The Biological Collections Ontology
type: Ontology
version IRI: bco.owl
Contributor: Barry Smith
Contributor: Biocode Commons Ontology Hackathon members
Contributor: John Deck
Contributor: John Wieczorek
Contributor: Ramona Walls
Contributor: Robert Guralnick
license: http://creativecommons.org/publicdomain/zero/1.0/
comment: This is the editor's version of the ontology. Use with caution. For the live version of the ontology, use http://purl.obolibrary.org/obo/bco.owl. The Biological Collections Ontology was originally created at the Biocode Commons Hackathon at GSC14. Older versions can be viewed at http://code.google.com/p/biocode-commons/source/browse/#svn%2Ftrunk%2Fontologies%2Fbiocollections. Some of the classes in this ontology may be replaced by existing or newly requested terms from OBI or other ontologies.

taxonomic inventory metadata preferred name
type: AnnotationProperty
sub property of: alternative term

BCO preferred label
type: AnnotationProperty

dwc_bco mapping
type: AnnotationProperty

BFO OWL specification label
type: AnnotationProperty
definition: Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification.
curator note: Really of interest to developers only

BFO CLIF specification label
type: AnnotationProperty
definition: Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
definition source: Person:Alan Ruttenberg
curator note: Really of interest to developers only

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

example of usage
type: AnnotationProperty
editor preferred label: example
has curation status: ready for release
definition: A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

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

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

definition
type: AnnotationProperty
editor preferred label: definition
editor preferred label: textual definition
has curation status: ready for release
definition: The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
editor note: 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
label: textual definition

editor note
type: AnnotationProperty
editor preferred label: editor note
has curation status: ready for release
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.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obfoundry.org/obo/obi>

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

alternative term
type: AnnotationProperty
editor preferred label: alternative term
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)
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

definition source
type: AnnotationProperty
editor preferred label: 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
term 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>

has obsolescence reason
type: AnnotationProperty
editor preferred label: has obsolescence reason
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 editor: PERSON:Alan Ruttenberg
term editor: PERSON:Melanie Courtot

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

term tracker item
type: AnnotationProperty
editor preferred label: term tracker item
example of usage: the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
has curation status: pending final vetting
definition: An IRI or similar locator for a request or discussion of an ontology term.
term editor: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
definition source: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
comment: The 'tracker item' can associate a tracker with a specific ontology term.

ontology term requester
type: AnnotationProperty
has curation status: pending final vetting
definition: The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
term editor: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
definition source: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
comment: The 'term requester' can credit the person, organization or project who request the ontology term.

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

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

expand expression to
type: AnnotationProperty
editor preferred label: 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
term editor: Chris Mungall

expand assertion to
type: AnnotationProperty
editor preferred label: expand assertion to
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)"
definition: A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
term editor: Chris Mungall

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

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

OBO foundry unique label
type: AnnotationProperty
editor preferred label: OBO foundry unique label
has curation status: pending final vetting
definition: An alternative name for a class or property which is unique across the OBO Foundry.
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 .
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Bjoern Peters
term editor: PERSON:Chris Mungall
term editor: PERSON:Melanie Courtot
definition source: GROUP:OBO Foundry <http://obofoundry.org/>

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

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

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

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

elucidation
type: AnnotationProperty
editor preferred label: elucidation
term editor: person:Alan Ruttenberg
definition source: Person:Barry Smith
elucidation: Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms

has associated axiom(nl)
type: AnnotationProperty
editor preferred label: has associated axiom(nl)
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: An axiom associated with a term expressed using natural language

has associated axiom(fol)
type: AnnotationProperty
editor preferred label: has associated axiom(fol)
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: An axiom expressed in first order logic using CLIF syntax

is allocated id range
type: AnnotationProperty
editor preferred label: is allocated id range
definition: Add as annotation triples in the granting ontology
definition: Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999"
term editor: PERSON:Alan Ruttenberg

may be identical to
type: AnnotationProperty
definition: A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged.
term editor: David Osumi-Sutherland
term tracker item: #40
ontology term requester: VFB
creation date: 2018-09-21T16:43:39Z
comment: Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance.

scheduled for obsoletion on or after
type: AnnotationProperty
definition: Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date.
term editor: Chris Mungall, Jie Zheng
term tracker item: https://github.com/geneontology/go-ontology/issues/15532
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/32
ontology term requester: GO ontology
range: dateTime

has axiom label
type: AnnotationProperty
editor preferred label: has axiom id
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI

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

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

ISA alternative term
type: AnnotationProperty
editor preferred label: ISA alternative term
has curation status: ready for release
definition: An alternative term used by the ISA tools project (http://isa-tools.org).
editor note: Requested by Alejandra Gonzalez-Beltran https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178
term editor: Person: Alejandra Gonzalez-Beltran
term editor: Person: Philippe Rocca-Serra
definition source: ISA tools project (http://isa-tools.org)

IEDB alternative term
type: AnnotationProperty
editor preferred label: IEDB alternative term
has curation status: ready for release
definition: An alternative term used by the IEDB.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB

temporal interpretation
type: AnnotationProperty
definition: An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

license
type: AnnotationProperty
term editor: Mark Miller
date: 2018-05-11T13:47:29Z

dwc_terms status
type: AnnotationProperty

has_alternative_id
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

in_subset
type: AnnotationProperty

obsolete has role
type: ObjectProperty
definition: The relationship between an independent continuant and a role. Slightly more specific than the parent class bearer of.
has obsolescence reason: to be replaced with external ontology term
comment: This property was originally created in OBI, but in OBI it was deprecated and replaced by BFO:0000087. However, BFO:0000087 was replaced by 'has role at some time', which is not yet part of a stable release. Once the BFO role has been tested and released, it may replace 'has role' in both BCO and OBI. There are currently two versions of 'has role', the old one from BFO (which is used in OBI's definition of specimen) and the RO version. For consistency with OBI, we have used the BFO relation in BCO, but this should be resolved at a higher level.
deprecated: true

derives from by planned process
type: ObjectProperty
sub property of: topObjectProperty
type: TransitiveProperty
has obsolescence reason: to be replaced with external ontology term
deprecated: true

is derived into by planned process
type: ObjectProperty
sub property of: topObjectProperty
type: TransitiveProperty
editor note: This property used an old version of the has input relation, so it has been deprecated.
has obsolescence reason: to be replaced with external ontology term
deprecated: true

to taxon
type: ObjectProperty
sub property of: is about
domain: identification assertion
range: Taxon
comment: This relation is used specifically to link a taxonomic association to a taxon and is used with the of organism relation.

of organism
type: ObjectProperty
sub property of: is about
domain: identification assertion
range: organismal entity
comment: This relation specifically links an identification association to an organismal entity and is used together with the to taxon relation.

member of taxon
type: ObjectProperty
sub property of: part of
property chain axiom:
  inverse of: of organism
property chain axiom: to taxon
comment: A shortcut relation to an organsimal entity to a taxon or taxa.

part of
type: ObjectProperty
equivalent property:
  inverse of: has part
inverse of: has part
type: TransitiveProperty
editor preferred label: is part of
example of usage: my brain is part of my body (continuant parthood, two material entities)
example of usage: my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
example of usage: this day is part of this year (occurrent parthood)
definition: a core relation that holds between a part and its whole
editor note: Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
editor note: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
editor note: Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
alternative term: part_of
temporal interpretation: axiom holds for all times

has part
type: ObjectProperty
equivalent property:
  inverse of: part of
type: TransitiveProperty
editor preferred label: has part
example of usage: my body has part my brain (continuant parthood, two material entities)
example of usage: my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
example of usage: this year has part this day (occurrent parthood)
definition: a core relation that holds between a whole and its part
editor note: Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
editor note: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
editor note: Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
alternative term: has_part
temporal interpretation: axiom holds for all times

realized in
type: ObjectProperty
equivalent property:
  inverse of: realizes
inverse of: realizes
domain: realizable entity
range: process
editor preferred label: realized in
example of usage: this disease is realized in this disease course
example of usage: this fragility is realized in this shattering
example of usage: this investigator role is realized in this investigation
alternative term: is realized by
alternative term: realized_in
elucidation: [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
comment: Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process

realizes
type: ObjectProperty
equivalent property:
  inverse of: realized in
domain: process
range: realizable entity
editor preferred label: realizes
example of usage: this disease course realizes this disease
example of usage: this investigation realizes this investigator role
example of usage: this shattering realizes this fragility
elucidation: to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
comment: Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process

occurs in
type: ObjectProperty
equivalent property:
  inverse of: contains process
inverse of: contains process
domain: occurrent
range: independent continuant
property chain axiom: part of
editor preferred label: occurs in
definition: b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
alternative term: occurs_in
alternative term: unfolds in
alternative term: unfolds_in
comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant

contains process
type: ObjectProperty
equivalent property:
  inverse of: occurs in
editor preferred label: site of
definition: [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant

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

denotes
type: ObjectProperty
sub property of: is about
inverse of: denoted by
domain: information content entity
range: entity
example of usage: A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named.
definition: 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
editor note: 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r
term editor: person:Alan Ruttenberg
definition source: Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan

denoted by
type: ObjectProperty
domain: entity
range: information content entity
definition: inverse of the relation 'denotes'
term editor: Person: Jie Zheng, Chris Stoeckert, Mike Conlon
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/206

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

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

is_specified_output_of
type: ObjectProperty
equivalent property:
  inverse of: has_specified_output
sub property of: participates in
range: planned process
editor preferred label: is_specified_output_of
has curation status: ready for release
definition: A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
term editor: Alan Ruttenberg
term editor: PERSON:Bjoern Peters
imported from: obi.owl

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

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

objective_achieved_by
type: ObjectProperty
domain: objective specification
range: planned process
editor preferred label: objective_achieved_by
has curation status: ready for release
definition: This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
term editor: OBI
definition source: OBI

has value specification
type: ObjectProperty
sub property of: has part
domain: information content entity
range: value specification
editor preferred label: has value specification
has curation status: FossilSpecimen
definition: A relation between an information content entity and a value specification that specifies its value.
term editor: PERSON: James A. Overton
definition source: OBI

inheres in
type: ObjectProperty
equivalent property:
  inverse of: bearer of
inverse of: bearer of
editor preferred label: inheres in
example of usage: this fragility inheres in this vase
example of usage: this red color inheres in this apple
definition: a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
editor note: A dependent inheres in its bearer at all times for which the dependent exists.
alternative term: inheres_in
temporal interpretation: axiom holds for all times

bearer of
type: ObjectProperty
equivalent property:
  inverse of: inheres in
range: specifically dependent continuant
editor preferred label: bearer of
example of usage: this apple is bearer of this red color
example of usage: this vase is bearer of this fragility
definition: a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
editor note: A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
alternative term: bearer_of
alternative term: is bearer of
temporal interpretation: axiom holds for all times

participates in
type: ObjectProperty
equivalent property:
  inverse of: has participant
inverse of: has participant
domain: continuant
range: occurrent
editor preferred label: participates in
example of usage: this blood clot participates in this blood coagulation
example of usage: this input material (or this output material) participates in this process
example of usage: this investigator participates in this investigation
definition: a relation between a continuant and a process, in which the continuant is somehow involved in the process
alternative term: participates_in

has participant
type: ObjectProperty
equivalent property:
  inverse of: participates in
domain: occurrent
range: continuant
editor preferred label: has participant
example of usage: this blood coagulation has participant this blood clot
example of usage: this investigation has participant this investigator
example of usage: this process has participant this input material (or this output material)
definition: a relation between a process and a continuant, in which the continuant is somehow involved in the process
editor note: Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
alternative term: has_participant
Source: http://www.obofoundry.org/ro/#OBO_REL:has_participant

is concretized as
type: ObjectProperty
equivalent property:
  inverse of: concretizes
inverse of: concretizes
domain: generically dependent continuant
range: specifically dependent continuant
example of usage: A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
example of usage: An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
definition: A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.

concretizes
type: ObjectProperty
equivalent property:
  inverse of: is concretized as
domain: specifically dependent continuant
range: generically dependent continuant
example of usage: A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
example of usage: An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
definition: A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.

function of
type: ObjectProperty
equivalent property:
  inverse of: has function
sub property of: inheres in
inverse of: has function
domain: function
example of usage: this catalysis function is a function of this enzyme
definition: a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
editor note: A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
alternative term: function_of
alternative term: is function of

quality of
type: ObjectProperty
equivalent property:
  inverse of: has quality
sub property of: inheres in
inverse of: has quality
example of usage: this red color is a quality of this apple
definition: a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
editor note: A quality inheres in its bearer at all times for which the quality exists.
alternative term: is quality of
alternative term: quality_of

role of
type: ObjectProperty
equivalent property:
  inverse of: has role
sub property of: inheres in
inverse of: has role
example of usage: this investigator role is a role of this person
definition: a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
editor note: A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
alternative term: is role of
alternative term: role_of

has function
type: ObjectProperty
equivalent property:
  inverse of: function of
sub property of: bearer of
domain: independent continuant
range: function
example of usage: this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
definition: a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
editor note: A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
alternative term: has_function

has quality
type: ObjectProperty
equivalent property:
  inverse of: quality of
sub property of: bearer of
range: quality
example of usage: this apple has quality this red color
definition: a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
editor note: A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
alternative term: has_quality

has role
type: ObjectProperty
equivalent property:
  inverse of: role of
sub property of: bearer of
domain: independent continuant
range: role
example of usage: this person has role this investigator role (more colloquially: this person has this role of investigator)
definition: a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
editor note: A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
alternative term: has_role

has disposition
type: ObjectProperty
equivalent property:
  inverse of: disposition of
sub property of: bearer of
inverse of: disposition of
domain: independent continuant
range: disposition
definition: a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence

disposition of
type: ObjectProperty
equivalent property:
  inverse of: has disposition
sub property of: inheres in

derives from
type: ObjectProperty
equivalent property:
  inverse of: derives into
sub property of: topObjectProperty
inverse of: derives into
domain: independent continuant
range: independent continuant
editor preferred label: derives from
example of usage: this cell derives from this parent cell (cell division)
example of usage: this nucleus derives from this parent nucleus (nuclear division)
has curation status: pending final vetting
definition: a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
editor note: This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
alternative term: derives_from
imported from: ro.owl

derives into
type: ObjectProperty
equivalent property:
  inverse of: derives from
example of usage: this parent cell derives into this cell (cell division)
example of usage: this parent nucleus derives into this nucleus (nuclear division)
has curation status: pending final vetting
definition: a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
editor note: This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.
alternative term: derives_into

location of
type: ObjectProperty
equivalent property:
  inverse of: located in
inverse of: located in
type: TransitiveProperty
editor preferred label: is location of
example of usage: my head is the location of my brain
example of usage: this cage is the location of this rat
definition: a relation between two independent continuants, the location and the target, in which the target is entirely within the location
editor note: Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
alternative term: location_of
temporal interpretation: axiom holds for all times

located in
type: ObjectProperty
equivalent property:
  inverse of: location of
type: TransitiveProperty
domain: independent continuant
domain: Class
  intersection of: independent continuant
  intersection of: Class
    complement of: spatial region
range: independent continuant
range: Class
  intersection of: independent continuant
  intersection of: Class
    complement of: spatial region
editor preferred label: located in
example of usage: my brain is located in my head
example of usage: this rat is located in this cage
definition: a relation between two independent continuants, the target and the location, in which the target is entirely within the location
editor note: Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
editor note: Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
alternative term: located_in
temporal interpretation: axiom holds for all times
Source: http://www.obofoundry.org/ro/#OBO_REL:located_in

Axiom
annotated source: located in
annotated property: domain
annotated target: independent continuant
editor note: This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.

Axiom
annotated source: located in
annotated property: range
annotated target: independent continuant
editor note: This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.

2D boundary of
type: ObjectProperty
equivalent property:
  inverse of: has 2D boundary
inverse of: has 2D boundary
example of usage: the surface of my skin is a 2D boundary of my body
definition: a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity
editor note: A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
editor note: Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
alternative term: 2D_boundary_of
alternative term: boundary of
alternative term: is 2D boundary of
alternative term: is boundary of
temporal interpretation: axiom holds for all times

has 2D boundary
type: ObjectProperty
equivalent property:
  inverse of: 2D boundary of
domain: material entity
range: immaterial entity
example of usage: my body has 2D boundary the surface of my skin
definition: a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity
editor note: A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
editor note: Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
alternative term: has boundary
alternative term: has_2D_boundary
temporal interpretation: axiom holds for all times

member of
type: ObjectProperty
equivalent property:
  inverse of: has member
sub property of: part of
inverse of: has member
example of usage: An organism that is a member of a population of organisms
definition: is member of is a mereological relation between a item and a collection.
alternative term: is member of
alternative term: member part of
definition source: SIO
temporal interpretation: axiom holds for all times

has member
type: ObjectProperty
equivalent property:
  inverse of: member of
sub property of: has part
type: IrreflexiveProperty
definition: has member is a mereological relation between a collection and an item.
definition source: SIO
temporal interpretation: axiom holds for all times

bibliographicCitation
type: DatatypeProperty
comment: Organizational term to help define related terms. Do not use for data annotation with Darwin Core.

date
type: DatatypeProperty
comment: Organizational term to help define related terms. Do not use for data annotation with Darwin Core.

Accepted Name Usage
type: DatatypeProperty
description: Example: "Tamias minimus" valid name for "Eutamias minimus"
has version: acceptedNameUsage-2009-09-21
issued: 2008-11-19
modified: 2009-09-21
replaces: acceptedScientificName-2009-07-06
abcd equivalence: not in ABCD
organized in class: Taxon
dwc_terms status: recommended
comment: The full name, with authorship and date information if known, of the currently valid (zoological) or accepted (botanical) taxon.

According To
type: DatatypeProperty
has version: accordingTo-2009-01-21
issued: 2009-01-21
modified: 2009-01-21
abcd equivalence: not in ABCD
dwc_terms status: recommended
comment: Abstract term to attribute information to a source.
comment: Organizational term to help define related terms. Do not use for data annotation.

Associated Media
type: DatatypeProperty
description: Example: "http://arctos.database.museum/SpecimenImages/UAMObs/Mamm/2/P7291179.JPG"
has version: associatedMedia-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: ImageURL-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/MultimediaObjects
organized in class: Occurrence
dwc_terms status: recommended
comment: A list (concatenated and separated) of identifiers (publication, global unique identifier, URI) of media associated with the Occurrence.

Associated Occurrences
type: DatatypeProperty
description: Example: "sibling of FMNH:Mammal:1234; sibling of FMNH:Mammal:1235"
has version: associatedOccurrences-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: RelatedCatalogedItems-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociatedUnitSourceInstitutionCode + DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociatedUnitSourceName + DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociatedUnitID
organized in class: Occurrence
dwc_terms status: recommended
comment: A list (concatenated and separated) of identifiers of other Occurrence records and their associations to this Occurrence.

Associated Organisms
type: DatatypeProperty
description: The recommended best practice is to separate the values with a vertical bar (' | '). Examples: "sibling of MXA-232", "mother of MXA-231 | mother of MXA-232".
has version: associatedOrganisms-2014-10-23
issued: 2014-10-23
modified: 2014-10-23
abcd equivalence: not in ABCD
decision: Decision-2014-10-26 14
organized in class: Organism
dwc_terms status: recommended
comment: A list (concatenated and separated) of identifiers of other Organisms and their associations to this Organism.

Associated References
type: DatatypeProperty
description: Examples: "http://www.sciencemag.org/cgi/content/abstract/322/5899/261", "Christopher J. Conroy, Jennifer L. Neuwald. 2008. Phylogeographic study of the California vole, Microtus californicus Journal of Mammalogy, 89(3):755-767."
has version: associatedReferences-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/UnitReferences
organized in class: Occurrence
dwc_terms status: recommended
comment: A list (concatenated and separated) of identifiers (publication, bibliographic reference, global unique identifier, URI) of literature associated with the Occurrence.

Associated Sequences
type: DatatypeProperty
description: Example: "GenBank: U34853.1"
has version: associatedSequences-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: GenBankNumber-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/Sequences/Sequence/ID-in-Database + constant
organized in class: Occurrence
dwc_terms status: recommended
comment: A list (concatenated and separated) of identifiers (publication, global unique identifier, URI) of genetic sequence information associated with the Occurrence.

Associated Taxa
type: DatatypeProperty
description: Example: "host: Quercus alba"
has version: associatedTaxa-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/Synecology/AssociatedTaxa
organized in class: Occurrence
dwc_terms status: recommended
comment: A list (concatenated and separated) of identifiers or names of taxa and their associations with the Occurrence.

Basis of Record
type: DatatypeProperty
description: Examples: "PreservedSpecimen", "FossilSpecimen", "LivingSpecimen", "HumanObservation", "MachineObservation"
has version: basisOfRecord-2009-12-07
issued: 2008-11-19
modified: 2009-12-07
replaces: basisOfRecord-2009-09-11
abcd equivalence: DataSets/DataSet/Units/Unit/RecordBasis
decision: Decision-2009-12-07 2
organized in class: all
dwc_terms status: recommended
comment: The specific nature of the data record - a subtype of the dcterms:type. Recommended best practice is to use a controlled vocabulary such as the Darwin Core Type Vocabulary (http://rs.tdwg.org/dwc/terms/type-vocabulary/index.htm).

Bed
type: DatatypeProperty
has version: http://rs.tdwg.org/dwc/terms/history/#bed-2009-04-24
issued: 2009-04-24
modified: 2009-07-06
replaces: http://rs.tdwg.org/dwc/terms/Bed-2005-07-03
abcd equivalence: not in ABCD
organized in class: Geological Context
dwc_terms status: recommended
comment: The full name of the lithostratigraphic bed from which the cataloged item was collected.

Behavior
type: DatatypeProperty
description: Examples: "roosting", "foraging", "running"
has version: behavior-2009-04-24
issued: 2009-03-06
modified: 2009-04-24
abcd equivalence: not in ABCD
organized in class: Occurrence
dwc_terms status: recommended
comment: A description of the behavior shown by the subject at the time the Occurrence was recorded. Recommended best practice is to use a controlled vocabulary.

Catalog Number
type: DatatypeProperty
description: Examples: "2008.1334", "145732a", "145732"
has version: catalogNumber-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: CatalogNumber-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/UnitID
organized in class: Occurrence
dwc_terms status: recommended
comment: An identifier (preferably unique) for the record within the data set or collection.

Class
type: DatatypeProperty
description: Examples: "Mammalia", "Hepaticopsida"
has version: class-2009-08-24
issued: 2008-11-19
modified: 2009-08-24
replaces: class-2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/HigherTaxa/HigherTaxon/HigherTaxonName with HigherTaxa/HigherTaxon/HigherTaxonRank = classis
organized in class: Taxon
dwc_terms status: recommended
comment: The full scientific name of the class in which the taxon is classified.

Collection Code
type: DatatypeProperty
description: Examples: "Mammals", "Hildebrandt", "eBird"
has version: collectionCode-2009-09-11
issued: 2008-11-19
modified: 2013-10-04
replaces: collectionCode-2009-08-24
abcd equivalence: DataSets/DataSet/Units/Unit/SourceID
organized in class: all
dwc_terms status: recommended
comment: The name, acronym, coden, or initialism identifying the collection or data set from which the record was derived.

Collection ID
type: DatatypeProperty
description: Example: "urn:lsid:biocol.org:col:34818"
has version: collectionID-2009-09-11
issued: 2008-11-19
modified: 2013-10-04
abcd equivalence: DataSets/DataSet/Units/Unit/SourceID
organized in class: all
dwc_terms status: recommended
comment: An identifier for the collection or dataset from which the record was derived. For physical specimens, the recommended best practice is to use the identifier in a collections registry such as the Biodiversity Collections Index (http://www.biodiversitycollectionsindex.org/).

Continent
type: DatatypeProperty
description: Examples: "Africa", "Antarctica", "Asia", "Europe", "North America", "Oceania", "South America"
has version: continent-2009-04-24
issued: 2008-11-19
modified: 2013-10-04
replaces: Continent-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/NamedAreas/NamedArea/AreaName with NamedAreas/NamedArea/AreaClass= Continent
organized in class: Location
dwc_terms status: recommended
comment: The name of the continent in which the Location occurs. Recommended best practice is to use a controlled vocabulary such as the Getty Thesaurus of Geographic Names.

Coordinate Precision
type: DatatypeProperty
description: Examples: "0.00001" (normal GPS limit for decimal degrees), "0.000278" (nearest second), "0.01667" (nearest minute), "1.0" (nearest degree)
has version: coordinatePrecision-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: CoordinatePrecision-2003-06-13
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/CoordinatesLatLong/ISOAccuracy or DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/CoordinatesLatLong/AccuracyStatement
organized in class: Location
dwc_terms status: recommended
comment: A decimal representation of the precision of the coordinates given in the decimalLatitude and decimalLongitude.

Coordinate Uncertainty In Meters
type: DatatypeProperty
description: Examples: "30" (reasonable lower limit of a GPS reading under good conditions if the actual precision was not recorded at the time), "71" (uncertainty for a UTM coordinate having 100 meter precision and a known spatial reference system).
has version: coordinateUncertaintyInMeters-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: CoordinateUncertaintyInMeters-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/CoordinatesLatLon/CoordinateErrorDistanceInMeters
organized in class: Location
dwc_terms status: recommended
comment: The horizontal distance (in meters) from the given decimalLatitude and decimalLongitude describing the smallest circle containing the whole of the Location. Leave the value empty if the uncertainty is unknown, cannot be estimated, or is not applicable (because there are no coordinates). Zero is not a valid value for this term.

Country
type: DatatypeProperty
description: Examples: "Denmark", "Colombia", "España"
has version: country-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: Country-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/Country/Name
organized in class: Location
dwc_terms status: recommended
comment: The name of the country or major administrative unit in which the Location occurs. Recommended best practice is to use a controlled vocabulary such as the Getty Thesaurus of Geographic Names.

Country Code
type: DatatypeProperty
description: Examples: "AR" for Argentina, "SV" for El Salvador
has version: countryCode-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/Country/ISO3166Code
organized in class: Location
dwc_terms status: recommended
comment: The standard code for the country in which the Location occurs. Recommended best practice is to use ISO 3166-1-alpha-2 country codes.

County
type: DatatypeProperty
description: Examples: "Missoula", "Los Lagos", "Mataró"
has version: county-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: County-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/NamedAreas/NamedArea/AreaName with NamedAreas/NamedArea/AreaClass= County
organized in class: Location
dwc_terms status: recommended
comment: The full, unabbreviated name of the next smaller administrative region than stateProvince (county, shire, department, etc.) in which the Location occurs.

Data Generalizations
type: DatatypeProperty
description: Example: "Coordinates generalized from original GPS coordinates to the nearest half degree grid cell"
has version: dataGeneralizations-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: Generalizations-2008-11-19
abcd equivalence: not in ABCD
organized in class: all
dwc_terms status: recommended
comment: Actions taken to make the shared data less specific or complete than in its original form. Suggests that alternative data of higher quality may be available on request.

Dataset Name
type: DatatypeProperty
description: Examples: "Grinnell Resurvey Mammals", "Lacey Ctenomys Recaptures"
has version: datasetName-2009-09-11
issued: 2009-09-11
modified: 2009-09-11
abcd equivalence: DataSets/DataSet/Units/Unit/SourceID
organized in class: all
dwc_terms status: recommended
comment: The name identifying the data set from which the record was derived.

Date Identified
type: DatatypeProperty
sub property of: date
description: Examples: "1963-03-08T14:07-0600" is 8 Mar 1963 2:07pm in the time zone six hours earlier than UTC, "2009-02-20T08:40Z" is 20 Feb 2009 8:40am UTC, "1809-02-12" is 12 Feb 1809, "1906-06" is Jun 1906, "1971" is just that year, "2007-03-01T13:00:00Z/2008-05-11T15:30:00Z" is the interval between 1 Mar 2007 1pm UTC and 11 May 2008 3:30pm UTC, "2007-11-13/15" is the interval between 13 Nov 2007 and 15 Nov 2007.
has version: dateIdentified-2009-08-24
issued: 2008-11-19
modified: 2009-08-24
replaces: dateIdentified-2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/Identifications/Identification/Date/DateText
organized in class: Identification
dwc_terms status: recommended
comment: The date on which the subject was identified as representing the Taxon. Recommended best practice is to use an encoding scheme, such as ISO 8601:2004(E).

Day
type: DatatypeProperty
description: Examples: "9", "28"
has version: day-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: DayCollected-2003-06-17
abcd equivalence: accessible from DataSets/DataSet/Units/Unit/Gathering/ISODateTimeBegin
organized in class: Event
dwc_terms status: recommended
comment: The integer day of the month on which the Event occurred.

Decimal Latitude
type: DatatypeProperty
description: Example: "-41.0983423"
has version: decimalLatitude-2009-04-24
issued: 2008-11-19
modified: 2009-07-06
replaces: DecimalLatitude-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/CoordinatesLatLon/LatitudeDecimal
organized in class: Location
dwc_terms status: recommended
comment: The geographic latitude (in decimal degrees, using the spatial reference system given in geodeticDatum) of the geographic center of a Location. Positive values are north of the Equator, negative values are south of it. Legal values lie between -90 and 90, inclusive.

Decimal Longitude
type: DatatypeProperty
description: Example: "-121.1761111"
has version: decimalLongitude-2009-04-24
issued: 2008-11-19
modified: 2009-07-06
replaces: DecimalLongitude-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/CoordinatesLatLon/LongitudeDecimal
organized in class: Location
dwc_terms status: recommended
comment: The geographic longitude (in decimal degrees, using the spatial reference system given in geodeticDatum) of the geographic center of a Location. Positive values are east of the Greenwich Meridian, negative values are west of it. Legal values lie between -180 and 180, inclusive.

Disposition
type: DatatypeProperty
description: Examples: "in collection", "missing", "voucher elsewhere", "duplicates elsewhere"
has version: disposition-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: Disposition-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/SpecimenUnit/Disposition
organized in class: Occurrence
dwc_terms status: recommended
comment: The current state of a specimen with respect to the collection identified in collectionCode or collectionID. Recommended best practice is to use a controlled vocabulary.

Dynamic Properties
type: DatatypeProperty
description: Examples: "tragusLengthInMeters=0.014; weightInGrams=120", "heightInMeters=1.5", "natureOfID=expert identification; identificationEvidence=cytochrome B sequence", "relativeHumidity=28; airTemperatureInC=22; sampleSizeInKilograms=10", "aspectHeading=277; slopeInDegrees=6", "iucnStatus=vulnerable; taxonDistribution=Neuquen, Argentina"
has version: dynamicProperties-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: Attributes-2007-04-17
abcd equivalence: not in ABCD
organized in class: all
dwc_terms status: recommended
comment: A list (concatenated and separated) of additional measurements, facts, characteristics, or assertions about the record. Meant to provide a mechanism for structured content such as key-value pairs.

Earliest Age Or Lowest Stage
type: DatatypeProperty
description: Examples: "Atlantic", "Boreal", "Skullrockian"
has version: earliestAgeOrLowestStage-2009-04-24
issued: 2009-04-24
modified: 2009-07-06
replaces: EarliestAgeOrLowestStage-2005-07-03
abcd equivalence: not in ABCD
organized in class: Geological Context
dwc_terms status: recommended
comment: The full name of the earliest possible geochronologic age or lowest chronostratigraphic stage attributable to the stratigraphic horizon from which the cataloged item was collected.

Earliest Eon Or Lowest Eonothem
type: DatatypeProperty
description: Examples: "Phanerozoic", "Proterozoic"
has version: earliestEonOrLowestEonothem-2009-04-24
issued: 2009-04-24
modified: 2009-07-06
replaces: EarliestEonOrLowestEonothem-2005-07-03
abcd equivalence: not in ABCD
organized in class: Geological Context
dwc_terms status: recommended
comment: The full name of the earliest possible geochronologic eon or lowest chrono-stratigraphic eonothem or the informal name ("Precambrian") attributable to the stratigraphic horizon from which the cataloged item was collected.

Earliest Epoch Or Lowest Series
type: DatatypeProperty
description: Examples: "Holocene", "Pleistocene", "Ibexian Series"
has version: earliestEpochOrLowestSeries-2009-04-24
issued: 2009-04-24
modified: 2009-07-06
replaces: EarliestEpochOrLowestSeries-2005-07-03
abcd equivalence: not in ABCD
organized in class: Geological Context
dwc_terms status: recommended
comment: The full name of the earliest possible geochronologic epoch or lowest chronostratigraphic series attributable to the stratigraphic horizon from which the cataloged item was collected.

Earliest Era Or Lowest Erathem
type: DatatypeProperty
description: Examples: "Cenozoic", "Mesozoic"
has version: earliestEraOrLowestErathem-2009-04-24
issued: 2009-04-24
modified: 2009-07-06
replaces: EarliestEraOrLowestErathem-2005-07-03
abcd equivalence: not in ABCD
organized in class: Geological Context
dwc_terms status: recommended
comment: The full name of the earliest possible geochronologic era or lowest chronostratigraphic erathem attributable to the stratigraphic horizon from which the cataloged item was collected.

Earliest Period Or Lowest System
type: DatatypeProperty
description: Examples: "Neogene", "Tertiary", "Quaternary"
has version: earliestPeriodOrLowestSystem-2009-04-24
issued: 2009-04-24
modified: 2009-07-06
replaces: EarliestPeriodOrLowestSystem-2005-07-03
abcd equivalence: not in ABCD
organized in class: Geological Context
dwc_terms status: recommended
comment: The full name of the earliest possible geochronologic period or lowest chronostratigraphic system attributable to the stratigraphic horizon from which the cataloged item was collected.

End Day Of Year
type: DatatypeProperty
description: Examples: "1" (=1 Jan), "366" (=31 Dec), "365" (=30 Dec in a leap year, 31 Dec in a non-leap year)
has version: endDayOfYear-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: DayOfYear-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/DateTime/DayNumberEnd
organized in class: Event
dwc_terms status: recommended
comment: The latest ordinal day of the year on which the Event occurred (1 for January 1, 365 for December 31, except in a leap year, in which case it is 366).

Establishment Means
type: DatatypeProperty
description: Examples: "native", "introduced", "naturalised", "invasive", "managed"
has version: establishmentMeans-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/EstablishmentMeans
organized in class: Occurrence
dwc_terms status: recommended
comment: The process by which the biological individual(s) represented in the Occurrence became established at the location. Recommended best practice is to use a controlled vocabulary.

Event Date
type: DatatypeProperty
sub property of: date
description: Examples: "1963-03-08T14:07-0600" is 8 Mar 1963 2:07pm in the time zone six hours earlier than UTC, "2009-02-20T08:40Z" is 20 Feb 2009 8:40am UTC, "1809-02-12" is 12 Feb 1809, "1906-06" is Jun 1906, "1971" is just that year, "2007-03-01T13:00:00Z/2008-05-11T15:30:00Z" is the interval between 1 Mar 2007 1pm UTC and 11 May 2008 3:30pm UTC, "2007-11-13/15" is the interval between 13 Nov 2007 and 15 Nov 2007.
has version: eventDate-2009-04-24
issued: 2009-04-24
modified: 2009-07-01
replaces: EarliestDateCollected-2007-04-17
replaces: LatestDateCollected-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/ISODateTimeBegin
organized in class: Event
dwc_terms status: recommended
comment: The date-time or interval during which an Event occurred. For occurrences, this is the date-time when the event was recorded. Not suitable for a time in a geological context. Recommended best practice is to use an encoding scheme, such as ISO 8601:2004(E).

Event Remarks
type: DatatypeProperty
description: Example: "after the recent rains the river is nearly at flood stage"
has version: eventRemarks-2009-04-24
issued: 2009-01-18
modified: 2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/Notes
organized in class: Event
dwc_terms status: recommended
comment: Comments or notes about the Event.

Event Time
type: DatatypeProperty
description: Examples: "14:07-0600" is 2:07pm in the time zone six hours earlier than UTC, "08:40:21Z" is 8:40:21am UTC, "13:00:00Z/15:30:00Z" is the interval between 1pm UTC and 3:30pm UTC.
has version: eventTime-2009-04-24
issued: 2009-04-24
modified: 2009-04-24
replaces: EndTimeOfDay-2005-07-10
replaces: StartTimeOfDay-2005-07-10
abcd equivalence: accessible from DataSets/DataSet/Units/Unit/Gathering/ISODateTimeBegin and DataSets/DataSet/Units/Unit/Gathering/ISODateTimeEnd
organized in class: Event
dwc_terms status: recommended
comment: The time or interval during which an Event occurred. Recommended best practice is to use an encoding scheme, such as ISO 8601:2004(E).

