
A scalar measurement datum that is the result of measurement of mass quality
hypothesis textual entity
A textual entity that expresses an assertion that is intended to be tested.
time measurement datum
A scalar measurement datum that is the result of measuring a temporal interval
postal address
A textual entity that is used as directive to deliver something to a person, or organization
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
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
Person:Chris Stoeckart
author role
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.
data item extraction from journal article
a planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing
documenting
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
Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
a planned process in which a document is created or added to by including the specified input in it.
wikipedia http://en.wikipedia.org/wiki/Documenting
line graph
A line graph is a type of graph created by connecting a series of data points together with a line.
WEB: http://en.wikipedia.org/wiki/Line_chart
line chart
assigning a centrally registered identifier
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.
Person:Melanie Courtot
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
associating information with a CRID in the CRID registry
A planned process in which a CRID registry associates an information content entity with a CRID symbol
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.
MC, 20101124: deprecated following discussion at IAO call 20101124. Term was deemed not necessary - no use case for now.
CRID symbol
A symbol that is part_of a CRID and that is sufficient to look up a record from the CRID's registry.
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.
Original proposal from Bjoern, discussions at IAO calls
PERSON: Bill Hogan
PMID:12345, 12345 in a database column which has header "pubmedID"
CRID
Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation.
An information content entity that consists of a CRID symbol and additional information about which CRID registry it belongs.
Entries in a Column of which the header is "Pubmed ID"
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.
The following URL: "http://www.ncbi.nlm.nih.gov/pubmed/19918065"
The following sentence contains a CRID: "The article with Pubmed ID: 19918065".
CRID registry
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.
IAO call, 20101124: PubMed registry is an instance of CRID registry
looking up a CRID
A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol
time stamped measurement datum
time sampled measurement data set
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.
experimental time series
pmid:20604925 - time-lapse live cell microscopy
written name
"Bill Clinton"
"The Eiffel Tower"
"United States of America"
A textual entity that denotes a particular in reality.
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.
software method
A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task.
PERSON: Michel Dumontier
software module
A software module is software composed of a collection of software methods.
PERSON: Melanei Courtot
software library
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.
software application
A software application is software that can be directly executed by some processing unit.
software script
A software script is software whose instructions can be executed using a software interpreter.
Cricetinae
Phodopus
Phodopus sungorus
Muridae
Mus
Mus musculus
Rattus
Rattus norvegicus
Viruses
Asteroideae
Heliantheae
Mutisieae
Obtectomera
Rhodobacter
canis group
phagocytophilum group
Rhodobacter sphaeroides
mitosporic Filobasidiales
Thlaspi caerulescens
Cryptococcus [NCBITaxon:107441]
Parvoviridae
Dependovirus
Adeno-associated virus - 2
Rhodospirillum
Rhodospirillum rubrum
Chloroflexaceae
Nectriaceae
Chloroflexus
Chloroflexus aurantiacus
Coronaviridae
Coronavirus
Penaeoidea
pseudomallei group
Cyanobacteria
Chroococcales
Synechococcus
Polytrichopsida
Populus tremula
Synechocystis
spotted fever group
typhus group
Synechocystis sp.
Saccharomyces kudriavzevii
Saccharomyces mikatae
Funariidae
Synechocystis sp. PCC 6803
Oscillatoriales
Nostocales
Nostocaceae
Anabaena
Anabaena variabilis
Teleostomi
Euteleostomi
Nostoc
Sphingobacteria
mitosporic Saccharomycetales
Populus tomentosa
Brucellaceae
Sulfolobaceae
Deinococcales
Coxiellaceae
Legionellales
Burkholderiaceae
unclassified Burkholderiales
Thermoanaerobacter tengcongensis
Chromadorea
Bombyciformes
Acidithiobacillus
Trichodesmium
Trichodesmium erythraeum
Paracoccidioides brasiliensis
Proteobacteria
Neoteleostei
Eurypterygii
Ctenosquamata
Acanthomorpha
Euacanthomorpha
Holacanthopterygii
Gammaproteobacteria
Firmicutes
Leuconostoc
Leuconostoc mesenteroides
Oenococcus oeni
Pediococcus
Pediococcus pentosaceus
Staphylococcus
Staphylococcus aureus
Polytrichum juniperinum
Deinococcus-Thermus
Deinococcus
Deinococcus radiodurans
Euacanthopterygii
Streptococcaceae
Streptococcus
Streptococcus gordonii
Streptococcus suis
Streptococcus mutans
Streptococcus agalactiae
Streptophytina
Streptococcus pneumoniae
Magnetospirillum
Streptococcus pyogenes
Thlaspi
Burkholderia mallei
Penaeus
Coffea
Coffea arabica
Burkholderia fungorum
Enterococcus
Enterococcus faecalis
Enterococcus faecium
Gerbera
Xanthomonadales
Pseudomonadaceae
Alteromonadales
Vibrionales
Pasteurellales
Lactococcus
Lactococcus lactis
Spirochaetales
Pseudomonas aeruginosa group
Pseudomonas fluorescens group
Pseudomonas putida group
Spirochaetaceae
Borrelia
Pteridaceae
Bacillales
Bacillus
Borrelia burgdorferi
Bacillus anthracis
Pinus [NCBITaxon:139271]
Bacillus cereus
Bacillus subtilis
Mycetozoa
Methanothermobacter
Methanothermobacter thermautotrophicus
Ehrhartoideae
Pooideae
Panicoideae
PACCAD clade
Oryzeae
Poeae
Triticeae
Andropogoneae
Saccharomycotina
Pezizomycotina
Dothideomycetes et Chaetothyriomycetes incertae sedis
Eurotiomycetes
Sordariomycetes
Sordariomycetes incertae sedis
Schizosaccharomycetes
Magnaporthe
Magnaporthe grisea
Clostridium
Clostridium acetobutylicum
Clostridium botulinum
Clostridium sporogenes
Clostridium thermocellum
Moorella thermoacetica
Tremellomycetidae
Homobasidiomycetes
Caulobacter vibrioides
Plantaginaceae
Group 2 species
Treponema
Lactobacillus
Treponema denticola
Citrus aurantiifolia
Lactobacillus gasseri
Lactobacillus sakei
Treponema pallidum
Lactobacillus salivarius
Listeria
Phaseoleae
Trifolieae
Vicieae
Loteae
Listeria monocytogenes
Listeria innocua
Corynebacteriaceae
Actinomyces
Actinomyces naeslundii
Novosphingobium
Heterobasidiomycetes
Bifidobacterium
Ixoroideae
Coffeeae
Corynebacterium
Rosoideae
Corynebacterium glutamicum
Passeroidea
Thermoanaerobacter
Actinobacteria (class)
Mycobacteriaceae
Mycobacterium
Mycobacterium leprae
Mycobacterium tuberculosis
Gerbera hybrid cultivar
Deinococcaceae
Enterogona
Thermoprotei
Methanobacteria
Halobacteria
Thermoplasmata
Thermococci
Archaeoglobi
Psathyrellaceae
Coprinopsis
Drosophiliti
Entomoplasmatales
Actinopteri
Elopocephala
Clupeocephala
Otophysi
Cypriniphysi
Otocephala
Clostridia
Clostridiales
Peptococcaceae
Thermoanaerobacteriaceae
Bacillaceae
Listeriaceae
Alicyclobacillaceae
Lactobacillales
Neognathi
Salmonoidei
Anurophorinae
Cryptopygus
Cryptopygus antarcticus
Aquificae (class)
Magnetospirillum magnetotacticum
Streptomyces
Thermotogae (class)
Thermotogaceae
Deinococci
Orbiliomycetes
Orbiliales
Zinnia
Streptomyces coelicolor
Lepidium
Campylobacter
Desulfovibrionaceae
Pleuronichthys
Pleuronichthys verticalis
Corynebacterium glutamicum ATCC 13032
Campylobacter jejuni
Pancrustacea
Mandibulata
Bacteria
Sphingobacteriales
Aquificae
Chloroflexi
Thermotogae
Actinobacteria
Thermobifida fusca
Fusobacteria (class)
Fusobacterales
Fusobacteriaceae
Spirochaetes
Spirochaetes (class)
Actinomycetales
Chlamydiae
Chlamydiae (class)
Rhodospirillales
Rhodobacterales
Sphingomonadales
Caulobacterales
Herminiimonas arsenicoxydans
Actinomycetaceae
Streptomycetaceae
Methylophilales
Neisseriales
Rhodocyclales
Homo/Pan/Gorilla group
Mycoplasmatales
Pasteuria nishizawae
Helicobacter
Mycoplasmataceae
Mycoplasma
Mycoplasma genitalium
Helicobacter pylori
Streptococcus mutans UA159
Mycoplasma pneumoniae
Mycoplasma pulmonis
Ureaplasma
Ureaplasma urealyticum
Desulfovibrionales
Geobacteraceae
Campylobacterales
Mesoplasma florum
Archaea
Methanobacteriales
Methanobacteriaceae
Sylvia communis
Lymnaeoidea
Antirrhineae
Bifidobacterium longum
Mutisioideae
Methanosarcinaceae
Methanosarcina
Methanosarcina barkeri
Methanosarcina mazei
Methanococcoides
Hypocreomycetidae
Sordariomycetidae
Archaeoglobales
Archaeoglobaceae
Archaeoglobus
Archaeoglobus fulgidus
Halobacteriales
Halobacteriaceae
Halobacterium
Halobacterium salinarum
Halobacterium sp.
Burkholderiales Genera incertae sedis
Haloferax volcanii
Methanomicrobia
Acidithiobacillales
Acidithiobacillaceae
Haloferax
Thermococcales
Thermococcaceae
Pyrococcus
Thermoproteales
Thermoproteaceae
Thermoproteus
Thermoproteus tenax
Rhizobium/Agrobacterium group
Sinorhizobium/Ensifer group
Paxilineae
SARS coronavirus
Sulfolobales
Sulfolobus
Sulfolobus acidocaldarius
Sulfolobus solfataricus
Thermoplasmatales
Thermoplasma
Thermoplasma acidophilum
Rubus
magnoliids
Thermotoga
Thermotoga maritima
Brucella
Brucella abortus
Rutaceae
Xylella
Xylella fastidiosa
Saliceae
Moniliformopses
Thermotogales
Rubiaceae
Rubrobacterineae
Dechloromonas aromatica
Francisella
Xenopus [NCBITaxon:262014]
Francisella tularensis
Crocosphaera
Crocosphaera watsonii
Francisella tularensis subsp. novicida
Rickettsia sibirica subgroup
Citrus
Citrus sinensis
Aquifex
Nostoc punctiforme
Saccharomyces paradoxus
Saccharomyces pastorianus
Eukaryota
Bovinae
Coregonus
Rubrivivax
Rubrivivax gelatinosus
Ralstonia syzygii
Sinorhizobium
Alphaproteobacteria
Betaproteobacteria
Deltaproteobacteria
Geobacter
Geobacter metallireducens
Staphylococcus aureus subsp. aureus MSSA476
Burkholderia pseudomallei
Trichocomaceae
Pseudomonas
Pseudomonas aeruginosa
Phaeophyceae
Ectocarpales
Ectocarpaceae
Ectocarpus
Ectocarpus siliculosus
Crenarchaeota
Euryarchaeota
Salmonella enterica
Burkholderia cepacia
ssDNA viruses
Cryptococcus gattii
Methanococcoides burtonii
Pseudomonas fluorescens
Veillonella
Veillonella parvula
Epsilonproteobacteria
Ceratopteris
Ceratopteris thalictroides
Vitis vinifera
Hypocrea
Collembola
Lachancea
Pseudomonas putida
Mesobatrachia
Pipoidea
Herminiimonas
Chlorophyta
Chlamydomonadales
Ralstonia solanacearum
Chlamydomonadaceae
Chlamydomonas
Chlamydomonas reinhardtii
Cyprinoidea
Pleuronectoidei
Tetraodontiformes
Tetraodontoidei
Tetraodontidae
Takifugu
Takifugu rubripes
Schistosomatoidea
Schistosomatidae
Laurasiatheria
Euarchontoglires
Glires
Simiiformes
Cercopithecoidea
Hominoidea
Chlorophyceae
Saccharophagus
Embryophyta
Bifidobacteriaceae
Mollicutes
Acidaminococcaceae
Clostridiaceae
Rhodobacteraceae
Burkholderia
Methylophilaceae
Thiomonas
Xanthomonadaceae
Synechococcus elongatus
Chloroflexi (class)
Chloroflexales
Fusobacteria
Aquificales
Bryophyta
Polytrichales
Polytrichaceae
Polytrichum
Bryopsida
Funariales
Funariaceae
Physcomitrella
Physcomitrella patens
Buchnera
Rubus idaeus
Sophophora
melanogaster group
melanogaster subgroup
obscura group
pseudoobscura subgroup
Lycopodiophyta
Isoetopsida
Selaginellales
Teleostei
Euteleostei
Selaginellaceae
Acanthopterygii
Selaginella
Percomorpha
Tetradontoidea
Paracanthopterygii
Ostariophysi
Tetrapoda
Amniota
Theria
Sauria
Filicophyta
Filicales
Ralstonia pickettii
Filicopsida
Bartonella grahamii
Dictyosteliida
Viridiplantae
Coniferophyta
Lepidium sativum
Coniferales
Fungi/Metazoa group
Eremothecium gossypii
Eremothecium
Aspergillus terreus
Pinaceae
Onygenales
Metazoa
Bilateria
Acoelomata
Pseudocoelomata
Picea
Tylenchina
Tylenchoidea
Heteroderinae
Picea glauca
Coelomata
Protostomia
Neoptera
Pinus
Endopterygota
Pinus radiata
Deuterostomia
Sciurognathi
Carnivora
Alveolata
stramenopiles
Euglenozoa
Cricetidae
Muroidea
Xanthomonas
Felinae
Xanthomonas campestris
Streptomyces avermitilis
Entomoplasmataceae
Lactobacillaceae
Magnoliophyta
Rickettsieae
Xanthomonas campestris pv. campestris
Magnoliales
Magnoliaceae
Francisellaceae
Liriodendron
Liriodendron tulipifera
Zinnia elegans
Lotus japonicus
Schizosaccharomycetales
mitosporic Trichocomaceae
mitosporic Onygenales
Strongyloides ratti
Heterodera
Apoidea
Cannabaceae
Cannabis
Cannabis sativa
Fagales
Betula
Betula pendula
Cryptosporidiidae
Azotobacter group
Betulaceae
Azotobacter
ssRNA positive-strand viruses, no DNA stage
Azotobacter vinelandii
Streptophyta
Suina
Pecora
Equus subg. Equus
Rhizobiales
Agrobacterium
Rickettsia sibirica
Agrobacterium tumefaciens
BEP clade
Vitaceae
Vitis
Isotomidae
Sylviidae
Malpighiales
Neosartorya
Neosartorya fischeri
Desulfitobacterium
Salicaceae
Populus
Populus trichocarpa
Populus trichocarpa x Populus deltoides
Populus deltoides
Brassicales
Brassicaceae
Arabidopsis
Arabidopsis thaliana
Brassica
Brassica juncea
Brassica napus
Brassica rapa
Rosales
Rosaceae
Aedes/Ochlerotatus group
Ditrysia
Bombycoidea
Noctuoidea
Estrildidae
Viannia
Leishmania braziliensis species complex
Haplorrhini
Rhizobium
Feliformia
Caniformia
Fabaceae
Mesorhizobium loti
Papilionoideae
Sinorhizobium meliloti
Bartonella henselae
Rhizobium leguminosarum
Glycine
Glycine max
Leishmania [NCBITaxon:38568]
Leishmania infantum species complex
Leishmania donovani species complex
Leishmania major species complex
Leishmania mexicana species complex
Diprotodontia
Lotus
Medicago
Medicago sativa
Medicago truncatula
Poales
Pisum
Pisum sativum
Paracoccidioides
Trifolium
Trifolium repens
Murinae
Cyprininae
Rasborinae
Trypanozoon
Oryza sativa (indica cultivar-group)
Oryza sativa (japonica cultivar-group)
Linaceae
Linum
Linum usitatissimum
Thraupini
Parvovirinae
Estrildinae
Vitales
Methylobacillus
Moss Superclass V
Methylobacillus flagellatus
Gentianales
Mammalia
Solanales
Solanaceae
Capsicum
Capsicum annuum
Solanum lycopersicum
Nicotiana
Nicotiana benthamiana
Neosartorya fennelliae
Solanum
Solanum tuberosum
Glossata
Neolepidoptera
Heteroneura
Mycosphaerella
Rhodospirillaceae
Sphingomonadaceae
Lamiales
Antirrhinum
Antirrhinum majus
Neopterygii
Batrachia
Protacanthopterygii
Plasmodium (Vinckeia)
Plasmodium (Laverania)
Culicoidea
Sapindales
Asterales
Asteraceae
Rubrobacter
Aconoidasida
Eimeriorina
Candida dubliniensis
Solanoideae
Nicotianoideae
Nicotianeae
Capsiceae
Solaneae
Thiomonas sp. 3As
Moorella group
Trichoderma reesei QM6a
Sylvia
Dinosauria
Saurischia
Theropoda
Coelurosauria
Muscomorpha
Schizophora
Acalyptratae
Ephydroidea
Culicimorpha
Anophelinae
Culicinae
Drosophilinae
Cyanothece
Cyanothece sp. ATCC 51142
Moorella
Liliopsida
Cellia
Pyretophorus
gambiae species complex
Dictyostelium discoideum
Poaceae
Hordeum
Hordeum vulgare
Lolium
Lolium perenne
Oryza
Oryza sativa
Triticum
Triticum aestivum
Triticum turgidum subsp. durum
Triticum turgidum
Zea
Zea mays
Festuca
Festuca arundinacea
Staphylococcus aureus subsp. aureus
Mesoplasma
Oenococcus
Thermoplasmataceae
Moraxellaceae
Drosophilini
Drosophilina
Acinetobacter
Acinetobacter baumannii
Orbiliaceae
Tetraodon
commelinids
Fungi
Schizotrypanum
Agrotis
Agrotis segetum
Neisseriaceae
Neisseria
Neisseria gonorrhoeae
Neisseria meningitidis
Ralstonia
Geospiza
Geospiza conirostris
Geospiza fortis
Geospiza magnirostris
Geospiza scandens
Ascomycota
Saccharomycetes
Saccharomycetales
Saccharomycetaceae
Novosphingobium aromaticivorans
Schizosaccharomycetaceae
Schizosaccharomyces
Schizosaccharomyces pombe
Kluyveromyces
Kluyveromyces waltii
Pichia
Pichia pastoris
Lycopersicon
Saccharomyces
Saccharomyces bayanus
Rubrobacter xylanophilus
Saccharomyces cerevisiae
Desulfitobacterium hafniense
Lachancea kluyveri
Thermoplasma volcanium
Eurotiales
Aspergillus
Insecta
Aspergillus clavatus
Alcaligenaceae
Aspergillus niger
Aspergillus fumigatus
Heterodera glycines
Hypocreales
Gibberella
Hypocreaceae
Chlamydiae/Verrucomicrobia group
Chlamydiales
Sordariales
Neurospora
Neurospora crassa
Hypocrea jecorina
Sordaria
Sordaria macrospora
Sordariaceae
Ciona savignyi
Bordetella
Bordetella bronchiseptica
Bordetella pertussis
Basidiomycota
Festuca rubra
Ustilaginomycetes
Ustilaginales
Ustilaginaceae
Ustilago
Ustilago maydis
Leymus
Hymenomycetes
Aphyllophorales
Corticiaceae
Phanerochaete
Phanerochaete chrysosporium
Agaricales
Xanthomonas axonopodis
Coprinopsis cinerea
Stegomyia
Culicini
Paxillaceae
Paxillus
Pyrococcus horikoshii
mitosporic Orbiliaceae
Monacrosporium
Zymomonas
Zymomonas mobilis
Enterobacteriaceae
Mycosphaerella graminicola
Candida
Candida albicans
Candida glabrata
Pinus resinosa
Gibberella zeae
Panagrolaimoidea
Rhabditoidea
Peloderinae
Escherichia
Escherichia coli
Agrotis ipsilon
Kinetoplastida
Trypanosomatidae
Leishmania
Leishmania braziliensis
Leishmania donovani
Leishmania major
Leishmania mexicana
Leishmania infantum
Trypanosoma
Trypanosoma brucei
Trypanosoma cruzi
Dictyostelium
Apicomplexa
Coccidia
Burkholderia thailandensis
Coniferopsida
Tracheophyta
Spermatophyta
Cryptosporidium
Cryptosporidium parvum
Haemosporida
Plasmodium
Plasmodium berghei
Plasmodium falciparum
Salmonella
Salmonella enteritidis
Taeniopygia
Taeniopygia guttata
Coregonus clupeaformis
Salmonella typhi
Salmonella typhimurium
Eumetazoa
Neosartorya fischeri group
Platyhelminthes
Trematoda
Digenea
Strigeidida
Schistosoma
Schistosoma japonicum
Schistosoma mansoni
Emberizinae
Nematoda
Rhabditida
Caenorhabditis
Caenorhabditis briggsae
Caenorhabditis elegans
Rhabditidae
Strongyloididae
Strongyloides
Spirurida
Brugia
Brugia malayi
Yersinia
Ustilaginomycetidae
Filarioidea
Onchocercidae
Tylenchida
Heteroderidae
Yersinia pestis
Aquifex aeolicus
Vibrionaceae
Mollusca
Gastropoda
Buchnera sp.
Borrelia burgdorferi group
Aquificaceae
Pulmonata
Basommatophora
Planorbidae
Biomphalaria
Biomphalaria glabrata
Photobacterium
Vibrio
Arthropoda
Crustacea
Vibrio cholerae
Malacostraca
Eucarida
Decapoda
Dendrobranchiata
Penaeidae
Penaeus monodon
Mesorhizobium
Thermoanaerobacteriales
Bacteroidetes/Chlorobi group
delta/epsilon subdivisions
Boletales
Phyllobacteriaceae
Desulfuromonadales
Hexapoda
Lepidoptera
Bombycidae
Bombyx
Bombyx mori
Apinae
Noctuidae
Paxillus involutus
Pasteurellaceae
eudicotyledons
asterids
rosids
Actinobacillus
Diptera
Nematocera
Actinobacillus pleuropneumoniae
Culicidae
Aedes
Aedes aegypti
Anopheles
Anopheles gambiae
Fabales
Brachycera
Eumalacostraca
Drosophilidae
Drosophila
Drosophila erecta
Drosophila mauritiana
Drosophila melanogaster
Thiotrichales
Pseudomonadales
Alteromonadaceae
Helicobacteraceae
Campylobacteraceae
Drosophila orena
Drosophila pseudoobscura
Drosophila sechellia
Haemophilus
Drosophila simulans
Drosophila teissieri
Drosophila yakuba
Haemophilus influenzae
Dechloromonas
Hymenoptera
Apocrita
Photobacterium profundum
Aculeata
Monacrosporium haptotylum
Pasteurella
Apidae
Apis
Apis mellifera
Pasteurella multocida
Pterygota
Ferroplasma
Caulobacter
Oxalobacteraceae
Populus euphratica
Eucoccidiorida
Rhodocyclaceae
Rickettsiales
Anaplasma
Nidovirales
Caulobacteraceae
Chordata
Urochordata
Ascidiacea
Phlebobranchia
Cionidae
Ciona
Ciona intestinalis
Bartonellaceae
Stolidobranchia
Pyuridae
Bartonella
Herdmania
Herdmania momus
Vertebrata
Rickettsiaceae
Coxiella
Mycobacterium tuberculosis complex
Coxiella burnetii
Gnathostomata
Rickettsia
Rickettsia conorii
Rickettsia prowazekii
Rickettsia rickettsii
Euphyllophyta
Actinopterygii
Cypriniformes
Cyprinidae
Danio
Danio rerio
Cyprinus
Cyprinus carpio
Arthropleona
Entomobryoidea
Ellipura
Salmoniformes
Salmonidae
Oncorhynchus
Oncorhynchus mykiss
Salmo
Bartonella quintana
Salmo salar
Salmo trutta
Gadiformes
Gadidae
Gadus
Gadus morhua
Burkholderiales
Populus tremula x Populus alba
Chlamydiaceae
Chlamydia
Magnaporthaceae
Perciformes
Percoidei
Chlamydia trachomatis
Sparidae
Sparus
Sparus aurata
Leuconostocaceae
Enterococcaceae
Rhizobiaceae
Pleuronectiformes
Pleuronectidae
Platichthys
Platichthys flesus
Sarcopterygii
Amphibia
Apini
Anura
Pipidae
Xenopus
Xenopus laevis
Chlamydophila
Chlamydophila pneumoniae
Xenopodinae
Silurana
Xenopus tropicalis
Nocardiopsaceae
Thermobifida
Sauropsida
Fusobacterium
Archosauria
Rubrobacteridae
Rubrobacterales
Rubrobacteraceae
Actinobacteridae
Bifidobacteriales
Actinomycineae
Corynebacterineae
Streptomycineae
Streptosporangineae
Fusobacterium nucleatum
Dicondylia
Amphiesmenoptera
Citrus clementina
Triticum turgidum subsp. dicoccoides
Paxillus filamentosus
Pasteuria
Leymus cinereus
Leymus triticoides
Saccharophagus degradans
Bacillus cereus group
Bacillus halodurans
Geospiza difficilis
Desulfovibrio
Desulfovibrio desulfuricans
Aves
Burkholderia cepacia complex
Neognathae
Panarthropoda
Flexibacteraceae
Craniata
Galliformes
Phasianidae
Ferroplasmaceae
Gallus
Gallus gallus
Phasianinae
Filobasidiales
Staphylococcaceae
Bacilli
Passeriformes
Fringillidae
Enterobacteriales
Cetartiodactyla
core eudicotyledons
eurosids I
eurosids II
campanulids
lamiids
Acidithiobacillus ferrooxidans
Bartonella koehlerae
Metatheria
Xanthomonas axonopodis pv. citri
Macropodidae
Macropus
Mycosphaerellaceae
Macropus eugenii
Eutheria
Anaplasmataceae
Ehrlichia
Ehrlichia canis
Primates
Methanosarcinales
Platyrrhini
Anaplasma phagocytophilum
Callitrichinae
Callithrix
Callithrix jacchus
Cebidae
Noctuinae
Catarrhini
Cercopithecidae
Cercopithecinae
Macaca
Macaca fascicularis
Macaca fuscata
Macaca mulatta
Pan
Pan troglodytes
Pongo
Pongo pygmaeus
Hominidae
Homo
Homo sapiens
Canidae
Canis
Canis familiaris
Vulpes
Vulpes vulpes
Felidae
Felis
Felis catus
Ferroplasma acidarmanus
Bacteroidetes
Cytophaga
Perissodactyla
Equidae
Equus
Equus caballus
Suidae
Sus
Sus scrofa
Ruminantia
Cytophaga hutchinsonii
Festuca brevipila
Festuca rubra subsp. fallax
Festuca rubra subsp. littoralis
Bovidae
Bos
Bos taurus
Bos indicus
Ovis
Ovis aries
Caprinae
Tetraodon nigroviridis
Rodentia
role of being consumer safety officer
the role of a human being that is realized by enforcing regulations to ensure consumer safety
Consumer safety officer; Consumer Safety Officer Positions at FDA http://69.20.19.211/jobs/cso.htm
OBI, CDISC
Person charged with serving as CSO, FDA official who coordinates the review
fluorescent reporter intensity
A measurement datum that represents the output of a scanner measuring the intensity value for each fluorescent reporter.
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.
planned process
'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.)
6/11/9: Edited at workshop. Used to include: is initiated by an agent
Injecting mice with a vaccine in order to test its efficacy
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.
A processual entity that realizes a plan which is the concretization of a plan specification.
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)
regulator role
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
OBI
Person:Jennifer Fostel
a regulatory role involved with making and/or enforcing relevant legislation and governmental orders
biological feature identification objective
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.
regulation-assigned role
Approval letter
Person: Jennifer Fostel
Regulation-assigned role is a regulatory role defined by legislation or governmental orders
regulatory role
GROUP: Role branch
Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008
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.
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
material supplier role
Jackson Labs is an organization which provide mice as experimental material
Supplier role is a special kind of service, e.g. biobank
PERSON:Jennifer Fostel
a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation.
contract research organization role
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
list-mode data file
A list-mode data file is a binary digital entity where events are stored sequentially, parameter by parameter.
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.
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.
classified data set
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.
reference substance role
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
a role inhering in a material entity that is realized when characteristics or responses elicited by the substance are used for comparison or reference.
cytological stain role
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
haemotoxylin is a general purpose nuclear stain extracted from the wood of the logwood tree WEB: http://en.wikipedia.org/wiki/Haematoxylin
centrifuge pellet role
9Mar09 after discussion with process branch changed definition to include use of centrifuge;
Definition of pellet :the material concentrated at the bottom of a centrifuge tube after centrifugation. http://www.everythingbio.com/glos/definition.php?word=pellet
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..
clinical research coordinator role
a worker role comprised of handling the administrative duties of a trial or study.
supernatant role
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
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.
chromatography column
open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178
Chromatography column in chemistry is a tube and contents (typically glass) used to purify individual chemical compounds from mixtures of compounds. It is often used for preparative applications on scales from micrograms up to kilograms.
drug role
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.
Role Branch
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
pump valve switch
A pump valve switch is a cardinal part of a liquid chromatography instrument that controls the flow.
FG:I would assume this should be a pump valve control switch and it would not be specific to a liquid chromatography instrument
OBI Instrument branch
xenotransplantation
is the transplantation of living cells, tissues or \norgans from one species to another such as from pigs to humans
physical document
A physical document is an object serving as a record of information by means of symbolic marks.
a book is a physical document
waiting
BP: I have doubts about the utility of this.
We need a better handling/modeling of time (January 2008)
not actively doing anything to a material for a duration of time.
processed material
Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
Is a material entity that is created or changed during material processing.
chromatography device
a device that facilitates the separation of mixtures. The function of a chromatography device involves passing a mixture dissolved in a "mobile phase" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture and allows it to be isolated.
chromatography instrument
mass spectrometer
A mass spectrometer is an instrument which is used to measure the mass to charge ratio of ions. All mass spectrometers consist of three basic parts: an ion source, a mass analyzer, and a detector system. The stages within the mass spectrometer are: 1. Production of ions from the sample 2. Separation of ions with different masses 3. Detection of the number of ions of each mass produced 4.Collection of data to generate the mass spectrum
LCQ Fleet Ion Trap MSn manufactured by thermo fisher scientific
obsolete_platform
suggested for deprecation https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178
A platform is an object_aggregate that is the set of instruments and software needed to perform a process. definition_source: OBI.
platform
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
liquid chromatography mass spectrometry platform
A liquid chromatography mass spectrometry platform is a platform that is the collection of instrument, software and reagents needed to perform a liquid chromatography mass spectrometry protocol. definition_source: OBI.
microarray platform
A microarray platform is a platform that contains the instruments, software and reagents needed to perform a microarray protocol. definition_source: OBI.
ratio of collected to emitted light
Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
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
person:Kevin Clancy
software optimization objective
Software_optimization is a software_testing_objective role describing a study designed to identify the best software or parameters of the software.
notified body role
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.
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
The role of notified bodies presentation: http://ec.europa.eu/enterprise/electr_equipment/emc/revision/notified_bodies.pdf
allotransplantation
is the transplantation of organs between members of the same species.
gamma counter
A processed material which measures gamma radiation
trial monitor role
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.
a responsible party involved in planning, overseeing the conduct of a study or study component, and interpreting data from a study
positive reference substance role
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
MMS mutagen
polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether
PMID: 30799. J Histochem Cytochem. 1978 Sep;26(9):696-712. Acid lipase: a histochemical and biochemical study using triton X100-naphtyl palmitate micelles.
adapted from Wikipedia before possible import from CHEBI
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
investigation
Could add specific objective specification
Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation
a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
evaluant role
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
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)
When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role.
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
examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected")
reporting party role
MO:submitter mapped to this term. So, alternative term 'submitter' was added.
Person who prepares microarray data in MAGE-TAB format and submits to a database, such as ArrayExpress.
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
a study personnel role played by a party who reports the outcome of a study component
assay
Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
A planned process with the objective to produce information about some evaluant
measuring
scientific observation
quantitative confidence value
A data item which is used to indicate the degree of uncertainty about a measurement.
sample preparation for assay
A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI.
study
diagnosis textual entity
diagnosis is an assessment of a disease or injury, its likely prognosis and treatment.
unplanned occurrence effecting an investigation
Earthquake that destroys the lab, an outside investigator discovering an adverse effect of the reagants used
a process which is external in origin to the investigation that has an impact on the outcome.
eMedical record
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.
culture medium
a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.
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.
A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008
Person: Jennifer Fostel, Jie Zheng
electronic case report tabulation
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.
polystyrene tube
Polystyrene tubes can be used to contain tissue culture cells during centrifgation
a polystyrene tube is a test tube made of polystyrene
reagent role
www.answers.com/topic/reagent; November 2008
Buffer, dye, a catalyst, a solvating agent.
GROUP: Role Branch
a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances
role of regulator of chemical manufacturer
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
a regulator involved with making and enforcing legislation and governmental orders relevant to chemical manufacture
detector reagent role
19feb2009. not clear we need this term. originally if came from microarrays -- the probes on the array are termed detectors in some instances
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
a role which inheres in a molecular entity and is realized by the process of recording or registering a stimulus.
role of certified IRB professional
WEB: http://en.wikipedia.org/wiki/Certified_IRB_Professional
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
CIP= Certified IRB Professional; http://acronyms.thefreedictionary.com/Certified+IRB+Professional
patient role
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
GROUP:Role Branch
a hospitalized person; a person with controlled diabetes; the patient's role http://www.fertilityjourney.com/testingAndDiagnosis/theRightDoctor/thePatientsRole/index.asp?C=55245395146924652778
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
material processing
A cell lysis, production of a cloning vector, creating a buffer.
A planned process which results in physical changes in a specified input material
material transformation
protocol testing objective
Protocol_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different protocols.
study subject role
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.
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.
obsolete_role of being first subject treated
First subject treated
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
Rat 1A; first enrolled patient to receive treatment
first subject treated. First subject who receives the test article or placebo in a clinical trial.
measured expression level
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.
Examples are quantified data from an expression microarray experiment, PCR measurements, etc.
responsible party role
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
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
principal investigator role
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)
a responsible party role played by a person responsible for the overall conduct of a study
transplantation
a protocol application to replace an organ or tissue of an organism
biological vector role
6/12/2009 Alan made this a material to be added role, because it was, and because this speeded up reasoning
Feb 20, 2009. The material transmitted can be genetic information (as in cloning vector) or a pathogen (as in a disease vector)
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.
1983 Sci. Amer. Jan. 58/2 Plasmids are routinely used as vectors for introducing foreign DNA into bacteria.
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
pH indicator dye role
bromophenol blue has a pH indicator dye role
the role of a dye that is realized when the dye is used in an experiment to measure the pH in a material entity
phenol red in RPMI; pH=4 indicator dye (also carries reference role)
specimen role
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.
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.
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.
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
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.
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.
sequence feature identification objective
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.
intervention design
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.
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.
Philppe Rocca-Serra
worker role
"executes the study plan" includes the suppliers and manufacturers of reagents and other materials used in the study
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
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
Bernoulli trial
is an assay where the output data is a datum with one of two values denoted success and failure.
gene list
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.
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.
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.
number of particles in subset
A measurement datum measuring the number of subjects in a defined subset in a flow cytometer instrument. The datum has a qualitative role
number of lost events electronic
74, 0, 14 events lost due to data acquisition electronic coincidence.
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.
calibration substance role
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
pH buffer used to calibrate a pH meter bears a calibration substance role
molecular feature identification objective
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.
hardware testing objective
Hardware_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different hardware, e.g. scanner.
incubator
Incubators are used in microbiology for culturing (growing) bacteria and other microorganisms. Incubators in tissue culture rooms are used for culturing stem cells, lymphocytes, skin fibroblasts and other types of cells
a device in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlled
label role
Label role is a role which inheres in a material entity and which is realized in a detection of label assay
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
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
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
baseline participant role
a reference participant role which is realized by making the reference to qualities at the start of the study or intervention
Subject at time = 0; subject before a stress test.
role of independent data monitoring committee
a trial monitor role charged recommending whether to continue, modify, or end the trial
pathologist role
a worker role of being responsible for making the histopathology diagnoses associated with data from a study; this activity occurs outside the study timeline
supernatant collection system harvesting frame
a device that is designed for collecting 90% of the supernatant in a microplate well and separating the living cell with no stress, eliminating centrifugation and other similar techniques. It can be used in a variety of release assays with different radioactive isotopes, such as Cr51 or I125.
google
filter paper
a device manufacture with the intent to provide a porous unsized paper used for filtering.
cell co-culturing
A material combination in which cell cultures of two or more different types are are combined and allowed to culture as one.
Culturing cytotoxic T-lymphocytes together with target cells in order to study lysis of the target cells. See chromium_release_assay
role of Institutional Review Board
the role of a organization that is realized by members reviewing study designs for their agreement with regulations
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
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.
eSource document
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
crossover population role
a role realized when a participant serves as reference to itself
complete nutrient role
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.
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
radiolabel role
radiolabel
radiolabel role is a role which inheres in a material entity which is realized by the process of radioactivity detection
cDNA library
GROUP: PSI
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.
PERSON: Luisa Montecchi
PERSON: Philippe Rocca-Serra
PMID:6110205. collection of cDNA derived from mouse splenocytes.
PRS: 22022008. class moved under population, modification of definition and replacement of biomaterials in previous definition with 'material' addition of has_role restriction
electronic case report form
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.
placebo role
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
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.
Pill consisting of inert materials
autotransplantation
is the transplantation of tissue from one part of \nthe body to another in the same individual. )
parameter threshold
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
study group role
The group of randomized participants that are assigned to a treatment arm of the trial
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
p-value
May be outside the scope of OBI long term, is needed so is retained
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).
WEB: http://en.wikipedia.org/wiki/P-value
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.
population
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.
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
adapted from Oxford English Dictionnary
rem1: collection somehow always involve a selection process
nuclear magnetic resonance assay
an assay used to identify the chemical structure of a compound or biological macromolecule using an NMR instrument.
www.nature.com/nrd/journal/v2/n5/glossary/nrd1086_glossary.html OBI branch derived
imaging assay
An imaging assay is an assay to produce a picture of an entity. definition_source: OBI.
protocol optimization objective
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.
role of pathology review board
a worker role comprised of providing a confirmed and consensus diagnosis for histopathology results obtained during the investigation
microtiter plate
A microtiter plate with 6, 24, 96, 384 or 1536 sample wells used in the enzyme-linked immunosorbent assay (ELISA)
A microtiter_plate is a flat plate with multiple wells used as small test tubes.
microplate
role of impartial witness
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
According to GCP , an impartial witness should be present for an illiterate subject. PharmPK Discussion, http://www.boomer.org/pkin/PK06/PK2006253.html
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
biological replicate role
a reference participant role realized by equivalent treatment of participants
A member of a dose-time group; a patient in a given arm of a trial
radioactivity detection
An assay in which a material's radioactivity is measured.
Measurment of the radioactivity of a supernatant, as in chromium_release_assay.
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.
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.
The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress.
nutrient role
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.
Luria broth; vitamin A; A nutrient is a substance used in an organism's metabolism which must be taken in from the environment. Wikipedia.
Wikipedia, feb 29, 2008
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.
obsolete_dropout role
Will be modelled as defined material, ouput of some 'dropout or withdrawal process' instead of role
Dropout
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.
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)
health care provider role
a worker role of providing medical care either within or outside the study timeline
methodology testing objective
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.
analytical cytology data file
A digital entity intended to capture data in analytical cytology domain.
FCS file, ACS file, foo.fcs, foo.asc
proxy respondent role
Proxy respondent is a worker role of describing patient's symptoms or condition to medical personnel
fluorescence compensation matrix
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.
negative reference substance role
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
Saline solution
role of legally acceptable representative
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.
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
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]
investigation results report
An investigation report is a report on the results of an investigation.
cellular feature identification objective
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.
reference subject role
Saline treated rat; one of three identically-treated subjects
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
vital dye role
2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893048&group_id=177891&atid=886178
The role of a dye that is realized when used in an experiment to stain live cells
obsolete_blinded medication role
115 patients received ipilimumab and blinded medication
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
Will be modelled using a blinding process and specified output blinded medication instead
Blinded medication
Inert pill shaped like aspirin tablet
sub-investigator role
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
a worker role authorized to make study-related decisions and carry out tasks related to the study; this role occurs during the study timeline
data encoding
We (protocol application branch) placed this term because it kept getting bounced from data transformation and DENRIE
a documenting process to encode an information entity into a digital document
storage of measurement results from an assay into a text file, such as
enzymatic cleavage
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
enzymatic cleavage is a protocol application to digest the fraction of input material that is susceptible to that enzyme
hardware optimization objective
Hardware_optimization is a hardware_testing_objective describing a study designed to identify the best hardware.
obsolete_defined_material
Place holder class, Utility class to gather the defined classes
_defined_material
trial statistician role
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]
a worker role that analyzes data obtained during a trial or study; this role occurs after the trial or study is completed or terminated.
standard error
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.
see P-Value
antigen role
9Mar09 waiting for discussion with immunology terms
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
Antigen is a role played by material which when introduced into an immune-competent organism causes an immune response
software testing objective
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.
sponsor role
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
a responsible party role involved with any of the following activities: initiating, managing and funding a study
organization
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.
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.
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.
feed role
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.
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
technical replicate role
technical replicate role is realized when two portions from one evaluant are used in replicate runs of an assay
Aliquots of a tissue subjected to parallel assays
dye role
A substance used to color materials www.answers.com/topic/dye 19feb09
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
cluster
A data set which is a subset of data that are a similar to each other in some way.
Cluster of the lymphocytes population.
cohort role
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.
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).
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.
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
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.
artificially induced nucleic acid hybridization
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.
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
DNA extraction
A DNA extraction is a nucleic acid extraction where the desired output material is DNA.
plan
The plan of researcher X to perform an experiment according to a protocol.
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.
A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process.
AR, BP, JM, MC, PRS
branch derived
obsolete_sample population
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.
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.
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
recruited population
sample population
organism feature identification objective
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.
number of lost events computer
0, 125, 787 events lost due to computer busy.
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
protocol
OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
PMID: 18388943.Nat Protoc. 2008;3(4):612-8.Protocol for the induction of arthritis in C57BL/6 mice.
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.
role of regulator of consumables and medical devices
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
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
adding a material entity into a target
Class was renamed from 'administering substance', as this is commonly used only for additions into organisms.
Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water.
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'.
analyte role
Glucose in blood (measured in an assay to determine the concentration of glucose).
interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role
pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested.
qualities such as weight, color are not assayed but measured, so they do not fall into this category.
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
disease stage
Stage II breast cancer, The timepoint of recovery from a disease
a part of an occurrence of a disease process which is associated with position in the normal progression of the disease
intraperitoneal injection
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
precipitate
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
a precipitate is a material entity which is output of a precipitation process
precipited material
protein-protein interaction detection
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.
An assay with the objective to determine interactions between proteins, such as protein-protein binding.
transcription factor binding site identification
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
a planned process with objective to find DNA region specifically recognized by proteins that function as transcription factors
obsolete_enrollment
merged with 'enrollment of human subjects
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
IEDB
enrollment
enrollment is a process of identifying a set of objects for further use in an investigation based on a set of criteria or rules
adverse event trigger
eluate
Raman spectroscopic detection of haemoproteins in the eluate from high-performance liquid chromatography. J Chromatogr. 1983 Jan 7;254:285-8. PMID: 6298263
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
eluted material
need to add restriction to indicate: has_part some (material entity has_role mobile phase) need to add mobile phase as role
material to be added role
9 March 09 from discussion with PA branch
drug added to a buffer contained in a tube; substance injected into an animal;
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
obsolete_peritoneum
BP: should be imported in the future, but I need it now to demonstrate how to define intraperitoneal injection
is the serous membrane that forms the lining of the abdominal cavity
interpreting data
Identifiying and removing outliers from data by eye. Examining data to and deriving a new hypothesis.
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
planning
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'.
the process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment.
a process of creating or modifying a plan.
obsolete_documenting
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
histological sample preparation
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
inductive reasoning
wikipedia: http://en.wikipedia.org/wiki/Inductive_reasoning
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.
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.
mass analyzer
A Mass analyzer is a device that separates ions according to their mass-to-charge ratio. All mass spectrometers are based on dynamics of charged particles in electric and magnetic fields in vacuum where the two laws of Lorentz force law and Newton's second law of motion apply.
The mass analyzer of the Voyager-DE(tm) STR Biospectrometry Workstation
hypothesis driven investigation
is an investigation with the goal to test one or more hypothesis
hypothesis generating investigation
is an investigation in which data is generated and analyzed with the purpose of generating new hypothesis
ion source
An ion source is a device that is part of a mass spectrometer that ionizes the material under analysis. The ions are then transported by magnetic or electric fields to the mass analyzer. Techniques for ionization have been key to determining what types of samples can be analyzed by mass spectrometry. Electron ionization and chemical ionization are used for gases and vapors. In chemical ionization sources, the material is ionized by chemical ion-molecule reactions during collisions in the source. Two techniques often used with liquid and solid biological samples include electrospray ionization (due to John Fenn PMID 2675315.) and matrix-assisted laser desorption/ionization (MALDI, due to M. Karas and F. Hillenkamp (Measuring Mass: From Positive Rays to Proteins by Michael A. Grayson (Editor) (ISBN 0-941901-31-9))).
The ion source of a Voyager-DE‚Ñ¢ STR Biospectrometry Workstation
ion detector
An ion detector is a device that measures and records the charge induced or current produced when an ion passes by or hits a surface. In a scanning instrument the signal produced in the detector during the course of the scan versus where the instrument is in the scan (at what m/Q) will produce a mass spectrum, a record of ions as a function of m/Q.
The ion detector of the Voyager-DE(tm) STR Biospectrometry Workstation
metabolite profiling
Metabolite profiling of human colon carcinoma - deregulation of TCA cycle and amino acid turnover. Mol Cancer. 2008 Sep 18;7(1):72. PMID: 18799019
metabolite profiling is a process which aims at detecting and identifying chemical entities resulting from biochemical and cellular metabolism
light emission function
A light emission function is an excitation function to excite a material to a specific excitation state that it emits light.
record function
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
magnify function
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.
contain function
A contain function is a function to constrain a material entities location in space
heat function
A heat function is a function that increases the internal kinetic energy of a material
material separation function
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.
ionize process
2009-11-10. Tracker: http://en.wikipedia.org/wiki/Ionize
Electrospray ionization in mass spectrometry
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.
excitation function
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.
freeze function
A freeze function is a function to decrease the internal kinetic energy of a material below the freezing point of that type of material.
synthesizing function
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.
perturb function
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.
filter function
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
mechanical function
A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force).
gas filter function
A gas filter function is a filter function which prevents the flow of solid objects, defined by specific qualities, in a gas-solid mixture
liquid filter function
A liquid filter function is a filter function which prevents the flow of solid objects, defined by specific qualities, in a liquid-solid mixture
transfer function
A transfer function is a function to displace a material from one location to another.
electricity supply function
the function of supplying current during a neuroscience experiment.
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.
power supply
ionization function
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.
cool function
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.
connection function
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.
isoelectric focusing device
An isoelectric focusing device is a device in which isoelectric focusing can be performed. An isoelectric focussing device had the function to contain and control the contained environment and transfer electrical energy from a power supply to a separation medium and the charged material to be separated.
isoelectric focusing unit
thermostatic circulator
A thermostatic circulator is a device which cools or heats a circulating liquid. It has the function to contain control the contained environment and transfer energy from or to the circulating liquid
energy supply function
An energy supply function is a function to supply or transfer energy from an energy source to a consumer of the energy
information processor function
An information processor function is a function that converts information from one form to another, by a lossless process or an extraction process.
data processor function
signal conversion function
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.
blot module
A blot module is a device which has the function to conatin and facilitate the material transfer process blotting to be realised
signal amplification function
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.
image acquisition function
An image acquisition function is a function to acquire an image of a material
image acquisition device
An image acquisition device is a device which captures a digitized image of an object
solid support function
Taped, glued, pinned, dried or molecularly bonded to a solid support
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
display function
A display function is a function to present information by translating that information through some lookup process into visual form.
environment control function
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.
sort function
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.
gel dryer
A gel dryer is a device which has the function to contain and to control the contained environment to facilitate the drying of gels
primer role
(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
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.
PCR product
PCR products are the results of amplifcation process. Detection of a PCR products is used to detect DNA and RNA.
