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
description: The BCO supports the interoperability of biodiversity and biodiversity related data, including data on museum collections, environmental/metagenomic samples, and ecological surveys. A key aspect of the BCO is distinguishing among material samples (i.e. specimens), observing processes, and data about either of those entities.
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.
version info: 2021-11-14

taxonomic inventory metadata preferred name
type: AnnotationProperty
definition: The label used in Humbolt Core.
sub property of: alternative term

Axiom
annotated source: taxonomic inventory metadata preferred name
annotated property: definition
annotated target: The label used in Humbolt Core.
Source: ecog.02942

BCO preferred label
type: AnnotationProperty
definition: The label preferred for use with this ontology. To be added only with imported terms.

editor preferred term
type: AnnotationProperty
editor preferred term: editor preferred term
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>

example of usage
type: AnnotationProperty
editor preferred term: example
editor preferred term: example of usage
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 term: 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 term: 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 term: definition
editor preferred term: 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 term: 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>
definition source: GROUP:OBI:<http://purl.obofoundry.org/obo/obi>
has db xref: IAO:0000116
has OBO namespace: uberon
id: editor_note
is metadata tag: true
shorthand: editor_note

term editor
type: AnnotationProperty
editor preferred term: 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 term: 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 term: definition source
has curation status: ready for release
definition: Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
definition: 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 term: 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 term: 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 term: 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 term: 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 term: 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 term: expand expression to
example of usage: ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
definition: A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones
term editor: Chris Mungall

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

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

OBO foundry unique label
type: AnnotationProperty
editor preferred term: 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 term: 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 term: 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 term: 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 term: 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 term: 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 term: 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
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.
imported from: obi.owl
has curation status: ready for release
editor preferred term: has_specified_input
term editor: PERSON: Bjoern Peters
term editor: PERSON: Alan Ruttenberg
example of usage: see is_input_of example_of_usage
editor note: 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
term editor: PERSON: Melanie Coutot

has input
type: AnnotationProperty
type: ObjectProperty
sub property of: has participant
inverse of: input of
domain: process
in subset: valid for go ontology
term editor: Chris Mungall
in subset: ro-eco
alternative term: consumes
has curation status: pending final vetting
definition: p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
in subset: valid for go annotation extension
in subset: valid for gocam

is a defining property chain axiom
type: AnnotationProperty
definition: If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL

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.

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.

label
type: AnnotationProperty
editor preferred term: label

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

obsolete 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

obsotlete 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
definition: A relation used to link a taxonomic association to a taxon. Should be used with the of organism relation.

of organism
type: ObjectProperty
sub property of: is about
domain: identification assertion
range: organismal entity
definition: A relation used to link an identification association to an organismal entity. Should be 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
definition: A shortcut relation from an organsimal entity to a taxon.

part of
type: ObjectProperty
inverse of: has part
type: TransitiveProperty
editor preferred term: 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
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
RO_0001900: RO_0001901

has part
type: ObjectProperty
type: TransitiveProperty
editor preferred term: 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
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
RO_0001900: RO_0001901

realized in
type: ObjectProperty
inverse of: realizes
domain: realizable entity
range: process
editor preferred term: 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
domain: process
range: realizable entity
editor preferred term: 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

preceded by
type: ObjectProperty
sub property of: ends after
inverse of: precedes
type: TransitiveProperty
domain: occurrent
range: occurrent
editor preferred term: preceded by
definition: x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
editor note: An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
alternative term: is preceded by
alternative term: preceded_by
Source: http://www.obofoundry.org/ro/#OBO_REL:preceded_by
in subset: ro-eco

precedes
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
domain: occurrent
range: occurrent
editor preferred term: precedes
definition: x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
in subset: ro-eco

occurs in
type: ObjectProperty
inverse of: contains process
domain: occurrent
range: independent continuant
property chain axiom: part of
editor preferred term: 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
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
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
editor preferred term: 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: 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

is_specified_input_of
type: ObjectProperty
sub property of: participates in
range: planned process
editor preferred term: 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 term: 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 term: 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 term: 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 term: 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 term: 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 term: 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

characteristic of
type: ObjectProperty
inverse of: bearer of
type: FunctionalProperty
editor preferred term: inheres in
example of usage: this fragility inheres in this vase
example of usage: this fragility is a characteristic of this vase
example of usage: this red color inheres in this apple
example of usage: this red color is a characteristic of this apple
definition: a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
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
RO_0001900: RO_0001901
comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
label: inheres in

bearer of
type: ObjectProperty
type: InverseFunctionalProperty
range: specifically dependent continuant
editor preferred term: bearer of
example of usage: this apple is bearer of this red color
example of usage: this vase is bearer of this fragility
definition: Inverse of characteristic_of
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
RO_0001900: RO_0001901
label: has characteristic

participates in
type: ObjectProperty
inverse of: has participant
domain: continuant
range: occurrent
editor preferred term: 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
domain: occurrent
range: continuant
editor preferred term: 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
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
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
sub property of: characteristic of
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
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

quality of
type: ObjectProperty
sub property of: characteristic of
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
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

role of
type: ObjectProperty
sub property of: characteristic of
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
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

has function
type: ObjectProperty
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
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
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
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
sub property of: characteristic of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

derives from
type: ObjectProperty
sub property of: topObjectProperty
inverse of: derives into
domain: independent continuant
range: independent continuant
editor preferred term: 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
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
inverse of: located in
type: TransitiveProperty
editor preferred term: 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
alternative term: location_of
RO_0001900: RO_0001901

located in
type: ObjectProperty
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 term: 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
alternative term: located_in
RO_0001900: RO_0001901
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
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
RO_0001900: RO_0001901

has 2D boundary
type: ObjectProperty
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
RO_0001900: RO_0001901

directly regulated by
type: ObjectProperty
sub property of: regulated by
inverse of: directly regulates
created by: dos
creation date: 2017-09-17T13:52:24Z
comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.

Axiom
annotated source: directly regulated by
annotated property: comment
annotated target: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
has db xref: GOC:dos

ends after
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
term editor: David Osumi-Sutherland
in subset: ro-eco
comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)

immediately preceded by
type: ObjectProperty
sub property of: preceded by
inverse of: immediately precedes
term editor: David Osumi-Sutherland
alternative term: starts_at_end_of
comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)

immediately precedes
type: ObjectProperty
sub property of: precedes
term editor: David Osumi-Sutherland
alternative term: ends_at_start_of
alternative term: meets
RO_0002575: precedes
in subset: ro-eco
comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)

overlaps
type: ObjectProperty
sub property of: mereotopologically related to
has curation status: pending final vetting
definition: x overlaps y if and only if there exists some z such that x has part z and z part of y
expand expression to: http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
RO_0001900: RO_0001901
in subset: valid for go annotation extension
in subset: valid for gocam
in subset: ro-eco

regulates
type: ObjectProperty
sub property of: causally upstream of
inverse of: regulated by
type: TransitiveProperty
domain: process
range: process
property chain axiom: directly regulates
has curation status: pending final vetting
definition: process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2.
editor note: We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit
term editor: Chris Mungall
term editor: David Hill
term editor: Tanya Berardini
definition source: causal-relations
definition source: GO
curator note: Regulation precludes parthood; the regulatory process may not be within the regulated process.
OBO foundry unique label: regulates (processual)
elucidation: false
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

negatively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, negative effect
inverse of: negatively regulated by
definition: Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
term editor: Chris Mungall
definition source: causal-relations
OBO foundry unique label: negatively regulates (process to process)
RO_0004050: regulates
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

positively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, positive effect
inverse of: positively regulated by
type: TransitiveProperty
property chain axiom: negatively regulates
definition: Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
term editor: Chris Mungall
definition source: causal-relations
OBO foundry unique label: positively regulates (process to process)
RO_0004049: regulates
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

capable of
type: ObjectProperty
sub property of: capable of part of
domain: independent continuant
range: process
example of usage: mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
example of usage: osteoclast SubClassOf 'capable of' some 'bone resorption'
definition: A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
term editor: Chris Mungall
alternative term: has function realized in
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20123131
definition source: http://www.ncbi.nlm.nih.gov/pubmed/21208450
curator note: For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
in subset: ro-eco

capable of part of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal agent in process
definition: c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
term editor: Chris Mungall
alternative term: has function in

temporally related to
type: ObjectProperty
domain: occurrent
range: occurrent
has curation status: pending final vetting
term editor: Chris Mungall
definition source: Allen's interval algebra
curator note: Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
source: https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit
in subset: ro-eco
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.

acts upstream of
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of
example of usage: A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.
definition: c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.
in subset: valid for go gp2term

acts upstream of or within
type: ObjectProperty
sub property of: causal agent in process
property chain axiom: enables
property chain axiom: causally upstream of or within
example of usage: A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.
definition: c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.
has related synonym: affects
in subset: valid for go gp2term

causally upstream of, positive effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, positive effect
RO_0004049: causally upstream of
creator: cjm
in subset: valid for go annotation extension
in subset: valid for gocam
comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y

causally upstream of, negative effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, negative effect
RO_0004050: causally upstream of
creator: cjm
comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y

ecologically related to
type: ObjectProperty
definition: A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)
editor note: Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6
term editor: Chris Mungall
curator note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions
in subset: ro-eco

mereotopologically related to
type: ObjectProperty
definition: A mereological relationship or a topological relationship
term editor: Chris Mungall
curator note: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
RO_0001900: RO_0001901

enables
type: ObjectProperty
sub property of: capable of
inverse of: enabled by
example of usage: a particular instances of akt-2 enables some instance of protein kinase activity
term editor: Chris Mungall
alternative term: catalyzes
alternative term: executes
alternative term: has
alternative term: is catalyzing
alternative term: is executing
curator note: This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
curator note: This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time.
in subset: valid for go gp2term

functionally related to
type: ObjectProperty
definition: A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
term editor: Chris Mungall
curator note: This is a grouping relation that collects relations used for the purpose of connecting structure and function

enabled by
type: ObjectProperty
sub property of: has participant
sub property of: functionally related to
definition: inverse of enables
term editor: Chris Mungall
in subset: valid for gocam

regulated by
type: ObjectProperty
sub property of: causally downstream of or within
type: TransitiveProperty
domain: process
range: process
definition: inverse of regulates
term editor: Chris Mungall
OBO foundry unique label: regulated by (processual)
in subset: RO_0002259

negatively regulated by
type: ObjectProperty
sub property of: regulated by
definition: inverse of negatively regulates
term editor: Chris Mungall
in subset: RO_0002259

positively regulated by
type: ObjectProperty
sub property of: regulated by
definition: inverse of positively regulates
term editor: Chris Mungall
in subset: RO_0002259

member of
type: ObjectProperty
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
RO_0001900: RO_0001901

has member
type: ObjectProperty
sub property of: has part
type: IrreflexiveProperty
definition: has member is a mereological relation between a collection and an item.
definition source: SIO
RO_0001900: RO_0001901

input of
type: ObjectProperty
sub property of: participates in
sub property of: functionally related to
definition: inverse of has input
term editor: Chris Mungall
in subset: RO_0002259
in subset: ro-eco

causally downstream of
type: ObjectProperty
sub property of: preceded by
sub property of: causally downstream of or within
inverse of: causally upstream of
has curation status: requires discussion
definition: inverse of upstream of
term editor: Chris Mungall

immediately causally downstream of
type: ObjectProperty
sub property of: immediately preceded by
sub property of: causally downstream of
inverse of: immediately causally upstream of
has curation status: requires discussion
term editor: Chris Mungall

causally related to
type: ObjectProperty
has curation status: requires discussion
definition: This relation groups causal relations between material entities and causal relations between processes
editor note: This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yiel…
term editor: Chris Mungall
curator note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

causally upstream of
type: ObjectProperty
sub property of: precedes
sub property of: causally upstream of or within
type: TransitiveProperty
has curation status: requires discussion
definition: p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain
term editor: Chris Mungall
in subset: valid for go annotation extension
in subset: valid for gocam

immediately causally upstream of
type: ObjectProperty
sub property of: immediately precedes
sub property of: causally upstream of
has curation status: requires discussion
definition: p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q.
term editor: Chris Mungall
RO_0002575: causally upstream of

causally upstream of or within
type: ObjectProperty
sub property of: causal relation between processes
inverse of: causally downstream of or within
type: TransitiveProperty
definition: p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.
editor note: We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
term editor: Chris Mungall
alternative term: influences (processual)
has related synonym: affects

causally downstream of or within
type: ObjectProperty
sub property of: causal relation between processes
type: TransitiveProperty
definition: inverse of causally upstream of or within
term editor: Chris Mungall
definition source: causal-relations
in subset: RO_0002259

involved in regulation of
type: ObjectProperty
sub property of: acts upstream of
sub property of: involved in or involved in regulation of
property chain axiom: enables
property chain axiom: regulates
definition: c involved in regulation of p if c is involved in some p' and p' regulates some p
term editor: Chris Mungall

involved in positive regulation of
type: ObjectProperty
sub property of: involved in regulation of
property chain axiom: enables
property chain axiom: positively regulates
definition: c involved in regulation of p if c is involved in some p' and p' positively regulates some p
term editor: Chris Mungall
RO_0004049: involved in regulation of

involved in negative regulation of
type: ObjectProperty
sub property of: involved in regulation of
property chain axiom: enables
property chain axiom: negatively regulates
definition: c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
term editor: Chris Mungall
RO_0004050: involved in regulation of

involved in or involved in regulation of
type: ObjectProperty
sub property of: acts upstream of or within
sub property of: functionally related to
sub property of: causal agent in process
definition: c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
editor note: OWL does not allow defining object properties via a Union
term editor: Chris Mungall
alternative term: involved in or reguates

is active in
type: ObjectProperty
sub property of: overlaps
sub property of: functionally related to
property chain axiom: enables
property chain axiom: occurs in
example of usage: A protein that enables activity in a cytosol.
definition: c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
term editor: Chris Mungall
alternative term: executes activity in
has exact synonym: enables activity in