Family
type: DatatypeProperty
description: Examples: "Felidae", "Monocleaceae"
has version: family-2009-08-24
issued: 2008-11-19
modified: 2009-08-24
replaces: family-2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/HigherTaxa/HigherTaxon/HigherTaxonName with HigherTaxa/HigherTaxon/HigherTaxonRank = familia
organized in class: Taxon
dwc_terms status: recommended
comment: The full scientific name of the family in which the taxon is classified.

Field Notes
type: DatatypeProperty
description: Example: "notes available in Grinnell-Miller Library"
has version: fieldNotes-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: FieldNotes-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/FieldNotes
organized in class: Event
dwc_terms status: recommended
comment: One of a) an indicator of the existence of, b) a reference to (publication, URI), or c) the text of notes taken in the field about the Event.

Field Number
type: DatatypeProperty
description: Example: "RV Sol 87-03-08"
has version: fieldNumber-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: FieldNumber-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/Code
organized in class: Event
dwc_terms status: recommended
comment: An identifier given to the event in the field. Often serves as a link between field notes and the Event.

Footprint SRS
type: DatatypeProperty
description: Example: The WKT for the standard WGS84 SRS (EPSG:4326) is "GEOGCS["GCS_WGS_1984",DATUM["D_WGS_1984",SPHEROID["WGS_1984",6378137,298.257223563]],PRIMEM["Greenwich",0],UNIT["Degree",0.0174532925199433]]" without the enclosing quotes.
has version: footprintSRS-2009-07-06
issued: 2009-07-06
modified: 2009-07-06
abcd equivalence: not in ABCD
organized in class: Location
dwc_terms status: recommended
comment: A Well-Known Text (WKT) representation of the Spatial Reference System (SRS) for the footprintWKT of the Location. Do not use this term to describe the SRS of the decimalLatitude and decimalLongitude, even if it is the same as for the footprintWKT - use the geodeticDatum instead.

Footprint Spatial Fit
type: DatatypeProperty
description: Detailed explanations with graphical examples can be found in the "Guide to Best Practices for Georeferencing", Chapman and Wieczorek, eds. 2006 (http://www.gbif.org/prog/digit/Georeferencing).
has version: footprintSpatialFit-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: FootprintSpatialFit-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/FootprintSpatialFit (ABCD v2.06b)
organized in class: Location
dwc_terms status: recommended
comment: The ratio of the area of the footprint (footprintWKT) to the area of the true (original, or most specific) spatial representation of the Location. Legal values are 0, greater than or equal to 1, or undefined. A value of 1 is an exact match or 100% overlap. A value of 0 should be used if the given footprint does not completely contain the original representation. The footprintSpatialFit is undefined (and should be left blank) if the original representation is a point and the given is not that same point. If both the original and the given georeference are the same point, the footprintSpatialFit is 1.

Footprint WKT
type: DatatypeProperty
description: Example: the one-degree bounding box with opposite corners at (longitude=10, latitude=20) and (longitude=11, latitude=21) would be expressed in well-known text as POLYGON ((10 20, 11 20, 11 21, 10 21, 10 20))
has version: footprintWKT-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: FootprintWKT-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/FootprintWKT (ABCD v2.06b)
organized in class: Location
dwc_terms status: recommended
comment: A Well-Known Text (WKT) representation of the shape (footprint, geometry) that defines the Location. A Location may have both a point-radius representation (see decimalLatitude) and a footprint representation, and they may differ from each other.

Formation
type: DatatypeProperty
description: Examples: "Notch Peak Fromation", "House Limestone", "Fillmore Formation"
has version: formation-2009-04-24
issued: 2009-04-24
modified: 2009-07-06
replaces: Formation-2005-07-03
abcd equivalence: not in ABCD
organized in class: Geological Context
dwc_terms status: recommended
comment: The full name of the lithostratigraphic formation from which the cataloged item was collected.

Genus
type: DatatypeProperty
description: Examples: "Puma", "Monoclea"
has version: genus-2009-08-24
issued: 2008-11-19
modified: 2009-08-24
replaces: genus-2009-04-24
abcd equivalence: {DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Bacterial/GenusOrMonomial or DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Botanical/GenusOrMonomial or DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Viral/GenusOrMonomial or DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Zoological/GenusOrMonomial}
organized in class: Taxon
dwc_terms status: recommended
comment: The full scientific name of the genus in which the taxon is classified.

Geodetic Datum
type: DatatypeProperty
description: Examples: "EPSG:4326", "WGS84", "NAD27", "Campo Inchauspe", "European 1950", "Clarke 1866"
has version: geodeticDatum-2009-04-24
issued: 2008-11-19
modified: 2009-07-06
replaces: GeodeticDatum-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/CoordinatesLatLon/SpatialDatum
organized in class: Location
dwc_terms status: recommended
comment: The ellipsoid, geodetic datum, or spatial reference system (SRS) upon which the geographic coordinates given in decimalLatitude and decimalLongitude as based. Recommended best practice is use the EPSG code as a controlled vocabulary to provide an SRS, if known. Otherwise use a controlled vocabulary for the name or code of the geodetic datum, if known. Otherwise use a controlled vocabulary for the name or code of the ellipsoid, if known. If none of these is known, use the value "unknown".

Georeference Protocol
type: DatatypeProperty
description: Examples: "Guide to Best Practices for Georeferencing" (Chapman and Wieczorek, eds. 2006), Global Biodiversity Information Facility.", "MaNIS/HerpNet/ORNIS Georeferencing Guidelines", "Georeferencing Quick Reference Guide"
has version: georeferenceProtocol-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: GeoreferenceProtocol-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/CoordinateMethod
organized in class: Location
dwc_terms status: recommended
comment: A description or reference to the methods used to determine the spatial footprint, coordinates, and uncertainties.

Georeference Remarks
type: DatatypeProperty
description: Example: "assumed distance by road (Hwy. 101)"
has version: georeferenceRemarks-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: GeoreferenceRemarks-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/GeoreferenceRemarks
organized in class: Location
dwc_terms status: recommended
comment: Notes or comments about the spatial description determination, explaining assumptions made in addition or opposition to the those formalized in the method referred to in georeferenceProtocol.

Georeference Sources
type: DatatypeProperty
description: Examples: "USGS 1:24000 Florence Montana Quad; Terrametrics 2008 on Google Earth"
has version: georeferenceSources-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: GeoreferenceSources-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/GeoreferenceSources
organized in class: Location
dwc_terms status: recommended
comment: A list (concatenated and separated) of maps, gazetteers, or other resources used to georeference the Location, described specifically enough to allow anyone in the future to use the same resources.

Georeference Verification Status
type: DatatypeProperty
description: Examples: "requires verification", "verified by collector", "verified by curator".
has version: georeferenceVerificationStatus-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: GeoreferenceVerificationStatus-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/GeoreferenceVerificationStatus
organized in class: Location
dwc_terms status: recommended
comment: A categorical description of the extent to which the georeference has been verified to represent the best possible spatial description. Recommended best practice is to use a controlled vocabulary.

Georeferenced By
type: DatatypeProperty
sub property of: According To
description: Examples: "Kristina Yamamoto (MVZ); Janet Fang (MVZ)", "Brad Millen (ROM)"
has version: georeferencedBy-2009-04-24
issued: 2009-01-21
modified: 2009-04-24
abcd equivalence: not in ABCD
organized in class: Location
dwc_terms status: recommended
comment: A list (concatenated and separated) of names of people, groups, or organizations who determined the georeference (spatial representation) for the Location.

Georeferenced Date
type: DatatypeProperty
sub property of: date
description: Examples: "1963-03-08T14:07-0600" is 8 Mar 1963 2:07pm in the time zone six hours earlier than UTC, "2009-02-20T08:40Z" is 20 Feb 2009 8:40am UTC, "1809-02-12" is 12 Feb 1809, "1906-06" is Jun 1906, "1971" is just that year, "2007-03-01T13:00:00Z/2008-05-11T15:30:00Z" is the interval between 1 Mar 2007 1pm UTC and 11 May 2008 3:30pm UTC, "2007-11-13/15" is the interval between 13 Nov 2007 and 15 Nov 2007.
has version: georeferencedDate-2011-10-16
issued: 2011-10-16
modified: 2011-10-16
abcd equivalence: not in ABCD
decision: Decision-2011-10-16 9
organized in class: Location
dwc_terms status: recommended
comment: The date on which the Location was georeferenced. Recommended best practice is to use an encoding scheme, such as ISO 8601:2004(E).

Group
type: DatatypeProperty
has version: group-2009-04-24
issued: 2009-04-24
modified: 2009-07-06
replaces: Group-2005-07-03
abcd equivalence: not in ABCD
organized in class: Geological Context
dwc_terms status: recommended
comment: The full name of the lithostratigraphic group from which the cataloged item was collected.

Habitat
type: DatatypeProperty
description: Examples: "oak savanna", "pre-cordilleran steppe"
has version: habitat-2009-04-24
issued: 2008-11-19
modified: 2009-05-17
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/Biotope/Text
organized in class: Event
dwc_terms status: recommended
comment: A category or description of the habitat in which the Event occurred.

Higher Classification
type: DatatypeProperty
description: Example: "Animalia;Chordata;Vertebrata;Mammalia;Theria;Eutheria;Rodentia;Hystricognatha;Hystricognathi;Ctenomyidae;Ctenomyini;Ctenomys"
has version: higherClassification-2009-08-24
issued: 2008-11-19
modified: 2009-08-24
replaces: higherTaxonName-2009-04-24
abcd equivalence: not in ABCD
organized in class: Taxon
dwc_terms status: recommended
comment: A list (concatenated and separated) of taxa names terminating at the rank immediately superior to the taxon referenced in the taxon record. Recommended best practice is to order the list starting with the highest rank and separating the names for each rank with a semi-colon (";").

Higher Geography
type: DatatypeProperty
description: Example: "South America; Argentina; Patagonia; Parque Nacional Nahuel Huapi; Neuquén; Los Lagos" with accompanying values "South America" in Continent, "Argentina" in Country, "Neuquén" in StateProvince, and Los Lagos in County.
has version: higherGeography-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: HigherGeography-2007-04-17
abcd equivalence: {DataSets/DataSet/Units/Unit/Gathering/LocalityText or DataSets/DataSet/Units/Unit/Gathering/NamedAreas/NamedArea/AreaName}
organized in class: Location
dwc_terms status: recommended
comment: A list (concatenated and separated) of geographic names less specific than the information captured in the locality term.

Highest Biostratigraphic Zone
type: DatatypeProperty
has version: highestBiostratigraphicZone-2009-04-24
issued: 2009-04-24
modified: 2009-07-06
replaces: HighestBiostratigraphicZone-2005-07-03
abcd equivalence: not in ABCD
organized in class: Geological Context
dwc_terms status: recommended
comment: The full name of the highest possible geological biostratigraphic zone of the stratigraphic horizon from which the cataloged item was collected.

Identification Qualifier
type: DatatypeProperty
description: Examples: 1) For the determination "Quercus aff. agrifolia var. oxyadenia", identificationQualifier would be "aff. agrifolia var. oxyadenia" with accompanying values "Quercus" in genus, "agrifolia" in specificEpithet, "oxyadenia" in infraspecificEpithet, and "var." in rank. 2) For the determination "Quercus agrifolia cf. var. oxyadenia", identificationQualifier would be "cf. var. oxyadenia " with accompanying values "Quercus" in genus, "agrifolia" in specificEpithet, "oxyadenia" in infraspecificEpithet, and "var." in rank.
has version: identificationQualifier-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: IdentificationQualifier-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/IdentificationQualifier
organized in class: Identification
dwc_terms status: recommended
comment: A brief phrase or a standard term ("cf.", "aff.") to express the determiner's doubts about the Identification.

Identification References
type: DatatypeProperty
description: Example: "Aves del Noroeste Patagonico. Christie et al. 2004."
has version: identificationReferences-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/Identifications/Identification/References
organized in class: Identification
dwc_terms status: recommended
comment: A list (concatenated and separated) of references (publication, global unique identifier, URI) used in the Identification.

Identification Remarks
type: DatatypeProperty
description: Example: "Distinguished between Anthus correndera and Anthus hellmayri based on the comparative lengths of the uñas."
has version: identificationRemarks-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/Identifications/Identification/Notes
organized in class: Identification
dwc_terms status: recommended
comment: Comments or notes about the Identification.

Identification Verification Status
type: DatatypeProperty
description: Examples: "0", "4"
has version: identificationVerificationStatus-2011-10-16
issued: 2011-10-16
modified: 2011-10-16
abcd equivalence: not in ABCD
decision: Decision-2011-10-16 10
organized in class: Identification
dwc_terms status: recommended
comment: A categorical indicator of the extent to which the taxonomic identification has been verified to be correct. Recommended best practice is to use a controlled vocabulary such as that used in HISPID/ABCD.

Identified By
type: DatatypeProperty
sub property of: According To
description: Examples: "James L. Patton", "Theodore Pappenfuss; Robert Macey"
has version: identifiedBy-2009-08-24
issued: 2008-11-19
modified: 2009-08-24
replaces: identifiedBy-2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/Identifications/Identification/Identifiers/IdentifiersText
organized in class: Identification
dwc_terms status: recommended
comment: A list (concatenated and separated) of names of people, groups, or organizations who assigned the Taxon to the subject.

Individual Count
type: DatatypeProperty
description: Examples: "1", "25"
has version: individualCount-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: IndividualCount-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/SiteMeasurementsOrFacts/SiteMeasurementOrFact/MeasurementOrFactAtomised/LowerValue
organized in class: Occurrence
dwc_terms status: recommended
comment: The number of individuals represented present at the time of the Occurrence.

Information Withheld
type: DatatypeProperty
description: Examples: "location information not given for endangered species", "collector identities withheld", "ask about tissue samples"
has version: informationWithheld-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: InformationWithheld-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/InformationWithheld
organized in class: all
dwc_terms status: recommended
comment: Additional information that exists, but that has not been shared in the given record.

Infraspecific Epithet
type: DatatypeProperty
description: Examples: "concolor", "oxyadenia", "sayi"
has version: infraspecificEpithet-2009-08-24
issued: 2008-11-19
modified: 2009-08-24
replaces: infraspecificEpithet-2009-04-24
abcd equivalence: {DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Bacterial/SubspeciesEpithet or DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Botanical/SecondEpithet or DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Zoological/SubspeciesEpithet}
organized in class: Taxon
dwc_terms status: recommended
comment: The name of the lowest or terminal infraspecific epithet of the scientificName, excluding any rank designation.

Institution Code
type: DatatypeProperty
description: Examples: "MVZ", "FMNH", "AKN-CLO", "University of California Museum of Paleontology (UCMP)"
has version: institutionCode-2009-09-11
issued: 2008-11-19
modified: 2013-10-04
replaces: institutionCode-2009-08-24
abcd equivalence: DataSets/DataSet/Units/Unit/SourceInstitutionID
organized in class: all
dwc_terms status: recommended
comment: The name (or acronym) in use by the institution having custody of the object(s) or information referred to in the record.

Institution ID
type: DatatypeProperty
has version: institutionID-2009-09-11
issued: 2009-09-11
modified: 2013-10-04
abcd equivalence: DataSets/DataSet/Units/Unit/SourceInstitutionID
organized in class: all
dwc_terms status: recommended
comment: An identifier for the institution having custody of the object(s) or information referred to in the record.

Island
type: DatatypeProperty
description: Examples: "Isla Victoria", "Vancouver", "Viti Levu", "Zanzibar"
has version: island-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: Island-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/NamedAreas/NamedArea/AreaName with NamedAreas/NamedArea/AreaClass= Island
organized in class: Location
dwc_terms status: recommended
comment: The name of the island on or near which the Location occurs. Recommended best practice is to use a controlled vocabulary such as the Getty Thesaurus of Geographic Names.

Island Group
type: DatatypeProperty
description: Examples: "Alexander Archipelago", "Seychelles"
has version: islandGroup-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: IslandGroup-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/NamedAreas/NamedArea/AreaName with NamedAreas/NamedArea/AreaClass= Island group
organized in class: Location
dwc_terms status: recommended
comment: The name of the island group in which the Location occurs. Recommended best practice is to use a controlled vocabulary such as the Getty Thesaurus of Geographic Names.

Kingdom
type: DatatypeProperty
description: Examples: "Animalia", "Plantae"
has version: kingdom-2009-08-24
issued: 2008-11-19
modified: 2009-08-24
replaces: kingdom-2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/HigherTaxa/HigherTaxon/HigherTaxonName with HigherTaxa/HigherTaxon/HigherTaxonRank = regnum
organized in class: Taxon
dwc_terms status: recommended
comment: The full scientific name of the kingdom in which the taxon is classified.

Latest AgeOr Highest Stage
type: DatatypeProperty
description: Examples: "Atlantic", "Boreal", "Skullrockian"
has version: latestAgeOrHighestStage-2009-04-24
issued: 2009-04-24
modified: 2009-07-06
replaces: LatestAgeOrHighestStage-2005-07-03
abcd equivalence: not in ABCD
organized in class: Geological Context
dwc_terms status: recommended
comment: The full name of the latest possible geochronologic age or highest chronostratigraphic stage attributable to the stratigraphic horizon from which the cataloged item was collected.

Latest Eon Or Highest Eonothem
type: DatatypeProperty
description: Examples: "Phanerozoic", "Proterozoic"
has version: latestEonOrHighestEonothem-2009-04-24
issued: 2009-04-24
modified: 2009-07-06
replaces: LatestEonOrLowestEonothem-2005-07-03
abcd equivalence: not in ABCD
organized in class: Geological Context
dwc_terms status: recommended
comment: The full name of the latest possible geochronologic eon or highest chrono-stratigraphic eonothem or the informal name ("Precambrian") attributable to the stratigraphic horizon from which the cataloged item was collected.

Latest Epoch Or Highest Series
type: DatatypeProperty
description: Examples: "Holocene", "Pleistocene", "Ibexian Series"
has version: latestEpochOrHighestSeries-2009-04-24
issued: 2009-04-24
modified: 2009-07-06
replaces: LatestEpochOrHighestSeries-2005-07-03
abcd equivalence: not in ABCD
organized in class: Geological Context
dwc_terms status: recommended
comment: The full name of the latest possible geochronologic epoch or highest chronostratigraphic series attributable to the stratigraphic horizon from which the cataloged item was collected.

Latest Era Or Highest Erathem
type: DatatypeProperty
description: Examples: "Cenozoic", "Mesozoic"
has version: latestEraOrHighestErathem-2009-04-24
issued: 2009-04-24
modified: 2009-07-06
replaces: LatestEraOrHighestErathem-2005-07-03
abcd equivalence: not in ABCD
organized in class: Geological Context
dwc_terms status: recommended
comment: The full name of the latest possible geochronologic era or highest chronostratigraphic erathem attributable to the stratigraphic horizon from which the cataloged item was collected.

Latest Period Or Highest System
type: DatatypeProperty
description: Examples: "Neogene", "Tertiary", "Quaternary"
has version: latestPeriodOrHighestSystem-2009-04-24
issued: 2009-04-24
modified: 2009-07-06
replaces: LatestPeriodOrHighestSystem-2005-07-03
abcd equivalence: not in ABCD
organized in class: Geological Context
dwc_terms status: recommended
comment: The full name of the latest possible geochronologic period or highest chronostratigraphic system attributable to the stratigraphic horizon from which the cataloged item was collected.

Life Stage
type: DatatypeProperty
description: Examples: "egg", "eft", "juvenile", "adult", "2 adults 4 juveniles"
has version: lifeStage-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: LifeStage-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/MycologicalUnit/MycologicalSexualStage or DataSets/DataSet/Units/Unit/MycologicalUnit/MycologicalLiveStages/MycologicalLiveStage (Note DwC spec uses ”MycologicalLifeStage” or DataSets/DataSet/Units/Unit/ZoologicalUnit/PhasesOrStages/PhaseOrStage
organized in class: Occurrence
dwc_terms status: recommended
comment: The age class or life stage of the biological individual(s) at the time the Occurrence was recorded. Recommended best practice is to use a controlled vocabulary.

Lithostratigraphic Terms
type: DatatypeProperty
has version: lithostratigraphicTerms-2009-04-24
issued: 2009-04-24
modified: 2009-07-06
replaces: LithostratigraphicTerms-2005-07-03
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/Stratigraphy/LithostratigraphicTerms
organized in class: Geological Context
dwc_terms status: recommended
comment: The combination of all litho-stratigraphic names for the rock from which the cataloged item was collected.

Locality
type: DatatypeProperty
description: Example: "Bariloche, 25 km NNE via Ruta Nacional 40 (=Ruta 237)"
has version: locality-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: Locality-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/NamedAreas/NamedArea/AreaName
organized in class: Location
dwc_terms status: recommended
comment: The specific description of the place. Less specific geographic information can be provided in other geographic terms (higherGeography, continent, country, stateProvince, county, municipality, waterBody, island, islandGroup). This term may contain information modified from the original to correct perceived errors or standardize the description.

Location According To
type: DatatypeProperty
sub property of: According To
description: Examples: "Getty Thesaurus of Geographic Names", "GADM"
has version: locationAccordingTo-2009-08-24
issued: 2009-08-24
modified: 2009-08-24
abcd equivalence: not in ABCD
organized in class: Location
dwc_terms status: recommended
comment: Information about the source of this Location information. Could be a publication (gazetteer), institution, or team of individuals.

Location Remarks
type: DatatypeProperty
description: Example: "under water since 2005"
has version: locationRemarks-2009-04-24
issued: 2009-01-18
modified: 2009-04-24
replaces: SamplingLocationRemarks-2009-01-18
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/AreaDetail
organized in class: Location
dwc_terms status: recommended
comment: Comments or notes about the Location.

Lowest Biostratigraphic Zone
type: DatatypeProperty
has version: lowestBiostratigraphicZone-2009-04-24
issued: 2009-04-24
modified: 2009-07-06
replaces: LowestBiostratigraphicZone-2005-07-03
abcd equivalence: not in ABCD
organized in class: Geological Context
dwc_terms status: recommended
comment: The full name of the lowest possible geological biostratigraphic zone of the stratigraphic horizon from which the cataloged item was collected.

Maximum Depth In Meters
type: DatatypeProperty
description: Example: "200"
has version: maximumDepthInMeters-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: MaximumDepthInMeters-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/Depth/MeasurementOrFactAtomised/UpperValue
organized in class: Location
dwc_terms status: recommended
comment: The greater depth of a range of depth below the local surface, in meters.

Maximum Distance Above Surface In Meters
type: DatatypeProperty
description: Example: 1.5 meter sediment core from the bottom of a lake (at depth 20m) at 300m elevation; VerbatimElevation: "300m" MinimumElevationInMeters: "300", MaximumElevationInMeters: "300", VerbatimDepth: "20m", MinimumDepthInMeters: "20", MaximumDepthInMeters: "20", minimumDistanceAboveSurfaceInMeters: "0", maximumDistanceAboveSurfaceInMeters: "-1.5"
has version: maximumDistanceAboveSurfaceInMeters-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/Height/MeasurementOrFactAtomised/UpperValue
organized in class: Location
dwc_terms status: recommended
comment: The greater distance in a range of distance from a reference surface in the vertical direction, in meters. Use positive values for locations above the surface, negative values for locations below. If depth measures are given, the reference surface is the location given by the depth, otherwise the reference surface is the location given by the elevation.

Maximum Elevation In Meters
type: DatatypeProperty
description: Example: "200"
has version: maximumElevationInMeters-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: MaximumElevationInMeters-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/Altitude/MeasurementOrFactAtomised/UpperValue
organized in class: Location
dwc_terms status: recommended
comment: The upper limit of the range of elevation (altitude, usually above sea level), in meters.

Measurement Accuracy
type: DatatypeProperty
description: Examples: "0.01", "normal distribution with variation of 2 m"
has version: measurementAccuracy-2009-04-24
issued: 2009-01-18
modified: 2009-04-24
replaces: eventMeasurementAccuracy-2009-04-24
replaces: occurrenceMeasurementAccuracy-2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/MeasurementsOrFacts/MeasurementOrFact/MeasurementOrFactAtomised/Accuracy or DataSet/Units/Unit/Gathering/SiteMeasurementsOrFacts/SiteMeasurementOrFact/MeasurementOrFactAtomised/Accuracy or DataSets/DataSet/Units/Unit/Gathering/Aspect/Accuracy or DataSets/DataSet/Units/Unit/Gathering/Altitude/MeasurementOrFactAtomised/Accuracy or DataSets/DataSet/Units/Unit/Gathering/Depth/MeasurementOrFactAtomised/Accuracy or DataSets/DataSet/Units/Unit/Gathering/Biotope/MeasurementsOrFacts/MeasurementOrFactAtomised/Accuracy or DataSets/DataSet/Units/Unit/MeasurementsOrFacts/MeasurementOrFact/MeasurementOrFactAtomised/Accuracy
organized in class: Measurement or Fact
dwc_terms status: recommended
comment: The description of the potential error associated with the measurementValue.

Measurement Determined By
type: DatatypeProperty
sub property of: According To
description: Examples: "Javier de la Torre", "Julie Woodruff; Eileen Lacey"
has version: measurementDeterminedBy-2009-04-24
issued: 2009-01-23
modified: 2009-04-24
replaces: eventMeasurementDeterminedBy-2009-04-24
replaces: occurrenceMeasurementDeterminedBy-2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/MeasurementsOrFacts/MeasurementOrFact/MeasurementOrFactAtomised/MeasuredBy or DataSets/DataSet/Units/Unit/Gathering/Altitude/MeasurementOrFactAtomised/MeasuredBy or DataSets/DataSet/Units/Unit/Gathering/Depth/MeasurementOrFactAtomised/MeasuredBy or DataSets/DataSet/Units/Unit/Gathering/Height/MeasurementOrFactAtomised/MeasuredBy or DataSets/DataSet/Units/Unit/Gathering/SiteMeasurementsOrFacts/SiteMeasurementOrFact/MeasurementOrFactAtomised/MeasuredBy or DataSets/DataSet/Units/Unit/Gathering/Biotope/MeasurementsOrFacts/MeasurementOrFactAtomised/MeasuredBy
organized in class: Measurement or Fact
dwc_terms status: recommended
comment: A list (concatenated and separated) of names of people, groups, or organizations who determined the value of the MeasurementOrFact.

Measurement Determined Date
type: DatatypeProperty
sub property of: date
description: Examples: "1963-03-08T14:07-0600" is 8 Mar 1963 2:07pm in the time zone six hours earlier than UTC, "2009-02-20T08:40Z" is 20 Feb 2009 8:40am UTC, "1809-02-12" is 12 Feb 1809, "1906-06" is Jun 1906, "1971" is just that year, "2007-03-01T13:00:00Z/2008-05-11T15:30:00Z" is the interval between 1 Mar 2007 1pm UTC and 11 May 2008 3:30pm UTC, "2007-11-13/15" is the interval between 13 Nov 2007 and 15 Nov 2007.
has version: measurementDeterminedDate-2009-04-24
issued: 2009-01-23
modified: 2009-04-24
replaces: eventMeasurementDeterminedDate-2009-04-24
replaces: occurrenceMeasurementDeterminedDate-2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/MeasurementsOrFacts/MeasurementOrFact/MeasurementOrFactAtomised/MeasurementDateTime or DataSets/DataSet/Units/Unit/Gathering/Altitude/MeasurementOrFactAtomised/MeasurementDateTime or DataSets/DataSet/Units/Unit/Gathering/Depth/MeasurementOrFactAtomised/MeasurementDateTime or DataSets/DataSet/Units/Unit/Gathering/Height/MeasurementOrFactAtomised/MeasurementDateTime or DataSets/DataSet/Units/Unit/Gathering/SiteMeasurementsOrFacts/SiteMeasurementOrFact/MeasurementOrFactAtomised/MeasurementDateTime or DataSets/DataSet/Units/Unit/Gathering/Biotope/MeasurementsOrFacts/MeasurementOrFactAtomised/MeasurementDateTime
organized in class: Measurement or Fact
dwc_terms status: recommended
comment: The date on which the MeasurementOrFact was made. Recommended best practice is to use an encoding scheme, such as ISO 8601:2004(E).

Measurement Method
type: DatatypeProperty
description: Examples: "minimum convex polygon around burrow entrances" for a home range area, "barometric altimeter" for an elevation
has version: measurementMethod-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
abcd equivalence: /DataSets/DataSet/Units/Unit/MeasurementsOrFacts/MeasurementOrFact/MeasurementOrFactAtomised/Method or /DataSets/DataSet/Units/Unit/Gathering/Biotope/MeasurementsOrFacts/MeasurementOrFactAtomised/Method or /DataSets/DataSet/Units/Unit/Gathering/SiteMeasurementsOrFacts/SiteMeasurementOrFact/MeasurementOrFactAtomised/Method
organized in class: Measurement or Fact
dwc_terms status: recommended
comment: A description of or reference to (publication, URI) the method or protocol used to determine the measurement, fact, characteristic, or assertion.

Measurement Remarks
type: DatatypeProperty
description: Example: "tip of tail missing"
has version: measurementRemarks-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: eventMeasurementRemarks-2009-04-24
replaces: occurrenceMeasurementRemarks-2009-04-24
abcd equivalence: not in ABCD
organized in class: Measurement or Fact
dwc_terms status: recommended
comment: Comments or notes accompanying the MeasurementOrFact.

Measurement Type
type: DatatypeProperty
description: Examples: "tail length", "temperature", "trap line length", "survey area", "trap type"
has version: measurementType-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: eventMeasurementType-2009-04-24
replaces: occurrenceMeasurementType-2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/MeasurementsOrFacts/MeasurementOrFact/MeasurementOrFactAtomised/Parameter or DataSets/DataSet/Units/Unit/Gathering/SiteMeasurementsOrFacts/MeasurementOrFact/MeasurementOrFactAtomised/Parameter
organized in class: Measurement or Fact
dwc_terms status: recommended
comment: The nature of the measurement, fact, characteristic, or assertion. Recommended best practice is to use a controlled vocabulary.

Measurement Unit
type: DatatypeProperty
description: Examples: "mm", "C", "km", "ha"
has version: measurementUnit-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: eventMeasurementUnit-2009-04-24
replaces: occurrenceMeasurementUnit-2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/SiteMeasurementsOrFacts/MeasurementOrFact/MeasurementOrFactAtomised/UnitOfMeasurement or DataSets/DataSet/Units/Unit/Gathering/SiteMeasurementsOrFacts/MeasurementOrFact/MeasurementOrFactAtomised/UnitOfMeasurement
organized in class: Measurement or Fact
dwc_terms status: recommended
comment: The units associated with the measurementValue. Recommended best practice is to use the International System of Units (SI).

Measurement Value
type: DatatypeProperty
description: Examples: "45", "20", "1", "14.5", "UV-light"
has version: measurementValue-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: eventMeasurementValue-2009-04-24
replaces: occurrenceMeasurementValue-2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/MeasurementsOrFacts/MeasurementOrFact/MeasurementOrFactAtomised/LowerValue or DataSets/DataSet/Units/Unit/MeasurementsOrFacts/MeasurementOrFact/MeasurementOrFactAtomised/UpperValue or DataSets/DataSet/Units/Unit/Gathering/SiteMeasurementsOrFacts/SiteMeasurementOrFact/MeasurementOrFactAtomised/LowerValue or DataSets/DataSet/Units/Unit/Gathering/SiteMeasurementsOrFacts/SiteMeasurementOrFact/MeasurementOrFactAtomised/UpperValue or DataSets/DataSet/Units/Unit/Gathering/Altitude/MeasurementOrFactAtomised/LowerValue or DataSets/DataSet/Units/Unit/Gathering/Altitude/MeasurementOrFactAtomised/UpperValue or DataSets/DataSet/Units/Unit/Gathering/Depth/MeasurementOrFactAtomised/LowerValue or DataSets/DataSet/Units/Unit/Gathering/Depth/MeasurementOrFactAtomised/UpperValue or DataSets/DataSet/Units/Unit/Gathering/Biotope/MeasurementsOrFacts/MeasurementOrFactAtomised/LowerValue or DataSets/DataSet/Units/Unit/Gathering/Biotope/MeasurementsOrFacts/MeasurementOrFactAtomised/UpperValue or DataSets/DataSet/Units/Unit/Gathering/Height/MeasurementOrFactAtomised/LowerValue or DataSets/DataSet/Units/Unit/Gathering/Height/MeasurementOrFactAtomised/UpperValue
organized in class: Measurement or Fact
dwc_terms status: recommended
comment: The value of the measurement, fact, characteristic, or assertion.

Member
type: DatatypeProperty
description: Examples: "Lava Dam Member", "Hellnmaria Member"
has version: member-2009-04-24
issued: 2009-04-24
modified: 2009-07-06
replaces: Member-2005-07-03
abcd equivalence: not in ABCD
organized in class: Geological Context
dwc_terms status: recommended
comment: The full name of the lithostratigraphic member from which the cataloged item was collected.

Minimum Depth In Meters
type: DatatypeProperty
description: Example: "100"
has version: minimumDepthInMeters-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: MinimumDepthInMeters-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/Depth/MeasurementOrFactAtomised/LowerValue
organized in class: Location
dwc_terms status: recommended
comment: The lesser depth of a range of depth below the local surface, in meters.

Minimum Distance Above Surface In Meters
type: DatatypeProperty
description: Example: 1.5 meter sediment core from the bottom of a lake (at depth 20m) at 300m elevation; VerbatimElevation: "300m" MinimumElevationInMeters: "300", MaximumElevationInMeters: "300", VerbatimDepth: "20m", MinimumDepthInMeters: "20", MaximumDepthInMeters: "20", minimumDistanceAboveSurfaceInMeters: "0", maximumDistanceAboveSurfaceInMeters: "-1.5"
has version: minimumDistanceAboveSurfaceInMeters-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/Height/MeasurementOrFactAtomised/LowerValue
organized in class: Location
dwc_terms status: recommended
comment: The lesser distance in a range of distance from a reference surface in the vertical direction, in meters. Use positive values for locations above the surface, negative values for locations below. If depth measures are given, the reference surface is the location given by the depth, otherwise the reference surface is the location given by the elevation.

Minimum Elevation In Meters
type: DatatypeProperty
description: Example: "100"
has version: minimumElevationInMeters-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: MinimumElevationInMeters-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/Altitude/MeasurementOrFactAtomised/LowerValue
organized in class: Location
dwc_terms status: recommended
comment: The lower limit of the range of elevation (altitude, usually above sea level), in meters.

Month
type: DatatypeProperty
description: Examples: "1" (=January), "10" (=October)
has version: month-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: MonthCollected-2003-06-17
abcd equivalence: accessible from DataSets/DataSet/Units/Unit/Gathering/ISODateTimeBegin
organized in class: Event
dwc_terms status: recommended
comment: The ordinal month in which the Event occurred.

Municipality
type: DatatypeProperty
description: Examples: "Holzminden"
has version: municipality-2009-08-24
issued: 2008-11-19
modified: 2009-08-24
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/NamedAreas/NamedArea/AreaName
organized in class: Location
dwc_terms status: recommended
comment: The full, unabbreviated name of the next smaller administrative region than county (city, municipality, etc.) in which the Location occurs. Do not use this term for a nearby named place that does not contain the actual location.

Name According To
type: DatatypeProperty
sub property of: According To
description: Example: "McCranie, J. R., D. B. Wake, and L. D. Wilson. 1996. The taxonomic status of Bolitoglossa schmidti, with comments on the biology of the Mesoamerican salamander Bolitoglossa dofleini (Caudata: Plethodontidae). Carib. J. Sci. 32:395-398.", "Werner Greuter 2008", "Lilljeborg 1861, Upsala Univ. Arsskrift, Math. Naturvet., pp. 4, 5"
has version: nameAccordingTo-2009-09-21
issued: 2008-11-19
modified: 2009-09-21
replaces: taxonAccordingTo-2009-04-24
abcd equivalence: not in ABCD
organized in class: Taxon
dwc_terms status: recommended
comment: The reference to the source in which the specific taxon concept circumscription is defined or implied - traditionally signified by the Latin "sensu" or "sec." (from secundum, meaning "according to"). For taxa that result from identifications, a reference to the keys, monographs, experts and other sources should be given.