We are using PCR and not the written out words, as this is the most common used.
is double stranded DNA that is the specified output of a polymerase chain reaction
viral RNA extraction
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
The extraction of RNA from an input material that specifically isolates viral RNA
nucleic acid template role
a model or standard for making comparisons; wordnet.princeton.edu/perl/webwn 19 feb 2009
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.
recombinant plasmid
a plasmid in which extraneous DNA has been inserted.
cloning vector role
pBluescript plays the role of a cloning vector
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.
cell cycle synchronization
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.
a process with the objective to obtain a cell culture in which all cells are in the same stage of the cell cycle
polymerase chain reaction
Opisthorchis viverrini: Detection by polymerase chain reaction (PCR) in human stool samples. Exp Parasitol. 2008 Sep 9. PMID: 18805413
PCR
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.
cloning insert role
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"
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.
measuring glucose concentration in blood serum
An assay that determines the concentration of glucose molecules in a blood serum sample
reverse transcriptase
enzyme and has_function some GO:0003964 (RNA-directed DNA polymerase activity)
obsolete_trypsinized material
A material entity that has undergone a process of digestion with trypsin
decided to be deprecated on Aug 2, 2010 dev call
Test Class: to evaluate OBI design pattern
syringe
Accuracy of oral liquid measuring devices: comparison of dosing cup and oral dosing syringe.Ann Pharmacother. 2008 Jan;42(1):46-52. Epub 2007 Dec 4. PMID: 18056832
a processed material which is used to introduce or draw fluids from a material entity. A syringe is made of a piston and body. the movement of the piston in the body determines the amount/volume of fluid to inject or draw
extract
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
an extract is a material entity which results from an extraction process
extracted material
transcription profiling assay
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
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
gene expression profiling
averaging objective
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.
An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation.
injection
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
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.
enzyme
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.
(protein or rna) or has_part (protein or rna) and has_function some GO:0003824 (catalytic activity)
intraperitoneal administration
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
The administration of a substance into the peritoneum of an organism
plasmid
plasmid = DNA and has_quality circular and has_function (is_realized_as some gene expression) GO:0010467
injection into organ section
A process in which an input substance is injected into a organ section.
Staining a specimen of human lung tissue with hematoxylin and eosin in order as a preparative step in histology
polyacrylamide gel
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
a material entity resulting from the polymerization of acrylamide with TEMED in some buffer solution
DNA sequence feature detection
An assay with the objective to determine a sequence feature of DNA
should be a defined class where interpretation of data generated by assay qualifies a DNA sequence
adding material objective
creating a mouse infected with LCM virus
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
genotyping assay
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
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.
genotype profiling, SNP genotyping
needle
Ovarian carcinoma presenting with axillary lymph node metastasis: A case diagnosed by fine-needle aspiration and brief review of the literature. Diagn Cytopathol. 2008 Oct 16. PMID: 18925569
a needle is a sharp, hollow device used to penetrate tissue or soft material. When attached to a syringe. it allows delivery of a specific volume of liquid or gaseous mixture.
analyte measurement objective
The objective to measure the concentration of glucose in a blood sample
is an assay objective to determine the presence or concentration of an analyte in the evaluant
DNA sequence variation detection
Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform. Nucleic Acids Res. 2006;34(18):e121. PMID: 17000641
DNA sequence variation detection is a process which aims at finding changes (expansion, amplification, deletion, mutation) in sequence of DNA molecule.
agarose gel
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
a material entity resulting from the polymerization of agarose after heating agarose suspended in some buffer solution
assay objective
the objective to determine the weight of a mouse.
is the specification of an objective to determine a specified type of information about an evaluated entity (independent continuant bearing evaluant role)
obsolete_heart
The heart is a muscular organ found in all vertebrates that is responsible for pumping blood throughout the blood vessels by repeated, rhythmic contractions
unused class. decided to be deprecated on Aug 2, 2010 dev call. Will be imported when need.
MC: should be imported
heart
analyte assay
PERSON:Bjoern Peters PERSON:Helen Parkinson PERSON:Philippe Rocca-Serra PERSON:Alan Ruttenberg GROUP:OBI Planned process branch
PERSON:Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Alan Ruttenberg
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'))
An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant.
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: 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
target of material addition role
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.
peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application.
target of material addition role is a role realized by an entity into which a material is added in a material addition process
mass measurement assay
The patients was weighed and mass was determined to be 47 kilograms
a process to determine the mass of an evaluant
obsolete_identification
Alan Ruttenberg 2010/11/22: After OBI call. A specific identification objective should be used instead, as necessary
See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3302925&group_id=177891&atid=886178
DNA cleavage assay for the identification of topoisomerase I inhibitors. Nat Protoc. 2008;3(11):1736-50. PMID: 18927559
a process by which the identity (what a thing is) of a material entity is established within a certain confidence interval
intra cellular electrophysiology recording
An intracellular electrophysiology recording is a process where the recording location of the electrode is intracellular
packed column
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.
obsolete_defined_output
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 subclass: normalized data set - A normalized data set is a data set that is produced as the output of a normalization data transformation.
regulatory agency
A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government.
normalized data set
A data set that is produced as the output of a normalization data transformation.
measure function
A glucometer measures blood glucose concentration, the glucometer has a measure function.
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.
extracellular electrophysiology recording
An extracellular electrophysiology recording is process where the recording location of the electrode is extracellular and data
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
consume data function
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.
material transformation objective
The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.
an objective specifiction that creates an specific output object from input materials.
artifact creation objective
manufacturing
Manufacturing implies reproducibility and responsibility AR
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
This includes a single scientist making a processed material for personal use.
manufacturing objective
is the objective to manufacture a material of a certain function (device)
column chromatography detector
There is a wide range of detectors available for both GC and LC each having their own particular areas of application. In general the more catholic the response, the less sensitive the detector and the most sensitive detectors are those that have a specific response. The performance of all detectors should be properly specified so that the user can determine which is most suitable for a specific application. Such specifications are also essential to compare the performance of different detectors supplied by alternative instrument manufactures. Detector specifications should be presented in a standard form and in standard units, so that detectors can be compared that function on widely different principles.
chromatography detector, defined class/xps
Bruker autosampler
A Bruker autosampler is an autosampler made by Bruker.
organic acid column
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.
thermal conductivity detector
TCD, hot wire detector
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).
Bruker US 2 NMR magnet
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.
NMR instrument
protein column
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.
refactor as defined class
solvent mixer
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.
check on definition !
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
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.
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.
a planned process that realizes the concretization of a study design
injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design.
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.
Bruker NMR Case sample changer
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.
nano pump system
A pump system optimized for nano flow chromatography.
Bruker AutoClean system
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.
washing system/NMR tube washing system, XPS: device has function washing
manual injection system
The traditional hardware system that allows a human to inject a sample into an inlet by hand, using a syringe.
Varian GEMINI spectrometer
An older Varian Broadband NMR spectrometer.
column connector
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.
solid NMR probe
An NMR probe that is designed to hold a solid sample.
NMR device
Bruker high resolution probe
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.
HR Probe
NMR probe
chromatography detector
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.
normal phase column
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.
APOLLO console
NMR instrument/NMR console
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.
NMR sample holder
An NMR sample holder is the part of an NMR instrument, which carries the NMR probe,sample tube and the nmr sample.
Any instrument that is used to carry out a chromatography experiment.
chromatography device, defined class?
continuous wave NMR instrument
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).
fourier transformation NMR instrument
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.
nitrogen phosphorous detector
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.
cation exchange column
A cation exchange column is a chromatography column that is used in cation exchange chromatography.
direct detection NMR probe
An NMR probe designed to allow the direct detection of acquisition nuclei.
Bruker B-ACS system
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.
rapid resolution column
A rapid resolution column is a chromatography column as marketed by Agilent, which is used with a rapid resolution cartridge to ensure a fast chromatography process with good separation resolution.
liquid chromatography autosampler
Designed to perform capillary LC with injection of sample volumes ranging from nL to L.
vacuum degasser
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.
capillary column
A capillary column is a thin tube with a small inner diameter, usually around 0.5 mm.
sample inlet
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.
NMR tube washing system
An automatic cleaning system for NMR tubes that removes previous probe and sample residues in order to allow for tube recycling.
NMR console
A component of an NMR instrument that controls the activities of the other components.
NMR instrument, TODO: same as or part of acquisition computer?
dual loop autosampler
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).
variable wavelength detector
A chromatography detector, that can detect signals within a certain range at user-defined wavelengths.
Bruker LC-NMR platform
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.
sample injection system
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.
multiple wavelength detector
A chromatography detector, that can detect many discrete wavelengths in parallel and produces a multiple wavelength chromatographic profile.
photoionization detector
PID
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.
gas generator
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.
gas chromatography equipment
column jacket
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.
electron capture detector
ECD
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.
reversed phase column
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.
injector lubricant
A lubricant used in liquid chromatography that eases sample injector penetration.
a process in which a population of cells with certain characteristics is isolated from a larger population
removing CD4+ cells from PBMCs using magnetic beads.
DISCOVERY console
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.
Bruker AMX series NMR instrument
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.
chromatofocusing column
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.
Part of an NMR instrument that detects the signals emitted from a sample. No single probe can perform the full range of experiments, and probes that are designed to perform more than one type of measurement usually suffer from performance compromises. The probe represents a rather fragile single point of failure that can render an NMR system completely unusable if the probe is dropped or otherwise damaged. Probes are usually characterised by Sample diameter and Frequency.\n alt The instrument that transmits and receives radiofrequency to and from the NMR sample.
NMR magnet
A magnet which induces a certain frequency (MHz) and which has a certain bore diameter.\n alt The NMR signal is a natural physical property of the certain atomic nuclei but it can only be detected with an external magnetic field. A magnet is a fundamental part of an NMR instrument which induces an electromagnetic force field (RF pulse) and by this excites and aligns the spins of the electrons of the NMR acquisition nucleus. It is usually a big (superconducting) electromagnet which is cooled by liquid helium and can be adjusted to a frequency between 200 and 950 MHz. The magnetic field strength is measured in Tesla or Gauss.
trap column
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.
flow probe
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.
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'
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
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.
flame ionization detector
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.
FID
vial
A vial is a cylindrical container often made from glass tubing.
magic angle spinning rotor
A rotor device that holds the NMR sample and enables the adjustment of the orientation of the rotation axis for a sample in a NMR instrument in the magic angle.
MAS rotor
Varian VXR spectrometer
A Varian NMR spectrometer.
splitless GC injector
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.
preparative autosampler
For preparative LC with injection of sample volumes ranging from L to mL ranges.
flow high resolution probe
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.
flow HR-probe
liquid chromatography valve
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.
JEOL NMR probe
An NMR probe that is manufactured by JEOL.
Bruker UltraShield Plus NMR magnet
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.
Bruker CryoProbe
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.
column cartridge
A device that binds the chromatography column and additional connector elements and / or valves or syringes into one physical unity for further processing.
chromatography device, check on definition !
affinity column
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.
tecmag NMR instrument
An NMR instrument that is manufactured by tecmag.
gel filtration column
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.
fraction collector
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.
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
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.
in-line filter
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.
imaging NMR probe
An NMR probe that is designed for generating pictures from sample states via NMR imaging.
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.
Bruker AC series NMR instrument
A series of older Bruker NMR magnets, now out of production.
Any device used in a gas chromatography experiment.
will become defined class/xps
syringe filter
A small membrane filter of defined pore size, that filters samples from a syringe.
Bruker SampleRail system
This Instrument system automatically prepares an NMR sample, inserts it into an NMR magnet, performs NMR experiments on the sample, and transports it back to the preparation system. The SampleRail fulfills the transporting tasks from the preparation system into the NMR magnet and back.
column compartment
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.
capillary pump system
A pump system optimized for capillary chromatography.
evaporative light scattering detector
The evaporative light scattering detector, as its name implies, utilizes a spray that continuously atomizes the column eluent into small droplets. These droplets are allowed to evaporate, leaving the solutes as fine particulate matter suspended in the atomizing gas.
a process in which cells with a single nucleus are isolated from a blood sample
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.
column cartridger
A chromatography device where the column cartridge is inserted into and stabilised.
nitrogen generator
A gas generator that generates nitrogen gas.
needle assembly
The needle assembly attached to the autosampler, comprises the injector needle that feeds a sample or carrier gas into the inlet
reverse transcribed polymerase chain reaction
3/21/10, BP:Modified definition to clarify that this is not the assay, but the material transformation
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
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.
reverse transcription polymerase chain reaction
Bruker Capillary LC-NMR platform
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.
gas chromatography oven
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.
autosampler
An optional part of an NMR instrument used to hold samples prior to NMR analysis and that sequentially loads these samples into the analytical part of the NMR instrument. \n alt The autosampler is an automatic sample changer device.
isocratic pump system
A pump system optimized for isocratic chromatography.
flash pump system
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).
Varian UNITY INOVA spectrometer
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.
liquid NMR probe
An NMR probe that is designed to hold a liquid sample.
ion exchange column
An ion exchange column is a chromatography column that is used in ion exchange chromatography and anion or cation exchange resins to enable separation.
Bruker NMR probe
An NMR probe that is manufactured by Bruker.
NMR device, TODO: May need no definition.
anion trap column
An anion trap column is a trap column and ion-exchange column which contains cationic anion-exchange resins.
fluorescene detector
A single wavelength detector, where the excitation light wavelength is normally a mercury lamp generated high intensity UV light at 253.7 nm. Many substances that fluoresce will be excited by light of this wavelength and hence be detected.
tecmag EAGLE probe
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.
electrical conductivity detector
The electrical conductivity detector measures the conductivity of the mobile phase. There is usually background conductivity which must be backed-off by suitable electronic adjustments. If the mobile phase contains buffers, the detector gives a base signal that completely overwhelms that from any solute usually making detection impossible. Thus, the electrical conductivity detector a bulk property detector. and senses all ions whether they are from a solute or from the mobile phase. In order to prevent polarization of the sensing electrodes, AC voltages must be used and so it is the impedance not the resistance of the electrode system that is actually measured. From a physical chemistry stand point the conductivity of a solution is more important than its resistance. However, it is the resistance (impedance) of the electrode system that determines the current across it. The resistance of any conductor varies directly as its length and inversely as its cross sectional area.
An Instrument which is used to carry out a NMR analysis of some sample.
Bruker UltraShield NMR magnet
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.
piston-seal
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.
mass selective detector
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.
mass spectrometry detector
spin column
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.
Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process.
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.
transfer line
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.
gradient pump system
A pump system optimized for gradient chromatography.
high temperature column
A high temperature column is a chromatography column which is suitable for and withstands very high temperatures in chromatography ovens.
Bruker Ultrastabilized NMR magnet
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.
scattered molecular aggregate
the sodium and chloride ions in a glass of salt water
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
Collective
obsolete_molecular concentration
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.
Discussion in Karslruhe, Oct 2008, with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg.
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.
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.
logical definition in OBI: 'quality of related physical entities' ('inheres in' some material_entity) and (towards some 'scattered molecular aggregate')
the phosphate concentration should be 0.1M
NMR sample tube
The sample-tube holds the NMR sample and sits in the nmr probe. It is usually a glass tube of 5-20mm diameter.
Varian UNITY spectrometer
The predecessor series of the Varian UNITY INOVA spectrometer.
AVANCE II spectrometer
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.
y-column connector
A column connector that connects one column on one side with two columns at the other side, hence building a Y shaped structure.
Bruker LC-NMR/MS platform
Includes the connection to a high-resolution TOF-LC-MS system.
refractive index detector
For analyzing non-UV absorbing substances, such as carbohydrates, lipids and polymers. This is also the detector of choice for gel permeation chromatography. The refractive index detector is one of the least sensitive LC detectors. It is very sensitive to changes in ambient temperature, pressure changes, flow-rate changes and can not be used for gradient elution. Despite these many disadvantages, this detector is extremely useful for detecting those compounds that are nonionic, do not adsorb in the UV, and do not fluoresce. There are many optical systems used in refractive index detectors but one of the most common is the differential refractive index detector.
anion exchange column
An anion exchange column is a chromatography column that is used in anion exchange chromatography and which enables the separation of anion mixtures.
plunger column
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.
flame photometric detector
FPD
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.
chromatography pump system
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).
Bruker 1mm MicroProbe
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.
Bruker BEST NMR system
Bruker Efficient Sample Transfer NMR
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.
chromatography detector filter
An optical filter that is used to obtain monochromatic light of a defined wavelength from detector lamps.
cation trap column
A cation trap column is a trap column and ion-exchange column which contains anionic cation-exchange resins.
column adapter
An Adapter that enabled the connection of a column to additional devices.
pulsed amperometric detector
A chromatography detector as used by high-performance anion exchange chromatography that provides sensitive and specific detection of carbohydrates. Pulsed Electrochemical Detection (PED) allows simple, sensitive, and direct detection of numerous polar aliphatic compounds, especially carbohydrates. This technique exploits the electrocatalytic activity of noble metal electrode surfaces to oxidize various polar functional groups. In PED, multi-step potential-time waveforms at Au and Pt electrodes realize amperometric/coulometric detection while maintaining uniform and reproducible electrode activity. The response mechanisms in PED are dominated by the surface properties of the electrode, and, as a consequence, members of each chemical class of compounds produce virtually identical voltammetric responses. Thus, the full potential is realized when combined with high performance liquid chromatography (HPLC).
PAD
Bruker NMR instrument
An NMR instrument that is manufactured by Bruker.
Bruker NMR magnet
An NMR magnet that is manufactured by Bruker.
ozone-induced chemiluminescence detector
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.
tecmag NMR console
An NMR console manufactured by tecmac.
JEOL NMR instrument
An NMR instrument that is manufactured by JEOL.
chromatography consumable
A chromatography consumable is a consumable that is used in a chromatography experiment.
column frit
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).
liquid chromatography column
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.
detector lamp
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.
chart recorder
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.
open tubular column
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.
high resolution magic angle spin probe
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.
high resolution MAS, hr-MAS
hydrogen generator
A gas generator that generates hydrogen gas.
glass column
A glass column is a chromatography column made out of glass that is usually used for larger scale and preparative liquid chromatography separations.
auto injector
A gas chromatography device that can auto-inject a small number of samples an inlet.
Varian NMR instrument
An NMR instrument that is manufactured by Varian.
Bruker MATCH tube holder system
Bruker Multiple Adjustable Tube Clamp Holder
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.
Bruker SPE-NMR platform
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.
guard column
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.
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
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
high resolution probe with automatic tuning and matching
High Resolution Probes with Automatic Tuning and Matching, HR_probe_with_ATM
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.
fluorine-induced chemiluminescence detector
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.
size exclusion column
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.
chromatography splitter
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.
Bruker micro imaging probe
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.
custom made column
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.
gel permeation column
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.
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
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.
Bruker SampleJet system
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.
JEOL ECX NMR spectrometer
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.
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.
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
quaternary pump system
A pump system that pump and mix up to four different solvents in parallel.
carbon nanotube column
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.
Bruker solid magic angle spinning probe
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.
solid MAS probe
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
hematology is a process studying blood and blood producing organs relying on a variety of techniques and instruments
Varian MERCURY spectrometer
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.
Bruker Metabolic Profiler
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.
column heater
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.
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
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.
JEOL CapNMR probe
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.
acquisition computer
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.
gas chromatography detector
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.
gas purifier
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.
The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood.
is an objective to transform a material entity into spatially separated components.
indirect detection probe
An NMR probe designed to allow the indirect detection of acquisition nuclei.
JEOL ECA NMR spectrometer
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.
atomic emission detector
AED
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.
clustered data set
A clustered data set is the output of a K means clustering data transformation
data set with assigned discovered class labels
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.
data set of features
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.
differential expression analysis data transformation
A differential expression analysis data transformation is a data transformation that has objective differential expression analysis and that consists of
4/10/2011BP: It seems to me that the editor notes refer to a previous version, and are no longer relevant.
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
a portion of urine collected from an organism
are we happy calling collection of urine a material separation?
Mixing two fluids. Adding salt into water. Injecting a mouse with PBS.
created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes.
is a material processing with the objective to combine two or more material entities as input into a single material entity as output.
fuzzy clustering objective
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.
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
a quality inheres_in some device and is concretization of some (device_setting_specification and is_about a quality of the device
a material entity derived from a portion of blood collected from an organism
blood drawn from a human for glucose assay
data set of predicted values according to fitted curve
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.
2009-02-28: work on this term has been finalized during the OBI workshop winter 2009
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.
5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
a planned process with the objective of obtaining specimen.
background corrected data set
A data set that is produced as the output of a background correction data transformation.
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.
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.
It is possible to add further restrictions, such as utilizing a plate as part of the assay.
error corrected data set
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).
class prediction data transformation
supervised classification data transformation
A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction.
PERSON: James Malone
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.
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.
Permeabilizing T cells and staining them with fluorescent labeled anti-IFN-gamma antibodies
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.
background correction data transformation
A background correction data transformation (sometimes called supervised classification) is a data transformation that has the objective background correction.
2/26/09 RESOLVE: Need to add a restriction for the 'MHC multimer' as a reagent used
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
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.
error correction data transformation
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.
2/26/09: RESOLVE: need to replace 'molecular entities' in the logical definition with 'tritiated thymidine'
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.
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.
a material obtained from an organism in order to be a representative of the whole
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.
statistical hypothesis test
A statistical hypothesis test data transformation is a data transformation that has objective statistical hypothesis test.
center value
A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data.
statistical hypothesis test objective
WEB: http://en.wikipedia.org/wiki/Statistical_hypothesis_testing
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
reduced dimension data set
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.
The objective to obtain multiple aliquots of an enzyme preparation.
is the objective to separate material into multiple portions, each of which contains a similar composition of the input material.
average value
A data item that is produced as the output of an averaging data transformation and represents the average value of the input data.
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
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.
putting a mouse in the blender. Not: putting a mouse on a scale
separation into different composition objective
The objective to obtain cells contained in a sample of blood.
We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives
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)
Study result is an information content entity that is a specified data output of a study.
A specimen creation objective is to obtain a material entity for potential use as an input during an investigation
The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
creating a mixture of molecules in solution
is a process with the objective to prepare a liquid solution of one or more chemicals at desired concentrations.
is an objective to obtain an output material that contains several input materials.
Cloning vectors are commercially available and supplied in linearized form with 3' dT overhangs
Nucleotide overhang cloning is the process of inserting nucleic acid into a vector using nucleotide overhangs used to prevent self ligation
A rodent care protocol is an animal protocol in which the animals being taken care of are rodents.
Keeping mice in the UCSD animals facility at 20 - 25 degrees celsius, in cages of 4 animals each and providing food twice daily.
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.
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.
PMID: 19419533. Arabidopsis RNA immunoprecipitation. Terzi LC, Simpson GG. Plant J. 2009 Jul;59(1):163-8.
is a process which realizes a material separation objective by relying on antibodies to specifically binding to material entity
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.
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
Methylated DNA immunoprecipitation sequencing assay
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.
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.
In an investigation, this will typically be part of an animal care process
animal feeding is a process in which animals are provided with food
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.
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
PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR. Methods. 2009 Jul;48(3):249-57.
is a DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation
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.
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.
5/22 Need to explore if there are GO / other classes exist that capture this. We need it now for cloning experiments
A DNA ligase is an enzyme that covalently joins two compatible pieces of DNA through the cleavage of an ATP molecule
Need to point out more specifically that survival / death is measured.
Survival assessment is an assay that measures the occurrence of death events in one or more organisms that are monitored over time
A support vector machine is a data transformation with a class prediction objective based on the construction of a separating hyperplane that maximizes the margin between two data sets of vectors in n-dimensional space.
A self-organizing map (SOM) is an artificial neural network with objective class discovery that uses a neighborhood function to preserve the topological properties of a dataset to produce low-dimensional (typically 2) discretized representation of the training data set. A set of artificial neurons learn to map points in an input space to coordinates in an output space. The input space can have different dimensions and topology from the output space, and the SOM will attempt to preserve these.
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.
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
PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR.Methods. 2009 Jul;48(3):249-57.
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
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.
PMID 4773306. Niall HD (1973). "Automated Edman degradation: the protein sequenator". Meth. Enzymol. 27: 942-1010
adapted from Wikipedia (http://en.wikipedia.org/wiki/Edman_degradation)
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.
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.
adapted from Wikipedia and Applied Biosystems web site
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
decision tree building data transformation
A decision tree building data transformation is a data transformation that has objective decision tree induction.
a process that realizes an animal care protocol that specifies how animals are kept and maintained
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
this should be a child of 'chromosome' if we import that from another source
is a DNA sequencer which is manufactured by Li-Cor corporation and enable automated chain termination based DNA sequencing
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.
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.
A pathogen challenge is the administration of a live pathogenic organism to a host
WEB: http://www.broadinstitute.org/cancer/software/genepattern/
a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks.
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.
For example, if the nodes are cities, then the edges may have numerical values that correspond to the distances between the cities.
WEB: http://mitpress.mit.edu/books/FLAOH/cbnhtml/glossary-G.html
An animal care protocol is a protocol which specifies the environment in which animals are being kept in captivity for research purposes
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.
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.
chromatin immunoprecipitation sequencing assay
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
is a DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry
6 April 2009: from the Vaccine Community
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
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
vaccine preparation is a planned process with specified output a vaccine
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'.
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
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
The role a material entity plays when it is co-administered with an immunogen in order to enhance the immune response to the immunogen.
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.
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.
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.
adapted from information provided by Solid web site
is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs
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.
is a DNA sequencing which relies on DNA ligase activity to perform chain extension during the sequencing reaction step.
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, Smith MA, Ernest Sohna Sohna J, Spence EJ, Stevens K, Sutton N, Szajkowski L, Tregidgo CL, Turcatti G, Vandevondele S, Verhovsky Y, Virk SM, Wakelin S, Walcott GC, Wang J, Worsley GJ, Yan J, Yau L, Zuerlein M, Rogers J, Mullikin JC, Hurles ME, McCooke NJ, West JS, Oaks FL, Lundberg PL, Klenerman D, Durbin R, Smith AJ. Nature. 2008 Nov 6;456(7218):53-9.
adapted from Wikipedia and Illumina / Solexa web site (SS_DNAsequencing.pdf document available on july 2009)
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.
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
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
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
Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold
k-nearest neighbors
A k-nearest neighbors is a data transformation which achieves a class discovery or partitioning objective, in which an input data object with vector y is assigned to a class label based upon the k closest training data set points to y; where k is the largest value that class label is assigned.
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.
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.
Note: 'cloning vector role' is really a function. Should be dealt with globally
Pyrosequencing sheds light on DNA sequencing. PMID: 1115661. Ronaghi M. Genome Res. 2001 Jan;11(1):3-11. Review.
Wikipedia (http://en.wikipedia.org/wiki/Pyrosequencing) and Roche 454 life science web site
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.
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.
The enzyme EcoR1 cuts DNA at the canonical cleavage site CAATTG
an enzyme that has a specific target cleavage sites within nucleic acids
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.
is a DNA sequencing which relies on DNA polymerase activity to perform chain extension during the sequencing reaction step.
a material consisting of 14.5% protein, 8.5% fat and 9.5% fiber produced to feed rodents
is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs
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.
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.
Studen't t-test is a data transformation with the objective of a statistical hypothesis test in which the test statistic has a Student's t distribution if the null hypothesis is true. It is applied when the population is assumed to be normally distributed but the sample sizes are small enough that the statistic on which inference is based is not normally distributed because it relies on an uncertain estimate of standard deviation rather than on a precisely known value.
WEB: http://en.wikipedia.org/wiki/T-test
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.
A material sample role is a specimen role borne by a material entity that is the output of a material sampling process.
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.
topologically preserved clustered data set
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.
the output data set generated from a self-organizing map.
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
an assay with the objective to determine information about an immune response
A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity
A material entity that has the material sample role
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.
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.
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.
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.
CART
A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure.
BOOK: David J. Hand, Heikki Mannila and Padhraic Smyth (2001) Principles of Data Mining.
independent variable specification
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.
Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables
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.
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
dependent variable specification
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.
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.
A 'blue top' test tube that contains anticoagulant for storing blood specimens'
controlled variable specification
WEB: http://en.wikipedia.org/wiki/Control_variable
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
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.
human antithrombin-III (AT-III) in blood assay
An assay to measure the amount of antithrombin III in blood.
PMID:19696660#The antithrombin-III (AT-III) was determined using a Berichrom(r) Antithrombin-III (A) kit.
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
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.
adapted from wikipedia http://en.wikipedia.org/wiki/Survival_rate
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
A multiple testing correction objectives is a data transformation objective where the aim is to correct for a set of statistical inferences considered simultaneously
Application of the Bonferroni correction
multiple comparison correction objective
A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set.
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
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
A measurement device with the function to measure and record the level/amount of glucose in a blood sample
Diabetic patients use glucometers to determine their glucose levels
10/14/09, BP: This should be linked to the 'purified' 'currently conferred quality
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
the objective to obtain a pure fraction of a specific peptide when running an HPLC on a crude synthesis of peptides.
SIINFEKL' is the primary structure of a peptide
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
Insert selection by BamHI methyltransferase protection in P1 phage-based cloning
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.
A process in which bonds are created that link one polymer to another
cross linking can be used as a probe to link proteins together, to check protein protein interactions
A measurement datum which represents information about an ordered series of action potentials in an organism's CNS measured over time.
Measurement of temporal regularity of spike train responses in auditory nerve fibers of the green treefrog
needs more work to see exactly what the data set looks like - HP
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
PMID:19696660#The prothrombin time (PT) was quantitatively determined using RecombiPlasTin (Instrumentation Laboratory Company, Lexington, Massachusetts, USA).
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.
Is a process in which the tertiary or secondary structure of a polymer is disrupted
informing investigator of subject study arm
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
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.
antithrombin-III (AT-III) berichrome assay
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
todo Reagents from Berichrom(r) Antithrombin III (A) and standard human plasma
is the objective to maintain some or all of the qualities of a material over time.
Helen Parkinson, Jessica Turner, Dirk Derom
The presentation of a flashing light to a monkey during reward training
a planned process in which an organism is exposed to some stimulus with the intent to invoke an action
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.
PMID:19696660#Antifactor-Xa (anti-Xa) was determined using spectrolyse heparin (Xa) (Trinity Biotech plc, Bray, County Wicklow, Ireland).
DNA that has been produced in an enzymatic amplification process
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.
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.
a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues.
measuring neural activity in the caudate nucleus
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
The process of measuring neural activity in the caudate nucleus
to be treated with active ingredient role
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
Role of a patient in a group treated with an active substance in a clinical trial
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.
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
A micro-electrode recording device used to record extracellular action potentialsin monkey caudate nucleus
An electrode of very fine caliber consisting usually of a fine wire or a glass tube of capillary diameter drawn to a fine point and filled with saline or a metal used in physiological experiments to stimulate or record action currents of extracellular or intracellular origin in the nervous system.
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).
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.
the process of using pH buffer adjust a pH meter
anticoagulant tube storage of blood specimen
Storage of a blood specimen in a tube with anticoagulant
activated partial thromboplastin time (aPTT) assay
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.
PMID:19696660#The activated partial thromboplastin time (aPTT) was determined using Dade Actin FSL activated PTT reagent.
A pill in the form of a small rounded gelatinous container with medicine inside.
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
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
PMID:19696660#The thrombin time was determined using thromboclotin assay kit.
Isolation of a YAC clone covering a cluster of nine S100 genes on human chromosome 1q21
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
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
09/28/2009 Alan Ruttenberg. Needed because we have to have a process to scope blinding over
A planned process, part of a study design execution, during which the treatment of subjects is ongoing
A dose of medicine or placebo in the form of a small pellet.
An organization formed with a goal to have its members conduct investigations
The SALK institute is a research organization.
obsolete_primary structure of sequence macromolecule
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 .
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
These are all placeholders and should be replaced by SO terms
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.)
a quality of a DNA residue that has a methyl group attached to it
A ruler, a microarray scanner, a Geiger counter.
a processed material created to have the function to measure
Extraction of chromosomal DNA from mammalian cells by first isolating nucei
The output of an extraction process in which DNA molecules above a molecular weight cutoff are purified in order to exclude DNA from organellas.
A person or organization that has a manufacturer role
A test tube is a device consisting of a glass or plastic tubing, open at the top, usually with a rounded U-shaped bottom which has the function to contain material
An adding a material entity to target with the entity is a pill and the target is the mouth
a process with that achieves the objective to maintain some or all of the characteristics of an input material over time
2010-01-31: Philippe Rocca-Serra placeholder
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
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
subject agrees they understand informed consent document
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
A process in which a subject receives an informed consent document and agrees that they have understood it
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
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.
The Sysmex CA-6000 automated coagulation analyzer is a random access instrument that is capable of performing 20 clot-based and chromogenic assays
A medical organization at which sick or injured people are given clinical care
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]
modified from the wording of the wordnet 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
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
fucoidan bears a test substance role in a study to test safety taking a certain dosage of it orally
A RNA extraction process typically involving the use of poly dT oligomers in which the desired output material is polyA RNA.
A RNA extraction process in which the desired output material is RNA in the organelle(s).
Replaced by CHEBI_59051 Diethylpyrocarbonate
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.
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.
a information content entity created to indicate that information about something is not available to the person recording it.
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
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.
A RNA extraction process in which total cellular and organelle RNA are extracted.
intracellular material detection by flow cytometry assay
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.
A primer in a PCR reaction. A probe on an Affymetrix chip.
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
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.
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.
a record indicating that the biological sex of an organism is not known.
A RNA extraction process in which the desired output material is RNA in the cytoplasm.
2010-01-31: Philippe Rocca-Serra: Need to add a restriction taking into account probe and transcript information
PMID: 18428227. Analysis of RNA by northern blot hybridization. Brown T, Mackey K. Curr Protoc Hum Genet. 2001 Nov;Appendix 3:Appendix 3K.
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
Likelihood-ratio is a data transformation which tests whether there is evidence of the need to move from a simple model to a more complicated one (where the simple model is nested within the complicated one); tests of the goodness-of-fit between two models.
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.
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)
A serum neutralization of viral infectivity assay which done in a 96-well plate.
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.
Establishment of HeLa immortal cell line
is a planned process in which the objective is to generate a cell line from a natural population of cells which are already immortal
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.
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.
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.)
single-nucleotide-resolution nucleic acid structure mapping assay
2010-01-31: Philippe Rocca-Serra: OBI needs to review 'structure assay' as currently defined. Need to get feedback from Kevin Clancy.
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.
The viral hemagglutination assay (HA) is a quantification of viruses by hemagglutination.
WEB: http://en.wikipedia.org/wiki/Hemagglutination_assay
serum neutralization of viral infectivity assay
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.
MC, 20100217: I added influenza neutralization assay as alternative term. This should be tagged with a community specific value, eg "influenza ontology" or else.
WEB: http://www.virology.ws/2009/05/28/influenza-microneutralization-assay/
a specimen that was taken from a live organism
material obtained through a liver biopsy from a human patient
MO_705 premortem
detection of specific nucleic acids with complementary probes
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.
Primer based PCR assay, Norther blot, Southern Blot, RNAse protection assay
WEB: http://www.virology.ws/2009/05/27/influenza-hemagglutination-inhibition-assay/
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.
viral hemeagglutination inhibition assay
A RNA extract that is the output of a RNA extraction process in which RNA molecules found in the cytoplasm are extracted.
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.)
Production of a cell line for the purposes of experimentation e.g. EBV transformation of PBMs
is the planned process of experimentally creating a cell line which is capable of dividing indefinitely in vitro. Has specified output cell line
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.
PMID: 8713846. Random primed 32P-labeling of DNA. Smith DR. Methods Mol Biol. 1996;58:27-9.
Person: Bjoern Peters Person: Chris Stoeckert
a labeling in which random primers are used to uniformly label input DNA
need to add Klenow subunit of DNA polymerase I under material entity
an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen.
An assay that measures the rate in which a target cell population is killed by effector cells.
in vivo cell mediated cell killing assay
An assay that measures the rate in which a target cell population is killed by effector cells within an organism
injecting CFSE labeled target cells with and without loaded influenza peptide into a mouse, and comparing the recovery rate.
secondary structure of sequence macromolecule
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
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.
A RNA extraction process in which the desired output material is RNA in the nucleus.
survival curve
An assay which measures the rate of proliferation of input cells
Measuring the amount of tritiated thymidine incorporated by dividing cells as a proxy for cell proliferation.
Note that cell proliferation assays can often be a part of another assay. For example, to detect an analyte with a cell culture bioassay.
2010-01-31: Philippe Rocca-Serra: need extra work on 'labeled probe'
2010-01-31: Philippe Rocca-Serra: departure from naming convention as the assay is named after Edwin Southern.
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.
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.
real time polymerase chain reaction assay
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.
WEB: http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction
quantitative real time polymerase chain reaction
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.
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,
A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen.
Extraction of total RNA from cells with Qiagen mini RNeasy kit.
PMID: 15630685: Single molecule studies of RNA secondary structure: AFM of TYMV viral RNA.
PMID:2446263. Probing the structure of RNAs in solution. Nucleic Acids Res. 1987 Nov 25;15(22):9109-28.
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
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.
Extraction of organellar RNA from plant cells using organellar RNA binding protein.
a specimen that was taken from a dead organism
MO_416 postmortem
in vitro cell mediated cell killing assay
An assay that measures the rate in which a target cell population is killed by effector cells in a cell culture.
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).
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.'
Tracker request: https://sourceforge.net/tracker/?func=detail&aid=2946262&group_id=177891&atid=886178
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'.
The clumping or clustering of red blood cells caused by certain viruses, antibodies, or other substances
WEB: http://medical-dictionary.thefreedictionary.com/hemagglutination
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.
The planned process of providing material entities to be used in an investigation.
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
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.
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.
WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf
type of sample used in the PCIRN influenza network
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.
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.
real time reverse-transcription polymerase chain reaction assay
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)
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
crystallizing an antibody:antigen complex, and recording the diffraction pattern of a synchrotron beam, and assembling the 3d complex structure based on homologous complexes.
promoter activity detection by reporter gene assay
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.
An assay in which expression of a reporter gene is detected that was inserted under the control of a promoter of interest.
A speciemn which derives from nasopharyngeal mucosa after aspiration.
2010/3/3 Alan Ruttenberg: There is a question of whether we should have a separate objective to "prepare for maintenance"
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
MO_481 frozen_storage
An assay that uses a flow cytometer to detect fluorescence in individual particles that flow by a laser in solution.
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.
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.
A culture medium containing iron, phenol red, amino acids, salts, glucose and vitamins.
Logical definition should contain all components listed in textual definition at some point.
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
may later be refined with more specific list of organisms
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.
Using a Luminex machine to detect IFN-gamma and IL-10 in the supernatant of a cell culture
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.
A specimen that has been frozen in order to store it.
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
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.
A specimen that has been modified in order to be able to detect it in future experiments
infectious agent
is a material entity bearing the disposition to infect an organism
a storage process with input material entity and output freeze dried material for long time storage
can link to freezing-dying equipment, such as freeze-dryer, rotary evaporator, if needed
A material separation function is a function that decreases the resolution between two or more material entities.
A stirrer has a material combination function
EBI provides training on databases and tools and has a training service provider role
a service provider role which is realized by a servicer provider organization performing some training
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.
A measurement device that is used to calculate the heat flow of a chemical reaction or physical change.
the part of the execution of an intervention design study which is varied between two or more subjects in the study
A device with a separation function realized in a planed process
A device that produces a three-dimensional image or picture of functional processes in the body. It detects pairs of gamma rays emitted indirectly by a positron-emitting radionuclide (tracer), which is introduced into the body on a biologically active molecule.
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
A device that is used to physically interact with a sample under a microscope, where a level of precision of movement is necessary that cannot be achieved by the unaided human hand.
A person or organization who provides access to a DNA sequencer.
a service provider role which is realized by a servicer provider organization performing access to some material
A measurement datum that is reported on a categorical scale
a process that achieves a training objective
e.g. a training course run by a vendor on their instrument, a training service on a assay by a core facility
A microscope that produces an image of an object by targeting it with an electro-magnetic beam in the visible frequency range
A biologist who uses a sequencing services fulfills the role of a service consumer
a role which inheres in a person who uses a service
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
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.
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
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.
The Edinburgh handedness assay is a specific method of determing handedness
A device that supports another device such as a precision instrument by isolating it from vibration that is transmitted from the floor.
a function to remove viable organisms from an input material
Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer.
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
A device that measures and displayes signal voltages, usually as a two-dimensional graph of one or more electrical potential differences (vertical axis) plotted as a function of time or of some other voltage (horizontal axis).
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
is realized in a planned process where the bearer participates
the role of the DNA sequencer to which someone gets access to a period of time, e.g. by payment, or other mechanism
a specimen that is output of a paraffin storage process in which specimen is embedded in paraffin
This is meant to include all kinds of material administrations, including vaccinations, chemical compounds etc.
an intervention design in which the treatment is the administration of a compound
The administration of a substance into the mouth of an organism
A specimen that has been intentionally physically modified.
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
A device used in the first step in making electrodes, that applies constant tension on a glass capillary tube and eventually breaks it while heating it; this produces a very fine point on the capillary tube.
An assay in which a person makes a statement that indicates what handedness he has from a choice of different categories.
A preparation device that uses a vibrating razor blade to cut through tissue.
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?
A function that is realized when a reagent is automatically added to some research material.
An automatic tissue processor automatically applies antibodies and buffers to histological tissue preparations.
PERSON: Nicole Vasilevsky, Matthew Brush
A reagent application function that is realized when a molecular tracer, such as an antibody or probe is automatically transferred to a biological specimen.
Immunohistochemical labeling of tissue sections by an autostainer staining system.
A training objective is fulfilled by e.f. a bioconductor tutorial which instructs the user in the use of a package
An training objective which is fulfilled by the provision of some training
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.
A label that is part of a categorical datum and that indicates the category of that datum
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.
An assay in which a measurement is made by observing entities located in a live cell.
a specimen that is output of a lyophilization storage process in which specimen is lyophilized for storage.
An assay in which a measurement is made by observing entities located in an organism.
Measuring the rate in which cells that are pulsed with a peptide are killed inside a mouse by peptide specific cytotoxic T cells.
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?)
A device that can be used to restrict the location of material entities over time
A device is a processed material which is designed to perform some function or functions
A voltmeter is a measurement device which is intended to perform some measure function.
food should not classify as a device - counter example for using manufacturer and not device. macroscopic only
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.
a directive information entity that describes the dose that will be administered to a target
a protocol specifying to administer 1 ml of vaccine to a mouse
A measurement datum which is the result of combining multiple datum. For example, a mean or summary score.
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.
JZ: can we defined it logically as the output of some data transformation, like aggragate data transformation?
Person: Jessica Turner
a specimen that is output of a specimen creation process used for an investigation without storage.
a processed material created to have a function and which requires electrical power to execute
sequence data
A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.
example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search.
cell-cell binding detection by flow cytometry assay
An assay which uses a flow cytometer to detect pairs of cells that are interacting by staining them with different fluorescent labels.
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.
handedness categorical measurement datum
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
a storage process with input organism or anatomical entity and paraffin and output material embedded in paraffin for long term storage
need to specify paraffin or wax is one of specified input of the process
an assay in which a measurement is made by observing entities located in a container.
DNA sequencing of a sample by a core lab which returns data to the consumer
a service provider role which is realized by a servicer provider organization performing a protocol execution
a specimen that is output of a process that cell culture inoculated into agar for long term storage.
An image acquisition device that generates a three-dimensional image of the inside of an object from a large series of two-dimensional X-ray images taken around a single axis of rotation.
The administration of a substance into the intranasal mucosis of an organism
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.
An organism has been injected 1ml of vaccine
A study design in which the independent variable is the environmental condition in which the specimen is growing
obsolete_DNA sequencing training service
03/22/2010:workshop: there is a user requirement that not in all cases of the training the trainee gains the skills.
A training process with the objective to provide a trainee with the skill to run DNA sequencing experiments
obsolete_general scalar measurement datum
4/10/2011 BP: It is unclear to me why we need this, and don't just use the scalar measurement datum.
Diagnosing that a patient has pneumonia based on information on measurements of temperature, sound of breathing, and patient complaining about a headache.
The interpretation of the information available about bodily features (clinical picture) of a patient resulting in a diagnosis
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.
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.
A microscope that produces an image of an object by targeting it with an electron beam
PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113
Eagle-i will supply better English 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.
A sequencing centre has a service provision objective
An objective which is fulfilled by the provision of some service e.g. a training service
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
Staining cells in a tissue slice with a dye.
The directed combination of a material entity with a specimen.
an objective which aims to create a device with a specified function
PERSON:Richard Scheuermann, Jie Zheng, Bjoern Peters
Right now this may be incomplete. Should also cover e.g. sound, light as well.
The collection of material entities and their qualities that are located near a live organism, tissue or cell and can influence its growth.
Need to clarify if this is a document or a directive information entity (or what their connection is))
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.
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.
Merriam-Webster
PERSON: Jessica Turner
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.
A device formed by conducting material or by a mesh of such material, that blocks out external static electric fields.
Wikipedia http://en.wikipedia.org/wiki/Faraday_cage
a storage process with input cell culture and agar and output agar stab for long time storage
need to specify that agar is one of input for this process
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
single nucleotide resolution mapping assay using RNAse CL3
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
single nucleotide resolution mapping assay using CMCT probe
A planned process that captures an image of an object.
Taking a polaroid picture of a patients skin lesion; Using a digital camera to take a picture of a gel
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
single nucleotide resolution mapping assay using Fe-MP probe
obsolete_qualitative binding detection assay
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.
PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum
An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.
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
single nucleotide resolution mapping assay using ENU probe
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
single nucleotide resolution mapping assay using RNAse V1
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
single nucleotide resolution mapping assay using Kethoxal probe
single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
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.
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
single nucleotide resolution mapping assay using DMS probe
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
single nucleotide resolution mapping assay using DNAse I
single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
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.
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
single nucleotide resolution mapping assay using Rhodium probe
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
single nucleotide resolution mapping assay using RNA adenosine deaminase I
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
single nucleotide resolution mapping assay using Lead probe
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
single nucleotide resolution mapping assay using RNAse T2
an assay of changes in phenotype due to increased or decreased dosage of a single allele of a gene.
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
single nucleotide resolution mapping assay using Fe-BABE probe
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
single nucleotide resolution mapping assay using RNAse U2
binding constant determination assay
Determination of KD value for an antibody binding a protein using a BIACORE assay.
A binding assay where the specified output is a binding constant
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
single nucleotide resolution mapping assay using NMIA probe
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
single nucleotide resolution mapping assay using Terbium probe
A planed process with objective of obtaining quantified values from an image.
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
single nucleotide resolution mapping assay using OH-radical probe
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
single nucleotide resolution mapping assay using RNAse T1
An image acquisition process that generate an image from the array.
A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics)
a device which has a function to emit light.
A perturbation device is a device which is designed to perform a perturb function
A growth chamber is an environmental control device.
An environmental control device is a device which has the function to control some aspect of the environment such as temperature, or humidity.
single nucleotide resolution mapping assay using Nuclease S1
a function that allows specific identification of individual speciment from one another.
e.g the function of a bar code reader used to read slide bar codes
A specimen fixation function is a function that holds or fastens an entity in a fixed position.
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
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
A current amplification function is an amplification function that increases the amplitude of a current.
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.
a transfer unction where the transfer requires work to move the entity, often against a gradient.
A cell harvester has a cell transfer function.
is a transfer function that displaces cells from one place to another
A device that records the patterns of pulse waves inside blood vessels.
A device that is used to transfer nucleic acids from agarose gels onto a membrane, based on the movement of buffer from a reservoir through the gel and the blotting membrane to a stack of dry blotting paper by capillary force. The molecules are carried to the blotting membrane on which they are adsorbed.
A device or system that supports a biologically active environment. ALAN SAYS NOT AN INSTRUMENT
A device that is used to measure the pH (acidity or alkalinity) of a liquid.
An image acquisition device that takes video or still photographs, or both, digitally by recording images via an electronic image sensor.
A device for dropping and immobilizing a solution of biomolecules, for example, nucleic acids such as probe DNA, mRNA, and peptide nucleic acid (PNA), and proteins on a DNA microarray surface to manufacture a DNA microarray.
A device that is used to isolate and collect RNA for subsequent molecular analysis.
The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas.
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.
A device that moves charged particles through a medium by using an electric field induced by electrodes.
A device that is used to produce targeted molecular pharmaceuticals for use in positron emission tomography.
A confocal microscope that uses a Nipkow disk, a mechanical, geometrically operating image scanning device.
An oligonucleotide synthesizer that is used to custom-build DNA molecules to contain a particular sequence of nucleotides.
high performance liquid chromatography instrument
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.
A measurement device that detects biological, chemical or physical events of samples in microtiter plates.
A microplate reader that is used for enzyme-linked immunosorbent assays (ELISA).
A robotic device that is used to excise spots from gels.
A device that is used to apply microwave irradiation to chemical reactions.
A device that measures the degree of darkness (the optical density) of a photographic or semitransparent material or of a reflecting surface.
A device that is used to automatically stain tissue sections on slides or tissue specimens.