Axiom
annotated source: is active in
annotated property: propertyChainAxiom
annotated target: enables
annotated target: occurs in
is a defining property chain axiom: true

Axiom
annotated source: is active in
annotated property: definition
annotated target: c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
has db xref: GOC:cjm
has db xref: GOC:dos

interacts with
type: ObjectProperty
type: SymmetricProperty
domain: material entity
range: material entity
definition: A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
editor note: Considering relabeling as 'pairwise interacts with'
editor note: This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
term editor: Chris Mungall
curator note: Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.
has exact synonym: in pairwise interaction with
in subset: ro-eco

molecularly interacts with
type: ObjectProperty
sub property of: interacts with
type: SymmetricProperty
definition: An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.
term editor: Chris Mungall
alternative term: binds
alternative term: molecularly binds with

phosphorylates
type: ObjectProperty
sub property of: molecularly interacts with
editor note: Axiomatization to GO to be added later
term editor: Chris Mungall
alternative term: An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.

directly regulates activity of
type: ObjectProperty
sub property of: molecularly interacts with
sub property of: regulates activity of
domain: material entity
range: material entity
property chain axiom: enables
property chain axiom: regulates
property chain axiom: enabled by
definition: The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.
term editor: Chris Mungall
term editor: Vasundra Touré
has exact synonym: molecularly controls

helper property (not for use in curation)
type: ObjectProperty
term editor: Chris Mungall
curator note: This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.

is kinase activity
type: ObjectProperty
sub property of: molecular interaction relation helper property
term editor: Chris Mungall

causal agent in process
type: ObjectProperty
sub property of: causal relation between material entity and a process
inverse of: process has causal agent
definition: A relationship between a material entity and a process where the material entity has some causal role that influences the process
definition source: causal-relations

causal relation between processes
type: ObjectProperty
sub property of: causally related to
domain: occurrent
range: occurrent
definition: p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.
term editor: Chris Mungall
definition source: causal-relations
curator note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

causal relation between entities
type: ObjectProperty
sub property of: causally related to
domain: continuant
range: continuant
editor note: The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
term editor: Chris Mungall
definition source: causal-relations
curator note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

causally influenced by
type: ObjectProperty
sub property of: causal relation between entities
inverse of: causally influences
term editor: Chris Mungall
definition source: causal-relations
OBO foundry unique label: causally influenced by (entity-centric)

interaction relation helper property
type: ObjectProperty
sub property of: helper property (not for use in curation)
term editor: Chris Mungall

molecular interaction relation helper property
type: ObjectProperty
sub property of: interaction relation helper property
term editor: Chris Mungall

causally influences
type: ObjectProperty
sub property of: causal relation between entities
domain: continuant
range: continuant
property chain axiom: enables
property chain axiom: causally upstream of
property chain axiom: has input
property chain axiom: enabled by
definition: The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).
term editor: Chris Mungall
term editor: Vasundra Touré
definition source: causal-relations
OBO foundry unique label: causally influences (entity-centric)

directly regulates
type: ObjectProperty
sub property of: regulates
sub property of: immediately causally upstream of
definition: Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
term editor: Chris Mungall
definition source: causal-relations
OBO foundry unique label: directly regulates (processual)
RO_0002575: regulates
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

causal relation between material entity and a process
type: ObjectProperty
sub property of: causally related to
domain: material entity
range: process
definition: A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
editor note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
term editor: Chris Mungall
definition source: causal-relations

capable of regulating
type: ObjectProperty
sub property of: causal agent in process
property chain axiom: capable of
property chain axiom: regulates
example of usage: pyrethroid -> growth
definition: Holds between c and p if and only if c is capable of some activity a, and a regulates p.
definition source: causal-relations

capable of negatively regulating
type: ObjectProperty
sub property of: capable of regulating
property chain axiom: capable of
property chain axiom: negatively regulates
definition: Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
definition source: causal-relations

capable of positively regulating
type: ObjectProperty
sub property of: capable of regulating
property chain axiom: capable of
property chain axiom: positively regulates
example of usage: renin -> arteriolar smooth muscle contraction
definition: Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
definition source: causal-relations

process has causal agent
type: ObjectProperty
sub property of: causally related to
definition: Inverse of 'causal agent in process'
definition source: causal-relations

acts upstream of or within, positive effect
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of or within, positive effect
RO_0004049: acts upstream of or within
created by: cjm
creation date: 2018-01-26T23:49:30Z
in subset: valid for go gp2term

acts upstream of or within, negative effect
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of or within, negative effect
RO_0004050: acts upstream of or within
created by: cjm
creation date: 2018-01-26T23:49:51Z
in subset: valid for go gp2term

acts upstream of, positive effect
type: ObjectProperty
sub property of: acts upstream of
sub property of: acts upstream of or within, positive effect
property chain axiom: enables
property chain axiom: causally upstream of, positive effect
definition: c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive
RO_0004049: acts upstream of
created by: cjm
creation date: 2018-01-26T23:53:14Z
in subset: valid for go gp2term

acts upstream of, negative effect
type: ObjectProperty
sub property of: acts upstream of
sub property of: acts upstream of or within, negative effect
property chain axiom: enables
property chain axiom: causally upstream of, negative effect
definition: c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative
RO_0004050: acts upstream of
created by: cjm
creation date: 2018-01-26T23:53:22Z
in subset: valid for go gp2term

causally upstream of or within, negative effect
type: ObjectProperty
sub property of: causally upstream of or within
RO_0004050: causally upstream of or within
created by: cjm
creation date: 2018-03-13T23:55:05Z

causally upstream of or within, positive effect
type: ObjectProperty
sub property of: causally upstream of or within
RO_0004049: causally upstream of or within
created by: cjm
creation date: 2018-03-13T23:55:19Z

DEPRECATED inheres in
type: ObjectProperty
inverse of: DEPRECATED bearer of
comment: DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information.
deprecated: true

DEPRECATED bearer of
type: ObjectProperty
deprecated: true

regulates activity of
type: ObjectProperty
sub property of: causally influences
domain: material entity
range: material entity
definition: The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.
term editor: Vasundra Touré

Accepted Taxon
type: DatatypeProperty
domain: Taxon
comment: The currently valid (zoological) or accepted (botanical) name for the ScientificName.
deprecated: True

Accepted Taxon ID
type: DatatypeProperty
domain: Taxon
comment: A global unique identifier for the parent to the AcceptedTaxon.
deprecated: True

Access Constraints
type: DatatypeProperty
domain: Sample
description: Example: "not-for-profit use only".
comment: A description of constraints on the use of the data as shared or access to further data that is not shared.
deprecated: True

Catalog Number Numeric
type: DatatypeProperty
domain: Occurrence
comment: The numeric value of the catalogNumber, used to facilitate numerical sorting and searching by ranges.
deprecated: True

Earliest Date Collected
type: DatatypeProperty
domain: Event
description: Date may be used to express temporal information at any level of granularity. Recommended best practice is to use an encoding scheme, such as the W3CDTF profile of ISO 8601 [W3CDTF].
comment: The earliest date-time in a period during which a event occurred. If the event is recorded as occurring at a single date-time, populate both EarliestDateCollected and LatestDateCollected with the same value. Recommended best practice is to use an encoding scheme, such as ISO 8601:2004(E).
deprecated: True

End Time of Day
type: DatatypeProperty
domain: Event
description: Examples: "12.0" (= noon), "13.5" (= 1:30pm)
comment: The time of day when the event ended, expressed as decimal hours from midnight, local time.
deprecated: True

Event Attribute Accuracy
type: DatatypeProperty
domain: Event Attribute
description: Example: "0.01", "normal distribution with variation of 2 m"
comment: The description of the error associated with the EventAttributeValue.
deprecated: True

Event Attribute Determined By
type: DatatypeProperty
domain: Event Attribute
description: Example: "Robert Hijmans"
comment: The agent responsible for having determined the value of the measurement or characteristic of the sampling event.
deprecated: True

Event Attribute Determined Date
type: DatatypeProperty
domain: Event Attribute
description: Date may be used to express temporal information at any level of granularity. Recommended best practice is to use an encoding scheme, such as the W3CDTF profile of ISO 8601 [W3CDTF].
comment: The date on which the the measurement or characteristic of the sampling event was made.
deprecated: True

Event Attribute ID
type: DatatypeProperty
domain: Event Attribute
comment: An identifier for the event attribute. May be a global unique identifier or an identifier specific to the data set.
deprecated: True

Event Attribute Remarks
type: DatatypeProperty
domain: Event Attribute
description: Example: "temperature taken at 15:00"
comment: Comments or notes accompanying the measurement or characteristic of the sampling event.
deprecated: True

Event Attribute Type
type: DatatypeProperty
domain: Event Attribute
description: Example: "Temperature"
comment: The nature of the measurement or characteristic of the sampling event. Recommended best practice is to use a controlled vocabulary.
deprecated: True

Event Attribute Unit
type: DatatypeProperty
domain: Event Attribute
description: Example: "C"
comment: The units for the value of the measurement or characteristic of the sampling event. Recommended best practice is to use International System of Units (SI) units.
deprecated: True

Event Attribute
type: DatatypeProperty
domain: Event Attribute
description: Example: "22"
comment: The value of the measurement or characteristic of the sampling event.
deprecated: True

Generalizations
type: DatatypeProperty
domain: all
description: Examples: "Coordinates generalized from original GPS coordinates to the nearest half degree grid cell", "locality information given only to nearest county".
comment: Actions taken to make the data as shared less specific or complete than in its original form. Suggests that alternative data of highly quality may be available on request.
deprecated: True

Higher Taxon
type: DatatypeProperty
domain: Taxon
description: Example: "Animalia, Chordata, Vertebrata, Mammalia, Theria, Eutheria, Rodentia, Hystricognatha, Hystricognathi, Ctenomyidae, Ctenomyini, Ctenomys".
comment: A list (concatenated and separated) of the names for the taxonomic ranks less specific than the ScientificName.
deprecated: True

Higher Taxon ID
type: DatatypeProperty
domain: Taxon
comment: A global unique identifier for the parent to the taxon.
deprecated: True

Latest Date Collected
type: DatatypeProperty
domain: Event
description: Date may be used to express temporal information at any level of granularity. Recommended best practice is to use an encoding scheme, such as the W3CDTF profile of ISO 8601 [W3CDTF].
comment: The latest date-time in a period during which a event occurred. If the event is recorded as occurring at a single date-time, populate both EarliestDateCollected and LatestDateCollected with the same value. Recommended best practice is to use an encoding scheme, such as ISO 8601:2004(E).
deprecated: True

Previous Identifications
type: DatatypeProperty
domain: Identification
description: Example: "Anthus correndera".
comment: A list (concatenated and separated) of previous ScientificNames to which the sample was identified.
deprecated: True

Related Basis of Record
type: DatatypeProperty
domain: Resource Relationship
description: Example: "PreservedSpecimen"
comment: The nature of the related resource. Recommended best practice is to use the same controlled vocabulary as for basisOfRecord.
deprecated: True

Sample Attribute Accuracy
type: DatatypeProperty
domain: Sample Attribute
description: Example: "0.01", "normal distribution with variation of 2 m"
comment: The description of the error associated with the SampleAttributeValue.
deprecated: True