Name Published In
type: DatatypeProperty
sub property of: bibliographicCitation
description: Examples: "Pearson O. P., and M. I. Christie. 1985. Historia Natural, 5(37):388", "Forel, Auguste, Diagnosies provisoires de quelques espèces nouvelles de fourmis de Madagascar, récoltées par M. Grandidier., Annales de la Societe Entomologique de Belgique, Comptes-rendus des Seances 30, 1886"
has version: namePublishedIn-2009-09-21
issued: 2008-11-19
modified: 2009-09-21
replaces: namePublishedIn-2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/SpecimenUnit/NomenclaturalTypeDesignations/NomenclaturalTypeDesignation/NomenclaturalReference/TitleCitation
organized in class: Taxon
dwc_terms status: recommended
comment: A reference for the publication in which the scientificName was originally established under the rules of the associated nomenclaturalCode.

Name Published In Year
type: DatatypeProperty
description: Examples: "1915", "2008"
has version: namePublishedInYear-2011-10-16
issued: 2011-10-16
modified: 2011-10-16
abcd equivalence: not in ABCD
decision: Decision-2011-10-16 8
organized in class: Taxon
dwc_terms status: recommended
comment: The four-digit year in which the scientificName was published.

Nomenclatural Code
type: DatatypeProperty
description: Examples: "ICBN", "ICZN", "BC", "ICNCP", "BioCode", "ICZN; ICBN"
has version: nomenclaturalCode-2009-09-21
issued: 2008-11-19
modified: 2009-09-21
replaces: NomenclaturalCode-2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/Code
organized in class: Taxon
dwc_terms status: recommended
comment: The nomenclatural code (or codes in the case of an ambiregnal name) under which the scientificName is constructed. Recommended best practice is to use a controlled vocabulary.

Nomenclatural Status
type: DatatypeProperty
description: Examples: "nom. ambig.", "nom. illeg.", "nom. subnud."
has version: nomenclaturalStatus-2009-04-24
issued: 2009-01-18
modified: 2009-04-24
abcd equivalence: (DataSets/DataSet/Units/Unit/SpecimenUnit/NomenclaturalTypeDesignations/NomenclaturalTypeDesignation/NomenclaturalReference/TitleCitation) pro parte
organized in class: Taxon
dwc_terms status: recommended
comment: The status related to the original publication of the name and its conformance to the relevant rules of nomenclature. It is based essentially on an algorithm according to the business rules of the code. It requires no taxonomic opinion.

Occurrence Remarks
type: DatatypeProperty
description: Example: "found dead on road"
has version: occurrenceRemarks-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: SampleRemarks-2009-01-18
abcd equivalence: DataSets/DataSet/Units/Unit/Notes
organized in class: Occurrence
dwc_terms status: recommended
comment: Comments or notes about the Occurrence.

Occurrence Status
type: DatatypeProperty
description: Examples: "present", "absent"
has version: occurrenceStatus-2009-09-17
issued: 2009-09-17
modified: 2009-09-17
abcd equivalence: not in ABCD
organized in class: Occurrence
dwc_terms status: recommended
comment: A statement about the presence or absence of a Taxon at a Location. Recommended best practice is to use a controlled vocabulary.

Order
type: DatatypeProperty
description: Examples: "Carnivora", "Monocleales"
has version: order-2009-08-24
issued: 2008-11-19
modified: 2009-08-24
replaces: order-2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/HigherTaxa/HigherTaxon/HigherTaxonName with HigherTaxa/HigherTaxon/HigherTaxonRank = ordo
organized in class: Taxon
dwc_terms status: recommended
comment: The full scientific name of the order in which the taxon is classified.

Organism Name
type: DatatypeProperty
description: Examples: "Huberta", "Boab Prison Tree", "J pod".
has version: organismName-2014-10-23
issued: 2014-10-23
modified: 2014-10-23
abcd equivalence: not in ABCD
decision: Decision-2014-10-26 14
organized in class: Organism
dwc_terms status: recommended
comment: A description of the kind of Organism instance. Can be used to indicate whether the Organism instance represents a discrete organism or if it represents a particular type of aggregation. Recommended best practice is to use a controlled vocabulary.

Organism Quantity
type: DatatypeProperty
description: An organismQuantity must have a corresponding organismQuantityType, e.g., "27" for organismQuantity with "individuals" for organismQuantityType; "12.5" for organismQuantity with "%biomass" for organismQuantityType; "r" for organismQuantity with "BraunBlanquetScale" for organismQuantityType.
has version: organismQuantity-2014-12-23
issued: 2014-11-07
modified: 2015-03-19
abcd equivalence: not in ABCD
decision: Decision-2015-03-19 18
organized in class: Occurrence
dwc_terms status: recommended
comment: A number or enumeration value for the quantity of organisms.

Organism Quantity Type
type: DatatypeProperty
description: An organismQuantityType must have a corresponding organismQuantity, e.g., "27" for organismQuantity with "individuals" for organismQuantityType; "12.5" for organismQuantity with "%biomass" for organismQuantityType; "r" for organismQuantity with "BraunBlanquetScale" for organismQuantityType.
has version: organismQuantityType-2014-12-23
issued: 2014-11-07
modified: 2015-03-19
abcd equivalence: not in ABCD
decision: Decision-2015-03-19 18
organized in class: Occurrence
dwc_terms status: recommended
comment: The type of quantification system used for the quantity of organisms.

Organism Remarks
type: DatatypeProperty
description: Example: "One of a litter of six."
has version: organismName-2014-10-23
issued: 2014-10-23
modified: 2014-10-23
abcd equivalence: not in ABCD
decision: Decision-2014-10-26 14
organized in class: Organism
dwc_terms status: recommended
comment: Comments or notes about the Organism instance.

Organism Scope
type: DatatypeProperty
description: This term is not intended to be used to specify a type of taxon. To describe the kind of Organism using a URI object in RDF, use rdf:type (http://www.w3.org/1999/02/22-rdf-syntax-ns#type) instead. Examples: "multicellular organism", "virus", "clone" "pack", "colony".
has version: organismScope-2014-10-23
issued: 2014-10-23
modified: 2014-10-23
abcd equivalence: not in ABCD
decision: Decision-2014-10-26 14
organized in class: Organism
dwc_terms status: recommended
comment: A textual name or label assigned to an Organism instance.

Original Name Usage
type: DatatypeProperty
description: Examples: "Pinus abies", "Gasterosteus saltatrix Linnaeus 1768"
has version: originalNameUsage-2009-09-21
issued: 2008-11-19
modified: 2009-09-21
replaces: basionym-2009-04-24
abcd equivalence: not in ABCD
organized in class: Taxon
dwc_terms status: recommended
comment: The taxon name, with authorship and date information if known, as it originally appeared when first established under the rules of the associated nomenclaturalCode. The basionym (botany) or basonym (bacteriology) of the scientificName or the senior/earlier homonym for replaced names.

Other Catalog Numbers
type: DatatypeProperty
description: Examples: "FMNH:Mammal:1234", "NPS YELLO6778; MBG 33424"
has version: otherCatalogNumbers-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: OtherCatalogNumbers-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/SpecimenUnit/History/PreviousUnitsText
organized in class: Occurrence
dwc_terms status: recommended
comment: A list (concatenated and separated) of previous or alternate fully qualified catalog numbers or other human-used identifiers for the same Occurrence, whether in the current or any other data set or collection.

Owner Institution Code
type: DatatypeProperty
description: Examples: "NPS", "APN", "InBio"
has version: ownerInstitutionCode-2009-08-24
issued: 2009-08-24
modified: 2013-10-04
abcd equivalence: not in ABCD
organized in class: all
dwc_terms status: recommended
comment: The name (or acronym) in use by the institution having ownership of the object(s) or information referred to in the record.

Parent Name Usage
type: DatatypeProperty
description: Examples: "Rubiaceae", "Gruiformes", "Testudinae"
has version: parentNameUsage-2009-09-21
issued: 2009-08-24
modified: 2009-09-21
abcd equivalence: DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/HigherTaxa/HigherTaxon/HigherTaxonName
organized in class: Taxon
dwc_terms status: recommended
comment: The full name, with authorship and date information if known, of the direct, most proximate higher-rank parent taxon (in a classification) of the most specific element of the scientificName.

Phylum
type: DatatypeProperty
description: Examples: "Chordata" (phylum), "Bryophyta" (division)
has version: phylum-2009-08-24
issued: 2008-11-19
modified: 2009-08-24
replaces: phylum-2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/HigherTaxa/HigherTaxon/HigherTaxonName with HigherTaxa/HigherTaxon/HigherTaxonRank = phylum
organized in class: Taxon
dwc_terms status: recommended
comment: The full scientific name of the phylum or division in which the taxon is classified.

Point Radius Spatial Fit
type: DatatypeProperty
description: Detailed explanations with graphical examples can be found in the "Guide to Best Practices for Georeferencing", Chapman and Wieczorek, eds. 2006 (http://www.gbif.org/prog/digit/Georeferencing).
has version: pointRadiusSpatialFit-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: PointRadiusSpatialFit-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/PointRadiusSpatialFit
organized in class: Location
dwc_terms status: recommended
comment: The ratio of the area of the point-radius (decimalLatitude, decimalLongitude, coordinateUncertaintyInMeters) to the area of the true (original, or most specific) spatial representation of the Location. Legal values are 0, greater than or equal to 1, or undefined. A value of 1 is an exact match or 100% overlap. A value of 0 should be used if the given point-radius does not completely contain the original representation. The pointRadiusSpatialFit is undefined (and should be left blank) if the original representation is a point without uncertainty and the given georeference is not that same point (without uncertainty). If both the original and the given georeference are the same point, the pointRadiusSpatialFit is 1.

Preparations
type: DatatypeProperty
description: Examples: "skin; skull; skeleton", "whole animal (ETOH); tissue (EDTA)", "fossil", "cast", "photograph", "DNA extract"
has version: preparations-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: Preparations-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/SpecimenUnit/Preparations/PreparationsText
organized in class: Occurrence
dwc_terms status: recommended
comment: A list (concatenated and separated) of preparations and preservation methods for a specimen.

Previous Identifications
type: DatatypeProperty
description: Example: "Anthus sp., field ID by G. Iglesias; Anthus correndera, expert ID by C. Cicero 2009-02-12 based on morphology"
has version: previousIdentifications-2009-05-18
issued: 2008-11-19
modified: 2009-05-18
replaces: previousIdentifications-2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/Identifications/Identification with PreferredFlag = false
organized in class: Occurrence
dwc_terms status: recommended
comment: A list (concatenated and separated) of previous assignments of names to the Occurrence.

Record Number
type: DatatypeProperty
description: Example: "OPP 7101"
has version: recordNumber-2009-04-24
issued: 2008-11-19
modified: 2009-05-18
replaces: CollectorNumber-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/CollectorsFieldNumber
organized in class: Occurrence
dwc_terms status: recommended
comment: An identifier given to the Occurrence at the time it was recorded. Often serves as a link between field notes and an Occurrence record, such as a specimen collector's number.

Recorded By
type: DatatypeProperty
sub property of: According To
description: Example: "Oliver P. Pearson; Anita K. Pearson" where the value in recordNumber "OPP 7101" corresponds to the number for the specimen in the field catalog (collector number) of Oliver P. Pearson.
has version: recordedBy-2009-04-24
issued: 2008-11-19
modified: 2009-05-18
replaces: Collector-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/GatheringAgents/GatheringAgentsText
organized in class: Occurrence
dwc_terms status: recommended
comment: A list (concatenated and separated) of names of people, groups, or organizations responsible for recording the original Occurrence. The primary collector or observer, especially one who applies a personal identifier (recordNumber), should be listed first.

Relationship According To
type: DatatypeProperty
sub property of: According To
description: Example: "Julie Woodruff"
has version: relationshipAccordingTo-2009-04-24
issued: 2009-04-24
modified: 2009-04-24
abcd equivalence: not in ABCD
organized in class: Resource Relationship
dwc_terms status: recommended
comment: The source (person, organization, publication, reference) establishing the relationship between the two resources.

Relationship Established Date
type: DatatypeProperty
sub property of: date
description: Examples: "1963-03-08T14:07-0600" is 8 Mar 1963 2:07pm in the time zone six hours earlier than UTC, "2009-02-20T08:40Z" is 20 Feb 2009 8:40am UTC, "1809-02-12" is 12 Feb 1809, "1906-06" is Jun 1906, "1971" is just that year, "2007-03-01T13:00:00Z/2008-05-11T15:30:00Z" is the interval between 1 Mar 2007 1pm UTC and 11 May 2008 3:30pm UTC, "2007-11-13/15" is the interval between 13 Nov 2007 and 15 Nov 2007.
has version: relationshipEstablishedDate-2009-04-24
issued: 2009-04-24
modified: 2009-04-24
abcd equivalence: not in ABCD
organized in class: Resource Relationship
dwc_terms status: recommended
comment: The date-time on which the relationship between the two resources was established. Recommended best practice is to use an encoding scheme, such as ISO 8601:2004(E).

Relationship Of Resource
type: DatatypeProperty
description: Examples: "duplicate of", "mother of", "endoparasite of", "host to", "sibling of", "valid synonym of", "located within"
has version: relationshipOfResource-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociationType
organized in class: Resource Relationship
dwc_terms status: recommended
comment: The relationship of the resource identified by relatedResourceID to the subject (optionally identified by the resourceID). Recommended best practice is to use a controlled vocabulary.

Relationship Remarks
type: DatatypeProperty
description: Examples: "mother and offspring collected from the same nest", "pollinator captured in the act"
has version: relationshipRemarks-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/Associations/UnitAssociation/Comments
organized in class: Resource Relationship
dwc_terms status: recommended
comment: Comments or notes about the relationship between the two resources.

Reproductive Condition
type: DatatypeProperty
description: Examples" "non-reproductive", "pregnant", "in bloom", "fruit-bearing"
has version: reproductiveCondition-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
abcd equivalence: not in ABCD
organized in class: Occurrence
dwc_terms status: recommended
comment: The reproductive condition of the biological individual(s) represented in the Occurrence. Recommended best practice is to use a controlled vocabulary.

Sample Size Unit
type: DatatypeProperty
description: A sampleSizeUnit must have a corresponding sampleSizeValue, e.g., "5" for sampleSizeValue with "metre" for sampleSizeUnit. Examples: "minute", "hour", "day", "metre", "square metre", "cubic metre". Recommended best practice is to use a controlled vocabulary such as the Ontology of Units of Measure http://www.wurvoc.org/vocabularies/om-1.8/ of SI units, derived units, or other non-SI units accepted for use within the SI (e.g., minute, hour, day, litre).
has version: sampleSizeUnit-2014-12-23
issued: 2014-11-07
modified: 2015-03-19
abcd equivalence: not in ABCD
decision: Decision-2015-03-19 18
organized in class: Event
dwc_terms status: recommended
comment: The unit of measurement of the size (time duration, length, area, or volume) of a sample in a sampling event.

Sample Size Value
type: DatatypeProperty
description: A sampleSizeValue must have a corresponding sampleSizeUnit. Example: "5" for sampleSizeValue with "metre" for sampleSizeUnit.
has version: sampleSizeValue-2014-12-23
issued: 2014-11-07
modified: 2015-03-19
abcd equivalence: not in ABCD
decision: Decision-2015-03-19 18
organized in class: Event
dwc_terms status: recommended
comment: A numeric value for a measurement of the size (time duration, length, area, or volume) of a sample in a sampling event.

Sampling Effort
type: DatatypeProperty
description: Examples: "40 trap-nights", "10 observer-hours; 10 km by foot; 30 km by car"
has version: samplingEffort-2009-08-24
issued: 2009-08-24
modified: 2009-08-24
abcd equivalence: not in ABCD
organized in class: Event
dwc_terms status: recommended
comment: The amount of effort expended during an Event.

Sampling Protocol
type: DatatypeProperty
description: Examples: "UV light trap", "mist net", "bottom trawl", "ad hoc observation", "point count", "Penguins from space: faecal stains reveal the location of emperor penguin colonies, http://dx.doi.org/10.1111/j.1466-8238.2009.00467.x", "Takats et al. 2001. Guidelines for Nocturnal Owl Monitoring in North America. Beaverhill Bird Observatory and Bird Studies Canada, Edmonton, Alberta. 32 pp.", "http://www.bsc-eoc.org/download/Owl.pdf"
has version: samplingProtocol-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: CollectingMethod-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/Method
organized in class: Event
dwc_terms status: recommended
comment: The name of, reference to, or description of the method or protocol used during an Event.

Scientific Name
type: DatatypeProperty
description: Examples: "Coleoptera" (order), "Vespertilionidae" (family), "Manis" (genus), "Ctenomys sociabilis" (genus + specificEpithet), "Ambystoma tigrinum diaboli" (genus + specificEpithet + infraspecificEpithet), "Roptrocerus typographi (Györfi, 1952)" (genus + specificEpithet + scientificNameAuthorship), "Quercus agrifolia var. oxyadenia (Torr.) J.T. Howell" (genus + specificEpithet + taxonRank + infraspecificEpithet + scientificNameAuthorship)
has version: scientificName-2009-09-21
issued: 2008-11-19
modified: 2009-09-21
replaces: scientificName-2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/FullScientificNameString
organized in class: Taxon
dwc_terms status: recommended
comment: The full scientific name, with authorship and date information if known. When forming part of an Identification, this should be the name in lowest level taxonomic rank that can be determined. This term should not contain identification qualifications, which should instead be supplied in the IdentificationQualifier term.

Scientific Name Authorship
type: DatatypeProperty
description: Example: "(Torr.) J.T. Howell", "(Martinovský) Tzvelev", "(Györfi, 1952)"
has version: scientificNameAuthorship-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: AuthorYearOfScientificName-2007-04-17
abcd equivalence: {DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Bacterial/ParentheticalAuthorTeamAndYear + DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Bacterial/AuthorTeamAndYear} or {DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Botanical/AuthorTeamParenthesis + DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Botanical/AuthorTeam} or {DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Zoological/AuthorTeamOriginalAndYear + [= or] DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Zoological/AuthorTeamParenthesisAndYear}
organized in class: Taxon
dwc_terms status: recommended
comment: The authorship information for the scientificName formatted according to the conventions of the applicable nomenclaturalCode.

Sex
type: DatatypeProperty
description: Examples: "female", "hermaphrodite", "8 males, 4 females"
has version: sex-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: Sex-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/Sex
organized in class: Occurrence
dwc_terms status: recommended
comment: The sex of the biological individual(s) represented in the Occurrence. Recommended best practice is to use a controlled vocabulary.

Specific Epithet
type: DatatypeProperty
description: Examples: "concolor", "gottschei"
has version: specificEpithet-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: SpecificEpithet-2007-04-17
abcd equivalence: {DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Bacterial/SpeciesEpithet or DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Botanical/FirstEpithet or DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Zoological/SpeciesEpithet}
organized in class: Taxon
dwc_terms status: recommended
comment: The name of the first or species epithet of the scientificName.

Start Day Of Year
type: DatatypeProperty
description: Examples: "1" (=1 Jan), "366" (=31 Dec), "365" (=30 Dec in a leap year, 31 Dec in a non-leap year)
has version: startDayOfYear-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: DayOfYear-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/DateTime/DayNumberBegin
organized in class: Event
dwc_terms status: recommended
comment: The earliest ordinal day of the year on which the Event occurred (1 for January 1, 365 for December 31, except in a leap year, in which case it is 366).

State Province
type: DatatypeProperty
description: Examples: "Montana", "Minas Gerais", "Córdoba"
has version: stateProvince-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: StateProvince-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/NamedAreas/NamedArea/AreaName with NamedAreas/NamedArea/AreaClass= State or = Province (etc.)
organized in class: Location
dwc_terms status: recommended
comment: The name of the next smaller administrative region than country (state, province, canton, department, region, etc.) in which the Location occurs.

Subgenus
type: DatatypeProperty
description: Examples: "Strobus (Pinus)", "Puma (Puma)" "Loligo (Amerigo)", "Hieracium subgen. Pilosella"
has version: subgenus-2009-08-24
issued: 2008-11-19
modified: 2009-08-24
replaces: subgenus-2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Zoological/Subgenus
organized in class: Taxon
dwc_terms status: recommended
comment: The full scientific name of the subgenus in which the taxon is classified. Values should include the genus to avoid homonym confusion.

Taxon Rank
type: DatatypeProperty
description: Examples: "subspecies", "varietas", "forma", "species", "genus"
has version: taxonRank-2009-09-21
issued: 2008-11-19
modified: 2009-09-21
replaces: scientificNameRank-2009-07-06
abcd equivalence: DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Botanical/Rank
organized in class: Taxon
dwc_terms status: recommended
comment: The taxonomic rank of the most specific name in the scientificName. Recommended best practice is to use a controlled vocabulary.

Taxon Remarks
type: DatatypeProperty
description: Example: "this name is a misspelling in common use"
has version: taxonRemarks-2009-08-24
issued: 2008-11-19
modified: 2009-08-24
replaces: taxonRemarks-2009-04-24
abcd equivalence: not in ABCD
organized in class: Taxon
dwc_terms status: recommended
comment: Comments or notes about the taxon or name.

Taxonomic Status
type: DatatypeProperty
description: Examples: "invalid", "misapplied", "homotypic synonym", "accepted"
has version: taxonomicStatus-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
abcd equivalence: not in ABCD
organized in class: Taxon
dwc_terms status: recommended
comment: The status of the use of the scientificName as a label for a taxon. Requires taxonomic opinion to define the scope of a taxon. Rules of priority then are used to define the taxonomic status of the nomenclature contained in that scope, combined with the experts opinion. It must be linked to a specific taxonomic reference that defines the concept. Recommended best practice is to use a controlled vocabulary.

Type Status
type: DatatypeProperty
description: Example: "holotype of Ctenomys sociabilis. Pearson O. P., and M. I. Christie. 1985. Historia Natural, 5(37):388"
has version: typeStatus-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: TypeStatus-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/SpecimenUnit/NomenclaturalTypeDesignations/NomenclaturalTypeText
organized in class: Identification
dwc_terms status: recommended
comment: A list (concatenated and separated) of nomenclatural types (type status, typified scientific name, publication) applied to the subject.

Verbatim Coordinate System
type: DatatypeProperty
description: Examples: "decimal degrees", "degrees decimal minutes", "degrees minutes seconds", "UTM"
has version: verbatimCoordinateSystem-2009-04-24
issued: 2008-11-19
modified: 2009-07-06
replaces: VerbatimCoordinateSystem-2007-04-17
abcd equivalence: (partly) DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/CoordinatesGrid/GridCellSystem
organized in class: Location
dwc_terms status: recommended
comment: The spatial coordinate system for the verbatimLatitude and verbatimLongitude or the verbatimCoordinates of the Location. Recommended best practice is to use a controlled vocabulary.

Verbatim Coordinates
type: DatatypeProperty
description: Examples: "41 05 54S 121 05 34W", "17T 630000 4833400"
has version: verbatimCoordinates-2009-04-24
issued: 2008-11-19
modified: 2009-07-06
replaces: VerbatimCoordinates-2007-04-17
abcd equivalence: {DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/CoordinatesLatLon/CoordinatesText or DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/CoordinatesUTM/UTMText}
organized in class: Location
dwc_terms status: recommended
comment: The verbatim original spatial coordinates of the Location. The coordinate ellipsoid, geodeticDatum, or full Spatial Reference System (SRS) for these coordinates should be stored in verbatimSRS and the coordinate system should be stored in verbatimCoordinateSystem.

Verbatim Depth
type: DatatypeProperty
description: Example: "100-200 m"
has version: verbatimDepth-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: VerbatimDepth-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/Depth/MeasurementOrFactText
organized in class: Location
dwc_terms status: recommended
comment: The original description of the depth below the local surface.

Verbatim Elevation
type: DatatypeProperty
description: Example: "100-200 m"
has version: verbatimElevation-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: VerbatimElevation-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/Altitude/MeasurementOrFactText
organized in class: Location
dwc_terms status: recommended
comment: The original description of the elevation (altitude, usually above sea level) of the Location.

Verbatim EventDate
type: DatatypeProperty
description: Examples: "spring 1910", "Marzo 2002", "1999-03-XX", "17IV1934"
has version: verbatimEventDate-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: VerbatimCollectingDate-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/DateTime/DateText
organized in class: Event
dwc_terms status: recommended
comment: The verbatim original representation of the date and time information for an Event.

Verbatim Latitude
type: DatatypeProperty
description: Example: "41 05 54.03S"
has version: verbatimLatitude-2009-04-24
issued: 2008-11-19
modified: 2009-07-06
replaces: VerbatimLatitude-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/CoordinatesLatLon/VerbatimLatitude
organized in class: Location
dwc_terms status: recommended
comment: The verbatim original latitude of the Location. The coordinate ellipsoid, geodeticDatum, or full Spatial Reference System (SRS) for these coordinates should be stored in verbatimSRS and the coordinate system should be stored in verbatimCoordinateSystem.

Verbatim Locality
type: DatatypeProperty
description: Example: "25 km NNE Bariloche por R. Nac. 237"
has version: verbatimLocality-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/NamedAreas/NamedArea/AreaName
organized in class: Location
dwc_terms status: recommended
comment: The original textual description of the place.

Verbatim Longitude
type: DatatypeProperty
description: Example: "121d 10' 34" W"
has version: verbatimLongitude-2009-04-24
issued: 2008-11-19
modified: 2009-07-06
replaces: VerbatimLongitude-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/CoordinatesLatLon/VerbatimLongitude
organized in class: Location
dwc_terms status: recommended
comment: The verbatim original longitude of the Location. The coordinate ellipsoid, geodeticDatum, or full Spatial Reference System (SRS) for these coordinates should be stored in verbatimSRS and the coordinate system should be stored in verbatimCoordinateSystem.

Verbatim SRS
type: DatatypeProperty
description: Examples: "EPSG:4326", "WGS84", "NAD27", "Campo Inchauspe", "European 1950", "Clarke 1866"
has version: verbatimSRS-2009-07-06
issued: 2009-07-06
modified: 2009-07-06
abcd equivalence: not in ABCD
organized in class: Location
dwc_terms status: recommended
comment: The ellipsoid, geodetic datum, or spatial reference system (SRS) upon which coordinates given in verbatimLatitude and verbatimLongitude, or verbatimCoordinates are based. Recommended best practice is use the EPSG code as a controlled vocabulary to provide an SRS, if known. Otherwise use a controlled vocabulary for the name or code of the geodetic datum, if known. Otherwise use a controlled vocabulary for the name or code of the ellipsoid, if known. If none of these is known, use the value "unknown".

Verbatim Taxon Rank
type: DatatypeProperty
description: Examples: "Agamospecies", "sub-lesus", "prole", "apomict", "nothogrex", "sp.", "subsp.", "var."
has version: verbatimRank-2009-09-21
issued: 2009-07-06
modified: 2009-09-21
replaces: verbatimScientificNameRank-2009-07-06
abcd equivalence: not in ABCD
organized in class: Taxon
dwc_terms status: recommended
comment: The taxonomic rank of the most specific name in the scientificName as it appears in the original record.

Vernacular Name
type: DatatypeProperty
description: Examples: "Andean Condor", "Condor Andino", "American Eagle", "Gänsegeier"
has version: vernacularName-2009-07-06
issued: 2009-07-06
modified: 2009-07-06
abcd equivalence: not in ABCD
organized in class: Taxon
dwc_terms status: recommended
comment: A common or vernacular name.

Water Body
type: DatatypeProperty
description: Examples: "Indian Ocean", "Baltic Sea", "Hudson River"
has version: waterBody-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: WaterBody-2007-04-17
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/NamedAreas/NamedArea/AreaName with NamedAreas/NamedArea/AreaClass= Water body
organized in class: Location
dwc_terms status: recommended
comment: The name of the water body in which the Location occurs. Recommended best practice is to use a controlled vocabulary such as the Getty Thesaurus of Geographic Names.

Year
type: DatatypeProperty
description: Example: "2008"
has version: year-2009-04-24
issued: 2008-11-19
modified: 2009-04-24
replaces: YearCollected-2003-06-17
abcd equivalence: accessible from DataSets/DataSet/Units/Unit/Gathering/ISODateTimeBegin
organized in class: Event
dwc_terms status: recommended
comment: The four-digit year in which the Event occurred, according to the Common Era Calendar.

observing process
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: information content entity
taxonomic inventory metadata preferred name: sighting
example of usage: A trip camera capture of an image of a jaguar is an observation, because it is "selected" by the camera as worthy of obsevation simply by virtue of moving in front of the camera.
example of usage: Observing and recording the presence or absence of butterflies during a transect walk.
example of usage: Seeing three pelicans flying overhead on Christmas day and report them as part of the Christmas Bird Count.
has curation status: pending final vetting
definition: A process in which a person or machine sees or detects a material entity and selects it as worthy of observation, and which has as output an information content entity about the selected material entity.
editor note: This class replaces class bco_0000003, which was made obsolete because of identifier format.
editor note: We are having conversation with OBI developers about how this term relates to OBI:assay (). Is it equivalent, broader, narrower? What does it mean to be the input to an observation.
creator: Biocode Commons Ontology Hackathon
comment: An observing process is distinguished from a specimen collecting process in by having an information content entity as an output rather than a specimen. The information artifact may be written or recorded or just be stored in someone's head (specifically depenedent upon that person). In the context of a taxonomic inventory, an observing process may be called a sighting, which is an ad hoc reporting of, typically, a single taxon occurrence, usually motivated by rarity, individual interest in the taxon, or atypicality of circumstances.

submitting process
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: material entity
example of usage: a curator submitting a herbarium speciman to a museum
example of usage: a researcher submitting a water sample to a laboratory storage collection
has curation status: requires discussion
definition: A planned process whereby a person submits a material sample to an organization.
editor note: false
creator: Biocode Commons Ontology Hackathon

locality description
type: Class
subclass of: information content entity
has curation status: requires discussion
definition: An information artifact that is about a spatio-temporal region at which a process (such as collecting process, observing process, or material sampling process) occured.
editor note: This term replaces the obsolete class bco_0000025, but with the correct identifier format.
creator: Biocode Commons Ontology Hackathon
comment: Darwin Core needs to describe both the site and time where some activity occurred as an information content entity (e.g., in recording data from a lab notebook),therefore, we made locality description about a spatial temporal region, rather than a site.

museum collection
type: Class
subclass of: object aggregate
subclass of: Restriction
  on property: has part
  some values from: specimen
example of usage: The herbarium collection at the New York Botanical Garden.
example of usage: the painting collection at the Louvre Museum
has curation status: requires discussion
definition: An object aggregate that has as member part a material sample that is located in museum as a result of a process of curation.
editor note: This term replaced bco_0000031, which was made obsolete because of incorrect identifier format.
creator: Biocode Commons Ontology Hackathon
comment: Intent is to document biodiversity for research and education. The class museum collection has meaning that is much broader than biological collections. It would probably be better to import this term from another, more general ontology and create a specific subclass for natural history museum collection.

organismal museum collection
type: Class
subclass of: museum collection
example of usage: the insect collection at the Smithsonian Institution
has curation status: requires discussion
definition: A museum collection that has as member part a material sample that was derived from an organism.
editor note: This term replaced bco_0000032, which was made obsolete because of incorrect identifier format.
creator: Biocode Commons Ontology Hackathon

taxonomic identification process
type: Class
equivalent class: Identification
subclass of: Identification
example of usage: Associating a museum specimen with a specific taxonomic concept based on its characters.
example of usage: Using BLAST to identify the taxa present in an environmental (metagenomic) sample.
example of usage: Using DNA barcoding to identify a plant species.
example of usage: Using a key to identify a plant in the field.
has curation status: pending final vetting
definition: A planned process by which an organismal entity is associated with a taxon or taxa.
editor note: Need to add a relation for has specified output some taxonomic association.
editor note: This term replaces bco_0000042, which was made obsolete because of incorrect identifier format.
creator: Biocode Commons Ontology Hackathon

material target of observation
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: BFO_0000087
    some values from: material target of observation role
subclass of: material entity
subclass of: Restriction
  on property: BFO_0000087
  some values from: material target of observation role
example of usage: A bird observed during a Christmas Bird Count
example of usage: A bird observed during a transect walk.
example of usage: A tree is forest plot that is measured for diameter at breast height (DBH).
example of usage: An lizard observed in the field that is not collected but whose location is recorded in a field notebook.
has curation status: requires discussion
definition: A material entity that has a target of observation role, that is, a material entity that is the input of some observing process.
editor note: This term replaces bco_0000044, which was made obsolete because of incorrect identifier format.
creator: Biocode Commons Ontology Hackathon

material target of observation role
type: Class
equivalent class: Class
  intersection of: role
  intersection of: Restriction
    on property: realized in
    some values from: observing process
subclass of: role
subclass of: Restriction
  on property: realized in
  some values from: observing process
example of usage: the role borne by a bird during a Christmas Bird Count
has curation status: pending final vetting
definition: A role that is borne by some material entity and is realized by the material entity being the input of an observing process.
editor note: This term replaced bco_0000046, which was made obsolete because of incorrect identifier format.
creator: Biocode Commons Ontology Hackathon

taxonomic inventory process
type: Class
equivalent class: Class
  intersection of: observing process
  intersection of: Restriction
    on property: has_specified_output
    some values from: taxonomic inventory
subclass of: observing process
subclass of: Restriction
  on property: has_specified_output
  some values from: taxonomic inventory
taxonomic inventory metadata preferred name: inventory type
has curation status: uncurated
definition: A planned process by which a taxonomic inventory is created.
creator: Taxonomic Inventory Metadata Workshop
comment: not sure if this should be a type of assay or a type of planned process

Axiom
annotated source: taxonomic inventory process
annotated property: definition
annotated target: A planned process by which a taxonomic inventory is created.
definition source: http://onlinelibrary.wiley.com/doi/10.1111/ecog.02942/full

taxonomic inventory
type: Class
equivalent class: Class
  intersection of: information content entity
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: taxonomic inventory process
subclass of: information content entity
subclass of: Restriction
  on property: is_specified_output_of
  some values from: taxonomic inventory process
example of usage: "The Flora of North America"
example of usage: The butterflies of Great Britain
example of usage: The plants of Yosemite National Park
has curation status: pending final vetting
definition: A list of names ascribed to biological entities of specified organismal scope recorded over some defined spatial and temporal scope following a described sampling protocol and sampling effort, potentially including values indicating abundance or biomass of the biological entities
creator: Taxonomic Inventory Metadata Workshop
Source: https://docs.google.com/spreadsheet/ccc
comment: The biological entities are almost always species and the organismal scope typically a taxon but potentially also an ecologically or functionally defined grouping (e.g. ‘water birds’ or ‘trees’) or other operational unit (e.g. genes). The list would typically contain multiple entities, but may be as short as a single entity or, if a sampling effort focused on a certain taxon yielded no results, even contain none.

restricted search taxonomic inventory process
type: Class
subclass of: taxonomic inventory process
taxonomic inventory metadata preferred name: restricted search
example of usage: Pollard transect-- "walk a 1km transect at a slow&steady pace, and report on all TOI within 5m in front, and 2.5m on either side of you."
has curation status: ready for release
definition: A taxonomic inventory process that is restricted to plots, transects, or points, in which a person or group of people is comprehensively covering the entire area, usually with a well-described survey time or pace. The search is restricted to a defined and human-scale geospatial area (usually traversable within a time course of less than a day) within which there is an expectation of a comprehensive accounting of the taxonomic items of interest.
creator: Taxonomic Inventory Metadata Workshop

Axiom
annotated source: restricted search taxonomic inventory process
annotated property: definition
annotated target: A taxonomic inventory process that is restricted to plots, transects, or points, in which a person or group of people is comprehensively covering the entire area, usually with a well-described survey time or pace. The search is restricted to a defined and human-scale geospatial area (usually traversable within a time course of less than a day) within which there is an expectation of a comprehensive accounting of the taxonomic items of interest.
definition source: http://onlinelibrary.wiley.com/doi/10.1111/ecog.02942/full

open search taxonomic inventory process
type: Class
subclass of: taxonomic inventory process
taxonomic inventory metadata preferred name: open search
example of usage: Individual Christmas Bird Count by some team. Organized field trip to a State Park.
has curation status: ready for release
definition: A taxonomic inventory process in which the search is restricted within a larger defined geographic area, but where effort isn't even or complete across the region, and thus not a comprehensive accounting of taxa of interest. Temporal duration is typically longer than restricted searches, lasting hours to several days.
creator: Taxonomic Inventory Metadata Workshop

Axiom
annotated source: open search taxonomic inventory process
annotated property: definition
annotated target: A taxonomic inventory process in which the search is restricted within a larger defined geographic area, but where effort isn't even or complete across the region, and thus not a comprehensive accounting of taxa of interest. Temporal duration is typically longer than restricted searches, lasting hours to several days.
definition source: http://onlinelibrary.wiley.com/doi/10.1111/ecog.02942/full

opportunistic search taxonomic inventory process
type: Class
subclass of: taxonomic inventory process
taxonomic inventory metadata preferred name: opportunistic search
example of usage: Many E-Bird lists are of this nature; useful supplementary information is that observers should state whether they documented every taxon of interest they saw.
has curation status: ready for release
definition: A taxonomic inventory process that is a more casual reporting of occurrences of taxa of interest, still intended to be a comprehensive accounting of the taxa of interest, but with no pre-specified investment of effort nor planned trajectory for discovery, thus of often idiosyncratic length or spatial scope.
creator: Taxonomic Inventory Metadata Workshop
comment: This is more typically used to report multiple sightings, where the motivation is to record presence and abundance, rather than for individual anecdotal occurrences that are noteworthy.

