Ontology
default language: en
version info: $Revision$
version IRI: ontology-metadata.owl

data item
type: Class
subclass of: information content entity

information content entity
type: Class
subclass of: GenericallyDependentContinuant

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

named class expression
type: denotator type
editor note: 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
definition: A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
definition editor: Alan Ruttenberg

universal
type: denotator type
definition source: A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
definition editor: Alan Ruttenberg
editor note: 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.

defined class
type: denotator type
editor note: "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.
definition editor: Alan Ruttenberg
definition editor: A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal

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

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

pending final vetting
type: curation status specification
definition: 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 definition editor.

failed exploratory term
type: obsolescence reason specification
definition: The term was used used in an attempt to structure part of the ontology but in retrospect failed to do a good job
definition editor: Person:Alan Ruttenberg

terms merged
type: obsolescence reason specification
editor note: An editor note should explain what were the merged terms and the reason for the merge.

term split
type: obsolescence reason specification
editor note: 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
type: obsolescence reason specification
editor note: We expect to be able to mine these new reasons and add instances as required.
editor note: This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason.

placeholder removed
type: obsolescence reason specification

term imported
type: obsolescence reason specification
editor note: 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.

curation status specification
type: Class
definition source: OBI_0000266
has curation status: pending final vetting
editor note: Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
editor preferred term: curation status specification
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition: The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
definition editor: PERSON:Bill Bug
equivalent class: Class
  one of: requires discussion
  one of: uncurated
  one of: to be replaced with external ontology term
  one of: ready for release
  one of: metadata complete
  one of: example to be eventually removed
  one of: metadata incomplete
  one of: pending final vetting
  one of: organizational term
subclass of: data about an ontology part

requires discussion
type: NamedIndividual
definition source: group:OBI
type: curation status specification
definition editor: Alan Ruttenberg
definition: 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.

uncurated
type: curation status specification
definition: Nothing done yet beyond assigning a unique class ID and proposing a preferred term.

to be replaced with external ontology term
type: NamedIndividual
type: curation status specification
definition editor: Alan Ruttenberg
definition: Terms with this status should eventually replaced with a term from another ontology.
definition source: group:OBI

ready for release
type: curation status specification
definition: 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 complete
type: curation status specification
definition: 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.

example to be eventually removed
type: curation status specification

metadata incomplete
type: curation status specification
definition: Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.

organizational term
type: curation status specification
definition: term created to ease viewing/sort terms for development purpose, and will not be included in a release

core
type: Subset
definition: Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
definition editor: PERSON: Melanie Courtot
definition editor: PERSON: Alan Ruttenberg

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

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

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

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

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

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

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

definition editor
type: AnnotationProperty
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
editor preferred term: definition editor
definition: Name of editor entering the definition in the file. The definition editor is a point of contact for information regarding the term. The definition editor may be, but is not always, the author of the definition, which may have been worked upon by several people
definition editor: PERSON:Daniel Schober
has curation status: ready for release

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

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

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

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

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

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

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

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

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

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

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