Sample Attribute Determined By
type: DatatypeProperty
domain: Sample Attribute
description: Example: "Javier de la Torre"
comment: The agent responsible for having determined the value of the measurement or characteristic of the sample.
deprecated: True

Sample Attribute Determined Date
type: DatatypeProperty
domain: Sample Attribute
description: Date may be used to express temporal information at any level of granularity. Recommended best practice is to use an encoding scheme, such as the W3CDTF profile of ISO 8601 [W3CDTF].
comment: The date on which the the measurement or characteristic of the sample was made.
deprecated: True

Sample Attribute Remarks
type: DatatypeProperty
domain: Sample Attribute
description: Example: "tip of tail missing"
comment: Comments or notes accompanying the measurement or characteristic of the sample.
deprecated: True

Sample Attribute Unit
type: DatatypeProperty
domain: Sample Attribute
description: Example: "mm"
comment: The units for the value of the measurement or characteristic of the sample. Recommended best practice is to use International System of Units (SI) units.
deprecated: True

Sample Attribute Value
type: DatatypeProperty
domain: Sample Attribute
description: Example: "45"
comment: The value of the measurement or characteristic of the sample.
deprecated: True

Sample Remarks
type: DatatypeProperty
domain: Sample
description: Example: "found dead on road"
comment: Comments or notes about the sample or record.
deprecated: True

Sample Attribute ID
type: DatatypeProperty
domain: Sample Attribute
comment: An identifier for the sampling attribute. May be a global unique identifier or an identifier specific to the data set.
deprecated: True

Sample Attribute Type
type: DatatypeProperty
domain: Sample Attribute
description: Example: "tail length"
comment: The nature of the measurement or characteristic of the sample. Recommended best practice is to use a controlled vocabulary.
deprecated: True

Sampling Event Attributes
type: DatatypeProperty
domain: Sampling Event
description: Example: "Relative humidity: 28 %; Temperature: 22 C; Sample size: 10 kg"
comment: A list (concatenated and separated) of additional measurements or characteristics of the sampling event.
deprecated: True

Sampling Event ID
type: DatatypeProperty
domain: Sampling Event
comment: An identifier for the sampling event. May be a global unique identifier or an identifier specific to the data set.
deprecated: True

Sampling Event Remarks
type: DatatypeProperty
domain: Sampling Event
description: Example: "found dead on road"
comment: Comments or notes about the sampling event.
deprecated: True

Sampling Location ID
type: DatatypeProperty
domain: Location
description: Example: "MVZ:LocID:12345"
comment: An identifier for the sampling location. May be a global unique identifier or an identifier specific to the data set.
deprecated: True

Sampling Location Remarks
type: DatatypeProperty
domain: Location
description: Example: "under water since 2005"
comment: Comments or notes about the sampling location.
deprecated: True

Start Time of Day
type: DatatypeProperty
domain: Event
description: Examples: "12.0" (= noon), "13.5" (= 1:30pm)
comment: The time of day when the event began, expressed as decimal hours from midnight, local time.
deprecated: True

Taxon ID
type: DatatypeProperty
domain: Taxon
comment: A global unique identifier for the taxon (name in a classification).
deprecated: True

Accepted Name Usage
type: DatatypeProperty
domain: Taxon
description: The full scientific name, with authorship and date information if known, of the accepted (botanical) or valid (zoological) name in cases where the provided scientificName is considered by the reference indicated in the accordingTo property, or of the content provider, to be a synonym or misapplied name. When applied to an Organism or Occurrence, this term should be used in cases where a content provider regards the provided scientificName to be inconsistent with the taxonomic perspective of the content provider. For example, there are many discrepancies within specimen collections and observation datasets between the recorded name (e.g., the most recent identification from an expert who examined a specimen, or a field identification for an observed organism), and the name asserted by the content provider to be taxonomically accepted.
example of usage: `Tamias minimus` (valid name for Eutamias minimus).
comment: The full name, with authorship and date information if known, of the currently valid (zoological) or accepted (botanical) taxon.

Accepted Name Usage ID
type: DatatypeProperty
domain: Taxon
description: This term should be used for synonyms or misapplied names to refer to the taxonID of a Taxon record that represents the accepted (botanical) or valid (zoological) name. For Darwin Core Archives the related record should be present locally in the same archive.
example of usage: `tsn:41107` (ITIS), `urn:lsid:ipni.org:names:320035-2` (IPNI), `2704179` (GBIF), `6W3C4` (COL)
comment: An identifier for the name usage (documented meaning of the name according to a source) of the currently valid (zoological) or accepted (botanical) taxon.

Accepted Scientific Name
type: DatatypeProperty
domain: Taxon
description: Example: "Tamias minimus" valid name for "Eutamias minimus"
comment: The currently valid (zoological) or accepted (botanical) name for the scientificName.
deprecated: True

Accepted Scientific Name ID
type: DatatypeProperty
domain: Taxon
comment: A unique identifier for the acceptedScientificName.
deprecated: True

Accepted Taxon ID
type: DatatypeProperty
domain: Taxon
description: Example: "8fa58e08-08de-4ac1-b69c-1235340b7001"
comment: An identifier for the name of the currently valid (zoological) or accepted (botanical) taxon. See acceptedTaxon.
deprecated: True

Accepted Taxon Name
type: DatatypeProperty
domain: Taxon
description: Example: "Tamias minimus" valid name for "Eutamias minimus"
comment: The currently valid (zoological) or accepted (botanical) name for the scientificName.
deprecated: True

Accepted Taxon Name ID
type: DatatypeProperty
domain: Taxon
comment: A unique identifier for the acceptedTaxonName.
deprecated: True

According To
type: DatatypeProperty
comment: Abstract term to attribute information to a source.
deprecated: True

Accuracy
type: DatatypeProperty
comment: Abstract term to capture error information about a measurement or fact.
deprecated: True

Associated Media
type: DatatypeProperty
domain: Occurrence
example of usage: `https://arctos.database.museum/media/10520962 | https://arctos.database.museum/media/10520964`
comment: A list (concatenated and separated) of identifiers (publication, global unique identifier, URI) of media associated with the Occurrence.

Associated Occurrences
type: DatatypeProperty
domain: Occurrence
description: This term can be used to provide a list of associations to other Occurrences. Note that the ResourceRelationship class is an alternative means of representing associations, and with more detail. Recommended best practice is to separate the values in a list with space vertical bar space ( | ).
example of usage: `"parasite collected from":"https://arctos.database.museum/guid/MSB:Mamm:215895?seid=950760"`, `"encounter previous to":"http://arctos.database.museum/guid/MSB:Mamm:292063?seid=3175067" | "encounter previous to":"http://arctos.database.museum/guid/MSB:Mamm:292063?seid=3177393" | "encounter previous to":"http://arctos.database.museum/guid/MSB:Mamm:292063?seid=3177394" | "encounter previous to":"http://arctos.database.museum/guid/MSB:Mamm:292063?seid=3177392" | "encounter previous to":"http://arctos.database.museum/guid/MSB:Mamm:292063?seid=3609139"`
comment: A list (concatenated and separated) of identifiers of other Occurrence records and their associations to this Occurrence.

Associated Organisms
type: DatatypeProperty
domain: Organism
description: This term can be used to provide a list of associations to other Organisms. Note that the ResourceRelationship class is an alternative means of representing associations, and with more detail. Recommended best practice is to separate the values in a list with space vertical bar space ( | ).
example of usage: `"sibling of":"http://arctos.database.museum/guid/DMNS:Mamm:14171"`, `"parent of":"http://arctos.database.museum/guid/MSB:Mamm:196208" | "parent of":"http://arctos.database.museum/guid/MSB:Mamm:196523" | "sibling of":"http://arctos.database.museum/guid/MSB:Mamm:142638"`
comment: A list (concatenated and separated) of identifiers of other Organisms and the associations of this Organism to each of them.

Associated References
type: DatatypeProperty
domain: Occurrence
description: Recommended best practice is to separate the values in a list with space vertical bar space ( | ). Note that the ResourceRelationship class is an alternative means of representing associations, and with more detail. Note also that the intended usage of the term dcterms:references in Darwin Core when applied to an Occurrence is to point to the definitive source representation of that Occurrence if one is available. Note also that the intended usage of dcterms:bibliographicCitation in Darwin Core when applied to an Occurrence is to provide the preferred way to cite the Occurrence itself.
example of usage: `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.`, `Steven R. Hoofer and Ronald A. Van Den Bussche. 2001. Phylogenetic Relationships of Plecotine Bats and Allies Based on Mitochondrial Ribosomal Sequences. Journal of Mammalogy 82(1):131-137. | Walker, Faith M., Jeffrey T. Foster, Kevin P. Drees, Carol L. Chambers. 2014. Spotted bat (Euderma maculatum) microsatellite discovery using illumina sequencing. Conservation Genetics Resources.`
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
domain: Occurrence
example of usage: `http://www.ncbi.nlm.nih.gov/nuccore/U34853.1`, `http://www.ncbi.nlm.nih.gov/nuccore/GU328060 | http://www.ncbi.nlm.nih.gov/nuccore/AF326093`
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
domain: Occurrence
description: This term can be used to provide a list of associations to Taxa other than the one defined in the Occurrence. Note that the ResourceRelationship class is an alternative means of representing associations, and with more detail. This term is not apt for establishing relationships between Taxa, only between specific Occurrences of an Organism with other Taxa. Recommended best practice is to separate the values in a list with space vertical bar space ( | ).
example of usage: `"host":"Quercus alba"`, `"host":"gbif.org/species/2879737"`,`"parasitoid of":"Cyclocephala signaticollis" | "predator of":"Apis mellifera"`
comment: A list (concatenated and separated) of identifiers or names of taxa and the associations of this Occurrence to each of them.

Basionym
type: DatatypeProperty
domain: Taxon
description: Example: "Pinus abies"
comment: The basionym (botany) or basonym (bacteriology) of the scientificName.
deprecated: True

Basionym ID
type: DatatypeProperty
domain: Taxon
comment: A unique identifier for the basionym (botany) or basonym (bacteriology) of the scientificName.
deprecated: True

Basis of Record
type: DatatypeProperty
domain: terms
description: Recommended best practice is to use the standard label of one of the Darwin Core classes.
example of usage: `PreservedSpecimen`, `FossilSpecimen`, `LivingSpecimen`, `MaterialSample`, `Event`, `HumanObservation`, `MachineObservation`, `Taxon`, `Occurrence`, `MaterialCitation`
comment: The specific nature of the data record.

Bed
type: DatatypeProperty
domain: Geological Context
example of usage: `Harlem coal`
comment: The full name of the lithostratigraphic bed from which the cataloged item was collected.

Behavior
type: DatatypeProperty
domain: Occurrence
example of usage: `roosting`, `foraging`, `running`
comment: The behavior shown by the subject at the time the Occurrence was recorded.

Binomial
type: DatatypeProperty
domain: Taxon
description: Example: "Ctenomys sociabilis"
comment: The combination of genus and first (species) epithet of the scientificName.
deprecated: True

Catalog Number
type: DatatypeProperty
domain: Occurrence
example of usage: `145732`, `145732a`, `2008.1334`, `R-4313`
comment: An identifier (preferably unique) for the record within the data set or collection.

Class
type: DatatypeProperty
domain: Taxon
example of usage: `Mammalia`, `Hepaticopsida`
comment: The full scientific name of the class in which the taxon is classified.

Collection Code
type: DatatypeProperty
domain: terms
example of usage: `Mammals`, `Hildebrandt`, `EBIRD`, `VP`
comment: The name, acronym, coden, or initialism identifying the collection or data set from which the record was derived.

Collection ID
type: DatatypeProperty
domain: terms
description: For physical specimens, the recommended best practice is to use an identifier from a collections registry such as the Global Registry of Biodiversity Repositories (http://grbio.org/).
example of usage: `http://biocol.org/urn:lsid:biocol.org:col:1001`, `http://grbio.org/cool/p5fp-c036`
comment: An identifier for the collection or dataset from which the record was derived.

Continent
type: DatatypeProperty
domain: Location
description: Recommended best practice is to use a controlled vocabulary such as the Getty Thesaurus of Geographic Names.
example of usage: `Africa`, `Antarctica`, `Asia`, `Europe`, `North America`, `Oceania`, `South America`
comment: The name of the continent in which the Location occurs.

Coordinate Precision
type: DatatypeProperty
domain: Location
example of usage: `0.00001` (normal GPS limit for decimal degrees). `0.000278` (nearest second). `0.01667` (nearest minute). `1.0` (nearest degree).
comment: A decimal representation of the precision of the coordinates given in the decimalLatitude and decimalLongitude.