A device for processing histological tissue having a tissue carrier basket suspended from a turntable overlying a plurality of beakers suspended from a carrier plate. The turntable is raised, indexed, and lowered by a suitable driving mechanism to move the tissue basket sequentially through the beakers. Timers can each be programmed to control the movement of the turntable to provide various different cycles for processing the tissue. Some of the beakers are received in individual thermal baths to heat and control the temperature of the substances received in the beakers for treating the tissue.
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.
A balance that consists of a metal plate on which to place an object and a digital readout of the measurement of its mass.
A device or system in which perfusion units are integrated.
A nuclear medicine tomographic imaging device that uses gamma rays to provide 3D information, typically presented as cross-sectional slices through the specimen but with the ability to be freely reformatted or manipulated as required.
array manufacturer role
a manufacturer role which is played by the person or organization that manufactured the array
MO_695 array_manufacturer
PERSON: Chris Stoeckert, Jie Zheng
A device that is used to measure ionizing radiation.
A confocal microscope that uses a programmable spatial light modulator for generating an arbitrary pattern of conjugate illumination and detection apertures.
Verveer et al, Journal of Microscopy, vol. 189, pt. 3, pp. 192-8
A device consisting of a vessel, similar in construction to a vacuum flask, that is used to maintain cold cryogenic temperatures. FIX THIS DEFINITION
A glass cutting and breaking device that is used to produce glass knives used in ultramicrotomy.
A device that is used for the fixation or stabilization of biological materials as the first step in specimen preparation for electron microscopy.
A device that creates an appropriate environment for nucleic acid hybridization.
An incubating device that provides shaking motion for biomedical applications (e.g., cell cultures).
A device that is used to image¬†small¬†laboratory¬†animals (e.g., rats and mice) in vivo.
An image acquisition device that is responsive to an infrared emissive target within a given field of view.
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.
A device used in electrophysiology that allows the study of single or multiple ion channels in cells.
A device that is used to acquire images of laboratory gels.
A device that is used for the separation of proteins.
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.
A device that is used to effect the transition of a substance into a glass.
An image acquisition device that uses ionizing electromagnetic radiation such as X-rays to view objects.
A device that consists of a radiosensitive detector and a means of recording the effects of radiation on the detector.
A device that is used to freeze dry material.
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.
A hardness testing device that is used in light-optical microscopes.
A microplate reader that can detect multiple types of absorbance, luminescence or fluorescence.
A balance that is used to compare the weights of two bodies, to determine the difference in mass (or weight).
A group of linked computers, working together closely so that in many respects they form a single computer.
A device that is used to sharpen knives used in microtomy.
A device that provides shaking motion for microplates.
A device for automatically analyzing blood coagulation in a clinical laboratory.
laser capture microdissection microscope
A microscope that uses low-energy laser beams and special transfer film to lift single cells from a tissue.
A liquid handling device that provides automatic liquid extraction.
A device that is used to visualize subcutaneous body structures including tendons, muscles, joints, vessels and internal organs.
A device that is used for the imaging of immunoblots.
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.
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.
electron paramagnetic resonance spectrometer
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.
A device that provides three-dimensional motion for biomedical applications (e.g., gel trays).
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.
A microscope that forms images of surfaces using a physical probe that scans the specimen.
A gel electrophoresis system that is used to separate very large molecules of DNA.
A device that is used to perform paraffin embedding of tissue specimens.
An device that is used to determine the order of nucleotides in nucleic acid sequences.
A device that is used to acquire and image bead array data.
An PCR instrument that enables both detection and quantification of one or more specific sequences in a DNA sample.
A device that is used for the warming of paraffin embedding medium.
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.
J. Black, Microbiology, Prentice Hall (1993) pg. 334; http://en.wikipedia.org/wiki/Autoclave
A device that is used to wash immunoassays in microwell strips and plates with professional accuracy. WHAT IS PROFESSIONAL ACCURACY??
nucleic acid extraction/purification instrument
A device that is used to isolate and collect nucleic acids (DNA or RNA) for subsequent molecular analysis.
A microplate washer that is used for enzyme-linked immunosorbent assays (ELISA).
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.
A device that is used to isolate and collect DNA for subsequent molecular analysis.
A pipetting system that has a plurality of tip fittings and is used for multi-well plate applications.
A device that is used to harvest cells from microplates and deposit samples on a filter mat. NOT AN INSTRUMENT?
A compact fluorometer that can be carried or moved with ease.
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.
A device that is used for the dissection of tissues under magnification.
A device that is used to fabricate glass micropipettes.
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.
A microscope that uses optics and a charge-coupled device (CCD) camera to output a digital image to a monitor.
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.
A microinjection device that is used to measure very small volumes of liquids.
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.
A device that heats materials in a vacuum.
A device that is used to heat microscope slides.
An electrophoresis system that is used to separate ionic species by their charge and frictional forces and mass.
denaturing high-performance liquid chromatography instrument
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.
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.
A measuring instrument that is used to determine the weight or mass of an object.
A tool for measuring adsorption of material onto planar metal (typically gold and silver) surfaces or onto the surface of metal nanoparticles.
An device that is used to determine the order of amino acids in protein sequences.
A device that is used to generate X-rays.
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
spike-in quality control role
MO_937 spike_quality_control
PERSON: Chris Stoeckert, Jie Zheng, Bjoern Peter
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
individual organism identifier
MO_169 Individual
a CRID symbol used to distinguish one individual organism from another.
dye swap quality control role
MO_524 dye_swap_quality_control
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
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.
binding constant
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.
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
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".
binding complex 3D structure determination assay
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.
Determination of a 3D structure of an antibody binding a protein by X-Ray crystallography, which identifies the specific binding site of the antibody.
binding assay
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.
An assay with the objective to characterize the disposition of two or more material entities to form a complex.
PERSON:Bjoern Peters, Randi Vita, Jason Greenbaum
cell culture expansion
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.
MO_758 grow
a processual entity that results in the increase of cell numbers
including grow of yeast and bacteria
gene knock out
MO_771 gene_knock_out
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.
gene knock in
MO_437 gene_knock_in
WEB: http://en.wikipedia.org/wiki/Gene_Knock-in
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.
chromosomal substitution
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'.
MO_995 chromosomal_substitution
genetically modified material
PERSON: Jie Zheng
a material entity, organism or cell, that is the output of a genetic transformation process.
term is proposed by BP on Oct 25, 2010 dev call
transfection
a genetic transformation which relies on the use of physical, electrical and chemical phenomena to introduce DNA or RNA into a cell
genetic transformation objective
suggested to be added by BP and AR during Oct 25, 2010 dev call
Person: Jie Zheng
a material transformation objective aims to create genetically modified organism or cell
induced mutation
MO_564 induced_mutation
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.
A measurement datum that describes the structural orientation of a material entity in 3D space.
PERSON: Jason Greenbaum, Randi Vita, Bjoern Peters
The atom coordinates found in a PDB (Protein Data Bank) file, generated by X Ray crystallography or NMR.
age since planting measurement datum
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.
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
age since hatching measurement datum
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.
age measurement assay
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.
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.
age since egg laying measurement datum
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.
assay validation objective
GROUP: Penn Group
an objective specification to check the accuracy or the quality of the results of an assay by comparison with independent results
age since germination measurement datum
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.
Definition of germination comes from GO. However, the term is deprecated from GO now because it is a grouping term without biological significance.
validation by reverse transcription PCR design
MO_986 reverse_transcription_PCR_quality_control
a study design in which checks the accuracy or the quality of the result of an assay by comparing with reverse transcription PCR results
age since eclosion measurement datum
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.
age since sowing measurement datum
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.
age since coitus measurement datum
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.
validation by real time PCR design
MO_434 real_time_PCR_quality_control
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
age measurement datum
A time measurement datum that is the result of measurement of age of an organism
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
PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng
discussed on Nov 15, dev call All subtype will be defined by textual definition now.
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
age since fertilization measurement datum
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.
Definition of fertilization comes from GO.
age since birth measurement datum
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.
reverse transcription polymerase chain reaction assay
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.
The time it takes for 50% of a class of stochastic processes to occur.
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.
A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer.
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
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.
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.
selective organism creation objective
WEB: wikipedia http://en.wikipedia.org/wiki/Cultivar http://en.wikipedia.org/wiki/Ecotype http://en.wikipedia.org/wiki/Strain_%28biology%29
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.
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.
An immunization in which an individual epitope is administered into a host organism.
Injection of a peptide T cell epitope into a mouse
PERSON:Bjoern Peters, Jason Greenbaum, Randi Vita
BP 12/21:Created based on a request from Melanie
RNA sequencing is a sequencing process which uses ribonucleic acid as input and results in a the creation of RNA sequence information artifact
efficacy of epitope intervention experiment
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.
epitope protection from infectious challenge experiment
An epitope protection experiment in which the ability of the epitope to protect the host from an infection is assessed.
half maximal effective concentration (EC50)
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.
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.
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.
A binding datum that states that there is no significant disposition of two or more entities to form a complex
epitope protection from tumor challenge experiment
An epitope protection experiment in which the ability of the epitope to protect the host from developing tumors is assessed.
an epitope intervention experiment that tests the efficacy of inducing an immune epitope response to prevent disease in a host.
selectively maintained organism
An organism that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms
Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Jie Zheng, Chris Stoeckert
MO_9 StrainOrLine, MO_71 Ecotype, MO_124 Cultivar
epitope protection from infectious challenge experiment based on pathogen burden
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.
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')
An assay in which the presence or amount of an infectious agent in an input material is detected in an evaluant
Bjoern Peters, Randi Vita, Jason Greenbaum
Culturing a sputum sample on agar medium to detect bacterial growth; Stain slices of liver from a mouse to count presence of infectious centers.
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.
epitope protection experiment based on survival
an epitope protection experiment that determines the success of the epitope intervention based on increased survival of the host.
an epitope intervention experiment that tests the ability of inducing an epitope immune response to treat an existing disease in the host.
half maximal inhibitory concentration (IC50)
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.
Interpolating that at a dose of IC50=12 nM, half of the binding of a comptetitive ligand is inhibited.
An administration in vivo to either actively or passively immunize an organism in order to induce a response against a specific immune epitope
epitope specific cytokine production by T cells
A process of cytokine production by T cells resulting from the recognition of a T cell epitope.
Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
ELISPOT assay of epitope specific transforming growth factor-beta production by T cells
An ELISPOT assay that measures epitope specific transforming growth factor-beta production by T cells
Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
operator variation design
A study design that assesses the operator performance and relation to data consistency and quality.
MO_519 operator_variation_design
cytometric bead array assay of epitope specific IP-10 production by T cells
A cytometric bead array assay that measures epitope specific IP-10 production by T cells
comparative genome hybridization by array design
A study design that detects genomic copy number variations using microarray technology.
MO_856 comparative_genome_hybridization_design
assay of epitope specific interleukin-27 production by T cells
An assay that measures epitope specific interleukin-27 production by T cells
in vivo design
A study design that is conducted entirely in a living organism, e.g. a compound treatment in a mouse model.
MO_454 in_vivo_design
genotyping by high throughput sequencing design
A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using high througput sequencing techniques.
epitope specific tolerance induction by T cells
A process of tolerance induction by T cells resulting from the recognition of a T cell epitope.
innate behavior design
A study design in which the innate behavior of the organism is examined, e.g. path finding in bees.
MO_355 innate_behavior_design
detection of specific nucleic acids with complementary probes of epitope specific transforming growth factor-beta production by T cells
A detection of specific nucleic acids with complementary probes that measures epitope specific transforming growth factor-beta production by T cells
SNP microarray
a DNA microarray used to detect polymorphisms in DNA samples
cell component comparison design
A study design that compares samples from different cell components.
MO_1019 cell_component_comparison_design
ELISPOT assay of epitope specific granulocyte macrophage colony-stimulating factor production by T cells
An ELISPOT assay that measures epitope specific granulocyte macrophage colony-stimulating factor production by T cells
epitope specific macrophage inflammatory protein-1 alpha production by T cells
A process of macrophage inflammatory protein-1 alpha production by T cells resulting from the recognition of a T cell epitope.
A process of T cell activation resulting from the recognition of a T cell epitope.
assay of epitope specific interleukin-10 production by T cells
An assay that measures epitope specific interleukin-10 production by T cells
cytometric bead array assay of epitope specific transforming growth factor-beta production by T cells
A cytometric bead array assay that measures epitope specific transforming growth factor-beta production by T cells
ex vivo design
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.
MO_808 ex_vivo_design
epitope specific type IV hypersensitivity by T cells
A process of type IV hypersensitivity by T cells resulting from the recognition of a T cell epitope.
normalization testing design
A study design that tests different normalization procedures.
MO_729 normalization_testing_design
intracellular staining assay of epitope specific perforin production
An intracellular staining assay that measures epitope specific perforin production
cell culture analyte detection bioassay of epitope specific interleukin-2 production by T cells
A cell culture analyte detection bioassay that measures epitope specific interleukin-2 production by T cells
assay of epitope specific interleukin-22 production by T cells
An assay that measures epitope specific interleukin-22 production by T cells
assay of epitope specific interleukin-8 production by T cells
An assay that measures epitope specific interleukin-8 production by T cells
epitope specific chemokine (C-C motif) ligand 1 production by T cells
A process of chemokine (C-C motif) ligand 1 production by T cells resulting from the recognition of a T cell epitope.
cell culture analyte detection bioassay of epitope specific interleukin-10 production by T cells
A cell culture analyte detection bioassay that measures epitope specific interleukin-10 production by T cells
ChIP-chip by SNP array assay
An assay where chromatin immunoprecipitation (ChIP) is used in combination with SNP microarray technology
EFO_0002764 ChIP-chip by SNP array
ELISA of epitope specific RANTES production by T cells
An ELISA that measures epitope specific RANTES production by T cells
cytometric bead array assay of epitope specific interleukin-1 beta production by T cells
A cytometric bead array assay that measures epitope specific interleukin-1 beta production by T cells
genetic population background information
Group: OBI group
a genetic characteristics information which is a part of genotype information that identifies the population of organisms
genotype information 'C57BL/6J Hnf1a+/-' in this case, C57BL/6J is the genetic population background information
proposed and discussed on San Diego OBI workshop, March 2011
environmental history design
A study design in which some aspect of the organism's environmental history is studied, such as exposure to teratogen, radiation, climate etc.
ELISPOT assay of epitope specific interleukin-6 production by T cells
An ELISPOT assay that measures epitope specific interleukin-6 production by T cells
assay of epitope specific T cell enhancement of B cell mediated immune response
An assay that measures epitope specific T cell enhancement of B cell mediated immune response
surface plasmon resonance assay of MHC:epitope complex binding to TCR
A surface plasmon resonance assay that measures MHC:epitope complex binding to TCR
assay of epitope specific interleukin-5 production by T cells
An assay that measures epitope specific interleukin-5 production by T cells
ELISA of epitope specific transforming growth factor-beta production by T cells
An ELISA that measures epitope specific transforming growth factor-beta production by T cells
assay of epitope specific RANTES production by T cells
An assay that measures epitope specific RANTES production by T cells
assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells
An assay that measures epitope specific granulocyte macrophage colony stimulating factor production by T cells
epigenetic modification identification objective
A molecular feature identification objective that aims to detect epigenetic modifications, such as DNA methylation, histone modifications.
Chris Stoeckert, Jie Zheng
Person: Chris Stoeckert
transcription profiling by tiling array assay
An assay in which the transcriptome of a biological sample is analysed using a tiling path array.
EFO_0002769 transcription profiling by tiling array
ELISA of epitope specific interleukin-22 production by T cells
An ELISA that measures epitope specific interleukin-22 production by T cells
assay of epitope specific interleukin-21 production by T cells
An assay that measures epitope specific interleukin-21 production by T cells
ELISA of epitope specific interleukin-9 production by T cells
An ELISA that measures epitope specific interleukin-9 production by T cells
transcription profiling by high thoughput sequencing design
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
Group: ArrayExpress production team
intracellular cytokine staining assay of epitope specific interleukin-6 production by T cells
An intracellular cytokine staining assay that measures epitope specific interleukin-6 production by T cells
cell culture analyte detection bioassay of epitope specific interleukin-4 production by T cells
A cell culture analyte detection bioassay that measures epitope specific interleukin-4 production by T cells
detection of specific nucleic acids with complementary probes of epitope specific tumor necrosis factor production by T cells
A detection of specific nucleic acids with complementary probes that measures epitope specific tumor necrosis factor production by T cells
cytometric bead array assay of epitope specific monocyte chemotactic protein-1 production by T cells
A cytometric bead array assay that measures epitope specific monocyte chemotactic protein-1 production by T cells
ELISA of epitope specific interleukin-23 production by T cells
An ELISA that measures epitope specific interleukin-23 production by T cells
detection of specific nucleic acids with complementary probes of epitope specific perforin production
A detection of specific nucleic acids with complementary probes that measures epitope specific perforin production
ELISA of epitope specific tumor necrosis factor superfamily cytokine production by T cells
An ELISA that measures epitope specific tumor necrosis factor superfamily cytokine production by T cells
genotyping by high throughput sequencing assay
An assay in which high througput sequencer is used to detect polymorphisms in DNA samples
EFO_0002771: genotyping by high throughput sequencing
ChIP-chip assay
WEB: http://en.wikipedia.org/wiki/ChIP-on-chip
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.
epitope specific T cell tolerance induction
A process of T cell tolerance induction resulting from the recognition of a T cell epitope.
intracellular material detection by flow cytometry assay of epitope specific cytotoxic T cell degranulation
An intracellular material detection by flow cytometry assay that measures epitope specific cytotoxic T cell degranulation
assay of epitope specific interleukin-13 production by T cells
An assay that measures epitope specific interleukin-13 production by T cells
array platform variation design
A study design in which the array platform is compared, e.g. Agilent versus Affymetrix.
MO_899 array_platform_variation_design
assay of epitope specific interleukin-9 production by T cells
An assay that measures epitope specific interleukin-9 production by T cells
epitope specific interleukin-3 production by T cells
A process of interleukin-3 production by T cells resulting from the recognition of a T cell epitope.
detection of specific nucleic acids with complementary probes of epitope specific interleukin-5 production by T cells
A detection of specific nucleic acids with complementary probes that measures epitope specific interleukin-5 production by T cells
epitope specific lymphotoxin A production by T cells
A process of lymphotoxin A production by T cells resulting from the recognition of a T cell epitope.
epitope specific interleukin-1 alpha production by T cells
A process of interleukin-1 alpha production by T cells resulting from the recognition of a T cell epitope.
ChIP-seq design
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.
Person: Chris Stoeckert, Jie Zheng
translational bias design
A study design that characterizes the association of transcripts and translation machinery.
MO_939 translational_bias_design
ELISA of epitope specific interleukin-3 production by T cells
An ELISA that measures epitope specific interleukin-3 production by T cells
ELISA of epitope specific interleukin-1 alpha production by T cells
An ELISA that measures epitope specific interleukin-1 alpha production by T cells
epitope specific interleukin-27 production by T cells
A process of interleukin-27 production by T cells resulting from the recognition of a T cell epitope.
assay of epitope specific helper T cell enhancement of T cell mediated immune response
An assay that measures epitope specific helper T cell enhancement of T cell mediated immune response
assay of epitope specific transforming growth factor-beta production by T cells
An assay that measures epitope specific transforming growth factor-beta production by T cells
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
PERS:Philippe Rocca-Serra
adapted from wikipedia (http://en.wikipedia.org/wiki/Familywise_error_rate)
DNA methylation profiling by high throughput sequencing assay
EFO_0002761 methylation profiling by high throughput sequencing
Group: ArrayExpress production team, James Malone, Helen Parkinson
An assay in which the methylation state of DNA is determined and is compared between samples using sequencing based technology
epitope specific transforming growth factor-beta production by T cells
A process of transforming growth factor-beta production by T cells resulting from the recognition of a T cell epitope.
detection of specific nucleic acids with complementary probes of epitope specific interleukin-12 production by T cells
A detection of specific nucleic acids with complementary probes that measures epitope specific interleukin-12 production by T cells
assay of epitope specific cytotoxic T cell degranulation
An assay that measures epitope specific cytotoxic T cell degranulation
cell culture analyte detection bioassay of epitope specific transforming growth factor-beta production by T cells
A cell culture analyte detection bioassay that measures epitope specific transforming growth factor-beta production by T cells
RNA-seq assay
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
EFO_0002770 transcription profiling by high throughput sequencing
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
transcription profiling by high throughput sequencing
ELISPOT assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells
An ELISPOT assay that measures epitope specific tumor necrosis factor superfamily cytokine production by T cells
cell culture analyte detection bioassay of epitope specific interleukin-5 production by T cells
A cell culture analyte detection bioassay that measures epitope specific interleukin-5 production by T cells
genotyping by array assay
An assay in which an array is used to detect polymorphisms in DNA samples
EFO_0002767: genotyping by array
epitope specific interleukin-16 production by T cells
A process of interleukin-16 production by T cells resulting from the recognition of a T cell epitope.
assay of epitope specific chemokine (C-C motif) ligand 1 production by T cells
An assay that measures epitope specific chemokine (C-C motif) ligand 1 production by T cells
detection of specific nucleic acids with complementary probes of epitope specific interleukin-2 production by T cells
A detection of specific nucleic acids with complementary probes that measures epitope specific interleukin-2 production by T cells
DNA methylation profiling by array design
A study design in which the methylation state of DNA is determined and is compared between samples using array technology.
GROUP: ArrayExpress production team
detection of specific nucleic acids with complementary probes of epitope specific interleukin-22 production by T cells
A detection of specific nucleic acids with complementary probes that measures epitope specific interleukin-22 production by T cells
assay of epitope specific interleukin-16 production by T cells
An assay that measures epitope specific interleukin-16 production by T cells
ELISA of epitope specific IP-10 production by T cells
An ELISA that measures epitope specific IP-10 production by T cells
translation profiling assay
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.
EFO_0001033 translation profiling
ELISA of epitope specific interleukin-15 production by T cells
An ELISA that measures epitope specific interleukin-15 production by T cells
cytometric bead array assay of epitope specific interleukin-12 production by T cells
A cytometric bead array assay that measures epitope specific interleukin-12 production by T cells
in vitro design
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.
MO_347 in_vitro_design
RNAi profiling by array design
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.
ELISA of epitope specific lymphotoxin A production by T cells
An ELISA that measures epitope specific lymphotoxin A production by T cells
cytometric bead array assay of epitope specific interleukin-5 production by T cells
A cytometric bead array assay that measures epitope specific interleukin-5 production by T cells
transcription profiling by array design
A study design that identifies forms and abundance of transcripts in the genome using microarray technology.
detection of specific nucleic acids with complementary probes of epitope specific interleukin-17 production by T cells
A detection of specific nucleic acids with complementary probes that measures epitope specific interleukin-17 production by T cells
assay of epitope specific interleukin-15 production by T cells
An assay that measures epitope specific interleukin-15 production by T cells
disease state design
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.
MO_902 disease_state_design
wild type organism genotype information
C57BL/6J wild type
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.
assay of epitope specific interleukin-17 production by T cells
An assay that measures epitope specific interleukin-17 production by T cells
cytometric bead array assay of epitope specific interleukin-17 production by T cells
A cytometric bead array assay that measures epitope specific interleukin-17 production by T cells
cytometric bead array assay of epitope specific interleukin-10 production by T cells
A cytometric bead array assay that measures epitope specific interleukin-10 production by T cells
detection of specific nucleic acids with complementary probes of epitope specific interleukin-21 production by T cells
A detection of specific nucleic acids with complementary probes that measures epitope specific interleukin-21 production by T cells
intracellular cytokine staining assay of epitope specific interleukin-5 production by T cells
An intracellular cytokine staining assay that measures epitope specific interleukin-5 production by T cells
cytometric bead array assay of epitope specific interleukin-2 production by T cells
A cytometric bead array assay that measures epitope specific interleukin-2 production by T cells
cell culture analyte detection bioassay of epitope specific interleukin-16 production by T cells
A cell culture analyte detection bioassay that measures epitope specific interleukin-16 production by T cells
ELISA of epitope specific macrophage inflammatory protein-1 alpha production by T cells
An ELISA that measures epitope specific macrophage inflammatory protein-1 alpha production by T cells
intracellular cytokine staining assay of epitope specific granulocyte macrophage colony-stimulating factor production by T cells
An intracellular cytokine staining assay that measures epitope specific granulocyte macrophage colony-stimulating factor production by T cells
RNAi profiling by array assay
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.
EFO_0001030 RNAi profiling by array
genotype information
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
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.
discussed on San Diego OBI workshop, March 2011
RNA stability design
A study design that examines the stability and/or decay of RNA transcripts.
MO_553 RNA_stability_design
tiling microarray
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.
assay of epitope specific IP-10 production by T cells
An assay that measures epitope specific IP-10 production by T cells
intracellular cytokine staining assay of epitope specific interleukin-13 production by T cells
An intracellular cytokine staining assay that measures epitope specific interleukin-13 production by T cells
species comparison design
A study design that assays differences between distinct species.
MO_675 species_design
X-ray crystallography assay of MHC:epitope complex binding to TCR
A X-ray crystallography assay that measures MHC:epitope complex binding to TCR
transcription profiling by RT-PCR design
A study design which aims to examine the transcriptome of a biological sample by reverse transcription PCR (RT-PCR).
epitope specific T cell enhancement of B cell mediated immune response
A process of T cell enhancement of B cell mediated immune response resulting from the recognition of a T cell epitope.
ELISA of epitope specific chemokine (C-C motif) ligand 1 production by T cells
An ELISA that measures epitope specific chemokine (C-C motif) ligand 1 production by T cells
epitope specific interleukin-21 production by T cells
A process of interleukin-21 production by T cells resulting from the recognition of a T cell epitope.
cell-cell binding detection by flow cytometry assay of MHC:epitope complex binding to TCR
A cell-cell binding detection by flow cytometry assay that measures MHC:epitope complex binding to TCR
proteomic profiling by array assay
An assay that proteins in a sample are detected, quantified or otherwise analysed, e.g. antibody profiling using an array based technology
EFO_0002765 proteomic profiling by array
cell culture analyte detection bioassay of epitope specific interferon-gamma production by T cells
A cell culture analyte detection bioassay that measures epitope specific interferon-gamma production by T cells
ELISPOT assay of epitope specific granzyme B production by T cells
An ELISPOT assay that measures epitope specific granzyme B production by T cells
microRNA profiling by array design
A study design in which a microRNA array is used to analyse the microRNA component of the transcriptome.
assay of T cell epitope specific tolerance induction
An assay that measures epitope specific tolerance induction by T cells
detection of specific nucleic acids with complementary probes of epitope specific RANTES production by T cells
A detection of specific nucleic acids with complementary probes that measures epitope specific RANTES production by T cells
cytometric bead array assay of epitope specific interleukin-4 production by T cells
A cytometric bead array assay that measures epitope specific interleukin-4 production by T cells
assay of epitope specific lymphotoxin A production by T cells
An assay that measures epitope specific lymphotoxin A production by T cells
organism development design
A study design that assays events associated with development. Development applies to organism(s) acquiring a mature state.
MO_892 development_or_differentiation_design
family history design
A study design in which the family history such as traits, characteristics, susceptibility to disease is studied.
MO_544 family_history_design
ELISA of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
An ELISA that measures epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
transcription profiling identification objective
A molecular feature identification objective that aims to characterize the abundance of transcripts
Group: Penn Group
DNA methylation profiling by array assay
An assay in which the methylation state of DNA is determined and is compared between samples using array technology
EFO_0002759 methylation profiling by array
assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells
An assay that measures epitope specific macrophage inflammatory protein-1 alpha production by T cells
epitope specific granulocyte colony stimulating factor production by T cells
A process of granulocyte colony stimulating factor production by T cells resulting from the recognition of a T cell epitope.
microRNA profiling by array assay
An assay in which a microRNA array is used to analyse the microRNA component of the transcriptome.
EFO_0000753 microRNA profiling by array
quality control testing design
A study design in which some aspects of the experiment is quality controlled for the purposes of quality assurance.
MO_981 quality_control_testing_design
clinical history design
A study design that the organism's clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. is studied.
MO_832 clinical_history_design
detection of specific nucleic acids with complementary probes of epitope specific interleukin-4 production by T cells
A detection of specific nucleic acids with complementary probes that measures epitope specific interleukin-4 production by T cells
cell culture analyte detection bioassay of epitope specific granulocyte macrophage colony-stimulating factor production by T cells
A cell culture analyte detection bioassay that measures epitope specific granulocyte macrophage colony-stimulating factor production by T cells
intracellular cytokine staining assay of epitope specific interleukin-21 production by T cells
An intracellular cytokine staining assay that measures epitope specific interleukin-21 production by T cells
detection of specific nucleic acids with complementary probes of epitope specific monocyte chemotactic protein-1 production by T cells
A detection of specific nucleic acids with complementary probes that measures epitope specific monocyte chemotactic protein-1 production by T cells
ELISA of epitope specific monocyte chemotactic protein-1 production by T cells
An ELISA that measures epitope specific monocyte chemotactic protein-1 production by T cells
assay of epitope specific chemokine (C-C motif) ligand 4 production by T cells
An assay that measures epitope specific chemokine (C-C motif) ligand 4 production by T cells
ELISA of epitope specific interleukin-21 production by T cells
An ELISA that measures epitope specific interleukin-21 production by T cells
assay of epitope specific type IV hypersensitivity by T cells
An assay that measures epitope specific type IV hypersensitivity by T cells
cytometric bead array assay of epitope specific interleukin-13 production by T cells
A cytometric bead array assay that measures epitope specific interleukin-13 production by T cells
detection of specific nucleic acids with complementary probes of epitope specific interferon-gamma production by T cells
A detection of specific nucleic acids with complementary probes that measures epitope specific interferon-gamma production by T cells
epitope specific tumor necrosis factor superfamily cytokine production by T cells
A process of tumor necrosis factor superfamily cytokine production by T cells resulting from the recognition of a T cell epitope.
allele information
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.
genotype information 'C57BL/6J Hnf1a+/-' in this case, Hnf1a+/- is the allele information
cytometric bead array assay of epitope specific tumor necrosis factor production by T cells
A cytometric bead array assay that measures epitope specific tumor necrosis factor production by T cells
ELISPOT assay of epitope specific interleukin-17 production by T cells
An ELISPOT assay that measures epitope specific interleukin-17 production by T cells
detection of specific nucleic acids with complementary probes of epitope specific interferon-beta production by T cells
A detection of specific nucleic acids with complementary probes that measures epitope specific interferon-beta production by T cells
detection of specific nucleic acids with complementary probes of epitope specific granulocyte macrophage colony-stimulating factor production by T cells
A detection of specific nucleic acids with complementary probes that measures epitope specific granulocyte macrophage colony-stimulating factor production by T cells
post-transcriptional modification design
A study design in which a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting.
MO_392 cellular_modification_design
post transcription modification design? or more clear RNAi design / antibody targeting design? need to check the use cases
ELISA of epitope specific interleukin-8 production by T cells
An ELISA that measures epitope specific interleukin-8 production by T cells
cytometric bead array assay of epitope specific interleukin-6 production by T cells
A cytometric bead array assay that measures epitope specific interleukin-6 production by T cells
transcription profiling by RT-PCR assay
An assay in which the transcriptome of a biological sample is analysed by reverse transcription PCR (RT-PCR)
EFO_0002943: transcription profiling by RT-PCR
Person: Anna Farne
epitope specific chemokine (C-C motif) ligand 4 production by T cells
A process of chemokine (C-C motif) ligand 4 production by T cells resulting from the recognition of a T cell epitope.
assay of epitope specific interleukin-23 production by T cells
An assay that measures epitope specific interleukin-23 production by T cells
genetic alteration information
a genetic characteristics information that is about known changes or the lack thereof from the genetic background, including allele information, duplication, insertion, deletion, etc.
cellular process design
A study design that aims to study the processes that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
MO_810 cellular_process_design
epitope specific RANTES production by T cells
A process of RANTES production by T cells resulting from the recognition of a T cell epitope.
detection of specific nucleic acids with complementary probes of epitope specific interleukin-10 production by T cells
A detection of specific nucleic acids with complementary probes that measures epitope specific interleukin-10 production by T cells
cytometric bead array assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells
A cytometric bead array assay that measures epitope specific tumor necrosis factor superfamily cytokine production by T cells
wild type allele information
MO_605 genotype
an allele information that is about the allele found most frequently in natural populations, or in standard laboratory stocks for a given organism.
intracellular cytokine staining assay of epitope specific chemokine (C-C motif) ligand 4 production by T cells
An intracellular cytokine staining assay that measures epitope specific chemokine (C-C motif) ligand 4 production by T cells
epitope specific granzyme B production by T cells
A process of granzyme B production by T cells resulting from the recognition of a T cell epitope.
epitope specific interleukin-8 production by T cells
A process of interleukin-8 production by T cells resulting from the recognition of a T cell epitope.
injury design
A study design in which the response of an organism(s) to injury or damage is studied.
MO_726 injury_design
intracellular cytokine staining assay of epitope specific interleukin-3 production by T cells
An intracellular cytokine staining assay that measures epitope specific interleukin-3 production by T cells
organism status comparison design
A study design that compares samples from live and dead organisms.
MO_841 organism_status_design
ELISA of epitope specific chemokine (C-C motif) ligand 4 production by T cells
An ELISA that measures epitope specific chemokine (C-C motif) ligand 4 production by T cells
cytometric bead array assay of epitope specific interferon-gamma production by T cells
A cytometric bead array assay that measures epitope specific interferon-gamma production by T cells
assay of epitope specific interleukin-18 production by T cells
An assay that measures epitope specific interleukin-18 production by T cells
epitope specific interleukin-23 production by T cells
A process of interleukin-23 production by T cells resulting from the recognition of a T cell epitope.
detection of specific nucleic acids with complementary probes of epitope specific interleukin-27 production by T cells
A detection of specific nucleic acids with complementary probes that measures epitope specific interleukin-27 production by T cells
detection of specific nucleic acids with complementary probes of epitope specific IP-10 production by T cells
A detection of specific nucleic acids with complementary probes that measures epitope specific IP-10 production by T cells
cell culture analyte detection bioassay of epitope specific interleukin-3 production by T cells
A cell culture analyte detection bioassay that measures epitope specific interleukin-3 production by T cells
intracellular cytokine staining assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells
An intracellular cytokine staining assay that measures epitope specific tumor necrosis factor superfamily cytokine production by T cells
epitope specific monocyte chemotactic protein-1 production by T cells
A process of monocyte chemotactic protein-1 production by T cells resulting from the recognition of a T cell epitope.
genotyping by array design
A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using microarray technology.
assay of epitope specific interleukin-1 alpha production by T cells
An assay that measures epitope specific interleukin-1 alpha production by T cells
detection of specific nucleic acids with complementary probes of epitope specific interleukin-6 production by T cells
A detection of specific nucleic acids with complementary probes that measures epitope specific interleukin-6 production by T cells
assay of epitope specific interferon-beta production by T cells
An assay that measures epitope specific interferon-beta production by T cells
assay of epitope specific interleukin-12 production by T cells
An assay that measures epitope specific interleukin-12 production by T cells
in vivo cell mediated cell killing assay of epitope specific T cell mediated cytotoxicity
An in vivo cell mediated cell killing assay that measures epitope specific T cell mediated cytotoxicity
comparative genomic hybridization by array assay
An assay in which changes in DNA sequence copy number are analysed using a microarray. For example the analysis of LOH in tumor cells vs a non diseased sample or the comparison of clinical isolated of disease causing bacteria.
EFO_0000749: comparative genomic hybridization by array
Person: James Malone
array CGH
epitope specific cytotoxic T cell degranulation
A process of cytotoxic T cell degranulation resulting from the recognition of a T cell epitope.
detection of specific nucleic acids with complementary probes of epitope specific interleukin-23 production by T cells
A detection of specific nucleic acids with complementary probes that measures epitope specific interleukin-23 production by T cells
stimulus or stress design
A study design in which the response of an organism(s) to the stress or stimulus is studied, e.g. osmotic stress, heat shock, radiation exposure, behavioral treatment etc.
MO_568 stimulus_or_stress_design
cytometric bead array assay of epitope specific granulocyte colony stimulating factor production by T cells
A cytometric bead array assay that measures epitope specific granulocyte colony stimulating factor production by T cells
protein and DNA interaction identification objective
A sequence feature identification objective that aims to characterize the interactions between protein and DNA which includes identification of transcription factor binding sites.
MO_933 binding_site_identification_design
epitope specific interleukin-22 production by T cells
A process of interleukin-22 production by T cells resulting from the recognition of a T cell epitope.
assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells
An assay that measures epitope specific tumor necrosis factor superfamily cytokine production by T cells
protocol optimization design
A study design where different protocols or protocol parameters are compared aims to find an optimized protocol
MO_934 optimization_design
Promoter activity detection by reporter gene assay of epitope specific interleukin-2 production by T cells
A Promoter activity detection by reporter gene assay that measures epitope specific interleukin-2 production by T cells
ChIP-chip design
A study design which aims to identify protein binding sites in genomic DNA by a combination of chromatin immunoprecipitation and DNA microarray (chip) assays.
genetic characteristics information
MO definition: The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes. examples in ArrayExpress wild_type MutaMouse (CD2F1 mice with lambda-gt10LacZ integration) AlfpCre; SNF5 flox/knockout p53 knock out C57Bl/6 gp130lox/lox MLC2vCRE/+ fer-15; fem-1 df/df pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid)
MO_66 IndividualGeneticCharacteristics
a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes.
cytometric bead array assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells
A cytometric bead array assay that measures epitope specific macrophage inflammatory protein-1 alpha production by T cells
assay of epitope specific interleukin-3 production by T cells
An assay that measures epitope specific interleukin-3 production by T cells
assay of epitope specific T cell activation
An assay that measures epitope specific T cell activation
imprinting design
A study design where differences in genetic imprinting of maternally- and paternally-inherited chromosomes (e.g., due to in vivo differences in chemical modification and/or chromatin structure) are compared.
MO_914 imprinting_design
cell cycle design
A study design that assays events that occur in relation to the cell cycle, which is the period between the formation of a cell, by division of its mother cell and the time when the cell itself divides to form two daughter cells.
MO_822 cell_cycle_design
translation profiling design
A study design in which surface-bound, translationally competent ribosome complexes are used to generate a translation profile for mRNA, where 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.
cell type comparison design
A study design that compares cells of different type, for example different cell lines.
MO_764 cell_type_comparison_design
cytometric bead array assay of epitope specific RANTES production by T cells
A cytometric bead array assay that measures epitope specific RANTES production by T cells
cell culture analyte detection bioassay of epitope specific interleukin-6 production by T cells
A cell culture analyte detection bioassay that measures epitope specific interleukin-6 production by T cells
assay of epitope specific interferon-gamma production by T cells
An assay that measures epitope specific interferon-gamma production by T cells
epitope specific interleukin-9 production by T cells
A process of interleukin-9 production by T cells resulting from the recognition of a T cell epitope.
assay of epitope specific tumor necrosis factor production by T cells
An assay that measures epitope specific tumor necrosis factor production by T cells
ChIP-chip by tiling array design
A study design which aims to identify protein binding sites in genomic DNA by a combination of chromatin immunoprecipitation and tiling microarray (chip) assays.
dose response design
A study design that examines the relationship between the size of the administered dose and the extent of the response.
MO_485 dose_response_design
ChIP-chip by tiling array assay
An assay where chromatin immunoprecipitation (ChIP) is used in combination with tiling microarray technology
EFO_0002762 ChIP-chip by tiling array
epitope specific helper T cell enhancement of T cell mediated immune response
A process of helper T cell enhancement of T cell mediated immune response resulting from the recognition of a T cell epitope.
epitope specific interferon-beta production by T cells
A process of interferon-beta production by T cells resulting from the recognition of a T cell epitope.
organism part comparison design
A study design that compares tissues, regions, organs within or between organisms
MO_953 organism_part_comparison_design
intracellular material detection of epitope specific granzyme B production by T cells
An intracellular staining assay that measures epitope specific granzyme B production by T cells
protein binding site identification design
A study design that investigates protein binding sites on nucleic acids.
sex comparison design
A study design that assays differences associated with an organism's sex, gender or mating type.
MO_575 sex_design
transcription profiling by tiling array design
A study design in which gene expression on a genome-wide basis is evaluated, without bias toward coding or noncoding regions, using tiling arrays containing oligonucleotides that are either overlapping or spaced at regular intervals.
cell differentiation design
A study design that assays events associated with cell development or differentiation.
transcription profiling design
A study design that identifies forms and abundance of transcripts in the genome.
operon identification design
A study design that identifies locations and members of operons in a genome.
MO_772 operon_identification_design
radio immuno assay of epitope specific interferon-gamma production by T cells
A radio immuno assay that measures epitope specific interferon-gamma production by T cells
DNA methylation profiling by high throughput sequencing design
A study design in which the methylation state of DNA is determined and is compared between samples using high throughput sequencing technology.
assay of epitope specific granzyme B production by T cells
An assay that measures epitope specific granzyme B production by T cells
intracellular cytokine staining assay of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
An intracellular cytokine staining assay that measures epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
ELISA of epitope specific macrophage inflammatory protein-1 gamma production by T cells
An ELISA that measures epitope specific macrophage inflammatory protein-1 gamma production by T cells
epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
A process of chemokine (C-X-C motif) ligand 9 production by T cells resulting from the recognition of a T cell epitope.
all pairs design
A study design in which all specimens are compared to every other specimen.
MO_565 all_pairs
proteomic profiling by array design
A study design in which proteins in a sample are detected, quantified or otherwise analysed, e.g. antibody profiling using an array based technology
PMID: 20483222. Comp Biochem Physiol Part D Genomics Proteomics. 2008 Sep;3(3):234-42. Analysis of Sus scrofa liver proteome and identification of proteins differentially expressed between genders, and conventional and genetically enhanced lines. "After controlling the false discovery rate (FDR</=0.1) using the Storey q value only four proteins (EPHX1, CAT, PAH, ST13) were shown to be differentially expressed between genders (Males/Females) and two proteins (SELENBP2, TAGLN) were differentially expressed between two lines (Transgenic/Conventional pigs)"
A quantitative confidence value that measures the minimum false discovery rate that is incurred when calling that test significant. To compute q-values, it is necessary to know the p-value produced by a test and possibly set a false discovery rate level.
Adapted from several sources, including http://.en/wikipedia.org/wiki/False_discovery_rate http://svitsrv25.epfl.ch/R-doc/library/qvalue.html
FDR adjusted p-value
genotyping design
A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs.
MO_560 genotyping_design
assay of epitope specific interleukin-2 production by T cells
An assay that measures epitope specific interleukin-2 production by T cells
epitope specific interleukin-15 production by T cells
A process of interleukin-15 production by T cells resulting from the recognition of a T cell epitope.
epitope specific macrophage inflammatory protein-1 gamma production by T cells
A process of macrophage inflammatory protein-1 gamma production by T cells resulting from the recognition of a T cell epitope.
individual genetic characteristics comparison design
A study design where genotype, haplotype, or other individual genetic characteristics are compared.
MO_527 individual_genetic_characteristics_design
assay of epitope specific interleukin-1 beta production by T cells
An assay that measures epitope specific interleukin-1 beta production by T cells
assay of epitope specific interleukin-4 production by T cells
An assay that measures epitope specific interleukin-4 production by T cells
assay of epitope specific interleukin-6 production by T cells
An assay that measures epitope specific interleukin-6 production by T cells
cell culture analyte detection bioassay of epitope specific tumor necrosis factor production by T cells
A cell culture analyte detection bioassay that measures epitope specific tumor necrosis factor production by T cells
intracellular cytokine staining assay of epitope specific lymphotoxin A production by T cells
An intracellular cytokine staining assay that measures epitope specific lymphotoxin A production by T cells
pathogenicity design
A study design in which an infective agent such as a bacterium, virus, protozoan, fungus etc. infects a host organism(s) and the infective agent is assayed.
MO_807 pathogenicity_design
ELISPOT assay of epitope specific interleukin-5 production by T cells
An ELISPOT assay that measures epitope specific interleukin-5 production by T cells
assay of epitope specific macrophage inflammatory protein-1 gamma production by T cells
An assay that measures epitope specific macrophage inflammatory protein-1 gamma production by T cells
cytometric bead array assay of epitope specific interleukin-8 production by T cells
A cytometric bead array assay that measures epitope specific interleukin-8 production by T cells
assay of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
An assay that measures epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
genetic modification design
A study design in which an organism(s) is studied that has had genetic material removed, rearranged, mutagenized or added, such as in a knock out.
MO_447 genetic_modification_design
ELISA of epitope specific granzyme B production by T cells
An ELISA that measures epitope specific granzyme B production by T cells
epitope specific IP-10 production by T cells
A process of IP-10 production by T cells resulting from the recognition of a T cell epitope.
transcription profiling by array assay
An assay in which the transcriptome of a biological sample is analysed using array technology.
EFO_0002768: transcription profiling by array
strain comparison design
A study design that assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species.
MO_462 strain_or_line_design
assay of epitope specific monocyte chemotactic protein-1 production by T cells
An assay that measures epitope specific monocyte chemotactic protein-1 production by T cells
intracellular cytokine staining assay of epitope specific interleukin-12 production by T cells
An intracellular cytokine staining assay that measures epitope specific interleukin-12 production by T cells
Date: 2011-06-27; Spreadsheet: All AssayTypes.xls; Worksheet: T cell Assay Template; Mappings: assay_mappings.owl
T cell epitope disease exacerbation experiment
An epitope disease exacerbation experiment in which the evaluated response is made by T cells
PERSON: Randi Vita, Jason Greenbaum, Bjoern Peters
cell specimen
A specimen primarily composed of cells collected from a multicellular organism or a cell culture
monospecific T cell recognition of eluted MHC ligand assay
An assay in which the presence of a specific ligand in an elute is detected using the response of T cells that are known to be monospecific for that ligand as a readout
Using proliferation of a T cell line specific for SIINFEKL in response to material eluted from a cell as evidence that SIINFEKL was presented by MHC on that cell.
epitope specific interleukin-17F production by T cells
A process of interleukin-17F production by T cells resulting from the recognition of a T cell epitope.
Date: 2011-06-27; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
T cell epitope specific immune intervention
An epitope specific immune intervention in which the induced response targets a T cell epitope
Injecting a mouse with peptide SIINFEKL to induce a T cell response against the peptide
specimen with known storage state
A specimen for which it is known whether it has been subjected to storage of a specified type.
T cell epitope protection from tumor challenge
An epitope protection experiment in which the ability of T cell epitope responses to protect the host from developing tumors is assessed.
lowess group transformation
A lowess transformation where a potentially different normalization curve is generated and used for two or more groups (delineated by some criteria); criteria could include blocks (e.g. print-tip groups) on an array, or the day on which mass spectrometry was performed.
T cell epitope protection from infectious challenge based on pathogen burden
An epitope protection from infectious challenge experiment in which T cell responses are induced and the readout is a reduction in the presence of pathogens in the host compared to controls.
An assay in which a phage display library is panned to select phages that bind a molecule of interest, the phage encoded peptide/proteins are sequenced.
Randi Vita, Jason Greenbaum, Bjoern Peters
Selecting phages from a commercial library that produce peptides binding to an antibody of interest, sequencing those peptides.
lowess transformation
A data transformation of normalizing ratio data by using a locally weighted polynomial regression (typically after a log transformation). The regression can be performed on log ratios resulting from the relation of two data sets versus the average log intensity data from the same two data sets or it can be performed on raw or log transformed values from one data set versus values from another. The goal could be to remove intensity-dependent dye-specific effects from the set of pair wise ratios. This method can be applied globally, or limited by one or more specified criteria.
mass spectrometry of eluted MHC ligand assay
The identification of ligands eluted from MHC molecules using mass spectrometry
tissue specimen
A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm).
IEDB, http://en.wikipedia.org/wiki/Phage_display
Jason Greenbaum, Randi Vita, Bjoern Peters
Phage display library panning is a process in which a diverse collection of phages encoding peptides or proteins are screened and the ones encoding active peptides/proteins are selected in an iterative process similar to natural selection.
Screening a libray of M13 phages displaying random peptide sequences for binding to the MHC molecule HLA-A*02:02 resulting in a subset of phages that encode peptides that bind.
lowess global transformation
A lowess transformation where the same normalization curve is used for all members of the data set; e.g. Features on an array, picked spots on a gel, or measured metabolites in a sample.
intracellular cytokine staining assay of epitope specific transforming growth factor-beta production by T cells
An intracellular cytokine staining assay that measures epitope specific transforming growth factor-beta production by T cells
cell collecting
A planned process that collects cells from culture.
efficacy of T cell epitope intervention experiment
An epitope intervention experiment in which the induced immune response is targeting a T cell epitope
A mixture containing MHC molecules that was purified to remove non-MHC molecular entities.