Axiom
annotated source: opportunistic search taxonomic inventory process
annotated property: definition
annotated target: A taxonomic inventory process that is a more casual reporting of occurrences of taxa of interest, still intended to be a comprehensive accounting of the taxa of interest, but with no pre-specified investment of effort nor planned trajectory for discovery, thus of often idiosyncratic length or spatial scope.
definition source: http://onlinelibrary.wiley.com/doi/10.1111/ecog.02942/full

trap or sample taxonomic inventory process
type: Class
subclass of: taxonomic inventory process
taxonomic inventory metadata preferred name: trap or sample inventory
example of usage: an inventory of insects in a area using pheremone traps
example of usage: an inventory of the large mammals of a park based on camera traps
example of usage: inventories based on trawl samples
has curation status: ready for release
definition: A taxonomic inventory process that is typically restricted in geospatial extent that involves either the physical extraction of some evidence of the presence of the taxa of interest, such as a whole organisms, scat, fur, other material samples or information artifacts such as photographs or sound recordings
creator: Taxonomic Inventory Metadata Workshop
comment: Can be highly targeted and or baited (pheromone trap), or general (pitfall). Trap events can either be "triggered" but of long-term deployment, or rigorously temporally specified (left out overnight).

Axiom
annotated source: trap or sample taxonomic inventory process
annotated property: definition
annotated target: A taxonomic inventory process that is typically restricted in geospatial extent that involves either the physical extraction of some evidence of the presence of the taxa of interest, such as a whole organisms, scat, fur, other material samples or information artifacts such as photographs or sound recordings
definition source: http://onlinelibrary.wiley.com/doi/10.1111/ecog.02942/full

adventitious taxonomic inventory process
type: Class
subclass of: taxonomic inventory process
taxonomic inventory metadata preferred name: incidental or adventitious inventory
example of usage: data from ecological studies in which presence of some taxa is recorded to clarify population or community parameters
has curation status: ready for release
definition: A taxonomic inventory process in which taxon occurrences are recorded as co-variates of another study, or by happenstance, and later compiled as a taxonomic inventory.
creator: Taxonomic Inventory Metadata Workshop

Axiom
annotated source: adventitious taxonomic inventory process
annotated property: definition
annotated target: A taxonomic inventory process in which taxon occurrences are recorded as co-variates of another study, or by happenstance, and later compiled as a taxonomic inventory.
definition source: http://onlinelibrary.wiley.com/doi/10.1111/ecog.02942/full

compilation taxonomic inventory process
type: Class
subclass of: taxonomic inventory process
taxonomic inventory metadata preferred name: compilation inventory
example of usage: Atlases and Checklists
has curation status: uncurated
definition: A taxonomic inventory process in which a list of taxa of interest is assembled from various combinations of existing taxonomic inventories, rather than generated de novo from observations or samples.
creator: Taxonomic Inventory Metadata Workshop
comment: A compiliation taxonomic inventory process is typically required to document the occurences of taxa of interest over large geospatial areas, or to derive the most comprehensive accounting of presence and absence of taxa of interest in a larger region.

Axiom
annotated source: compilation taxonomic inventory process
annotated property: definition
annotated target: A taxonomic inventory process in which a list of taxa of interest is assembled from various combinations of existing taxonomic inventories, rather than generated de novo from observations or samples.
definition source: http://onlinelibrary.wiley.com/doi/10.1111/ecog.02942/full

museum
type: Class
subclass of: organization
subclass of: Restriction
  on property: has part
  some values from: museum collection
example of usage: The Louvre Museum
example of usage: The Smithsonian Institution
has curation status: ready for release
definition: An institution that cares for (conserves) a collection of artifacts and other objects of scientific, artistic, cultural, or historical importance.
definition source: ISBN:9780759105096
comment: A museum may make its collections available for public viewing through exhibits that may be permanent or temporary. The class museum has meaning that is much broader than biological collecitons. It may be better to import this term from another, more general ontology and create a specific subclass for natural history museum.

obsolete fossil specimen
type: Class
subclass of: Obsolete Class
example of usage: a fossil housed in a natural history museum
definition: A specimen that is derived from a fossil.
has obsolescence reason: failed exploratory term
deprecated: true

obsolete living specimen
type: Class
subclass of: Obsolete Class
example of usage: a bacterial culture in a culture collection
example of usage: a tree in an arboretum
example of usage: an animal in a zoo
example of usage: germplasm
definition: A specimen that is alive.
has obsolescence reason: failed exploratory term
deprecated: true

obsolete preserved specimen
type: Class
subclass of: Obsolete Class
definition: A specimen that has been preserved.
has obsolescence reason: failed exploratory term
deprecated: true

obsolete darwin core class
type: Class
subclass of: Obsolete Class
has obsolescence reason: failed exploratory term
deprecated: true

human observation process
type: Class
subclass of: observing process
example of usage: a biologist recording an observation of an animal in a field notebook
example of usage: an entomologist recording the presense of butterflies while walking a transect
has curation status: metadata incomplete
definition: An observing process in which the observing entity consists of one or more humans.
comment: May be able to use the has agent = has active participant relationship for defining this. May want to work with OBI to define this term in a more general sense for investigations.

machine observation process
type: Class
subclass of: observing process
example of usage: a camera trap recording the presence of a jaguar
example of usage: a sensor periodically recording the surface temperature of a leaf over several hours
has curation status: metadata incomplete
definition: An observing process in which the observing entity consists of one or more machines.
comment: May want to work with OBI to define this term in a more general sense for investigations.

identification assertion
type: Class
subclass of: data item
subclass of: Restriction
  on property: to taxon
  some values from: Taxon
subclass of: Restriction
  on property: of organism
  some values from: organismal entity
definition: A data item that is the output of a taxonomic identification process and associates some organismal entity with a taxon or taxa.
definition source: PPO hackathon Sep. 2016.

entity
type: Class
disjoint with: Obsolete Class
BFO OWL specification label: entity
BFO CLIF specification label: Entity
example of usage: Julius Caesar
example of usage: Verdi’s Requiem
example of usage: the Second World War
example of usage: your body mass index
editor note: BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
editor note: Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
elucidation: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])

Axiom
annotated source: entity
annotated property: editor note
annotated target: Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000004
comment: per discussion with Barry Smith

Axiom
annotated source: entity
annotated property: elucidation
annotated target: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/001-001

continuant
type: Class
subclass of: entity
disjoint with: occurrent
disjoint with: Restriction
  on property: part of
  some values from: occurrent
BFO OWL specification label: continuant
BFO CLIF specification label: Continuant
definition: An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
editor note: BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
editor note: Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
elucidation: A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
has associated axiom(nl): if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
has associated axiom(nl): if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
has associated axiom(nl): if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
has associated axiom(fol): (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
has associated axiom(fol): (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]

Axiom
annotated source: continuant
annotated property: editor note
annotated target: Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000007

Axiom
annotated source: continuant
annotated property: elucidation
annotated target: A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/008-002

Axiom
annotated source: continuant
annotated property: has associated axiom(nl)
annotated target: if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/126-001

Axiom
annotated source: continuant
annotated property: has associated axiom(nl)
annotated target: if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/009-002

Axiom
annotated source: continuant
annotated property: has associated axiom(nl)
annotated target: if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/011-002

Axiom
annotated source: continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/009-002

Axiom
annotated source: continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/126-001

Axiom
annotated source: continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/008-002

Axiom
annotated source: continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/011-002

occurrent
type: Class
subclass of: entity
disjoint with: Restriction
  on property: part of
  some values from: continuant
BFO OWL specification label: occurrent
BFO CLIF specification label: Occurrent
definition: An entity that has temporal parts and that happens, unfolds or develops through time.
editor note: BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
editor note: BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
editor note: Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
editor note: Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
elucidation: An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
has associated axiom(nl): Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
has associated axiom(nl): b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
has associated axiom(fol): (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
has associated axiom(fol): (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]

Axiom
annotated source: occurrent
annotated property: editor note
annotated target: Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000006
comment: per discussion with Barry Smith

Axiom
annotated source: occurrent
annotated property: editor note
annotated target: Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000012

Axiom
annotated source: occurrent
annotated property: elucidation
annotated target: An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/077-002

Axiom
annotated source: occurrent
annotated property: has associated axiom(nl)
annotated target: Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/108-001

Axiom
annotated source: occurrent
annotated property: has associated axiom(nl)
annotated target: b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/079-001

Axiom
annotated source: occurrent
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/108-001

Axiom
annotated source: occurrent
annotated property: has associated axiom(fol)
annotated target: (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/079-001

independent continuant
type: Class
subclass of: continuant
disjoint with: specifically dependent continuant
disjoint with: generically dependent continuant
BFO OWL specification label: ic
BFO CLIF specification label: IndependentContinuant
example of usage: a chair
example of usage: a heart
example of usage: a leg
example of usage: a molecule
example of usage: a spatial region
example of usage: an atom
example of usage: an orchestra.
example of usage: an organism
example of usage: the bottom right portion of a human torso
example of usage: the interior of your mouth
definition: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
definition: b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
has associated axiom(nl): For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
has associated axiom(nl): For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
has associated axiom(fol): (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
has associated axiom(fol): (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
has associated axiom(fol): (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]

Axiom
annotated source: independent continuant
annotated property: definition
annotated target: b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/017-002

Axiom
annotated source: independent continuant
annotated property: has associated axiom(nl)
annotated target: For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/134-001

Axiom
annotated source: independent continuant
annotated property: has associated axiom(nl)
annotated target: For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/018-002

Axiom
annotated source: independent continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/134-001

Axiom
annotated source: independent continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/018-002

Axiom
annotated source: independent continuant
annotated property: has associated axiom(fol)
annotated target: (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/017-002

obsolete dependent continuant
type: Class
subclass of: Obsolete Class
definition: A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities.
deprecated: true

spatial region
type: Class
equivalent class: Location
subclass of: Location
BFO OWL specification label: s-region
BFO CLIF specification label: SpatialRegion
editor note: BFO 2 Reference: Spatial regions do not participate in processes.
editor note: Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
elucidation: A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
has associated axiom(nl): All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
has associated axiom(fol): (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
has associated axiom(fol): (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]

Axiom
annotated source: spatial region
annotated property: editor note
annotated target: Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000002
comment: per discussion with Barry Smith

Axiom
annotated source: spatial region
annotated property: elucidation
annotated target: A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/035-001

Axiom
annotated source: spatial region
annotated property: has associated axiom(nl)
annotated target: All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/036-001

Axiom
annotated source: spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/036-001

Axiom
annotated source: spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/035-001

process
type: Class
equivalent class: Event
subclass of: Event
BFO OWL specification label: process
BFO CLIF specification label: Process
example of usage: a process of cell-division, \ a beating of the heart
example of usage: a process of meiosis
example of usage: a process of sleeping
example of usage: the course of a disease
example of usage: the flight of a bird
example of usage: the life of an organism
example of usage: your process of aging.
definition: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
definition: p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
editor note: BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
has associated axiom(fol): (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]

Axiom
annotated source: process
annotated property: definition
annotated target: p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/083-003

Axiom
annotated source: process
annotated property: has associated axiom(fol)
annotated target: (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/083-003

disposition
type: Class
subclass of: realizable entity
disjoint with: role
BFO OWL specification label: disposition
BFO CLIF specification label: Disposition
example of usage: an atom of element X has the disposition to decay to an atom of element Y
example of usage: certain people have a predisposition to colon cancer
example of usage: children are innately disposed to categorize objects in certain ways.
example of usage: the cell wall is disposed to filter chemicals in endocytosis and exocytosis
editor note: BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
elucidation: b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
has associated axiom(nl): If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
has associated axiom(fol): (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
has associated axiom(fol): (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]

Axiom
annotated source: disposition
annotated property: elucidation
annotated target: b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/062-002

Axiom
annotated source: disposition
annotated property: has associated axiom(nl)
annotated target: If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/063-002

Axiom
annotated source: disposition
annotated property: has associated axiom(fol)
annotated target: (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/063-002

Axiom
annotated source: disposition
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/062-002

realizable entity
type: Class
subclass of: specifically dependent continuant
disjoint with: quality
BFO OWL specification label: realizable
BFO CLIF specification label: RealizableEntity
example of usage: the disposition of this piece of metal to conduct electricity.
example of usage: the disposition of your blood to coagulate
example of usage: the function of your reproductive organs
example of usage: the role of being a doctor
example of usage: the role of this boundary to delineate where Utah and Colorado meet
definition: A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
elucidation: To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
has associated axiom(nl): All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
has associated axiom(fol): (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
has associated axiom(fol): (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]

Axiom
annotated source: realizable entity
annotated property: elucidation
annotated target: To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/058-002

Axiom
annotated source: realizable entity
annotated property: has associated axiom(nl)
annotated target: All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/060-002

Axiom
annotated source: realizable entity
annotated property: has associated axiom(fol)
annotated target: (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/060-002

Axiom
annotated source: realizable entity
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/058-002

quality
type: Class
subclass of: specifically dependent continuant
BFO OWL specification label: quality
BFO CLIF specification label: Quality
example of usage: the ambient temperature of this portion of air
example of usage: the color of a tomato
example of usage: the length of the circumference of your waist
example of usage: the mass of this piece of gold.
example of usage: the shape of your nose
example of usage: the shape of your nostril
elucidation: a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
has associated axiom(nl): If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
has associated axiom(fol): (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
has associated axiom(fol): (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]

Axiom
annotated source: quality
annotated property: elucidation
annotated target: a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/055-001

Axiom
annotated source: quality
annotated property: has associated axiom(nl)
annotated target: If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/105-001

Axiom
annotated source: quality
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/055-001

Axiom
annotated source: quality
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/105-001

specifically dependent continuant
type: Class
subclass of: continuant
disjoint with: generically dependent continuant
BFO OWL specification label: sdc
BFO CLIF specification label: SpecificallyDependentContinuant
example of usage: Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
example of usage: of one-sided specifically dependent continuants: the mass of this tomato
example of usage: of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
example of usage: the disposition of this fish to decay
example of usage: the function of this heart: to pump blood
example of usage: the mutual dependence of proton donors and acceptors in chemical reactions [79
example of usage: the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
example of usage: the pink color of a medium rare piece of grilled filet mignon at its center
example of usage: the role of being a doctor
example of usage: the shape of this hole.
example of usage: the smell of this portion of mozzarella
definition: A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
definition: b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
definition: b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
editor note: Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
has associated axiom(fol): (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]
has associated axiom(fol): (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]

Axiom
annotated source: specifically dependent continuant
annotated property: definition
annotated target: b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/131-004

Axiom
annotated source: specifically dependent continuant
annotated property: definition
annotated target: b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/050-003

Axiom
annotated source: specifically dependent continuant
annotated property: editor note
annotated target: Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000005
comment: per discussion with Barry Smith

Axiom
annotated source: specifically dependent continuant
annotated property: has associated axiom(fol)
annotated target: (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/131-004

Axiom
annotated source: specifically dependent continuant
annotated property: has associated axiom(fol)
annotated target: (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/050-003

role
type: Class
subclass of: realizable entity
BFO OWL specification label: role
BFO CLIF specification label: Role
example of usage: John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
example of usage: the priest role
example of usage: the role of a boundary to demarcate two neighboring administrative territories
example of usage: the role of a building in serving as a military target
example of usage: the role of a stone in marking a property boundary
example of usage: the role of subject in a clinical trial
example of usage: the student role
definition: A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
editor note: BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
elucidation: b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
has associated axiom(fol): (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]

Axiom
annotated source: role
annotated property: elucidation
annotated target: b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/061-001

Axiom
annotated source: role
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/061-001

object aggregate
type: Class
subclass of: material entity
BFO OWL specification label: object-aggregate
BFO CLIF specification label: ObjectAggregate
example of usage: a collection of cells in a blood biobank.
example of usage: a swarm of bees is an aggregate of members who are linked together through natural bonds
example of usage: a symphony orchestra
example of usage: an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)
example of usage: defined by fiat: the aggregate of members of an organization
example of usage: defined through physical attachment: the aggregate of atoms in a lump of granite
example of usage: defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
example of usage: defined via attributive delimitations such as: the patients in this hospital
example of usage: the aggregate of bearings in a constant velocity axle joint
example of usage: the aggregate of blood cells in your body
example of usage: the nitrogen atoms in the atmosphere
example of usage: the restaurants in Palo Alto
example of usage: your collection of Meissen ceramic plates.
editor note: An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
editor note: BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee).
definition source: ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
elucidation: b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
has associated axiom(fol): (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]

Axiom
annotated source: object aggregate
annotated property: editor note
annotated target: An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000011

Axiom
annotated source: object aggregate
annotated property: editor note
annotated target: An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000301

Axiom
annotated source: object aggregate
annotated property: definition source
annotated target: ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000300

Axiom
annotated source: object aggregate
annotated property: elucidation
annotated target: b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/025-004

Axiom
annotated source: object aggregate
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/025-004

object
type: Class
subclass of: material entity
BFO OWL specification label: object
BFO CLIF specification label: Object
example of usage: atom
example of usage: cell
example of usage: cells and organisms
example of usage: engineered artifacts
example of usage: grain of sand
example of usage: molecule
example of usage: organelle
example of usage: organism
example of usage: planet
example of usage: solid portions of matter
example of usage: star
editor note: BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting.
editor note: BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below).
editor note: BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47
editor note: BFO 2 Reference: an object is a maximal causally unified material entity
editor note: BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74
elucidation: b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])

Axiom
annotated source: object
annotated property: elucidation
annotated target: b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/024-001

generically dependent continuant
type: Class
subclass of: continuant
BFO OWL specification label: gdc
BFO CLIF specification label: GenericallyDependentContinuant
example of usage: The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
example of usage: the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
example of usage: the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
definition: A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
definition: b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
has associated axiom(fol): (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]

Axiom
annotated source: generically dependent continuant
annotated property: definition
annotated target: b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/074-001

Axiom
annotated source: generically dependent continuant
annotated property: has associated axiom(fol)
annotated target: (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/074-001

function
type: Class
subclass of: disposition
BFO OWL specification label: function
BFO CLIF specification label: Function
example of usage: the function of a hammer to drive in nails
example of usage: the function of a heart pacemaker to regulate the beating of a heart through electricity
example of usage: the function of amylase in saliva to break down starch into sugar
editor note: BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
elucidation: A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
has associated axiom(fol): (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]

Axiom
annotated source: function
annotated property: elucidation
annotated target: A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/064-001

Axiom
annotated source: function
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/064-001

material entity
type: Class
subclass of: independent continuant
disjoint with: immaterial entity
BFO OWL specification label: material
BFO CLIF specification label: MaterialEntity
example of usage: a flame
example of usage: a forest fire
example of usage: a human being
example of usage: a hurricane
example of usage: a photon
example of usage: a puff of smoke
example of usage: a sea wave
example of usage: a tornado
example of usage: an aggregate of human beings.
example of usage: an energy wave
example of usage: an epidemic
example of usage: the undetached arm of a human being
definition: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
editor note: BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
editor note: BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
editor note: BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
elucidation: A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
has associated axiom(nl): Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
has associated axiom(nl): every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
has associated axiom(fol): (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
has associated axiom(fol): (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
has associated axiom(fol): (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]

Axiom
annotated source: material entity
annotated property: elucidation
annotated target: A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/019-002

Axiom
annotated source: material entity
annotated property: has associated axiom(nl)
annotated target: Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/020-002

Axiom
annotated source: material entity
annotated property: has associated axiom(nl)
annotated target: every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/021-002

Axiom
annotated source: material entity
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/019-002

Axiom
annotated source: material entity
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/021-002

Axiom
annotated source: material entity
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/020-002

immaterial entity
type: Class
subclass of: independent continuant
BFO OWL specification label: immaterial
BFO CLIF specification label: ImmaterialEntity
editor note: BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10

organism or virus or viroid
type: Class
subclass of: organismal entity
definition: Material anatomical entity that is a member of an individual species or is a viral or viroid particle.
term editor: Melissa Haendel
imported from: Common Anatomy Reference Onotology - CARO2
OBO foundry unique label: organism or virus
IAO created by: Melissa Haendel
IAO creation date: 9/18/11

peptide
type: Class
subclass of: macromolecule
editor preferred label: peptide
definition: Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc.
imported from: chebi.owl

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

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

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

ribonucleic acid
type: Class
subclass of: nucleic acid
editor preferred label: ribonucleic acid
definition: High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
imported from: chebi.owl

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

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

cultured cell
type: Class
subclass of: experimentally modified cell in vitro
subclass of: Class
  union of: Restriction
    on property: is_specified_output_of
    some values from: establishing cell culture
  union of: Restriction
    on property: derives from
    some values from: Restriction
      on property: is_specified_output_of
      some values from: establishing cell culture
editor preferred label: cultured cell
definition: A cell in vitro that is or has been maintained or propagated as part of a cell culture.
imported from: cl.owl

B cell
type: Class
subclass of: lymphocyte
editor preferred label: B cell
definition: A lymphocyte of B lineage with the phenotype CD19-positive, CD20-positive, and capable of B cell mediated immunity.
imported from: cl.owl

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

experimentally modified cell in vitro
type: Class
subclass of: cell
subclass of: processed material
editor preferred label: experimentally modified cell in vitro
definition: A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.
imported from: cl.owl

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

construction
type: Class
subclass of: astronomical body part
definition: A feature that has been constructed by deliberate human effort.
editor note: "constructed" should probably be made something like a quality and this class obsoleted or filled only by inference
has_exact_synonym: constructed feature

Axiom
annotated source: construction
annotated property: definition
annotated target: A feature that has been constructed by deliberate human effort.
has db xref: MA:ma

environmental feature
type: Class
subclass of: material entity
definition: A material entity which determines an environmental system.
has_obo_namespace: ENVO
id: ENVO:00002297
comment: A material entity determines an environmental system when its removal would cause the collapse of that system. For example, a seamount determines a seamount environment, acting as its 'hub'. This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised.

Axiom
annotated source: environmental feature
annotated property: definition
annotated target: A material entity which determines an environmental system.
has db xref: DOI:10.1186/2041-1480-4-43
has db xref: NM:nm
has db xref: ORCID:0000-0002-4366-3088

human dwelling
type: Class
subclass of: construction
definition: A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning.
editor note: See https://github.com/EnvironmentOntology/envo/issues/264 for discussion. This definition needs a lot of clean up and links to household and related classes must be made to form logical definitions for inference to work.
editor note: Subclasses will be added by inference.

Axiom
annotated source: human dwelling
annotated property: definition
annotated target: A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning.
has db xref: https://en.wikipedia.org/wiki/Dwelling accessed 11/25/2015

astronomical body part
type: Class
subclass of: environmental feature
definition: A material part of an astronomical body.
in_subset: envoAstro
in_subset: envoPolar

GO:molecular_function
type: Class
subclass of: process
subclass of: Event
editor preferred label: molecular_function
definition: A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.
imported from: go.owl

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

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

protein-containing complex
type: Class
subclass of: material entity
subclass of: Restriction
  on property: has part
  some values from: protein
editor preferred label: protein-containing complex
example of usage: A ribosome is a protein complex.
definition: A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.
alternative term: protein complex
imported from: go.owl

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

objective specification
type: Class
subclass of: directive information entity
editor preferred label: objective specification
example of usage: In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
has curation status: ready for release
definition: a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
editor note: 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."
editor note: 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that.
editor note: Answers the question, why did you do this experiment?
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Barry Smith
term editor: PERSON: Bjoern Peters
term editor: PERSON: Jennifer Fostel
alternative term: goal specification
definition source: OBI Plan and Planned Process/Roles Branch
definition source: OBI_0000217

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

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

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

information carrier
type: Class
equivalent class: Class
  intersection of: quality
  intersection of: Restriction
    on property: concretizes
    some values from: information content entity
subclass of: quality
subclass of: Restriction
  on property: concretizes
  some values from: information content entity
editor preferred label: information carrier
example of usage: In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case.
has curation status: pending final vetting
definition: A quality of an information bearer that imparts the information content
editor note: 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'.
editor note: 2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it.
term editor: PERSON: Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy

data item
type: Class
subclass of: information content entity
editor preferred label: data item
example of usage: Data items include counts of things, analyte concentrations, and statistical summaries.
has curation status: pending final vetting
definition: a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
editor note: 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
editor note: 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
editor note: 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
editor note: 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
editor note: JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jonathan Rees
alternative term: data

information content entity
type: Class
subclass of: generically dependent continuant
subclass of: Restriction
  on property: is about
  some values from: entity
editor preferred label: information content entity
example of usage: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
has curation status: ready for release
definition: A generically dependent continuant that is about some thing.
editor note: 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
editor note: information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
term editor: PERSON: Chris Stoeckert
definition source: OBI_0000142

directive information entity
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is about
  some values from: realizable entity
has curation status: ready for release
definition: An information content entity whose concretizations indicate to their bearer how to realize them in a process.
editor note: 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
editor note: 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.
editor note: 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
editor note: Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters

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

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

algorithm
type: Class
subclass of: plan specification
editor preferred label: algorithm
example of usage: PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
has curation status: FossilSpecimen
definition: A plan specification which describes the inputs and 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.
term editor: Philippe Rocca-Serra
term editor: PlanAndPlannedProcess Branch
definition source: OBI_0000270
definition source: adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)

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

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

data set
type: Class
subclass of: data item
editor preferred label: data set
example of usage: Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
has curation status: pending final vetting
definition: A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
editor note: 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type
editor note: 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.
term editor: person:Allyson Lister
term editor: person:Chris Stoeckert
definition source: OBI_0000042
definition source: group:OBI

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

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

plan specification
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: has part
  some values from: objective specification
subclass of: Restriction
  on property: has part
  some values from: action specification
editor preferred label: plan specification
example of usage: PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
has curation status: ready for release
definition: A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
editor note: 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
editor note: 2014-03-31: A plan specification can have other parts, such as conditional specifications.
editor note: Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
term editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch
definition source: OBI_0000344
comment: 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them

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

material information bearer
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: bearer of
    some values from: Restriction
      on property: concretizes
      some values from: information content entity
subclass of: material entity
subclass of: Restriction
  on property: bearer of
  some values from: Restriction
    on property: concretizes
    some values from: information content entity
editor preferred label: material information bearer
example of usage: A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier.
example of usage: a brain
example of usage: a hard drive
has curation status: ready for release
definition: A material entity in which a concretization of an information content entity inheres.
term editor: GROUP: IAO

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

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

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

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

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

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

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

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

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

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

denotator type
type: Class
equivalent class: Class
  one of: universal
  one of: defined class
  one of: named class expression
subclass of: data about an ontology part
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.
definition: A denotator type indicates how a term should be interpreted from an ontological perspective.
term editor: Alan Ruttenberg
definition source: Barry Smith, Werner Ceusters

ontology module
type: Class
subclass of: data about an ontology part
editor note: I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it.
alternative term: ontology file
curator note: This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology.
created by: cjm
creation date: 2018-05-20T20:55:03Z

base ontology module
type: Class
subclass of: ontology module
definition: An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies.
created by: cjm
creation date: 2018-05-20T20:55:30Z

editors ontology module
type: Class
subclass of: ontology module
definition: An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users.
alternative term: source ontology module
created by: cjm
creation date: 2018-05-20T20:55:47Z

main release ontology module
type: Class
subclass of: ontology module
definition: An ontology module that is intended to be the primary release product and the one consumed by the majority of tools.
editor note: TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module
created by: cjm
creation date: 2018-05-20T20:56:13Z

bridge ontology module
type: Class
subclass of: ontology module
definition: An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module.
created by: cjm
creation date: 2018-05-20T20:56:23Z

import ontology module
type: Class
subclass of: subset ontology module
definition: A subset ontology module that is intended to be imported from another ontology.
editor note: TODO: add axioms that indicate this is the output of a module extraction process.
alternative term: import file
created by: cjm
creation date: 2018-05-20T20:56:47Z

subset ontology module
type: Class
subclass of: ontology module
definition: An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms.
alternative term: ontology slim
alternative term: subset ontology
created by: cjm
creation date: 2018-05-20T20:58:11Z

curation subset ontology module
type: Class
subclass of: subset ontology module
definition: A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation.
created by: cjm
creation date: 2018-05-20T20:58:38Z

analysis subset ontology module
type: Class
subclass of: subset ontology module
definition: An ontology module that is intended for usage in analysis or discovery applications.
created by: cjm
creation date: 2018-05-20T20:58:49Z

single layer subset ontology module
type: Class
subclass of: subset ontology module
definition: A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint.
alternative term: ribbon subset
created by: cjm
creation date: 2018-05-20T20:59:19Z

exclusion subset ontology module
type: Class
subclass of: subset ontology module
definition: A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes.
alternative term: antislim
created by: cjm
creation date: 2018-05-20T20:59:57Z

external import ontology module
type: Class
subclass of: import ontology module
definition: An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach.
alternative term: external import
created by: cjm
creation date: 2018-05-20T21:00:14Z

species subset ontology module
type: Class
subclass of: subset ontology module
definition: A subset ontology that is crafted to either include or exclude a taxonomic grouping of species.
alternative term: taxon subset
created by: cjm
creation date: 2018-05-20T21:14:16Z

reasoned ontology module
type: Class
subclass of: ontology module
definition: An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available.
created by: cjm
creation date: 2018-05-20T21:20:33Z

generated ontology module
type: Class
subclass of: ontology module
definition: An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV.
editor note: TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process
created by: cjm
creation date: 2018-05-20T21:21:12Z

template generated ontology module
type: Class
subclass of: generated ontology module
definition: An ontology module that is automatically generated from a template specification and fillers for slots in that template.
created by: cjm
creation date: 2018-05-20T21:21:21Z

taxonomic bridge ontology module
type: Class
subclass of: bridge ontology module
created by: cjm
creation date: 2018-05-20T21:28:15Z

ontology module subsetted by expressivity
type: Class
subclass of: subset ontology module
created by: cjm
creation date: 2018-05-22T04:15:54Z

obo basic subset ontology module
type: Class
subclass of: ontology module subsetted by expressivity
definition: A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). An ontology is OBO Basic if and only if it has the following characteristics: DAG Unidirectional No Dangling Clauses Fully Asserted Fully Labeled No equivalence axioms Singly labeled edges No qualifier lists No disjointness axioms No owl-axioms header No imports
created by: cjm
creation date: 2018-05-22T04:16:10Z

ontology module subsetted by OWL profile
type: Class
subclass of: ontology module subsetted by expressivity
created by: cjm
creation date: 2018-05-22T04:16:28Z

EL++ ontology module
type: Class
subclass of: ontology module subsetted by OWL profile
created by: cjm
creation date: 2018-05-22T04:16:48Z

Viruses
type: Class
subclass of: organism
editor preferred label: Viruses
imported from: ncbitaxon.owl
has rank: NCBITaxon superkingdom
has db xref: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Vira
has_related_synonym: Viridae
has_related_synonym: viruses

Axiom
annotated source: Viruses
annotated property: has_related_synonym
annotated target: Vira
has synonym type: synonym

Axiom
annotated source: Viruses
annotated property: has_related_synonym
annotated target: Viridae
has synonym type: synonym

Axiom
annotated source: Viruses
annotated property: has_related_synonym
annotated target: viruses
has synonym type: blast name

Teleostomi
type: Class
subclass of: Gnathostomata <vertebrate>
has db xref: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Euteleostomi
type: Class
subclass of: Teleostomi
editor preferred label: Euteleostomi
alternative term: bony vertebrates
imported from: ncbitaxon.owl
has_alternative_id: NCBITaxon:40673
has db xref: GC_ID:1
has_exact_synonym: bony vertebrates
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Euteleostomi
annotated property: has_exact_synonym
annotated target: bony vertebrates
has synonym type: genbank common name

cellular organisms
type: Class
has db xref: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: biota

Axiom
annotated source: cellular organisms
annotated property: has_related_synonym
annotated target: biota
has synonym type: synonym

Dipnotetrapodomorpha
type: Class
subclass of: Sarcopterygii
has db xref: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Boreoeutheria
type: Class
subclass of: Eutheria
has db xref: GC_ID:1
has db xref: PMID:11743200
has db xref: PMID:11791233
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Boreotheria

Axiom
annotated source: Boreoeutheria
annotated property: has_related_synonym
annotated target: Boreotheria
has synonym type: synonym

Bacteria
type: Class
subclass of: cellular organisms
subclass of: organism
editor preferred label: Bacteria
alternative term: eubacteria
imported from: ncbitaxon.owl
has rank: NCBITaxon superkingdom
has db xref: GC_ID:11
has db xref: PMID:10425795
has db xref: PMID:10425796
has db xref: PMID:10425797
has db xref: PMID:10490293
has db xref: PMID:10843050
has db xref: PMID:10939651
has db xref: PMID:10939673
has db xref: PMID:10939677
has db xref: PMID:11211268
has db xref: PMID:11321083
has db xref: PMID:11321113
has db xref: PMID:11411719
has db xref: PMID:11540071
has db xref: PMID:11542017
has db xref: PMID:11542087
has db xref: PMID:11760965
has db xref: PMID:12054223
has db xref: PMID:2112744
has db xref: PMID:270744
has db xref: PMID:8123559
has db xref: PMID:8590690
has db xref: PMID:9103655
has db xref: PMID:9336922
has_exact_synonym: eubacteria
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Monera
has_related_synonym: Procaryotae
has_related_synonym: Prokaryota
has_related_synonym: Prokaryotae
has_related_synonym: bacteria
has_related_synonym: prokaryote
has_related_synonym: prokaryotes

Axiom
annotated source: Bacteria
annotated property: has_exact_synonym
annotated target: eubacteria
has synonym type: genbank common name

Axiom
annotated source: Bacteria
annotated property: has_related_synonym
annotated target: Monera
has synonym type: in part

Axiom
annotated source: Bacteria
annotated property: has_related_synonym
annotated target: Procaryotae
has synonym type: in part

Axiom
annotated source: Bacteria
annotated property: has_related_synonym
annotated target: Prokaryota
has synonym type: in part

Axiom
annotated source: Bacteria
annotated property: has_related_synonym
annotated target: Prokaryotae
has synonym type: in part

Axiom
annotated source: Bacteria
annotated property: has_related_synonym
annotated target: bacteria
has synonym type: blast name

Axiom
annotated source: Bacteria
annotated property: has_related_synonym
annotated target: prokaryote
has synonym type: in part

Axiom
annotated source: Bacteria
annotated property: has_related_synonym
annotated target: prokaryotes
has synonym type: in part

Homininae
type: Class
subclass of: Hominidae
has rank: NCBITaxon subfamily
has db xref: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Homo/Pan/Gorilla group

Axiom
annotated source: Homininae
annotated property: has_related_synonym
annotated target: Homo/Pan/Gorilla group
has synonym type: synonym

Archaea
type: Class
subclass of: cellular organisms
subclass of: organism
editor preferred label: Archaea
imported from: ncbitaxon.owl
has rank: NCBITaxon superkingdom
has db xref: GC_ID:11
has db xref: PMID:10425795
has db xref: PMID:10425796
has db xref: PMID:10425797
has db xref: PMID:10490293
has db xref: PMID:10843050
has db xref: PMID:10939651
has db xref: PMID:10939673
has db xref: PMID:10939677
has db xref: PMID:11211268
has db xref: PMID:11321083
has db xref: PMID:11321113
has db xref: PMID:11411719
has db xref: PMID:11540071
has db xref: PMID:11541975
has db xref: PMID:11542064
has db xref: PMID:11542149
has db xref: PMID:11760965
has db xref: PMID:12054223
has db xref: PMID:2112744
has db xref: PMID:25527841
has db xref: PMID:270744
has db xref: PMID:8123559
has db xref: PMID:8590690
has db xref: PMID:9103655
has db xref: PMID:9336922
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Archaebacteria
has_related_synonym: Mendosicutes
has_related_synonym: Metabacteria
has_related_synonym: Monera
has_related_synonym: Procaryotae
has_related_synonym: Prokaryota
has_related_synonym: Prokaryotae
has_related_synonym: archaea
has_related_synonym: prokaryote
has_related_synonym: prokaryotes