Coordinate Uncertainty In Meters
type: DatatypeProperty
domain: Location
example of usage: `30` (reasonable lower limit on or after 2020-05-01 of a GPS reading under good conditions if the actual precision was not recorded at the time). `100` (reasonable lower limit before 2020-05-01 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).
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
domain: Location
description: Recommended best practice is to use a controlled vocabulary such as the Getty Thesaurus of Geographic Names. Recommended best practice is to leave this field blank if the Location spans multiple entities at this administrative level or if the Location might be in one or another of multiple possible entities at this level. Multiplicity and uncertainty of the geographic entity can be captured either in the term higherGeography or in the term locality, or both.
example of usage: `Denmark`, `Colombia`, `España`
comment: The name of the country or major administrative unit in which the Location occurs.

Country Code
type: DatatypeProperty
domain: Location
description: Recommended best practice is to use an ISO 3166-1-alpha-2 country code.
example of usage: `AR`, `SV`
comment: The standard code for the country in which the Location occurs.

County
type: DatatypeProperty
domain: Location
description: Recommended best practice is to use a controlled vocabulary such as the Getty Thesaurus of Geographic Names.
example of usage: `Missoula`, `Los Lagos`, `Mataró`
comment: The full, unabbreviated name of the next smaller administrative region than stateProvince (county, shire, department, etc.) in which the Location occurs.

Cultivar Epithet
type: DatatypeProperty
domain: Taxon
description: According to the Rules of the Cultivated Plant Code, a cultivar name consists of a botanical name followed by a cultivar epithet. The value given as the cultivarEpithet should exclude any quotes. The term taxonRank should be used to indicate which type of cultivated plant name (e.g. cultivar, cultivar group, grex) is concerned. This epithet, including any enclosing apostrophes or suffix, should be provided in scientificName as well.
example of usage: `King Edward` (for scientificName "Solanum tuberosum 'King Edward'" and taxonRank "cultivar"); `Mishmiense` (for scientificName "Rhododendron boothii Mishmiense Group" and taxonRank "cultivar group"); `Atlantis` (for scientificName "Paphiopedilum Atlantis grex" and taxonRank "grex").
comment: Part of the name of a cultivar, cultivar group or grex that follows the scientific name.

Data Generalizations
type: DatatypeProperty
domain: terms
example of usage: `Coordinates generalized from original GPS coordinates to the nearest half degree grid cell`.
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 ID
type: DatatypeProperty
domain: terms
example of usage: `b15d4952-7d20-46f1-8a3e-556a512b04c5`
comment: An identifier for the set of data. May be a global unique identifier or an identifier specific to a collection or institution.

Dataset Name
type: DatatypeProperty
domain: terms
example of usage: `Grinnell Resurvey Mammals`, `Lacey Ctenomys Recaptures`
comment: The name identifying the data set from which the record was derived.

Date Identified
type: DatatypeProperty
domain: Identification
description: Recommended best practice is to use a date that conforms to ISO 8601-1:2019.
example of usage: `1963-03-08T14:07-0600` (8 Mar 1963 at 2:07pm in the time zone six hours earlier than UTC). `2009-02-20T08:40Z` (20 February 2009 8:40am UTC). `2018-08-29T15:19` (3:19pm local time on 29 August 2018). `1809-02-12` (some time during 12 February 1809). `1906-06` (some time in June 1906). `1971` (some time in the year 1971). `2007-03-01T13:00:00Z/2008-05-11T15:30:00Z` (some time during the interval between 1 March 2007 1pm UTC and 11 May 2008 3:30pm UTC). `1900/1909` (some time during the interval between the beginning of the year 1900 and the end of the year 1909). `2007-11-13/15` (some time in the interval between 13 November 2007 and 15 November 2007).
comment: The date on which the subject was determined as representing the Taxon.

Day
type: DatatypeProperty
domain: Event
example of usage: `9`, `28`
comment: The integer day of the month on which the Event occurred.

Decimal Latitude
type: DatatypeProperty
domain: Location
example of usage: `-41.0983423`
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
domain: Location
example of usage: `-121.1761111`
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.

Degree of Establishment
type: DatatypeProperty
domain: Occurrence
description: Recommended best practice is to use controlled value strings from the controlled vocabulary designated for use with this term, listed at http://rs.tdwg.org/dwc/doc/doe/. For details, refer to https://doi.org/10.3897/biss.3.38084
example of usage: `native`, `captive`, `cultivated`, `released`, `failing`, `casual`, `reproducing`, `established`, `colonising`, `invasive`, `widespreadInvasive`
comment: The degree to which an Organism survives, reproduces, and expands its range at the given place and time.

Disposition
type: DatatypeProperty
domain: Occurrence
description: Recommended best practice is to use a controlled vocabulary.
example of usage: `in collection`, `missing`, `voucher elsewhere`, `duplicates elsewhere`
comment: The current state of a specimen with respect to the collection identified in collectionCode or collectionID.

Dynamic Properties
type: DatatypeProperty
domain: terms
description: Recommended best practice is to use a key:value encoding schema for a data interchange format such as JSON.
example of usage: `{"heightInMeters":1.5}`, `{"tragusLengthInMeters":0.014, "weightInGrams":120}`, `{"natureOfID":"expert identification", "identificationEvidence":"cytochrome B sequence"}`, `{"relativeHumidity":28, "airTemperatureInCelsius":22, "sampleSizeInKilograms":10}`, `{"aspectHeading":277, "slopeInDegrees":6}`, `{"iucnStatus":"vulnerable", "taxonDistribution":"Neuquén, Argentina"}`
comment: A list of additional measurements, facts, characteristics, or assertions about the record. Meant to provide a mechanism for structured content.

Earliest Age Or Lowest Stage
type: DatatypeProperty
domain: Geological Context
example of usage: `Atlantic`, `Boreal`, `Skullrockian`
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
domain: Geological Context
example of usage: `Phanerozoic`, `Proterozoic`
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
domain: Geological Context
example of usage: `Holocene`, `Pleistocene`, `Ibexian Series`
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
domain: Geological Context
example of usage: `Cenozoic`, `Mesozoic`
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
domain: Geological Context
example of usage: `Neogene`, `Tertiary`, `Quaternary`
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
domain: Event
example of usage: `1` (1 January). `32` (1 February). `366` (31 December). `365` (30 December in a leap year, 31 December in a non-leap year).
comment: The latest integer 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
domain: Occurrence
description: Recommended best practice is to use controlled value strings from the controlled vocabulary designated for use with this term, listed at http://rs.tdwg.org/dwc/doc/em/. For details, refer to https://doi.org/10.3897/biss.3.38084
example of usage: `native`, `nativeReintroduced`, `introduced`, `introducedAssistedColonisation`, `vagrant`, `uncertain`
comment: Statement about whether an organism or organisms have been introduced to a given place and time through the direct or indirect activity of modern humans.

Event Attributes
type: DatatypeProperty
domain: Event
description: Example: "Relative humidity: 28 %; Temperature: 22 C; Sample size: 10 kg"
comment: A list (concatenated and separated) of additional measurements or characteristics of the Event.
deprecated: True

Event Date
type: DatatypeProperty
domain: Event
description: Recommended best practice is to use a date that conforms to ISO 8601-1:2019.
example of usage: `1963-03-08T14:07-0600` (8 Mar 1963 at 2:07pm in the time zone six hours earlier than UTC). `2009-02-20T08:40Z` (20 February 2009 8:40am UTC). `2018-08-29T15:19` (3:19pm local time on 29 August 2018). `1809-02-12` (some time during 12 February 1809). `1906-06` (some time in June 1906). `1971` (some time in the year 1971). `2007-03-01T13:00:00Z/2008-05-11T15:30:00Z` (some time during the interval between 1 March 2007 1pm UTC and 11 May 2008 3:30pm UTC). `1900/1909` (some time during the interval between the beginning of the year 1900 and the end of the year 1909). `2007-11-13/15` (some time in the interval between 13 November 2007 and 15 November 2007).
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.

Event ID
type: DatatypeProperty
domain: Event
example of usage: `INBO:VIS:Ev:00009375`
comment: An identifier for the set of information associated with an Event (something that occurs at a place and time). May be a global unique identifier or an identifier specific to the data set.

Event Measurement Accuracy
type: DatatypeProperty
domain: Event Measurement
description: Example: "0.01", "normal distribution with variation of 2 m"
comment: The description of the error associated with the EventAttributeValue.
deprecated: True

Event Measurement Determined By
type: DatatypeProperty
domain: Event Measurement
description: Example: "Robert Hijmans"
comment: The agent responsible for having determined the value of the measurement or characteristic of the event.
deprecated: True

Event Measurement Determined Date
type: DatatypeProperty
domain: Event Measurement
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.
comment: The date on which the the measurement or characteristic of the event was made. Recommended best practice is to use an encoding scheme, such as ISO 8601:2004(E).
deprecated: True

Event Measurement ID
type: DatatypeProperty
domain: Event Measurement
comment: An identifier for the event attribute. May be a global unique identifier or an identifier specific to the data set.
deprecated: True

Event Measurement Remarks
type: DatatypeProperty
domain: Event Measurement
description: Example: "temperature taken at 15:00"
comment: Comments or notes accompanying the measurement or characteristic of the event.
deprecated: True

Event Measurement Type
type: DatatypeProperty
domain: Event Measurement
description: Example: "temperature"
comment: The nature of the measurement or characteristic of the event. Recommended best practice is to use a controlled vocabulary.
deprecated: True

Event Measurement Unit
type: DatatypeProperty
domain: Event Measurement
description: Example: "C"
comment: The units for the value of the measurement or characteristic of the event. Recommended best practice is to use International System of Units (SI) units.
deprecated: True

Event Measurement Value
type: DatatypeProperty
domain: Event Measurement
description: Example: "22"
comment: The value of the measurement or characteristic of the event.
deprecated: True

Event Remarks
type: DatatypeProperty
domain: Event
example of usage: `After the recent rains the river is nearly at flood stage.`
comment: Comments or notes about the Event.

Event Time
type: DatatypeProperty
domain: Event
description: Recommended best practice is to use a date that conforms to ISO 8601-1:2019.
example of usage: `14:07-0600` (2:07pm in the time zone six hours earlier than UTC). `08:40:21Z` (8:40:21am UTC). `13:00:00Z/15:30:00Z` (the interval between 1pm UTC and 3:30pm UTC).
comment: The time or interval during which an Event occurred.

Family
type: DatatypeProperty
domain: Taxon
example of usage: `Felidae`, `Monocleaceae`
comment: The full scientific name of the family in which the taxon is classified.

Field Notes
type: DatatypeProperty
domain: Event
example of usage: `Notes available in the Grinnell-Miller Library.`
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
domain: Event
example of usage: `RV Sol 87-03-08`
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
domain: Location
description: Recommended best practice is to use the EPSG code of the 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`. It is also permitted to provide the SRS in Well-Known-Text, especially if no EPSG code provides the necessary values for the attributes of the SRS. Do not use this term to describe the SRS of the decimalLatitude and decimalLongitude, nor of any verbatim coordinates - use the geodeticDatum and verbatimSRS instead.
example of usage: `epsg:4326`, `GEOGCS["GCS_WGS_1984", DATUM["D_WGS_1984", SPHEROID["WGS_1984",6378137,298.257223563]], PRIMEM["Greenwich",0], UNIT["Degree",0.0174532925199433]]` (WKT for the standard WGS84 Spatial Reference System EPSG:4326)
comment: The ellipsoid, geodetic datum, or spatial reference system (SRS) upon which the geometry given in footprintWKT is based.

Footprint Spatial Fit
type: DatatypeProperty
domain: Location
description: Detailed explanations with graphical examples can be found in the Georeferencing Best Practices, Chapman and Wieczorek, 2020 (https://doi.org/10.15468/doc-gg7h-s853).
example of usage: `0`, `1`, `1.5708`
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 empty) 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 footprintSpatialFit is 1.

Footprint WKT
type: DatatypeProperty
domain: Location
example of usage: `POLYGON ((10 20, 11 20, 11 21, 10 21, 10 20))` (the one-degree bounding box with opposite corners at longitude=10, latitude=20 and longitude=11, latitude=21)
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
domain: Geological Context
example of usage: `Notch Peak Formation`, `House Limestone`, `Fillmore Formation`
comment: The full name of the lithostratigraphic formation from which the cataloged item was collected.

Generic Name
type: DatatypeProperty
domain: Taxon
description: For synonyms the accepted genus and the genus part of the name may be different. The term genericName should be used together with specificEpithet to form a binomial and with infraspecificEpithet to form a trinomial. The term genericName should only be used for combinations. Uninomials of generic rank do not have a genericName.
example of usage: `Felis` (for scientificName "Felis concolor", with accompanying values of "Puma concolor" in acceptedNameUsage and "Puma" in genus).
comment: The genus part of the scientificName without authorship.