BP: 06/09/11: This needs to be coordinated with the broader treatment of 'purified materials' in general.
HLA A*0201 that was purified from cell lysate using an HLA class I specific antibody
disposition to be bound by an MHC protein complex
Is the disposition borne by a material entity that is realized in a process of being bound in the antigen binding grove of an MHC protein complex.
B cell epitope specific immune intervention
An epitope specific immune intervention in which the induced response targets a B cell epitope
Injecting a mouse with recombinant antibody targeting an anthrax epitope
An efficacy of epitope intervention experiment that tests the ability of the intervention to decrease an existing immune response
mass spectrometry of MHC ligands eluted from whole cells assay
An assay in which ligands are eluted from MHC molecules expressed on the cell surface, and the specific ligands are identified by mass spectrometry.
cytometric bead array of epitope specific granulocyte macrophage colony-stimulating factor production by T cells
A cytometric bead array assay that measures epitope specific granulocyte macrophage colony-stimulating factor production by T cells
binding assay that uses radioactivity detection as an indicator of binding
T cell epitope protection experiment based on survival
An epitope protection experiment based on survival in which the evaluated responses are made by T cells
cell bound MHC competitive binding assay using T cell epitope recognition assay
An assay in which a T cell line known to respond to a certain MHC:epitope combination is incubated with the known epitope, another ligand to be evaluated and the MHC to determine if the evaluant can outcompete the known reactive epitope which indicates that the evaluant binds the MHC.
Incubating OT-1 cells together with their specific epitope SIINFEKL and its restricting MHC H-2 Kb and titrating in different amounts of the peptide SSSNFAKL and reading out proliferation to determine if SSSNFAKL binds H-2 Kb
T cell response inhibition MHC binding assay
linear amplification
An enzymatic amplification which amplifies nucleic acid sequence by making many copies off the same template.
An example is the use of the T7 promoter for amplification by transcribing many RNA copies.
assay of epitope specific T cell helper activity
An assay that measures the ability of epitope specific helper T cells to enhance either B cell or T cell adaptive immune response function
intracellular cytokine staining assay of epitope specific interleukin-22 production by T cells
An intracellular cytokine staining assay that measures epitope specific interleukin-22 production by T cells
assay of epitope specific perforin release by T cells
An assay that measures the production of perforin by T cells in response to the recognition of a T cell epitope
atmosphere
A growth environment pertaining to the atmospheric conditions that is used to culture or grow an organism.
binding assay that uses fluorescence detection as an indicator of binding
T cell recognition of HPLC fractionated MHC ligand eluate compared to synthetic ligand assay
An assay in which an HPL chromatography is run to separate an input mixture of ligands eluted from MHC into fractions. These fractions are tested for recognition by T cells and compared to the recognition of a synthetic ligand that is presumed to be the recognized epitope. Identical HPLC fractionation and T cell recognition patterns confirm that the specific ligand was presented by MHC molecules.
PERSON: Randi Vita; Bjoern Peters; Jason Greenbaum; Jorg Calis
Using a laser to stimulate a cell culture that was previously labeled with fluorescent antibodies to detect light emmission at a different wavelength in order to determine the presence of surface markers the antibodies are specific for.
an assay in which a materials fluorescence is determined
epitope specific perforin production by T cells
Should be linked to a GO process, which will be requested by IEDB team. Along with granzyme B production, should be tied to T cell degranulation
The production of perforin, an immune mediator molecule involved in T cell degranulation, resulting from the recognition of a T cell epitope.
6/13/11 BP: The disposition referenced is the one of the ligand to bind the molecule. This along with binding as a function / process needs to be figured out with GO which is inconsistent at this point.
The peptide SIINFEKL binding to an empty murine H-2 Kb molecule to form a complex.
The process in which a ligand binds to an MHC molecule to form a stable complex
dissection
A planned process that separates and isolates tissues for surgical purposes, or for the analysis or study of their structures.
purification
A planned process 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
specimen with pre- or post-mortem status
A specimen that has been established to be taken from a live (pre-mortem) or dead (post-mortem) organism.
organizational term, used in description of specimen that is created from known pre- or post-mortem status
An epitope treatment experiment in which the evaluated response is made by T cells
sampling time measurement datum
A time measurement datum when an observation is made or a sample is taken from a material as measured from some reference point.
MO_738 timepoint
time point
Edman degradation of eluted MHC ligand assay
An assay in which ligands are eluted from MHC molecules and identified by Edman degradation
mass spectrometry of ligands eluted from secreted MHC assay
An assay in which cells are utilized that express a form of MHC molecules that are secreted into the cell culture supernatant. The soluble MHC is harvested, ligands are eluted from the MHC molecules and individual ligands identified by mass spectrometry.
disposition to be a product of antigen processing and presentation
A disposition of a material entity to be presented by MHC molecules on the cell surface as a result of antigen processing by an antigen presenting cell.
The disposition of the peptide AALKNLPLI to be created from the source protein long-chain-fatty-acid--CoA ligase 3 in murine macrophages through cleavage before residue 599 and after residue 607 by the proteasome and subsequent transport into the ER.
cytometric bead array assay of epitope specific interleukin-17A production by T cells
A cytometric bead array assay that measures epitope specific interleukin-17A production by T cells
Date: 2011-11-10; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: assay_mappings.owl
purified MHC competitive binding assay using radioactivity detection
Date: 2011-10-21; Spreadsheet: MHCAssays.xls; Worksheet: assay template; Mappings: MHC_assay_mappings.owl
competitive inhibition of binding assay measuring MHC ligand binding by radioactivity detection using MHC derived from a purified MHC molecule preparation
A scalar measurement datum that indicates the lowest concentration at which a specific compound significantly inhibits a process from occurring compared to in the absence of the compound.
Bjoern Peters, coordinated with Albert Goldfain
Created following request by Albert Goldfain
A material processing service in which a service provider makes physical modifications to a specified input material, such that at least one of the specified outputs of this process is a modified version of a specified input material.
Here we need to go back to the defintoin of storage process. It has object specification which is material maintenance. Not necessareley a material maintenance is needed in a storage process.
cell lysate MHC direct binding assay measuring half maximal effective concentration (EC50) [nM] using radioactivity detection
Date: 2011-10-21; Spreadsheet: MHCAssays.xls; Worksheet: assay template; Mappings: MHC_unit_assay_mappings.owl
direct binding assay measuring half maximal effective concentration (EC50) of MHC ligand binding by radioactivity detection using MHC derived from a cell lysate
cell bound MHC competitive binding assay measuring half maximal inhibitory concentration (IC50) [nM] using radioactivity detection
competitive inhibition of binding assay measuring half maximal inhibitory concentration (IC50) of MHC ligand binding by radioactivity detection using MHC derived from a cell
epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells
A process of tumor necrosis factor (ligand) superfamily member 11 production by T cells resulting from the recognition of a T cell epitope.
Date: 2011-11-10; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: assay_mappings.owl
cell lysate MHC direct binding assay using fluorescence detection
direct binding assay measuring MHC ligand binding by fluorescence detection using MHC derived from a cell lysate
cell bound MHC competitive binding assay measuring half maximal inhibitory concentration (IC50) [nM] using fluorescence detection
competitive inhibition of binding assay measuring half maximal inhibitory concentration (IC50) of MHC ligand binding by fluorescence detection using MHC derived from a cell
ELISA of epitope specific granulocyte colony stimulating factor production by T cells
An ELISA that measures epitope specific granulocyte colony stimulating factor production by T cells
sequence assembly algorithm
An algorithm used to assemble individual sequence reads into larger contiguous sequences (contigs). Assembly details include but are not limited to assembler type (overlap-layout-consensus, deBruijn), assembler version, and any relevant quality control information such as per cent known genes/ESTs captured.
BRC
cytometric bead array assay of epitope specific interleukin-17F production by T cells
A cytometric bead array assay that measures epitope specific interleukin-17F production by T cells
cell bound MHC direct binding assay measuring equilibrium association constant (KA) [1/M] using fluorescence detection
direct binding assay measuring equilibrium association constant (KA) of MHC ligand binding by fluorescence detection using MHC derived from a cell
A 3d structural organization datum capturing the results of X-ray crystallography or NMR experiment that is formatted as specified by the Protein Databank (http://www.wwpdb.org/docs.html). A PDB file can describe the structure of multiple molecules, each of which has a different chain identifier assigned.
PERSON: Bjoern Peters, Dorjee Tamang, Jason Greenbaum
The file found in the pdb with the identifier 3pe4 http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=3pe4
epitope specific interleukin-17A production by T cells
A process of interleukin-17A production by T cells resulting from the recognition of a T cell epitope.
A service in which the service provider assists the consumer in activities directly or indirectly associated with the production and analysis of experimental research data.
An help desk for an instrument or a software.
A service performing DNA sequencing, a service preforming cell analysis. A service performing cell line immortalization
A service which has a material entity as specified input and/or specified output.
A service in which a service consumer provides some input data and a service provider transforms, models, or interprets the input data and returns this generated data as output.
Statistaical analysis service, data visualization service
A service that has some information content entity as input and output.
Data analysis service such statistical abalysis or storage service such data backup.
Information content entity was used as specified input and output since it was more appropriate then data item or dataset.
purified MHC direct binding assay measuring half life of binding datum [min] using fluorescence detection
direct binding assay measuring half life of binding datum of MHC ligand binding by fluorescence detection using MHC derived from a purified MHC molecule preparation
cytometric bead array assay of epitope specific interleukin-9 production by T cells
A cytometric bead array assay that measures epitope specific interleukin-9 production by T cells
A storage service in which a service consumer provides data as input which a service provider stores and returns as output in its original form.
purified MHC competitive binding assay using fluorescence detection
competitive inhibition of binding assay measuring MHC ligand binding by fluorescence detection using MHC derived from a purified MHC molecule preparation
epitope specific interleukin-7 production by T cells
A process of interleukin-7 production by T cells resulting from the recognition of a T cell epitope.
A binding constant defined as the ratio of kon over koff (on-rate of binding divided by off-rate)
KD = 32 nM is the equilibrium dissociation rate found for peptide SIINFEKL binding to H-2 Kb
purified MHC competitive binding assay measuring equilibrium dissociation constant (KD) [nM] using fluorescence detection
competitive inhibition of binding assay measuring equilibrium dissociation constant (KD) of MHC ligand binding by fluorescence detection using MHC derived from a purified MHC molecule preparation
A service in which the service provider offers educational materials or events, such as courses, workshops or graduate programs, to the service consumer.
A service that offers training for a specific instrument or technique. A course to learn how to use a microscope
cell bound MHC competitive binding assay measuring equilibrium dissociation constant (KD) [nM] using fluorescence detection
competitive inhibition of binding assay measuring equilibrium dissociation constant (KD) of MHC ligand binding by fluorescence detection using MHC derived from a cell
T cell recognition of eluted MHC ligand assay
An assay that identifies an MHC ligand using a T cell response assay as a readout
purified MHC direct binding assay measuring binding on rate measurement datum (kon) [nM^-1 s^-1] using fluorescence detection
direct binding assay measuring binding on rate measurement datum (kon) of MHC ligand binding by fluorescence detection using MHC derived from a purified MHC molecule preparation
detection of specific nucleic acids with complementary probes of epitope specific interleukin-13 production by T cells
A detection of specific nucleic acids with complementary probes that measures epitope specific interleukin-13 production by T cells
purified MHC direct binding assay measuring equilibrium dissociation constant (KD) approximated by EC50 [nM] using fluorescence detection
Date: 2011-10-21; Spreadsheet: MHCAssays.xls; Worksheet: assay template; Mappings: MHC_organizational_assay_mappings.owl
direct binding assay measuring equilibrium dissociation constant (KD) approximated by EC50 of MHC ligand binding by fluorescence detection using MHC derived from a purified MHC molecule preparation
cell lysate MHC competitive binding assay measuring equilibrium dissociation constant (KD) [nM] using radioactivity detection
competitive inhibition of binding assay measuring equilibrium dissociation constant (KD) of MHC ligand binding by radioactivity detection using MHC derived from a cell lysate
intracellular cytokine staining assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells
An intracellular cytokine staining assay that measures epitope specific macrophage inflammatory protein-1 alpha production by T cells
6/1/2012: We will utilize 'comparative qualities' once they are available in BFO2
Interpreting data from assays that evaluate the qualities or dispositions inhering in an organism or organism part and comparing it to data from other organisms to make a conclusion about a phenotypic difference
A service in which a service consumer provides some input material and a service provider performs some analysis of this material to generate data that is returned to the service consumer.
Services performing DNA sequencing or Cell Analysis
A binding constant defined as the ratio of koff over kon (off-rate of binding divided by on-rate)
KA = 10^-12 M^-1 is the equilibirum association constant maximally found for antibody binding to haptens.
cell bound MHC competitive binding assay measuring equilibrium dissociation constant (KD) [nM] using radioactivity detection
competitive inhibition of binding assay measuring equilibrium dissociation constant (KD) of MHC ligand binding by radioactivity detection using MHC derived from a cell
assay measuring MHC ligand binding using MHC derived from a cell
A service in which a service consumer receives the right to use a resource (instrument, database, software, etc) that is owned or managed by a service provider. Ownership of the accessed resource remains with the service provider during and after provision of service.
A service that provides acess to a mass spectrometer.
Need to come up wiht a proper logical defintion. One option woudl be to dfine provides_access_to property as shortcut of participants in a process.
intracellular cytokine staining assay of epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells
An intracellular cytokine staining assay that measures epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells
MHC binding constant determination assay
A binding assay that determines a binding constant for the interaction between an MHC molecule and its ligand
A scalar measurement datum that represents the number of events occuring over a time interval
The rate of disassociation of a peptide from a complex with an MHC molecule measured by the ratio of bound and unbound peptide per unit of time.
assay measuring MHC ligand binding using MHC derived from a purified MHC molecule preparation
cell lysate MHC direct binding assay using radioactivity detection
direct binding assay measuring MHC ligand binding by radioactivity detection using MHC derived from a cell lysate
A service that offers liquid nitrogen stroage.
A storage service in which a service consumer provides some material as input which a service provider stores and returns as output.
cell bound MHC direct binding assay measuring half life of binding datum [min] using radioactivity detection
direct binding assay measuring half life of binding datum of MHC ligand binding by radioactivity detection using MHC derived from a cell
cell bound MHC direct binding assay measuring half life of binding datum [min] using fluorescence detection
direct binding assay measuring half life of binding datum of MHC ligand binding by fluorescence detection using MHC derived from a cell
cell lysate MHC binding constant determination assay
An assay that measures the affinity of a ligand to a MHC in a cell lysate preparation and that quantifies the affinity with a binding constant.
cell bound MHC direct binding assay measuring half maximal effective concentration (EC50) [nM] using fluorescence detection
direct binding assay measuring half maximal effective concentration (EC50) of MHC ligand binding by fluorescence detection using MHC derived from a cell
intracellular cytokine staining assay of epitope specific interleukin-17F production by T cells
An intracellular cytokine staining assay that measures epitope specific interleukin-17F production by T cells
A service for cell line creation. A service providing cel line immortalization.
A service in which a service provider makes physical changes to a specified input material entity with the objective of producing a new material entity form input materials, or modifying the input material entity, and returning this as output to the service consumer.
purified MHC competitive binding assay measuring equilibrium dissociation constant (KD) approximated by IC50 [nM] using radioactivity detection
competitive inhibition of binding assay measuring equilibrium dissociation constant (KD) approximated by IC50 of MHC ligand binding by radioactivity detection using MHC derived from a purified MHC molecule preparation
cell lysate MHC direct binding assay measuring half life of binding datum [min] using radioactivity detection
direct binding assay measuring half life of binding datum of MHC ligand binding by radioactivity detection using MHC derived from a cell lysate
50% dissociation of binding temperature (Tm)
A binding datum that specifies the temperature at which half of the binding partners are forming a complex and the other half are unbound.
Preparing a complex of a purified HLA-A*02:01 bound to a specific peptide ligand, varying the temperature while detecting the fraction of bound complexes with a complex conformation specific antibody, and interpolating the temperature at which 50% of complexes are dissociated.
cell lysate MHC direct binding assay measuring binding off rate measurement datum (koff) [s^-1] using radioactivity detection
direct binding assay measuring binding off rate measurement datum (koff) of MHC ligand binding by radioactivity detection using MHC derived from a cell lysate
purified MHC competitive binding assay measuring half maximal inhibitory concentration (IC50) [nM] using radioactivity detection
competitive inhibition of binding assay measuring half maximal inhibitory concentration (IC50) of MHC ligand binding by radioactivity detection using MHC derived from a purified MHC molecule preparation
purified MHC direct binding assay measuring binding off rate measurement datum (koff) [s^-1] using fluorescence detection
direct binding assay measuring binding off rate measurement datum (koff) of MHC ligand binding by fluorescence detection using MHC derived from a purified MHC molecule preparation
assay of epitope specific vascular endothelial growth factor production by T cells
An assay that measures epitope specific vascular endothelial growth factor production by T cells
equilibrium dissociation constant (KD) approximated by IC50
A measurement of an IC50 value under specific assay conditions approximates KD, namely the binding reaction is at an equilibrium, there is a single population of sites on the receptor that competitor and ligand are binding to, and the concentration of the receptor must be much less than the KD for the competitor and the ligand. In this case, according to Cheng and Prussoff, KD = IC50 / (1 + Lstot / KDs), in which Lstot is the total concentration of the labeled competitor and KDs is the KD value of that competitor.
cell bound MHC binding constant determination assay
An assay that measures the affinity of a ligand to MHC moleculs bound to the cell surface and that quantifies the affinity with a binding constant.
8/29/11 call: This is added after a request from Melanie and Yu. They should review it further. This should be a child of 'sequence data', and as of the current definition will infer there.
A sequence data item that is about the primary structure of DNA
The part of a FASTA file that contains the letters ACTGGGAA
cell lysate MHC competitive binding assay using radioactivity detection
competitive inhibition of binding assay measuring MHC ligand binding by radioactivity detection using MHC derived from a cell lysate
assigning gene property based on phenotypic assessment
Interpreting data from assays that evaluate the qualities or dispositions inhering in an organism or organism part and comparing it to data from other organisms that have a defined genetic difference, and assigning a property to the product of the targeted gene as a result.
purified MHC binding constant determination assay
An assay that measures the affinity of a ligand to a purified MHC complex preparation and that quantifies the affinity with a binding constant.
cytometric bead array assay of epitope specific interleukin-22 production by T cells
A cytometric bead array assay that measures epitope specific interleukin-22 production by T cells
ELISA of epitope specific vascular endothelial growth factor production by T cells
An ELISA that measures epitope specific vascular endothelial growth factor production by T cells
assay measuring MHC ligand binding using MHC derived from a cell lysate
A service in which a service provider facilitates the transport of some material entity to a specified destination for the service consumer.
equilibrium dissociation constant (KD) approximated by EC50
A measurement of an EC50 value under specific assay conditions approximates KD, namely the binding reaction is at an equilibrium, and the concentration of the receptor must be much less than the KD for the ligand.
Assay Development: Fundamentals and Practices, By Ge Wu, page 74
direct binding assay measuring MHC ligand binding using MHC derived from a cell
A half life datum of the time it takes for 50% of bound complexes in an ensemble to disassociate in absence of re-association.
The 45 minute period in which one half of the complexes formed by peptide ligand bound to a HLA-A*0201molecule disassociate.
purified MHC direct binding assay using phage display binding assay
direct binding assay measuring MHC ligand binding by phage display binding assay using MHC derived from a purified MHC molecule preparation
cytometric bead array assay of epitope specific interleukin-7 production by T cells
A cytometric bead array assay that measures epitope specific interleukin-7 production by T cells
purified MHC direct binding assay measuring half life of binding datum [min] using radioactivity detection
direct binding assay measuring half life of binding datum of MHC ligand binding by radioactivity detection using MHC derived from a purified MHC molecule preparation
assay of epitope specific interleukin-7 production by T cells
An assay that measures epitope specific interleukin-7 production by T cells
9/28/11 BP: The disposition referenced is the one of the ligand to bind the molecule. This along with binding as a function / process needs to be figured out with GO which is inconsistent at this point.
A peptide binding to an MHC molecule to form a complex.
The process of material entities forming complexes.
intracellular cytokine staining assay of epitope specific interleukin-17A production by T cells
An intracellular cytokine staining assay that measures epitope specific interleukin-17A production by T cells
purified MHC direct binding assay using fluorescence detection
direct binding assay measuring MHC ligand binding by fluorescence detection using MHC derived from a purified MHC molecule preparation
Detecting the binding of a fluorescently labeled antibody to a peptide bound to the bottom of an ELISA plate, by incubating the antibody in the well, washing the plate, and detecing fluorescence which is a proxy for the presence of the bound antibody.
a binding assay that measures the formation or disassociation of a complex of 2 material entities directly without use of a competitve ligand.
purified MHC direct binding assay measuring half maximal effective concentration (EC50) [nM] using fluorescence detection
direct binding assay measuring half maximal effective concentration (EC50) of MHC ligand binding by fluorescence detection using MHC derived from a purified MHC molecule preparation
A binding assay that detects the inhibition of binding between 2 material entities known to form a complex by the addition of a third material entity of interest.
Detecting the inhibition of binding of a fluorescently labeled antibody to its known protein ligand bound to the bottom of an ELISA plate, by incubating the antibody in the presence of a peptide of interest, adding it to the plate, washing the plate, and detecing fluorescence which is a proxy for the presence of the bound antibody. Reduction in binding due to the presence of the peptide indicates that the antibody binds the peptide.
cell bound MHC competitive binding assay using fluorescence detection
competitive inhibition of binding assay measuring MHC ligand binding by fluorescence detection using MHC derived from a cell
3D structure determination of MHC:ligand complex assay
direct binding assay measuring MHC ligand binding by binding complex 3D structure determination assay using MHC derived from a purified MHC molecule preparation
A 3D structural organization datum that is part of a PDB file and has a specific chain identifier that identifies the entire information on a subset of the material entities
The 'D' chain in the PDB file 2BSE identifies the heavy chain of the antibody in the protein:antibody complex
cell bound MHC competitive binding assay measuring half maximal inhibitory concentration (IC50) [nM] using T cell epitope recognition assay
competitive inhibition of binding assay measuring half maximal inhibitory concentration (IC50) of MHC ligand binding by T cell epitope recognition assay using MHC derived from a cell
A database management service, a web hosting service.
A maintenance service in which a service provider actively manages or maintains data or a database for the service consumer. Maintenance of the data is performed to maintain its integrity or enhance its quality or utility for the consumer, but new data is not generated as a result of the maintenance.
cell bound MHC competitive binding assay using radioactivity detection
competitive inhibition of binding assay measuring MHC ligand binding by radioactivity detection using MHC derived from a cell
assay of epitope specific granulocyte colony stimulating factor production by T cells
An assay that measures epitope specific granulocyte colony stimulating factor production by T cells
cytometric bead array assay of epitope specific interleukin-21 production by T cells
A cytometric bead array assay that measures epitope specific interleukin-21 production by T cells
cell bound MHC direct binding assay using radioactivity detection
direct binding assay measuring MHC ligand binding by radioactivity detection using MHC derived from a cell
binding off rate measurement datum (koff)
A rate measurement datum of how quickly bound complexes disassociate
purified MHC direct binding assay measuring 50% dissociation of binding temperature (Tm) [°C] using fluorescence detection
direct binding assay measuring 50% dissociation of binding temperature (Tm) of MHC ligand binding by fluorescence detection using MHC derived from a purified MHC molecule preparation
A rate measurement datum of how quickly bound complexes form
cell bound MHC direct binding assay using fluorescence detection
direct binding assay measuring MHC ligand binding by fluorescence detection using MHC derived from a cell
assay of epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells
An assay that measures epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells
purified MHC direct binding assay using radioactivity detection
direct binding assay measuring MHC ligand binding by radioactivity detection using MHC derived from a purified MHC molecule preparation
intracellular cytokine staining assay of epitope specific interleukin-8 production by T cells
An intracellular cytokine staining assay that measures epitope specific interleukin-8 production by T cells
cytometric bead array assay of epitope specific interleukin-23 production by T cells
A cytometric bead array assay that measures epitope specific interleukin-23 production by T cells
direct binding assay measuring MHC ligand binding using MHC derived from a purified MHC molecule preparation
epitope specific vascular endothelial growth factor production by T cells
A process of vascular endothelial growth factor production by T cells resulting from the recognition of a T cell epitope.
purified MHC competitive binding assay measuring half maximal inhibitory concentration (IC50) [nM] using fluorescence detection
competitive inhibition of binding assay measuring half maximal inhibitory concentration (IC50) of MHC ligand binding by fluorescence detection using MHC derived from a purified MHC molecule preparation
GenBank ID
A CRID symbol uniquely indentifies the submitted GeneBank sequence record.
investigation description
A textual entity that describes an investigation.
Penn Group
project description
specimen identifier
A CRID symbol denotes a specimen and used to distinguish one specimen from another in an investigation.
specimen ID
PubMed ID
A CRID symbol that is sufficient to look up a citation from the PubMed, a literature database of life sciences and biomedical information.
PMID
PubMed Identifier
Website: http://en.wikipedia.org/wiki/Wikipedia:PMID
average depth of sequence coverage
An average value of the depth of sequence coverage based both on external (e.g. Cot-based size estimates) and internal (average coverage in the assembly) measures of genome size.
specimen creation time measurement datum
A time measurement datum that is the measure of the time when the specimens are collected.
collection date
latitude coordinate measurement datum
A measurement datum that is the measure of the latitude coordinate of a site.
latitude
longitude coordinate measurement datum
A measurement datum that is the measure of the longitude coordinate of a site.
longitude
investigation title
A textual entity that denotes an investigation.
Person:Chris Stoeckert, Jie Zheng
project title
organism identification objective
A biological feature identification objective to identify the organism species in a specimen.
organism identification assay
An assay that identifies the organism species in a specimen.
sequence annotation algorithm
An algorithm used to identify sequence features (e.g. protein coding regions) in the assembled contig sequence. This may also include a description of any manual curation that may have generated or validated the annotation.
Bioinformatics Resource Center
An organization that is one of the Internet-based research centers established and funded by NIAID (the National Institute of Allergy and Infectious Diseases). The Bioinformatics Resource Centers (BRCs) were formed in response to the threats posed by emerging and re-emerging pathogens, particularly CDC Category A, B, and C pathogens, and their potential use in bioterrorism. The intention of NIAID in funding these bioinformatics centers is to assist researchers involved in the experimental characterization of such pathogens and the formation of drugs, vaccines, or diagnostic tools to combat them.
Website: http://en.wikipedia.org/wiki/Bioinformatics_Resource_Centers
country name
A textual entity that denotes a geographic location that is a site or part of a site that is identified as a country in the political geography.
Website: http://en.wikipedia.org/wiki/Country
investigation identifier
A CRID symbol used to identify an investigation.
Person: Chris Stoeckert, Jie Zhneg
project ID
grant identifier
A CRID symbol used to identify a grant.
grant ID
Detection of the presence of an blood group A specific antibodies by passing a serum sample through an affinity column containing blood group A carbohydrate, and quantifying the protein content eluted from the column.
the use of a biomaterial's preferential affinity for either the mobile phase or the stationary phase to separate it from other materials and thereby detect its presence in an input material
Using an electron microscope to generate an image of a material
Using gold labeled antibodies to stain a mouse brain slice and use electron microscopy to generate an image that shows the location of the antibodies.
2/23/12: BP It sucks to have to refer to 'immunoglobulin complex, circulating' rather than 'antibody'
2/23/12: BP The example describes a more specific type (immunohistochemistry assay), but we need this more general one as well. If somebody specifically needs immunohistochemistry, it should be created as a child class.
A detection of label assay in which the label is attached to an antibody so that substances are marked based on the antibody's binding specificity.
Detection of the presence of VCAM molecules on the surface of cells in a histology slide using an enzyme-linked antibody followed by enzyme activation to release a dye.
A material entity that is generated by a purification process in which an input material is separated to obtain a fraction with a higher concentration of a desired component
A mixture of peptide molecules that has been run through an HPLC column to remove 65
A solution of a proteins is titrated into a solution containing a specific antibody. The heat released upon their interaction (ΔH) is monitored over time where each peak represents a heat change associated with the injection of a small volume of sample into the reaction cell. As successive amounts of the ligand are titrated into the cell, the quantity of heat absorbed or released is in direct proportion to the amount of binding. As the system reaches saturation, the heat signal diminishes until only heats of dilution are observed. A binding curve is then obtained from a plot of the heats from each injection against the ratio of protein and antibody in the cell .
Measurement of the heat generated or absorbed during a binding event, which allows determination of binding constants (KB), reaction stoichiometry (n), enthalpy (∆H) and entropy (ΔS).
antibody binding detection by fluorescence quenching
An assay in which binding affinity is measured by detecing a change in fluorescence (usually quenching) that occurs upon binding of the antibody to the ligand. The fluorescent signal that is affected by binding is either from an exogenous fluorophore attached to the ligand, or is the intrisic fluorescence of aromatic (tryptophan) residues on the binding site of the antibody (no conjugated fluorophore necessary) or, less commonly, on the ligand binding region (epitope).
Detection a decrease in the fluorescence of Cholera toxin B protein following incubation with a Fab fragment of antibody TE 34 (PubMed ID: 2450576)
grant
A plan specification of organization A to give money to organization B so that B conducts investigations. Organization A has funder role and Organization B has research organization role.
Discussed on Feb 13, 2012 dev call. Details see the tracker: https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891&atid=886178
Group: OBI
B cell epitope specific antigen inhibition of epitope:antibody binding measuring equilibrium dissociation constant (KD) approximated by IC50 [nM] assay
Antigen inhibition assay measuring epitope specfic immunoglobulin equilibrium dissociation constant (KD) approximated by IC50 in nM
Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Assay Template; Mapping: ebcell_specific_mappings.owl
B cell epitope specific Ig-mediated histamine release assay
An assay measuring B cell epitope specific histamine secretion mediated by immunoglobulin
B cell epitope specific immunoglobulin-mediated antigen activation assay
6/7/2012:BP: Ideally, this assay should also be tied to a biological process of activation of whatever the antigen is (typically a protein). We did not find that yet.
An assay measuring activation of an antigen as a result of immunoglobulin binding
B cell epitope specific complement-dependent cytotoxicity assay
An assay measuring B cell epitope specific complement-dependent cytotoxicity
B cell epitope specific antibody-dependent cellular cytotoxicity assay
An assay measuring B cell epitope specific antibody-dependent cellular cytotoxicity
B cell epitope specific immunoglobulin-mediated neutralization assay
An assay measuring B cell epitope specific immunoglobulin-mediated neutralization
B cell epitope specific opsonization assay
An assay measuring B cell epitope specific opsonization
B cell epitope specific calorimetry assay
An assay that measures epitope specific antibody binding using a calorimetric assay
B cell epitope specific electron microscopy measuring 3D structure assay
An assay that measures the 3D structure of an epitope specific antibody binding event using electron microscopy imaging
B cell epitope specific nuclear magnetic resonance (NMR) measuring 3D structure assay
An assay that measures epitope specific antibody binding using a nuclear magnetic resonance assay
B cell epitope specific antibody cross blocking assay
An assay that measures epitope specific antibody binding using a antibody cross-blocking assay
B cell epitope specific radio immuno assay (RIA)
An assay that measures epitope specific antibody binding using a radio immuno assay
B cell epitope specific western blot analysis
An assay that measures epitope specific antibody binding using western blot analysis
B cell epitope specific surface plasmon resonance (SPR) assay
An assay that measures epitope specific antibody binding using a surface plasmon resonance assay
B cell epitope specific immuno staining assay
An assay that measures epitope specific antibody binding using an immuno staining assay
B cell epitope specific immunoprecipitation assay
An assay that measures epitope specific antibody binding using immunoprecipitation assay
B cell epitope specific mass spectrometry assay
An assay that measures epitope specific antibody binding using mass spectrometry assay
B cell epitope specific phage display assay
An assay that measures epitope specific antibody binding using phage display binding assay
B cell epitope specific electron microscopy assay
An assay that measures epitope specific antibody binding using electron microscopy imaging
An assay that measures epitope specific antibody binding using ELISA
An assay that measures epitope specific antibody binding using ELISPOT
B cell epitope specific flow cytometry assay
An assay that measures epitope specific antibody binding using a flow cytometry assay
intracellular cytokine staining assay of epitope specific granzyme A production by T cells
An intracellular cytokine staining assay that measures epitope specific granzyme A production by T cells
Date: 2012-06-24; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: MMExpressionsTcell.txt
B cell epitope specific chromatography assay
An assay that measures epitope specific antibody binding using analytical chromatography
B cell epitope nuclear magnetic resonance (NMR)
Date: 2012-04-12; Spreadsheet: BcellAssays.xls; Worksheet: Assay Template; Mapping: ebcell_specific_mappings.owl
ELISA of epitope specific granulysin production by T cells
An ELISA that measures epitope specific granulysin production by T cells
intracellular cytokine staining assay of epitope specific granulysin production by T cells
An intracellular cytokine staining assay that measures epitope specific granulysin production by T cells
cell bound MHC direct binding assay measuring binding off rate measurement datum (koff) [s^-1] using fluorescence detection
Date: 2012-6-24; Spreadsheet: MHCAssays.xls; Worksheet: assay template; Mappings: MMExpressionsmhcbindunits.txt
direct binding assay measuring binding off rate measurement datum (koff) of MHC ligand binding by fluorescence detection using MHC derived from a cell
cell bound MHC direct binding assay measuring binding on rate measurement datum (kon) [nM^-1 s^-1] using fluorescence detection
direct binding assay measuring binding on rate measurement datum (kon) of MHC ligand binding by fluorescence detection using MHC derived from a cell
purified MHC competitive binding assay measuring equilibrium dissociation constant (KD) approximated by IC50 [nM] using fluorescence detection
competitive inhibition of binding assay measuring equilibrium dissociation constant (KD) approximated by IC50 of MHC ligand binding by fluorescence detection using MHC derived from a purified MHC molecule preparation
split-ubiquitin assay
PERSON:Philippe Rocca-Serra; Marcus Chibucos
Split-ubiquitin two-hybrid assay to analyze protein-protein interactions at the endosome: application to Saccharomyces cerevisiae Bro1 interacting with ESCRT complexes, the Doa4 ubiquitin hydrolase, and the Rsp5 ubiquitin ligase. Nikko E, AndrÈ B. Eukaryot Cell. 2007 Aug;6(8):1266-77. Epub 2007 May 18. PMID: 17513562
adapted from wikipedia
add regulatory region DNA binding;sequence-specific DNA binding;obo:GO:0000975;obo:GO:0043565;
is a kind of yeast 2 hybrid system which enables membrane soluble proteins to be screened. two integral membrane proteins to be studied are fused to two different ubiquitin moieties: a C-terminal ubiquitin moiety (\"Cub\", residues 35–76) and an N-terminal ubiquitin moiety (\"Nub\", residues 1–34). These fused proteins are called the bait and prey, respectively. In addition to being fused to an integral membrane protein, the Cub moiety is also fused to a transcription factor (TF) that can be cleaved off by ubiquitin specific proteases. Upon bait–prey interaction, Nub and Cub-moieties assemble, reconstituting the split-ubiquitin. The reconstituted split-ubiquitin molecule is recognized by ubiquitin specific proteases, which cleave off the reporter protein, allowing it to induce the transcription of reporter genes.
far-Western blot
Studying protein-protein interactions via blot overlay or Far Western blot. Hall RA. Methods Mol Biol. 2004;261:167-74. Review. PMID: 15064457
adapted from ECO, PMID:18079728
is a adaptation on the western blot assay to explore protein-protein interaction. The assay involves separating target proteins on an SDS-PAGE gel, blotting to a membrane, hybridization with a protein probe and visualization using a probe-directed antibody.
RNA protection assay
Absolute concentrations of mRNA for type I and type VI collagen in the canine meniscus in normal and ACL-deficient knee joints obtained by RNase protection assay. Wildey GM, Billetz AC, Matyas JR, Adams ME, McDevitt CA. J Orthop Res. 2001 Jul;19(4):650-8. PMID: 11518275
RPA is a technique to assess the presence and estimate abundance of transcript species by first creating an homo or heteroduplex by adding a specific, complementary sequence to the sequence of interest and then exposing the mixture of ribonuclease, which will degrade only single stranded molecules. A detection step will reveal if the sample contained a sequence of interest.
RPA; RNAse protection assay
adapted from wikipedia + PMID:16491611
electrophoretic mobility shift assay
EMSA,gel shift assay, gel mobility shift assay, band shift assay, gel retardation assay
Electrophoretic mobility shift assay reveals a novel recognition sequence for Setaria italica NAC protein. Puranik S, Kumar K, Srivastava PS, Prasad M. Plant Signal Behav. 2011 Oct;6(10):1588-90. Epub 2011 Oct 1. PMID: 21918373
is an assay which aims to provide information about Protein-DNA or Protein-RNA interaction and which used gel electrophoresis and relies on the fact the molecular interactions will cause the heterodimer to be retarded on the gel when compared to controls corresponding to protein extract alone and protein extract + neutral nucleic acid.
gene knock-down assay
is an assay which transiently disrupts gene transcripts by expressing antisense RNA constructs or delivering RNA interfering molecules in cells.
nano-cap analysis of gene expression
Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. PMID:20543846
PMID: 20543846
nano-CAGE
nano-CAGE is a type of CAGE developed to work from very low amount (nanogram scale) of mRNA samples
cap analysis of gene expression
5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing. Takahashi H, Lassmann T, Murata M, Carninci P. Nat Protoc. 2012 Feb 23;7(3):542-61. doi: 10.1038/nprot.2012.005. PMID: 22362160
CAGE
Cap analysis gene expression is an assay which aims at monitoring RNA transcript abundances in biological samples by extracting 5' ends of capped transcripts, RTPCR and sequence those. Copy numbers of CAGE tags provide a way of quantification and provide a measure of expression of the transcriptome
ELISA of epitope specific interleukin-17A production by T cells
An ELISA that measures epitope specific interleukin-17A production by T cells
detection of specific nucleic acids with complementary probes of epitope specific interleukin-7 production by T cells
A detection of specific nucleic acids with complementary probes that measures epitope specific interleukin-7 production by T cells
Date: 2012-06-18; Spreadsheet: All AssayTypes.xls; Worksheet: Assay Template; Mappings: MMExpressionsTcell.txt
epitope specific granulysin production by T cells
A process of granulysin production by T cells resulting from the recognition of a T cell epitope.
Date: 2011-6-24; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt
epitope specific granzyme A production by T cells
A process of granzyme A production by T cells resulting from the recognition of a T cell epitope.
yeast 2-hybrid
Strong FANCA/FANCG but weak FANCA/FANCC interaction in the yeast 2-hybrid system. Reuter T, Herterich S, Bernhard O, Hoehn H, Gross HJ. Blood. 2000 Jan 15;95(2):719-20. PMID: 10627486
Y2H
add regulatory region DNA binding;GO:0043565;
yeast 2 hybrid screen is an assay meant to discover protein–protein interactions and protein–DNA interactions by testing for physical interactions (such as binding) between two proteins or a single protein and a DNA molecule, respectively. The premise behind the test is the activation of downstream reporter gene(s) by the binding of a transcription factor onto an upstream activating sequence (UAS). For two-hybrid screening, the transcription factor is split into two separate fragments, called the binding domain (BD) and activating domain (AD). The BD is the domain responsible for binding to the UAS and the AD is the domain responsible for the activation of transcription.[1][2] The Y2H is thus a protein-fragment complementation assay.
Sos-recruitment assay
SRS
The Sos-recruitment system as a tool to analyze cellular localization of plant proteins: membrane localization of Arabidopsis thaliana PEPINO/PASTICCINO2. Schˆnhofer-Merl S, Torres-Ruiz RA. Mol Genet Genomics. 2010 May;283(5):439-49. Epub 2010 Mar 19. PMID: 20300944
adapted from the original publication by Aronheim et al, 1997. PMID: 9154808
is a kind of yeast 2 hybrid system where mammalian guanyl nucleotide exchange factor (GEF) Sos is recruited to the Saccharomyces cerevisiae plasma membrane harboring a temperature-sensitive Ras GEF, Cdc25-2, allowing growth at the nonpermissive temperature. Using the Sos recruitment system, interacting proteins for targeted domain can be detected.
yeast one-hybrid
PMID: 22218861
The one-hybrid variation of this technique is designed to investigate protein–DNA interactions and uses a single fusion protein in which the AD is linked directly to the binding domain.
Y1H
Yeast one-hybrid assays for gene-centered human gene regulatory network mapping. Nat Methods. 2011 Oct 30;8(12):1050-2. doi: 10.1038/nmeth.1764. PMID: 22037702
add regulatory region DNA binding;obo:GO:0000975;
bacterial one-hybrid
is a method for identifying the sequence-specific target site of a DNA-binding domain. In this system, a given transcription factor (TF) is expressed as a fusion to a subunit of RNA polymerase. In parallel, a library of randomized oligonucleotides representing potential TF target sequences, is cloned into a separate vector containing the selectable genes HIS3 and URA3. If the DNA-binding domain (bait) binds a potential DNA target site (prey) in vivo, it will recruit RNA polymerase to the promoter and activate transcription of the reporter genes in that clone. The two reporter genes, HIS3 and URA3, allow for positive and negative selections, respectively. At the end of the process, positive clones are sequenced and examined with motif-finding tools in order to resolve the favoured DNA target sequence
A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. Noyes MB, Meng X, Wakabayashi A, Sinha S, Brodsky MH, Wolfe SA. Nucleic Acids Res. 2008 May;36(8):2547-60. Epub 2008 Mar 10. PMID: 18332042
B1H
fluorescence in-situ hybridization
Duplication of intrachromosomal insertion segments 4q32→q35 confirmed by comparative genomic hybridization and fluorescent in situ hybridization.PMID:22384449
FISH
is an in-situ hybridization assay that uses fluorescence as means of detection chromosomal integrity
methylation-specific polymerase chain reaction
MSP
Methylation status of breast cancer resistance protein detected by methylation-specific polymerase chain reaction analysis is correlated inversely with its expression in drug-resistant lung cancer cells. PMID: 18219662
is an assay which uses initial modification of DNA by sodium bisulfite, converting all unmethylated, but not methylated, cytosines to uracil, and subsequent amplification with primers specific for methylated versus unmethylated DNA.
amplification of intermethylated sites (AIMS) assay
amplification of intermethylated sites (AIMS) is an assay appropriate for genome-wide estimates of DNA methylation and the discovery of specific methylated sequences. AIMS is based on the differential enzymatic digestion of genomic DNA with methylation-sensitive and methylation-insensitive isoschizomers followed by restrained PCR amplification of methylated sequences.
AIMS assay,intermethylated site amplification
Analysis of DNA methylation by amplification of intermethylated sites (AIMS).PMID:18987810
PMID: 18987810
in-situ hybridization
ISH
Use of in situ hybridization to examine gene expression in the embryonic, neonatal, and adult urogenital system. PMID:22639265
is an assay using artificially induced nucleic hybridization to localize a specific DNA or RNA sequence in a portion or section of tissue
contact representative role
A role inhering in a person who represents an institution, organization, or service provider and realized when communication is directed at them about the entity they represent.
Discussed on May 7, 2012 dev call propose:contact role, type of organization role, and create shortcut relation between 'organization role' and 'organization' ? Whether it works for communicating author in manuscript or not? Tracker: https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891&atid=886178
cytochalasin-induced inhibition of actin polymerization assay
add ;actin filament polymerization obo:GO:0070358;
is an assay which uses compound cytochalasin (CHEBI: 23528) to block actin polymerization-dependent cell motility (GO:0070358) and actin filament polymerization (GO:0030041).
molecular function identification objective
OBI group
PERSON:Philippe Rocca-Serra
is an objective specification which aims to discover molecular function realized by a molecular entity
cellular structure feature identification objective
is an objective specification which aims to discover cellular structure properties
B cell epitope reduction of fertility experiment
An assay measuring reduction of fertility after a B cell epitope intervention
B cell epitope specific induction of tolerance assay
An assay that measures epitope specific tolerance induction by a B cell epitope
B cell epitope induction of hypersensitivity experiment
An assay measuring hypersentitivity after a B cell epitope intervention
B cell epitope specific immune complex formation assay
An assay that measures B cell epitope specific agglutination
B cell epitope protection experiment based on survival
An assay measuring survival after challenge after a B cell epitope intervention
An assay measuring decreased disease symptoms after treatment with a B cell epitope intervention
efficacy of B cell epitope intervention experiment
An assay measuring the efficacy of a B cell epitope intervention
A competiive binding assay in which two antibodies that are known to bind the same antigen are tested for the ability of one antibody to inhibit binding of the other antibody to the antigen, thereby determining if they have overlapping binding sites.
Testing two antibodies that bind the HBV core protein for the ability of one antibody pre-incubated with the protein in solution to inhibit binding to the other antibody which is plate-bound in an ELISA format.
An assay with the objective to determine presence of an analyte by mixing a solution of antigen and antibody and separating out bound antigen:antibody complexes using immunoprecipitation. Either the antibody has known specificy, and the antigen mixture is tested for the presence of a specific antigen, or the antigen solution is well defined and the antibody solution is tested for the presence of antigen specific antibodies.
Determining if a cell is producing a protein using a protein specific antibody to immunoprecipitate the cell lysate. Determining if the serum of a patient contains antibodies against HBV core protein by immunoprecipitating purified HBV core protein with the patients serum.
antigen inhibition of epitope:antibody binding assay
A competetive binding assay in which an antigen is being tested for its ability to inhibit the binding of an antibody to its known epitope.
Testing if an antibody generated by immunization with a peptide from HBV core protein can be blocked from binding that peptide by competition with fully folded HBV core protein in order to determine ability to recognize the peptide in the native structure.
Binding of the LA5 antibody to a discontinuous set of amino acid residues on the surface of the D8 protein of Vaccinia virus
a process of an immunoglobulin complex binding to a material entity at the immunoglobulin complementarity determining region (CDR).
B cell epitope binding to antibody assay
An assay in which a material entity is tested for binding to an antibody.
B cell epitope specific activation of additional immune response in vitro
An assay that detects an immune response process that is triggered as a result of an antibody:epitope complex formation
B cell epitope specific neutralization of antigen in vitro assay
An assay that detects the inhibition of the activity of an antigen as a result of being bound by immunoglobulins.
B cell epitope dependent biological activity assay
An assay that detects a biological process that is triggered by antibody:epitope binding events, rather than measuring the binding event itself.
immunoglobulin mediated histamine release
4/26/12, BP: We want to import this from GO, which currently only has IgE mediated histamine release. We have requested the term, but need to use this as a placeholder in the meanwhile.
The release of histamine by cells stimulated through their Fc receptors which are loaded with immunoglobulins.