Axiom
annotated source: Archaea
annotated property: has_related_synonym
annotated target: Archaebacteria
has synonym type: synonym

Axiom
annotated source: Archaea
annotated property: has_related_synonym
annotated target: Mendosicutes
has synonym type: synonym

Axiom
annotated source: Archaea
annotated property: has_related_synonym
annotated target: Metabacteria
has synonym type: synonym

Axiom
annotated source: Archaea
annotated property: has_related_synonym
annotated target: Monera
has synonym type: in part

Axiom
annotated source: Archaea
annotated property: has_related_synonym
annotated target: Procaryotae
has synonym type: in part

Axiom
annotated source: Archaea
annotated property: has_related_synonym
annotated target: Prokaryota
has synonym type: in part

Axiom
annotated source: Archaea
annotated property: has_related_synonym
annotated target: Prokaryotae
has synonym type: in part

Axiom
annotated source: Archaea
annotated property: has_related_synonym
annotated target: archaea
has synonym type: blast name

Axiom
annotated source: Archaea
annotated property: has_related_synonym
annotated target: prokaryote
has synonym type: in part

Axiom
annotated source: Archaea
annotated property: has_related_synonym
annotated target: prokaryotes
has synonym type: in part

Eukaryota
type: Class
subclass of: cellular organisms
subclass of: organism
editor preferred label: Eukaryota
alternative term: eucaryotes
alternative term: eukaryotes
imported from: ncbitaxon.owl
has rank: NCBITaxon superkingdom
has db xref: GC_ID:1
has db xref: PMID:23020233
has_exact_synonym: eucaryotes
has_exact_synonym: eukaryotes
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Eucarya
has_related_synonym: Eucaryotae
has_related_synonym: Eukarya
has_related_synonym: Eukaryotae
has_related_synonym: eukaryotes

Axiom
annotated source: Eukaryota
annotated property: has_exact_synonym
annotated target: eucaryotes
has synonym type: genbank common name

Axiom
annotated source: Eukaryota
annotated property: has_exact_synonym
annotated target: eukaryotes
has synonym type: common name

Axiom
annotated source: Eukaryota
annotated property: has_related_synonym
annotated target: Eucarya
has synonym type: synonym

Axiom
annotated source: Eukaryota
annotated property: has_related_synonym
annotated target: Eucaryotae
has synonym type: synonym

Axiom
annotated source: Eukaryota
annotated property: has_related_synonym
annotated target: Eukarya
has synonym type: synonym

Axiom
annotated source: Eukaryota
annotated property: has_related_synonym
annotated target: Eukaryotae
has synonym type: synonym

Axiom
annotated source: Eukaryota
annotated property: has_related_synonym
annotated target: eukaryotes
has synonym type: blast name

Euarchontoglires
type: Class
subclass of: Boreoeutheria
editor preferred label: Euarchontoglires
imported from: ncbitaxon.owl
has rank: NCBITaxon superorder
has db xref: GC_ID:1
has db xref: PMID:11214319
has db xref: PMID:12082125
has db xref: PMID:12878460
has db xref: PMID:15522813
has_obo_namespace: ncbi_taxonomy

Simiiformes
type: Class
subclass of: Haplorrhini
has rank: NCBITaxon infraorder
has db xref: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Anthropoidea

Axiom
annotated source: Simiiformes
annotated property: has_related_synonym
annotated target: Anthropoidea
has synonym type: synonym

Hominoidea
type: Class
subclass of: Catarrhini
has rank: NCBITaxon superfamily
has db xref: GC_ID:1
has_exact_synonym: ape
has_exact_synonym: apes
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Hominoidea
annotated property: has_exact_synonym
annotated target: ape
has synonym type: common name

Axiom
annotated source: Hominoidea
annotated property: has_exact_synonym
annotated target: apes
has synonym type: genbank common name

Tetrapoda
type: Class
subclass of: Dipnotetrapodomorpha
editor preferred label: Tetrapoda
alternative term: tetrapods
imported from: ncbitaxon.owl
has db xref: GC_ID:1
has_exact_synonym: tetrapods
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Tetrapoda
annotated property: has_exact_synonym
annotated target: tetrapods
has synonym type: genbank common name

Amniota
type: Class
subclass of: Tetrapoda
editor preferred label: Amniota
alternative term: amniotes
imported from: ncbitaxon.owl
has db xref: GC_ID:1
has_exact_synonym: amniotes
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Amniota
annotated property: has_exact_synonym
annotated target: amniotes
has synonym type: genbank common name

Theria <Mammalia>
type: Class
subclass of: Mammalia
has db xref: GC_ID:1
has_exact_synonym: Theria
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Theria <Mammalia>
annotated property: has_exact_synonym
annotated target: Theria
has synonym type: scientific name

Opisthokonta
type: Class
subclass of: Eukaryota
editor preferred label: Opisthokonta
imported from: ncbitaxon.owl
has db xref: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Fungi/Metazoa group
has_related_synonym: opisthokonts

Axiom
annotated source: Opisthokonta
annotated property: has_related_synonym
annotated target: Fungi/Metazoa group
has synonym type: synonym

Axiom
annotated source: Opisthokonta
annotated property: has_related_synonym
annotated target: opisthokonts
has synonym type: synonym

Metazoa
type: Class
subclass of: Opisthokonta
has rank: NCBITaxon kingdom
has db xref: GC_ID:1
has_exact_synonym: metazoans
has_exact_synonym: multicellular animals
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Animalia
has_related_synonym: animals

Axiom
annotated source: Metazoa
annotated property: has_exact_synonym
annotated target: metazoans
has synonym type: genbank common name

Axiom
annotated source: Metazoa
annotated property: has_exact_synonym
annotated target: multicellular animals
has synonym type: common name

Axiom
annotated source: Metazoa
annotated property: has_related_synonym
annotated target: Animalia
has synonym type: synonym

Axiom
annotated source: Metazoa
annotated property: has_related_synonym
annotated target: animals
has synonym type: blast name

Bilateria
type: Class
subclass of: Eumetazoa
editor preferred label: Bilateria
imported from: ncbitaxon.owl
has db xref: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Deuterostomia
type: Class
subclass of: Bilateria
has db xref: GC_ID:1
has_exact_synonym: deuterostomes
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Deuterostomia
annotated property: has_exact_synonym
annotated target: deuterostomes
has synonym type: common name

Haplorrhini
type: Class
subclass of: Primates
has rank: NCBITaxon suborder
has db xref: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Mammalia
type: Class
subclass of: Amniota
editor preferred label: Mammalia
alternative term: mammals
imported from: ncbitaxon.owl
has rank: NCBITaxon class
has db xref: GC_ID:1
has_exact_synonym: mammals
has_obo_namespace: ncbi_taxonomy
has_related_synonym: mammals

Axiom
annotated source: Mammalia
annotated property: has_exact_synonym
annotated target: mammals
has synonym type: genbank common name

Axiom
annotated source: Mammalia
annotated property: has_related_synonym
annotated target: mammals
has synonym type: blast name

Eumetazoa
type: Class
subclass of: Metazoa
has db xref: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Chordata
type: Class
subclass of: Deuterostomia
has rank: NCBITaxon phylum
has db xref: GC_ID:1
has_exact_synonym: chordates
has_obo_namespace: ncbi_taxonomy
has_related_synonym: chordates

Axiom
annotated source: Chordata
annotated property: has_exact_synonym
annotated target: chordates
has synonym type: genbank common name

Axiom
annotated source: Chordata
annotated property: has_related_synonym
annotated target: chordates
has synonym type: blast name

Vertebrata <Metazoa>
type: Class
subclass of: Craniata <chordata>
editor preferred label: Vertebrata <Metazoa>
alternative term: Vertebrata
alternative term: vertebrates
imported from: ncbitaxon.owl
has db xref: GC_ID:1
has_exact_synonym: Vertebrata
has_exact_synonym: vertebrates
has_obo_namespace: ncbi_taxonomy
has_related_synonym: vertebrates

Axiom
annotated source: Vertebrata <Metazoa>
annotated property: has_exact_synonym
annotated target: Vertebrata
has synonym type: scientific name

Axiom
annotated source: Vertebrata <Metazoa>
annotated property: has_exact_synonym
annotated target: vertebrates
has synonym type: genbank common name

Axiom
annotated source: Vertebrata <Metazoa>
annotated property: has_related_synonym
annotated target: vertebrates
has synonym type: blast name

Gnathostomata <vertebrate>
type: Class
subclass of: Vertebrata <Metazoa>
has db xref: GC_ID:1
has_exact_synonym: Gnathostomata
has_exact_synonym: jawed vertebrates
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Gnathostomata <vertebrate>
annotated property: has_exact_synonym
annotated target: Gnathostomata
has synonym type: scientific name

Axiom
annotated source: Gnathostomata <vertebrate>
annotated property: has_exact_synonym
annotated target: jawed vertebrates
has synonym type: genbank common name

Sarcopterygii
type: Class
subclass of: Euteleostomi
has rank: NCBITaxon superclass
has db xref: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Craniata <chordata>
type: Class
subclass of: Chordata
has rank: NCBITaxon subphylum
has db xref: GC_ID:1
has_exact_synonym: Craniata
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Craniata <chordata>
annotated property: has_exact_synonym
annotated target: Craniata
has synonym type: scientific name

Eutheria
type: Class
subclass of: Theria <Mammalia>
has db xref: GC_ID:1
has_exact_synonym: eutherian mammals
has_exact_synonym: placental mammals
has_exact_synonym: placentals
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Placentalia
has_related_synonym: placentals

Axiom
annotated source: Eutheria
annotated property: has_exact_synonym
annotated target: eutherian mammals
has synonym type: common name

Axiom
annotated source: Eutheria
annotated property: has_exact_synonym
annotated target: placental mammals
has synonym type: common name

Axiom
annotated source: Eutheria
annotated property: has_exact_synonym
annotated target: placentals
has synonym type: genbank common name

Axiom
annotated source: Eutheria
annotated property: has_related_synonym
annotated target: Placentalia
has synonym type: synonym

Axiom
annotated source: Eutheria
annotated property: has_related_synonym
annotated target: placentals
has synonym type: blast name

Primates
type: Class
subclass of: Euarchontoglires
has rank: NCBITaxon order
has db xref: GC_ID:1
has_exact_synonym: primate
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Primata
has_related_synonym: primates

Axiom
annotated source: Primates
annotated property: has_exact_synonym
annotated target: primate
has synonym type: equivalent name

Axiom
annotated source: Primates
annotated property: has_related_synonym
annotated target: Primata
has synonym type: synonym

Axiom
annotated source: Primates
annotated property: has_related_synonym
annotated target: primates
has synonym type: blast name

Catarrhini
type: Class
subclass of: Simiiformes
has rank: NCBITaxon parvorder
has db xref: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Hominidae
type: Class
subclass of: Hominoidea
has rank: NCBITaxon family
has db xref: GC_ID:1
has_exact_synonym: great apes
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Pongidae

Axiom
annotated source: Hominidae
annotated property: has_exact_synonym
annotated target: great apes
has synonym type: genbank common name

Axiom
annotated source: Hominidae
annotated property: has_related_synonym
annotated target: Pongidae
has synonym type: synonym

Homo
type: Class
subclass of: Homininae
has rank: NCBITaxon genus
has db xref: GC_ID:1
has_exact_synonym: humans
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Homo
annotated property: has_exact_synonym
annotated target: humans
has synonym type: common name

Homo sapiens
type: Class
subclass of: Homo
editor preferred label: Homo sapiens
alternative term: human
alternative term: human being
alternative term: man
imported from: ncbitaxon.owl
has rank: NCBITaxon species
has db xref: GC_ID:1
has_exact_synonym: human
has_exact_synonym: man
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Home sapiens
has_related_synonym: Homo sampiens
has_related_synonym: Homo sapeins
has_related_synonym: Homo sapian
has_related_synonym: Homo sapians
has_related_synonym: Homo sapien
has_related_synonym: Homo sapience
has_related_synonym: Homo sapiense
has_related_synonym: Homo sapients
has_related_synonym: Homo sapines
has_related_synonym: Homo spaiens
has_related_synonym: Homo spiens
has_related_synonym: Humo sapiens

Axiom
annotated source: Homo sapiens
annotated property: has_exact_synonym
annotated target: human
has synonym type: genbank common name

Axiom
annotated source: Homo sapiens
annotated property: has_exact_synonym
annotated target: man
has synonym type: common name

Axiom
annotated source: Homo sapiens
annotated property: has_related_synonym
annotated target: Home sapiens
has synonym type: misspelling

Axiom
annotated source: Homo sapiens
annotated property: has_related_synonym
annotated target: Homo sampiens
has synonym type: misspelling

Axiom
annotated source: Homo sapiens
annotated property: has_related_synonym
annotated target: Homo sapeins
has synonym type: misspelling

Axiom
annotated source: Homo sapiens
annotated property: has_related_synonym
annotated target: Homo sapian
has synonym type: misspelling

Axiom
annotated source: Homo sapiens
annotated property: has_related_synonym
annotated target: Homo sapians
has synonym type: misspelling

Axiom
annotated source: Homo sapiens
annotated property: has_related_synonym
annotated target: Homo sapien
has synonym type: misspelling

Axiom
annotated source: Homo sapiens
annotated property: has_related_synonym
annotated target: Homo sapience
has synonym type: misspelling

Axiom
annotated source: Homo sapiens
annotated property: has_related_synonym
annotated target: Homo sapiense
has synonym type: misspelling

Axiom
annotated source: Homo sapiens
annotated property: has_related_synonym
annotated target: Homo sapients
has synonym type: misspelling

Axiom
annotated source: Homo sapiens
annotated property: has_related_synonym
annotated target: Homo sapines
has synonym type: misspelling

Axiom
annotated source: Homo sapiens
annotated property: has_related_synonym
annotated target: Homo spaiens
has synonym type: misspelling

Axiom
annotated source: Homo sapiens
annotated property: has_related_synonym
annotated target: Homo spiens
has synonym type: misspelling

Axiom
annotated source: Homo sapiens
annotated property: has_related_synonym
annotated target: Humo sapiens
has synonym type: misspelling

planned process
type: Class
equivalent class: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: plan specification
subclass of: process
subclass of: Event
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: plan specification
editor preferred label: planned process
example of usage: Injecting mice with a vaccine in order to test its efficacy
has curation status: ready for release
definition: A processual entity that realizes a plan which is the concretization of a plan specification.
editor note: 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
editor note: We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
term editor: Bjoern Peters
definition source: branch derived
curator note: 6/11/9: Edited at workshop. Used to include: is initiated by an agent
curator note: This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
imported from: obi.owl

regulator role
type: Class
subclass of: regulatory role
editor preferred label: regulator role
example of usage: Fact sheet - Regulating the companies The role of the regulator. Ofwat is the economic regulator of the water and sewerage industry in England and Wales. http://www.ofwat.gov.uk/aptrix/ofwat/publish.nsf/Content/roleofregulator_factsheet170805
has curation status: FossilSpecimen
definition: a regulatory role involved with making and/or enforcing relevant legislation and governmental orders
term editor: Person:Jennifer Fostel
alternative term: regulator
definition source: OBI

regulatory role
type: Class
subclass of: role
editor preferred label: regulatory role
example of usage: Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008
has curation status: FossilSpecimen
definition: a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body.
term editor: GROUP: Role branch
definition source: OBI, CDISC
curator note: govt agents responsible for creating regulations; proxies for enforcing regulations. CDISC definition: regulatory authorities. Bodies having the power to regulate. NOTE: In the ICH GCP guideline the term includes the authorities that review submitted clinical data and those that conduct inspections. These bodies are sometimes referred to as competent

material supplier role
type: Class
subclass of: service provider role
editor preferred label: material supplier role
example of usage: Jackson Labs is an organization which provide mice as experimental material
has curation status: FossilSpecimen
definition: a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation.
editor note: Supplier role is a special kind of service, e.g. biobank
term editor: PERSON:Jennifer Fostel
alternative term: material provider role
alternative term: supplier

classified data set
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: class prediction data transformation
subclass of: data set
subclass of: Restriction
  on property: is_specified_output_of
  some values from: class prediction data transformation
editor preferred label: classified data set
has curation status: pending final vetting
definition: A data set that is produced as the output of a class prediction data transformation and consists of a data set with assigned class labels.
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
alternative term: data set with assigned class labels

processed material
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: material processing
subclass of: material entity
subclass of: Restriction
  on property: is_specified_output_of
  some values from: material processing
editor preferred label: processed material
example of usage: Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
has curation status: ready for release
definition: Is a material entity that is created or changed during material processing.
term editor: PERSON: Alan Ruttenberg

evaluant role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: material entity
subclass of: Restriction
  on property: realized in
  all values from: assay
editor preferred label: evaluant role
example of usage: When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source.
has curation status: ready for release
definition: a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role
editor note: Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is)
editor note: examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected")
term editor: GROUP: Role Branch
definition source: OBI
curator note: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.

assay
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: planned process
subclass of: Restriction
  on property: realizes
  some values from: evaluant role
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: has role
      some values from: evaluant role
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: material entity
        intersection of: Restriction
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
disjoint with: data transformation
editor preferred label: assay
example of usage: Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
has curation status: ready for release
definition: A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
editor note: 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation.
term editor: PlanAndPlannedProcess Branch
alternative term: measuring
alternative term: scientific observation
definition source: OBI branch derived
ISA alternative term: study assay
IEDB alternative term: any method

culture medium
type: Class
subclass of: processed material
editor preferred label: culture medium
example of usage: A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008
has curation status: ready for release
definition: a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.
editor note: changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178 Modification made by JZ.
term editor: Person: Jennifer Fostel, Jie Zheng
definition source: OBI

material processing
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: processed material
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: Restriction
  on property: has_specified_input
  all values from: material entity
editor preferred label: material processing
example of usage: A cell lysis, production of a cloning vector, creating a buffer.
has curation status: ready for release
definition: A planned process which results in physical changes in a specified input material
term editor: PERSON: Bjoern Peters
term editor: PERSON: Frank Gibson
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Melanie Courtot
term editor: PERSON: Philippe Rocca Serra
alternative term: material transformation
definition source: OBI branch derived

specimen role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
editor preferred label: specimen role
example of usage: liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.
has curation status: ready for release
definition: a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation
editor note: 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role.
editor note: Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
editor note: blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen.
editor note: parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject.
term editor: GROUP: Role Branch
alternative term: material sample
definition source: OBI

imaging assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has_specified_output
  some values from: image
editor preferred label: imaging assay
has curation status: pending final vetting
definition: An assay that produces a picture of an entity.
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived

organization
type: Class
subclass of: material entity
editor preferred label: organization
example of usage: PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
has curation status: ready for release
definition: An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
editor note: BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Philippe Rocca-Serra
term editor: PERSON: Susanna Sansone
definition source: GROUP: OBI

protocol
type: Class
subclass of: plan specification
editor preferred label: protocol
example of usage: PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR.
has curation status: ready for release
definition: A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
ISA alternative term: study protocol

reverse transcriptase
type: Class
equivalent class: Class
  intersection of: enzyme
  intersection of: Restriction
    on property: has function
    some values from: Restriction
      on property: realized in
      all values from: RNA-directed DNA polymerase activity
subclass of: enzyme
subclass of: Restriction
  on property: has function
  some values from: Restriction
    on property: realized in
    all values from: RNA-directed DNA polymerase activity
editor preferred label: reverse transcriptase
has curation status: pending final vetting
definition: enzyme and has_function some GO:0003964 (RNA-directed DNA polymerase activity)
term editor: person:Melanie Courtot
definition source: group:OBI

extract
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: extraction
editor preferred label: extract
example of usage: Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923
has curation status: FossilSpecimen
definition: an extract is a material entity which results from an extraction process
term editor: PERSON: Philippe Rocca-Serra
alternative term: extracted material
definition source: GROUP: OBI Biomatrial Branch

enzyme
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Class
    union of: ribonucleic acid
    union of: protein-containing complex
    union of: protein
    union of: Restriction
      on property: has part
      some values from: ribonucleic acid
    union of: Restriction
      on property: has part
      some values from: protein-containing complex
    union of: Restriction
      on property: has part
      some values from: protein
  intersection of: Restriction
    on property: has function
    some values from: Restriction
      on property: realized in
      all values from: catalytic activity
subclass of: material entity
subclass of: Restriction
  on property: has function
  some values from: Restriction
    on property: realized in
    all values from: catalytic activity
editor preferred label: enzyme
has curation status: pending final vetting
definition: (protein or rna) or has_part (protein or rna) and has_function some GO:0003824 (catalytic activity)
editor note: MC: known issue: enzyme doesn't classify under material entity for now as it isn't stated that anything that has_part some material entity is a material entity. If we add as equivalent classes to material entity has_part some material entity and part_of some material entity (each one in his own necessary and sufficient block) Pellet in P3 doesn't classify any more.
term editor: person: Melanie Courtot
definition source: GROUP:OBI

assay objective
type: Class
subclass of: objective specification
editor preferred label: assay objective
example of usage: the objective to determine the weight of a mouse.
has curation status: ready for release
definition: an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role)
term editor: PPPB branch
definition source: PPPB branch

regulatory agency
type: Class
equivalent class: Class
  intersection of: organization
  intersection of: Restriction
    on property: has role
    some values from: regulator role
subclass of: organization
subclass of: Restriction
  on property: has role
  some values from: regulator role
editor preferred label: regulatory agency
example of usage: The US Environmental Protection Agency
has curation status: ready for release
definition: A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government.
term editor: GROUP: OBI Biomaterial Branch
definition source: WEB: en.wikipedia.org/wiki/Regulator

measure function
type: Class
subclass of: function
subclass of: Restriction
  on property: function of
  some values from: processed material
subclass of: Restriction
  on property: realized in
  all values from: Restriction
    on property: has_specified_output
    some values from: measurement datum
editor preferred label: measure function
example of usage: A glucometer measures blood glucose concentration, the glucometer has a measure function.
has curation status: ready for release
definition: Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference.
term editor: PERSON: Daniel Schober
term editor: PERSON: Helen Parkinson
term editor: PERSON: Melanie Courtot
term editor: PERSON:Frank Gibson

material transformation objective
type: Class
subclass of: objective specification
editor preferred label: material transformation objective
example of usage: The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.
has curation status: ready for release
definition: an objective specifiction that creates an specific output object from input materials.
term editor: PERSON: Bjoern Peters
term editor: PERSON: Frank Gibson
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Melanie Courtot
term editor: PERSON: Philippe Rocca-Serra
alternative term: artifact creation objective
definition source: GROUP: OBI PlanAndPlannedProcess Branch

manufacturing
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: manufacturing objective
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: manufacturing objective
editor preferred label: manufacturing
has curation status: ready for release
definition: Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process
editor note: Manufacturing implies reproducibility and responsibility AR
editor note: This includes a single scientist making a processed material for personal use.
term editor: PERSON: Bjoern Peters
term editor: PERSON: Frank Gibson
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Melanie Courtot
term editor: PERSON: Philippe Rocca-Serra
definition source: GROUP: OBI PlanAndPlannedProcess Branch

manufacturing objective
type: Class
subclass of: material transformation objective
editor preferred label: manufacturing objective
has curation status: ready for release
definition: is the objective to manufacture a material of a certain function (device)
term editor: PERSON: Bjoern Peters
term editor: PERSON: Frank Gibson
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Melanie Courtot
term editor: PERSON: Philippe Rocca-Serra
definition source: GROUP: OBI PlanAndPlannedProcess Branch

manufacturer role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: Class
    union of: Homo sapiens
    union of: organization
subclass of: Restriction
  on property: realized in
  all values from: manufacturing
editor preferred label: manufacturer role
example of usage: With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role.
has curation status: metadata incomplete
definition: Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process.
term editor: GROUP: Role Branch
definition source: OBI

material separation objective
type: Class
equivalent class: Class
  union of: portioning objective
  union of: separation into different composition objective
subclass of: material transformation objective
editor preferred label: material separation objective
example of usage: The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood.
has curation status: ready for release
definition: is an objective to transform a material entity into spatially separated components.
term editor: PPPB branch
definition source: PPPB branch

clustered data set
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: class discovery data transformation
subclass of: data set
subclass of: Restriction
  on property: is_specified_output_of
  some values from: class discovery data transformation
editor preferred label: clustered data set
example of usage: A clustered data set is the output of a K means clustering data transformation
has curation status: pending final vetting
definition: A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels.
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
alternative term: data set with assigned discovered class labels
curator note: AR thinks could be a data item instead

specimen collection process
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: specimen collection objective
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: specimen
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: specimen collection objective
BCO preferred label: specimen collection process
editor preferred label: specimen collection process
example of usage: drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation
has curation status: ready for release
definition: A planned process with the objective of collecting a specimen.
editor note: Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
editor note: Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role.
editor note: Philly2013: The specimen_role for the specimen is created during the specimen collection process.
editor note: label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/
term editor: Bjoern Peters
alternative term: specimen collection
curator note: 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
curator note: 6/9/09: used at workshop

class prediction data transformation
type: Class
equivalent class: Class
  union of: Restriction
    on property: has_specified_output
    some values from: classified data set
  union of: Restriction
    on property: achieves_planned_objective
    some values from: class prediction objective
subclass of: data transformation
editor preferred label: class prediction data transformation
has curation status: ready for release
definition: A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction.
term editor: James Malone
alternative term: supervised classification data transformation
definition source: PERSON: James Malone

sample from organism
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: collecting specimen from organism
  intersection of: Restriction
    on property: has role
    some values from: material sample role
subclass of: material sample
subclass of: specimen from organism
subclass of: Restriction
  on property: is_specified_output_of
  some values from: collecting specimen from organism
subclass of: Restriction
  on property: derives from
  some values from: material anatomical entity
editor preferred label: sample from organism
has curation status: example to be eventually removed
definition: a material obtained from an organism in order to be a representative of the whole
editor note: 5/29: This is a helper class for now
editor note: we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about.

portioning objective
type: Class
subclass of: material separation objective
disjoint with: separation into different composition objective
editor preferred label: portioning objective
example of usage: The objective to obtain multiple aliquots of an enzyme preparation.
has curation status: metadata incomplete
definition: A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material.

separation into different composition objective
type: Class
subclass of: material separation objective
editor preferred label: separation into different composition objective
example of usage: The objective to obtain cells contained in a sample of blood.
has curation status: FossilSpecimen
definition: A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities).
editor note: We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives

specimen collection objective
type: Class
subclass of: objective specification
editor preferred label: specimen collection objective
example of usage: The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
has curation status: ready for release
definition: A objective specification to obtain a material entity for potential use as an input during an investigation.
term editor: Bjoern Peters
definition source: Bjoern Peters

support vector machine
type: Class
subclass of: class prediction data transformation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: class prediction objective
editor preferred label: support vector machine
has curation status: metadata incomplete
definition: 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.
term editor: James Malone
term editor: Ryan Brinkman
alternative term: SVM
definition source: PERSON: Ryan Brinkman

decision tree induction objective
type: Class
subclass of: data transformation objective
editor preferred label: decision tree induction objective
has curation status: metadata incomplete
definition: A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made.
term editor: James Malone

decision tree building data transformation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: decision tree induction objective
subclass of: data transformation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: decision tree induction objective
editor preferred label: decision tree building data transformation
has curation status: FossilSpecimen
definition: A decision tree building data transformation is a data transformation that has objective decision tree induction.
term editor: James Malone
definition source: PERSON: James Malone

GenePattern software
type: Class
subclass of: software
editor preferred label: GenePattern software
has curation status: FossilSpecimen
definition: a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks.
term editor: James Malone
term editor: Person:Helen Parkinson
definition source: WEB: http://www.broadinstitute.org/cancer/software/genepattern/

peak matching
type: Class
subclass of: data transformation
editor preferred label: peak matching
has curation status: metadata incomplete
definition: 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
term editor: James Malone
term editor: Ryan Brinkman
definition source: PERSON: Ryan Brinkman

k-nearest neighbors
type: Class
subclass of: partitioning data transformation
subclass of: class discovery data transformation
subclass of: Class
  intersection of: Restriction
    on property: has_specified_output
    some values from: clustered data set
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: class discovery objective
editor preferred label: k-nearest neighbors
has curation status: pending final vetting
definition: 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.
term editor: James Malone
alternative term: k-NN
definition source: PERSON: James Malone

material sample role
type: Class
subclass of: specimen role
editor preferred label: material sample role
example of usage: a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
has curation status: pending final vetting
definition: A material sample role is a specimen role borne by a material entity that is the output of a material sampling process.
editor note: 7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off.

material sampling process
type: Class
equivalent class: Class
  intersection of: specimen collection process
  intersection of: Restriction
    on property: has_specified_input
    some values from: material entity
  intersection of: Restriction
    on property: has_specified_output
    some values from: material sample
subclass of: specimen collection process
subclass of: Restriction
  on property: has_specified_output
  some values from: material sample
editor preferred label: material sampling process
has curation status: metadata incomplete
definition: A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity
alternative term: sample collection
alternative term: sampling
term tracker item: https://github.com/obi-ontology/obi/issues/1002

material sample
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: material sample role
subclass of: specimen
subclass of: Material Sample
subclass of: Restriction
  on property: has role
  some values from: material sample role
editor preferred label: material sample
example of usage: blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
has curation status: metadata incomplete
definition: A material entity that has the material sample role
term editor: OBI: workshop
alternative term: sample population
ISA alternative term: sample

CART
type: Class
subclass of: decision tree building data transformation
editor preferred label: CART
has curation status: ready for release
definition: A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure.
term editor: James Malone
alternative term: classification and regression trees
definition source: BOOK: David J. Hand, Heikki Mannila and Padhraic Smyth (2001) Principles of Data Mining.

statistical model validation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: cross validation objective
subclass of: partitioning data transformation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: cross validation objective
editor preferred label: statistical model validation
example of usage: Using the expression levels of 20 proteins to predict whether a cancer patient will respond to a drug. A practical goal would be to determine which subset of the 20 features should be used to produce the best predictive model. - wikipedia
has curation status: FossilSpecimen
definition: A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set.
term editor: Helen Parkinson
definition source: http://en.wikipedia.org/wiki/Cross-validation_%28statistics%29

material maintenance objective
type: Class
subclass of: objective specification
editor preferred label: material maintenance objective
has curation status: ready for release
definition: An objective specification maintains some or all of the qualities of a material over time.
term editor: PERSON: Bjoern Peters
definition source: PERSON: Bjoern Peters

primary structure of DNA macromolecule
type: Class
equivalent class: Restriction
  on property: is concretized as
  some values from: Restriction
    on property: inheres in
    some values from: deoxyribonucleic acid
subclass of: region
subclass of: Restriction
  on property: is concretized as
  some values from: Restriction
    on property: inheres in
    some values from: deoxyribonucleic acid
editor preferred label: primary structure of DNA macromolecule
has curation status: metadata incomplete
definition: a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues.
editor note: placeholder for SO
term editor: BP et al

measurement device
type: Class
equivalent class: Class
  intersection of: device
  intersection of: Restriction
    on property: has function
    some values from: measure function
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred label: measurement device
example of usage: A ruler, a microarray scanner, a Geiger counter.
has curation status: ready for release
definition: A device in which a measure function inheres.
term editor: GROUP:OBI Philly workshop
definition source: OBI

manufacturer
type: Class
equivalent class: Class
  intersection of: Class
    union of: Homo sapiens
    union of: organization
  intersection of: Restriction
    on property: has role
    some values from: manufacturer role
subclass of: material entity
subclass of: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: manufacturer
has curation status: metadata incomplete
definition: A person or organization that has a manufacturer role

material maintenance
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
subclass of: planned process
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
editor preferred label: material maintenance
has curation status: metadata incomplete
definition: a process with that achieves the objective to maintain some or all of the characteristics of an input material over time

primary structure of RNA molecule
type: Class
equivalent class: Restriction
  on property: is concretized as
  some values from: Restriction
    on property: inheres in
    some values from: ribonucleic acid
subclass of: region
subclass of: Restriction
  on property: is concretized as
  some values from: Restriction
    on property: inheres in
    some values from: ribonucleic acid
editor preferred label: primary structure of RNA molecule
has curation status: metadata incomplete
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
term editor: Person:Bjoern Peters

service provider role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: Class
    union of: Homo sapiens
    union of: organization
subclass of: Restriction
  on property: realized in
  all values from: planned process
editor preferred label: service provider role
example of usage: Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer.
has curation status: metadata incomplete
definition: is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person
term editor: PERSON:Helen Parkinson

processed specimen
type: Class
equivalent class: Class
  intersection of: processed material
  intersection of: specimen
subclass of: processed material
subclass of: specimen
subclass of: Material Sample
editor preferred label: processed specimen
example of usage: A tissue sample that has been sliced and stained for a histology study. A blood specimen that has been centrifuged to obtain the white blood cells.
has curation status: ready for release
definition: A specimen that has been intentionally physically modified.
term editor: Bjoern Peters
definition source: Bjoern Peters
comment: A tissue sample that has been sliced and stained for a histology study.

categorical label
type: Class
subclass of: datum label
editor preferred label: categorical label
example of usage: The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels.
has curation status: FossilSpecimen
definition: A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale.
term editor: Bjoern Peters
definition source: Bjoern Peters

device
type: Class
subclass of: processed material
subclass of: Restriction
  on property: has function
  some values from: function
editor preferred label: device
example of usage: A voltmeter is a measurement device which is intended to perform some measure function.
example of usage: An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
has curation status: ready for release
definition: A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
editor note: 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent…
term editor: PERSON: Helen Parkinson
alternative term: instrument
definition source: OBI development call 2012-12-17.

sequence data
type: Class
subclass of: Class
  intersection of: measurement datum
  intersection of: Restriction
    on property: is about
    some values from: region
editor preferred label: sequence data
example of usage: example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search.
has curation status: FossilSpecimen
definition: A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.
term editor: Person:Chris Stoeckert
definition source: GROUP: OBI

questionnaire
type: Class
subclass of: document
editor preferred label: questionnaire
has curation status: FossilSpecimen
definition: A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study.
editor note: JT: It plays a role in collecting data that could be fleshed out more; but I'm thinking it is, in itself, an edited document. JZ: based on textual definition of edited document, it can be defined as N&S. I prefer to leave questionnaire as a document now. We can add more restrictions in the future and use that to determine it is an edited document or not.
editor note: Need to clarify if this is a document or a directive information entity (or what their connection is))
term editor: PERSON: Jessica Turner
definition source: Merriam-Webster

nucleic acid extract
type: Class
subclass of: extract
subclass of: processed specimen
subclass of: Class
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: nucleic acid extraction
  intersection of: Restriction
    on property: has role
    some values from: specimen role
subclass of: Restriction
  on property: has grain
  some values from: nucleic acid
editor preferred label: nucleic acid extract
has curation status: FossilSpecimen
definition: An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.
term editor: PERSON: Jie Zheng
definition source: UPenn Group

nucleic acid sequencer
type: Class
subclass of: measurement device
editor preferred label: nucleic acid sequencer
has curation status: FossilSpecimen
definition: An device that is used to determine the order of nucleotides in nucleic acid sequences.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

protein sequencer
type: Class
subclass of: measurement device
editor preferred label: protein sequencer
has curation status: FossilSpecimen
definition: An device that is used to determine the order of amino acids in protein sequences.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

specimen from organism
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has role
    some values from: specimen role
  intersection of: Restriction
    on property: derives from
    some values from: Class
      union of: material anatomical entity
      union of: anatomical cluster
subclass of: specimen
subclass of: Material Sample
subclass of: Restriction
  on property: derives from
  some values from: Class
    union of: material anatomical entity
    union of: anatomical cluster
editor preferred label: specimen from organism
has curation status: ready for release
definition: 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).
term editor: PERSON: Chris Stoeckert, Jie Zheng
alternative term: tissue specimen
definition source: MO_954 organism_part