Genus
type: DatatypeProperty
domain: Taxon
example of usage: `Puma`, `Monoclea`
comment: The full scientific name of the genus in which the taxon is classified.

Geodetic Datum
type: DatatypeProperty
domain: Location
description: Recommended best practice is to use the EPSG code of the 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`.
example of usage: `EPSG:4326`, `WGS84`, `NAD27`, `Campo Inchauspe`, `European 1950`, `Clarke 1866`, `unknown`
comment: The ellipsoid, geodetic datum, or spatial reference system (SRS) upon which the geographic coordinates given in decimalLatitude and decimalLongitude as based.

Geological Context ID
type: DatatypeProperty
domain: Geological Context
example of usage: `https://opencontext.org/subjects/e54377f7-4452-4315-b676-40679b10c4d9`
comment: An identifier for the set of information associated with a GeologicalContext (the location within a geological context, such as stratigraphy). May be a global unique identifier or an identifier specific to the data set.

Georeference Protocol
type: DatatypeProperty
domain: Location
example of usage: `Georeferencing Quick Reference Guide (Zermoglio et al. 2020, https://doi.org/10.35035/e09p-h128)`
comment: A description or reference to the methods used to determine the spatial footprint, coordinates, and uncertainties.

Georeference Remarks
type: DatatypeProperty
domain: Location
example of usage: `Assumed distance by road (Hwy. 101)`.
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
domain: Location
description: Recommended best practice is to separate the values in a list with space vertical bar space (` | `).
example of usage: `https://www.geonames.org/`, `USGS 1:24000 Florence Montana Quad 1967 | Terrametrics 2008 on Google Earth`, `GeoLocate`
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
domain: Occurrence
description: Recommended best practice is to use a controlled vocabulary.
example of usage: `unable to georeference`, `requires georeference`, `requires verification`, `verified by data custodian`, `verified by contributor`
comment: A categorical description of the extent to which the georeference has been verified to represent the best possible spatial description for the Location of the Occurrence.

Georeferenced By
type: DatatypeProperty
domain: Location
description: Recommended best practice is to separate the values in a list with space vertical bar space (` | `).
example of usage: `Brad Millen (ROM)`, `Kristina Yamamoto | Janet Fang`
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
domain: Location
description: Recommended best practice is to use a date that conforms to ISO 8601-1:2019.
example of usage: `1963-03-08T14:07-0600` (8 Mar 1963 at 2:07pm in the time zone six hours earlier than UTC). `2009-02-20T08:40Z` (20 February 2009 8:40am UTC). `2018-08-29T15:19` (3:19pm local time on 29 August 2018). `1809-02-12` (some time during 12 February 1809). `1906-06` (some time in June 1906). `1971` (some time in the year 1971). `2007-03-01T13:00:00Z/2008-05-11T15:30:00Z` (some time during the interval between 1 March 2007 1pm UTC and 11 May 2008 3:30pm UTC). `1900/1909` (some time during the interval between the beginning of the year 1900 and the end of the year 1909). `2007-11-13/15` (some time in the interval between 13 November 2007 and 15 November 2007).
comment: The date on which the Location was georeferenced.

Group
type: DatatypeProperty
domain: Geological Context
example of usage: `Bathurst`, `Lower Wealden`
comment: The full name of the lithostratigraphic group from which the cataloged item was collected.

Habitat
type: DatatypeProperty
domain: Event
example of usage: `oak savanna`, `pre-cordilleran steppe`
comment: A category or description of the habitat in which the Event occurred.

Higher Classification
type: DatatypeProperty
domain: Taxon
description: Recommended best practice is to separate the values in a list with space vertical bar space (` | `), with terms in order from the highest taxonomic rank to the lowest.
example of usage: `Plantae | Tracheophyta | Magnoliopsida | Ranunculales | Ranunculaceae | Ranunculus`, `Animalia`, `Animalia | Chordata | Vertebrata | Mammalia | Theria | Eutheria | Rodentia | Hystricognatha | Hystricognathi | Ctenomyidae | Ctenomyini | Ctenomys`
comment: A list (concatenated and separated) of taxa names terminating at the rank immediately superior to the taxon referenced in the taxon record.

Higher Geography
type: DatatypeProperty
domain: Location
description: Recommended best practice is to separate the values in a list with space vertical bar space (` | `), with terms in order from least specific to most specific.
example of usage: `North Atlantic Ocean`. `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.
comment: A list (concatenated and separated) of geographic names less specific than the information captured in the locality term.

Higher Geography ID
type: DatatypeProperty
domain: Location
description: Recommended best practice is to use a persistent identifier from a controlled vocabulary such as the Getty Thesaurus of Geographic Names.
example of usage: `http://vocab.getty.edu/tgn/1002002` (Antártida e Islas del Atlántico Sur, Territorio Nacional de la Tierra del Fuego, Argentina).
comment: An identifier for the geographic region within which the Location occurred.

Higher Taxon Name
type: DatatypeProperty
domain: Taxon
description: Example: "Animalia; Chordata; Vertebrata; Mammalia; Theria; Eutheria; Rodentia; Hystricognatha; Hystricognathi; Ctenomyidae; Ctenomyini; Ctenomys"
comment: A list (concatenated and separated) of the names for the taxonomic ranks less specific than that given in the scientificName.
deprecated: True

Higher Taxon Name ID
type: DatatypeProperty
domain: Taxon
comment: A unique identifier for the name of the next higher rank than the scientificName in a taxonomic classification. See higherTaxonName.
deprecated: True

Higher Taxon Concept ID
type: DatatypeProperty
domain: Taxon
comment: A unique identifier for the taxon concept less specific than that given in the taxonConceptID.
deprecated: True

Highest Biostratigraphic Zone
type: DatatypeProperty
domain: Geological Context
example of usage: `Blancan`
comment: The full name of the highest possible geological biostratigraphic zone of the stratigraphic horizon from which the cataloged item was collected.

Identification Attributes
type: DatatypeProperty
domain: Identification
description: Example: "natureOfID=expert identification; identificationEvidence=cytochrome B sequence"
comment: A list (concatenated and separated) of additional measurements, facts, characteristics, or assertions about the Identification.
deprecated: True

Identification ID
type: DatatypeProperty
domain: Identification
example of usage: `9992`
comment: An identifier for the Identification (the body of information associated with the assignment of a scientific name). May be a global unique identifier or an identifier specific to the data set.

Identification Qualifier
type: DatatypeProperty
domain: Identification
example of usage: `aff. agrifolia var. oxyadenia` (for `Quercus aff. agrifolia var. oxyadenia` with accompanying values `Quercus` in genus, `agrifolia` in specificEpithet, `oxyadenia` in infraspecificEpithet, and `var.` in taxonRank. `cf. var. oxyadenia` for `Quercus agrifolia cf. var. oxyadenia` with accompanying values `Quercus` in genus, `agrifolia` in specificEpithet, `oxyadenia` in infraspecificEpithet, and `var.` in taxonRank.
comment: A brief phrase or a standard term ("cf.", "aff.") to express the determiner's doubts about the Identification.

Identification References
type: DatatypeProperty
domain: Identification
description: Recommended best practice is to separate the values in a list with space vertical bar space (` | `).
example of usage: `Aves del Noroeste Patagonico. Christie et al. 2004.`, `Stebbins, R. Field Guide to Western Reptiles and Amphibians. 3rd Edition. 2003. | Irschick, D.J. and Shaffer, H.B. (1997). The polytypic species revisited: Morphological differentiation among tiger salamanders (Ambystoma tigrinum) (Amphibia: Caudata). Herpetologica, 53(1), 30-49.`
comment: A list (concatenated and separated) of references (publication, global unique identifier, URI) used in the Identification.

Identification Remarks
type: DatatypeProperty
domain: Identification
example of usage: `Distinguished between Anthus correndera and Anthus hellmayri based on the comparative lengths of the uñas.`
comment: Comments or notes about the Identification.

Identification Verification Status
type: DatatypeProperty
domain: Identification
description: Recommended best practice is to use a controlled vocabulary such as that used in HISPID and ABCD.
example of usage: `0` ("unverified" in HISPID/ABCD).
comment: A categorical indicator of the extent to which the taxonomic identification has been verified to be correct.

Identified By
type: DatatypeProperty
domain: Identification
description: Recommended best practice is to separate the values in a list with space vertical bar space (` | `).
example of usage: `James L. Patton`, `Theodore Pappenfuss | Robert Macey`
comment: A list (concatenated and separated) of names of people, groups, or organizations who assigned the Taxon to the subject.

Identified By ID
type: DatatypeProperty
domain: Identification
description: Recommended best practice is to provide a single identifier that disambiguates the details of the identifying agent. If a list is used, the order of the identifiers on the list should not be assumed to convey any semantics. Recommended best practice is to separate the values in a list with space vertical bar space ( | ).
example of usage: `https://orcid.org/0000-0002-1825-0097` (for an individual), `https://orcid.org/0000-0002-1825-0097 | https://orcid.org/0000-0002-1825-0098` (for a list of people).
comment: A list (concatenated and separated) of the globally unique identifier for the person, people, groups, or organizations responsible for assigning the Taxon to the subject.

Individual Count
type: DatatypeProperty
domain: Occurrence
example of usage: `0`, `1`, `25`
comment: The number of individuals present at the time of the Occurrence.

Individual ID
type: DatatypeProperty
domain: Occurrence
description: Examples: "U.amer. 44", "Smedley", "Orca J 23"
comment: An identifier for an individual or named group of individual organisms represented in the Occurrence. Meant to accommodate resampling of the same individual or group for monitoring purposes. May be a global unique identifier or an identifier specific to a data set.
deprecated: True

Information Withheld
type: DatatypeProperty
domain: terms
example of usage: `location information not given for endangered species`, `collector identities withheld | ask about tissue samples`
comment: Additional information that exists, but that has not been shared in the given record.

Infrageneric Epithet
type: DatatypeProperty
domain: Taxon
description: The term infragenericEpithet should be used in conjunction with genericName, specificEpithet, infraspecificEpithet, taxonRank and scientificNameAuthorship to represent the individual elements of the complete scientificName. It can be used to indicate the subgenus placement of a species, which in zoology is often given in parentheses. Can also be used to share infrageneric names such as botanical sections (e.g., `Vicia sect. Cracca`).
example of usage: `Abacetillus` (for scientificName "Abacetus (Abacetillus) ambiguus", `Cracca` (for scientificName "Vicia sect. Cracca")
comment: The infrageneric part of a binomial name at ranks above species but below genus.

Infraspecific Epithet
type: DatatypeProperty
domain: Taxon
description: In botany, where there can be more than one infraspecific rank, name strings may be provided, in literature and in identifications, that have more than two epithets. Only the last of these epithets is the infraspecificEpithet and only the first and the last epithets belong to the scientificName. For example: the infraspecificEpithet in the string "Indigofera charlieriana subsp. sessilis var. scaberrima" is `scaberrima` and the scientificName is `Indigophera charlieriana var. scaberrima`.
example of usage: `concolor` (for scientificName "Puma concolor concolor"), `oxyadenia` (for scientificName "Quercus agrifolia var. oxyadenia"), `laxa` (for scientificName "Cheilanthes hirta f. laxa"), `scaberrima` (for scientificName "Indigofera charlieriana var. scaberrima").
comment: The name of the lowest or terminal infraspecific epithet of the scientificName, excluding any rank designation.

Institution Code
type: DatatypeProperty
domain: terms
example of usage: `MVZ`, `FMNH`, `CLO`, `UCMP`
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
domain: terms
description: For physical specimens, the recommended best practice is to use an identifier from a collections registry such as the Global Registry of Biodiversity Repositories (http://grbio.org/).
example of usage: `http://biocol.org/urn:lsid:biocol.org:col:34777`, `http://grbio.org/cool/km06-gtbn`
comment: An identifier for the institution having custody of the object(s) or information referred to in the record.

Island
type: DatatypeProperty
domain: Location
description: Recommended best practice is to use a controlled vocabulary such as the Getty Thesaurus of Geographic Names.
example of usage: `Nosy Be`, `Bikini Atoll`, `Vancouver`, `Viti Levu`, `Zanzibar`
comment: The name of the island on or near which the Location occurs.

Island Group
type: DatatypeProperty
domain: Location
description: Recommended best practice is to use a controlled vocabulary such as the Getty Thesaurus of Geographic Names.
example of usage: `Alexander Archipelago`, `Archipiélago Diego Ramírez`, `Seychelles`
comment: The name of the island group in which the Location occurs.