B cell epitope equilibrium dissociation constant (KD) determination assay
A B cell epitope recognition assay measuring equilibrium dissociation constant (KD)
B cell epitope binding constant determination assay
A B cell epitope recognition assay measuring a binding constant
An assay measuring protection after challenge after a B cell epitope intervention
B cell epitope disease exacerbation experiment
An assay measuring disease symptom exacerbation after a B cell epitope intervention
Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl
opsonization resulting from antibody binding to epitope
B cell epitope specific immunoglobulin-mediated neutralization
immunoglobulin-mediated neutralization resulting from antibody binding to epitope
B cell epitope competitive binding assay
A competitive inhibition of binding assay using a assay
B cell epitope specific complement-dependent cytotoxicity
complement-dependent cytotoxicity resulting from antibody binding to epitope
B cell epitope specific antibody-dependent cellular cytotoxicity
antibody-dependent cellular cytotoxicity resulting from antibody binding to epitope
B cell epitope binding binding on rate measurement datum (kon) determination assay
A B cell epitope recognition assay measuring binding on rate measurement datum (kon)
B cell epitope equilibrium association constant (KA) determination assay
A B cell epitope recognition assay measuring equilibrium association constant (KA)
B cell epitope specific immune complex formation
immune complex formation resulting from antibody binding to epitope
B cell epitope 3D structure determination of antibody:epitope complex assay
A B cell epitope recognition assay measuring 3D structural organization datum
B cell epitope specific hypersensitivity
hypersensitivity resulting from antibody binding to epitope
B cell epitope binding off rate measurement datum (koff) determination assay
A B cell epitope recognition assay measuring binding off rate measurement datum (koff)
B cell epitope specific hemagglutination inhibition assay
An assay that measures epitope specific antibody binding using a viral hemagglutination inhibition assay
B cell epitope specific histamine secretion mediated by immunoglobulin
histamine secretion mediated by immunoglobulin resulting from antibody binding to epitope
B cell epitope fluorescence immuno assay (FIA)
An assay that measures epitope specific antibody binding detection by fluorescence quenching
B cell epitope specific radio immuno assay (RIA) measuring KD [nM]
radio immuno assay measuring epitope specfic immunoglobulin equilibrium dissociation constant (KD) in nM
B cell epitope specific ELISA measuring KD [nM]
ELISA measuring epitope specfic immunoglobulin equilibrium dissociation constant (KD) in nM
B cell epitope specific fluorescence immuno assay (FIA) measuring KD [nM]
antibody binding detection by fluorescence quenching measuring epitope specfic immunoglobulin equilibrium dissociation constant (KD) in nM
B cell epitope specific surface plasmon resonance (SPR) measuring KA [1/nM] assay
surface plasmon resonance assay measuring epitope specfic immunoglobulin equilibrium association constant (KA) in nM^-1
B cell epitope specific surface plasmon resonance (SPR) measuring KD [nM] assay
surface plasmon resonance assay measuring epitope specfic immunoglobulin equilibrium dissociation constant (KD) in nM
B cell epitope specific fluorescence immuno assay (FIA) measuring KA [1/nM]
antibody binding detection by fluorescence quenching assay measuring epitope specfic immunoglobulin equilibrium association constant (KA) in nM^-1
B cell epitope specific calorimetry measuring KA [1/nM] assay
calorimetric assay measuring epitope specfic immunoglobulin equilibrium association constant (KA) in nM^-1
B cell epitope specific calorimetry measuring KD [nM] assay
calorimetric assay measuring epitope specfic immunoglobulin equilibrium dissociation constant (KD) in nM
B cell epitope specific ELISA measuring KA [1/nM] assay
ELISA measuring epitope specfic immunoglobulin equilibrium association constant (KA) in nM^-1
B cell epitope specific radio immuno assay (RIA) measuring KA [1/nM]
radio immuno assay measuring epitope specfic immunoglobulin equilibrium association constant (KA) in nM^-1
B cell epitope specific X-ray crystallography assay
A X-ray crystallography assay measuring epitope specfic antibody binding event in Ã…
B cell epitope specific X-ray crystallography measuring 3D structure assay
A X-ray crystallography assay measuring the 3D structure of an epitope specfic antibody binding event in Ã…
B cell epitope specific surface plasmon resonance (SPR) measuring koff (kd) [1/s] assay
surface plasmon resonance assay measuring epitope specfic immunoglobulin binding off rate measurement datum (koff) in s^-1
B cell epitope specific fluorescence immuno assay (FIA) measuring koff [1/s]
antibody binding detection by fluorescence quenching assay measuring epitope specfic immunoglobulin binding off rate measurement datum (koff) in s^-1
B cell epitope specific surface plasmon resonance measuring kon ka [M^-1 s^-1]
surface plasmon resonance assay measuring epitope specfic immunoglobulin binding on rate measurement datum (kon) in M^-1 s^-1
B cell epitope specific fluorescence immuno assay (FIA) measuring kon [M^-1 s^-1]
antibody binding detection by fluorescence quenching assay measuring epitope specfic immunoglobulin binding on rate measurement datum (kon) in M^-1 s^-1
The function of a device realized when administering a substance in vivo, applied particularly to the forcible insertion of a liquid or gas by means of a syringe, pump, etc.
adapted from WEB: http://www.dictionary.net/injection
Epstein Barr virus transformed B cell
A material entity which results from viral transformation process using EBV as transformation agent when applied to B-cell entity
PMID: 8777380. Expression of thyroid peroxidase in EBV-transformed B cell lines using adenovirus.Thyroid. 1996 Feb;6(1):23-8.
chimera
An organism which contains cells or tissues with a different genotype
PERSON: Helen Parkinson
obsolete_anatomical entity
13-02-2009: Biomaterial branch: change of label and definition following discussions at the OBI winter meeting 2009. It was felt that 'macroscopic part of multicellular organism' introduce an impractical delineation. IMPORTANT NOTE: OBI 'anatomical entity' would essentially correspond to FMA 'material anatomical entity' rather than FMA 'physical anatomical entity'. OBI does not include 'immaterial anatomical entity' as it would clash with the parent class 'material entity' DOCUMENTATION NOTE: OBI anatomical entity granularity level excludes cell and biological molecules.
Biom call - January 2009 - Issues: parasites are not macroscopic part or organism. fetus is_a macroscopic part (but this is up for discussion)
equivalent classes 'portion of tissue' or 'multi-tissue structure' or 'portion of organism substance' Superclasses material_entity part_of some organism
10/20/09: This class and all subclasses are currently problematic. They should all be imported from other OBO foundry ontologies. (FMA / CARO / UBERON). Currently two problems exist: There is no cross species anatomy that covers all the entities we need. Secondly: there is not good boundary between anatomical entities and smaller parts in FMA. Currently we will use anatomical entities as if they are valid across species.
An anatomical entity is a material entity that is part of a multicellular organism, and which is large enough so that it forms an identifiable structure in the organism. Specifically, it excludes granular parts of the organism, such as atoms, molecules, cells, which can be removed from the organism without affecting it. It is defined as the union of 'multi-tissue structure', 'body substance' and 'portion of tissue'
Tina Boussard
Tissue, organ, system, sperm, blood or body location (arm).
not super happy about liquids (blood, sperm), as they seem to be 'granular' somewhat, and not form a structure.
blood plasma specimen
03/21/2010: BP, blood plasma is defined as the output of certain separation processes, so this is in the domain of OBI, not FMA.
PERSON: Maura Gasparetto
PMID: 18217225.Sex Transm Dis. 2008 Jan;35(1):55-60. Review.Human immunodeficiency virus viral load in blood plasma and semen: review and implications of empirical findings.
WEB: http://en.wikipedia.org/wiki/Blood_plasma
a material entity which corresponds to the liquid component of blood, in which the blood cells are suspended.
plasma
blood serum specimen
A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors.
PMID: 18229666.Adv Med Sci. 2007;52 Suppl 1:204-6.Antioxidant activity of blood serum and saliva in patients with periodontal disease treated due to epilepsy.
organism
10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI.
A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
WEB: http://en.wikipedia.org/wiki/Organism
animal
fungus
plant
virus
immortal cell
GROUP: OBI Biomaterial Branch
a cell derived from a multicellular organism that has the potential to replicate indefinitely
a single Hela cell
obsolete_fragment derived from protein
BP:03/21/2010:obsoleted as the class is no longer necessary, and we would otherwise need all kinds of 'fragment derived from' classes. Instead, use composite terms with the relationship 'derived from' some protein OR derived from some part_of protein.
A material entity which is derived from a protein
GROUP: IEDB
PRS:22022008. result from protocol_application where input=protein and output=polypeptide or peptide (to capture: derives_from protein)
fragment derived from protein
original term: protein fragment split into synthetic polypeptide and fragment derived from protein THE DEFINITION OF THIS SUGGESTS WE COVER THIS ALREADY IN PEPTIDE/POLYPETIDE. DO WE NEED THIS AND CAN WE DEAL WITH IT IN SOME OTHER WAY? JAMES
the peptide with sequence SIINFEKL, which is eluted from a cell expressing hen egg lysozyme
phosphate buffered saline solution
PBS buffer
PERSON: Tina Boussard
PMID: 16279733.Dent Mater J. 2005 Sep;24(3):414-21.PBS buffer solutions with different pH values can change porosity of DNA-chitosan complexes.
Phosphate buffered saline (abbreviated PBS) is a buffer solution commonly used in biochemistry. It is a salty solution containing sodium chloride, sodium phosphate and in some preparations potassium chloride and potassium phosphate. The buffer helps to maintain a constant pH. The concentration usually matches the human body (isotonic).
WEB: http://en.wikipedia.org/wiki/Phosphate_buffered_saline
specimen
Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
A material entity that has the specimen role.
cell line cell
A material entity that represents generations of a primary culture.
immortalized cell line culture
An immortalized cell line is a cell line that is able to replicate indefinitely as a result of an in vitro cell line immortalization process
Isolation and characterization of an immortalized oral keratinocyte cell line of mouse origin. Arch Oral Biol. 2008 Nov;53(11):1091-100. Epub 2008 Aug 21. PMID: 1872191
xenograft
A material entity which results from the transplantation of living cells, tissues or organs from on organism of one species to an organism of another species.
Human xenotransplantation (e.g. from pig to human) offers a potential treatment for end-stage organ failure, a significant health problem in parts of the industrialized world
WEB: http://en.wikipedia.org/wiki/Xenograft
xenotransplant
cell culture
Jurkat cell line in RPMI w/ 10% FCS. PBMCs were purified from blood sample and put into tissue culture media. Purification of recombinant human growth hormone from CHO cell culture supernatant by Gradiflow preparative electrophoresis technology. Protein Expr Purif. 2003 Nov;32(1):126-34. PMID: 14680949
a cell culture is a material entity consisting of a population of cells that is maintained in vitro
primary cell culture
a primary cell culture is a cell culture where the cells derive from a fresh tissue source.
spleen cells put directly into culture Cold storage of biopsies from wild endangered native Chilean species in field conditions and subsequent isolation of primary culture cell lines. In Vitro Cell Dev Biol Anim. 2008 Jul 2. PMID: 18594934
cell line culture
HeLa cells Changes in ultrastructure and endogenous ionic channels activity during culture of HEK 293 cell line. Eur J Pharmacol. 2007 Jul 12;567(1-2):10-8. PMID: 17482592
a cell line culture is a cell culture where the cells grown are from a cell line, long term culture of cells that are replicating continuously. The cell population is homogenous but not clonal
clonal cell culture
a clonal cell culture is a cell culture in which all cells can be assumed to be identical, tracking back to a single ancestor cell.
cell cut Stem cell functions assessed in clonal culture. Soc Gen Physiol Ser. 1988;43:39-45. Review. PMID: 3077557
screening library
7/13/09: Need to clarify if this meets reagent role definition
PMID: 15615535.J Med Chem. 2004 Dec 30;47(27):6864-74.A screening library for peptide activated G-protein coupled receptors. 1. The test set. [cdna_library, phage display library]
PRS: 22-02-2008: while working on definition of cDNA library and looking at current example of usage, a screening library should be a defined class -> any material library which has input_role in a screening protocol application change biomaterial to material in definition
a screening library is a collection of materials engineered to identify qualities of a subset of its members during a screening process?
synthetic peptide
PRS:22-02-2008: a chebi entity which has output role in a synthesis protocol application
a synthetic peptide is an material entity which is artificially engineered and results from the synthesis of a chain of amino acids which may also be found in natural protein and be identical in sequence to a protein fragment
changed from synthetic polypeptide to peptide, to get rid of the restriction of having more than 10 amino acids (required by Chebi).
original term: protein fragment split into synthetic polypeptide and fragment derived from protein DS: Is this synthetic an oxymoron to the biomaterial?
the synthesized peptide SIINFEKL which also occurs in hen-egg lysozyme
organ section
A liver slice used in a perfusion experiment. Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ section study with long-term functional evaluation. Clin Otolaryngol Allied Sci. 1995 Apr;20(2):145-9. PMID: 7634521
A processed material which derives from an organ and results from a process of dissection or histological sample preparation a portion(formerly an organ section is portion of an organ removed from the context of the organ)
GROUP: CEBS
bronchial alveolar lavage
BAL
Group of biomaterials present in the bronchial aveolar space of an organism which are collected through lavage including the reagents used to for the lavage process, organisms, cells, and cellular secretions present in the bronchial aveolar space.
solution containing lung derived T cells, eosinophils, and TNFa.
obsolete_polymer
MC, 20100316: Replaced by Chebi polymer and usage polymerization also fixed.
TERM: CHEBI:33839
A scattered aggregate of glucose molecules in a liquid
data transformation
The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
A data transformation is a process which produces output data from input data
Branch editors
Ryan Brinkman
data analysis
data processing
logistic-log curve fitting
A logistic-log curve fitting is a curve fitting where a curve of the form y=d+((a-d)/(1+(x/c)^b)) is obtained, where a, b, c, and d are determined so to optimize its fit to the input data points (x_1, y_1), (x_2, y_2), ..., (x_n, y_n).
ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1448
Typically used in an enzyme-linked immunosorbent assay (ELISA) to model the relationship between optical density (OD) and dilution. In this case a and d correspond to the theoretical OD of the assay at zero and infinite concentrations, respectively; c is the dilution associated with the point of symmetry of the sigmoid and is located at the midpoint of the assay found at the inflection point of the curve; b is a curvature parameter and is related to the slope of the curve.
logit-log curve fitting
A logit-log curve fitting is a curve fitting where first the limits y_0 an y_infty of y when x->0 and x->infinity, respectively, are estimated from the input data points (x_1, y_1), (x_2,y_2), ..., (x_n, y_n). Then a curve with equation log((y-y_0)/(y_infty-y))=a+b log(x) is obtained, where a and b are determined to optimize its fit to the input data points.
The above definition refers to the 'fully specified' logit-log model. The reduced form of this, when it is assumed that y_0=0, is named 'partially specified' logit-log model.
Typically used in an enzyme-linked immunosorbent assay (ELISA) to model the relationship between optical density (OD) and dilution. In this case OD_0 (also referred to OD_min) and OD_infty (also referred to OD_max) correspond to the theoretical OD of the assay at zero and infinite concentrations, respectively.
log-log curve fitting
A log-log curve fitting is a curve fitting where first a logarithmic transformation is applied both to the x and the y coordinates of the input data points (x_1, y_1), (x_2, y_2), ..., (x_n, y_n), and then coefficients a and b are determined to optimize the fit of log(y)=a+b*log(x) to these input data points.
ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1446
Typically used in an enzyme-linked immunosorbent assay (ELISA) to model the relationship between optical density (OD) and dilution.
feature extraction objective
A feature extraction objective is a data transformation objective where the aim of the data transformation is to generate quantified values from a scanned image.
TERM: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#feature_extraction
biexponential transformation
A biexponential transformation is a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation B(y)-x=0, where B denotes a b transformation.
Joseph Spliden
This type of transformation is typically used in flow cytometry.
WEB: http://flowcyt.sourceforge.net/gating/latest.pdf
box-cox transformation
A box-cox transformation is a data transformation according to the methods of Box and Cox as described in the article Box, G. E. P. and Cox, D.R. (1964) An analysis of transformations. Journal of Royal Statistical Society, Series B, vol. 26, pp. 211-246.
ARTICLE: Box, G. E. P. and Cox, D.R. (1964), "An analysis of transformations", Journal of Royal Statistical Society, Series B, vol. 26, pp. 211-246.
hyperlog transformation
A hyperlog transformation ia a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation EH(y)-x=0, where EH denotes an eh transformation.
ARTICLE: Bagwell C.B. (2006), "Hyperlog - a flexible log-like transform for negative, zero, and positive valued data", Cytometry A 64, 34-42."
loess scale group transformation one-channel
A loess scale group transformation one-channel is a loess scale group transformation consisting in the application of a scale adjustment following a loess group transformation one-channel, to render the M group variances similar.
Loess scale group normalization applied to data from two one-channel expression microarray assays.
OTHER: Editor's adjustment based on MGED Ontology term
logical transformation
A logical transformation is a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation S(y)-x=0, where S denotes an s transformation.
loess scale group transformation two-channel
A loess scale group transformation two-channel is a loess scale group transformation consisting in the application of a scale adjustment following a loess group transformation two-channel, to render the M group variances similar.
Loess scale group normalization applied to data from a two-channel expression microarray assay.
OTHER: Adjusted from MGED Ontology
loess global transformation one-channel
A loess global transformation one-channel is a loess global transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays.
Loess global normalization applied to data from two one-channel expression microarray assays, where the curve is obtained using all reporters. The goal is to remove intensity-dependent biases.
OTHER: Editor's generalization based on MGED Ontology term
split-scale transformation
A split-scale transformation is a data transformation which is an application of a function f described as follows to a (one dimensional) real number input. f(x)=a*x+b if x=for x>t; where log denotes a logarithmic transformation and a, b, c, d, r, t are real constants, with a, c, d, r, t positive, chosen so that f is continuous with a continuous derivative at the transition point t.
loess global transformation two-channel
A loess global transformation two-channel is a loess global transformation in the special case where the input the result of an MA transformation applied to intensities from the two channels of a two-channel assay.
Loess global normalization applied to data from a two-channel expression microarray assay, where the curve is obtained using all reporters. The goal is to remove intensity-dependent biases.
sine transformation
A sine transformation is a data transformation which consists in applying the sine function to a (one dimensional) real number input. The sine function is one of the basic trigonometric functions and a definition is provided, e.g., at http://mathworld.wolfram.com/Sine.html.
WEB: http://mathworld.wolfram.com/Sine.html
sine(0)=0, sine(pi/2)=1, sine(pi)=0, sine(3*pi/2)=-1, sine(pi/6)=1/2, sine(x+2*k*pi)=sine(x) where k is any integer, etc.
cosine transformation
A cosine transformation is a data transformation which consists in applying the cosine function to a (one dimensional) real number input. The cosine function is one of the basic trigonometric functions and a definition is provided, e.g., at http://mathworld.wolfram.com/Cosine.html.
WEB: http://mathworld.wolfram.com/Cosine.html
cosine(0)=1, cosine(pi/2)=0, cosine(pi)=-1, cosine(3*pi/2)=0, cosine(pi/3)=1/2, cosine(x+2*k*pi)=cosine(x) where k is any integer, etc.
loess group transformation one-channel
A loess group transformation one-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays.
loess group transformation two-channel
A loess group transformation two-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from the two channels of a two-channel assay.
homogeneous polynomial transformation
A homogeneous polynomial transformation is a polynomial transformation where all the term of the polynomial have the same degree.
WEB: http://mathworld.wolfram.com/HomogeneousPolynomial.html
a*x, with a non-zero, is a homogeneous polynomial of degree 1 in 1 variable, a*x^2, with a non-zero, is a homogeneous polynomial of degree 2 in 1 variable; a_1*x_1+...+a_n*x_n, with at least one of the a_i's non-zero, is a homogeneous polynomial of degree one in n variables; a*x_n^3+b*x_1*x_2*x_3, with at least one of a and b non-zero, is a homogeneous polynomial of degree 3 in n variables.
linlog transformation
A linlog transformation is a data transformation, described in PMID 16646782, whose input is a matrix [y_ik] and whose output is a matrix obtained by applying formula (9) of this paper, where values below an appropriately determined threshold (dependent on the row i) are transformed via a polynomial of degree 1, and values above this threshold are transformed via a logarithm.
PMID: 16646782
This can be used for microarray normalization, e.g. to normalize the data from a two-channel expression microarray assay, as described in PMID 16646782.
variance stabilizing transformation
A variance stabilizing transformation is a data transformation, described in PMID 12169536, whose input is a matrix [y_ik] and whose output is a matrix obtained by applying formula (6) in this paper. One of the goals is to obtain an output matrix whose rows have equal variances. The method relies on various assumptions described in the paper.
PMID: 12169536
This can be used for expression microarray assay normalization and it is referred to as "variance stabilizing normalization", according to the procedure described e.g. in PMID 12169536.
variance stabilising transformation
loess global transformation
A loess global transformation is a loess transformation where only one loess fitting is performed, utilizing one subset of (or possibly all of) the data points in the input so that there is only one resulting loess curve y=f(x) which is used for the transformation.
loess group transformation
A loess group transformation is a loess transformation where the input is partitioned into groups and for each group a loess fitting is performed, utilizing a subset of (or possibly all of) the data points in that group. Thus, a collection of loess curves y=f_i(x) is generated, one per group. Each (x, y) in the input is transformed into (x, y-f_i(x)), where f_i(x) is the curve corresponding to the group to which that data point belongs.
loess scale group transformation
A loess scale group transformation is a data transformation consisting in the application of a scale adjustment following a loess group transformation, to render the group variances for the second variable (y) similar. Has objective scaling.
total intensity transformation single
A total intensity transformation single is a data transformation that takes as input an n-dimensional (real) vector and multiplies each component of this vector by a coefficient, where the coefficient is obtained by taking the sum of the input components or of a subset of these, multiplied by a constant of choice.
Note that if the word "sum" is replaced by the word "mean" in the definition, the resulting definition is equivalent.
This can be used as a simple normalization method for expression microarray assays. For example, each intensity from a one-channel microarray assay is multiplied by a constant so that the output mean intensity over the microarray equals a desired target T (the multiplicative constant in this case is the T/(mean intensity)).
total intensity transformation paired
A total intensity transformation paired is a data transformation that takes as input two n-dimensional (real) vectors and multiplies each component of the first vector by a coefficient, where the coefficient is obtained by taking the ratio of the sum of the second input components or of a subset of these by the sum of the first input components or of a subset of these (the same subset is used for the two vectors).
This can be used as a simple normalization method for the two channels from a two-channel expression microarray assay or from two related one-channel expression microarray assays.
quantile transformation
A quantile transformation is a data transformation that takes as input a collection of data sets, where each can be thought as an n-dimensional (real) vector, and which transforms each data set so that the resulting output data sets have equal quantiles.
PERSON: Elisabetta Manduchi
This can be used for expression microarray assay normalization and it is referred to as "quantile normalization", according to the procedure described e.g. in PMID 12538238.
mean centering
A mean centering is a data transformation that takes as input an n-dimensional (real) vector, performs a mean calculation on its components, and subtracts the resulting mean from each component of the input.
This can be used as a normalization method in expression microarray assays. For example, given a two-channel microarray assay, the log ratios of the two channels (M values) can be mean-centered.
mean centring
median centering
A median centering is a data transformation that takes as input an n-dimensional (real) vector, performs a median calculation on its components, and subtracts the resulting median from each component of the input.
This can be used as a normalization method in expression microarray assays. For example, given a two-channel microarray assay, the log ratios of the two channels (M values) can be median-centered.
median centring
differential expression analysis objective
A differential expression analysis objective is a data transformation objective whose input consists of expression levels of entities (such as transcripts or proteins), or of sets of such expression levels, under two or more conditions and whose output reflects which of these are likely to have different expression across such conditions.
Analyses implemented by the SAM (http://www-stat.stanford.edu/~tibs/SAM), PaGE (www.cbil.upenn.edu/PaGE) or GSEA (www.broad.mit.edu/gsea/) algorithms and software
K-fold cross validation method
K-fold cross-validation randomly partitions the original sample into K subsamples. Of the K subsamples, a single subsample is retained as the validation data for testing the model, and the remaining K − 1 subsamples are used as training data. The cross-validation process is then repeated K times (the folds), with each of the K subsamples used exactly once as the validation data. The K results from the folds then can be averaged (or otherwise combined) to produce a single estimation. The advantage of this method over repeated random sub-sampling is that all observations are used for both training and validation, and each observation is used for validation exactly once. 10-fold cross-validation is commonly used
leave one out cross validation method
2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893049&group_id=177891&atid=886178
The authors conducted leave-one-out cross validation to estimate the strength and accuracy of the differentially expressed filtered genes. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/3/368
is a data transformation : leave-one-out cross-validation (LOOCV) involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data
jackknifing method
Jacknifing is a re-sampling data transformation process used to estimate the precision of sampling statistics and is a resampling method
simple weighting procedure is suggested for combining information over alleles and loci, and sample variances may be estimated by a jackknife procedure
jackknifing
boostrapping
Although widely accepted that high throughput biological data are typically highly noisy, the effects that this uncertainty has upon the conclusions we draw from these data are often overlooked. However, in order to assign any degree of confidence to our conclusions, we must quantify these effects. Bootstrap resampling is one method by which this may be achieved.
Bootstrapping is a data transformation process which estimates the precision of sampling statistics by drawing randomly with replacement from a set of data points
Bootstrapping is a statistical method for estimating the sampling distribution of a statistic by sampling with replacement from the original data, most often with the purpose of deriving robust estimates of standard errors and confidence intervals of a population parameter like a mean, median, proportion, odds ratio, correlation coefficient or regression coefficient
Benjamini and Hochberg false discovery rate correction method
A data transformation process in which the Benjamini and Hochberg method sequential p-value procedure is applied with the aim of correcting false discovery rate
Statistical significance of the 8 most represented biological processes (GO level 4) among E7 6 month upregulated genes following analysis with DAVID software; Benjamini-Hochberg FDR (false discovery rate)
2011-03-31: [PRS]. specified input and output of dt which were missing
pareto scaling
A pareto scaling is a data transformation that divides all measurements of a variable by the square root of the standard deviation of that variable.
modular decomposition
Molecular decomposition is the partition of a network into distinct subgraphs for the purpose of identifying functional clusters. The network data is run through any of several existing algorithms designed to partition a network into distinct subgraphs for the purpose of isolating groups of functionally linked biological elements such as proteins.
editor
k-means clustering
A k-means clustering is a data transformation which achieves a class discovery or partitioning objective, which takes as input a collection of objects (represented as points in multidimensional space) and which partitions them into a specified number k of clusters. The algorithm attempts to find the centers of natural clusters in the data. The most common form of the algorithm starts by partitioning the input points into k initial sets, either at random or using some heuristic data. It then calculates the mean point, or centroid, of each set. It constructs a new partition by associating each point with the closest centroid. Then the centroids are recalculated for the new clusters, and the algorithm repeated by alternate applications of these two steps until convergence, which is obtained when the points no longer switch clusters (or alternatively centroids are no longer changed).
WEB: http://en.wikipedia.org/wiki/K-means
hierarchical clustering
A hierarchical clustering is a data transformation which achieves a class discovery objective, which takes as input data item and builds a hierarchy of clusters. The traditional representation of this hierarchy is a tree (visualized by a dendrogram), with the individual input objects at one end (leaves) and a single cluster containing every object at the other (root).
WEB: http://en.wikipedia.org/wiki/Data_clustering#Hierarchical_clustering
average linkage hierarchical clustering
An average linkage hierarchical clustering is an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the average distance between objects from the first cluster and objects from the second cluster.
complete linkage hierarchical clustering
an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the maximum distance between objects from the first cluster and objects from the second cluster.
single linkage hierarchical clustering
A single linkage hierarchical clustering is an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the minimum distance between objects from the first cluster and objects from the second cluster.
Benjamini and Yekutieli false discovery rate correction method
A data transformation in which the Benjamini and Yekutieli method is applied with the aim of correcting false discovery rate
The expression set was compared univariately between the stroke patients and controls, gene list was generated using False Discovery Rate correction (Benjamini and Yekutieli)
dimensionality reduction
A dimensionality reduction is data partitioning which transforms each input m-dimensional vector (x_1, x_2, ..., x_m) into an output n-dimensional vector (y_1, y_2, ..., y_n), where n is smaller than m.
principal components analysis dimensionality reduction
A principal components analysis dimensionality reduction is a dimensionality reduction achieved by applying principal components analysis and by keeping low-order principal components and excluding higher-order ones.
pca data reduction
probabilistic algorithm
A probabilistic algorithm is one which involves an element of probability or randomness in the transformation of the data.
expectation maximization
EM is a probabilistic algorithm used to estimate the maximum likelihood of parameters from existing data where the model involves unobserved latent variables. The input to this method is the data model for which the estimation is performed over and the output is an approximated probability function.
global modularity calculation
A network graph quality calculation in which an input data set of subgraph modules and their in-degree and out-degree qualities is used to calculate the average modularity of subgraphs within the network.
PERSON: Richard Scheuermann
dye swap merge
A dye swap merge is a replicate analysis which takes as input data from paired two-channel microarray assays where the sample labeled with one dye in the first assay is labeled with the other dye in the second assay and vice versa. The output for each reporter is obtained by combining its (raw or possibly pre-processed) M values in the two assays, where the M value in an assay is defined as the difference of the log intensities in the two channels. This can be used as a normalization step, when appropriate assumptions are met.
moving average
A moving average is a data transformation in which center calculations, usually mean calculations, are performed on values within a sliding window across the input data set.
The moving average is often used to handle data from tiling arrays.
replicate analysis
A replicate analysis is a data transformation in which data from replicates are combined, e.g. through descriptive statistics calculations, and the results might be utilized for a variety of purposes, like assessing reproducibility, identifying outliers, normalizing, etc.
PERSON:Elisabetta Manduchi
Replicate analysis can be used in microarray analysis to identify and potentially exclude low quality data.
b cell epitope prediction
A B cell epitope prediction takes as input an antigen sequence, and through an analysis of this sequence, produces as output a prediction of the likelihood the biomaterial is a B Cell Epitope.
mhc binding prediction
An MHC binding prediction takes an input of a biomaterial sequence and through an analysis of this sequence, produces as output a prediction of the likelihood that the biomaterial will bind to an MHC molecule.
t cell epitope prediction
A T cell epitope prediction takes as input an antigen sequence, and through an analysis of this sequence, produces as output a prediction of the likelihood the biomaterial is a T cell epitope.
data imputation
ARTICLE: Little, RJA and Rubin, DB (2002). Statistical Analysis with Missing Data, Second Edition. John Wiley: Hoboken New Jersey, pp. 59-60.
Imputation is a means of filling in missing data values from a predictive distribution of the missing values. The predictive distribution can be created either based on a formal statistical model (i,e, a multivariate normal distribution) or an algorithm.
continuum mass spectrum
A continuum mass spectrum is a data transformation that contains the full profile of the detected signals for a given ion.
PERSON: Tina Hernandez-Boussard
characteristic path length calculation
Quantifying subgraph navigability based on shortest-path length averaged over all pairs of subgraph vertices
centroid mass spectrum
A centroid mass spectrum is a data transformation in which many points are used to delineate a mass spectral peak, is converted into mass-centroided data by a data compression algorithm. The centroided mass peak is located at the weighted center of mass of the profile peak. The normalized area of the peak provides the mass intensity data.
Person:Tina Hernandez-Boussard
Holm-Bonferroni family-wise error rate correction method
WEB: http://en.wikipedia.org/wiki/Holm%E2%80%93Bonferroni_method
a data transformation that performs more than one hypothesis test simultaneously, a closed-test procedure, that controls the familywise error rate for all the k hypotheses at level α in the strong sense. Objective: multiple testing correction
t-tests were used with the type I error adjusted for multiple comparisons, Holm's correction (HOLM 1979), and false discovery rate, http://www.genetics.org/cgi/content/full/172/2/1179
2011-03-14: [PRS]. Class Label has been changed to address the conflict with the definition Also added restriction to specify the output to be a FWER adjusted p-value The 'editor preferred term' should be removed
edge weighting
Edge weighting is the substitution or transformation of edge length using numerical data. Data input include a symmetric adjacency matrix for a network and a second data set, for example a list of interactor pairs and a confidence score associated with the experimental detection of each pair's interaction. Each element in the adjacency matrix is transformed or replaced with the corresponding number in the second data set. Output data are a modified adjacency matrix reflecting the transformed state of the network.
was classified under algorithm class which is not acceptable super-class TO BE DEALT WITH STILL BY RICHARD. JAMES
loess transformation
A loess transformation is a data transformation that takes as input a collection of real number pairs (x, y) and, after performing (one or more) loess fittings, utilizes the resulting curves to transform each (x, y) in the input into (x, y-f(x)) where f(x) is one of the fitted curves.
curve fitting data transformation
A curve fitting is a data transformation that has objective curve fitting and that consists of finding a curve which matches a series of data points and possibly other constraints.
WEB: http://en.wikipedia.org/wiki/Curve_fitting
family wise error rate correction method
A family wise error rate correction method is a multiple testing procedure that controls the probability of at least one false positive.
Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19
2011-03-31: [PRS]. creating a defined class by specifying the necessary output of dt allows correct classification of FWER dt
FWER correction
submatrix extraction
A submatrix extraction is a projection whose input is a matrix and whose output is a matrix obtained by selecting certain rows and columns from the input. (Note that, if one represents the input matrix as a vector obtained by concatenating its rows, then extracting a submatrix is equivalent to projecting this vector into that composed by the entries belonging to the rows and columns of interest from the input matrix.)
Note that this can be considered as a special case of projection if one represents the input matrix as a vector obtained by concatenating its rows. Then extracting a submatrix is equivalent to projecting this vector into the entries belonging to the rows and columns of interest from the input matrix.
WEB: http://en.wikipedia.org/wiki/Submatrix
When presented with the data from an expression microarray experiment in the form of a matrix, whose rows correspond to genes and whose columns correspond to samples, if one filters some of the genes and/or some of the samples out, the resulting data set corresponds to a submatrix of the original set.
row submatrix extraction
A row submatrix extraction is a submatrix extraction where all the columns of the input matrix are retained and selection only occurs on the rows.
When presented with the data from an expression microarray experiment in the form of a matrix, whose rows correspond to genes and whose columns correspond to samples, if one filters some of the genes out, the resulting data set corresponds to a row submatrix of the original set.
column submatrix extraction
A column submatrix extraction is a submatrix extraction where all the rows of the input matrix are retained and selection only occurs on the columns.
When presented with the data from an expression microarray experiment in the form of a matrix, whose rows correspond to genes and whose columns correspond to samples, if one filters some of the samples out, the resulting data set corresponds to a column submatrix of the original set.
gating
Gating is a property-based vector selection with the objective of partitioning a data vector set into vector subsets based on dimension values of individual vectors (events), in which vectors represent individual physical particles (often cells) of a sample and dimension values represent light intensity qualities as measured by flow cytometry.
Josef Spidlen
PERSON: Josef Spidlen
PERSON: Ryan Brinkman
descriptive statistical calculation objective
A descriptive statistical calculation objective is a data transformation objective which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability.
PERSON: Monnie McGee
mean calculation
A mean calculation 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.
From Monnie's file comments - need to add moment_calculation and center_calculation roles but they don't exist yet - (editor note added by James Jan 2008)
network analysis
A data transformation that takes as input data that describes biological networks in terms of the node (a.k.a. vertex) and edge graph elements and their characteristics and generates as output properties of the constituent nodes and edges, the sub-graphs, and the entire network.
sequence analysis objective
A sequence analysis objective is a data transformation objective which aims to analyse some ordered biological data for sequential patterns.
longitudinal data analysis
Longitudinal analysis is a data transformation used to perform repeated observations of the same items over long periods of time.
survival analysis objective
A data transformation objective which has the data transformation aims to model time to event data (where events are e.g. death and or disease recurrence); the purpose of survival analysis is to model the underlying distribution of event times and to assess the dependence of the event time on other explanatory variables
mass spectrometry analysis
A data transformation which has the objective of spectrum analysis.
spread calculation data transformation
A spread calculation is a data transformation that has objective spread calculation.
Kaplan Meier
a nonparametric (actuarial) data transformation technique for estimating time-related events. It is a univariate analysis that estimates the probability of the proportion of subjects in remission at a particular time, starting from the initiation of active date (time zero), and takes into account those lost to follow-up or not yet in remission at end of study (censored)
multiple testing correction method
A multiple testing correction method is a hypothesis test performed simultaneously on M > 1 hypotheses. Multiple testing procedures produce a set of rejected hypotheses that is an estimate for the set of false null hypotheses while controlling for a suitably define Type I error rate
PAPER: Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 9-10.
multiple testing procedure
inter-rater reliability objective
A study was conducted to determine the inter-rater reliability of common clinical examination procedures proposed to identify patients with lumbar segmental instability. Examples include joint-probability of agreement, Cohen's kappa and the related Fleiss' kappa, inter-rater correlation, concordance correlation coefficient and intra-class correlation.
a data transformation objective of determining the concordance or agreement between human judges.
Westfall and Young family wise error rate correction
Is a data transformation process in which the Westfall and Young method is applied with the aim of controlling for multiple testing
PRS: 2011-03-31: set specified input and specified output to the data transformation
Westfall and Young FWER correction
polynomial transformation
A polynomial transformation is a data transformation that is obtained through a polynomial, where a polynomial is a mathematical expression involving a sum of powers in one or more variables multiplied by coefficients (e.g. see http://mathworld.wolfram.com/Polynomial.html). The number of variables and the degree are properties of a polynomial. The degree of a polynomial is the highest power of its terms, where the terms of a polynomial are the individual summands with the coefficients omitted.
WEB: http://mathworld.wolfram.com/Polynomial.html
a*x+b, with a non-zero, is a polynomial of degree one in one variable; a*x^2+b*x+c, with a nonzero, is a polynomial of degree 2 in 1 variable; a*x*y+b*y+c, with a non-zero, is a polynomial of degree 2 in 2 variables (x and y); a_1*x_1+...+a_n*x_n+b, with at least one of the a_i's non-zero, is a polynomial of degree one in n variables
logarithmic transformation
A logarithmic transformation is a data transformation consisting in the application of the logarithm function with a given base a (where a>0 and a is not equal to 1) to a (one dimensional) positive real number input. The logarithm function with base a can be defined as the inverse of the exponential function with the same base. See e.g. http://en.wikipedia.org/wiki/Logarithm.
WEB: http://en.wikipedia.org/wiki/Logarithm
exponential transformation
An exponential transformation is a data transformation consisting in the application of the exponential function with a given base a (where a>0 and a is typically not equal to 1) to a (one dimensional) real number input. For alternative definitions and properties of this function see, e.g., http://en.wikipedia.org/wiki/Exponential_function and http://en.wikipedia.org/wiki/Characterizations_of_the_exponential_function.
WEB: http://en.wikipedia.org/wiki/Characterizations_of_the_exponential_function
WEB: http://en.wikipedia.org/wiki/Exponential_function
non-negative matrix factorization
Non negative matrix factorization is a data transformation in which factorises a matrix and which forces that all elements must be equal to or greater than zero.
Non-negative matrix factorization is used in text mining where document-term matrix is constructed with the weights of various terms (typically weighted word frequency information) from a set of documents. This matrix is factored into a term-feature and a feature-document matrix.
soft independent modeling of class analogy analysis
SIMCA
Soft independent modeling by class analogy (SIMCA) is a descriptive statistics method for supervised classification of data. The method requires a training data set consisting of samples (or objects) with a set of attributes and their class membership. The term soft refers to the fact the classifier can identify samples as belonging to multiple classes and not necessarily producing a classification of samples into non-overlapping classes.
WEB: http://en.wikipedia.org/wiki/Soft_independent_modelling_of_class_analogies
discriminant function analysis
Discriminant function analysis is a form of discriminant analysis used to determine which variables discriminate between two or more naturally occurring groups. Analysis is used to determine which variable(s) are the best predictors of a particular outcome.
WEB: http://www.statsoft.com/textbook/stdiscan.html
canonical variate analysis
CVA
WEB: http://en.wikipedia.org/wiki/Canonical_analysis
canonical variate analysis is a form of discriminant analysis that takes several continuous predictor variables and uses the entire set to predict several criterion variables, each of which is also continuous. CVA simultaneously calculates a linear composite of all x variables and a linear composite of all y variables. Unlike other multivariate techniques, these weighted composites are derived in pairs. Each linear combination is called a canonical variate and takes the general linear form.
linear discriminant functional analysis
Linear discriminant functional analysis (LDFA) is a multivariate technique used in special applications where there are several intact groups (random assignment may be impossible) and they have been measured on several independent measures. Thus, you will want to describe how these groups differ on the basis of these measures. In this case, classification and prediction is the main objective.
regression analysis method
BOOK: Richard A. Berk, Regression Analysis: A Constructive Critique, Sage Publications (2004) 978-0761929048
Regression analysis is a descriptive statistics technique that examines the relation of a dependent variable (response variable) to specified independent variables (explanatory variables). Regression analysis can be used as a descriptive method of data analysis (such as curve fitting) without relying on any assumptions about underlying processes generating the data.
multiple linear regression analysis
multiple linear regression is a regression method that models the relationship between a dependent variable Y, independent variables Xi, i = 1, ..., p, and a random term epsilon. The model can be written as Y = \beta_0 + \beta_1 X_1 + \beta_2 X_2 + \cdots +\beta_p X_p + \varepsilon where \beta_0 = 0 is the intercept ("constant" term), the \beta_i s are the respective parameters of independent variables, and p is the number of parameters to be estimated in the linear regression.
principal component regression
The Principal Component Regression method is a regression analysis method that combines the Principal Component Analysis (PCA)spectral decomposition with an Inverse Least Squares (ILS) regression method to create a quantitative model for complex samples. Unlike quantitation methods based directly on Beer's Law which attempt to calculate the absorbtivity coefficients for the constituents of interest from a direct regression of the constituent concentrations onto the spectroscopic responses, the PCR method regresses the concentrations on the PCA scores.
WEB: : http://www.thermo.com/com/cda/resources/resources_detail/1,2166,13414,00.html
partial least square regression analysis
ARTICLE: de Jong, S. (1993). SIMPLS: An alternative approach to partial least squares regression. Chemometrics and Intelligent Laboratory Systems, 18: 251-263.
PLS-RA
Partial least squares regression is an extension of the multiple linear regression model (see, e.g., Multiple Regression or General Stepwise Regression). In its simplest form, a linear model specifies the (linear) relationship between a dependent (response) variable Y, and a set of predictor variables, the X's, so that Y = b0 + b1X1 + b2X2 + ... + bpXp In this equation b0 is the regression coefficient for the intercept and the bi values are the regression coefficients (for variables 1 through p) computed from the data.
discriminant analysis
Discriminant function analysis is used to determine which variables discriminate between two or more naturally occurring groups. Analysis is used to determine which variable(s) are the best predictors of a particular outcome.
partial least square discriminant analysis
PLS Discriminant Analysis (PLS-DA) is a discriminant analysis performed in order to sharpen the separation between groups of observations, by hopefully rotating PCA (Principal Components Analysis) components such that a maximum separation among classes is obtained, and to understand which variables carry the class separating information.
WEB: http://www.camo.com/rt/Resources/pls-da.html
PLS-DA
eh transformation
An eh transformation is a data transformation obtained by applying the function EH described in what follows to a (one dimensional) real number input. EH(x)=exp(x*d/r)+b*(d/r)*x-1, if x>=0, and EH(x)=-exp(-x*d/r)+b*(d/r)*x+1, otherwise. Here exp denotes an exponential transformation and b, d, r are positive real constants with the objective of normalization.
b transformation
A b transformation is a data transformation obtained by applying the function B described in what follows to a (one dimensional) real number input. B(x)= a*exp(b*x)-c*exp(-d*x)+f, where exp denotes an exponential transformation and a, b, c, d, f are real constants with a, b, c, d positive with the objective of normalization.
s transformation
An s transformation is a data transformation obtained by applying the function S described in what follows to a (one dimensional) real number input. S(x)=T*exp(w-m)*(exp(x-w)-(p^2)*exp((w-x)/p)+p^2-1) if x>=w, S(x)=-S(w-x) otherwise; where exp denotes an exponential_transformations, 'p^' denotes the exponential transformation with base p; T, w, m, p are real constants with T, m, and p positive and w non-negative, and where w and p are related by w=2p*ln(p)(p+1) with the objective of normalization.
data visualization
Generation of a heatmap from a microarray dataset
Possible future hierarchy might include this: information_encoding >data_encoding >>image_encoding
An planned process that creates images, diagrams or animations from the input data.
visualization
similarity calculation
A similarity calculation is a data transformation that attaches to each pair of objects in the input a number that is meant to reflect how 'close' or 'similar' those objects are.
euclidean distance calculation
An euclidean distance calculation is a similarity calculation that attaches to each pair of real number vectors of the same dimension n the square root of the sum of the square differences between corresponding components. The smaller this number, the more similar the two vectors are considered.
pearson correlation coefficient calculation
A pearson correlation coefficient calculation is a similarity calculation which attaches to each pair of random variables X and Y the ratio of their covariance by the product of their standard deviations. Given a series of n measurements of X and Y written as x_i and y_i where i = 1, 2, ..., n, then their Pearson correlation coefficient refers to the "sample correlation coefficient" and is written as the sum over i of the ratios (x_i-xbar)*(y_i-ybar)/((n-1)*s_x*s_y) where xbar and ybar are the sample means of X and Y , s_x and s_y are the sample standard deviations of X and Y. The closer the pearson correlation coefficient is to 1, the more similar the inputs are considered.
WEB: http://en.wikipedia.org/wiki/Correlation
loess fitting
A loess fitting is a curve fitting obtained by localized regression. The latter refers to fitting a polynomial (straight line, quadratic, cubic, etc) to data values within a window covering a fraction of the total number of observations. As the window slides along the axis, a new polynomial is fit to the observations falling within the window. This continues until all points are fit with a local polynomial. The results are then smoothed together to form a curve. The smoothness of loess fits is controlled by a smoothing parameter (often denoted as alpha, usually between 1/4 and 1) and the degree of the polynomial that is fitted by the method (usually denoted by lambda).
ARTICLE: Mathematical details of loess fits are given in Cleveland, William (1993) Visualizing Data. Hobart Press, Summit, New Jersey, pp. 94-101.
mode calculation
A mode calculation is a descriptive statistics calculation in which the mode is calculated which is the most common value in a data set. It is most often used as a measure of center for discrete data.
From Monnie's file comments - need to add center_calculation role but it doesn't exist yet - (editor note added by James Jan 2008)
quantile calculation
A quantile calculation is a descriptive statistics calculation in which the kth quantile is the data value for which an approximate k fraction of the data is less than or equal to that value. See http://www.stat.wvu.edu/SRS/Modules/Quantiles/quantiles.html for details.
WEB: http://www.stat.wvu.edu/SRS/Modules/Quantiles/quantiles.html
median calculation
A median calculation is a descriptive statistics calculation in which the midpoint of the data set (the 0.5 quantile) is calculated. First, the observations are sorted in increasing order. For an odd number of observations, the median is the middle value of the sorted data. For an even number of observations, the median is the average of the two middle values.
variance calculation
A variance calculation is a descriptive statistics calculation in which the variance is defined as the average squared distance of each observation in the data set to the mean of the data set. It is also known as the second central moment.
From Monnie's file comments - need to add spread_calculation and moment_calculation roles but they don't exist yet - (editor note added by James Jan 2008)
standard deviation calculation
A standard deviation calculation is a descriptive statistics calculation defined as the square root of the variance. Also thought of as the average distance of each value to the mean.
From Monnie's file comments - need to add spread calculation role but they doesn't exist yet - (editor note added by James Jan 2008)
interquartile-range calculation
The interquartile range is a descriptive statistics calculation defined as the difference between the 0.75 quantile and the 0.25 quantile for a set of data.
skewness calculation
A skewness calculation is a descriptive statistics calculation defined as a parameter that describes how much a distribution (or a data set) varies from a bell-shaped curve. See http://www.riskglossary.com/link/skewness.htm for details. It is also known as the third central moment
From Monnie's file comments - need to add moment calculation role but they doesn't exist yet - (editor note added by James Jan 2008)
WEB: http://www.riskglossary.com/link/skewness.htm
kurtosis calculation
A kurtosis calculation is a descriptive statistics calculation defined as a parameter that measures how large or small the tails of a distribution are relative to the mean. For details, see http://davidmlane.com/hyperstat/A53638.html
WEB: http://davidmlane.com/hyperstat/A53638.html
data combination
A data transformation in which individual input data elements and values are merged together into a output set of data elements and values.
network graph construction
A network analysis in which an input data set describing objects and relationships between objects is transformed into an output representation of these objects as nodes and the relationships as edges of a network graph.
weighted network graph construction
A network graph construction in which an input data set describing objects and quantitative relationships between objects is transformed into and output representation of these objects as nodes and the quantitative relationships as weighted edges of a network graph.
directed network graph construction
A network graph construction in which an input data set describing objects and directional relationships between objects is transformed into and output representation of these objects as nodes and the directional relationships as directed edges of a network graph.
node quality calculation
A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of one of the node objects in the network.
node degree calculation
A node quality calculation in which an input data set describing object nodes and relationship edges between object nodes is used to enumerate the number of unique relationships of an individual object node.
quantitative node degree calculation
A node quality calculation in which an input data set describing object nodes and quantitative relationship edges between object nodes is used to sum all of the quantitative relationships of an individual object node.
node in-degree calculation
A node quality calculation in which an input data set describing object nodes and directional relationship edges between object nodes is used to enumerate the number of unique relationships pointing into an individual object node.
node out-degree calculation
A node quality calculation in which an input data set describing object nodes and directional relationship edges between object nodes is used to enumerate the number of unique relationships pointing out of an individual object node.
node shortest path identification
A node quality calculation in which a path describing the shortest path needed to transverse through connected nodes and edges to arrive at a specific target node in the network.
edge quality calculation
A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of one of the edge relationships in the network.
edge betweenness calculation
An edge quality calculation in which the input is a data sets of shortest paths between all pairs of node in the network and the output is the sum of all shortest paths that traverse the specific edge.
network subgraph quality calculation
A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of a subgraph partition of the network.
subgraph degree calculation
A network subgraph quality calculation in which an input data set describing subgraphs and relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships of an individual subgraph.
quantitative subgraph degree calculation
A network subgraph quality calculation in which an input data set describing subgraphs and quantitative relationship edges between subgraphs and other network objects is used to sum the quantitative relationships of an individual subgraph.
mathematical feature
This class is temporary and will be placed outside of data transformation ultimately (if it still remains at all after review)
feature is a (parent_class) that describes a characteristic, trait or quality of a data transformation
log base
The log base is a feature of a logarithmic function which is defined in http://en.wikipedia.org/wiki/Logarithm. Its value can be any positive real number different from 1.
subgraph in-degree calculation
A network subgraph quality calculation in which an input data set describing subgraphs and directional relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships pointing into an individual subgraph.
subgraph out-degree calculation
A network subgraph quality calculation in which an input data set describing subgraphs and relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships pointing out of an individual subgraph.
intra subgraph connectivity calculation
A network subgraph quality calculation in which an input data set describing internal nodes, edges and node degrees is used to determine the average node degree within the subgraph.
subgraph modularity calculation
A network subgraph quality calculation in which an input data set of subgraph in-degree and out-degree qualities is used to calculate the ratio of indegree to outdegree as a measure of modularity.
network graph quality calculation
A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of the network as a whole.
unit-variance scaling
A unit-variance scaling is a data transformation that divides all measurements of a variable by the standard deviation of that variable.
autoscaling
An MA transformation is a data transformation which takes as input a collection of data points (g_1, r_1), (g_2, r_2), ..., (g_n, r_n) with the r_i and g_i positive real numbers, and whose output is the collection of data points (A_1, M_1), (A_2, M_2), ..., (A_n, M_n) where, for each i, A_i=(log(g_i)+log(r_i))/2 and M_i=log(r_i)-log(g_i). Here log denotes a logarithmic transformation.