DNA sequence data
type: Class
subclass of: sequence data
subclass of: Restriction
  on property: is about
  some values from: primary structure of DNA macromolecule
editor preferred label: DNA sequence data
example of usage: The part of a FASTA file that contains the letters ACTGGGAA
has curation status: FossilSpecimen
definition: A sequence data item that is about the primary structure of DNA
term editor: OBI call; Bjoern Peters
definition source: OBI call; Melanie Courtout
curator note: 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.

cell freezing medium
type: Class
subclass of: processed material
editor preferred label: cell freezing medium
has curation status: FossilSpecimen
definition: A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles.
term editor: PERSON: Matthew Brush

categorical value specification
type: Class
subclass of: value specification
editor preferred label: categorical value specification
has curation status: metadata incomplete
definition: A value specification that is specifies one category out of a fixed number of nominal categories
term editor: PERSON:Bjoern Peters

value specification
type: Class
subclass of: information content entity
editor preferred label: value specification
example of usage: The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
has curation status: ready for release
definition: An information content entity that specifies a value within a classification scheme or on a quantitative scale.
editor note: This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement.
term editor: PERSON:Bjoern Peters

cytometry assay
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: Class
        intersection of: evaluant role
        intersection of: Restriction
    intersection of: Restriction
      on property: has_specified_input
      some values from: Class
        intersection of: cell
        intersection of: Restriction
subclass of: assay
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: evaluant role
    intersection of: Restriction
      on property: role of
      some values from: cell
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: cell
    intersection of: Restriction
      on property: has role
      some values from: evaluant role
editor preferred label: cytometry assay
example of usage: An intracellular material detection by flow cytometry assay measuring peforin inside a culture of T cells.
has curation status: FossilSpecimen
definition: An assay that measures properties of cells.
term editor: IEDB
definition source: IEDB

collection of specimens
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has member
    all values from: specimen
subclass of: material entity
editor preferred label: collection of specimens
example of usage: Blood cells collected from multiple donors over the course of a study.
has curation status: pending final vetting
definition: A material entity that has two or more specimens as its parts.
editor note: Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: OBIB, OBI
Source: Biobank

histologic grade according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: histologic grade according to AJCC 7th edition
example of usage: G4: Undifferentiated
example of usage: G1:Well differentiated
has curation status: FossilSpecimen
definition: A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

histologic grade according to the Fuhrman Nuclear Grading System
type: Class
subclass of: categorical value specification
editor preferred label: histologic grade according to the Fuhrman Nuclear Grading System
has curation status: FossilSpecimen
definition: A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Histologic Grade (Fuhrman Nuclear Grading System)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

histologic grade for ovarian tumor
type: Class
subclass of: categorical value specification
editor preferred label: histologic grade for ovarian tumor
has curation status: FossilSpecimen
definition: A categorical value specification that is a histologic grade assigned to a ovarian tumor.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

histologic grade for ovarian tumor according to a two-tier grading system
type: Class
subclass of: histologic grade for ovarian tumor
editor preferred label: histologic grade for ovarian tumor according to a two-tier grading system
has curation status: FossilSpecimen
definition: A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

histologic grade for ovarian tumor according to the World Health Organization
type: Class
subclass of: histologic grade for ovarian tumor
editor preferred label: histologic grade for ovarian tumor according to the World Health Organization
has curation status: FossilSpecimen
definition: A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO).
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
has curation status: FossilSpecimen
definition: A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
term editor: Chris Stoeckert, Helena Ellis
alternative term: pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

pathologic primary tumor stage for lung according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic primary tumor stage for lung according to AJCC 7th edition
has curation status: FossilSpecimen
definition: A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
term editor: Chris Stoeckert, Helena Ellis
alternative term: pT: Pathologic spread lung primary tumor (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

pathologic primary tumor stage for kidney according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic primary tumor stage for kidney according to AJCC 7th edition
has curation status: FossilSpecimen
definition: A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
term editor: Chris Stoeckert, Helena Ellis
alternative term: pT: Pathologic spread kidney primary tumor (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

pathologic primary tumor stage for ovary according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic primary tumor stage for ovary according to AJCC 7th edition
has curation status: FossilSpecimen
definition: A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
term editor: Chris Stoeckert, Helena Ellis
alternative term: pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

pathologic lymph node stage for colon and rectum according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic lymph node stage for colon and rectum according to AJCC 7th edition
has curation status: FossilSpecimen
definition: A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
term editor: Chris Stoeckert, Helena Ellis
alternative term: pN: Pathologic spread colon lymph nodes (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

pathologic lymph node stage for lung according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic lymph node stage for lung according to AJCC 7th edition
has curation status: FossilSpecimen
definition: A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
term editor: Chris Stoeckert, Helena Ellis
alternative term: pN: Pathologic spread colon lymph nodes (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

pathologic lymph node stage for kidney according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic lymph node stage for kidney according to AJCC 7th edition
has curation status: FossilSpecimen
definition: A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
term editor: Chris Stoeckert, Helena Ellis
alternative term: pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

pathologic lymph node stage for ovary according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic lymph node stage for ovary according to AJCC 7th edition
has curation status: FossilSpecimen
definition: A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
term editor: Chris Stoeckert, Helena Ellis
alternative term: pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

pathologic distant metastases stage for colon according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic distant metastases stage for colon according to AJCC 7th edition
has curation status: FossilSpecimen
definition: A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
term editor: Chris Stoeckert, Helena Ellis
alternative term: M: colon distant metastases (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

pathologic distant metastases stage for lung according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic distant metastases stage for lung according to AJCC 7th edition
has curation status: FossilSpecimen
definition: A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
term editor: Chris Stoeckert, Helena Ellis
alternative term: M: lung distant metastases (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

pathologic distant metastases stage for kidney according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic distant metastases stage for kidney according to AJCC 7th edition
has curation status: FossilSpecimen
definition: A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
term editor: Chris Stoeckert, Helena Ellis
alternative term: M: kidney distant Metastases (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

pathologic distant metastases stage for ovary according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic distant metastases stage for ovary according to AJCC 7th edition
has curation status: FossilSpecimen
definition: A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
term editor: Chris Stoeckert, Helena Ellis
alternative term: M: ovarian distant metastases (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

clinical tumor stage group according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: clinical tumor stage group according to AJCC 7th edition
has curation status: FossilSpecimen
definition: A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Clinical tumor stage group (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

International Federation of Gynecology and Obstetrics cervical cancer stage value specification
type: Class
subclass of: categorical value specification
editor preferred label: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
has curation status: FossilSpecimen
definition: A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Clinical FIGO stage
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
type: Class
subclass of: categorical value specification
editor preferred label: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
has curation status: FossilSpecimen
definition: A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Pathologic Tumor Stage Grouping for ovarian cancer (FIGO)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

performance status value specification
type: Class
subclass of: categorical value specification
editor preferred label: performance status value specification
has curation status: FossilSpecimen
definition: A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life).
term editor: Chris Stoeckert, Helena Ellis
alternative term: Performance Status Scale
definition source: https://en.wikipedia.org/wiki/Performance_status
ontology term requester: NCI BBRB

Eastern Cooperative Oncology Group score value specification
type: Class
subclass of: performance status value specification
editor preferred label: Eastern Cooperative Oncology Group score value specification
has curation status: FossilSpecimen
definition: A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient.
term editor: Chris Stoeckert, Helena Ellis
alternative term: ECOG score
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

Karnofsky score vaue specification
type: Class
subclass of: performance status value specification
editor preferred label: Karnofsky score vaue specification
has curation status: FossilSpecimen
definition: A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Karnofsky Score
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

Epstein Barr virus transformed B cell
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: Class
      intersection of: establishing cell culture
      intersection of: Restriction
        on property: has_specified_input
        some values from: Viruses
  intersection of: Restriction
    on property: derives from
    all values from: B cell
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: establishing cell culture
    intersection of: Restriction
      on property: has_specified_input
      some values from: Viruses
editor preferred label: Epstein Barr virus transformed B cell
example of usage: PMID: 8777380. Expression of thyroid peroxidase in EBV-transformed B cell lines using adenovirus.Thyroid. 1996 Feb;6(1):23-8.
has curation status: FossilSpecimen
definition: A material entity which results from viral transformation process using EBV as transformation agent when applied to B-cell entity
term editor: PERSON: Susanna Sansone
definition source: GROUP: OBI Biomaterial Branch

organism
type: Class
equivalent class: Class
  union of: Viruses
  union of: Bacteria
  union of: Archaea
  union of: Eukaryota
subclass of: material entity
editor preferred label: organism
example of usage: animal
example of usage: fungus
example of usage: plant
example of usage: virus
has curation status: ready for release
definition: 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.
editor note: 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')
editor note: 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.
term editor: GROUP: OBI Biomaterial Branch
definition source: WEB: http://en.wikipedia.org/wiki/Organism

specimen
type: Class
equivalent class: Material Sample
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: specimen role
subclass of: Material Sample
editor preferred label: specimen
example of usage: A herbarium or museum specimen.
example of usage: A jar of water, the microbes that were filtered from that water, the DNA extracted from those microbes, a subsample of that DNA.
example of usage: Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
has curation status: ready for release
definition: A material entity that has the specimen role.
editor note: Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
term editor: PERSON: James Malone
term editor: PERSON: Philippe Rocca-Serra
definition source: GROUP: OBI Biomaterial Branch

cultured cell population
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: maintaining cell culture
subclass of: Restriction
  on property: has grain
  some values from: cultured cell
subclass of: Restriction
  on property: has grain
  all values from: cultured cell
editor preferred label: cultured cell population
example of usage: A cultured cell population applied in an experiment: "293 cells expressing TrkA were serum-starved for 18 hours and then neurotrophins were added for 10 min before cell harvest." (Lee, Ramee, et al. "Regulation of cell survival by secreted proneurotrophins." Science 294.5548 (2001): 1945-1948). A cultured cell population maintained in vitro: "Rat cortical neurons from 15 day embryos are grown in dissociated cell culture and maintained in vitro for 8–12 weeks" (Dichter, Marc A. "Rat cortical neurons in cell culture: culture methods, cell morphology, electrophysiology, and synapse formation." Brain Research 149.2 (1978): 279-293).
has curation status: FossilSpecimen
definition: A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history.
editor note: 2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line.
term editor: PERSON:Matthew Brush
alternative term: cell culture sample
definition source: PERSON:Matthew Brush
comment: The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally.

data transformation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: data transformation objective
subclass of: planned process
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: Class
      intersection of: algorithm
      intersection of: Restriction
        on property: has part
        some values from: objective specification
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: data transformation objective
subclass of: Restriction
  on property: has_specified_input
  all values from: data item
editor preferred label: data transformation
example of usage: 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.
has curation status: ready for release
definition: A planned process that produces output data from input data.
term editor: Elisabetta Manduchi
term editor: Helen Parkinson
term editor: James Malone
term editor: Melanie Courtot
term editor: Philippe Rocca-Serra
term editor: Richard Scheuermann
term editor: Ryan Brinkman
term editor: Tina Hernandez-Boussard
alternative term: data analysis
alternative term: data processing
definition source: Branch editors

leave one out cross validation method
type: Class
subclass of: statistical model validation
editor preferred label: leave one out cross validation method
example of usage: 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
has curation status: metadata incomplete
definition: 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
editor note: 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893049&group_id=177891&atid=886178
term editor: Person:Helen Parkinson

k-means clustering
type: Class
subclass of: partitioning data transformation
subclass of: class discovery data transformation
subclass of: Class
  intersection of: Restriction
    on property: has_specified_output
    some values from: clustered data set
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: class discovery objective
editor preferred label: k-means clustering
has curation status: pending final vetting
definition: 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).
term editor: Elisabetta Manduchi
term editor: James Malone
term editor: Philippe Rocca-Serra
definition source: WEB: http://en.wikipedia.org/wiki/K-means

hierarchical clustering
type: Class
subclass of: class discovery data transformation
subclass of: Class
  intersection of: Restriction
    on property: has_specified_output
    some values from: clustered data set
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: class discovery objective
editor preferred label: hierarchical clustering
has curation status: pending final vetting
definition: 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).
term editor: James Malone
definition source: WEB: http://en.wikipedia.org/wiki/Data_clustering#Hierarchical_clustering

dimensionality reduction
type: Class
subclass of: class discovery data transformation
subclass of: Class
  intersection of: Restriction
    on property: has_specified_output
    some values from: clustered data set
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: class discovery objective
editor preferred label: dimensionality reduction
has curation status: ready for release
definition: 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.
term editor: Elisabetta Manduchi
term editor: James Malone
term editor: Melanie Courtot
term editor: Philippe Rocca-Serra
alternative term: data projection
definition source: PERSON: Elisabetta Manduchi
definition source: PERSON: James Malone
definition source: PERSON: Melanie Courtot

principal components analysis dimensionality reduction
type: Class
subclass of: dimensionality reduction
editor preferred label: principal components analysis dimensionality reduction
has curation status: ready for release
definition: 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.
term editor: Elisabetta Manduchi
term editor: James Malone
term editor: Melanie Courtot
term editor: Philippe Rocca-Serra
alternative term: pca data reduction
definition source: PERSON: Elisabetta Manduchi
definition source: PERSON: James Malone
definition source: PERSON: Melanie Courtot

data visualization
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: data item
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    union of: graph
    union of: image
subclass of: Restriction
  on property: has_specified_input
  all values from: data item
subclass of: Restriction
  on property: has_specified_output
  all values from: Class
    union of: graph
    union of: image
editor preferred label: data visualization
example of usage: Generation of a heatmap from a microarray dataset
has curation status: ready for release
definition: An planned process that creates images, diagrams or animations from the input data.
term editor: Elisabetta Manduchi
term editor: James Malone
term editor: Melanie Courtot
term editor: Tina Boussard
alternative term: data encoding as image
alternative term: visualization
definition source: PERSON: Elisabetta Manduchi
definition source: PERSON: James Malone
definition source: PERSON: Melanie Courtot
definition source: PERSON: Tina Boussard
curator note: Possible future hierarchy might include this: information_encoding >data_encoding >>image_encoding

data transformation objective
type: Class
subclass of: objective specification
editor preferred label: data transformation objective
example of usage: normalize objective
has curation status: ready for release
definition: An objective specification to transformation input data into output data
editor note: Modified definition in 2013 Philly OBI workshop
term editor: James Malone
definition source: PERSON: James Malone

partitioning data transformation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: partitioning objective
subclass of: data transformation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: partitioning objective
editor preferred label: partitioning data transformation
has curation status: metadata incomplete
definition: A partitioning data transformation is a data transformation that has objective partitioning.
term editor: James Malone
definition source: PERSON: James Malone

partitioning objective
type: Class
subclass of: data transformation objective
editor preferred label: partitioning objective
example of usage: A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets.
has curation status: ready for release
definition: 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.
term editor: Elisabetta Manduchi
term editor: James Malone
definition source: PERSON: Elisabetta Manduchi

class discovery data transformation
type: Class
equivalent class: Class
  union of: Restriction
    on property: has_specified_output
    some values from: clustered data set
  union of: Restriction
    on property: achieves_planned_objective
    some values from: class discovery objective
subclass of: data transformation
editor preferred label: class discovery data transformation
has curation status: ready for release
definition: A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery.
term editor: James Malone
alternative term: clustering data transformation
alternative term: unsupervised classification data transformation
definition source: PERSON: James Malone

class discovery objective
type: Class
subclass of: data transformation objective
editor preferred label: class discovery objective
has curation status: ready for release
definition: 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.
term editor: James Malone
alternative term: clustering objective
alternative term: discriminant analysis objective
alternative term: unsupervised classification objective
definition source: PERSON: Elisabetta Manduchi
definition source: PERSON: James Malone

class prediction objective
type: Class
subclass of: data transformation objective
editor preferred label: class prediction objective
has curation status: ready for release
definition: 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.
term editor: James Malone
alternative term: classification objective
alternative term: supervised classification objective
definition source: PERSON: Elisabetta Manduchi
definition source: PERSON: James Malone

cross validation objective
type: Class
subclass of: partitioning objective
editor preferred label: cross validation objective
has curation status: pending final vetting
definition: 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.
term editor: James Malone
alternative term: rotation estimation objective
definition source: WEB: http://en.wikipedia.org/wiki/Cross_validation

clustered data visualization
type: Class
subclass of: data visualization
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    union of: dot plot
    union of: histogram
    union of: heatmap
    union of: dendrogram
    union of: scatter plot
subclass of: Restriction
  on property: has_specified_input
  all values from: clustered data set
editor preferred label: clustered data visualization
has curation status: metadata incomplete
definition: 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.
term editor: James Malone

extraction
type: Class
subclass of: material component separation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: separation into different composition objective
editor preferred label: extraction
example of usage: nucleic acid extraction using phenol chloroform
has curation status: metadata incomplete
definition: A material separation in which a desired component of an input material is separated from the remainder
editor note: 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.
term editor: Person:Bjoern Peters
term editor: Philippe Rocca-Serra

DNA sequencer
type: Class
subclass of: measurement device
editor preferred label: DNA sequencer
example of usage: ABI 377 DNA Sequencer, ABI 310 DNA Sequencer
has curation status: ready for release
definition: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
term editor: Trish Whetzel
definition source: MO

collecting specimen from organism
type: Class
subclass of: specimen collection process
subclass of: Restriction
  on property: has_specified_input
  some values from: organism
editor preferred label: collecting specimen from organism
example of usage: taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient
has curation status: ready for release
definition: a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation
term editor: PERSON:Bjoern Peters
definition source: IEDB

material component separation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material separation objective
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material separation objective
editor preferred label: material component separation
example of usage: 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
has curation status: ready for release
definition: a material processing in which components of an input material become segregated in space
term editor: Bjoern Peters
definition source: IEDB

maintaining cell culture
type: Class
subclass of: material maintenance
subclass of: Restriction
  on property: has_specified_input
  some values from: cultured cell population
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: culture medium
    union of: cell freezing medium
subclass of: Restriction
  on property: has_specified_output
  some values from: cultured cell population
editor preferred label: maintaining cell culture
example of usage: 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
has curation status: pending final vetting
definition: a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived

establishing cell culture
type: Class
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: cell
subclass of: Restriction
  on property: has_specified_input
  some values from: culture medium
subclass of: Restriction
  on property: has_specified_output
  some values from: cultured cell population
editor preferred label: 'establishing cell culture'
has curation status: FossilSpecimen
definition: a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line).
term editor: PERSON:Matthew Brush
definition source: PERSON:Matthew Brush
comment: A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms.

sequencing assay
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: Class
        intersection of: function
        intersection of: Restriction
    intersection of: Restriction
      on property: has_specified_input
      some values from: Class
        union of: nucleic acid sequencer
        union of: protein sequencer
        union of: DNA sequencer
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: Class
        intersection of: evaluant role
        intersection of: Restriction
    intersection of: Restriction
      on property: has_specified_input
      some values from: Class
        intersection of: Class
        intersection of: Restriction
  intersection of: Restriction
    on property: has_specified_output
    some values from: sequence data
  intersection of: Restriction
    on property: has_specified_output
    some values from: Restriction
      on property: is about
      some values from: region
subclass of: assay
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: function
    intersection of: Restriction
      on property: inheres in
      some values from: Class
        union of: nucleic acid sequencer
        union of: protein sequencer
        union of: DNA sequencer
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: evaluant role
    intersection of: Restriction
      on property: role of
      some values from: Class
        union of: nucleic acid extract
        union of: Restriction
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: Class
      union of: nucleic acid extract
      union of: Restriction
        on property: has part
        some values from: protein
    intersection of: Restriction
      on property: has role
      some values from: evaluant role
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: nucleic acid sequencer
    union of: protein sequencer
    union of: DNA sequencer
subclass of: Restriction
  on property: has_specified_output
  some values from: sequence data
editor preferred label: sequencing assay
example of usage: The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template
has curation status: pending final vetting
definition: An assay the uses chemical or biochemical means to infer the sequence of a biomaterial
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived

nucleic acid extraction
type: Class
subclass of: extraction
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: sample from organism
    union of: organism
    union of: cultured cell population
subclass of: Restriction
  on property: has_specified_output
  some values from: nucleic acid
editor preferred label: nucleic acid extraction
example of usage: 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.
has curation status: pending final vetting
definition: a material separation to recover the nucleic acid fraction of an input material
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
curator note: requested by Helen Parkinson for MO. Could be defined class

quality
type: Class
definition: A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
has_alternative_id: PATO:0000072
has_exact_synonym: trait
has_obo_namespace: quality
id: PATO:0000001

Axiom
annotated source: quality
annotated property: definition
annotated target: A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
has db xref: PATOC:GVG

behavioral quality
type: Class
subclass of: organismal quality
editor preferred label: behavioral quality
definition: 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.
imported from: pato.owl

physical object quality
type: Class
subclass of: quality
editor preferred label: physical object quality
definition: A quality which inheres in a continuant.
imported from: pato.owl
has_alternative_id: PATO:0001237
has_alternative_id: PATO:0001238
has db xref: snap:Quality
has_exact_synonym: monadic quality of a continuant
has_exact_synonym: multiply inhering quality of a physical entity
has_exact_synonym: quality of a continuant
has_exact_synonym: quality of a single physical entity
has_exact_synonym: quality of an object
has_exact_synonym: quality of continuant
has narrow synonym: monadic quality of an object
has narrow synonym: monadic quality of continuant
has_obo_namespace: quality
id: PATO:0001241
comment: Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles.

Axiom
annotated source: physical object quality
annotated property: definition
annotated target: A quality which inheres in a continuant.
has db xref: PATOC:GVG

organismal quality
type: Class
subclass of: physical object quality
editor preferred label: organismal quality
definition: A quality that inheres in an entire organism or part of an organism.
imported from: pato.owl

handedness
type: Class
subclass of: behavioral quality
editor preferred label: handedness
definition: 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.
imported from: pato.owl

left handedness
type: Class
subclass of: handedness
editor preferred label: left handedness
definition: 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.
imported from: pato.owl

right handedness
type: Class
subclass of: handedness
editor preferred label: right handedness
definition: 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.
imported from: pato.owl

ambidextrous handedness
type: Class
subclass of: handedness
editor preferred label: ambidextrous handedness
definition: 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.
imported from: pato.owl

collection of organisms
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has member
    all values from: organism or virus or viroid
  intersection of: Restriction
    on property: has member
    min qualified cardinality: 2
    on class: organism or virus or viroid
subclass of: object aggregate
subclass of: organismal entity
subclass of: Restriction
  on property: has member
  some values from: organism or virus or viroid
example of usage: Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family.
has curation status: pending final vetting
definition: A material entity that consists of two or more organisms, viruses, or viroids.
alternative term: group of organism
alternative term: organism collection
comment: May be of the same or different species.

species as a collection of organisms
type: Class
subclass of: single-species collection of organisms
has curation status: FossilSpecimen
definition: A collection of organisms that has as parts every organism of given species and no organisms of any other species.
editor note: At the moment there is no way to specify in an OWL axiom that the collection includes every individual of a species. This should be added, if possible.
comment: This term is neutral with respect to which organisms are included in a species. Membership will depend on the species concept and the taxonomic assertions used to define the species. These criteria must be specified by the user.

single-species collection of organisms
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has member
    all values from: organism or virus or viroid
  intersection of: Restriction
    on property: has member
    all values from: Restriction
      on property: member of
      qualified cardinality: 1
      on class: species as a collection of organisms
  intersection of: Restriction
    on property: has member
    min qualified cardinality: 2
    on class: organism or virus or viroid
subclass of: collection of organisms
has curation status: FossilSpecimen
definition: A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species.
alternative term: collection of organisms of the same species

household
type: Class
subclass of: organismal entity
subclass of: Class
  intersection of: Restriction
    on property: has member
    all values from: Homo sapiens
  intersection of: Restriction
    on property: has member
    min qualified cardinality: 1
    on class: Homo sapiens
subclass of: Restriction
  on property: RO_0002321
  some values from: human dwelling
has curation status: metadata incomplete
definition: An organismal entity that consists of one or more people who live in the same dwelling and also share at meals or living accommodation, and may consist of a single family or some other grouping of people.
term editor: Person: Jie Zheng
definition source: WEB: http://en.wikipedia.org/wiki/Household

collection of humans
type: Class
equivalent class: Class
  intersection of: single-species collection of organisms
  intersection of: Restriction
    on property: has member
    all values from: Homo sapiens
  intersection of: Restriction
    on property: has member
    min qualified cardinality: 2
    on class: Homo sapiens
subclass of: single-species collection of organisms
subclass of: Restriction
  on property: has member
  some values from: Homo sapiens
has curation status: pending final vetting
definition: A collection of organisms of the same species that has as members only humans.
alternative term: human community
alternative term: human population

agricultural household
type: Class
subclass of: household
has curation status: metadata incomplete
definition: A household in which the majority of the income of its members is derived from agricultural activities.
editor note: This is a more narrow definition in which the majority of income of a house comes from agricultural activities, as opposed to the broad definition in which any income comes from agricultural activities. The narrow definition was chosen to be consistent with the SDGIO (UN Sustainable Development Goals) which requested this term.

organismal entity
type: Class
equivalent class: Class
  union of: organism or virus or viroid
  union of: collection of organisms
subclass of: material entity
has curation status: FossilSpecimen
definition: A material entity that is one or more organisms, viruses or viroids.

protein
type: Class
subclass of: peptide
editor preferred label: protein
example of usage: antithrombin III is a protein
definition: An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA.
imported from: pr.owl

region
type: Class
subclass of: generically dependent continuant
editor preferred label: region
definition: 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.
alternative term: primary structure of sequence macromolecule
alternative term: sequence
imported from: so.owl

material anatomical entity
type: Class
subclass of: material entity
editor preferred label: material anatomical entity
definition: Anatomical entity that has mass.
imported from: uberon.owl

anatomical cluster
type: Class
subclass of: material entity
editor preferred label: anatomical cluster
definition: Anatomical group that has its parts adjacent to one another.
imported from: uberon.owl

length unit
type: Class
subclass of: measurement unit label
editor preferred label: length unit
definition: A unit which is a standard measure of the distance between two points.
imported from: uo.owl

mass unit
type: Class
subclass of: measurement unit label
editor preferred label: mass unit
definition: A unit which is a standard measure of the amount of matter/energy of a physical object.
imported from: uo.owl

time unit
type: Class
subclass of: measurement unit label
editor preferred label: time unit
definition: A unit which is a standard measure of the dimension in which events occur in sequence.
imported from: uo.owl

temperature unit
type: Class
subclass of: measurement unit label
editor preferred label: temperature unit
definition: A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter.
imported from: uo.owl

substance unit
type: Class
subclass of: measurement unit label
editor preferred label: substance unit
definition: A unit which is a standardised quantity of an element or compound with uniform composition.
imported from: uo.owl

concentration unit
type: Class
subclass of: measurement unit label
editor preferred label: concentration unit
definition: A unit which represents a standard measurement of how much of a given substance there is mixed with another substance.
imported from: uo.owl

volume unit
type: Class
subclass of: measurement unit label
editor preferred label: volume unit
definition: A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas.
imported from: uo.owl

frequency unit
type: Class
subclass of: measurement unit label
editor preferred label: frequency unit
definition: A unit which is a standard measure of the number of repetitive actions in a particular time.
imported from: uo.owl

volumetric flow rate unit
type: Class
subclass of: measurement unit label
editor preferred label: volumetric flow rate unit
definition: A unit which is a standard measure of the volume of fluid which passes through a given surface per unit time .
imported from: uo.owl

rate unit
type: Class
subclass of: measurement unit label
editor preferred label: rate unit
definition: A unit which represents a standard measurement occurrence of a process per unit time.
imported from: uo.owl

obsolete evidence role
type: Class
subclass of: Obsolete Class
example of usage: A museum specimen that serves as evidence for a taxonomic identification process bears an evidence role.
definition: A role that is borne by some entity as a result of the entity providing evidence to support an assertion.
has obsolescence reason: to be replaced with external ontology term
comment: Will be replaced by an external ontology class.
deprecated: true

obsolete persistent evidence role
type: Class
subclass of: Obsolete Class
definition: An evidence role that persists through time.
comment: Could add relation that persistant evidence role is specifically dependent on a museum material samples. Deprecated because we do not need this term. Can use OBI:evidence role. Not clear what it means for an evidence role to persist through time.
deprecated: true

obsolete collecting process
type: Class
subclass of: Obsolete Class
has obsolescence reason: terms merged
comment: This term is now redundant and is merged with material sampling process http://purl.obolibrary.org/obo/bco_0000022.
deprecated: true

obsolete observing process
type: Class
subclass of: Obsolete Class
taxonomic inventory metadata preferred name: sighting
example of usage: A trip camera capture of an image of a jaguar is an observation, because it is "selected" by the camera as worthy of obsevation simply by virtue of moving in front of the camera.
example of usage: Observing and recording the presence or absence of butterflies during a transect walk.
example of usage: Seeing three pelicans flying overhead on Christmas day and report them as part of the Christmas Bird Count.
definition: A process in which a person or machine sees or detects a material entity and selects it as worthy of observation, and which has as output an information content entity about the selected material entity.
editor note: This class was made obsolete because of the incorrect identifier format. It has been replaced by BCO_0000003.
has obsolescence reason: incorrect identifier format, replaced
creator: Biocode Commons Ontology Hackathon
comment: The information artifact may written or recorded or just be stored in someone's head (specifically depenedent upon that person). In the context of a taxonomic inventory, an observing process may be called a sighting, and is an ad hoc reporting of, typically, a single taxon occurrence, usually motivated by rarity, individual interest in the taxon, or atypicality of circumstances.
deprecated: true

obsolete being there process
type: Class
subclass of: Obsolete Class
definition: A process of existing in a particular spatio-temporal region.
has obsolescence reason: failed exploratory term
comment: This term was originally developed at the Semantics of Biodiversity workshop in 5/2012. It is no longer needed for the BCO.
deprecated: true

obsolete printed report
type: Class
subclass of: Obsolete Class
example of usage: a book
example of usage: a field notebook
has curation status: uncurated
has obsolescence reason: to be replaced with external ontology term
creator: Biocode Commons Ontology Hackathon
comment: IAO has the term document, which is defined as "A collection of information content entities intended to be understood together as a whole" and has as examples journal article, patent application, laboratory notebook, and book. IAO also has a term for report, but it is not defined. With this term, we want to describe the physical object that corresponds to some information content entity, together with the information content contained in the document or report. This class may be less important for modeling collection data, but could be important for efforts to get hand written (specifically dependent) reports into an electronic (generically dependent) report, and monitoring that process.
deprecated: true

obolete printed observational report
type: Class
subclass of: obsolete printed report
example of usage: A field notebook.
has curation status: uncurated
definition: A printed report that records the outcome of some observing process.
has obsolescence reason: incorrect identifier format, replaced
creator: Biocode Commons Ontology Hackathon
deprecated: true

obsolete selecting process
type: Class
subclass of: Obsolete Class
example of usage: Filtering sea water to extract only organisms smaller than a certain size.
example of usage: deciding which branch to collect for a herbarium specimen
definition: A process by which a person or machine decides that a particular material entity as worthy of collection or observation.
has obsolescence reason: to be replaced with external ontology term
creator: Biocode Commons Ontology Hackathon
comment: The criteria for selection may be specified in a protocol or may be ad hoc. Should be replaced by OBI:selection, but first OBI needs to fix the definition.
deprecated: true

obsolete submitting process
type: Class
subclass of: Obsolete Class
example of usage: a curator submitting a herbarium speciman to a museum
example of usage: a researcher submitting a water sample to a laboratory storage collection
definition: A planned process whereby a person submits a material sample to an organization.
editor note: This term was made obsolete because it had the incorrect identifier format. It has been replaced by BCO_0000016.
has obsolescence reason: incorrect identifier format, replaced
creator: Biocode Commons Ontology Hackathon
deprecated: true

obsolete physical extraction process
type: Class
subclass of: Obsolete Class
example of usage: picking leaves from a plant
example of usage: removing a fish from the ocean with a net
example of usage: removing dna from cells
definition: A process that involves removing a material entity from its original site to another site.
has obsolescence reason: to be replaced with external ontology term
creator: Biocode Commons Ontology Hackathon
comment: Considered acquisition in OBI, but that is about taking possession. Physical extraction may involve taking pocession, but it may also just involve extraction of something that is already posessed (e.g. of dna from cells).
deprecated: true

obsolete material sampling process
type: Class
subclass of: Obsolete Class
example of usage: collecting plant parts for herbarium specimens
example of usage: collecting sea water samples as part of Ocean Sampling Day
definition: A planned process that includes selecting a material entity for study, physically extracting the material entity, and submitting the material entity to some institution for preservation or study.
alternative term: collecting event
has obsolescence reason: failed exploratory term
creator: Biocode Commons Ontology Hackathon
comment: This term has been replaced by OBI:specimen collection.
deprecated: true

obsolete data sampling process
type: Class
subclass of: Obsolete Class
has obsolescence reason: failed exploratory term
comment: This term has been deprecated until it is determined whether or not it is needed in the BCO. Should probably be replaced by a term from OBI or IAO.
deprecated: true

obsolete statistical sampling process
type: Class
subclass of: Obsolete Class
has obsolescence reason: failed exploratory term
comment: This term has been deprecated until it is determined whether or not it is needed in the BCO. Should probably be replaced by a term from OBI or IAO.
deprecated: true

obsolete locality description
type: Class
subclass of: Obsolete Class
definition: An information artifact that is about a spatio-temporal region at which a process (such as collecting process, observing process, or material sampling process) occured.
editor note: This term was deprecated because it has the wrong ID format. It is replaced by BCO_0000025.
has obsolescence reason: incorrect identifier format, replaced
creator: Biocode Commons Ontology Hackathon
comment: Darwin Core needs to describe both the site and time where some activity occurred as an information content entity (e.g., in recording data from a lab notebook),therefore, we made locality description about a spatial temporal region, rather than a site.
deprecated: true

obsolete material sample role
type: Class
subclass of: Obsolete Class
example of usage: the role borne by a branch when it becomes a herbarium specimen
definition: A role that is borne by some material entity and is realized by the material entity being the output of a material sampling process.
has obsolescence reason: failed exploratory term
creator: Biocode Commons Ontology Hackathon
comment: This term has been replaced by OBI:specimen role.
deprecated: true

obsolete successful material sampling process
type: Class
subclass of: Obsolete Class
definition: A sampling process that has as output some material sample.
has obsolescence reason: failed exploratory term
comment: Do not need this class. By virtue of the existance of the material sample, we know that the sampling process was successful.
deprecated: true

obsolete unsuccessful material sampling process
type: Class
subclass of: Obsolete Class
definition: A material sampling process that has as output exactly zero material samples.
has obsolescence reason: failed exploratory term
comment: Do not need this class. By virtue of the absence of the material sample, we know that the sampling process was unsuccessful.
deprecated: true

obsolete museum collection entity
type: Class
subclass of: Obsolete Class
has obsolescence reason: failed exploratory term
comment: At the GSC14 hackathon in 09/2012, we decided to deprecate this term.
deprecated: true

obsolete organismal museum collection entity
type: Class
subclass of: obsolete museum collection entity
definition: A museum collections entity that derives from an organismal entity, has a persistent evidence role and 'depends on' a process of collecting.
has obsolescence reason: failed exploratory term
comment: The label for this on the original diagram was 'collection object'. However, not all entities in collections will fit the defition of 'object', so 'collection entity is probably a better name. The relation 'depends on' cannot really be used here. Old BFO has 'inverse depends on', but this is not in the current BFO. See dwc_bfo2_new.owl for the original logical definition. At the GSC14 hackathon in 09/2012, we decided to deprecate this term.
deprecated: true

obsolete museum collection
type: Class
subclass of: Obsolete Class
example of usage: The herbarium collection at the New York Botanical Garden.
example of usage: the painting collection at the Louvre Museum
has curation status: requires discussion
definition: An object aggregate that has as member part a material sample that is located in museum as a result of a process of curation.
editor note: This term was made obsolete because of incorrect identifier format. It has been replaced by BCO_0000031.
has obsolescence reason: incorrect identifier format, replaced
creator: Biocode Commons Ontology Hackathon
comment: Intent is to document biodiversity for research and education. The class museum collection has meaning that is much broader than biological collections. It would probably be better to import this term from another, more general ontology and create a specific subclass for natural history museum collection.
deprecated: true