Kingdom
type: DatatypeProperty
domain: Taxon
example of usage: `Animalia`, `Archaea`, `Bacteria`, `Chromista`, `Fungi`, `Plantae`, `Protozoa`, `Viruses`
comment: The full scientific name of the kingdom in which the taxon is classified.

Latest AgeOr Highest Stage
type: DatatypeProperty
domain: Geological Context
example of usage: `Atlantic`, `Boreal`, `Skullrockian`
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
domain: Geological Context
example of usage: `Phanerozoic`, `Proterozoic`
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
domain: Geological Context
example of usage: `Holocene`, `Pleistocene`, `Ibexian Series`
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
domain: Geological Context
example of usage: `Cenozoic`, `Mesozoic`
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
domain: Geological Context
example of usage: `Neogene`, `Tertiary`, `Quaternary`
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
domain: Occurrence
description: Recommended best practice is to use a controlled vocabulary.
example of usage: `zygote`, `larva`, `juvenile`, `adult`, `seedling`, `flowering`, `fruiting`
comment: The age class or life stage of the Organism(s) at the time the Occurrence was recorded.

Lithostratigraphic Terms
type: DatatypeProperty
domain: Geological Context
example of usage: `Pleistocene-Weichselien`
comment: The combination of all litho-stratigraphic names for the rock from which the cataloged item was collected.

Locality
type: DatatypeProperty
domain: Location
description: 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.
example of usage: `Bariloche, 25 km NNE via Ruta Nacional 40 (=Ruta 237)`, `Queets Rainforest, Olympic National Park`
comment: The specific description of the place.

Location According To
type: DatatypeProperty
domain: Location
example of usage: `Getty Thesaurus of Geographic Names`, `GADM`
comment: Information about the source of this Location information. Could be a publication (gazetteer), institution, or team of individuals.

Location Attributes
type: DatatypeProperty
domain: Location
description: Example: "aspectheading=277; slopeindegrees=6"
comment: A list (concatenated and separated) of additional measurements, facts, characteristics, or assertions about the location.
deprecated: True

Location ID
type: DatatypeProperty
domain: Location
example of usage: `https://opencontext.org/subjects/768A875F-E205-4D0B-DE55-BAB7598D0FD1`
comment: An identifier for the set of location information (data associated with dcterms:Location). May be a global unique identifier or an identifier specific to the data set.

Location Remarks
type: DatatypeProperty
domain: Location
example of usage: `under water since 2005`
comment: Comments or notes about the Location.

Lowest Biostratigraphic Zone
type: DatatypeProperty
domain: Geological Context
example of usage: `Maastrichtian`
comment: The full name of the lowest possible geological biostratigraphic zone of the stratigraphic horizon from which the cataloged item was collected.

Material Sample ID
type: DatatypeProperty
domain: Material Sample
description: Recommended best practice is to use a persistent, globally unique identifier.
example of usage: `06809dc5-f143-459a-be1a-6f03e63fc083`
comment: An identifier for the MaterialSample (as opposed to a particular digital record of the material sample). In the absence of a persistent global unique identifier, construct one from a combination of identifiers in the record that will most closely make the materialSampleID globally unique.

Maximum Depth In Meters
type: DatatypeProperty
domain: Location
example of usage: `0`, `200`
comment: The greater depth of a range of depth below the local surface, in meters.

Maximum Distance Above Surface In Meters
type: DatatypeProperty
domain: Location
example of usage: `-1.5` (below the surface). `4.2` (above the surface). For a 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`.
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
domain: Location
example of usage: `-205`, `1236`
comment: The upper limit of the range of elevation (altitude, usually above sea level), in meters.

Measurement Accuracy
type: DatatypeProperty
domain: Measurement or Fact
example of usage: `0.01`, `normal distribution with variation of 2 m`
comment: The description of the potential error associated with the measurementValue.

Measurement Determined By
type: DatatypeProperty
domain: Measurement or Fact
description: Recommended best practice is to separate the values in a list with space vertical bar space (` | `).
example of usage: `Rob Guralnick`, `Peter Desmet | Stijn Van Hoey`
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
domain: Measurement or Fact
description: Recommended best practice is to use a date that conforms to ISO 8601-1:2019.
example of usage: `1963-03-08T14:07-0600` (8 Mar 1963 at 2:07pm in the time zone six hours earlier than UTC). `2009-02-20T08:40Z` (20 February 2009 8:40am UTC). `2018-08-29T15:19` (3:19pm local time on 29 August 2018). `1809-02-12` (some time during 12 February 1809). `1906-06` (some time in June 1906). `1971` (some time in the year 1971). `2007-03-01T13:00:00Z/2008-05-11T15:30:00Z` (some time during the interval between 1 March 2007 1pm UTC and 11 May 2008 3:30pm UTC). `1900/1909` (some time during the interval between the beginning of the year 1900 and the end of the year 1909). `2007-11-13/15` (some time in the interval between 13 November 2007 and 15 November 2007).
comment: The date on which the MeasurementOrFact was made.

Measurement ID
type: DatatypeProperty
domain: Measurement or Fact
example of usage: `9c752d22-b09a-11e8-96f8-529269fb1459`
comment: An identifier for the MeasurementOrFact (information pertaining to measurements, facts, characteristics, or assertions). May be a global unique identifier or an identifier specific to the data set.

Measurement Method
type: DatatypeProperty
domain: Measurement or Fact
example of usage: `minimum convex polygon around burrow entrances` (for a home range area). `barometric altimeter` (for an elevation).
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
domain: Measurement or Fact
example of usage: `tip of tail missing`
comment: Comments or notes accompanying the MeasurementOrFact.

Measurement Type
type: DatatypeProperty
domain: Measurement or Fact
description: Recommended best practice is to use a controlled vocabulary.
example of usage: `tail length`, `temperature`, `trap line length`, `survey area`, `trap type`
comment: The nature of the measurement, fact, characteristic, or assertion.

Measurement Unit
type: DatatypeProperty
domain: Measurement or Fact
description: Recommended best practice is to use the International System of Units (SI).
example of usage: `mm`, `C`, `km`, `ha`
comment: The units associated with the measurementValue.

Measurement Value
type: DatatypeProperty
domain: Measurement or Fact
example of usage: `45`, `20`, `1`, `14.5`, `UV-light`
comment: The value of the measurement, fact, characteristic, or assertion.

Member
type: DatatypeProperty
domain: Geological Context
example of usage: `Lava Dam Member`, `Hellnmaria Member`
comment: The full name of the lithostratigraphic member from which the cataloged item was collected.

Minimum Depth In Meters
type: DatatypeProperty
domain: Location
example of usage: `0`, `100`
comment: The lesser depth of a range of depth below the local surface, in meters.

Minimum Distance Above Surface In Meters
type: DatatypeProperty
domain: Location
example of usage: `-1.5` (below the surface). `4.2` (above the surface). For a 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`.
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
domain: Location
example of usage: `-100`, `802`
comment: The lower limit of the range of elevation (altitude, usually above sea level), in meters.

Month
type: DatatypeProperty
domain: Event
example of usage: `1` (January). `10` (October).
comment: The integer month in which the Event occurred.

Municipality
type: DatatypeProperty
domain: Location
description: Recommended best practice is to use a controlled vocabulary such as the Getty Thesaurus of Geographic Names.
example of usage: `Holzminden`, `Araçatuba`, `Ga-Segonyana`
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
domain: Taxon
description: This term provides context to the `scientificName`. Together with the `scientificName`, separated by ‘sensu’ or ‘sec.’, it forms the taxon concept label, which may be seen as having the same relationship to `taxonConceptID` as, for example, `acceptedNameUsage` has to `acceptedNameUsageID`. When not provided, in Taxon Core data sets the `nameAccordingTo` can be taken to be the data set. In this case the data set mostly provides sufficient context to infer the delimitation of the taxon and its relationship with other taxa. In Occurrence Core data sets, when not provided, `nameAccordingTo` can be an underlying taxonomy of the data set, e.g. Plants of the World Online (http://powo.science.kew.org/) for vascular plant records in iNaturalist (in which case it should be provided), or, which is the case for most `PreservedSpecimen` data sets, the `Identification`, in which case there is no further context.
example of usage: `Franz NM, Cardona-Duque J (2013) Description of two new species and phylogenetic reassessment of Perelleschus Wibmer & O’Brien, 1986 (Coleoptera: Curculionidae), with a complete taxonomic concept history of Perelleschus sec. Franz & Cardona-Duque, 2013. Syst Biodivers. 11: 209–236.` (as the full citation of the Franz & Cardona-Duque (2013) in Perelleschus splendida sec. Franz & Cardona-Duque (2013))
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 According To ID
type: DatatypeProperty
domain: Taxon
example of usage: `https://doi.org/10.1016/S0269-915X(97)80026-2`
comment: An identifier for the source in which the specific taxon concept circumscription is defined or implied. See nameAccordingTo.

Name Publication ID
type: DatatypeProperty
domain: Taxon
description: Example: "http://hdl.handle.net/10199/7"
comment: A resolvable globally unique identifier for the original publication of the scientificName.
deprecated: True

Name Published In
type: DatatypeProperty
domain: Taxon
example of usage: `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`
comment: A reference for the publication in which the scientificName was originally established under the rules of the associated nomenclaturalCode.

Name Published In ID
type: DatatypeProperty
domain: Taxon
comment: An identifier for the publication in which the scientificName was originally established under the rules of the associated nomenclaturalCode.

Name Published In Year
type: DatatypeProperty
domain: Taxon
example of usage: `1915`, `2008`
comment: The four-digit year in which the scientificName was published.

Nomenclatural Code
type: DatatypeProperty
domain: Taxon
description: Recommended best practice is to use a controlled vocabulary.
example of usage: `ICN`, `ICZN`, `BC`, `ICNCP`, `BioCode`
comment: The nomenclatural code (or codes in the case of an ambiregnal name) under which the scientificName is constructed.

Nomenclatural Status
type: DatatypeProperty
domain: Taxon
example of usage: `nom. ambig.`, `nom. illeg.`, `nom. subnud.`
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 Attributes
type: DatatypeProperty
domain: Occurrence
description: Examples: "Tragus length: 14mm; Weight: 120g", "Height: 1-1.5 meters tall; flowers yellow; uncommon".
comment: A list (concatenated and separated) of additional measurements, facts, characteristics, or assertions about the Occurrence.
deprecated: True

Occurrence Details
type: DatatypeProperty
domain: Occurrence
description: Example: "http://mvzarctos.berkeley.edu/guid/MVZ:Mamm:165861"
comment: A reference (publication, URI) to the most detailed information available about the Occurrence.
deprecated: True

Occurrence ID
type: DatatypeProperty
domain: Occurrence
description: Recommended best practice is to use a persistent, globally unique identifier.
example of usage: `http://arctos.database.museum/guid/MSB:Mamm:233627`, `000866d2-c177-4648-a200-ead4007051b9`, `urn:catalog:UWBM:Bird:89776`
comment: An identifier for the Occurrence (as opposed to a particular digital record of the occurrence). In the absence of a persistent global unique identifier, construct one from a combination of identifiers in the record that will most closely make the occurrenceID globally unique.

Occurrence Measurement Accuracy
type: DatatypeProperty
domain: Occurrence Measurement
description: Example: "0.01", "normal distribution with variation of 2 m"
comment: The description of the error associated with the occurrenceAttributeValue.
deprecated: True

Occurrence Measurement Determined By
type: DatatypeProperty
domain: Occurrence Measurement
description: Example: "Javier de la Torre"
comment: The agent responsible for having determined the value of the measurement or characteristic of the occurrence.
deprecated: True

Occurrence Measurement Determined Date
type: DatatypeProperty
domain: Occurrence Measurement
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.
comment: The date on which the the measurement or characteristic of the occurrence was made. Recommended best practice is to use an encoding scheme, such as ISO 8601:2004(E).
deprecated: True

Occurrence Measurement ID
type: DatatypeProperty
domain: Occurrence Measurement
comment: An identifier for the occurrence attribute. May be a global unique identifier or an identifier specific to the data set.
deprecated: True

Occurrence Measurement Remarks
type: DatatypeProperty
domain: Occurrence Measurement
description: Example: "tip of tail missing"
comment: Comments or notes accompanying the measurement or characteristic of the occurrence.
deprecated: True

Occurrence Measurement Type
type: DatatypeProperty
domain: Occurrence Measurement
description: Example: "tail length"
comment: The nature of the measurement or characteristic of the occurrence. Recommended best practice is to use a controlled vocabulary.
deprecated: True

Occurrence Measurement Unit
type: DatatypeProperty
domain: Occurrence Measurement
description: Example: "mm"
comment: The units for the value of the measurement or characteristic of the occurrence. Recommended best practice is to use International System of Units (SI) units.
deprecated: True

Occurrence Measurement Value
type: DatatypeProperty
domain: Occurrence Measurement
description: Example: "45"
comment: The value of the measurement or characteristic of the occurrence.
deprecated: True

Occurrence Remarks
type: DatatypeProperty
domain: Occurrence
example of usage: `found dead on road`
comment: Comments or notes about the Occurrence.