MA transformations are typically used in microarray data analyses. In this context, the g_i and r_i represent the reporter intensities in the two channels of a 2-channel assay or the reporter intensities in two related one-channel assays. Typically the base used for the logarithm is 2.
exponential base
The exponential base is a feature of an exponential function which is defined in http://en.wikipedia.org/wiki/Exponential_function. Its value can be any positive real number (typically different from 1).
polynomial degree
The polynomial degree is a feature of a polynomial function defined as the highest power of the polynomial's terms, where the terms of a polynomial are the individual summands with the coefficients omitted.
number of variables
The number of variables is a feature of any function (including polynomial functions) with domain contained in an n-dimensional vector space and is defined as n, the dimension of such space.
agglomerative hierarchical clustering
An agglomerative hierarchical clustering is a hierarchical clustering which starts with separate clusters and then successively combines these clusters until there is only one cluster remaining.
divisive hierarchical clustering
A divisive hierarchical clustering is a hierarchical clustering which starts with a single cluster and then successively splits resulting clusters until only clusters of individual objects remain.
data partitioning
Data partitioning is a data transformation with the objective of partitioning or separating input data into output subsets.
data vector reduction objective
Data vector reduction is a data transformation objective in which k m-dimensional input vectors are reduced to j m-dimensional output vectors, where j is smaller than k.
PERSON: Richard H. Scheuermann
Richard H. Scheuermann
generalized family wise error rate correction method
A generalized FWER correction method is a multiple testing procedure that controls the probability of at least k+1 false positives, where k is a user-supplied integer.
gFWER correction
quantile number of false positives correction method
A quantile number of false positives correction method is a MTP that controls for the pth quantile of the distribution of the number of false positives out of the total number of tests performed'
QNFP
tail probability for the proportion of false positives correction method
A TPPFP correction method is a MTP that controls the probability that the proportion of false positives among all rejected hypotheses is no greater than a constant q, where q is between 0 and 1.
Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 20
TPPFP correction method
false discovery rate correction method
Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21 and http://www.wikidoc.org/index.php/False_discovery_rate
The false discovery rate is a data transformation used in multiple hypothesis testing to correct for multiple comparisons. It controls the expected proportion of incorrectly rejected null hypotheses (type I errors) in a list of rejected hypotheses. It is a less conservative comparison procedure with greater power than familywise error rate (FWER) control, at a cost of increasing the likelihood of obtaining type I errors. .
2011-03-31: [PRS]. creating a defined class by specifying the necessary output of dt allows correct classification of FDR dt
FDR correction method
proportion of expected false positives correction method
A proportion of expected false positives correction method is a multiple testing procedure that controls the ratio of the expected value of the numbers of false positives to the expected value of the numbers of rejected hypotheses.
Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21
PEFP correction method
quantile proportion of false positives correction method
A quantile proportion of false positives correction method is a multiple testing procedure that controls the pth quantile of the distribution of the proportion of false positives among the rejected hypothesis (false discovery rate).
QPFP correction method
data transformation objective
A data transformation objective is an objective specification that a data transformation may have towards which the realization of that transformation is directed.
normalize objective
data normalization objective
A normalization objective is a data transformation objective where the aim is to remove systematic sources of variation to put the data on equal footing in order to create a common base for comparisons.
Quantile transformation which has normalization objective can be used for expression microarray assay normalization and it is referred to as "quantile normalization", according to the procedure described e.g. in PMID 12538238.
correction objective
A correction objective is a data transformation objective where the aim is to correct for error, noise or other impairments to the input of the data transformation or derived from the data transformation itself
Type I error correction
normalization data transformation
A normalization data transformation is a data transformation that has objective normalization.
averaging data transformation
An averaging data transformation is a data transformation that has objective averaging.
partitioning data transformation
A partitioning data transformation is a data transformation that has objective partitioning.
partitioning objective
A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets.
A partitioning objective is a data transformation objective where the aim is to generate a collection of disjoint non-empty subsets whose union equals a non-empty input set.
background correction objective
A background correction objective is a data transformation objective where the aim is to remove irrelevant contributions from the measured signal, e.g. those due to instrument noise or sample preparation.
curve fitting objective
A curve fitting objective is a data transformation objective in which the aim is to find a curve which matches a series of data points and possibly other constraints.
class discovery data transformation
unsupervised classification data transformation
A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery.
Fisher's exact test is a data transformation used to determine if there are nonrandom associations between two Fisher's exact test is a statistical significance test used in the analysis of contingency tables where sample sizes are small where the significance of the deviation from a null hypothesis can be calculated exactly, rather than relying on an approximation that becomes exact in the limit as the sample size grows to infinity, as with many statistical tests.
center calculation objective
A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set.
A mean calculation which has center calculation objective is a data transformation in which the center of the input data is discovered through the calculation of a mean average.
class discovery objective
A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic.
discriminant analysis objective
unsupervised classification objective
class prediction objective
A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data.
supervised classification objective
spread calculation objective
Spread calculation can be achieved by use of a standard deviation, which measures distance from the mean
is a data transformation objective whereby the aim is to the calculate the spread of a dataset, spread is a descriptive statistic which describes the variability of values in a data set
Awaiting English definition from Monnie McGee
center calculation data transformation
A center calculation data transformation is a data transformation that has objective of center calculation.
data vector reduction data transformation
A data vector reduction is a data transformation that has objective data vector reduction and that consists of reducing the input vectors k to a smaller number of output vectors j, where j<k.
scaling objective
Scaling gene expression data for cross platform analysis http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-454-4_13
is a data transformation objective where all, or some of a data set is adjusted by some data transformation according to some scale, for example a user defined minimum or maximum
descriptive statistical calculation data transformation
A descriptive statistical calculation data transformation is a data transformation that has objective descriptive statistical calculation and which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability.
scaling data transformation
A scaling data transformation is a data transformation that has objective scaling.
error correction objective
Application of a multiple testing correction method
An error correction objective is a data transformation objective where the aim is to remove (correct for) erroneous contributions arising from the input data, or the transformation itself.
James Malone, Helen Parkinson
sequence analysis data transformation
A sequence analysis data transformation is a data transformation that has objective sequence analysis and has the aim of analysing ordered biological data for sequential patterns.
cross validation objective
WEB: http://en.wikipedia.org/wiki/Cross_validation
A cross validation objective is a data transformation objective in which the aim is to partition a sample of data into subsets such that the analysis is initially performed on a single subset, while the other subset(s) are retained for subsequent use in confirming and validating the initial analysis.
rotation estimation objective
merging objective
A merging objective is a data transformation objective in which the data transformation has the aim of performing a union of two or more sets.
combining objective
merging of columns from two different data sets
A data visualization which has input of a clustered data set and produces an output of a report graph which is capable of rendering data of this type.
Adata visualization which has input of a gene list and produces an output of a report graph which is capable of rendering data of this type.
A data visualization which has input of a classified data set and produces an output of a report graph which is capable of rendering data of this type.
A data visualization which has input of a background corrected data set and produces an output of a report graph which is capable of rendering data of this type.
A data transformation which has the objective of performing survival analysis.
Proportional hazards model is a data transformation model to estimate the effects of different covariates influencing the times-to-failure of a system.
WEB: http://en.wikipedia.org/wiki/Cox_proportional_hazards_model
A data transformation objective in which correlation is obtained (often measured as a correlation coefficient, ρ) which indicates the strength and direction of a relationship between two random variables.
Calculation of characteristic path length in mass spectrometry
is a data transformation objective where the aim is to analyse some aspect of spectral data by some data transformation process.
A precursor ion is selected in the first stage, allowed to fragment and then all resultant masses are scanned in the second mass analyzer and detected in the detector that is positioned after the second mass analyzer. This experiment is commonly performed to identify transitions used for quantification by tandem MS.
Tandem mass spectrometry is a data transformation that uses two or more analyzers separated by a region in which ions can be induced to fragment by transfer of energy (frequently by collision with other molecules).
Gas chromatography mass spectrometry is a data transformation combining mass spectrometry and gas chromatography for the qualitative as well as quantitative determinations of compounds.
The chi-square test is a data transformation with the objective of statistical hypothesis testing, in which the sampling distribution of the test statistic is a chi-square distribution when the null hypothesis is true, or any in which this is asymptotically true, meaning that the sampling distribution (if the null hypothesis is true) can be made to approximate a chi-square distribution as closely as desired by making the sample size large enough.
ANOVA or analysis of variance is a data transformation in which a statistical test of whether the means of several groups are all equal.
sequential design
Any design in which the decision as to whether to enroll the next patient, pair of patients, or block of patients is determined by whether the cumulative treatment difference for all previous patients is within specified limits. Enrollment is continued if the difference does not exceed the limits. It is terminated if it does
MUSC
PMID: 17710740.Pharm Stat. 2007 Aug 20.Sequential design approaches for bioequivalence studies with crossover designs.
Provenance: OCI
observation design
PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study.
observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists.
obsolete_collection (of entities of organismal origin)
03/17/2010: obsoleted (on call), and replaced by 'material entity' and/or specimen. No need for the 'collection' part of this class any more after merging bfo:aggregate object into material entity, and by dealing with 'specimen' rather than with entities of organismal origin.
2009-11-04, MC: Entity of organismal origin has been deprecated a while ago. We still have collection (of entities of organismal origin). I am not sure we could replace with collection of material entity without altering the meaning (i.e. deprecating the class). In addition, if we do deprecate that class, should we just assert the children under material entity?
PMID: 18037794. Magn Reson Med Sci. 2007;6(3):139-46. Imaging of a large collection of human embryo using a super-parallel MR microscope.[the Orsay Museum has a nice collection of Impressionnist paintings]
PRS: How can we distinguish with 'collection' as the process of collecting entities, (eg. data collection, urine collection)
a collection is a bfo:aggregate object, that is a set of material object of the same kind
added during 22-02-2008 biomaterial call to distinguish library and population
collection (of entities of organismal origin)
set, group, ensemble
pool of specimens
A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish.
check with advisors as to how to represent multiple instances of any class? a set of specimens which have been gathered from one or more sample_populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish
chemical solution
A material entity that is made up of at least 2 scattered molecular aggregates, one playing the role of solvent and the other one playing the role of solute.
PMID: 18289311.Anesth Analg. 2008 Apr;106(4):1078-86.Less impairment of hemostasis and reduced blood loss in pigs after resuscitation from hemorrhagic shock using the small-volume concept with hypertonic saline/hydroxyethyl starch as compared to administration of 4% gelatin or 6% hydroxyethyl starch solution.
liquid chemical solution
buffer role
A buffer of carbonic acid (H2CO3) and bicarbonate (HCO3−) is present in blood plasma, to maintain a pH between 7.35 and 7.45. http://en.wikipedia.org/wiki/Buffer_solution
a role which inheres in some molecular entity realized during the process of buffering
solvent role
adpated from wikipedia (http://en.wikipedia.org/wiki/Solvatation)
PMID: 18373502.Transfusion. 2008 Mar 25. Solvent/detergent treatment of platelet concentrates enhances the release of growth factors.
solvent role is a role which inheres in a molecular entity capable of ensuring the dissolution of another chemical entity and realized by the process of solvation
solute role
adapted from wikipedia (http://en.wikipedia.org/wiki/Solute)
PMID: 18380397.Pharmazie. 2008 Feb;63(2):113-21.Deviations of drug solubility in water-cosolvent mixtures from the Jouyban-Acree model--effect of solute structure.
solute role is a role played by a chemical entity which is dissolved by another chemical entity (the solvent) when creating a solution
comet assay
PMID: 18326531.Mutagenesis. 2008 Mar 6.Recommendations for design of the rat comet assay.
PMID:7686265 .Mutat Res. 1993 Jul;288(1):47-63.The single cell gel electrophoresis assay (comet assay): a European review.
SCGE assay
a comet assay is an assay which utilizes gel electrophoresis on cell exposed to a challenge with the objective to assess DNA damage (DNA breakage) by determining the size and shape of DNA migration in cell placed in an electric field in specific conditions.
single cell gel electrophoresis assay
PCR-SSCP assay
PMID: 17334176.Hum Exp Toxicol. 2007 Jan;26(1):9-18.Is there a role for PCR-SSCP among the methods for missense mutation detection of TP53 gene?
PMID: 18219595.Mol Biotechnol. 2008 Feb;38(2):155-63.PCR-SSCP: a method for the molecular analysis of genetic diseases.
a PCR-SSCP assay is an assay that identifies DNA sequence variation (mutation, deletion, insertions) using gel electrophoresis technique and denaturating conditions on target DNA sequences amplified using polymerase chain reaction procedure.
polymerase chain reaction-single strand conformation polymorphism assay
obsolete_liver
PMID: 2104732. Caudate lobe of the liver: anatomy, embryology, and pathology. AJR Am J Roentgenol. 1990 Jan;154(1):87-93.
PRS: Test. added for evaluation and validation of possible imports from CARO (or other anatomical resources)
liver
liver is an anatomical entity which constituent are mainly hepatocytes, which has a function of detoxification, hematopoietic center, glucose and fat metabolism management. liver is only found in animals , all Vertebrates and some families of invertebrates
obsolete_adipose tissue
PMID: 18435934.Fatty acid composition of adipose tissue and blood in humans and its use as a biomarker of dietary intake.Prog Lipid Res. 2008 Apr 4.
PRS: this class has been added during major biomaterial.owl cleanup for evaluation and testing of imports from CARO
adipose tissue
adipose tissue is a tissue which main constituents are adipocytes. adipose tissue can be classified base on its location (site) but also based on adipocyte subtypes (brown or white) which reflect functional differences and is only found in animals, Vertebrates or invertebrates.
denatured polymer
Is a polymer which has lost secondary or tertiary structure
decapitated organism
OBI Biomaterial
Ovarian development induced in decapitated female Culex pipiens pallens mosquitoes by infusion of physiological quantities of 20-hydroxyecdysone together with amino acids. J Insect Physiol. 1998 May;44(5-6):525-528. PMID: 12770172
decapitated organism is an organism which has had it's head removed
validated information
PMID: 20084519: "..Three of four interactions were validated via functional magnetic resonance imaging (fMRI) in an independent sample of healthy controls;..."
an information content entity which results from a validation process aimed at confirming a claim, a finding or a predicted information entity about a material entity or a process by experimental means.
curated information
2009-11-10 Bjoern Peters. Need to check if this was intended. overlap with 'edited information', and has the same logical restrictions.
2010-01-31 Philippe Rocca-Serra: restriction now changed to be the output of a digital curation process + reflected in example of usage and reference
A information content entity that has undergone a digital curation performed by a curator for accuracy checks and compliance with curation requirements. Information which has been assessed for accuracy by domain experts.
PMID: 17344875: A curated compendium of phosphorylation motifs.Nat Biotechnol. 2007 Mar;25(3):285-6.
randomized group participant role
A person enrolled in a randomized clinical trial bears a randomized group participant role
a role that borne by an organism and realized by some group randomization process
methylated polymer
A methylated polymer which has artificially acquired one or more methyl groups
Binding and penetration of methylated DNA into primary and transformed human cells. Ann N Y Acad Sci. 2008 Aug;1137:36-40. PMID: 18837922
genetically modified organism
A protocol for removal of antibiotic resistance cassettes from human embryonic stem cells genetically modified by homologous recombination or transgenesis. Nat Protoc. 2008;3(10):1550-8. PMID: 18802436
an organism that is the output of a genetic transformation process
predicted data item
BP 12/21: Edited the incomplete definition from Philippe. It is still unclear to me if this should be a data item at all, or an information content entity. This will be important, because if we exclude predictions from data items, we will run into issues that we willl have to duplicate things like 'weight datum' etc. all of which can be predicted.
A data item that was generated on the basis of a calculation or logical reasoning
mean-centered data
a data item which has been processed by a mean centering data transformation where each output value is produced by subtracting the mean from the inout value
edited document
A document which is the output of a document editing process
The OBI manuscript is (much) edited imformation
dissolved material entity
A material entity that has been going through a process of being put into solution
Salt molecules that have been mixed into water
extraction
A material separation in which a desired component of an input material is separated from the remainder
nucleic acid extraction using phenol chloroform
Current the output of material processing defined as the molecular entity, main component in the output material entity, rather than the material entity that have grain molecular entity. 'nucleic acid extract' is the output of 'nucleic acid extraction' and has grain 'nucleic acid'. However, the output of 'nucleic acid extraction' is 'nucleic acid' rather than 'nucleic acid extract'. We are aware of this issue and will work it out in the future.
filtration
OBI-Branch: adapted from wikipedia and wordnet
PMID: 18524968.Filtration of CSF improves isolation of Mycobacteria.J Clin Microbiol. 2008 Jun 4.
filtration is a process which separates components suspended in a fluid based on granularity properties relying on a filter device
centrifugation
adapted from http://www.fao.org/DOCREP/003/X3910E/X3910E06.htm
PMID: 18428461.Purification of oligodendrocytes and their progenitors using immunomagnetic separation and Percoll gradient centrifugation. Curr Protoc Neurosci. 2001 May;Chapter 3:Unit 3.12.
centrifugation is a process separating molecules by size or density using centrifugal forces generated by a spinning rotor. G-forces of several hundred thousand times gravity are generated in ultracentrifugation
staining
adapted from Wikipedia: http://en.wikipedia.org/wiki/Staining
PMID: 18540298. Role of modified bleach method in staining of acid-fast bacilli in lymph node aspirates. Acta Cytol. 2008 May-Jun;52(3):325-8.
Staining is a process which results in the addition a class-specific (DNA, proteins, lipids, carbohydrates) dye to a substrate to qualify or quantify the presence of a specific compound.
washing
PMID: 6874122. Dialysis leucopenia--no correction after prolonged washing of the membrane. Int J Artif Organs. 1983 May;6(3):113-4.
washing is a process by which a material entity acting as contaminant (e.g. excess staining reagent) is removed by application of one or more cycles of solution in flow.
irradiation
adapted from wikipedia (http://en.wikipedia.org/wiki/Irradiation)
PMID: 18563778.Histological and modeling study of skin thermal injury to 2.0 mum laser irradiation.Lasers Surg Med. 2008 Jun 18;40(5):358-370.
irradiation is a process by which a material entity is exposed to radiative energy, which could be ionizing radiation (such as gamma rays or X-rays) or not such as UV light or microwaves
polymerization
PMID: 18517209. The electronic role of DNA-functionalized carbon nanotubes: efficacy for in situ polymerization of conducting polymer nanocomposites. J Am Chem Soc. 2008 Jun 25;130(25):7921-8. Epub 2008 Jun 3.
PRS:22102008: need to import catalyst from CHEBI 35223
polymerization is process by which molecular entity of small mass are aggregated in motifs over the course of a chemical reaction catalyzed by enzymes or other molecular entities acting as catalyst. polymerization results in molecular entity of high molecular weight
trypsination
The use of mild trypsinization conditions in the detachment of endothelial cells to promote subsequent endothelialization on synthetic surfaces. Biomaterials. 2007 Sep;28(27):3928-35. PMID: 17570483
trypsination is a protease cleavage which uses enzyme trypsin to act on proteins present in an input material entity
enzymatic ligation
An enzymatic ligation is a planned process in which molecules are joined by covalent bonds through the action of an material entity with a ligase activity
PMID: 17853876. Enzymatic ligation assisted by nucleases: simultaneous ligation and digestion promote the ordered assembly of DNA. Nat Protoc. 2007;2(9):2198-202.
storage
A maintenance process by which material entities that are not actively metabolizing are placed in well identified location and possibly under controlled environment in ad-hoc devices/structures in order to preserve and protect them from decay/alteration and maintain availability
PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10.
cell lysis
BP, JG, RV: There is also a need for the unplanned cell lysis, which is probably not in the scope of OBI, but should be linked to from this process.
adapted from wikipedia [http://en.wikipedia.org/wiki/Lysis]
PMID: 18484276.Cell lysis with dimethyl sulphoxide produces stable homogeneous solutions in the dichlorofluorescein oxidative stress assay. Free Radic Res. 2008 May;42(5):435-41.
cell lysis is a process by which cell membrane integrity of live cells is compromised and leads to cell death. Cell lysis may be achieved by means of viral action or osmotic shock.
electrocution
PMID: 9587208. Electrocution of horses and cattle. Vet Rec. 1998 Apr 4;142(14):376.
electrocution is process by which electric current is applied to a material with quality alive and result the termination of life process.
cervical dislocation
PMID: 18246869. Loss of cortical function in mice after decapitation, cervical dislocation, potassium chloride injection, and CO2 inhalation. Comp Med. 2007 Dec;57(6):570-3
PRS:21102008: Input must be restricted to Vertebrates (requires import from NCBI tax)
cervical dislocation is a process by which a Vertebrate organism has its life terminated by rupturing spinal cord between cervical vertebrae induced by excessive mechanical torsion
asphyxiation
PMID: 18246869. Loss of cortical function in mice after decapitation, cervical dislocation, potassium chloride injection, and CO2 inhalation. Comp Med. 2007 Dec;57(6):570-
asphyxiation is a process by which oxygen supplies are restricted (by mechanical, e.g obstructing airways or chemical means, e.g. increasing CO2 partial pressure) resulting in termination of life in oxygen reliant organisms.
intentional overdosing
In vivo measurement of tumor blood oxygenation by near-infrared spectroscopy: immediate effects of pentobarbital overdose or carmustine treatment. J Neurooncol. 1994;22(3):209-20. PMID: 7760097
intentional overdosing is a process by which an excess dose of a chemical compound is given with the intent of causing death
lethal injection
decapitation
decapitation is a process by which the head of a living organism is physically removed from the body, usually resulting in rapid death (in the case of Rhodnius prolixus, it might take a bit longer..)
group randomization
adapted from wikipedia [http://en.wikipedia.org/wiki/Randomization]
A group assignment which relies on chance to assign materials to a group of materials in order to avoid bias in experimental set up.
PMID: 18349405. Randomization reveals unexpected acute leukemias in Southwest Oncology Group prostate cancer trial. J Clin Oncol. 2008 Mar 20;26(9):1532-6.
obsolete_activation
Alan Ruttenberg 2010/11/22: After OBI call, this is too broad a term, and in any case would be in the scope of GO
PMID: 18566411.Activation of the JAK/STAT-1 Signaling Pathway by IFN-{gamma} Can Down-Regulate Functional Expression of the MHC Class I-Related Neonatal Fc Receptor for IgG.J Immunol. 2008 Jul 1;181(1):449-63.
a process by which a material entity status is modified and conferred a capability of reacting (this sounds like a circular definition , hugh!)
immobilization
PMID: 18562258. The immobilization of proteins on biodegradable fibers via biotin-streptavidin bridges.Acta Biomater. 2008 May 23.
immbolization is a process by which material entity become (possibly covalently but not necessarily) attached to the surface of another material entity used a substratum.
nucleic acid hybridization
adapted from wikipedia [http://en.wikipedia.org/wiki/Nucleic_acid_hybridization]
PMID: 18555787.Quantitative analysis of DNA hybridization in a flowthrough microarray for molecular testing. Anal Biochem. 2008 May 27.
a planned process by which totally or partially complementary, single-stranded nucleic acids are combined into a single molecule called heteroduplex or homoduplex to an extent depending on the amount of complementarity.
elution
PMID: 18549238.Theory and Application of the Two-Mode Gradient Elution in Liquid Chromatography Involving Simultaneous Changes in Temperature and Mobile-Phase Composition.Anal Chem. 2008 Jun 13.
the process of extracting one material from another by washing with a solvent to remove adsorbed material from an adsorbent (as in washing of loaded ion-exchange resins to remove captured ions)
DNA Subtraction
PMID: 10718422. Identification of genes overexpressed in head and neck squamous cell carcinoma using a combination of complementary DNA subtraction and microarray analysis. Laryngoscope. 2000 Mar;110(3 Pt 1):374-81
a material separation process by which repetitive genomic DNA is removed during the construction of cDNA library.
document editing
Wax DB, Beilin Y, Hossain S, Lin HM, Reich DL. Manual editing of automatically recorded data in an anesthesia information management system. Anesthesiology. 2008 Nov;109(5):811-5. PMID: 18946292
is a planned process with specified input original document and specified output edited document
prediction
Prediction of TF target sites based on atomistic models of protein-DNA complexes. BMC Bioinformatics. 2008 Oct 16;9(1):436. PMID: 18922190
a process by which an event or an entity is described before it actually happens or is being discovered and identified.
validation
PMID: 18557814 . Chemical and genetic validation of dihydrofolate reductase-thymidylate synthase as a drug target in African trypanosomes. Mol Microbiol. 2008 Jun 16.
a planned process with objective to check that the accuracy or the quality of a claim or prediction satisfies some criteria and which is assessed by comparing with independent results
electroporation
PMID: 18551712. Microfluidic electroporation for selective release of intracellular molecules at the single-cell level. Electrophoresis. 2008 Jun 13.
a process in which a significant increase in the electrical conductivity and permeability of the cell plasma membrane caused by an externally applied electrical field. It is usually used in molecular biology as a way of introducing some substance into a cell, such as loading it with a molecular probe, a drug that can change the cell's function, or a piece of coding DNA
digital curation
Digital curation is the process of establishing and developing long term repositories of digital assets for current and future reference by researchers, scientists, and historians, and scholars generally.
PMID: 16901087. Supporting the curation of biological databases with reusable text mining.Genome Inform. 2005;16(2):32-44.
A10-Analyzer
A A10 is a flow_cytometer_analyser manufactured by Apogee. It uses an arc lamp as a light source, with choices of 75W Xe, 75W Xe/Hg or 100W Hg arc lamps. It has filters and collectors for up to three fluorescent parameters and two scatter parameters. It uses analog electronics. The A10 can be used for measuring the properties of individual cells.
John Quinn
A40-MiniFCM
A A40-MiniFCM is a flow_cytometer_analyser that allows for the choice of one of four lasers (375nm, 405nm,488nm, 532nm, 635nm), and PMTs and filters for collecting up to four parameters. It uses digital electronics. A military version of this cytometer is available as well. The A40-MiniFCM is geared towards the most demanding applications such as archaea, bacteria and large virus.
analog-to-digital converter
A-D
A2D
An analog-to-digital_converter is an instrument that converts an infinite resolution analog signal to a finite resolution digital signal.
The analog to digital converter transformed the analog output from the photomultiplier tube to a digital signal for collection.
flow cytometer analyzer
An analyser is a flow_cytometer that is used to measure properties of particles (whole cells, nuclei, chromosomes, diatoms, plankton, bacteria, viruses) by moving these particles through a detection chamber. An analyser is used to collect data for analysis.
FACS Calibur, Luminex 100
arc lamp
Arc lamp is a light source that produces light by an electric arc (or voltaic arc). The lamp consists of two electrodes typically made of tungsten which are separated by a gas. The type of lamp is often named by the gas contained in the bulb; including neon, argon, xenon, krypton, sodium, metal halide, and mercury. The electric arc in an arc lamp consists of gas which is initially ionized by a voltage and is therefore electrically conductive. To start an arc lamp, usually a very high voltage is needed to ignite or strike the arc. This requires an electrical circuit sometimes called an igniter, which is part of a larger circuit called the ballast. The ballast supplies a suitable voltage and current to the lamp as its electrical characteristics change with temperature and time. Older cytometers may use arc lamps to irradiate particles at the interrogation point.
The Jablochkoff Candle
argon ion laser
An argon-ion laser is an ion laser that uses argon ions as the lasing medium. These lasers are used primarily to emit light at wave lengths of 458 nm, 488 nm or 514.5 nm, though it is possible to use them to emit several wavelengths of blue and green light. Argon-ion lasers can emit light at many different wave lenghts, and excite a number of different flourochromes.
argon ion laser in a cytometer
avalanche photodiode
An avalanche photodiode is typically used to collect photons emitted by forward scatter because it is far less sensitive, and less likely o be burned out, than a PMT. A photodiode with high quantum efficiency and a mechanism for producing gains as high as a few thousand.
C30644E - InGaAs Avalanche Photodiode
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
Bactiflow
A Bactiflow is a flow_cytometer_analyser manufactured by Chemunex SA. It is a cell counter for bacteria and other micro organisms. Bacteria are stained with a fluorochrome and the number of particles that fluoresce are counted. The system uses digital electronics, a single laser and a single detector. An ALS version is available as well - Automatic Labeling System. The Bactiflow is specialized cytometer used exclusively for counting microbes.
band pass filter
530/30 BP filter, 585/42 BP filter
A band pass filter is an optical filter that passes wavelengths of light within a certain range and rejects (attenuates) frequencies outside that range. The passed wavelengths are indicated in the specifications of the filter and its name. A 480/20 band-pass filter pass light with at wavelengths of 460 to 500 nm and attenuates all others.
Person:John Quinn
BioSorter1000
A BioSorter1000 is a flow_cytometer_sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 1000 is an instrument for analyzing and sorting objects from 200-600 microns in diameter.
BioSorter 1000 at TSRI Flow Cytometry Core Facility
BioSorter2000
A BioSorter2000 is a sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 2000 is an instrument for analyzing and sorting objects from 500 microns to 1.5 millimeters in diameter.
BioSorter 2000 at TSRI Flow Cytometry Core Facility
BioSorter250
A BioSorter250 is a flow_cytometer_sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 250 is an instrument for analyzing and sorting objects from 40-200 microns in diameter.
BioSorter 250 at TSRI Flow Cytometry Core Facility
BioSorter500
A BioSorter500 is a flow_cytometer_sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 500 is an instrument for analyzing and sorting objects from 100-250 microns in diameter and less than 2mm in length.
BioSorter 500 at TSRI Flow Cytometry Core Facility
Cell Lab Quanta SC
A Cell Lab Quanta SC is a flow_cytometer_analyser manufactured by Becman Coulter. It features a mercury arc lamp optimized at 366, 405, and 435 nm, and a 488 nm laser diode. It has filters and PMTs to collect up to 3 fluorescent parameters, and a photodiode for side scatter detection. This cytometer uses Couter-Volume for cell size measurements. The Cell Lab Quanta SC can be used for measuring the properties of individual cells.
charge plate
LSR2 charge plate
Part of the fluidics subsystem. Charge plates are used or sorters. They create an charged electric field when particles deemed to be desired for further analysis are shaken form the piexo electric crystal. The charged particles are drawn toward the charged plate, and the altered drop location causes the particles to fall into a collection tube. Charge plates enable sorting.
cell sorter collection tube
LSR2 collection tube
Part of the fluidics subsystem. The collection tube is a vessel for capturing cells of interest that have been identified by a sorter. The collection tube is the end location of sorted cells.
Cyan
A Cyan is a flow_cytometer_analyser manufactured by Dako Cytomation. It features include digital electronics, three lasers: 488 nm, 635 nm, and 405 nm, and filters and collectors for nine fluorescent parameters and two scatter parameters. The Cyan can be used for measuring the properties of individual cells.
CYFlow ML
A CyFlow_ML is a flow_cytometer_analyser manufactured by Partec. It is a digital machine which uses 4 light sources: triple laser configurations including new powerful 200mW@488nm blue solid state laser + 100W UV lamp for highest resolution DNA analysis, and can collect 16 optical parameters: FSC1, FSC2, SSC, FL1-FL13. Ultracompact high end desktop multilaser Flow Cytometer for all applications in cell analysis and absolute counting.
CyFlow SL
a flow_cytometer_analyser manufactured by Partec. Its specs are: ultracompact and fully equipped mobile/portable instrument, dimensions [cm]: L 43 x H 16 x D 37, highest stability/robustness and highest precision, 5 optical parameters: FSC, SSC, FL-1, FL-2, FL-3, 20mW@488nm blue solid state laser , other laser light sources optional (UV, violet, green, red), WindowsTM XP FloMax (software for real time data acquisition, data display, and data evaluation), parallel 16 bit digital pulse processing Compact mobile Flow Cytometer for any kind of cell analysis and absolute volumetric counting. The CyFlow_SL allows to analyze forward and side scatter signals in combination with up to 3 fluorescence channels.
CyFlow SL3
A CyFlow_Sl3 is a flow_cytometer_analyser manufactured by Partec. Its specs are: ultracompact and fully equipped mobile/portable instrument, dimensions [cm]: L 43 x H 16 x D 37 , highest stability/robustness and highest precision, 5 optical parameters: FSC, SSC, FL-1, FL-2, FL-3, 20mW@488nm blue solid state laser, other laser light sources optional (UV, violet, green, red), WindowsTM XP FloMax (software for real time data acquisition, data display, and data evaluation), parallel 16 bit digital pulse processing. The CyFlow SL3 is a compact and dedicated portable Flow Cytometer for accurate and affordable cell analysis and true volumetric absolute counting in HIV Monitoring and AIDS patient follow-up by precise and direct CD4 and CD4% measurement.
CyFlow Space
A CyFlow_Space is a flow_cytometer_sorter manufactured by Partec. Its specs are: 8optical parameters, 6 colours:FSC, SSC, FL1-FL6 , 3laser light sources: 200mW@488nm blue solid state laser 25mW@635nm red diode laser 50mW@405nm violet or 8mW@375nm ultraviolet diode laser _ultracompact desktop high end instrument. Parallel 16bit digital pulse processing. The CyFlow Space is a 6-Colour FCM System and Cell Sorter for Clinical Routine and Research.
CyFlow Space at TSRI Flow Cytometry Core Facility
CytoBuoy
A CytoBuoy is a flow_cytometer_analyser manufactured by Cyto Buoy Inc. They are the buoy mounted version of the CytoSense, equipped with wireless transmission of control and data files. They are a single laser, multi parameter instrument. Various types of micro-laser are offered; available measuring parameters are forward light scatter, side scatter, and fluorescence (max. 9 colour bands). The current series have 5 parameters.
CytoBuoy can be used to conduct extended and/or high frequency time series of phytoplankton distribution and abundance on fixed locations
John Quinn, Melanie Courtot
CytoSence
A CytoSense is a flow_cytometer_analyser manufactured by Cyto Buoy Inc. They are a single laser, multi parameter instrument. Various types of micro-laser are offered; available measuring parameters are forward light scatter, side scatter, and fluorescence (max. 9 colour bands). The current series have 5 parameters. The CytoSense is the basic instrument, which can be used for normal laboratory applications, as well as for autonomous monitoring with internal data logging or direct data transmission. The special instrument design and its splashproof housing allow operation on moving platforms and outdoor sites.
CytoSub
A CytoSub is a flow_cytometer_analyser manufactured by Cyto Buoy Inc. They are a single laser, multi parameter instrument. Various types of micro-laser are offered; available measuring parameters are forward light scatter, side scatter, and fluorescence (max. 9 colour bands). The current series have 5 parameters. The CytoSub is the submersible version equipped with a high pressure sample inlet loop and a high pressure housing to allow underwater operation down to 200 m, lowered on a cable or mounted on a flooded underwater vehicle.
dichroic filter
A dichroic filter is an optical filter which is used to selectively pass light of a small range of colors while reflecting other colors. A dichroic filter passes the specified range of light whereas a dichroic mirror reflects the specified range of light.
Cy3 Dichroic Filter
dichroic mirror
A dichroic mirror is an optical filter which is used to selectively reflect light of a small range of colors while passing other colors. A dichroic filter passes the specified range of light whereas a dichroic mirror reflects the specified range of light.
ViewLux Alexa 594 dichroic mirror
differential pressure gauge
LSR2 differential pressure gauge
Part of the fluidics subsystem. The differential pressure gauge monitors the difference between sample and sheath fluid pressures in systems where pressure is used to force the sample fluid to flow in the center of the sheath fluid. A differential pressure gauge can be used by the operator to make sure that the sample fluid is at a greater pressure than the sheath fluid, which maintains a core of sample fluid.
diode laser
A diode laser is a laser in which the active medium is a p-n junction semiconductor laser diode, similar to that found in a light-emitting diode. Laser diodes emit at wavelengths from 375 nm to 1800 nm, and wavelengths of over 3 micrometer have been demonstrated. A diode laser can by used to irradiate cells in a flow cytometer.
FAX-RS3-H0 diode laser manufactured by Diode Laser Concepts, Inc.
dye laser
A dye laser is a laser in which the lasing medium is a fluorescent dye, usually dissolved in an organic solvent such as ethanol or ethylene glycol. The particular dye used determines the wavelengths the laser can emit. The laser medium is places between two parallel mirrors for light emission amplification.
Rhodamine 101 dye laser used to irradiate cells in a flow cytometer.
FACS Calibur
"FACS Calibur at TFL, BCCRC, Vancouver"
"http://www.bdbiosciences.com/immunocytometry_systems/products/display_product.php?keyID=45, 2007-05-11"
The FACS Calibur is one of the most popular cytometers in use for research.
FACS Canto
A FACS_Canto is a flow_cytometer_analyser manufactured by Becton Dickinson. It features digital electronics, a solid state 488 nm, and a HeNe 633 nm lasers, and filters and PMTs for collecting up to 6 fluorescent parameters. The FACS_Canto is an analyser usually used in clinical applications.
FACS Canto2
A FACS_Canto2 is a flow_cytometer_analyser manufactured by BD. It features digital electronics, two solid state lasers at 488 and 633 nm with the option for a third 405 nm laser, and filters and collectors for measuring up to 8 fluorescent paramters with either the 2 or 3 laser option. The FACS_Canto2 is an analyser usually used in clinical applications.
FACS Scan
A FACS_Scan is a flow_cytometer_analyser manufactured by Becton Dickinson. IT features analog electronics, one 488 nm solid state laser, and the filters and PMTs to collect up to three fluorescent parameters The FACS_Scan is usually used for research applications.
FACSAria
A FASCSAria is a flow_cytometer_sorter manufactured by Becton Dickinson. It features digital electronics, a solid state 488 nm blue laser, a solid state 407 nm violet laser, and a HeNe (633 nm) ion laser. The Aria has the filters and PMTs to collect side scatter and 9 fluorescent parameters. The Aria has a photodiode detector for forward scatter collector. The flow cell is Quartz cuvette. The FACSAria is a sorter used to collect and analyse cells using up to 11 parameters.
FACSAria at TSRI Flow Cytometry Core Facility
FACSvantage
FACSvantage at TSRI Flow Cytometry Core Facility
The FACSvantage is a flow_cytometer_sorter manufactured by Becton Dickinson. It has analog electronics, three lasers (several options are available), and the filters and PMTs to collect 6 fluorescent parameters and side scatter, and a photodiode to collect forward scatter. The FACSvantage can be used to analyse, sort and collect cells.
FC 500
A FC_500 is a flow_cytometer_analyser manufactured by Beckman Coulter. It features digital electronics, 488 nm and 635 nm lasers, filters and PMTs for 5 fluorescent parameters, a diode for collecting side scatter and a solid state detector for forward scatter. The FC 500 is an analyser usually used for either research or clinical applications.
flow cell
Aparatus in the fluidic subsystem where the sheath and sample meet. Can be one of several types; jet-in-air, quartz cuvette, or a hybrid of the two. The sample flows through the center of a fluid column of sheath fluid in the flow cell.
Biofilm Flow Cell
flow cytometer
A flow_cytometer is an instrument for counting, examining and sorting microscopic particles in suspension. It allows simultaneous multiparametric analysis of the physical and/or chemical characteristics of single cells flowing through an optical and/or electronic detection apparatus. A flow cytometer is an instrument that can be used to quantitatively measure the properties of individual cells in a flowing medium.
fluid pressure regulator
LSR2 fluid pressure regulator
Part of the fluidic subsystem. The fluid pressure regulator maintains constant pressure within the sheath and or sample lines by filling the lines with enough gas to push the fluid at the desired rate. The gas is usually air, and less frequently nitrogen. In the sheath line, the gas is pushed into the sheath tank. In the sample line the gas is pushed into the collection tube. Fluid pressure regulators maintain great enough pressure to push sample fluid out of the tube and sheath fluid out of the sheath tank.
Person: John Quinn
gas laser
A gas laser is a laser in which the lasing medium is a gas. The laser medium is places between two parallel mirrors for light emission amplification. The gas is excited to emit light via an external light source or an electric current discharging through the gas.
helium-neon gas laser used to erradiate cells in a flow cytometer.
Guava EasyCyte Mini
A Guava_EasyCyte_Mini is a flow_cytometer_analyser that includes a single 488 nm laser, and filters and PMTs to collect up to 3 fluorescent parameters. It includes a photodiode forward scatter collector and an optional photodiode for side scatter collection.Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The mini accepts tubes only for inputting cells or beads. The Guava_EasyCyte_Mini cytometer is a small portable cytometer particularly useful for field measurement.
Guava EasyCyte Plus
A Guava_EasyCyte_Plus System is a flow_cytometer_analyser that includes a single 488 nm laser, and filters and PMTs to collect up to 4 fluorescent parameters. It includes a photodiode forward scatter collector and an optional photodiode for side scatter collection.Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The EasyCyte plus accepts 96 well plates as well as tubes. The Guava_EasyCyte_Plus cytometer is a small portable cytometer particularly useful for field measurement.
Guava Personal Cell Analysis
A Guava_Personal_Cell_Analysis System is a flow_cytometer_analyser that includes a single 532 nm laser, and filters and PMTs to collect up to 2 fluorescent parameters. It includes a photodiode forward scatter collector. Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The PCA96 uses only tubes to introduce specimen. The Guava PCA cytometer is a small portable cytometer particularly useful for field measurement.
Guava_PCA
Guava Personal Cell Analysis-96
Guava_PCA-96
The Guava_Personal_Cell_Analysis-96 Systems is a flow_cytometer_analyser that includes a single 532 nm laser, and filters and PMTs to collect up to 2 fluorescent parameters. It includes a photodiode forward scatter collector. Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The PCA96 uses either tubes or 96 well plates to introduce specimen. The Guava PCA -96 cytometer is a small portable cytometer particularly useful for field measurement.
helium cadmium ion laser
A helium-cadmium laser is a metal vapor laser that emits wavelengths of 442, 325 and 354 nms. This laser is a metal vapor laser. A helium-cadmium laser can by used to irradiate cells in a flow cytometer.
KIMMON HeCd 325nm laser
helium neon ion laser
A helium neon laser can by used to irradiate cells in a flow cytometer.
A helium-neon laser (HeNe) is an ion laser that uses helium and neon gas-ions as lasing medium. HeNe lasers emit at 543 nm and 633 nm most commonly and can also be used at 543, 594, and 611 nm.
Amnis ImageStream
It has both components, an Image cytometer and a flow cytometer.
The ImageStream is a multispectral_imaging_flow_cytometer manufactured by Amnis. Its has digital electronics, a single standard 488 nm solid state laser. In addition an optional 658 nm and your choice of either a 405 nm or 375 nm solid state laser can be added. Information is collected using cameras. The ImageStream system CCD camera produces six images of each cell, including darkfield, brightfield, and up to four fluorescent colors. Each image is used to calculate over 40 features, so a six-image assay results in ~250 morphometric and photometric features per cell. The ImageStream is a flow cytometer that takes pictures of the cells in flow. It has both components, an Image cytometer and a flow cytometer.
inFlux Analyzer
The inFlux Analyzer is a flow_cytometer_analyser manufactured by Cytopeia. It is a digital machine, with these laser options: Coherent 70, 90, 300 series water cooled lasers, solid state UV 355nm, Violet 408nm, Violet-Blue 479nm, Blue-488nm, Green-531nm, Red-635nm, Red-647nm. Filters and PMTs are used for all parameters (including forward light scatter), and up to 12 PMTs can be included. The Influx analyser can be used to measure the properties of individual cells.
Influx Cell Sorter
A Influx Cell Sorter is a flow_cytometer_sorter manufactured by Cytopeia. It is a digital machine, with these laser options: Coherent 70, 90, 300 series water cooled lasers, solid state UV 355nm, Violet 408nm, Violet-Blue 479nm, Blue-488nm, Green-531nm, Red-635nm, Red-647nm. The sorting is multi-way, index, and proportional sorting. Filters and PMTs are used for all parameters (including forward light scatter), and up to 12 PMTs can be included. The Influx cell sorter can be used to measure, sort, and collect ndividual cells.
Influx Cell Sorter at TSRI Flow Cytometry Core Facility
interrogation_point
Interrogation point in BD FACS Calibur
Point within the fluidic subsystem at which the laser intersects the stream, illuminating the cells where they emit their fluorescence and scatter the light. The laser irradiates the cell at the interrogation point.
http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm, 2007-05-11
ion laser
2 Watt Lexel 88 Argon Ion laser
An ion laser is a gas laser which uses an ionized gas as its lasing medium.
jet_in_air_flow_chamber
A flow cell in which the cells are pinched off as droplets and allowed to drop through the air. The laser intersects with the cell in mid-air. A jet in air flow chamber allows the laser to intersect with the cells without any intermittent media other than air.
Jet-in-air flow chamber in DakoCytomation MoFlo high-speed cell sorter
krypton ion laser
A krypton-ion laser is an ion laser that uses krypton as the lasing medium. These lasers can emit at 468, 476, 482, 520, 531, 568, 647 (the most powerful line), and 676 nm all at once. They have much lower gain than argon lasers however.
Lexel 95L krypton laser
LactoScope C4
A LactoScope_C4 is a spectrophotometer with which the composition of milk and milk products is analysed via infrared technology. The LactoScope determines the amount of the constituents fat, protein, lactose and the total solids content with extreme accuracy.
LactoScope C4 Automatic Economical
laser
A laser (acronym for light amplification by the stimulated emission of radiation) is a light source that emits photons of the same characteristics in a coherent beam. A laser uses a solid, liquid or gaseous lasing medium, that contains molecules, of which some atoms have electrons that emit photons of the same frequency when falling back to their normal orbital after excitation (pumping) by external means A laser is the most common way to irradiate a cell in a flow cytometer.
A laser is the most common way to irradiate a cell in a flow cytometer.
light amplification by the stimulated emission of radiation
light source
A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics). Light sources may include one of a variety of lamps (e.g., xenon, halogen, mercury). Most light sources are operated from line power, but some may be powered from batteries. They are mostly used in endoscopic, microscopic, and other examination and/or in surgical procedures. The light source is part of the optical subsystem. In a flow cytometer the light source directs high intensity light at particles at the interrogation point. The light source in a flow cytometer is usually a laser.
Elizabeth M. Goralczyk
Olga Tchuvatkina
logarithmic voltage amplifier
A logarithmic voltage amplifier is an analog electronic circuit that puts out a voltage or current proportional to the voltage or current at its input, with logarithmic proportionality. In an analog system, the logarithmic voltage amplifier is used to present parameters with a high dynamic range on a more useful scale.
HLVA-100 logarithmic voltage amplifier developed by FEMTO Messtechnik, GmbH
long pass filter
750 LP filter
A long pass filter is an optical filter that passes high wavelengths of light but attenuates (or reduces) wavelengths lower than the cutoff frequency. A long pass filter with a cutoff of 500 nm would pass all wavelengths greater than 500 nm.
LSR2
A LSR2 is a sorter manufactured by Becton Dickinson. It features digital electronics, a solid state 488 nm blue laser and optionally can also have any combination of solid state UV (355 nm) and violet (405 nm) lasers and the a HeNe (633 nm) ion laser. The LSR2 has the filters and PMTs to work with 13 fluorescent parameters. The LSR II is one of the most common sorters in use.
LSR2 at TSRI Flow Cytometry Core Facility
Luminex 100
The Luminex 100 is a flow_cytometer_analyser manufactured by Luminex. It is a single laser system (575 nm) with avalanche photodiodes in red and infrared and a single PMT for fluorescence. The flow chamber is a square quartz cuvette.