obsolete organismal museum collection
type: Class
subclass of: Obsolete Class
example of usage: the insect collection at the Smithsonian Institution
has curation status: requires discussion
definition: A museum collection that has as member part a material sample that was derived from an organism.
editor note: This term was made obsolete because of incorrect identifier format. It is replaced by BCO_0000031.
has obsolescence reason: incorrect identifier format, replaced
creator: Biocode Commons Ontology Hackathon
deprecated: true

obsolete institution
type: Class
subclass of: Obsolete Class
has obsolescence reason: to be replaced with external ontology term
comment: Replaced by OBI organization. Request institution as synonym in OBI.
deprecated: true

obsolete organismal entity
type: Class
subclass of: obsolete taxonomic identification process
definition: A material entity that derives from an organism or virus or viroid.
comment: This class is understood to mean: A material entity that is either an organism, a part of an organism, a collection of organisms, or a fossil. The relation 'organismal entity derives from organism' was in the original diagram. Subclasses of organismal entity include organism, and It is not clear if it is valid to that an organism derives from an organism (is the derives from relation reflexive?). At the GSC14 hackathon in 09/2012, we decided to deprecate this term.
deprecated: true

obsolete organism or virus or viroid
type: Class
subclass of: Obsolete Class
has obsolescence reason: to be replaced with external ontology term
comment: This terms was replaced by a term imported from CARO. The original diagram only had organsim, but DWC and GOs both need to include viruses and viroids.
deprecated: true

obsolete material sample
type: Class
subclass of: Obsolete Class
example of usage: A herbarium or museum specimen.
example of usage: A jar of water, the microbes that were filtered from that water, the DNA extracted from those microbes, a subsample of that DNA.
definition: A material entity that has a material sample role. A material entity takes on the material sample role by being the output of a material samping process. That is, is selected for study, collected, and submitted to an institution for preservation or study.
has obsolescence reason: failed exploratory term
creator: Biocode Commons Ontology Hackathon
comment: This term has been replaced by OBI:specimen.
deprecated: true

obsolete data sample
type: Class
subclass of: Obsolete Class
definition: An information content entity (?) that is the result of some data sampling process.
has obsolescence reason: failed exploratory term
comment: This term has been deprecated until it is determined whether or not it is needed in the BCO. Should probably be replaced by a term from OBI or IAO.
deprecated: true

obsolete statistical sample
type: Class
subclass of: Obsolete Class
has obsolescence reason: failed exploratory term
comment: This term has been deprecated until it is determined whether or not it is needed in the BCO. Should probably be replaced by a term from OBI or IAO.
deprecated: true

obsolete protocol governed sampling activity
type: Class
subclass of: Obsolete Class
has obsolescence reason: failed exploratory term
comment: If sampling is a OBI planned process, that captures that it is protocal governed.
deprecated: true

obsolete taxonomic identification process
type: Class
subclass of: Obsolete Class
example of usage: Associating a museum specimen with a specific taxonomic concept based on its characters.
example of usage: Using BLAST to identify the taxa present in an environmental (metagenomic) sample.
example of usage: Using DNA barcoding to identify a plant species.
example of usage: Using a key to identify a plant in the field.
definition: A process by which a material sample is associated with a taxon or taxa.
editor note: This term was made obsolete because of incorrect identifier format. It is replaced by BCO_0000042.
creator: Biocode Commons Ontology Hackathon
deprecated: true

obsolete process that yields a material representation of a material entity
type: Class
subclass of: Obsolete Class
editor note: This term was made obsolete because of incorrect identifier format. It should be replaced by an external ontology term.
has obsolescence reason: to be replaced with external ontology term
curator note: Consider term from OBI or IAO.
creator: Biocode Commons Ontology Hackathon
comment: Includes as output rubbings, casts, photographic prints, audio or video tapes. Needs a better name. Current name is the definition.
deprecated: true

obsolete material target of observation
type: Class
subclass of: Obsolete Class
example of usage: A bird observed during a Christmas Bird Count
example of usage: A bird observed during a transect walk.
example of usage: A tree is forest plot that is measured for diameter at breast height (DBH).
example of usage: An lizard observed in the field that is not collected but whose location is recorded in a field notebook.
definition: A material entity that has a target of observation role, that is, a material entity that is the input of some observing process.
editor note: This term was made obsolete because of incorrected identifier format. It is replaced by BCO_0000044.
has obsolescence reason: incorrect identifier format, replaced
creator: Biocode Commons Ontology Hackathon
deprecated: true

obsolete process that yields an information artifact that is a representation of a material entity
type: Class
subclass of: Obsolete Class
editor note: This term was made obsolete because of incorrect identifier format. It should be replaced by an external ontology term.
has obsolescence reason: to be replaced with external ontology term
curator note: Some instances of term could possibly be replaced by OBI:image acquisition. Maybe request another OBI term for audio recording acquisition.
creator: Biocode Commons Ontology Hackathon
comment: Includes audio recordings and photographs (which are information artifacts). Needs a better name. Current name is the definition.
deprecated: true

obsolete material target of observation role
type: Class
subclass of: Obsolete Class
example of usage: the role borne by a bird during a Christmas Bird Count
definition: A role that is borne by some material entity and is realized by the material entity being the input of an observing process.
editor note: This term was made obsolete because of incorrect identifier format. It is replaced by BCO_0000046.
has obsolescence reason: incorrect identifier format, replaced
creator: Biocode Commons Ontology Hackathon
deprecated: true

zooarcheological specimen
type: Class
subclass of: Preserved Specimen
example of usage: A set of gastropod and bivalve shells found in shell midden from an archaeological site in Alaska.
definition: A preserved specimen that is the output of an archaeological sampling process and is the remains of a part of some animal.
definition source: Rob Guralnick
comment: Zooarchaeological specimens are typically collections of biological material generated as part of an archaeological collecting process that is separate from the type of processes that would yield other kinds of samples or collections of samples. This process almost always entails collecting in-situ from archaeological sites where there is evidence of past human material culture.

archeobotanical specimen
type: Class
subclass of: Preserved Specimen
example of usage: Preserved seeds found in a storage jar at an archeological site.
definition: A preserved specimen that is the output of an archaeological sampling process and is the remains of a part of some plant.
definition source: Rob Guralnick
comment: Archaeologicalbotanical specimens are typically collections of biological material generated as part of an archaeological collecting process that is separate from the type of processes that would yield other kinds of samples or collections of samples. This process almost always entails collecting in-situ from archaeological sites where there is evidence of past human material culture.

VocabularyEncodingScheme
type: Class
subclass of: Obsolete Class
has obsolescence reason: failed exploratory term
deprecated: true

Location
type: Class
subclass of: spatial region
BCO preferred label: location of an event
has curation status: metadata incomplete
expand expression to: The site where a process occurs. In the context of Dawrin Core, this is generally where a specimen is collected, an organism is observed or a measurement is taken.

Event
type: Class
subclass of: process
BCO preferred label: event
description: Examples: A specimen collection process. A machine observation.
has version: Event-2014-10-23
issued: 2008-11-19
modified: 2014-10-23
replaces: Event-2009-04-29
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering
decision: Decision-2014-10-26 15
dwc_terms status: recommended
comment: An action that occurs at some location during some time.

Fossil Specimen
type: Class
subclass of: Preserved Specimen
BCO preferred label: fossil specimen
has version: FossilSpecimen-2014-10-23
issued: 2014-10-23
modified: 2014-10-23
replaces: FossilSpecimen-2011-10-16
abcd equivalence: RecordBasisEnum/FossileSpecimen
decision: Decision-2014-10-26 15
dwc_terms status: recommended
comment: A preserved specimen that is a fossil.

Geological Context
type: Class
BCO preferred label: geological context
has curation status: uncurated
description: Example: A lithostratigraphic layer.
has version: GeologicalContext-2014-10-23
issued: 2009-07-06
modified: 2014-10-23
replaces: GeologicalContext-2009-07-06
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/Stratigraphy
decision: Decision-2014-10-26 15
dwc_terms status: recommended
comment: Geological information, such as stratigraphy, that qualifies a region or place.

Human Observation
type: Class
subclass of: data item
BCO preferred label: human observation
has version: HumanObservation-2014-10-23
issued: 2014-10-23
modified: 2014-10-23
replaces: HumanObservation-2011-10-16
abcd equivalence: RecordBasisEnum/HumanObservation
decision: Decision-2014-10-26 15
dwc_terms status: recommended
comment: An output of a human observation process.

Identification
type: Class
subclass of: taxonomic identification process
BCO preferred label: identification
dwc_bco mapping: taxonomic identification process
has curation status: pending final vetting
description: Example: A subspecies determination of an organism.
has version: Identification-2014-10-23
issued: 2008-11-19
modified: 2014-10-23
replaces: Identification-2008-11-19
abcd equivalence: DataSets/DataSet/Units/Unit/Identifications/Identification
decision: Decision-2014-10-26 15
dwc_terms status: recommended
comment: A taxonomic determination (e.g., the assignment to a taxon).

Living Specimen
type: Class
subclass of: specimen
subclass of: Material Sample
BCO preferred label: living specimen
has version: LivingSpecimen-2014-10-23
issued: 2014-10-23
modified: 2014-10-23
replaces: LivingSpecimen-2011-10-16
abcd equivalence: RecordBasisEnum/LivingSpecimen
decision: Decision-2014-10-26 15
dwc_terms status: recommended
comment: A specimen that is alive.

Machine Observation
type: Class
subclass of: data item
BCO preferred label: machine observation
has version: MachineObservation-2014-10-23
issued: 2014-10-23
modified: 2014-10-23
replaces: MachineObservation-2011-10-16
abcd equivalence: RecordBasisEnum/MachineObservation
decision: Decision-2014-10-26 15
dwc_terms status: recommended
comment: An output of a machine observation process.

Material Sample
type: Class
subclass of: specimen
BCO preferred label: specimen
description: Examples: A whole organism preserved in a collection. A part of an organism isolated for some purpose. A soil sample. A marine microbial sample.
has version: MaterialSample-2014-10-23
issued: 2013-03-28
modified: 2014-10-23
replaces: MaterialSample-2013-03-28
abcd equivalence: DataSets/DataSet/Units/Unit
decision: Decision-2014-10-26 15
dwc_terms status: recommended
comment: A physical results of a sampling (or subsampling) event. In biological collections, the material sample is typically collected, and either preserved or destructively processed.

Measurement or Fact
type: Class
subclass of: Obsolete Class
has obsolescence reason: This term was not deprecated from the dwc terms vocabulary, merely from the dwcterms ontology, because it is not needed here.
description: Resources can be thought of as identifiable records or instances of classes and may include, but need not be limited to Occurrences, Organisms, MaterialSamples, Events, Locations, GeologicalContexts, Identifications, or Taxa. Examples: The weight of an organism in grams. The number of placental scars.
has version: MeasurementOrFact-2014-10-23
issued: 2009-04-24
modified: 2014-10-23
replaces: MeasurementOrFact-2009-04-24
abcd equivalence: Datasets/Dataset/Units/Unit/MeasurementsOrFacts or DataSets/DataSet/Units/Unit/Gathering/SiteMeasurementsOrFacts
decision: Decision-2014-10-26 15
dwc_terms status: recommended
comment: A measurement of or fact about an rdfs:Resource (http://www.w3.org/2000/01/rdf-schema#Resource).
deprecated: true

Occurrence
type: Class
BCO preferred label: occurrence
editor note: This Darwin Core class should not be used when annotating data with BCO. It is not mapped to BCO classes because its meaning is too ambiguous.
description: Examples: A wolf pack on the shore of Kluane Lake in 1988. A virus in a plant leaf in a the New York Botanical Garden at 15:29 on 2014-10-23. A fungus in Central Park in the summer of 1929.
has version: Occurrence-2014-10-23
issued: 2008-11-19
modified: 2014-10-23
replaces: Occurrence-2009-04-29
abcd equivalence: DataSets/DataSet/Units/Unit
decision: Decision-2014-10-26 15
dwc_terms status: recommended
comment: An existence of an Organism (sensu http://rs.tdwg.org/dwc/terms/Organism) at a particular place at a particular time.

Organism
type: Class
subclass of: organismal entity
BCO preferred label: organism
description: Instances of the Organism class are intended to facilitate linking of one or more Identification instances to one or more Occurrence instances. Therefore, things that are typically assigned scientific names (such as viruses, hybrids, and lichens) and aggregates whose occurrences are typically recorded (such as packs, clones, and colonies) are included in the scope of this class.
has version: Organism-2014-10-23
issued: 2014-10-23
modified: 2014-10-23
abcd equivalence: not in ABCD
decision: Decision-2014-10-26 14
dwc_terms status: recommended
comment: A particular organism or defined group of organisms considered to be taxonomically homogeneous.

Preserved Specimen
type: Class
subclass of: specimen
subclass of: Material Sample
BCO preferred label: preserved specimen
has version: PreservedSpecimen-2014-10-23
issued: 2014-10-23
modified: 2014-10-23
replaces: PreservedSpecimen-2011-10-16
abcd equivalence: RecordBasisEnum/PreservedSpecimen
decision: Decision-2014-10-26 15
dwc_terms status: recommended
comment: A specimen that has been preserved.

Resource Relationship
type: Class
subclass of: Obsolete Class
has obsolescence reason: This term was not deprecated from the dwc terms vocabulary, merely from the dwcterms ontology, because it is not needed here.
description: Resources can be thought of as identifiable records or instances of classes and may include, but need not be limited to Occurrences, Organisms, MaterialSamples, Events, Locations, GeologicalContexts, Identifications, or Taxa. Example: An instance of an Organism is the mother of another instance of an Organism.
has version: ResourceRelationship-2014-10-23
issued: 2008-11-19
modified: 2014-10-23
replaces: ResourceRelationship-2009-01-21
abcd equivalence: DataSets/DataSet/Units/Unit/Associations
decision: Decision-2014-10-26 15
dwc_terms status: recommended
comment: A relationship of one rdfs:Resource (http://www.w3.org/2000/01/rdf-schema#Resource) to another.
deprecated: true

Taxon
type: Class
subclass of: collection of organisms
BCO preferred label: taxon
description: Example: The genus Truncorotaloides as published by Brönnimann et al. in 1953 in the Journal of Paleontology Vol. 27(6) p. 817-820.
has version: Taxon-2014-10-23
issued: 2008-11-19
modified: 2014-10-23
replaces: Taxon-2009-09-21
abcd equivalence: no simple equivalent in ABCD
decision: Decision-2014-10-26 15
dwc_terms status: recommended
comment: A group of organisms (sensu http://purl.obolibrary.org/obo/OBI_0100026) considered by taxonomists to form a homogeneous unit.

Obsolete Class
type: Class
subclass of: Thing

specimen collection process X
type: NamedIndividual

material entity A
type: NamedIndividual
is_specified_input_of: specimen collection process X

material entity B
type: NamedIndividual
is_specified_input_of: specimen collection process Y
is_specified_output_of: specimen collection process X

material entity C
type: NamedIndividual
is_specified_output_of: specimen collection process Y

specimen collection process Y
type: NamedIndividual

example to be eventually removed
type: NamedIndividual
type: curation status specification

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

FossilSpecimen
type: NamedIndividual
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.
label: metadata complete

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

ready for release
type: NamedIndividual
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 incomplete
type: NamedIndividual
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.

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

pending final vetting
type: NamedIndividual
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 term editor.

core
type: NamedIndividual
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.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot

placeholder removed
type: NamedIndividual
type: obsolescence reason specification

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

term imported
type: NamedIndividual
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.

term split
type: NamedIndividual
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: NamedIndividual
type: obsolescence reason specification
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.
editor note: We expect to be able to mine these new reasons and add instances as required.
deprecated: true

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

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

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

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

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

Transformation-ML
type: NamedIndividual
type: data format specification
editor preferred label: Transformation-ML
example of usage: Transformation-ML file describing parameter transformations used in a GvHD experiment.
has curation status: pending final vetting
definition: 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)
term editor: person:Jennifer Fostel

ACS
type: NamedIndividual
type: data format specification
editor preferred label: ACS
example of usage: d06.acs, ACS1.0 data file of well D06 of plate 2 of part 1 of a GvHD experiment.
has curation status: pending final vetting
definition: 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/)
term editor: person:Jennifer Fostel
definition source: web-page:http://www.isac-net.org/content/view/607/150/

XML
type: NamedIndividual
type: data format specification
editor preferred label: XML
example of usage: RDF/XML file, OWL file, Compensation-ML file, WSDL document, SVG document
has curation status: pending final vetting
definition: XML is a format standard of a digital entity that is conformant with the W3C Extensible Markup Language Recommendation.(http://www.w3.org/XML/)
term editor: person:Jennifer Fostel
definition source: web-page:http://www.w3.org/XML/

RDF
type: NamedIndividual
type: data format specification
editor preferred label: RDF
example of usage: A FOAF file, a SKOS file, an OWL file.
has curation status: pending final vetting
definition: 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/)
term editor: person:Jennifer Fostel
definition source: web-page:http://www.w3.org/RDF/

zip
type: NamedIndividual
type: data format specification
editor preferred label: zip
example of usage: MagicDraw MDZIP archive, Java JAR file.
has curation status: pending final vetting
definition: 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/)
term editor: person:Jennifer Fostel
definition source: web-page:http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/

tar
type: NamedIndividual
type: data format specification
editor preferred label: tar
example of usage: Example.tar file.
has curation status: pending final vetting
definition: 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/)
term editor: person:Jennifer Fostel
definition source: web-page:http://www.gnu.org/software/tar/manual/

FCS
type: NamedIndividual
type: data format specification
editor preferred label: FCS
example of usage: d01.fcs, FCS3 data file of well D06 of plate 2 of part 1 of a GvHD experiment.
has curation status: pending final vetting
definition: FCS is a format standard of a digital entity that is conformant with the Flow Cytometry Data File Standard.(http://www.fcspress.com/)
term editor: person:Jennifer Fostel
definition source: web-page:http://www.fcspress.com/

Compensation-ML
type: NamedIndividual
type: data format specification
editor preferred label: Compensation-ML
example of usage: compfoo.xml, Compensation-ML file describing compensation used in a GvHD experiment
has curation status: pending final vetting
definition: 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)
term editor: person:Jennifer Fostel

Gating-ML
type: NamedIndividual
type: data format specification
editor preferred label: Gating-ML
example of usage: foogate.xml, Gating-ML file describing gates used in a GvHD experiment.
has curation status: pending final vetting
definition: Gating-ML is a format standard of a digital entity that is conformant with the Gating-ML standard. (http://www.flowcyt.org/gating/)
term editor: person:Jennifer Fostel
definition source: web-page:http://www.flowcyt.org/gating/

OWL
type: NamedIndividual
type: data format specification
editor preferred label: OWL
example of usage: OBI ontology file, Basic Formal Ontology file, BIRNLex file, BioPAX file.
has curation status: pending final vetting
definition: 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/)
term editor: person:Jennifer Fostel
definition source: web-page:http://www.w3.org/2004/OWL/

Affymetrix
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: material supplier role
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Affymetrix
example of usage: Affymetrix supplied microarray
has curation status: metadata incomplete
definition: An organization which supplies technology, tools and protocols for use in high throughput applications

Thermo
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Thermo
has curation status: metadata incomplete
term editor: Philippe Rocca-Serra

Waters
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Waters
has curation status: metadata incomplete
term editor: Philippe Rocca-Serra

BIO-RAD
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: BIO-RAD
has curation status: metadata incomplete
term editor: Philippe Rocca-Serra

GenePattern hierarchical clustering
type: NamedIndividual
type: hierarchical clustering
editor preferred label: GenePattern hierarchical clustering
has curation status: metadata incomplete
term editor: James Malone

Ambion
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Ambion
has curation status: metadata incomplete
term editor: Philippe Rocca-Serra

Helicos
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Helicos
has curation status: metadata incomplete
term editor: Philippe Rocca-Serra

Roche
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Roche
has curation status: metadata incomplete
term editor: Philippe Rocca-Serra

Illumina
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Illumina
has curation status: metadata incomplete
term editor: Philippe Rocca-Serra

GenePattern PCA
type: NamedIndividual
type: principal components analysis dimensionality reduction
editor preferred label: GenePattern PCA
has curation status: metadata incomplete

GenePattern module SVM
type: NamedIndividual
type: GenePattern software
is about: GenePattern SVM
editor preferred label: GenePattern module SVM
has curation status: metadata incomplete
definition: GenePattern module SVM is a GenePattern software module which is used to run a support vector machine data transformation.
term editor: James Malone
term editor: Ryan Brinkman

GenePattern k-nearest neighbors
type: NamedIndividual
type: k-nearest neighbors
editor preferred label: GenePattern k-nearest neighbors
has curation status: metadata incomplete
term editor: James Malone

GenePattern LOOCV
type: NamedIndividual
type: leave one out cross validation method
editor preferred label: GenePattern LOOCV
has curation status: metadata incomplete

GenePattern k-means clustering
type: NamedIndividual
type: k-means clustering
editor preferred label: GenePattern k-means clustering
has curation status: metadata incomplete
term editor: James Malone

Agilent
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Agilent
has curation status: metadata incomplete
term editor: Philippe Rocca-Serra

GenePattern module KMeansClustering
type: NamedIndividual
type: GenePattern software
is about: GenePattern k-means clustering
editor preferred label: GenePattern module KMeansClustering
has curation status: FossilSpecimen
definition: GenePattern module KMeansClustering is a GenePattern software module which is used to perform a k Means clustering data transformation.
term editor: James Malone
definition source: PERSON: James Malone

GenePattern CART
type: NamedIndividual
type: CART
editor preferred label: GenePattern CART
has curation status: metadata incomplete
term editor: James Malone

GenePattern module CARTXValidation
type: NamedIndividual
type: GenePattern software
is about: GenePattern LOOCV
is about: GenePattern CART
editor preferred label: GenePattern module CARTXValidation
has curation status: metadata incomplete
definition: GenePattern module CARTXValidation is a GenePattern software module which uses a CART decision tree induction with a leave one out cross validation data transformations.

Li-Cor
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Li-Cor
has curation status: metadata incomplete
term editor: Philippe Rocca-Serra

Bruker Corporation
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Bruker Corporation
has curation status: metadata incomplete
term editor: Philippe Rocca-Serra

GenePattern module KNNXValidation
type: NamedIndividual
type: GenePattern software
editor preferred label: GenePattern module KNNXValidation
has curation status: FossilSpecimen
definition: GenePattern module KNNXValidation is a GenePattern software module which uses a k-nearest neighbours clustering with a leave one out cross validation data transformations.
term editor: James Malone
definition source: PERSON: James Malone

GenePattern module PeakMatch
type: NamedIndividual
type: GenePattern software
is about: GenePattern peak matching
editor preferred label: GenePattern module PeakMatch
has curation status: metadata incomplete

GenePattern module KNN
type: NamedIndividual
type: GenePattern software
is about: GenePattern k-nearest neighbors
editor preferred label: GenePattern module KNN
has curation status: metadata incomplete
definition: GenePattern module KNN is a GenePattern software module which perform a k-nearest neighbors data transformation.
term editor: James Malone

GenePattern module HierarchicalClustering
type: NamedIndividual
type: GenePattern software
is about: GenePattern hierarchical clustering
editor preferred label: GenePattern module HierarchicalClustering
has curation status: metadata incomplete
definition: GenePattern module HierarchicalClustering is a GenePattern software module which is used to perform a hierarchical clustering data transformation.
term editor: James Malone
term editor: PERSON: James Malone

GenePattern SVM
type: NamedIndividual
type: support vector machine
editor preferred label: GenePattern SVM
has curation status: metadata incomplete
term editor: James Malone

Applied Biosystems
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Applied Biosystems
has curation status: metadata incomplete
term editor: Philippe Rocca-Serra

GenePattern module PCA
type: NamedIndividual
type: GenePattern software
is about: GenePattern PCA
editor preferred label: GenePattern module PCA
has curation status: FossilSpecimen
definition: GenePattern module PCA is a GenePattern software module which is used to perform a principal components analysis dimensionality reduction data transformation.
term editor: James Malone
definition source: PERSON: James Malone

GenePattern peak matching
type: NamedIndividual
type: peak matching
editor preferred label: GenePattern peak matching
has curation status: metadata incomplete
term editor: James Malone
term editor: Ryan Brinkman

Bruker Daltonics
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Bruker Daltonics
has curation status: metadata incomplete
term editor: Philippe Rocca-Serra

GenePattern HeatMapViewer data visualization
type: NamedIndividual
type: clustered data visualization
editor preferred label: GenePattern HeatMapViewer data visualization
has curation status: metadata incomplete
definition: The GenePattern process of generating Heat Maps from clustered data.
term editor: James Malone

GenePattern HierarchicalClusteringViewer data visualization
type: NamedIndividual
type: clustered data visualization
editor preferred label: GenePattern HierarchicalClusteringViewer data visualization
has curation status: metadata incomplete
definition: The GenePattern process of generating hierarchical clustering visualization from clustered data.
term editor: James Malone

GenePattern module HeatMapViewer
type: NamedIndividual
type: GenePattern software
is about: GenePattern HeatMapViewer data visualization
editor preferred label: GenePattern module HeatMapViewer
has curation status: metadata incomplete
definition: A GenePattern software module which is used to generate a heatmap view of data.
term editor: James Malone

GenePattern module HierarchicalClusteringViewer
type: NamedIndividual
type: GenePattern software
is about: GenePattern HierarchicalClusteringViewer data visualization
editor preferred label: GenePattern module HierarchicalClusteringViewer
has curation status: metadata incomplete
definition: A GenePattern software module which is used to generate a view of data that has been hierarchically clustered.
term editor: James Malone

Sysmex Corporation, Kobe, Japan
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Sysmex Corporation, Kobe, Japan
has curation status: FossilSpecimen
definition source: WEB:http://www.sysmex.com/@2009/08/06
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

U.S. Food and Drug Administration
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: regulator role
editor preferred label: U.S. Food and Drug Administration
has curation status: metadata incomplete
alternative term: FDA

right handed
type: NamedIndividual
type: categorical label
type: Restriction
  on property: denotes
  some values from: right handedness
editor preferred label: right handed
has curation status: metadata incomplete

ambidexterous
type: NamedIndividual
type: categorical label
type: Restriction
  on property: denotes
  some values from: ambidextrous handedness
editor preferred label: ambidexterous
has curation status: metadata incomplete

left handed
type: NamedIndividual
type: categorical label
type: Restriction
  on property: denotes
  some values from: left handedness
editor preferred label: left handed
has curation status: metadata incomplete

Edingburgh handedness inventory
type: NamedIndividual
type: questionnaire
editor preferred label: Edingburgh handedness inventory
has curation status: FossilSpecimen
definition: 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.
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Jessica Turner
definition source: PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113
definition source: WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html

eBioscience
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: eBioscience
has curation status: FossilSpecimen
definition: A supplier of flow cytometry analyzers
term editor: Karin Breuer
definition source: WEB:http://www.ebioscience.com/@2011/04/11

Cytopeia
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Cytopeia
has curation status: FossilSpecimen
definition: A supplier of flow cytometry analyzers
term editor: Karin Breuer
definition source: WEB:http://www.cytopeia.com/@2011/04/11

Exalpha Biological
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Exalpha Biological
has curation status: FossilSpecimen
definition: A supplier of flow cytometry analyzers
term editor: Karin Breuer
definition source: WEB:http://www.exalpha.com/@2011/04/11

Apogee Flow Systems
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Apogee Flow Systems
has curation status: FossilSpecimen
definition: A supplier of flow cytometry analyzers
term editor: Karin Breuer
definition source: WEB:http://www.apogeeflow.com/@2011/04/11

Exbio Antibodies
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Exbio Antibodies
has curation status: FossilSpecimen
definition: A supplier of flow cytometry analyzers
term editor: Karin Breuer
definition source: WEB:http://www.exbio.cz/@2011/04/11

Becton Dickinson (BD Biosciences)
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Becton Dickinson (BD Biosciences)
has curation status: FossilSpecimen
definition: A supplier of flow cytometry analyzers
term editor: Karin Breuer
definition source: WEB:http://www.bdbiosciences.com/@2011/04/11

Dako Cytomation
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Dako Cytomation
has curation status: FossilSpecimen
definition: A supplier of flow cytometry analyzers
term editor: Karin Breuer
definition source: WEB:http://www.dakousa.com/@2011/04/11

Millipore
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Millipore
has curation status: FossilSpecimen
definition: A supplier of flow cytometry analyzers
term editor: Karin Breuer
definition source: WEB:http://www.guavatechnologies.com/@2011/04/11

Antigenix
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Antigenix
has curation status: FossilSpecimen
definition: A supplier of flow cytometry analyzers
term editor: Karin Breuer
definition source: WEB:http://www.antigenix.com/@2011/04/11

Partec
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Partec
has curation status: FossilSpecimen
definition: A supplier of flow cytometry analyzers
term editor: Karin Breuer
definition source: WEB:http://www.partec.de/@2011/04/11

Beckman Coulter
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Beckman Coulter
has curation status: FossilSpecimen
definition: A supplier of flow cytometry analyzers
term editor: Karin Breuer
definition source: WEB:http://www.beckmancoulter.com/@2011/04/11

Advanced Instruments Inc. (AI Companies)
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Advanced Instruments Inc. (AI Companies)
has curation status: FossilSpecimen
definition: A supplier of flow cytometry analyzers
term editor: Karin Breuer
definition source: WEB:http://www.aicompanies.com/@2011/04/11

Miltenyi Biotec
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Miltenyi Biotec
has curation status: FossilSpecimen
definition: A supplier of flow cytometry analyzers
term editor: Karin Breuer
definition source: WEB:http://www.miltenyibiotec.com/@2011/04/11

AES Chemunex
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: AES Chemunex
has curation status: FossilSpecimen
definition: A supplier of flow cytometry analyzers
term editor: Karin Breuer
definition source: WEB:http://www.aeschemunex.com/@2011/04/11

Bentley Instruments
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Bentley Instruments
has curation status: FossilSpecimen
definition: A supplier of flow cytometry analyzers
term editor: Karin Breuer
definition source: WEB:http://bentleyinstruments.com/@2011/04/11

Invitrogen
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Invitrogen
has curation status: FossilSpecimen
definition: A supplier of flow cytometry analyzers
term editor: Karin Breuer
definition source: WEB:http://www.invitrogen.com/@2011/04/11

Luminex
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Luminex
has curation status: FossilSpecimen
definition: A supplier of flow cytometry analyzers
term editor: Karin Breuer
definition source: WEB:http://www.luminexcorp.com/@2011/04/11

CytoBuoy
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: CytoBuoy
has curation status: FossilSpecimen
definition: A supplier of flow cytometry analyzers
term editor: Karin Breuer
definition source: WEB:http://www.cytobuoy.com/@2011/04/11

Nimblegen
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Nimblegen
has curation status: metadata incomplete
definition: An organization that focuses on manufacturing target enrichment probe pools for DNA sequencing.
term editor: Person: Jie Zheng

Pacific Biosciences
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Pacific Biosciences
has curation status: metadata incomplete
definition: An organization that supplies tools for studying the synthesis and regulation of DNA, RNA and protein. It developed a powerful technology platform called single molecule real-time (SMRT) technology which enables real-time analysis of biomolecules with single molecule resolution.
term editor: Person: Jie Zheng

NanoString Technologies
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: NanoString Technologies
has curation status: metadata incomplete
definition: An organization that supplies life science tools for translational research and molecular diagnostics based on a novel digital molecular barcoding technology. The NanoString platform can provide simple, multiplexed digital profiling of single molecules.