Occurrence Status
type: DatatypeProperty
domain: Occurrence
description: For Occurrences, the default vocabulary is recommended to consist of "present" and "absent", but can be extended by implementers with good justification.
example of usage: `present`, `absent`
comment: A statement about the presence or absence of a Taxon at a Location.

Order
type: DatatypeProperty
domain: Taxon
example of usage: `Carnivora`, `Monocleales`
comment: The full scientific name of the order in which the taxon is classified.

Organism ID
type: DatatypeProperty
domain: Organism
example of usage: `http://arctos.database.museum/guid/WNMU:Mamm:1249`
comment: An identifier for the Organism instance (as opposed to a particular digital record of the Organism). May be a globally unique identifier or an identifier specific to the data set.

Organism Name
type: DatatypeProperty
domain: Organism
example of usage: `Huberta`, `Boab Prison Tree`, `J pod`
comment: A textual name or label assigned to an Organism instance.

Organism Quantity
type: DatatypeProperty
domain: Occurrence
description: An organismQuantity must have a corresponding organismQuantityType.
example of usage: `27` (organismQuantity) with `individuals` (organismQuantityType). `12.5` (organismQuantity) with `% biomass` (organismQuantityType). `r` (organismQuantity) with `Braun Blanquet Scale` (organismQuantityType). `many` (organismQuantity) with `individuals` (organismQuantityType).
comment: A number or enumeration value for the quantity of organisms.

Organism Quantity Type
type: DatatypeProperty
domain: Occurrence
description: A dwc:organismQuantityType must have a corresponding dwc:organismQuantity.
example of usage: `27` (organismQuantity) with `individuals` (organismQuantityType). `12.5` (organismQuantity) with `%biomass` (organismQuantityType). `r` (organismQuantity) with `BraunBlanquetScale` (organismQuantityType).
comment: The type of quantification system used for the quantity of organisms.

Organism Remarks
type: DatatypeProperty
domain: Organism
example of usage: `One of a litter of six`
comment: Comments or notes about the Organism instance.

Organism Scope
type: DatatypeProperty
domain: Organism
description: Recommended best practice is to use a controlled vocabulary. This term is not intended to be used to specify a type of taxon. To describe the kind of dwc:Organism using a URI object in RDF, use rdf:type (http://www.w3.org/1999/02/22-rdf-syntax-ns#type) instead.
example of usage: `multicellular organism`, `virus`, `clone`, `pack`, `colony`
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.

Original Name Usage
type: DatatypeProperty
domain: Taxon
description: The full scientific name, with authorship and date information if known, of the name usage in which the terminal element of the scientificName was originally established under the rules of the associated nomenclaturalCode. For example, for names governed by the ICNafp, this term would indicate the basionym of a record representing a subsequent combination. Unlike basionyms, however, this term can apply to scientific names at all ranks.
example of usage: `Pinus abies`, `Gasterosteus saltatrix Linnaeus 1768`
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.

Original Name Usage ID
type: DatatypeProperty
domain: Taxon
description: This term should be used to refer to the taxonID of a Taxon record that represents the usage of the terminal element of the scientificName as originally established under the rules of the associated nomenclaturalCode. For example, for names governed by the ICNafp, this term would establish the relationship between a record representing a subsequent combination and the record for its corresponding basionym. Unlike basionyms, however, this term can apply to scientific names at all ranks. For Darwin Core Archives the related record should be present locally in the same archive.
example of usage: `tsn:41107` (ITIS), `urn:lsid:ipni.org:names:320035-2` (IPNI), `2704179` (GBIF), `6W3C4` (COL)
comment: An identifier for the name usage (documented meaning of the name according to a source) in which the terminal element of the scientificName was originally established under the rules of the associated nomenclaturalCode.

Other Catalog Numbers
type: DatatypeProperty
domain: Occurrence
description: Recommended best practice is to separate the values in a list with space vertical bar space (` | `).
example of usage: `FMNH:Mammal:1234`, `NPS YELLO6778 | MBG 33424`
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
domain: terms
example of usage: `NPS`, `APN`, `InBio`
comment: The name (or acronym) in use by the institution having ownership of the object(s) or information referred to in the record.

Parent Event ID
type: DatatypeProperty
domain: Event
description: Use a globally unique identifier for a dwc:Event or an identifier for a dwc:Event that is specific to the data set.
example of usage: `A1` (parentEventID to identify the main Whittaker Plot in nested samples, each with its own eventID - `A1:1`, `A1:2`).
comment: An identifier for the broader Event that groups this and potentially other Events.

Parent Name Usage
type: DatatypeProperty
domain: Taxon
example of usage: `Rubiaceae`, `Gruiformes`, `Testudinae`
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.

Parent Name Usage ID
type: DatatypeProperty
domain: Taxon
description: This term should be used for accepted names to refer to the taxonID of a Taxon record that represents the next higher taxon rank in the same taxonomic classification. For Darwin Core Archives the related record should be present locally in the same archive.
example of usage: `tsn:41074` (ITIS), `urn:lsid:ipni.org:names:30001404-2` (IPNI), `2704173` (GBIF), `6T8N` (COL)
comment: An identifier for the name usage (documented meaning of the name according to a source) of the direct, most proximate higher-rank parent taxon (in a classification) of the most specific element of the scientificName.

Pathway
type: DatatypeProperty
domain: Occurrence
description: Recommended best practice is to use controlled value strings from the controlled vocabulary designated for use with this term, listed at http://rs.tdwg.org/dwc/doc/pw/. For details, refer to https://doi.org/10.3897/biss.3.38084
example of usage: `releasedForUse`, `otherEscape`, `transportContaminant`, `transportStowaway`, `corridor`, `unaided`
comment: The process by which an Organism came to be in a given place at a given time.

Phylum
type: DatatypeProperty
domain: Taxon
example of usage: `Chordata` (phylum). `Bryophyta` (division).
comment: The full scientific name of the phylum or division in which the taxon is classified.

Point Radius Spatial Fit
type: DatatypeProperty
domain: Location
description: Detailed explanations with graphical examples can be found in the Georeferencing Best Practices, Chapman and Wieczorek, 2020 (https://doi.org/10.15468/doc-gg7h-s853).
example of usage: `0`, `1`, `1.5708`
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 empty) 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
domain: Occurrence
description: Recommended best practice is to separate the values in a list with space vertical bar space (` | `).
example of usage: `fossil`, `cast`, `photograph`, `DNA extract`, `skin | skull | skeleton`, `whole animal (ETOH) | tissue (EDTA)`
comment: A list (concatenated and separated) of preparations and preservation methods for a specimen.

Previous Identifications
type: DatatypeProperty
domain: Organism
description: Recommended best practice is to separate the values in a list with space vertical bar space (` | `).
example of usage: `Chalepidae`, `Pinus abies`, `Anthus sp., field ID by G. Iglesias | Anthus correndera, expert ID by C. Cicero 2009-02-12 based on morphology`
comment: A list (concatenated and separated) of previous assignments of names to the Organism.

Record Number
type: DatatypeProperty
domain: Occurrence
example of usage: `OPP 7101`
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
domain: Occurrence
description: Recommended best practice is to separate the values in a list with space vertical bar space (` | `).
example of usage: `José E. Crespo`. `Oliver P. Pearson | Anita K. Pearson` (where the value in recordNumber `OPP 7101` corresponds to the collector number for the specimen in the field catalog of Oliver P. Pearson).
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.

Recorded By ID
type: DatatypeProperty
domain: Occurrence
description: Recommended best practice is to provide a single identifier that disambiguates the details of the identifying agent. If a list is used, it is recommended to separate the values in the list with space vertical bar space ( | ). The order of the identifiers on any list for this term can not be guaranteed to convey any semantics.
example of usage: `https://orcid.org/0000-0002-1825-0097` (for an individual); `https://orcid.org/0000-0002-1825-0097 | https://orcid.org/0000-0002-1825-0098` (for a list of people).
comment: A list (concatenated and separated) of the globally unique identifier for the person, people, groups, or organizations responsible for recording the original Occurrence.

Related Resource ID
type: DatatypeProperty
domain: Resource Relationship
example of usage: `dc609808-b09b-11e8-96f8-529269fb1459`
comment: An identifier for a related resource (the object, rather than the subject of the relationship).

Related Resource Type
type: DatatypeProperty
domain: Resource Relationship
description: Examples: "StillImage", "MovingImage", "Sound", PhysicalObject", "PreservedSpecimen", FossilSpecimen", LivingSpecimen", "HumanObservation", "MachineObservation", "Location", "Taxonomy", "NomeclaturalChecklist", "Publication"
comment: The type of the related resource. Recommended best practice is to use a controlled vocabulary.
deprecated: True

Relationship According To
type: DatatypeProperty
domain: Resource Relationship
example of usage: `Julie Woodruff`
comment: The source (person, organization, publication, reference) establishing the relationship between the two resources.

Relationship Established Date
type: DatatypeProperty
domain: Resource Relationship
description: Recommended best practice is to use a date that conforms to ISO 8601-1:2019.
example of usage: `1963-03-08T14:07-0600` (8 Mar 1963 at 2:07pm in the time zone six hours earlier than UTC). `2009-02-20T08:40Z` (20 February 2009 8:40am UTC). `2018-08-29T15:19` (3:19pm local time on 29 August 2018). `1809-02-12` (some time during 12 February 1809). `1906-06` (some time in June 1906). `1971` (some time in the year 1971). `2007-03-01T13:00:00Z/2008-05-11T15:30:00Z` (some time during the interval between 1 March 2007 1pm UTC and 11 May 2008 3:30pm UTC). `1900/1909` (some time during the interval between the beginning of the year 1900 and the end of the year 1909). `2007-11-13/15` (some time in the interval between 13 November 2007 and 15 November 2007).
comment: The date-time on which the relationship between the two resources was established.

Relationship Of Resource
type: DatatypeProperty
domain: Resource Relationship
description: Recommended best practice is to use a controlled vocabulary.
example of usage: `sameAs`, `duplicate of`, `mother of`, `offspring of`, `sibling of`, `parasite of`, `host of`, `valid synonym of`, `located within`, `pollinator of members of taxon`, `pollinated specific plant`, `pollinated by members of taxon`
comment: The relationship of the subject (identified by resourceID) to the object (identified by relatedResourceID).

Relationship Of Resource ID
type: DatatypeProperty
domain: Resource Relationship
description: Recommended best practice is to use the identifiers of the terms in a controlled vocabulary, such as the OBO Relation Ontology.
example of usage: `http://purl.obolibrary.org/obo/RO_0002456` (for the relation "pollinated by"), `http://purl.obolibrary.org/obo/RO_0002455` (for the relation "pollinates"), `https://www.inaturalist.org/observation_fields/879` (for the relation "eaten by")
comment: An identifier for the relationship type (predicate) that connects the subject identified by resourceID to its object identified by relatedResourceID.

Relationship Remarks
type: DatatypeProperty
domain: Resource Relationship
example of usage: `mother and offspring collected from the same nest`, `pollinator captured in the act`
comment: Comments or notes about the relationship between the two resources.

Reproductive Condition
type: DatatypeProperty
domain: Occurrence
description: Recommended best practice is to use a controlled vocabulary.
example of usage: `non-reproductive`, `pregnant`, `in bloom`, `fruit-bearing`
comment: The reproductive condition of the biological individual(s) represented in the Occurrence.

Resource ID
type: DatatypeProperty
domain: Resource Relationship
example of usage: `f809b9e0-b09b-11e8-96f8-529269fb1459`
comment: An identifier for the resource that is the subject of the relationship.

Resource Relationship ID
type: DatatypeProperty
domain: Resource Relationship
example of usage: `04b16710-b09c-11e8-96f8-529269fb1459`
comment: An identifier for an instance of relationship between one resource (the subject) and another (relatedResource, the object).

Sample Size Unit
type: DatatypeProperty
domain: Event
description: A sampleSizeUnit must have a corresponding sampleSizeValue, e.g., `5` for sampleSizeValue with `metre` for sampleSizeUnit.
example of usage: `minute`, `hour`, `day`, `metre`, `square metre`, `cubic metre`
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
domain: Event
description: A sampleSizeValue must have a corresponding sampleSizeUnit.
example of usage: `5` for sampleSizeValue with `metre` for sampleSizeUnit.
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
domain: Event
example of usage: `40 trap-nights`, `10 observer-hours`, `10 km by foot`, `30 km by car`
comment: The amount of effort expended during an Event.