Luminex 200
A Luminex_200 is a flow_cytometer_analyser manufactured by Luminex. The optical specifications are: Reporter laser: 532 nm, nominal output 10 - 15 mW, maximum 500 mW, frequency-doubled diode; mode of operation, continuous wave (CW). Classification laser: 635 nm, 9.1 __ 6%, maximum output 25 mW, diode; mode of operation, continuous wave (CW) Reporter detector: Photomultiplier tube, detection bandwidth of 565 - 585 nm Classification detector and doublet discriminator: Avalanche photo diodes with temperature compensation
MACS Quant
A MACS Quant is a flow_cytometer_analyser manufactured by Miltenyi. It uses digital electronics, and has three lasers of wavelengths 405 nm, 488 nm, and 635 nm. It has filters and detectors to collect 7 fluorescent parameters and 2 scatter parameters. The MACS Quant is an analyser usually used in research applications.
metal vapor laser
A metal vapor laser is a gas laser in which the lasing medium is metal vapor. A metal vapor laser can by used to irradiate cells in a flow cytometer.
Gold vapor laser, Helium-cadmium metal-vapor laser
mixed argon-krypton gas laser
A mixed argon krypton gas laser is an ion laser in which the lasing medium is a mixture of argon and krypton. A mixed argon-krypton laser can by used to irradiate cells in a flow cytometer.
argon-krypton laser in a cytometer
MoFlo
A MoFlo is a flow_cytometer_sorter manufactured by Dako Cytomation. It features digital electronics, the option to include several lasers (solid state 488 nm, 635 nm, and a 351 nm diode laser), and has the filtering and collection capacity for up to 10 flouresecent parameters. The MoFlo is an instrument that can be used to both analyze quantitatively and collect cells in a flowing medium.
MoFlo at TSRI Flow Cytometry Core Facility
multi-well plate
96 well plate, 48 multiwell plate
A particle deliver vessel. A multi-well plate is a vessel that can deliver multiple samples to a flow cytometer in a specified order. It must be used with a plate loader.
FG this is synonymous with microtiter plate
neodymium-YAG laser
A Neodymium-YAG (yttrium aluminum garnet) laser is a solid state laser in which the lasing medium is a solid rod of crystalline material pumped by a flash lamp or a diode laser. Typical output wavelengths are 355, 532, and 1064 nm. A neodymium-YAG laser can by used to irradiate cells in a flow cytometer.
Neodymium-YAG Laser in DURIP99 System
obscuration bar
Flow Cytometry: First Principles, by Alice Longobardi Givan, ISBN-10: 0471382248, ISBN-13: 978-0471382249
An obscuration bar is a an optical subsystem which is a strip of metal or other material that serves to block out direct light from the illuminating beam. The obscuration bar prevents the bright light scattered in the forward directions from burning out the collection device.
obscuration bar in a flow cytometer
optical filter
720 LP filter, 580/30 BP filter
An optical filter is an optical subsystem that selectively transmits light having certain properties (often, a particular range of wavelengths, that is, range of colours of light), while blocking the remainder. They are commonly used in photography, in many optical instruments, and to colour stage lighting Optical filters can be arranged to segregate and collect light by wave length.
optical subsystem
DS: Is 'subsystem' necessary or is 'optical_system' enough. Not sure its graph position since an optical subsystem is not necessarily an instrument, but more likely part of one.
Person: Daniel Schober
a device or part of a device that deals with the behavior and properties of light and the interaction of light with matter. Commonly optical subsystems consist of an excitation optics and collection optics. The excitation optics of a flow cytometer optical subsystem consist of the laser and lenses that are used to shape and focus the laser beam. The collections optics consist of a collection lens to collect light emitted from the particle laser beam interaction and a system of optical mirrors and filters to route specified wavelengths of the collected light to designated optical detectors. The optical subsystem in a flow cytometer consists of the equipment used to irradiate particles, and collect the light either emitted or scattered by those particles.
optical subsystem of a cytometer
particle delivery vessel
FC 500 particle delivery vessel
FG: this should be delted - particle delivery is a role that an object can play
Part of the fluidics subsystem. A particle delivery vessel is used to introduce either a single sample or multiple samples to a flow cytometer. The most common particle delivery vessel is a sample tube.
photodetector
A photodetector is a device used to detect and measure the intensity of radiant energy through photoelectric action. In a cytometer, photodetectors measure either the number of photons of laser light scattered on impact with a cell (for example), or the flourescence emitted by excitation of a fluorescent dye.
A photomultiplier tube, a photo diode
photodiode
A photodiode is a semiconductor photodetector used to detect light and generate an electrical current. Typically used in forward scatter (FSC) detection. The photodiode collects the forward light scatter in a cytometer.
Avalanche photodiode
photomultiplier tube
A photomultiplier is a device that is normally in the form of a tube, that uses a photocathode to convert photons into photoelectrons which are then amplified. PMTs are typically used to detect SSC and fluorescent parameters. Cytometers have a PMT for each color they can collect.
R9647 by manufactured by Hamamatsu
piezo electric crystal
think this is natural thing, not a device HP/JF
Apparatus in the fluidic subsystem of sorters that vibrates to break up the stream coming out of the flow chamber into droplets for sorting. The peizo electric crystal vibrates in a manner that breaks off droplets at regular intervals. Not all droplets contain a cell.
quartz piezoelectric crystal, topaz piezoelectric crystal, piezoelectric crystal in a sonar
plate loader
measurement function is not corret as discussed on April 26 dev call. Will add new function such as positioning function. Add to tracker will discuss in the future.
FC 500 plate loader
Part of the fluidics system. A plate loader positions the wells of a multi-well plate under the aspiration tube is a preset order. A plate loader is used for high throughput applications.
preamplifier
A preamplifier is part of the electronics subsystem. It converts the current output from its associated detector to a voltage. The preamplifier is the first stage in analog electronics signal processing.
Built in preamplifier in a Hamamatsu H9656 PMT
quartz cuvette flow chamber
A flow cell in which the laser irradiates the cell as it passes through a quartz cuvette. A quartz cuvette flow chamber can be used to allow the laser to irradiate cells.
CVF-Q-10 flow chamber, CV-Q-10 flow chamber
Reflection
A Reflection is a sorter manufactured by iCyte. It uses digital signal processing, and can be configured with lasers of the users choice from among these excitation wavelengths: 355, 405,488, 532, 635nm. It accommodates up to 48 traditional PMTs. Options include an acousto-optical tunable filter (AOTF) and 16 channel spectrometer (370 to 730 nm). The various detection components can be uniquely configured across multiple Highly Automated Parallel Sorting (HAPS) modules. The Reflection can be used to analyse, sort, and collect cells.
Reflection at TSRI Flow Cytometry Core Facility
cytometer sample tube
A particle delivery vessel. The cytometer sample tube is a vessel in which the sample is introduced to the cytometer. Frequently the tube is placed on the cytometer in such a manner that a seal is formed between the tube and cytometer, and gas is used to create enough pressure to push the sample out of the tube and into the cytometer.
sample tube in a cytometer
sheath tank
LSR2 sheath tank
Part of the fluidics system. The sheath tank is the vessel that holds the sheath fluid at a constant pressure, allowing for it to be pushed into the flow chamber at a constant rate. The sheath tank holds the pressurized sheath fluid.
short pass filter
620 SP filter
A short pass filter is an optical filter that passes low wavelengths of light but attenuates (or reduces) wavelengths higher than the cutoff frequency. A short pass filter with a cutoff of 500 nm would pass all wavelengths less than 500 nm.
solid state laser
A solid-state laser is a laser that uses a lasing medium that is a solid, rather than a liquid such as dye lasers or a gas such as gas lasers. Semiconductor-based diode lasers are also in the solid state, but are generally considered separately from solid-state lasers. The first laser developed was an optical pumped ruby crystal solid state laser.
Solid State Heat Capacity Laser developed at DOE's Lawrence Livermore National Laboratory for the USA Army's Space and Missile Defense Command
Somacount
A Somacount is a flow_cytometer_analyser manufactured by Bently Instruments. It is a specialized tool for counting somatic cells in milk by specifically staining them with Ethidium Bromide and counting the cells that fluoresce. It has one laser, and the filters and a PMT for the single parameter. There are three sizes available, the 150, 300, and 500 with the number indicating the maximum number of cells that can be analysed per hour. The Somacount is an example of a very specific use cytometer; it exclusively counts somatic cells in milk.
SomaScope
"http://www.aicompanies.com/DeltaCD/soma_auto_adv.htm, 2007-05-10"
SomaScope Mark II Automatic Economical
The SomaScope is an instrument to quantify somatic cells in milk.
flow cytometer sorter
A flow_cytometer_sorter is a flow_cytometer that analyzes and separates or sorts particles passing through (based on properties measured during analysis) to collect cells of interest.
BioSorter2000, LSR2
syringe pump
NE-1000 Single Syringe Pump
Part of the fluidics system. A syringe pump can be used to inject the sample fluid and cells into the sheath fluid in the flow chamber. Syringe pumps are useful for creating stable flow rates.
http://www.answers.com/topic/syringe, 2007-05-11
voltage amplifier
A voltage amplifier is a device that amplifies the voltage signal.
Linear amplifier, log amplifier, microwave amplifier
waste tank
LSR2 waste tank
Part of the fluidics systems. In analyzers the sheath and sample fluid, once analyzed is dumped into a waste tank. The waste tank is where the fluids passing through the cytometer end up after the analysis is finished.
DNA sequencer
A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
ABI 377 DNA Sequencer, ABI 310 DNA Sequencer
array scanner
An processed material which acquires images of fluorescence (induced with lasers) from labeled molecules on the surface of the microarray chip
GenePix 4200A, GenePix4000B
arrayer
BioRobotics Microgrid II TAS, Affymetrix GMS 417
MO_697 arrayer
a device which deposits biological material onto a substrate in a defined pattern.
centrifuge
A device with a rapidly rotating container that applies centrifugal force to its contents
computer
A computer is an instrument which manipulates (stores, retrieves, and processes) data according to a list of instructions.
Apple PowerBook, Dell OptiPlex
heating block
A heating block is an instrument or part of an instrument which raises or maintains the temperature of a sample to a defined constant temperature during certain parts of an assay
An instrument used to heat and/or maintain material at a set temperature.
homogenizer
A homogenizer is an instrument for the homogenization of various types of material, such as tissue, plant, food, soil, and many others.
mortar, blender
hybridization chamber
A device which is used to maintain constant contact of a liquid on an array. This can be either a glass vial or slide.
Glass Array Hybridization Cassette
MO_563 hybridization_chamber
hybridization station
A device which is used to maintain the temperature of one or more hybridization_chamber(s) at a defined, constant temperature.
Labnet Problot12
MO_497 hybridization station
liquid handler
Beckman BioMek 2000
DS: Is this class justified? Its a unnamed class. If so, put a fluidic_system and the fluidic_subsystem as subclasses. TW: This is required by MO. FG & DS: Capture as function. All: Needs to be reviewed, according to query use case. If we keep it its kept as unnamed owl class. The liquid handling class remains but as an undefined class with are unlikely to have children. It is expected that the reasoner would classifiy appropriate classes under this class that meet the have the liquid_handling function relation.
DS: Is this class justified? Its a unnamed class. If so, put a fluidic_system and the fluidic_subsystem as subclasses. TW: This is required by MO. FG: Or as function.
MO_868 liquid_handler
a device that is used for automated liquid transfer and handling.
liquid_handling_instrument
oligonucleotide synthesizer
An instrument used to chemically synthesize oligonucleotides.
Automated Multiplex Oligonucleotide Synthesizer
sonicator
An instrument that converts a variable electrical current to mechanical vibration of a metallic probe. The instrument is used for the lysis of cells, the mixing of compounds or solutions, or to create emulsions.
Sonicator 3000
spectrophotometer
A spectrophotometer is an instrument that measures the intensity of light as a function of the color, or more specifically, the wavelength of light, transmitted by a substance.
Helios Gamma Spectrophotometer
thermal cycler
An instrument that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time.
DNA_amplifier
PCR_machine
Piko(tm) 96-well Thermal Cycler
Polymerase_Chain_Reaction_ machine
thermocycler
vacuum dryer
An instrument which removes liquid by the application of negative pressure, i.e. vacuum.
Model 777 Microarray Oven
vortexer
A vortexer is an instrument that mixes small vials of liquid by creating a rotation of the liquid around its own center. It consists of an electric motor with the drive shaft oriented vertically and attached to a cupped rubber piece mounted slightly off-center. As the motor runs the rubber piece oscillates rapidly in a circular motion. When a test tube or other appropriate container is pressed into the rubber cup (or touched to its edge) the motion is transmitted to the liquid inside and a vortex is created.
VWR Genie 2
vortex_mixer
microarray wash station
ArrayIt(r) Microarray Wash Station
MO_626 wash_station
a device that is used to wash Affymetrix-type arrays.
temperature control bath
A temperature_control_bath is a device that has the function to regulate the temperature of a material, the function to contain fluid and the function to vary and maintain the temperature of the contained fluid. Heat exchange (energy transfer) between the material and the heating element is facilitated via the contained fluid. A temperature_control_bath is composed of a container, a heating element and/or a cooling element and a means to adjust the needed temperature. In most cases also a timer and a means to stir the fluid is provided as well.
DS: This was heated_bath. It was renamed to reflect the possability that the same bath can be used for cooling. We can now define the temperature variables and based on that infer if it is a cooling device or a heating device (also quite relative to surrounding temperature).
VWR Signature Deep-Chamber Heated Water Bath. A water bath is used for temperatures up to 100 degrees C. An oil bath is employed for temperatures over 100 degrees C.
molecular crosslinker
AL: if we intend that other ontologies can be used in conjunction with OBI, we shouldn't have such a general term used specifically for chemically joining two or more molecules. I'm sure there are other "crosslinkers" that are on a much different scale in engineering etc. I have moved the original label to be an alternative term, and have renamed the main label accordingly.
MO ?? cannot be found in MO
Stratalinker
a device that is able to chemically join two or more molecules.
image cytometer
An image_cytometer is an instrument for image-based study or measurement of cells.
The most common current application of image cytometry is for DNA analysis, followed by quantitation of immunohistochemical staining.
cytometer
A cytometer is an instrument for counting and measuring cells.
gel tank
CHEF gel box, slab gel box, capillary electrophoresis
Person:Kevin Clancy
a device which holds a gel and running buffers to allow electrophoresis to be performed. A gel tank has the function to contain and to control the contained environment and transfer energy from an energy supply through the running buffers to the gel matrix and the material with charged molecules in an electric field across a porous matrix or medium with the objective to separate the charged molecules.
electrophoresis box
electrophoresis unit
A AC/DC transformer that generates the reqired power for an electrophoresis apparatus
A power supply is an device or part of a device that permits the required application of a defined electrical charge to an instrument. The power supply may permit the defined application of a given amount of current for a defined length of time.
PERSON: Daniel Schober
PSU
electrical power supply
power pack
power supply unit
was power_pack, maps to SEP electrical_power_supply
fluorometer
A fluorometer is an instrument for the detection and measurement of parameters of fluoresence, which in turn are used to identify the presence and amount of specific molecules in the sample.
Kevin Lister
laser/detector in capillary electrophoresis apparatus, NanoDrop ND-3300
multispectral imaging flow cytometer
A multispectral_imaging_flow_cytometer is an instrument which combines quantitative image analysis and flow cytometry in a single platform. It measures the amount, location and movement of molecules on, in, or between cells, and the location and co-localization of multiple markers on or in cells. It can also quantitate morphologically distinct cell subpopulations.
MIFC
microarray
An affymetrix U133 array is a microarray. Microarrays include 1 and 2-color arrays, custom and commercial arrays (e.g, Affymetrix, Agilent, Nimblegen, Illumina, etc.) for expression profiling, DNA variant detection, protein binding, and other genomic and functional genomic assays.
A processed material that is made to be used in an analyte assay. It consists of a physical immobilisation matrix in which substances that bind the analyte are placed in regular spatial position.
DNA microarray
A DNA-microarray is a microarray that is used as a physical 2D immobilisation matrix for DNA sequences. DNA microarray-bound DNA fragments are used as targets for a hybridising probed sample.
DNA Chip
DNA-array
Moran G, Stokes C, Thewes S, Hube B, Coleman DC, Sullivan D (2004). "Comparative genomics using Candida albicans DNA microarrays reveals absence and divergence of virulence-associated genes in Candida dubliniensis". Microbiology 150: 3363-3382. doi:10.1099/mic.0.27221-0. PMID 15470115
protein microarray
A protein-microarray is a microarray, ususlly a piece of glass, on which different molecules of protein have been affixed at separate locations in an ordered manner. These are used to identify protein-protein or protein-small molecule interactions.
The most common protein microarray is the antibody microarray, where antibodies are spotted onto the protein chip and are used as capture molecules to detect proteins from cell lysate solutions.
droplet sorter
A droplet sorter is part_of a flow cytometer sorter that converts the carrier fluid stream into individual droplets, and these droplets are directed into separate locations for recovery (enriching the original sample for particles of interest based on qualities determined by gating) or disposal.
water bath
A water bath is a temperature control bath in which a water acts as contact medium enabling temperature transfer from the heating element or cooling element to the sample. The temperature can be controlled in the 0 to 100 degree centigrade range (under normal pressure).
A water bath was used to allow for cell incubation at 38 degree centigrade for 8 hours.
oil bath
An oil bath is a temperature control bath in which oil acts as contact medium for the temperature transfer (from heating or cooling elements to the sample).
An oil bath was used to allow for fast reaction of two chemical compounds during a 2 hour period.
digital-to-analog converter
A digital-to-analog_converter is an instrument that converts a finite resolution digital signal into an infinite resolution analog signal.
A digital-to-analog_converter is used to convert a computergenerated discrete signal into a continuous analog one, e.g. a sound.
microtome
A microtome is a mechanical instrument used to cut biological specimens into very thin segments for further treatment (e.g. ISH) and ultimately microscopic or histologic examination. Most microtomes provide cooling facilities (cryo-microtome) and use a steel blade to cut a slice of defined thickness. Some are automatic, and some are driven by hand.
PMID: 9974145.Serial sectioning of thick tissue with a novel vibrating blade microtome. Brain Res Brain Res Protoc. 1999 Jan;3(3):302-7.
microscope
A microscope is an instrument which magnifies the view on objects (too small to be viewed by the naked eye) under increased resolution. A microscope can be an optical instrument but also and electronic instrument. There are various kind of optical microscopes, e.g confocal microscope, epifluoresence microscope)
PMID:18466942. A light and transmission electron microscope study of hepatic portal tracts in the rhesus monkey (Macacus rhesus). Tissue Cell. 2008 May 6
microscope slide
PMID: 9668975.Microscope slide for enhanced analysis of DNA damage using the comet assay.
a microscope slide is a device usually made of glass which is used as a solid matrix for (biological) material deposited on its surface and which is compatible for use with a microscope instrument
animal cage
PMID: 18246864.Barthold SW.Effects of cage density on behavior in young adult mice.
a processed material which has the function to define a bounded habitat which is amenable to keeping animals.
laboratory cage
study design
A study design is a plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available.
a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design.
experimental design
rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol.
clinical study design
Clinical Research Glossary Version 4.0 CDICS glossary group
PMID: 17655677.J Cardiovasc Electrophysiol. 2007 Aug;18(9):965-71.Biventricular versus right ventricular pacing in patients with AV block (BLOCK HF): clinical study design and rationale.
Plan for the precise procedure to be followed in a clinical trial, including planned and actual timing of events, choice of control group, method of allocating treatments, blinding methods; assigns a subject to pass through one or more epochs in the course of a trial. Specific design elements, e.g., crossover, parallel; dose-escalation [Modified from Pocock, Clinical Trials: A Practical Approach]
The definition needs to be extended to other things than simply patients
repeated measure design
PMID: 10959922.J Biopharm Stat. 2000 Aug;10(3):433-45.Equivalence in test assay method comparisons for the repeated-measure, matched-pair design in medical device studies: statistical considerations.
a study design which use the same individuals and exposure them to a set of conditions. The effect of order and practice can be confounding factor in such designs
cross over design
(source: http://www.sbu.se/Filer/Content0/publikationer/1/literaturesearching_1993/glossary.html)
PMID: 17601993-Objective: HIV-infected patients with lipodystrophy (HIV-lipodystrophy) are insulin resistant and have elevated plasma free fatty acid (FFA) concentrations. We aimed to explore the mechanisms underlying FFA-induced insulin resistance in patients with HIV-lipodystrophy. Research Design and Methods: Using a randomized placebo-controlled cross-over design, we studied the effects of an overnight acipimox-induced suppression of FFA on glucose and FFA metabolism by using stable isotope labelled tracer techniques during basal conditions and a two-stage euglycemic, hyperinsulinemic clamp (20 mU insulin/m(2)/min; 50 mU insulin/m(2)/min) in nine patients with nondiabetic HIV-lipodystrophy. All patients received antiretroviral therapy. Biopsies from the vastus lateralis muscle were obtained during each stage of the clamp. Results: Acipimox treatment reduced basal FFA rate of appearance by 68.9% (52.6%-79.5%) and decreased plasma FFA concentration by 51.6 % (42.0%-58.9%), (both, P < 0.0001). Endogenous glucose production was not influenced by acipimox. During the clamp the increase in glucose-uptake was significantly greater after acipimox treatment compared to placebo (acipimox: 26.85 (18.09-39.86) vs placebo: 20.30 (13.67-30.13) mumol/kg/min; P < 0.01). Insulin increased phosphorylation of Akt (Thr(308)) and GSK-3beta (Ser(9)), decreased phosphorylation of glycogen synthase (GS) site 3a+b and increased GS-activity (I-form) in skeletal muscle (P < 0.01). Acipimox decreased phosphorylation of GS (site 3a+b) (P < 0.02) and increased GS-activity (P < 0.01) in muscle. Conclusion: The present study provides direct evidence that suppression of lipolysis in patients with HIV-lipodystrophy improves insulin-stimulated peripheral glucose-uptake. The increased glucose-uptake may in part be explained by increased dephosphorylation of GS (site 3a+b) resulting in increased GS activity.
a repeated measure design which ensures that experimental units receive, in sequence, the treatment (or the control), and then, after a specified time interval (aka *wash-out periods*), switch to the control (or treatment). In this design, subjects (patients in human context) serve as their own controls, and randomization may be used to determine the ordering which a subject receives the treatment and control
n-to-1 design
Adapted from http://www.childrens-mercy.org/stats/definitions/crossover.htm and source:http://symptomresearch.nih.gov/chapter_6/sec1/csss1pg1.htm)
N-of-1 design is a cross-over design in which the same patient is repeatedly randomised to receive either the experimental treatment or its control (Senn, 1993).
matched pairs design
A matched pair design is a study design which use groups of individuals associated (hence matched) to each other based on a set of criteria, one member going to one treatment, the other member receiving the other treatment.
PMID: 17288613-BSTRACT: BACKGROUND: Physicians in Canadian emergency departments (EDs) annually treat 185,000 alert and stable trauma victims who are at risk for cervical spine (C-spine) injury. However, only 0.9% of these patients have suffered a cervical spine fracture. Current use of radiography is not efficient. The Canadian C-Spine Rule is designed to allow physicians to be more selective and accurate in ordering C-spine radiography, and to rapidly clear the C-spine without the need for radiography in many patients. The goal of this phase III study is to evaluate the effectiveness of an active strategy to implement the Canadian C-Spine Rule into physician practice. Specific objectives are to: 1) determine clinical impact, 2) determine sustainability, 3) evaluate performance, and 4) conduct an economic evaluation. METHODS: We propose a matched-pair cluster design study that compares outcomes during three consecutive 12-months before, after, and decay periods at six pairs of intervention and control sites. These 12 hospital ED sites will be stratified as teaching or community hospitals, matched according to baseline C-spine radiography ordering rates, and then allocated within each pair to either intervention or control groups. During the after period at the intervention sites, simple and inexpensive strategies will be employed to actively implement the Canadian C-Spine Rule. The following outcomes will be assessed: 1) measures of clinical impact, 2) performance of the Canadian C-Spine Rule, and 3) economic measures. During the 12-month decay period, implementation strategies will continue, allowing us to evaluate the sustainability of the effect. We estimate a sample size of 4,800 patients in each period in order to have adequate power to evaluate the main outcomes. DISCUSSION: Phase I successfully derived the Canadian C-Spine Rule and phase II confirmed the accuracy and safety of the rule, hence, the potential for physicians to improve care. What remains unknown is the actual change in clinical behaviors that can be affected by implementation of the Canadian C-Spine Rule, and whether implementation can be achieved with simple and inexpensive measures. We believe that the Canadian C-Spine Rule has the potential to significantly reduce health care costs and improve the efficiency of patient flow in busy Canadian EDs.
parallel group design
A parallel group design or independent measure design is a study design which uses unique experimental unit each experimental group, in other word no two individuals are shared between experimental groups, hence also known as parallel group design. Subjects of a treatment group receive a unique combination of independent variable values making up a treatment
PMID: 17408389-Purpose: Proliferative vitreoretinopathy (PVR) is the most important reason for blindness following retinal detachment. Presently, vitreous tamponades such as gas or silicone oil cannot contact the lower part of the retina. A heavier-than-water tamponade displaces the inflammatory and PVR-stimulating environment from the inferior area of the retina. The Heavy Silicone Oil versus Standard Silicone Oil Study (HSO Study) is designed to answer the question of whether a heavier-than-water tamponade improves the prognosis of eyes with PVR of the lower retina. Methods: The HSO Study is a multicentre, randomized, prospective controlled clinical trial comparing two endotamponades within a two-arm parallel group design. Patients with inferiorly and posteriorly located PVR are randomized to either heavy silicone oil or standard silicone oil as a tamponading agent. Three hundred and fifty consecutive patients are recruited per group. After intraoperative re-attachment, patients are randomized to either standard silicone oil (1000 cSt or 5000 cSt) or Densiron((R)) as a tamponading agent. The main endpoint criteria are complete retinal attachment at 12 months and change of visual acuity (VA) 12 months postoperatively compared with the preoperative VA. Secondary endpoints include complete retinal attachment before endotamponade removal, quality of life analysis and the number of retina affecting re-operation within 1 year of follow-up. Results: The design and early recruitment phase of the study are described. Conclusions: The results of this study will uncover whether or not heavy silicone oil improves the prognosis of eyes with PVR.
independent measure design
randomized complete block design
A randomized complete block design is_a study design which assigns randomly treatments to block. The number of units per block equals the number of treatment so each block receives each treatment exactly once (hence the qualifier 'complete'). The design was originally devised from field trials used in agronomy and agriculture. The analysis assumes that there is no interaction between block and treatment. The method was then used in other settings So The randomised complete block design is a design in which the subjects are matched according to a variable which the experimenter wishes to control. The subjects are put into groups (blocks) of the same size as the number of treatments. The members of each block are then randomly assigned to different treatment groups.
http://www.stats.gla.ac.uk/steps/glossary/anova.html,(A researcher is carrying out a study of the effectiveness of four different skin creams for the treatment of a certain skin disease. He has eighty subjects and plans to divide them into 4 treatment groups of twenty subjects each. Using a randomised blocks& design, the subjects are assessed and put in blocks of four according to how severe their skin condition is; the four most severe cases are the first block, the next four most severe cases are the second block, and so on to the twentieth block. The four &members of each block are then randomly assigned, one to each of the four treatment groups. http://www.stats.gla.ac.uk/steps/glossary/anova.html#rbd))
balanced incomplete block design
PMID: 7622388.Health Educ Q. 1995 May;22(2):201-10.Balanced incomplete block design: description, case study, and implications for practice.
balanced incomplete block design is a kind of factorial design where all treatment pairs occur together within a block an equal number ?? times. ??ii' is the number of times treatment i occurs with i'
http://en.wikipedia.org/wiki/Block_design and http://www.stat.psu.edu/~jglenn/stat503/05_factorial/02_factorial_IBD.html
loop design
A loop experiment design is where labeled extracts are compared in consecutive pairs. synonym: circular design
MO_912
PMID: 12933549
Philippe Rocca-Serra on behalf of MO
reference design
A reference experiment design type is where all samples are compared to a common reference.
MO_699
latin square design
Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and
Latin square design is_a study design which allows in its simpler form controlling 2 levels of nuisance variables (also known as blocking variables).he 2 nuisance factors are divided into a tabular grid with the property that each row and each column receive each treatment exactly once.
PMID: 17582121-Our objective was to examine the effects of dietary cation-anion difference (DCAD) with different concentrations of dietary crude protein (CP) on performance and acid-base status in early lactation cows. Six lactating Holstein cows averaging 44 d in milk were used in a 6 x 6 Latin square design with a 2 x 3 factorial arrangement of treatments: DCAD of -3, 22, or 47 milliequivalents (Na + K - Cl - S)/100 g of dry matter (DM), and 16 or 19% CP on a DM basis. Linear increases with DCAD occurred in DM intake, milk fat percentage, 4% fat-corrected milk production, milk true protein, milk lactose, and milk solids-not-fat. Milk production itself was unaffected by DCAD. Jugular venous blood pH, base excess and HCO3(-) concentration, and urine pH increased, but jugular venous blood Cl- concentration, urine titratable acidity, and net acid excretion decreased linearly with increasing DCAD. An elevated ratio of coccygeal venous plasma essential AA to nonessential AA with increasing DCAD indicated that N metabolism in the rumen was affected, probably resulting in more microbial protein flowing to the small intestine. Cows fed 16% CP had lower urea N in milk than cows fed 19% CP; the same was true for urea N in coccygeal venous plasma and urine. Dry matter intake, milk production, milk composition, and acid-base status did not differ between the 16 and 19% CP treatments. It was concluded that DCAD affected DM intake and performance of dairy cows in early lactation. Feeding 16% dietary CP to cows in early lactation, compared with 19% CP, maintained lactation performance while reducing urea N excretion in milk and urine.
graeco latin square design
Greco-Latin square design is a study design which relates to Latin square design
PMID: 6846242-Beaton et al (Am J Clin Nutr 1979;32:2546-59) reported on the partitioning of variance in 1-day dietary data for the intake of energy, protein, total carbohydrate, total fat, classes of fatty acids, cholesterol, and alcohol. Using the same food intake data and the expanded National Heart, Lung and Blood Institute food composition data base, these analyses of sources of variance have been expanded to include classes of carbohydrate, vitamin A, vitamin C, thiamin, riboflavin, niacin, calcium, iron, total ash, caffeine, and crude fiber. The analyses relate to observed intakes (replicated six times) of 30 adult males and 30 adult females obtained under a paired Graeco-Latin square design with sequence of interview, interviewer, and day of the week as determinants. Neither sequence nor interviewer made consistent contribution to variance. In females, day of the week had a significant effect for several nutrients. The major partitioning of variance was between interindividual variation (between subjects) and intraindividual variation (within subjects) which included both true day-to-day variation in intake and methodological variation. For all except caffeine, the intraindividual variability of 1-day data was larger than the interindividual variability. For vitamin A, almost all of the variance was associated with day-to-day variability. One day data provide a very inadequate estimate of usual intake of individuals. In the design of nutrition studies it is critical that the intended use of dietary data be a major consideration in deciding on methodology. There is no ideal dietary method. There may be preferred methods for particular purposes.
only 2 articles in pubmed ->probably irrelevant
hyper graeco latin square design
PRS to do
no example found in pubmed->not in use in the community
factorial design
factorial design is_a study design which is used to evaluate two or more factors simultaneously. The treatments are combinations of levels of the factors. The advantages of factorial designs over one-factor-at-a-time experiments is that they are more efficient and they allow interactions to be detected. In statistics, a factorial design experiment is an experiment whose design consists of two or more factors, each with discrete possible values or levels, and whose experimental units take on all possible combinations of these levels across all such factors. Such an experiment allows studying the effect of each factor on the response variable, as well as the effects of interactions between factors on the response variable.
http://www.stats.gla.ac.uk/steps/glossary/anova.html#facdes And from wikipedia (01/03/2007): http://en.wikipedia.org/wiki/Factorial_experiment)
2x2 factorial design
PMID: 17561240
PMID: 17561240-The present experiment evaluates the effects of intermittent exposure to a social stimulus on ethanol and water drinking in rats. Four groups of rats were arranged in a 2x2 factorial design with 2 levels of Social procedure (Intermittent Social vs Continuous Social) and 2 levels of sipper Liquid (Ethanol vs Water). Intermittent Social groups received 35 trials per session. Each trial consisted of the insertion of the sipper tube for 10 s followed by lifting of the guillotine door for 15 s. The guillotine door separated the experimental rat from the conspecific rat in the wire mesh cage during the 60 s inter-trial interval. The Continuous Social groups received similar procedures except that the guillotine door was raised during the entire duration of the session. For the Ethanol groups, the concentrations of ethanol in the sipper [3, 4, 6, 8, 10, 12, 14, and 16% (vol/vol)] increased across sessions, while the Water groups received 0% ethanol (water) in the sipper throughout the experiment. Both Social procedures induced more intake of ethanol than water. The Intermittent Social procedure induced more ethanol intake at the two highest ethanol concentration blocks (10-12% and 14-16%) than the Continuous Social procedure, but this effect was not observed with water. Effects of social stimulation on ethanol drinking are discussed.
a factorial design which has 2 experimental factors (aka independent variables) and 2 factor levels per experimental factors
fractional factorial design
A fractional factorial design is_a study design in which only an adequately chosen fraction of the treatment combinations required for the complete factorial experiment is selected to be run
http://www.itl.nist.gov/div898/handbook/pri/section3/pri334.htm From ASQC (1983) Glossary & Tables for Statistical Quality Control
dye swap design
An experiment design type where the label orientations are reversed. exact synonym: flip dye, dye flip
MO_858
PMID: 17411393-Dye-specific bias effects, commonly observed in the two-color microarray platform, are normally corrected using the dye swap design. This design, however, is relatively expensive and labor-intensive. We propose a self-self hybridization design as an alternative to the dye swap design. In this design, the treated and control samples are labeled with Cy5 and Cy3 (or Cy3 and Cy5), respectively, without dye swap, along with a set of self-self hybridizations on the control sample. We compare this design with the dye swap design through investigation of mouse primary hepatocytes treated with three peroxisome proliferator-activated receptor-alpha (PPARalpha) agonists at three dose levels. Using Agilent's Whole Mouse Genome microarray, differentially expressed genes (DEG) were determined for both the self-self hybridization and dye swap designs. The DEG concordance between the two designs was over 80% across each dose treatment and chemical. Furthermore, 90% of DEG-associated biological pathways were in common between the designs, indicating that biological interpretations would be consistent. The reduced labor and expense for the self-self hybridization design make it an efficient substitute for the dye swap design. For example, in larger toxicogenomic studies, only about half the chips are required for the self-self hybridization design compared to that needed in the dye swap design.
replicate design
A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments.
MO_885
self vs self design
A study design that investigates variance and error estimates in the experimental system, and is where the same extract is compared.
MO_490
time series design
Groups of assays that are related as part of a time series.
MO_887
PMID: 14744830-Microarrays are powerful tools for surveying the expression levels of many thousands of genes simultaneously. They belong to the new genomics technologies which have important applications in the biological, agricultural and pharmaceutical sciences. There are myriad sources of uncertainty in microarray experiments, and rigorous experimental design is essential for fully realizing the potential of these valuable resources. Two questions frequently asked by biologists on the brink of conducting cDNA or two-colour, spotted microarray experiments are 'Which mRNA samples should be competitively hybridized together on the same slide?' and 'How many times should each slide be replicated?' Early experience has shown that whilst the field of classical experimental design has much to offer this emerging multi-disciplinary area, new approaches which accommodate features specific to the microarray context are needed. In this paper, we propose optimal designs for factorial and time course experiments, which are special designs arising quite frequently in microarray experimentation. Our criterion for optimality is statistical efficiency based on a new notion of admissible designs; our approach enables efficient designs to be selected subject to the information available on the effects of most interest to biologists, the number of arrays available for the experiment, and other resource or practical constraints, including limitations on the amount of mRNA probe. We show that our designs are superior to both the popular reference designs, which are highly inefficient, and to designs incorporating all possible direct pairwise comparisons. Moreover, our proposed designs represent a substantial practical improvement over classical experimental designs which work in terms of standard interactions and main effects. The latter do not provide a basis for meaningful inference on the effects of most interest to biologists, nor make the most efficient use of valuable and limited resources.
stopping rule
PMID: 17591081-BACKGROUND/AIMS: To investigate the viral kinetics of Chinese CHC patients received pegylated interferon plus ribavirin and examine the impact of HCV genotypes and severity of liver disease. METHODOLOGY: 65 treatment-naove CHC patients who finished a 24-week therapy with peginterferon (alpha-2b (1.5 mcg/kg/week) plus ribavirin (1000-1200 mg /day) and 24 weeks of follow-up were enrolled. Hepatic fibrosis was graded by the METAVIR scoring system. Serum quantitative HCV RNA was determined by Versant HCV RNA 3.0 assay (Bayer Inc.). RESULTS: Genotype non-1 patients responded quickly and a higher percentage of them achieved undetectable HCV RNA (< 615 IU/mL) at week 4 compared with genotype 1 patients (93% vs. 69%, p = 0.018). Degree of hepatic fibrosis significantly affected end-of-treatment and sustained response (SVR). For patients who did not achieve early virological response (EVR), the negative predictive value for SVR was 100%. In genotype 1 patients, undetectable HCV RNA by week 4 was a good marker to predict treatment response, with a positive predictive value of 84% and a negative predictive value of 82%. CONCLUSIONS: EVR can be applied to Chinese patients as an early stopping rule. A 24-week duration of pegylated IFN/ribavirin might be adequate for genotype 1 patients who rapidly responded to therapy.
a stopping rule (criterion) is_a *rule* which causes a *stopping process* to happen
compliance rule
a compliance rule is a rule which ensures a compliance process occurs
standard compliance rule
a standard compliance rule is a compliance rule which defines conformity to a representation standard
ethical standard compliance rule
an ethical standard compliance rule is_a *compliance rule* which enable a *ethical compliance process* to occur
eligibility rule
Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group
PMID: 17579629 -Eligibility criteria included: untreated ED-SCLC; age >/=70 and performance status 0-2, or age <70 and PS 3.
an eligibility rule (criterion) is_a *rule* which defines the positive and negative criteria decide an entity to enter a study and that will define the population of the study
inclusion rule
PMID: 17599746-RESULTS: Fifteen trials met our inclusion criteria. The summary effect size was 0.35 (95% confidence interval 0.14, 0.56). I(2) was 0.80.
an inclusion rule (criterion) is_ rule* in a protocol that prospective subjects must meet to be eligible for participation in a study
exclusion rule
PMID: 17600285-Exclusion criteria included the use of any topical ophthalmic or topical oral medication and/or history of ocular or oral surgery within the past six months.
an exclusion rule (criterion) is_a *eligibility rule* prospective subjects should not meet to be eligible for participation in a study
adding substance to cell culture
renamed from 'administering substance to cell culture', to reflect that administration is commonly used only for organisms
adding fetal calf serum to a 96 well plate containing a cell culture derived from a blood sample of a patient
is process in which a material substance is added to a cell culture
tumor grading
Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney
Determination of the grade (severity/stage) of a tumor sample, used in cancer biology to describe abnormalities/qualities of tumor cells or tissues. Values can be described by terms from NCI Thesaurus.
OBI branch derived; submitted by MO
grading of tumor
performing a clinical assessment
(maybe CIO)
a protocol application during which a series of tests are made of a patient leading to determination of disease state, or condition.
human subject enrollment
As with group assignment, should the specified output here be an organism which bears a role
A process of obtaining informed consent from a person (or designated legal guardian of the person) who meets the study design criteria to participate in an investigation.
criteria come from plan / clinical trial branch
enlisting familiy members of HIV patients into a study
collecting specimen from organism
a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation
taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient
killing
A protocol application in which an organism is intentionally put to death
CEBS, Biomaterial_branch
Terminal sacrifice of animals by cervical dislocation at the end of an investigation.
death status type
difficult to place this properly - JG. Death process (e.g. unscheduled death) is out of scope but should be added somewhere. All killings have death process as a part, but not all death processes are part of a killing.
euthanisia
life termination
sacrifice
administering substance in vivo
2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893050&group_id=177891&atid=886178
A process by which a substance is intentionally given to an organism
Balb/c mice received an intracameral or subconjunctival injection of trinitrophenylated spleen cells
Different routes and means of administration should go as children underneath this
injecting mice with 10 ug morphine intranasally, a patient taking two pills of 1 mg aspirin orally
needs roles such as perturber and perturbee (children of input role). Perturb is too strong. Host might be the name for one role. Others considered: Doner, Donated, Acceptor.
acquisition
5/31/2012 - OBI workshop: This process is not implying ownership of the material / information.
Alan Ruttenberg: 2009/11/01 - probably a duplicate for object acquisition. https://sourceforge.net/tracker/?func=detail&aid=2890523&group_id=177891&atid=886178
Downloading a 3D structure from the PDB. Purchasing antibodies from sigma.
This needs to be fleshed out and logical definitions added that will allow to place the children terms automatically under acquisition
the process of gaining posession of a continuant
exposure of material to environment
Alan says there will be problmes, e.g. with selection by survival
Putting cells in a freezer at -80C. Cy5-labeled DNA is irradiated with a laser to excite the fluorophore. Inducing a phase transition in a material by putting it in an environment with a specific temperature. Oxygen deprivation in a chamber.
a planned process in which an input material is exposed to a defined set of conditions in a controlled environment. The environment is a specified input.
material acquisition
The assumption is that the object already exists in its current state, e.g, an available mouse strain purchased from the Jackson Lab, this is the differentia from specimen creation
Acquiring 50 C57BL/6 mice in the investigators animal facilities. Purchasing 1 mg of peptides synthesized by Mimotopes at 80% purity. Getting a gift of purified CD4+ specific antibodies presented by Stephen Schoenberger at LIAI.
Bjoern Peters, Alan Ruttenberg, Helen Parkinson
the process of gaining posession of a material entity
acclimatization
A protocol application in which an object is left in an environment for some period of time, until some qualities of interest are in equilibrium with that environment.
placing mice in animal facility for 2 weeks prior to an experiment to accustom them to their environment, reducing stress
environmental material collection
Bjoern Peters, Alan Ruttenberg
Taking 1 liter of surface ocean water from the San Diego Mission Bay Jetty. Capturing mice living in rural Arkansas
environmental_material_collection is an acquisition where an object is taken from an environment and put into a storage container. Roles include, environment, thing collected, container, acquirer.
the researcher is very interested in the location
information acquisition
Gathering all influenza HA sequences from GenBank, Retrieveing HLA allele frequencies in the North American populations from dbMHC
the process of gaining posession of information
material component separation
Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification
a material processing in which components of an input material become segregated in space
group assignment
Assigning' to be treated with active ingredient role' to an organism during group assignment. The group is those organisms that have the same role in the context of an investigation
OBI Plan
group assignment is a process which has an organism as specified input and during which a role is assigned
pooling specimens
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=104564; Combining spleens of 20 mice, Combining supernatant from a cell culture obtained at different time points
like' is one of the things that you should be controling for in a well-designed experiment. The instances of material need to have the same class.
physical combination of several instances of like material
sample pooling
detection of label
Determination of the amount of phycoerytherin label present in a cell population stained with anti-CD8-PE in order to determine the percentage of CD8+ T cells present
the detection of the amount of a label which is a proxy for the detection of the labeled biomaterial
material portioning
a material processing in which the input substance is partitioned into a number of portions that are similar in composition.
aliquoting
apportioning
pouring 50 mL aliquots of fetal calf serum into conical tubes from a 500 mL stock
non-specific labeling
The addition of a reagent labeling the entire input biomaterial enabling future detection of the output biomaterial
The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies.
definition blessed by Allyson, Bjoern, Jay & Randi
histology
PRS:20090901: addition of alternative term = histopathology
PERSON:Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney
need to incorporate parts\n---\nThis is a very vague term, it should be in the same place as transcriptomics, proteomics metaboloimcs. It is the 'study' of tissues, not the process of studying tissues\n
the counting of the number of cells with fluorescent label at their surface to determine the percentage of the population which was activated
the visual examination of cells or tissue (or images of them) with an assessment regarding a quality of the cells or tissue. Parts are: staining, imaging, judgement
cell fixation
a protocol application to preserve defined qualities of cells or tissues (sample) which may otherwise change over time
http://www.tissuearray.org/CellLinesProtocolforTMA112.pdf; the treatment of CD8+ cells with methanol at -20oC; http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=16080188&dopt=AbstractPlus
should include capturing what qualities are being preserved
we could generalize this for other input materials
excision
Alan Ruttenberg, Kevin Clancy
Cutting out the portion of a gel which contains a DNA fragment
the use physical means to remove a portion of a substance from the rest
www.crohnsresource.com/glossary.jsp (via google define:resection)
non specific enzymatic cleavage
PERSON:Kevin Clancy
The use of agarase to digest an agar gel
a protocol application to digest the fraction of input material that is susceptible to that enzyme
maintaining cell culture
When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture
a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing
substance detection
any protocol which results in the detection of a specified substance
the detection of phycoerytherin by means of flow cytometry
longitudinal mass measurement assay
A process in which the mass of a material is measured at two or more time points
The comparison of the weight of vaccinated and non-vaccinated mice after infection with influenza A over 6 weeks post-infection
artificially induced cell membrane lysis
---\nThere is a more general 'membrane lysis', which could apply to artificial membranes etc. For this general membrane encapsulated objects would need to be defined.
a material transformation to break the membranes of cells, releasing the cells contents; input=>cells; output=>cell_lysate
http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=16080188&dopt=AbstractPlus; The destruction of cell membranes with detergent.
artificially induced reverse transcription
It could also be added that the reverse transcriptase is bearer of a GO:0003964 RNA-directed DNA polymerase activity, which is realized in this process.
The use of M-MLV reverse transcriptase from the Moloney murine leukemia virus to transcribe an RNA sample into cDNA
We need to indicate the relationship between the cDNA generated and the RNA that was used as a template. This may be outside of the OBI scope
a protocol with the objective to transcribe single-stranded RNA into complementary DNA (cDNA)
isolation of cell culture supernatant
Pouring out a portion of the fluid part of an adherant cell culture growing in a flask.; The centrifugation of a T cell culture followed by aspiration of the supernatant while the cellular pellet remains in the centrifuge tube.
This does not apply to the case where the cells are lysed
a protocol which results in the separation of supernatant material from a cell culture
experimental disease induction
a protocol application to induce a specific disease in an organism
could be defined class
the injection of mice with LCM virus iv to establish an LCMV infection. Witholding food from animals to induce starvation syndrome.
ELISPOT assay
2/26/09: RESOLVE: we need to specify the produced substance that is desired to be detected. Analyte does not work, as this is not a concentration, and this is not present at the start of the assay.
An assay in which the number of cells producing a material in a larger cell population are stained and counted. This is done by visualizing and counting the number of spots present on a surface via an antibody specific for the produced material. Each spot represents one cell producing the material of interest.
Determination of the frequency of cells producing IFN-gamma in response to viral peptides by placing effector cells on a anti IFN-gamma coated plate, and adding antigen presenting cells pulsed with a peptide. After washing, the bound IFN-gamma is detected with a secondary antibody linked to a dye that visualizes as one spot per cell.
ELISPOT
artificially induced DNA repair
---\nis this really a protocol?\n--> This as several other protocol applications is also a natural process. The fact that it is induced experimetnally by following a protocol makes it a protocol application. Need to make sure that labels don't conflict wi
a protocol application to repair damaged DNA molecules
the use of DNA repair enzymes uracil DNA glycosylase and 3-methyladenine DNA glycosylase to repair DNA strands
cell permeabilization
A protocol application to permeabilize cell membranes, allowing molecules to more easily pass through the membrane than was possible prior to the protocol application
Electroporation of HeLa cells to allow transfection with pUC19.
definition blessed by Jay, Alan, Randi
need to add output cell has_quality permeable
precipitation
The use of ethanol to precipitate DNA molecules from a solution containing DNA
a protocol application to cause a material to precipitate (becoming a solid) out of solution. Input is a solution, output is a solution plus a solid component (the precipitate)
establishing cell culture
Effects of establishing cell cultures and cell culture conditions on the proliferative life span of human fibroblasts isolated from different tissues and donors of different ages. Exp Cell Res. 2002 Apr 1;274(2):275-87. PMID: 11900488 When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the establishing_cell_culture step comprises preparing the cells at a certain dilution and plating them in a container with growth medium.
establishing a cell culture is a process which results in creating an in vitro environment in which cells are sustained from input material containing cells. input: cell-containing material, output cell culture, part of cell culturing. Cells are originally plated at a certain concentration referred to as seeding density.
cell culture splitting
The act of taking a cell culture of high density, counting the cells, removing part of the cells, and re-seeding a select number of the cells into new flasks with fresh tissue culture media.