Thermo Fisher Scientific
type: NamedIndividual
type: organization
editor preferred label: Thermo Fisher Scientific
has curation status: FossilSpecimen
definition: An organization that is an American multinational, biotechnology product development company, created in 2006 by the merger of Thermo Electron and Fisher Scientific.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://en.wikipedia.org/wiki/Thermo_Fisher_Scientific
ontology term requester: NCI BBRB

G1: Well differentiated
type: NamedIndividual
type: histologic grade according to AJCC 7th edition
editor preferred label: G1: Well differentiated
has curation status: FossilSpecimen
definition: A histologic grade according to AJCC 7th edition indicating that the tumor cells and the organization of the tumor tissue appear close to normal.
term editor: Chris Stoeckert, Helena Ellis
alternative term: G1
definition source: https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet
ontology term requester: NCI BBRB

G2: Moderately differentiated
type: NamedIndividual
type: histologic grade according to AJCC 7th edition
editor preferred label: G2: Moderately differentiated
has curation status: FossilSpecimen
definition: A histologic grade according to AJCC 7th edition indicating that the tumor cells are moderately differentiated and reflect an intermediate grade.
term editor: Chris Stoeckert, Helena Ellis
alternative term: G2
definition source: https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet
ontology term requester: NCI BBRB

G3: Poorly differentiated
type: NamedIndividual
type: histologic grade according to AJCC 7th edition
editor preferred label: G3: Poorly differentiated
has curation status: FossilSpecimen
definition: A histologic grade according to AJCC 7th edition indicating that the tumor cells are poorly differentiated and do not look like normal cells and tissue.
term editor: Chris Stoeckert, Helena Ellis
alternative term: G3
definition source: https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet
ontology term requester: NCI BBRB

G4: Undifferentiated
type: NamedIndividual
type: histologic grade according to AJCC 7th edition
editor preferred label: G4: Undifferentiated
has curation status: FossilSpecimen
definition: A histologic grade according to AJCC 7th edition indicating that the tumor cells are undifferentiated and do not look like normal cells and tissue.
term editor: Chris Stoeckert, Helena Ellis
alternative term: G4
definition source: https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet
ontology term requester: NCI BBRB

G1 (Fuhrman)
type: NamedIndividual
type: histologic grade according to the Fuhrman Nuclear Grading System
editor preferred label: G1 (Fuhrman)
has curation status: FossilSpecimen
definition: A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are round, uniform, approximately 10um and that nucleoli are inconspicuous or absent.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Grade 1
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

G2 (Fuhrman)
type: NamedIndividual
type: histologic grade according to the Fuhrman Nuclear Grading System
editor preferred label: G2 (Fuhrman)
has curation status: FossilSpecimen
definition: A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are slightly irregular, approximately 15um and nucleoli are evident.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Grade 2
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

G3 (Fuhrman)
type: NamedIndividual
type: histologic grade according to the Fuhrman Nuclear Grading System
editor preferred label: G3 (Fuhrman)
has curation status: FossilSpecimen
definition: A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are very irregular, approximately 20um and nucleoli large and prominent.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Grade 3
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

G4 (Fuhrman)
type: NamedIndividual
type: histologic grade according to the Fuhrman Nuclear Grading System
editor preferred label: G4 (Fuhrman)
has curation status: FossilSpecimen
definition: A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei arei bizarre and multilobulated, 20um or greater and nucleoli are prominent and chromatin clumped.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Grade 4
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

Low grade ovarian tumor
type: NamedIndividual
type: histologic grade for ovarian tumor according to a two-tier grading system
editor preferred label: Low grade ovarian tumor
has curation status: FossilSpecimen
definition: A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is low grade.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Low grade
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

High grade ovarian tumor
type: NamedIndividual
type: histologic grade for ovarian tumor according to a two-tier grading system
editor preferred label: High grade ovarian tumor
has curation status: FossilSpecimen
definition: A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is high grade.
term editor: Chris Stoeckert, Helena Ellis
alternative term: High grade
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

G1 (WHO)
type: NamedIndividual
type: histologic grade for ovarian tumor according to the World Health Organization
editor preferred label: G1 (WHO)
has curation status: FossilSpecimen
definition: A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is well differentiated.
term editor: Chris Stoeckert, Helena Ellis
alternative term: G1
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

G2 (WHO)
type: NamedIndividual
type: histologic grade for ovarian tumor according to the World Health Organization
editor preferred label: G2 (WHO)
has curation status: FossilSpecimen
definition: A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is moderately differentiated.
term editor: Chris Stoeckert, Helena Ellis
alternative term: G2
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

G3 (WHO)
type: NamedIndividual
type: histologic grade for ovarian tumor according to the World Health Organization
editor preferred label: G3 (WHO)
has curation status: FossilSpecimen
definition: A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is poorly differentiated.
term editor: Chris Stoeckert, Helena Ellis
alternative term: G3
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

G4 (WHO)
type: NamedIndividual
type: histologic grade for ovarian tumor according to the World Health Organization
editor preferred label: G4 (WHO)
has curation status: FossilSpecimen
definition: A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is undifferentiated.
term editor: Chris Stoeckert, Helena Ellis
alternative term: G4
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

pT0 (colon)
type: NamedIndividual
type: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
editor preferred label: pT0 (colon)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that there is no evidence of primary tumor.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/
ontology term requester: NCI BBRB

pTis (colon)
type: NamedIndividual
type: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
editor preferred label: pTis (colon)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating carcinoma in situ (intraepithelial or invasion of lamina propria).
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/
ontology term requester: NCI BBRB

pT1 (colon)
type: NamedIndividual
type: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
editor preferred label: pT1 (colon)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades submucosa.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/
ontology term requester: NCI BBRB

pT2 (colon)
type: NamedIndividual
type: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
editor preferred label: pT2 (colon)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades muscularis propria.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/
ontology term requester: NCI BBRB

pT3 (colon)
type: NamedIndividual
type: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
editor preferred label: pT3 (colon)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades subserosa or into non-peritionealized pericolic or perirectal tissues.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/
ontology term requester: NCI BBRB

pT4a (colon)
type: NamedIndividual
type: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
editor preferred label: pT4a (colon)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor perforates visceral peritoneum.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/
ontology term requester: NCI BBRB

pT4b (colon)
type: NamedIndividual
type: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
editor preferred label: pT4b (colon)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor directly invades other organs or structures.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/
ontology term requester: NCI BBRB

pT0 (lung)
type: NamedIndividual
type: pathologic primary tumor stage for lung according to AJCC 7th edition
editor preferred label: pT0 (lung)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that there is no evidence of primary tumor.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/
ontology term requester: NCI BBRB

pTis (lung)
type: NamedIndividual
type: pathologic primary tumor stage for lung according to AJCC 7th edition
editor preferred label: pTis (lung)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for lung according to AJCC 7th edition indicating carcinoma in situ.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/
ontology term requester: NCI BBRB

pT1 (lung)
type: NamedIndividual
type: pathologic primary tumor stage for lung according to AJCC 7th edition
editor preferred label: pT1 (lung)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 3 cm or less in greatest dimension, surrounded by lung or visceral pleura without bronchoscopic evidence of invasion more proximal than the lobar bronchus (i.e., not in the main bronchus).
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/
ontology term requester: NCI BBRB

pT1a (lung)
type: NamedIndividual
type: pathologic primary tumor stage for lung according to AJCC 7th edition
editor preferred label: pT1a (lung)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 2 cm or less in greatest dimension.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/
ontology term requester: NCI BBRB

pT1b (lung)
type: NamedIndividual
type: pathologic primary tumor stage for lung according to AJCC 7th edition
editor preferred label: pT1b (lung)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 2 cm but not more than 3 cm in greatest dimension.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/
ontology term requester: NCI BBRB

pT2 (lung)
type: NamedIndividual
type: pathologic primary tumor stage for lung according to AJCC 7th edition
editor preferred label: pT2 (lung)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 7 cm or the tumor has any of the following features: involves main bronchus, 2 cm or more distal to the carina, invades visceral pleura, associated with atelectasis or obstructive pneumonitis that extends to the hilar region but does not involve the entire lung.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/
ontology term requester: NCI BBRB

pT2a (lung)
type: NamedIndividual
type: pathologic primary tumor stage for lung according to AJCC 7th edition
editor preferred label: pT2a (lung)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 5 cm in greatest dimension.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/
ontology term requester: NCI BBRB

pT2b (lung)
type: NamedIndividual
type: pathologic primary tumor stage for lung according to AJCC 7th edition
editor preferred label: pT2b (lung)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 5 cm but not more than 7 cm in greatest dimension.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/
ontology term requester: NCI BBRB

pT3 (lung)
type: NamedIndividual
type: pathologic primary tumor stage for lung according to AJCC 7th edition
editor preferred label: pT3 (lung)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 7 cm or one that directly invades any of: parietal pleura, chest wall (including superior sulcus tumors), diaphragm, phrenic nerve, mediastinal pleura, parietal pericardiu or the tumor is in the main bronchus less than 2 cm distal to the carina but without involvement of the carina or there is associated atelectasis or obstructive pneumonitis of the entire lung or there is separate tumor nodule(s) in the same lobe as the primary.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/
ontology term requester: NCI BBRB

pT4 (lung)
type: NamedIndividual
type: pathologic primary tumor stage for lung according to AJCC 7th edition
editor preferred label: pT4 (lung)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor of any size that invades any of the following: mediastinum, heart, great vessels, trachea, recurrent laryngeal nerve, esophagus, vertebral body, carina or there is separate tumor nodule(s) in a different ipsilateral lobe to that of the primary.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/
ontology term requester: NCI BBRB

pT0 (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred label: pT0 (kidney)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that there is no evidence of primary tumor.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT1 (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred label: pT1 (kidney)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 7 cm or less in greatest dimension and limited to the kidney.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT1a (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred label: pT1a (kidney)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 4 cm or less.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT1b (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred label: pT1b (kidney)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 4 cm but not more than 7 cm.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT2 (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred label: pT2 (kidney)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm in greatest dimension and limited to the kidney.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT2a (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred label: pT2a (kidney)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm but not more than 10 cm.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT2b (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred label: pT2b (kidney)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 10 cm and limited to the kidney.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT3 (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred label: pT3 (kidney)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor extends into major veins or perinephric tissues but not into the ipsilateral adrenal gland and not beyond the Gerota fascia.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT3a (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred label: pT3a (kidney)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into the renal vein or its segmental (muscle containing) branches, or the tumor invades perirenal and/or renal sinus fat (peripelvic) fat but not beyond Gerota fascia.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT3b (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred label: pT3b (kidney)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava below diaphragm.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT3c (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred label: pT3c (kidney)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava above the diaphragm or Invades the wall of the vena cava.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT4 (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred label: pT4 (kidney)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor invades beyond Gerota fascia (including contiguous extension into the ipsilateral adrenal gland).
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT0 (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred label: pT0 (ovary)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that there is no evidence of primary tumor.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT1 (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred label: pT1 (ovary)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to the ovaries (one or both).
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT1a (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred label: pT1a (ovary)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one ovary; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT1b (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred label: pT1b (ovary)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to both ovaries; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT1c (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred label: pT1c (ovary)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one or both ovaries with capsule ruptured, tumor on ovarian surface, or malignant cells in ascites or peritoneal washings.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT2 (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred label: pT2 (ovary)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with pelvic extension.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT2a (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred label: pT2a (ovary)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension and/or implants on uterus and/or tube(s) and no malignant cells in ascites or peritoneal washings.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT2b (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred label: pT2b (ovary)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension to other pelvic tissues and no malignant cells in ascites or peritoneal washings.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT2c (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred label: pT2c (ovary)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has pelvic extension with malignant cells in ascites or peritoneal washings.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT3 (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred label: pT3 (ovary)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with microscopically confirmed peritoneal metastasis outside the pelvis and/or regional lymph node metastasis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT3a (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred label: pT3a (ovary)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has microscopic peritoneal metastasis beyond pelvis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT3b (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred label: pT3b (ovary)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has macroscopic peritoneal, metastatasis beyond pelvis, 2 cm or less in greatest dimension.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT3c (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred label: pT3c (ovary)
has curation status: FossilSpecimen
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has peritoneal metastasis beyond pelvis, more than 2 cm in greatest dimension and/or regional lymph node metastasis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pN0 (colon)
type: NamedIndividual
type: pathologic lymph node stage for colon and rectum according to AJCC 7th edition
editor preferred label: pN0 (colon)
has curation status: FossilSpecimen
definition: A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating no regional lymph node metastsis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/
ontology term requester: NCI BBRB

pN1 (colon)
type: NamedIndividual
type: pathologic lymph node stage for colon and rectum according to AJCC 7th edition
editor preferred label: pN1 (colon)
has curation status: FossilSpecimen
definition: A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1-3 regional lymph nodes.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/
ontology term requester: NCI BBRB

pN1a (colon)
type: NamedIndividual
type: pathologic lymph node stage for colon and rectum according to AJCC 7th edition
editor preferred label: pN1a (colon)
has curation status: FossilSpecimen
definition: A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1 regional lymph node.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/
ontology term requester: NCI BBRB

pN1b (colon)
type: NamedIndividual
type: pathologic lymph node stage for colon and rectum according to AJCC 7th edition
editor preferred label: pN1b (colon)
has curation status: FossilSpecimen
definition: A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 2-3 regional lymph nodes.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/
ontology term requester: NCI BBRB

pN1c (colon)
type: NamedIndividual
type: pathologic lymph node stage for colon and rectum according to AJCC 7th edition
editor preferred label: pN1c (colon)
has curation status: FossilSpecimen
definition: A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating tumor deposit(s), i.e., satellites in the subserosa, or in non-peritonealized pericolic or perirectal soft tissue without regional lymph node metastasis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/
ontology term requester: NCI BBRB

pN2 (colon)
type: NamedIndividual
type: pathologic lymph node stage for colon and rectum according to AJCC 7th edition
editor preferred label: pN2 (colon)
has curation status: FossilSpecimen
definition: A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 or more regional lymph nodes.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/
ontology term requester: NCI BBRB

pN2a (colon)
type: NamedIndividual
type: pathologic lymph node stage for colon and rectum according to AJCC 7th edition
editor preferred label: pN2a (colon)
has curation status: FossilSpecimen
definition: A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 to 6 regional lymph nodes.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/
ontology term requester: NCI BBRB

pN2b (colon)
type: NamedIndividual
type: pathologic lymph node stage for colon and rectum according to AJCC 7th edition
editor preferred label: pN2b (colon)
has curation status: FossilSpecimen
definition: A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 7 or more regional lymph nodes.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/
ontology term requester: NCI BBRB

pN0 (lung)
type: NamedIndividual
type: pathologic lymph node stage for lung according to AJCC 7th edition
editor preferred label: pN0 (lung)
has curation status: FossilSpecimen
definition: A pathologic lymph node stage for lung according to AJCC 7th edition indicating no regional lymph node metastasis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/
ontology term requester: NCI BBRB

pN1 (lung)
type: NamedIndividual
type: pathologic lymph node stage for lung according to AJCC 7th edition
editor preferred label: pN1 (lung)
has curation status: FossilSpecimen
definition: A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral peribronchial and/or ipsilateral hilar lymph nodes and intrapulmonary nodes, including involvement by direct extension.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/
ontology term requester: NCI BBRB

pN2 (lung)
type: NamedIndividual
type: pathologic lymph node stage for lung according to AJCC 7th edition
editor preferred label: pN2 (lung)
has curation status: FossilSpecimen
definition: A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral mediastinal and/or subcarinal lymph node(s).
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/
ontology term requester: NCI BBRB

pN3 (lung)
type: NamedIndividual
type: pathologic lymph node stage for lung according to AJCC 7th edition
editor preferred label: pN3 (lung)
has curation status: FossilSpecimen
definition: A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in contralateral mediastinal, contralateral hilar, ipsilateral or contralateral scalene, or supraclavicular lymph node(s).
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/
ontology term requester: NCI BBRB

pN0 (kidney)
type: NamedIndividual
type: pathologic lymph node stage for kidney according to AJCC 7th edition
editor preferred label: pN0 (kidney)
has curation status: FossilSpecimen
definition: A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is no regional lymph node metastasis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_n/
ontology term requester: NCI BBRB

pN1 (kidney)
type: NamedIndividual
type: pathologic lymph node stage for kidney according to AJCC 7th edition
editor preferred label: pN1 (kidney)
has curation status: FossilSpecimen
definition: A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is regional lymph node metastasis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_n/
ontology term requester: NCI BBRB

pN0 (ovary)
type: NamedIndividual
type: pathologic lymph node stage for ovary according to AJCC 7th edition
editor preferred label: pN0 (ovary)
has curation status: FossilSpecimen
definition: A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is no regional lymph node metastasis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_n/
ontology term requester: NCI BBRB

pN1 (ovary)
type: NamedIndividual
type: pathologic lymph node stage for ovary according to AJCC 7th edition
editor preferred label: pN1 (ovary)
has curation status: FossilSpecimen
definition: A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is regional lymph node metastasis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_n/
ontology term requester: NCI BBRB

cM0 (colon)
type: NamedIndividual
type: pathologic distant metastases stage for colon according to AJCC 7th edition
editor preferred label: cM0 (colon)
has curation status: FossilSpecimen
definition: A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there are no symptoms or signs of distant metastasis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://en.wikipedia.org/wiki/Cancer_staging#Pathological_M_Categorization_.28cM_and_pM.29
ontology term requester: NCI BBRB

cM1 (colon)
type: NamedIndividual
type: pathologic distant metastases stage for colon according to AJCC 7th edition
editor preferred label: cM1 (colon)
has curation status: FossilSpecimen
definition: A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is clinical evidence of distant metastases by history, physical examination, imaging studies, or invasive procedures, but without microscopic evidence of the presumed distant metastases.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://en.wikipedia.org/wiki/Cancer_staging#Pathological_M_Categorization_.28cM_and_pM.29
ontology term requester: NCI BBRB

cM1a (colon)
type: NamedIndividual
type: pathologic distant metastases stage for colon according to AJCC 7th edition
editor preferred label: cM1a (colon)
has curation status: FossilSpecimen
definition: A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ based on clinical assessment.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/
ontology term requester: NCI BBRB

cM1b (colon)
type: NamedIndividual
type: pathologic distant metastases stage for colon according to AJCC 7th edition
editor preferred label: cM1b (colon)
has curation status: FossilSpecimen
definition: A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum based on clinical assessment.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/
ontology term requester: NCI BBRB

pM1 (colon)
type: NamedIndividual
type: pathologic distant metastases stage for colon according to AJCC 7th edition
editor preferred label: pM1 (colon)
has curation status: FossilSpecimen
definition: A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is microscopic evidence confirming distant metastatic disease.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/
ontology term requester: NCI BBRB

pM1a (colon)
type: NamedIndividual
type: pathologic distant metastases stage for colon according to AJCC 7th edition
editor preferred label: pM1a (colon)
has curation status: FossilSpecimen
definition: A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ and histologically confirmed.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/
ontology term requester: NCI BBRB

pM1b (colon)
type: NamedIndividual
type: pathologic distant metastases stage for colon according to AJCC 7th edition
editor preferred label: pM1b (colon)
has curation status: FossilSpecimen
definition: A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum and histologically confirmed.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/
ontology term requester: NCI BBRB

cM0 (lung)
type: NamedIndividual
type: pathologic distant metastases stage for lung according to AJCC 7th edition
editor preferred label: cM0 (lung)
has curation status: FossilSpecimen
definition: A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is no distant metastasis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/
ontology term requester: NCI BBRB

cM1 (lung)
type: NamedIndividual
type: pathologic distant metastases stage for lung according to AJCC 7th edition
editor preferred label: cM1 (lung)
has curation status: FossilSpecimen
definition: A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/
ontology term requester: NCI BBRB

cM1a (lung)
type: NamedIndividual
type: pathologic distant metastases stage for lung according to AJCC 7th edition
editor preferred label: cM1a (lung)
has curation status: FossilSpecimen
definition: A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is based on clinical assessment and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/
ontology term requester: NCI BBRB

cM1b (lung)
type: NamedIndividual
type: pathologic distant metastases stage for lung according to AJCC 7th edition
editor preferred label: cM1b (lung)
has curation status: FossilSpecimen
definition: A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases based on clinical assessment.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/
ontology term requester: NCI BBRB

pM1 (lung)
type: NamedIndividual
type: pathologic distant metastases stage for lung according to AJCC 7th edition
editor preferred label: pM1 (lung)
has curation status: FossilSpecimen
definition: A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/
ontology term requester: NCI BBRB

pM1a (lung)
type: NamedIndividual
type: pathologic distant metastases stage for lung according to AJCC 7th edition
editor preferred label: pM1a (lung)
has curation status: FossilSpecimen
definition: A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is histologically confirmed and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/
ontology term requester: NCI BBRB

pM1b (lung)
type: NamedIndividual
type: pathologic distant metastases stage for lung according to AJCC 7th edition
editor preferred label: pM1b (lung)
has curation status: FossilSpecimen
definition: A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/
ontology term requester: NCI BBRB

cM0 (kidney)
type: NamedIndividual
type: pathologic distant metastases stage for kidney according to AJCC 7th edition
editor preferred label: cM0 (kidney)
has curation status: FossilSpecimen
definition: A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is no distant metastasis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/
ontology term requester: NCI BBRB

cM1 (kidney)
type: NamedIndividual
type: pathologic distant metastases stage for kidney according to AJCC 7th edition
editor preferred label: cM1 (kidney)
has curation status: FossilSpecimen
definition: A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/
ontology term requester: NCI BBRB

pM1 (kidney)
type: NamedIndividual
type: pathologic distant metastases stage for kidney according to AJCC 7th edition
editor preferred label: pM1 (kidney)
has curation status: FossilSpecimen
definition: A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/
ontology term requester: NCI BBRB

cM0 (ovary)
type: NamedIndividual
type: pathologic distant metastases stage for ovary according to AJCC 7th edition
editor preferred label: cM0 (ovary)
has curation status: FossilSpecimen
definition: A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is no distant metastasis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/
ontology term requester: NCI BBRB

cM1 (ovary)
type: NamedIndividual
type: pathologic distant metastases stage for ovary according to AJCC 7th edition
editor preferred label: cM1 (ovary)
has curation status: FossilSpecimen
definition: A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis based on clinical assessment.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/
ontology term requester: NCI BBRB

pM1 (ovary)
type: NamedIndividual
type: pathologic distant metastases stage for ovary according to AJCC 7th edition
editor preferred label: pM1 (ovary)
has curation status: FossilSpecimen
definition: A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis that is histologically confirmed.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/
ontology term requester: NCI BBRB

Occult Carcinoma (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred label: Occult Carcinoma (AJCC 7th)
has curation status: FossilSpecimen
definition: A clinical tumor stage group according to AJCC 7th edition indicating a small carcinoma, either asymptomatic or giving rise to metastases without symptoms due to the primary carcinoma.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Occult Carcinoma
definition source: http://www.medilexicon.com/dictionary/14371
ontology term requester: NCI BBRB

Stage 0 (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred label: Stage 0 (AJCC 7th)
has curation status: FossilSpecimen
definition: A clinical tumor stage group according to AJCC 7th edition indicating a carcinoma in situ (or melanoma in situ for melanoma of the skin or germ cell neoplasia in situ for testicular germ cell tumors) and generally is considered to have no metastatic potential.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Stage 0
definition source: https://en.wikipedia.org/wiki/Cancer_staging
ontology term requester: NCI BBRB

Stage I (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred label: Stage I (AJCC 7th)
has curation status: FossilSpecimen
definition: A clinical tumor stage group according to AJCC 7th edition indicating cancers that are smaller or less deeply invasive without regional disease or nodes.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Stage I
definition source: https://en.wikipedia.org/wiki/Cancer_staging
ontology term requester: NCI BBRB

Stage IIA (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred label: Stage IIA (AJCC 7th)
has curation status: FossilSpecimen
definition: A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIB and IIC.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IIA
definition source: https://en.wikipedia.org/wiki/Cancer_staging
ontology term requester: NCI BBRB

Stage IIB (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred label: Stage IIB (AJCC 7th)
has curation status: FossilSpecimen
definition: A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIC.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IIB
definition source: https://en.wikipedia.org/wiki/Cancer_staging
ontology term requester: NCI BBRB

Stage IIC (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred label: Stage IIC (AJCC 7th)
has curation status: FossilSpecimen
definition: A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIB.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IIC
definition source: https://en.wikipedia.org/wiki/Cancer_staging
ontology term requester: NCI BBRB

Stage IIIA (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred label: Stage IIIA (AJCC 7th)
has curation status: FossilSpecimen
definition: A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIB and IIIC.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IIIA
definition source: https://en.wikipedia.org/wiki/Cancer_staging
ontology term requester: NCI BBRB

Stage IIIB (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred label: Stage IIIB (AJCC 7th)
has curation status: FossilSpecimen
definition: A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIC.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IIIB
definition source: https://en.wikipedia.org/wiki/Cancer_staging
ontology term requester: NCI BBRB

Stage IIIC (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred label: Stage IIIC (AJCC 7th)
has curation status: FossilSpecimen
definition: A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIB.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IIIC
definition source: https://en.wikipedia.org/wiki/Cancer_staging
ontology term requester: NCI BBRB

Stage IVA (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred label: Stage IVA (AJCC 7th)
has curation status: FossilSpecimen
definition: A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVB.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IVA
definition source: https://en.wikipedia.org/wiki/Cancer_staging
ontology term requester: NCI BBRB

Stage IVB (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred label: Stage IVB (AJCC 7th)
has curation status: FossilSpecimen
definition: A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVA.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IVB
definition source: https://en.wikipedia.org/wiki/Cancer_staging
ontology term requester: NCI BBRB

Stage IA (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IA (FIGO)
has curation status: FossilSpecimen
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating invasive carcinoma which can be diagnosed only by microscopy, with deepest invasion <5 mm and the largest extension <7 mm.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IA
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IA1 (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IA1 (FIGO)
has curation status: FossilSpecimen
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of <3.0 mm in depth and extension of <7.0 mm.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IA1
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IA2 (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IA2 (FIGO)
has curation status: FossilSpecimen
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of >3.0 mm and not >5.0 mm with an extension of not >7.0 mm.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IA2
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IB (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IB (FIGO)
has curation status: FossilSpecimen
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesions limited to the cervix uteri or pre-clinical cancers greater than stage IA
term editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IB
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IB1 (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IB1 (FIGO)
has curation status: FossilSpecimen
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA <4.0 cm in greatest dimension.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IB1
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IB2 (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IB2 (FIGO)
has curation status: FossilSpecimen
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA >4.0 cm in greatest dimension.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IB2
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IIA (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IIA (FIGO)
has curation status: FossilSpecimen
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IIA
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IIA1 (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IIA1 (FIGO)
has curation status: FossilSpecimen
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion <4.0 cm in greatest dimension.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IIA1
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IIA2 (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IIA2 (FIGO)
has curation status: FossilSpecimen
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion >4.0 cm in greatest dimension.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IIA2
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IIB (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IIB (FIGO)
has curation status: FossilSpecimen
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina with obvious parametrial invasion.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IIB
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IIIA (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IIIA (FIGO)
has curation status: FossilSpecimen
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating tumour involves lower third of the vagina, with no extension to the pelvic wall.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IIIA
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IIIB (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IIIB (FIGO)
has curation status: FossilSpecimen
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating extension to the pelvic wall and/or hydronephrosis or non-functioning kidney.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IIIB
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IVA (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IVA (FIGO)
has curation status: FossilSpecimen
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread of the growth to adjacent organs.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IVA
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IVB (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IVB (FIGO)
has curation status: FossilSpecimen
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread to distant organs.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IVB
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage 1 (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage 1 (FIGO)
has curation status: FossilSpecimen
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1, N0, and M0.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Stage 1
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 1A (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage 1A (FIGO)
has curation status: FossilSpecimen
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1a, N0, and M0.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Stage 1A
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 1B (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage 1B (FIGO)
has curation status: FossilSpecimen
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1b, N0, and M0.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Stage 1B
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 1C (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage 1C (FIGO)
has curation status: FossilSpecimen
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1c, N0, and M0.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Stage 1C
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 2 (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage 2 (FIGO)
has curation status: FossilSpecimen
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2, N0, and M0.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Stage 2
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 2A (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage 2A (FIGO)
has curation status: FossilSpecimen
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2a, N0, and M0.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Stage 2A
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 2B (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage 2B (FIGO)
has curation status: FossilSpecimen
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2b, N0, and M0.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Stage 2B
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 2C (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage 2C (FIGO)
has curation status: FossilSpecimen
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2c, N0, and M0.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Stage 2C
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 3 (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage 3 (FIGO)
has curation status: FossilSpecimen
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3, N0, and M0) or (T3,3a,3b, NX, and M0).
term editor: Chris Stoeckert, Helena Ellis
alternative term: Stage 3
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 3A (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage 3A (FIGO)
has curation status: FossilSpecimen
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3a, N0, and M0 .
term editor: Chris Stoeckert, Helena Ellis
alternative term: Stage 3A
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 3B (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage 3B (FIGO)
has curation status: FossilSpecimen
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3b, N0, and M0 .
term editor: Chris Stoeckert, Helena Ellis
alternative term: Stage 3B
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 3C (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage 3C (FIGO)
has curation status: FossilSpecimen
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3c, N0,X and M0) or (any T, N1 and M0).
term editor: Chris Stoeckert, Helena Ellis
alternative term: Stage 3C
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 4 (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage 4 (FIGO)
has curation status: FossilSpecimen
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of any T, any N, and M1.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Stage 4
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage Unknown (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage Unknown (FIGO)
has curation status: FossilSpecimen
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T0, N0, and M0) or (T1,1a-1c,2,2a-2c, NX, and M0) or (TX, N0,X, M0).
term editor: Chris Stoeckert, Helena Ellis
alternative term: Stage Unknown
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

3: symptomatic in bed more than 50% of the day but not bed ridden
type: NamedIndividual
type: Eastern Cooperative Oncology Group score value specification
editor preferred label: 3: symptomatic in bed more than 50% of the day but not bed ridden
has curation status: FossilSpecimen
definition: An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and in bed for more than 50% of the day but is not bed ridden.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

2: symptomatic but in bed less than 50% of the day
type: NamedIndividual
type: Eastern Cooperative Oncology Group score value specification
editor preferred label: 2: symptomatic but in bed less than 50% of the day
has curation status: FossilSpecimen
definition: An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is in bed for less than 50% of the day.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

4: bed ridden
type: NamedIndividual
type: Eastern Cooperative Oncology Group score value specification
editor preferred label: 4: bed ridden
has curation status: FossilSpecimen
definition: An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and is bed ridden.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

0: asymptomatic
type: NamedIndividual
type: Eastern Cooperative Oncology Group score value specification
editor preferred label: 0: asymptomatic
has curation status: FossilSpecimen
definition: An Eastern Cooperative Oncology Group score value specification indicating a patient is asymptomatic.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

1: symptomatic but fully ambulatory
type: NamedIndividual
type: Eastern Cooperative Oncology Group score value specification
editor preferred label: 1: symptomatic but fully ambulatory
has curation status: FossilSpecimen
definition: An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is fully ambulatory.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

100: asymptomatic
type: NamedIndividual
type: Karnofsky score vaue specification
editor preferred label: 100: asymptomatic
has curation status: FossilSpecimen
definition: A Karnofsky score vaue specification indicating that a patient is asymptomatic.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

80-90: symptomatic but fully ambulatory
type: NamedIndividual
type: Karnofsky score vaue specification
editor preferred label: 80-90: symptomatic but fully ambulatory
has curation status: FossilSpecimen
definition: A Karnofsky score vaue specification indicating that a patient is symptomatic but fully ambulatory.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

60-70: symptomatic but in bed less than 50% of the day
type: NamedIndividual
type: Karnofsky score vaue specification
editor preferred label: 60-70: symptomatic but in bed less than 50% of the day
has curation status: FossilSpecimen
definition: A Karnofsky score vaue specification indicating that a patient is symptomatic but in bed less than 50% of the day.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

40-50: symptomatic, in bed more than 50% of the day, but not bed ridden
type: NamedIndividual
type: Karnofsky score vaue specification
editor preferred label: 40-50: symptomatic, in bed more than 50% of the day, but not bed ridden
has curation status: FossilSpecimen
definition: A Karnofsky score vaue specification indicating that a patient is symptomatic, in bed more than 50% of the day, but not bed ridden.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

axiom holds for all times
type: NamedIndividual
definition: ## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally' ## How to interpret (informal) First the "atemporal" FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation

meter
type: NamedIndividual
type: length unit
editor preferred label: meter
definition: 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.
alternative term: m
imported from: uo.owl

kilogram
type: NamedIndividual
type: mass unit
editor preferred label: kilogram
definition: A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France.
alternative term: kg
imported from: uo.owl

second
type: NamedIndividual
type: time unit
editor preferred label: second
definition: 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.
alternative term: s
alternative term: sec
imported from: uo.owl

centimeter
type: NamedIndividual
type: length unit
editor preferred label: centimeter
definition: A length unit which is equal to one hundredth of a meter or 10^[-2] m.
alternative term: cm
imported from: uo.owl

millimeter
type: NamedIndividual
type: length unit
editor preferred label: millimeter
definition: A length unit which is equal to one thousandth of a meter or 10^[-3] m.
alternative term: mm
imported from: uo.owl

micrometer
type: NamedIndividual
type: length unit
editor preferred label: micrometer
definition: A length unit which is equal to one millionth of a meter or 10^[-6] m.
alternative term: um
imported from: uo.owl

nanometer
type: NamedIndividual
type: length unit
editor preferred label: nanometer
definition: A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m.
alternative term: nm
imported from: uo.owl

angstrom
type: NamedIndividual
type: length unit
editor preferred label: angstrom
definition: A length unit which is equal to 10 [-10] m.
imported from: uo.owl

gram
type: NamedIndividual
type: mass unit
editor preferred label: gram
definition: A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg.
alternative term: g
imported from: uo.owl

milligram
type: NamedIndividual
type: mass unit
editor preferred label: milligram
definition: A mass unit which is equal to one thousandth of a gram or 10^[-3] g.
alternative term: mg
imported from: uo.owl

microgram
type: NamedIndividual
type: mass unit
editor preferred label: microgram
definition: A mass unit which is equal to one millionth of a gram or 10^[-6] g.
alternative term: ug
imported from: uo.owl

nanogram
type: NamedIndividual
type: mass unit
editor preferred label: nanogram
definition: A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g.
alternative term: ng
imported from: uo.owl

picogram
type: NamedIndividual
type: mass unit
editor preferred label: picogram
definition: A mass unit which is equal to 10^[-12] g.
alternative term: pg
imported from: uo.owl

degree Celsius
type: NamedIndividual
type: temperature unit
editor preferred label: degree Celsius
definition: 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.
alternative term: C
alternative term: degree C
imported from: uo.owl

minute
type: NamedIndividual
type: time unit
editor preferred label: minute
definition: A time unit which is equal to 60 seconds.
alternative term: min
imported from: uo.owl

hour
type: NamedIndividual
type: time unit
editor preferred label: hour
definition: A time unit which is equal to 3600 seconds or 60 minutes.
alternative term: h
alternative term: hr
imported from: uo.owl

day
type: NamedIndividual
type: time unit
editor preferred label: day
definition: A time unit which is equal to 24 hours.
imported from: uo.owl

week
type: NamedIndividual
type: time unit
editor preferred label: week
definition: A time unit which is equal to 7 days.
imported from: uo.owl

month
type: NamedIndividual
type: time unit
editor preferred label: month
definition: A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days.
imported from: uo.owl

year
type: NamedIndividual
type: time unit
editor preferred label: year
definition: A time unit which is equal to 12 months which is science is taken to be equal to 365.25 days.
imported from: uo.owl

micromole
type: NamedIndividual
type: substance unit
editor preferred label: micromole
definition: A substance unit equal to a millionth of a mol or 10^[-6] mol.
alternative term: umol
imported from: uo.owl

nanomole
type: NamedIndividual
type: substance unit
editor preferred label: nanomole
definition: A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol.
alternative term: nmol
imported from: uo.owl

picomole
type: NamedIndividual
type: substance unit
editor preferred label: picomole
definition: A substance unit equal to 10^[-12] mol.
alternative term: pmol
imported from: uo.owl

molar
type: NamedIndividual
type: concentration unit
editor preferred label: molar
definition: A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L).
alternative term: M
imported from: uo.owl

millimolar
type: NamedIndividual
type: concentration unit
editor preferred label: millimolar
definition: A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M.
alternative term: mM
imported from: uo.owl

micromolar
type: NamedIndividual
type: concentration unit
editor preferred label: micromolar
definition: A unit of molarity which is equal to one millionth of a molar or 10^[-6] M.
alternative term: uM
imported from: uo.owl

nanomolar
type: NamedIndividual
type: concentration unit
editor preferred label: nanomolar
definition: A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M.
alternative term: nM
imported from: uo.owl

picomolar
type: NamedIndividual
type: concentration unit
editor preferred label: picomolar
definition: A unit of molarity which is equal to 10^[-12] M.
alternative term: pM
imported from: uo.owl

cubic centimeter
type: NamedIndividual
type: volume unit
editor preferred label: cubic centimeter
definition: A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml.
alternative term: cc
imported from: uo.owl

milliliter
type: NamedIndividual
type: volume unit
editor preferred label: milliliter
definition: A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter.
alternative term: ml
imported from: uo.owl

liter
type: NamedIndividual
type: volume unit
editor preferred label: liter
definition: A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter.
alternative term: L
imported from: uo.owl

cubic decimeter
type: NamedIndividual
type: volume unit
editor preferred label: cubic decimeter
definition: A volume unit which is equal to one thousand of a cubic meter or 10^[-3] m^[3], or to 1 L.
imported from: uo.owl

microliter
type: NamedIndividual
type: volume unit
editor preferred label: microliter
definition: A volume unit which is equal to one millionth of a liter or 10^[-6] L.
alternative term: ul
imported from: uo.owl

nanoliter
type: NamedIndividual
type: volume unit
editor preferred label: nanoliter
definition: A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L.
alternative term: nl
imported from: uo.owl

picoliter
type: NamedIndividual
type: volume unit
editor preferred label: picoliter
definition: A volume unit which is equal to 10^[-12] L.
alternative term: pl
imported from: uo.owl

hertz
type: NamedIndividual
type: frequency unit
editor preferred label: hertz
definition: A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second.
imported from: uo.owl

mass percentage
type: NamedIndividual
type: concentration unit
editor preferred label: mass percentage
definition: A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture.
alternative term: % w/w
alternative term: percent weight pr weight
imported from: uo.owl

mass volume percentage
type: NamedIndividual
type: concentration unit
editor preferred label: mass volume percentage
definition: A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture.
alternative term: % w/v
alternative term: percent vol per vol
imported from: uo.owl

volume percentage
type: NamedIndividual
type: concentration unit
editor preferred label: volume percentage
definition: A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution.
alternative term: % v/v
alternative term: percent vol per vol
imported from: uo.owl

gram per liter
type: NamedIndividual
type: concentration unit
editor preferred label: gram per liter
definition: A mass unit density which is equal to mass of an object in grams divided by the volume in liters.
alternative term: g per L
alternative term: g/L
imported from: uo.owl

milligram per milliliter
type: NamedIndividual
type: concentration unit
editor preferred label: milligram per milliliter
definition: A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters.
alternative term: mg per ml
alternative term: mg/ml
imported from: uo.owl

degree Fahrenheit
type: NamedIndividual
type: temperature unit
editor preferred label: degree Fahrenheit
definition: A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius.
imported from: uo.owl

pH
type: NamedIndividual
type: concentration unit
editor preferred label: pH
definition: A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+).
imported from: uo.owl

milliliter per liter
type: NamedIndividual
type: concentration unit
editor preferred label: milliliter per liter
definition: A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution.
alternative term: ml per L
alternative term: ml/l
imported from: uo.owl

gram per deciliter
type: NamedIndividual
type: concentration unit
editor preferred label: gram per deciliter
definition: A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters.
alternative term: g/dl
imported from: uo.owl

colony forming unit per volume
type: NamedIndividual
type: concentration unit
editor preferred label: colony forming unit per volume
definition: A concentration unit which a measure of viable bacterial numbers in a given volume.
imported from: uo.owl

microliters per minute
type: NamedIndividual
type: volumetric flow rate unit
editor preferred label: microliters per minute
definition: A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute.
imported from: uo.owl

count per nanomolar second
type: NamedIndividual
type: rate unit
editor preferred label: count per nanomolar second
definition: A rate unit which is equal to one over one nanomolar second.
imported from: uo.owl

count per molar second
type: NamedIndividual
type: rate unit
editor preferred label: count per molar second
definition: A rate unit which is equal to one over one molar second.
imported from: uo.owl

count per nanomolar
type: NamedIndividual
type: rate unit
editor preferred label: count per nanomolar
definition: A rate unit which is equal to one over one nanomolar.
imported from: uo.owl

count per molar
type: NamedIndividual
type: rate unit
editor preferred label: count per molar
definition: A rate unit which is equal to one over one molar.
imported from: uo.owl

microgram per liter
type: NamedIndividual
type: concentration unit
editor preferred label: microgram per liter
definition: A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters.
alternative term: ng/ml
alternative term: ug/L
imported from: uo.owl

incorrect identifier format, replaced
type: NamedIndividual
type: curation status specification

Event
deprecated: false
has curation status: requires discussion