The act of taking part of a homogeneous cell culture and creating one or more additional separate cultures of similar qualities. input: cell_culture, output cell_culture min cardinality 2. part of cell culturing
labeling
The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies. The addition of anti-CD8-PE to a population of cells, to label the subpopulation cells that are CD8+.
the addition of a labeling reagent to an input biomaterial in order to detect the labeled material in the future
artificially induced methylation
A planned process of adding methyl groups to polymers
the use of enzymes to add methyl groups to DNA molecules
synthesis
This probably needs breaking down into more specific applications. The example given is already covered in reverse_transcription
making cDNA from nucleotides using RNA as a template
synthesize
the construction of a biomaterial from simpler biomaterials
concentrate
Evaporation of the solution containing DNA to increase the concentration of the DNA molecules
a protocol application to create an output material with an increased density of a material of interest that is part of the input material by separating other parts of the input material
recombinant plasmid cloning
The DNA fragment encoding the p35 gene from Mycobacterium avium complex was inserted into pcDNAII and expressed in E coli in order to study p35.
the insertion of a particular DNA fragment into a plasmid in order to make copies of a biomaterial
genetic transformation
The transduction of E. coli through the introduction of a plasmid encoding for M. avium p35
genetic modification
the introduction. alteration or integration of genetic material into a cell or organism
lavage
A protocol application to separate cells and/or cellular secretions from an anatomical space by the introduction and removal of fluid
This is not washing, in which case the material of interest is not the resulting fluid
the collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present
structure determination assay
The use of NMR Spectroscopy to determine the 3D-Structure of the binding of an epitope to an MHC molecule
a process that resulting in information on the 3-dimensional qualities of a biomaterial
preparative chromatography
PERSON:Kevin Clancy; Bjoern Peters
The use of gas chromatography in order separate out from an input sample of eggs a fraction that would be enriched for pesticides.
the use of a biomaterial's preferential affinity for either the mobile phase or the stationary phase to separate it from other materials of differing affinity
sequencing assay
The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template
has_output should be sequence of input; we don't have sequence well defined yet
the use of a chemical or biochemical means to infer the sequence of a biomaterial
vector mediated amplification
E coli expressing the gene for M avium p35 were cultured in order to produce p35.
The process of creating a copy of some biological entity in cell culture
DNA polymerase amplification
DNA polymerase amplification is an enzymatic amplification which uses DNA polymerase enzyme to make copies of a DNA contained in biomaterial used as input
The use of taq polymerase to amplify a DNA fragment during a PCR.
specific enzymatic cleavage
The use of a protease to digest a protein into peptides
gradient separation
a protocol application that uses different concentrations of materials in a defined order to create a gradient to facilitate the separation of an input material into its components with specific qualities
the use of a sucrose gradient to isolate mitochondria
dialysis
a protocol application that uses diffusion through a semi-permeable membrane to separate an input material into two fractions of different composition
the use of a dialysis bag of select pore size to remove salt from collagen isolated from mouse cartilage
electrophoresis
Loading a mixture of proteins into a polyacrylamide gel and the application of an electrical current to the gel to separate the proteins by size and change.
Need to define more terms like gel_separation, matrix,centrifugation, and the connection between the force used to separate materials and the medium or barriers.
a protocol application that uses an electrical potential to move material through a defined matrix in order to separate it by its resistance to movement and its charge
selection by survival
The insertion of a gene for antibiotic resistance into a cell population and subsequent growth in the presence of the antibiotic to select for those cells which were successfully transfected
the use of environmental conditions to select for the organism or cells that have a certain trait
DNA cleavage, restriction analysis
restriction enzyme assay
the use of enzymes to cut DNA molecules, the study of DNA through cleavage, mapping, and analysis of the fragments
the use of the restriction enzymes SalPI and PstI to cleave DNA into fragments, assay made up of components
protease cleavage
enzymatic digestion
protease cleavage is an enzymatic cleavage which relies on enzyme with protease activity to act on proteins and produce polypeptides (protein fragments).
the use of trypsin to cleave pepsin into peptide fragments
enzymatic DNA replication
the use of enzymes to duplicate DNA molecule any process used to make additional copies of a biomaterial
the use of enzymes to duplicate DNA molecules
enzymatic amplification
the use of a polymerase chain reaction to amplify a fragment of DNA
the use of enzymes to increase the number of molecules of a biomaterial
DNA transduction
The transfer of a recombinant bacterial plasmid into E.coli to facilitate amplification of a specific protein
a genetic transformation which relies on the use of lysogenic infection to transfer DNA sequences into an organism
DNA transfection
The use of electroporation to permeabilize a cell membrane in order to introduce a plasmid encoding for a labeled protein of interest
a transfection which relies on the use of physical, electrical and chemical phenomena to introduce DNA into a cell
vector mediated expression
Construction of pRSS1327 expression vector by molecular cloning of a 1327-bp cDNA, which includes sequences of the entire coding region for RSS, into pBluescript. Expression in Escherichia coli of a functional, full-length RSS was confirmed by immunoblot analysis and enzymatic activity.
needs defined relationship to cell culture
vector mediated expression sis the generation of copies of biomaterial by in a cell_culture modified for this purpose by insertion of an expression vector
recombinant vector cloning
a planned process with the objective to insert genetic material into a cloning vector for future replication of the inserted material
pa_branch (Alan, Randi, Kevin, Jay, Bjoern)
obsolete_defined processes
Place holder class, see editor note
Remove to simplify OBI release Discussed on 2012 Ann Arbor OBI wokshop
_defined processes
specific labeling
The addition of anti-CD8 antibody for an ICCS assay in order to selectively stain the CD8+ cells
a labeling in which the labeling reagent used has a specificity to bind only certain components of the input material
RNA extraction
A RNA extraction is a nucleic acid extraction where the desired output material is RNA
requested by Helen Parkinson for MO
nucleic acid extraction
Phenol / chlorophorm extraction disolvation of protein content folllowed by ethanol precipitation of the nucleic acid fraction over night in the fridge followed by centrifugation to obtain a nucleic acid pellet.
a material separation to recover the nucleic acid fraction of an input material
requested by Helen Parkinson for MO. Could be defined class
cell culture supernatant
Supernatant of a cell culture is a material entity which contains media, supplements, and secreted products of the cells and becomes the environment of cultivated cell.
solution containing RPMI, fetal calf sera, antibiotics, and monoclonal antibody UCHT1. Isolation of proliferation factor of immature T-cell clone in concanavalin A-stimulated splenocyte culture supernatant. Immunology. 2003 Jun;109(2):209-16. PMID: 12757615
cell pellet
A material entity which results from the aggregation of cells produced by the application of centrifugal force to a liquid containing cells in suspension
Detection of fetal DNA in a cell pellet after centrifugation of mountant. J Forensic Sci. 2003 Jan;48(1):135-6. PMID: 12570214
phage display library
PMID: 15905471.Nucleic Acids Res. 2005 May 19;33(9):e81.Oligonucleotide-assisted cleavage and ligation: a novel directional DNA cloning technology to capture cDNAs. Application in the construction of a human immune antibody phage-display library. [Phage display library encoding fragments of human antibodies. m-rna library encoding for 9-mer peptides]
WEB: http://www.immuneepitope.org/home.do
a phage display library is a collection of materials in which a mixture of genes or gene fragments is expressed and can be individually selected and amplified.
display library
cell lysate
The effect of vaccination with the lysate of heat-shocked tumor cells on nitric oxide production in BALB/c mice with fibrosarcoma tumor. Cell Biol Int. 2008 Jul;32(7):835-40. PMID: 18455932
PERSON: Susanna Sansone
PRS:22-02-2008: is a material which has output_role during lysis protocol-application. old defintion: A mixture (collection) of cell components created by rupturing of the cell wall resulting from a lysis process
a cell lysate is a material entity which is output of a cell lysis process
lysate
peptide construct
Multiple Antigenic Peptide (MAP) construct containing T and B cell epitopes from p. falciparum congugated to a central glycin A novel multivalent human CTL peptide construct elicits robust cellular immune responses in HLA-A*0201 transgenic mice: implications for HTLV-1 vaccine design. Vaccine. 2003 Jun 20;21(21-22):2767-81. PMID: 12798617
a material entity synthesized to contain a number of peptides conjugated together in a non-linear fashion
transgenic organism
HLA-A*0201 transgenic mice, Vaccinia virus expressing the LCMV gp protein Possible ecological risks of transgenic organism release when transgenes affect mating success: sexual selection and the Trojan gene hypothesis. Proc Natl Acad Sci U S A. 1999 Nov 23;96(24):13853-6. PMID: 10570162
PRS:22-02-2008: is a organism which has output_role during genetic modification of type (KO) protocol-application
a transgenic organism is material entity which derives from an organism which has been modified to express a gene not normally part of it
whole mount tissue
A whole organism preparation resulting from a histological preparation known as whole mount preparation where the whole specimen is mounted or spread on the microscope (glass) slide
PRS:22-02-2008: indicates the need to create a protocol application and distinguish it from this entity
PRS:22-02-2008: is a material which has output_role during whole mount preparation protocol-application
whole mount sample
bead
A globular or round particle of defined physicochemical properties and size which can be exploited as either the primary substance for detection or as a secondary solid platform for the attachment of bioactive molecules.
DS: Probably better modeled as a role.
Dynabeads are commercially available magnetic beads which are precoated with antibodies specific for select cellular receptors and are used to separate cell populations.
epitope
a material entity bearing the epitope role
obsolete_occurrence of disease
An occurrence of disease is a process involving pathologic changes within an organism
replaced by http://purl.obolibrary.org/obo/OGMS_0000022 'disease course' Details see https://sourceforge.net/tracker/?func=detail&aid=3515228&group_id=177891&atid=886178
host exposure to infectious agent
a process in which an infectious agent comes into physical contact with a host organism.
administration in vivo with infectious agent
is an administration of an infectious agent to a host organism
occurrence of infectious disease
Is an occurrence of a disease caused by an infection
disposition to cause an allergic reaction
The role borne by a material entity that is realized when it is recognized by the immune system and results in the occurrence of an allergic disease.
allergic reaction
an allergic reaction is an pathologic immune response by an organism to a non-self entity that is normally harmless(the allergen)
occurrence of allergy
The process of an allergic disease occurring in an organism.
T cell epitope ELISPOT IL-2 assay
A T cell epitope specific cytokine production assay that measures production of IL-2 by T cells utilizing the ELISPOT methodology.
epitope binding by adaptive immune receptor
is the process in which an adaptive immune receptor binds to a material entity (realizing its disposition). The binding affinity is significant enough to trigger an immune response. Specifically, transient non-specific binding of adaptive immune receptors occurring during immune surveillance is not considered significant binding.
Immunization in vivo
Process of administering an object playing the role of immunogen to a living organism
adaptive immune effector function
A function realized as an immune response, which inheres in a T cell, B cell or antibody which derives from or is produced by a cell with prior antigen experience.
living with infected household contact
a process in which a a human being lives in the same household as another human being that is known to be infected with an infectious agent
living in endemic area
a process in which a potential host organism lives in a geographic area in which an infectious agent is present to such a degree of frequency that contact is likely
pathogen release in laboratory accident
a process in which a an infectious agent maintained in a laboratory setting is not contained as planned, leading to potential exposure of human beings to the agent
Immunization in vitro
Process of administering an object playing the role of immunogen to a cell culture
infection
the detrimental process in which an infectious agent colonizes or replicates in a host environment
adaptive immune receptor
is a receptor produced by cells of the adaptive immune system with the purpose of binding epitopes.
immunogen
a material entity bearing the immunogen role
environmental exposure to infectious agent
Is a process in which an infectious agent is in direct contact with a potential host organism in its habitat. This is preceded by proximity to the infectious agent
host of immune response
A mouse that is vaccinated with a peptide and develops protective immunity. A human exposed to bacteria that are killed by pre-existing immune responses.
In immune response processes in the context of infectious diseases and allergy, there are often multiple organisms involved, which requires calling out the 'host'. This terminology is expanded to allergy, cancer and transplantation.
An organism in which an immune response process occurs.
293-T cell culture
A cell line derived from human embryonic kidney cells. This cell line contains the SV40 Large T-antigen, allowing episomal replication of transfected plasmids containing the SV40 origin of replication.
C1R cell culture
A cell line derived from human B cells. This cell line was created by EBV transformation (B-lymphoblastoid cell-line (BLCL)).
experimental infection of cell culture
is the administration of an infectious agent to a cell culture with the objective to have the agent colonize and replicate in culture
EL-4 cell culture
A cell line derived from mouse (C57BL/6N) lymphoma cells.
HeLa cell culture
A cell line derived from human cervical cancer cells.
JAWS II cell culture
A cell line derived from mouse dendritic cells.
antigen
is a material entity that has the antigen role
Jurkat cell culture
JY cell culture
The JY cell line is an Epstein-Barr virus (EBV)-immortalised b cell lymphoblastoid line.(wikipedia)
T cell epitope recognition assay
An assay in which a positive measurement indicates TCR recognition of an epitope:MHC context. Inputs to the assay include: 1) the assay antigen which contains the epitope, 2) TCR molecules 3) restricting MHC molecules.
RMA cell culture
A cell line derived from a mouse lymphoma, specifically a Rauscher virus-induced tumor.This cell ine is antigen processing-defective and expresses a very low level of MHC molecules on its surface.
T2 cell culture
A human T-B lymphoblastoid hybrid cell line
infectious disease
is a disease caused by an infectious agent
lymph node cell
A mixed cell population obtained by processing whole lymph node into individual cells, typically performed using a sieve. This population includes T cells, B cells, macrophages, and other cell types.
adherent cell culture
A mixed cell population that is characterized by its ability to bind to tissue culture flasks or plates. This population typically contains macrophages and other cells capable of playing the antigen presenting cell role.
PBMC cell culture
A mixed cell population obtained by processing whole blood. The cells are characterized by having a similar density and are largely mononuclear cells (includes T cells, B cells, and other cell types).
disposition to be bound by an adaptive immune receptor
Is the disposition borne by a material entity that is realized in a process of being bound by a adaptive immune receptor.
organ harvesting
The process of removing an organ from its source organism
CD3+ T cell culture
A T cell population characterized by expressing the CD3 molecule on its surface.
CD3- T cell culture
A T cell population characterized by not expressing the CD3 molecule on its surface.
allergy
is a disease in which an abnormally strong inflammatory immune response is triggered against non-self entities, and the immune response has no protective effect
CD4- T cell culture
A T cell population characterized by not expressing the CD4 molecule on its surface.
CD8- T cell culture
A T cell population characterized by not expressing the CD8 molecule on its surface.
CD4-/CD8- T cell culture
A T cell population characterized by not expressing the CD4 nor the CD8 molecule on its surface.
cancer
A disease characterized by abnormal and uncontrolled cell division
autoimmune disease
Is a disease characterized by an immune response of an organism against parts of itself
disease
placeholder to be imported from disease ontology
epitope specific IL-2 release by T cells
A biological process where T cells produce IL-2 resulting from the recognition of a T cell epitope.
MHC:epitope complex binding to TCR
a process of an MHC molecule binding to an entity playing the role of epitope to create an MHC:epitope complex which is then bound by a TCR molecule.
T cell epitope ELISPOT IFN-g assay
A T cell epitope specific cytokine production assay that measures production of IL-IFNg by T cells utilizing the ELISPOT methodology.
exposure resulting in immune reactivity
a process in which an organism (host) is exposed to some material entity, which results in an immune reactivity
immunogen role
any entity capable of eliciting an immune response when introduced to components of the immune system
host of immune response role
03/21/2010: This sense of 'host' is used not only in infectious diseases but also allergy, cancer, transplantation, etc. which is why it is needed separately from the 'host of infectious agent' meaning, which will be imported from IDO.
is a role borne by an organism. It is realized by the organism during an immunization or an immune response taking place inside or on the surface of the organism, and in which the responding or stimulated immune system is part of the host.
effector T cell function
The function inhering in a T cell that is realized in an immune response that results from the T cell receptor binding to the MHC:epitope complex.
antigen presentation function
should add a reference to the antigen processing and presentation process.
APC
a function inhering in a cell that expresses MHC molecules which is realized in the process of antigen processing and presentation of antigen derived parts by MHC molecules on the cell surface.
restricting MHC role
The role played by an MHC molecule by binding a material entity playing the role of epitope when that epitope/MHC molecule pair are recognized (bound) by a TCR molecule on the surface of a cell playing the role of effector cell.
donor
Definition modified by HP to deal with the case where an organ may be removed for donation but is not transplanted as intended.
A role which inheres in an organism or part thereof from which any part including cell, organ or tissue is removed with the intention that the donated part will be placed into another organism and/or cultured in vitro.
immune epitope carrier role
03/21/2010, BP: surveying the literature, this seems to be a messy term. Need to clarify what material entities can be carriers, and if only immunogenicity (not antigenicity) is effected by their presence.
A role inhering in a material entity that is covalently bound to an epitope in order to increase the epitopes immunogenicity.
adjuvant role
Adjuvant role is a role that inheres in a material entity and which is realized through a process of modifying a biological response.
disposition to infect an organism
Is a role borne by an agent, and realized when in contact with or inside another organism in which it is capable of replicating and causing disease
immunization
Infection with influenza (the immunogen) leading to B cells producing antibodies (the effector function) against surface regions of the HA protein (the epitope).
The process of an epitope that is part of or derived from an immunogen coming into contact with adaptive immune cells resulting in these cells acquiring immune effector functions specific for the epitope.
blood harvesting
A material separation where blood is taken from an organism.
L cell culture
A cell line derived from mouse fibroblasts.
A culture of PBMCs. A culture of Hela cells.
a cell culture including cells that have an antigen presentation function
A cell culture including cells that have an effector T cell function
10/26/09: This defined class is used as a 'macro expression' to reduce the size of the IEDB export
2010/02/24 Alan Ruttenberg: I think this might generate confusion as the common use of the term would consider something to be a specimen during the realization of the role, not only if it bears it. However having this class as a probe, or for display, or as a macro might be useful. Ideally we would mark or segregate such classes
A mixture of peptides that is being added into a cell culture.
a material that is added to another one in a material combination process
10/26/09: This defined class is used as a 'macro' to reduce the size of the IEDB export.
A cell culture into which a mixture of peptides is being added.
A material entity into which another is being added in a material combinatino process
environmental proximity to infectious agent
Is a process in which an infectious agent comes close enough to a potential host organism in its habitat that a contact can result
contact to pathogen carrying biological vector
a process in which a vector carrying an infectious agent comes close enough to a potential host organism that a contact can result
splenocyte
A mixed cell population obtained by processing whole spleen into individual cells, typically performed using a sieve or blender. This population includes T cells, B cells, macrophages, and other cell types.
P815 cell culture
A cell line derived from mouse mastocytoma.
assay antigen role
Any molecule recognized by the adaptive immune receptors? Recognized means bound with a certain affinity? From GO ag binding:Interacting selectively 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. see OBI_1110120 below
pathologic process
abnormal, harmful processes caused by or associated with a disease
T cell TCR:epitope:MHC binding assay
Any assay that measures the binding of a TCR molecule to an epitope:MHC complex.
MHC ligand processing and presentation assay
an assay that determines what ligands are processed and loaded onto MHC molecules by eluting ligands and identifying them
MHC:ligand binding assay
an assay that measures the binding of a ligand to an MHC molecule
B cell epitope recognition assay
is an assay that measures the binding of an epitope to an antibody or B cell receptor, or an immune response process resulting from such a binding event
immune epitope assay
10/26/09, BP: Strictly speaking, the definition would exclude MHC ligand elution and binding assays. Need to either expand this definition in scope, or move out those subclasses.
is an assay that measures the binding of an epitope to an adaptive immune receptor or a immune response process resulting from such a binding event
T cell epitope specific cytokine production assay
Any assay that measures the production of a cytokine by T cells resulting from the recognition of a T cell epitope.
T cell epitope specific killing assay
Any assay that measures the killing of an antigen presenting cell (APC) by a T cell that occurs in response to TCR on that T cell binding an epitope:MHC complex on that APC.
T cell epitope specific proliferation assay
Any assay that measures the proliferation of a T cell that occurs in response to TCR on that T cell binding an epitope:MHC complex.
A transmembrane glycoprotein that serves as a co-receptor for the T cell receptor.
This term does not belong in ONTIE. It should be imported from PRO, but there seems to be no appropriate term as of 08/17/2009.
T cell epitope chromium release assay
Is a T cell epitope specific killing assay which utilizes radiolabeled chromium in order to measure T cell mediated lysis of antigen presenting cells that occurs in response to TCR on that T cell binding an epitope:MHC complex on the APC.
T cell epitope ELISA IFN-g assay
A T cell epitope specific cytokine production assay that measures production of IFNg by T cells utilizing the ELISA methodology.
T cell epitope ELISA IL-2 assay
A T cell epitope specific cytokine production assay that measures production of IL-2 by T cells utilizing the ELISA methodology.
T cell epitope ELISA IL-4 assay
A T cell epitope specific cytokine production assay that measures production of IL-4 by T cells utilizing the ELISA methodology.
T cell epitope ELISA IL-5 assay
A T cell epitope specific cytokine production assay that measures production of IL-5 by T cells utilizing the ELISA methodology.
T cell epitope ELISA TNF assay
A T cell epitope specific cytokine production assay that measures production of TNF by T cells utilizing the ELISA methodology.
T cell epitope ELISA IL-10 assay
A T cell epitope specific cytokine production assay that measures production of IL-10 by T cells utilizing the ELISA methodology.
T cell epitope ELISA GM-CSF assay
A T cell epitope specific cytokine production assay that measures production of GM-CSF by T cells utilizing the ELISA methodology.
T cell epitope ELISA IL-6 assay
A T cell epitope specific cytokine production assay that measures production of IL-6 by T cells utilizing the ELISA methodology.
T cell epitope ELISA IL-13 assay
A T cell epitope specific cytokine production assay that measures production of IL-13 by T cells utilizing the ELISA methodology.
T cell epitope ELISA IL-12 assay
A T cell epitope specific cytokine production assay that measures production of IL-12 by T cells utilizing the ELISA methodology.
T cell epitope ELISA IL-1b assay
A T cell epitope specific cytokine production assay that measures production of IL-1b by T cells utilizing the ELISA methodology.
T cell epitope ELISA IL-17 assay
A T cell epitope specific cytokine production assay that measures production of IL-17 by T cells utilizing the ELISA methodology.
T cell epitope ELISA IL-18 assay
A T cell epitope specific cytokine production assay that measures production of IL-18 by T cells utilizing the ELISA methodology.
T cell epitope ELISPOT IL-4 assay
A T cell epitope specific cytokine production assay that measures production of IL-4 by T cells utilizing the ELISPOT methodology.
T cell epitope ELISPOT TNF assay
A T cell epitope specific cytokine production assay that measures production of TNF by T cells utilizing the ELISPOT methodology.
T cell epitope ELISPOT IL-10 assay
A T cell epitope specific cytokine production assay that measures production of IL-10 by T cells utilizing the ELISPOT methodology.
T cell epitope ELISPOT IL-13 assay
A T cell epitope specific cytokine production assay that measures production of IL-13 by T cells utilizing the ELISPOT methodology.
T cell epitope intracellular cytokine staining (ICS) IFN-g assay
A T cell epitope specific cytokine production assay that measures production of IFN-g by T cells utilizing the ICS methodology.
T cell epitope intracellular cytokine staining (ICS) IL-2 assay
A T cell epitope specific cytokine production assay that measures production of IL-2 by T cells utilizing the ICS methodology.
T cell epitope intracellular cytokine staining (ICS) TNF assay
A T cell epitope specific cytokine production assay that measures production of TNF by T cells utilizing the ICS methodology.
T cell epitope intracellular cytokine staining (ICS) IL-4 assay
A T cell epitope specific cytokine production assay that measures production of IL-4 by T cells utilizing the ICS methodology.
T cell epitope intracellular cytokine staining (ICS) IL-10 assay
A T cell epitope specific cytokine production assay that measures production of IL-10 by T cells utilizing the ICS methodology.
T cell epitope intracellular cytokine staining (ICS) IL-17 assay
A T cell epitope specific cytokine production assay that measures production of IL-17 by T cells utilizing the ICS methodology.
T cell epitope MHC tetramer/multimer staining assay
An assay that measures MHC:epitope complex binding to TCR utilizing flow cytometry. The MHC molecules are prepared into multimers, loaded with epitope, and are fluorescently labeled in order to visualize the T cells that bind. The data that is generated provides information on the presence of epitope specific T cells in the cell population that was tested.
T cell epitope (3H-Thymidine) cell proliferation assay
T cell epitope specific proliferation assay that measures T cell proliferation utilizing the Thymidine incorporation assay.
T cell epitope (BrdU) cell proliferation assay
T cell epitope specific proliferation assay that measures T cell proliferation utilizing the BrdU incorporation assay.
epitope specific T cell proliferation
A biological process where T cells proliferate resulting from the recognition of a T cell epitope.
epitope specific GM-CSF release by T cells
A biological process where T cells produce GM-CSF resulting from the recognition of a T cell epitope.
epitope specific IFN-g release by T cells
A biological process where T cells produce IFNg resulting from the recognition of a T cell epitope.
epitope specific IL-10 release by T cells
A biological process where T cells produce IL-10 resulting from the recognition of a T cell epitope.
epitope specific IL-12 release by T cells
A biological process where T cells produce IL-12 resulting from the recognition of a T cell epitope.
epitope specific IL-13 release by T cells
A biological process where T cells produce IL-13 resulting from the recognition of a T cell epitope.
epitope specific IL-17 release by T cells
A biological process where T cells produce IL-17 resulting from the recognition of a T cell epitope.
epitope specific IL-18 release by T cells
A biological process where T cells produce IL-18 resulting from the recognition of a T cell epitope.
epitope specific IL-1b release by T cells
A biological process where T cells produce IL-1b resulting from the recognition of a T cell epitope.
epitope specific IL-4 release by T cells
A biological process where T cells produce IL-4 resulting from the recognition of a T cell epitope.
A material entity bearing the disposition to cause an allergic reaction
epitope specific IL-5 release by T cells
A biological process where T cells produce IL-5 resulting from the recognition of a T cell epitope.
epitope specific IL-6 release by T cells
A biological process where T cells produce IL-6 resulting from the recognition of a T cell epitope.
epitope specific killing by T cells
A biological process where T cells lyse antigen presenting cells resulting from the recognition of a T cell epitope on MHC molecules of the antigen presenting cell.
epitope specific TNF release by T cells
A biological process where T cells produce TNF resulting from the recognition of a T cell epitope.
An IFN-g ELISPOT is an assay detecting ifn-gamma production
an assay that determines information about the production of the cytokine interferon gamma
A report about experiments in an investigation that characterize immune epitopes, and was submitted directly by the authors to the Immune Epitope Database (IEDB)
The report on "Identification of a dominant CD4 T cell epitope in the membrane lipoprotein Tul4 from Francisella tularensis LVS. " submitted by Valentino et al to the IEDB. The content of that report on the IEDB website is here: http://iedb.org/refId/1013357
chromium release assay
An assay in which radioactive chromium is absorbed by cells and released into supernatant when the cells die. The amount of radioactivity measured in the supernatant is a proxy for the number of cells that have died.
from http://cvi.asm.org/cgi/content/full/11/2/255 (and slightly simplified)\nAutologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target (5 x 10E4 cells/ml) and effector cells were added to triplicate wells of 96-well tissue culture plates, and 1:2 serial dilutions of effectors were made, producing effector-to-target (E:T) ratios of 100:1, 50:1, 25:1, and 12.5:1 (9). Spontaneous release of 51Cr was assessed by the incubation of target cells in medium alone, and maximum release of 51Cr was determined by the incubation of target cells in 0.1% Triton X-100 (Sigma-Aldrich).\nAfter a 4-h incubation of the effector cells with the target cells at 37 degrees C in 6% CO2, supernatants were collected following brief centrifugation. The supernatant was collected into filters of supernatant collection system harvesting frames (Molecular Devices Skatron, Sunnyvale, Calif.) and transferred to polystyrene tubes to be counted with the LKB 1272 Clinigamma counter (Wallac).\nPercent specific was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100.
A series of statements representing health-relevant qualities of a patient and of a patient's family.
replace 'OBI:occurrence of disease', need to add logical definition The axioms of OBI occurence of disease: Equivalent classes: realizes some disease Superclasses: 'has part' some 'pathologic process' 'has participant' some (organism and ('has role' some 'host of immune response role')) biological_process realizes some 'host of immune response role'
The totality of all processes through which a given disease instance is realized.
A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species.
A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder
age
A time quality inhering in a bearer by virtue of how long the bearer has existed.
fluorescence
A luminous flux quality inhering in a bearer by virtue of the bearer's emitting longer wavelength light following the absorption of shorter wavelength radiation; fluorescence is common with aromatic compounds with several rings joined together.
biological sex
An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved.
A 1-D extent quality which is equal to the distance between two points.
A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
temperature
A physical quality of the thermal energy of a system.
behavioral quality
An organismal quality inhering in a bearer by virtue of the bearer's behavior aggregate of the responses or reactions or movements in a given situation.
female
A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes.
male
A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes.
volume
A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies.
pressure
A physical quality that inheres in a bearer by virtue of the bearer's amount of force per unit area it exerts.
diluted
A concentration which relatively low.
damaged
A structural quality inhering in a bearer by virtue of the bearer being harmed or injured or spoiled, such that its functionality is impaired.
lateral to
A spatial quality inhering in a bearer by virtue of the bearer's being located toward the side relative to another entity.
ventral to
A spatial quality inhering in a bearer by virtue of the bearer's being located toward the abdomen of an organism relative to another entity.
dorsal to
A spatial quality inhering in a bearer by virtue of the bearer's being located toward the back or upper surface of an organism relative to another entity.
quality of a single physical entity
A physical object quality which inheres in a single-bearer.
quality of related physical entities
A physical entity quality which exists in relation towards some other entity.
mixed sex
A biological sex quality inhering in a population of multiple sexes.
biomaterial purity
A composition quality inhering in an bearer by virtue of the bearer's homogeneity of a biomaterial.
hermaphrodite
A biological sex quality inhering in an organism or a population with both male and female sexual organs in one individual.
a mating type (yeast)
A S. cerevisiae mating type cells that secrete a pheromone that in alpha haploids stimulates processes that lead to mating.
alpha mating type (yeast)
A S. cerevisiae mating type cells that secrete a pheromone that stimulates a haploids.
h minus
A S. pombe mating type determined by the mat1-Mc and mat1-Mi on the mat1 locus.
h plus
A S. pombe mating type determined by the mat1-Pc and mat1-Pi on the mat1 locus.
F mating type
A bacterial mating type indicating the presence of F plasmid in a bacterial cell.
F minus mating type
A bacterial mating type indicating the absence of F plasmid in a bacterial cell.
ploidy
A cellular quality inhering in a bearer by virtue of the bearer's number of homologous sets of chromosomes in the nucleus or primary chromosome-containing compartment of the cell, each set essentially coding for all the biological traits of the organism.
haploid
A ploidy quality inhering in a bearer by virtue of the bearer's containing a single set of homologous chromosomes.
polyploid
A ploidy quality inhering in a bearer by virtue of the bearer's containing more than two homologous sets of chromosomes.
aneuploid
A ploidy quality inhering in a bearer by virtue of the bearer's containing a non-integral multiple of the monoploid number, due to extra or missing chromosomes.
diploid
A ploidy quality inhering in a bearer by virtue of the bearer's having two copies (homologs) of each chromosome, usually one from the mother and one from the father.
cellular quality
A monadic quality of continuant that exists at the cellular level of organisation.
alive
A viability quality inhering in a bearer by virtue of the bearer's condition before death.
dead
A viability quality inhering in a bearer by virtue of the cessation of the bearer's life.
quality of a solid
A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity characterized by particles arranged such that their shape and volume are relatively stable.
quality of a gas
A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity consisting of particles that have neither a defined volume nor defined shape.
quality of a liquid
A physical quality inhering in an entity exhibiting the physical characteristics of an amorphous (non-crystalline) form of matter between a gas and a solid that has a definite volume, but no definite shape.
relational spatial quality
A quality of related physical entities inhering in a bearer by virtue of the bearer's pertaining to or involving or having the nature of space in relation to another entity.
anterior to
A spatial quality inhering in a bearer by virtue of the bearer's being located toward the front of an organism relative to another entity.
frontal
radioactive
A radiation quality inhering in bearer by virtue of the bearer's exhibiting or being caused by radioactivity.
left side of
A spatial quality inhering in a bearer by virtue of the bearer's being located on left side of from the a another entity.
right side of
A spatial quality inhering in a bearer by virtue of the bearer's being located on right side of a another entity.
frozen
A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point.
handedness
A behavioral quality inhering ina bearer by virtue of the bearer's unequal distribution of fine motor skill between its left and right hands or feet.
left handedness
Handedness where the organism preferentially uses the left hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot.
right handedness
Handedness where the organism preferentially uses the right hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot.
ambidextrous handedness
Handedness where the organism exhibits no overall dominance in the use of right or left hand or foot in the performance of tasks that require one hand or foot or a dominant hand or foot.
fluid flow rate
A physical quality inhering in a fluid (liquid or gas) by virtue of the amount of fluid which passes through a given surface per unit time.
protein
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA.
CD4 molecule
A protein that is a translation product of the CD4 gene or a 1:1 ortholog thereof. CD4 is an accessory protein for MHC class-II antigen/T-cell receptor interaction. It is the primary receptor for HIV-1. CD4 has four immunoglobulin-like domains in its extracellular region that share the same structure, but can differ in sequence.
CD3 subunit with immunoglobulin domain
A protein with a core domain composition consisting of an extracellular N-terminal domain that adopts an immunoglobulin fold, a transmembrane domain, and an intracellular C-terminal domain with a single copy of the Immunoreceptor tyrosine-based activation motif (PF02189) (ITAM). It constitutes the invariant subunit of the T cell antigen receptor (TCR). TCR is a surface receptor on T cells responsible for recognizing MHC-restricted antigens and initiating the cellular immune response.
double-stranded RNA-specific adenosine deaminase
A protein that is a translation product of the ADAR gene or a 1:1 ortholog thereof.
deoxyribonuclease-1
A protein that is a translation product of the DNASE1 gene or a 1:1 ortholog thereof.
glial cell line-derived neurotrophic factor
A protein that is a translation product of the GDNF gene or a 1:1 ortholog thereof.
ribonuclease T2
A protein that is a translation product of the RNASET2 gene or a 1:1 ortholog thereof.
DNA ligase
Definition defined by OBI developers: an enzyme that covalently joins two compatible pieces of DNA through the cleavage of an ATP molecule
A protein that is a translation product of the ligA gene or a 1:1 ortholog thereof.
T cell receptor co-receptor CD8
A protein complex that is a membrane-bound heterodimeric co-receptor for MHC class-I antigen/T-cell receptor interaction.
guanyl-specific ribonuclease T1
A protein that is a translation product of the Aspergillus oryzae rntA gene or a 1:1 ortholog thereof.
nuclease S1
A protein that is a translation product of the Aspergillus oryzae nucS gene or a 1:1 ortholog thereof.
ribonuclease U2
A protein that is a translation product of the Ustilago sphaerogena RNU2 gene or a 1:1 ortholog thereof.
ribonuclease V1
A protein with ribonuclease activity that is a constituent of cobra venom.
ribonuclease CL3
A protein with ribonuclease activity that is purified from chicken liver.
region
primary structure of sequence macromolecule
A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.
polypeptide
A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation.
circular
A quality of a nucleotide polymer that has no terminal nucleotide residues.
lymph node
Oval or bean shaped bodies (1 - 30 mm in diameter) located along the lymphatic system. Lymph nodes are garrisons of B, T, and other immune cells. Lymph nodes are found all through the body, and act as filters or traps for foreign particles. They contain white blood cells that use oxygen to process. Thus they are important in the proper functioning of the immune system. The lymph node is surrounded by a fibrous capsule, and inside the lymph node the fibrous capsule extends to form trabeculae. The substance of the lymph node is divided into the outer cortex and the inner medulla surrounded by the former all around except for at the hilum, where the medulla comes in direct contact with the surface. Thin reticular fibers, elastin and reticular fibers form a supporting meshwork called reticular network (RN) inside the node, within which the white blood cells (WBCs), most prominently, lymphocytes are tightly packed as follicles in the cortex. Elsewhere, there are only occasional WBCs. The RN provides not just the structural support, but also provide surface for adhesion of the dendritic cells, macrophages and lymphocytes. It allows for exchange of material with blood through the high endothelial venules and provides the growth and regulatory factors necessary for activation and maturation of immune cells[WP].
life cycle stage
A spatiotemporal region encompassing some part of the life cycle of an organism.
mouth
First portion of the digestive tract[WP]. The portion of the digestive that develops from the stomodeum
blood
Circulating body substance which consists of blood plasma and hemoglobin-carrying red blood cells. Excludes blood analogues (see UBERON:0000179 haemolymphatic fluid).
brain
The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals.[1] Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP].
Dense irregular connective tissue, which predominantly consists of adipocytes. Fat is stored in adipose tissue.
urine
Excretion in liquid state processed by the kidney.[FMA]
skeletal muscle tissue
Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA]. Striated muscle tissue under control of the somatic nervous system. It is one of three major muscle types, the others being cardiac and smooth muscle. As its name suggests, most skeletal muscle is attached to bones by bundles of collagen fibers known as tendons. Skeletal muscle is made up of individual components known as muscle fibers. These fibers are formed from the fusion of developmental myoblasts. The myofibers are long, cylindrical, multinucleated cells composed of actin and myosin myofibrils repeated as a sarcomere, the basic functional unit of the cell and responsible for skeletal muscle's striated appearance and forming the basic machinery necessary for muscle contraction. The term muscle refers to multiple bundles of muscle fibers held together by connective tissue[WP].
vein
Any of the tubular branching vessels that carry blood from the capillaries toward the heart.
caudate nucleus
Nucleus of brain which is an elongated crescent-shaped mass lying parallel and adjacent to the lateral ventricle throughout its extent.
putamen
Nucleus of brain which lies ventral to the caudate nucleus and internal capsule and medial to the external capsule. The putamen and caudate nucleus together form the dorsal striatum. It is also one of the structures that comprises the basal ganglia. Through various pathways, the putamen is connected to the substantia nigra and globus pallidus. The main function of the putamen is to regulate movements and influence various types of learning. It employs dopamine to perform its functions. The putamen also plays a role in degenerative neurological disorders, such as Parkinson's disease.
dermis
The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP].
hypodermis
Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP]. A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells[FMA].
spleen
Organ found in virtually all vertebrate animals with important roles in regard to red blood cells and the immune system.[1] In humans, it is located in the left upper quadrant of the abdomen. It removes old red blood cells and holds a reserve in case of hemorrhagic shock, especially in animals like horses (not in humans), while recycling iron.[2] It synthesizes antibodies in its white pulp and removes, from blood and lymph node circulation, antibody-coated bacteria along with antibody-coated blood cells.
An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].
peritoneum
A serous membrane that forms the lining of the abdominal cavity or the coelom - it covers most of the intra-abdominal (or coelomic) organs - in higher vertebrates and some invertebrates (annelids, for instance). It is composed of a layer of mesothelium supported by a thin layer of connective tissue. The peritoneum both supports the abdominal organs and serves as a conduit for their blood and lymph vessels and nerves[WP]. The smooth transparent serous membrane that lines the cavity of the abdomen of a mammal and is folded inward over the abdominal and pelvic viscera[BTO]. The endothelial lining of the ABDOMINAL CAVITY. The parietal peritoneum covers the inside of the ABDOMINAL WALL and the visceral peritoneum covers the bowel, the MESENTERY, and certain of the organs. The portion that covers the bowel becomes the serosal layer of the bowel wall[GAID].
left cerebral hemisphere
right cerebral hemisphere
mucosa of nasopharynx
A mucosa that is part of a nasopharynx [Obol].
mucosa of oropharynx
A mucosa that is part of a oropharynx [Obol].
length unit
A unit which is a standard measure of the distance between two points.
mass unit
A unit which is a standard measure of the amount of matter/energy of a physical object.
time unit
A unit which is a standard measure of the dimension in which events occur in sequence.
temperature unit
A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter.
substance unit
A unit which is a standardised quantity of an element or compound with uniform composition.
concentration unit
A unit which represents a standard measurement of how much of a given substance there is mixed with another substance.
volume unit
A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas.
frequency unit
A unit which is a standard measure of the number of repetitive actions in a particular time.
pressure unit
A unit which is a standard measure of the force applied to a given area.
volumetric flow rate unit
A unit which is a standard measure of the volume of fluid which passes through a given surface per unit time .
rate unit
A unit which represents a standard measurement occurrence of a process per unit time.
A vaccine is a processed material with the function that when administered, it prevents or ameliorates a disorder in a target organism by inducing or modifying adaptive immune responses specific to the antigens in the vaccine.
Vaccination is: an 'administering substance in vivo' that involves in adding vaccine into a host (e.g., human, mouse) in vivo with the intend to invoke a protective immune response.
example to be eventually removed
failed exploratory term
The term was used used in an attempt to structure part of the ontology but in retrospect failed to do a good job
metadata complete
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
organizational term
term created to ease viewing/sort terms for development purpose, and will not be included in a release
ready for release
Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
metadata incomplete
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
uncurated
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
pending final vetting
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
core
Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
placeholder removed
terms merged
An editor note should explain what were the merged terms and the reason for the merge.
term imported
This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.
term split
This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.
other
This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason.
We expect to be able to mine these new reasons and add instances as required.
A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
"definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
to be replaced with external ontology term
Terms with this status should eventually replaced with a term from another ontology.
requires discussion
A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
Transformation-ML
Transformation-ML file describing parameter transformations used in a GvHD experiment.
Transformation-ML is a format standard of a digital entity that is conformant with the Transformation-ML standard.(http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf)
ACS
ACS is a format standard of a digital entity that is conformant with the Analytical Cytometry Standard. (http://www.isac-net.org/content/view/607/150/)
d06.acs, ACS1.0 data file of well D06 of plate 2 of part 1 of a GvHD experiment.
XML
RDF/XML file, OWL file, Compensation-ML file, WSDL document, SVG document
XML is a format standard of a digital entity that is conformant with the W3C Extensible Markup Language Recommendation.(http://www.w3.org/XML/)
RDF
A FOAF file, a SKOS file, an OWL file.
RDF is a format standard of a digital entity that is conformant with the W3C Resource Description Framework RDF/XML Syntax specification.(http://www.w3.org/RDF/)
zip
MagicDraw MDZIP archive, Java JAR file.
zip is a format standard of a digital entity that is conformant with the PKWARE .ZIP file format specification (http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/)
tar
Example.tar file.
tar is a format standard of a digital entity that is conformant with the tape archive file format as standardized by POSIX.1-1998, POSIX.1-2001, or any other tar format compliant with the GNU tar specification. (http://www.gnu.org/software/tar/manual/)
FCS
FCS is a format standard of a digital entity that is conformant with the Flow Cytometry Data File Standard.(http://www.fcspress.com/)
d01.fcs, FCS3 data file of well D06 of plate 2 of part 1 of a GvHD experiment.
Compensation-ML
Compensation-ML is a format standard of a digital entity that is conformant with the Compensation-ML standard. (http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf)
compfoo.xml, Compensation-ML file describing compensation used in a GvHD experiment
Gating-ML
Gating-ML is a format standard of a digital entity that is conformant with the Gating-ML standard. (http://www.flowcyt.org/gating/)
foogate.xml, Gating-ML file describing gates used in a GvHD experiment.
OWL
OBI ontology file, Basic Formal Ontology file, BIRNLex file, BioPAX file.
OWL is a format standard of a digital entity that is conformant with the W3C Web Ontology Language specification.(http://www.w3.org/2004/OWL/)
obsolete_the supplier role of Affymetrix
Affymetrix
An organization which supplies technology, tools and protocols for use in high throughput applications
GenePattern module SVM is a GenePattern software module which is used to run a support vector machine data transformation.
GenePattern module KMeansClustering is a GenePattern software module which is used to perform a k Means clustering data transformation.
GenePattern module CARTXValidation is a GenePattern software module which uses a CART decision tree induction with a leave one out cross validation data transformations.
GenePattern module KNNXValidation is a GenePattern software module which uses a k-nearest neighbours clustering with a leave one out cross validation data transformations.
GenePattern module KNN is a GenePattern software module which perform a k-nearest neighbors data transformation.
GenePattern module HierarchicalClustering
GenePattern module HierarchicalClustering is a GenePattern software module which is used to perform a hierarchical clustering data transformation.
GenePattern module PCA is a GenePattern software module which is used to perform a principal components analysis dimensionality reduction data transformation.
GenePattern HeatMapViewer data visualization
The GenePattern process of generating Heat Maps from clustered data.
GenePattern HierarchicalClusteringViewer data visualization
The GenePattern process of generating hierarchical clustering visualization from clustered data.
A GenePattern software module which is used to generate a heatmap view of data.
GenePattern module HierarchicalClusteringViewer
A GenePattern software module which is used to generate a view of data that has been hierarchically clustered.
obsolete_the manufacturer role of Agilent
obsolete_manufacturer role of Bruker Daltonics
obsolete_the manufacturer role of Thermo
obsolete_the manufacturer role of Li-Cor
obsolete_the manufacturer role of Ambion
obsolete_the manufacturer role of BIO-RAD
obsolete_the manufacturer role of Illumina
obsolete_the manufacturer role of Helicos
obsolete_manufacturer role of Bruker Corporation
obsolete_the manufacturer role of Waters
obsolete_manufacturer role of applied biosystems
The Edinburgh Handedness Inventory is a set of questions used to assess the dominance of a person's right or left hand in everyday activities.
Advanced Instruments Inc. (AI Companies)
meter
A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second.
kilogram
A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France.
second
A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom.
centimeter
A length unit which is equal to one hundredth of a meter or 10^[-2] m.
millimeter
A length unit which is equal to one thousandth of a meter or 10^[-3] m.
micrometer
A length unit which is equal to one millionth of a meter or 10^[-6] m.
nanometer
A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m.
angstrom
A length unit which is equal to 10 [-10] m.
gram
A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg.
milligram
A mass unit which is equal to one thousandth of a gram or 10^[-3] g.
microgram
A mass unit which is equal to one millionth of a gram or 10^[-6] g.
nanogram
A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g.
picogram
A mass unit which is equal to 10^[-12] g.
degree celsius
A temperature unit which is equal to one Kelvin degree. However, they have their zeros at different points. The Centigrade scale has its zero at 273.15 K.
minute
A time unit which is equal to 60 seconds.
hour
A time unit which is equal to 3600 seconds or 60 minutes.
day
A time unit which is equal to 24 hours.
week
A time unit which is equal to 7 days.
month
A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which is science is taken to be equal to 30 days.
year
A time unit which is equal to 12 months which is science is taken to be equal to 365.25 days.
micromole
A substance unit equal to a millionth of a mol or 10^[-6] mol.
nanomole
A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol.
picomole
A substance unit equal to 10^[-12] mol.
molar
A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L).
millimolar
A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M.
micromolar
A unit of molarity which is equal to one millionth of a molar or 10^[-6] M.
nanomolar
A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M.
picomolar
A unit of molarity which is equal to 10^[-12] M.
cubic centimeter
A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml.
milliliter
A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter.
liter
A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter.
cubic decimeter
A volume unit which is equal to one thousand of a cubic meter or 10^[-3] m^[3], or to 1 L.
microliter
A volume unit which is equal to one millionth of a liter or 10^[-6] L.
nanoliter
A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L.
picoliter
A volume unit which is equal to 10^[-12] L.
hertz
A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second.
mass percentage
A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture.
mass volume percentage
A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture.
volume percentage
A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution.
gram per liter
A mass unit density which is equal to mass of an object in grams divided by the volume in liters.
milligram per milliliter
A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters.
A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+).
milliliter per liter
A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution.
gram per deciliter
A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters.
colony forming unit per volume
A concentration unit which a measure of viable bacterial numbers in a given volume.
microliters per minute
A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute.
count per nanomolar second
A rate unit which is equal to one over one nanomolar second.
count per molar second
A rate unit which is equal to one over one molar second.
count per nanomolar
1/nM
A rate unit which is equal to one over nanomolar.
count per molar
1/M
A rate unit which is equal to one over molar.
microgram per liter
A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters.
Barry Smith and Pierre Grenon: "The Cornucopia of Formal Ontological Relations"
Pierre Grenon: "Nuts in BFO's Nutshell: Revisions to the Bi-categorial Axiomatization of BFO"
Institute for Formal Ontology and Medical Information Science (IFOMIS)
Barry Smith: "Basic Tools of Formal Ontology"
Pierre Grenon: "BFO in a Nutshell: A Bi-categorial Axiomatization of BFO and Comparison with DOLCE"
Pierre Grenon, Barry Smith and Louis Goldberg: "Biodynamic Ontology: Applying BFO in the Biomedical Domain"
Barry Smith: "Beyond Concepts: Ontology as Reality Representation"
Pierre Grenon: "Spatio-temporality in Basic Formal Ontology: SNAP and SPAN, Upper-Level Ontology, and Framework for Formalization"