Sampling Protocol
type: DatatypeProperty
domain: Event
description: Recommended best practice is describe an Event with no more than one sampling protocol. In the case of a summary Event with multiple protocols, in which a specific protocol can not be attributed to specific Occurrences, the recommended best practice is to separate the values in a list with space vertical bar space ( | ).
example of usage: `UV light trap`, `mist net`, `bottom trawl`, `ad hoc observation | point count`, `Penguins from space: faecal stains reveal the location of emperor penguin colonies, https://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`
comment: The names of, references to, or descriptions of the methods or protocols used during an Event.

Scientific Name
type: DatatypeProperty
domain: Taxon
description: This term should not contain identification qualifications, which should instead be supplied in the IdentificationQualifier term. When applied to an Organism or Occurrence, this term should be used to represent the scientific name that was applied to the associated Organism in accordance with the Taxon to which it was or is currently identified.
example of usage: `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).
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
domain: Taxon
example of usage: `(Torr.) J.T. Howell`, `(Martinovský) Tzvelev`, `(Györfi, 1952)`
comment: The authorship information for the scientificName formatted according to the conventions of the applicable nomenclaturalCode.

Scientific Name ID
type: DatatypeProperty
domain: Taxon
example of usage: `urn:lsid:ipni.org:names:37829-1:1.3`
comment: An identifier for the nomenclatural (not taxonomic) details of a scientific name.

Scientific Name Rank
type: DatatypeProperty
domain: Taxon
description: Examples: "subsp.", "var.", "forma", "species", "genus"
comment: The taxonomic rank of the most specific name in the scientificName. Recommended best practice is to use a controlled vocabulary.
deprecated: True

Sex
type: DatatypeProperty
domain: Occurrence
description: Recommended best practice is to use a controlled vocabulary.
example of usage: `female`, `male`, `hermaphrodite`
comment: The sex of the biological individual(s) represented in the Occurrence.

Specific Epithet
type: DatatypeProperty
domain: Taxon
example of usage: `concolor`, `gottschei`
comment: The name of the first or species epithet of the scientificName.

Start Day Of Year
type: DatatypeProperty
domain: Event
example of usage: `1` (1 January). `366` (31 December), `365` (30 December in a leap year, 31 December in a non-leap year).
comment: The earliest integer 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
domain: Location
description: Recommended best practice is to use a controlled vocabulary such as the Getty Thesaurus of Geographic Names.
example of usage: `Montana`, `Minas Gerais`, `Córdoba`
comment: The name of the next smaller administrative region than country (state, province, canton, department, region, etc.) in which the Location occurs.

Subfamily
type: DatatypeProperty
domain: Taxon
example of usage: `Periptyctinae`, `Orchidoideae`, `Sphindociinae`
comment: The full scientific name of the subfamily in which the taxon is classified.

Subgenus
type: DatatypeProperty
domain: Taxon
example of usage: `Strobus`, `Amerigo`, `Pilosella`
comment: The full scientific name of the subgenus in which the taxon is classified. Values should include the genus to avoid homonym confusion.

Taxon According To
type: DatatypeProperty
domain: Taxon
comment: Information about the authorship of this taxon concept which uses the scientificName in their sense (secundum, sensu). Could be a publication (identification key), institution or team of individuals.
deprecated: True

Taxon Attributes
type: DatatypeProperty
domain: Taxon
description: Example: "iucnstatus=vulnerable; distribution=Neuquen, Argentina"
comment: A list (concatenated and separated) of additional measurements, facts, characteristics, or assertions about the taxon.
deprecated: True

Taxon Concept ID
type: DatatypeProperty
domain: Taxon
example of usage: `8fa58e08-08de-4ac1-b69c-1235340b7001`
comment: An identifier for the taxonomic concept to which the record refers - not for the nomenclatural details of a taxon.

Taxon ID
type: DatatypeProperty
domain: Taxon
example of usage: `8fa58e08-08de-4ac1-b69c-1235340b7001`, `32567`, `https://www.gbif.org/species/212`
comment: An identifier for the set of taxon information (data associated with the Taxon class). May be a global unique identifier or an identifier specific to the data set.

Taxon Name ID
type: DatatypeProperty
domain: Taxon
comment: A unique identifier for the scientificName.
deprecated: True

Taxon Rank
type: DatatypeProperty
domain: Taxon
description: Recommended best practice is to use a controlled vocabulary.
example of usage: `subspecies`, `varietas`, `forma`, `species`, `genus`
comment: The taxonomic rank of the most specific name in the scientificName.

Taxon Remarks
type: DatatypeProperty
domain: Taxon
example of usage: `this name is a misspelling in common use`
comment: Comments or notes about the taxon or name.

Taxonomic Status
type: DatatypeProperty
domain: Taxon
description: Recommended best practice is to use a controlled vocabulary.
example of usage: `invalid`, `misapplied`, `homotypic synonym`, `accepted`
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.

Type Status
type: DatatypeProperty
domain: Identification
description: Recommended best practice is to separate the values in a list with space vertical bar space (` | `).
example of usage: `holotype of Ctenomys sociabilis. Pearson O. P., and M. I. Christie. 1985. Historia Natural, 5(37):388`, `holotype of Pinus abies | holotype of Picea abies`
comment: A list (concatenated and separated) of nomenclatural types (type status, typified scientific name, publication) applied to the subject.

Verbatim Coordinate System
type: DatatypeProperty
domain: Location
description: Recommended best practice is to use a controlled vocabulary.
example of usage: `decimal degrees`, `degrees decimal minutes`, `degrees minutes seconds`, `UTM`
comment: The coordinate format for the verbatimLatitude and verbatimLongitude or the verbatimCoordinates of the Location.

Verbatim Coordinates
type: DatatypeProperty
domain: Location
example of usage: `41 05 54S 121 05 34W`, `17T 630000 4833400`
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
domain: Location
example of usage: `100-200 m`
comment: The original description of the depth below the local surface.

Verbatim Elevation
type: DatatypeProperty
domain: Location
example of usage: `100-200 m`
comment: The original description of the elevation (altitude, usually above sea level) of the Location.

Verbatim EventDate
type: DatatypeProperty
domain: Event
example of usage: `spring 1910`, `Marzo 2002`, `1999-03-XX`, `17IV1934`
comment: The verbatim original representation of the date and time information for an Event.

Verbatim Identification
type: DatatypeProperty
domain: Identification
description: This term is meant to allow the capture of an unaltered original identification/determination, including identification qualifiers, hybrid formulas, uncertainties, etc. This term is meant to be used in addition to `scientificName` (and `identificationQualifier` etc.), not instead of it.
example of usage: `Peromyscus sp.`, `Ministrymon sp. nov. 1`, `Anser anser X Branta canadensis`, `Pachyporidae?`
comment: A string representing the taxonomic identification as it appeared in the original record.

Verbatim Latitude
type: DatatypeProperty
domain: Location
example of usage: `41 05 54.03S`
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
domain: Location
example of usage: `25 km NNE Bariloche por R. Nac. 237`
comment: The original textual description of the place.

Verbatim Longitude
type: DatatypeProperty
domain: Location
example of usage: `121d 10' 34" W`
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
domain: Location
description: Recommended best practice is to use the EPSG code of the 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`.
example of usage: `unknown`, `EPSG:4326`, `WGS84`, `NAD27`, `Campo Inchauspe`, `European 1950`, `Clarke 1866`
comment: The ellipsoid, geodetic datum, or spatial reference system (SRS) upon which coordinates given in verbatimLatitude and verbatimLongitude, or verbatimCoordinates are based.

Verbatim Scientific Name Rank
type: DatatypeProperty
domain: Taxon
description: Examples: "Agamospecies", "sub-lesus", "prole", "apomict", "nothogrex".
comment: The taxonomic rank of the most specific name in the scientificName as it appears in the original record.
deprecated: True

Verbatim Taxon Rank
type: DatatypeProperty
domain: Taxon
example of usage: `Agamospecies`, `sub-lesus`, `prole`, `apomict`, `nothogrex`, `sp.`, `subsp.`, `var.`
comment: The taxonomic rank of the most specific name in the scientificName as it appears in the original record.

Vernacular Name
type: DatatypeProperty
domain: Taxon
example of usage: `Andean Condor`, `Condor Andino`, `American Eagle`, `Gänsegeier`
comment: A common or vernacular name.

Vertical Datum
type: DatatypeProperty
domain: Location
description: Recommended best practice is to use a controlled vocabulary.
example of usage: `EGM84`, `EGM96`, `EGM2008`, `PGM2000A`, `PGM2004`, `PGM2006`, `PGM2007`, `epsg:7030`, `unknown`
comment: The vertical datum used as the reference upon which the values in the elevation terms are based.

Water Body
type: DatatypeProperty
domain: Location
description: Recommended best practice is to use a controlled vocabulary such as the Getty Thesaurus of Geographic Names.
example of usage: `Indian Ocean`, `Baltic Sea`, `Hudson River`, `Lago Nahuel Huapi`
comment: The name of the water body in which the Location occurs.

Year
type: DatatypeProperty
domain: Event
example of usage: `1160`, `2008`
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 lizard observed in the field that is not collected but whose location is recorded in a field notebook.
example of usage: A tree is forest plot that is measured for diameter at breast height (DBH).
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_0000179: entity
BFO_0000180: 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_0000179: continuant
BFO_0000180: Continuant
editor preferred term: 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
imported from: pato.owl
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_0000179: occurrent
BFO_0000180: 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_0000179: ic
BFO_0000180: 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

spatial region
type: Class
equivalent class: Location
subclass of: Location
BFO_0000179: s-region
BFO_0000180: 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_0000179: process
BFO_0000180: 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

realizable entity
type: Class
subclass of: specifically dependent continuant
disjoint with: quality
BFO_0000179: realizable
BFO_0000180: 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.
term editor: https://orcid.org/0000-0001-8815-0078
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

specifically dependent continuant
type: Class
subclass of: continuant
disjoint with: generically dependent continuant
BFO_0000179: sdc
BFO_0000180: SpecificallyDependentContinuant
editor preferred term: specifically dependent continuant
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.
imported from: pato.owl
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_0000179: role
BFO_0000180: 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_0000179: object-aggregate
BFO_0000180: 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_0000179: object
BFO_0000180: 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_0000179: gdc
BFO_0000180: 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

material entity
type: Class
subclass of: independent continuant
disjoint with: immaterial entity
BFO_0000179: material
BFO_0000180: MaterialEntity
editor preferred term: material entity
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.
imported from: ido.owl
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_0000179: immaterial
BFO_0000180: 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

deoxyribonucleic acid
type: Class
subclass of: nucleic acid
editor preferred term: 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

nucleic acid
type: Class
subclass of: macromolecule
editor preferred term: 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 term: 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: material entity
editor preferred term: 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 term: 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: cell
subclass of: processed material
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 term: 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: cell
editor preferred term: B cell
definition: A lymphocyte of B lineage that is capable of B cell mediated immunity.
definition: A lymphocyte of B lineage with the phenotype CD19-positive, CD20-positive, and capable of B cell mediated immunity.
imported from: cl.owl

human dwelling
type: Class
subclass of: material entity
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

molecular_function
type: Class
subclass of: process
subclass of: Event
OBO foundry unique label: molecular process

catalytic activity
type: Class
subclass of: molecular_function

RNA-directed DNA polymerase activity
type: Class
subclass of: process
subclass of: Event
editor preferred term: 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

kinase activity
type: Class
subclass of: transferase activity, transferring phosphorus-containing groups
subclass of: Restriction
  on property: is kinase activity
  has self: true

transferase activity
type: Class
subclass of: catalytic activity

transferase activity, transferring phosphorus-containing groups
type: Class
subclass of: transferase activity

protein-containing complex
type: Class
subclass of: material entity
subclass of: Restriction
  on property: has part
  some values from: protein
editor preferred term: 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

objective specification
type: Class
subclass of: directive information entity
editor preferred term: 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

information carrier
type: Class
subclass of: specifically dependent continuant
editor preferred term: 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 term: data item
example of usage: Data items include counts of things, analyte concentrations, and statistical summaries.
has curation status: pending final vetting
definition: 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.
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
imported from: obi.owl

information content entity
type: Class
subclass of: generically dependent continuant
subclass of: Restriction
  on property: is about
  some values from: entity
editor preferred term: 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

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 term: 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

image
type: Class
subclass of: information content entity
editor preferred term: 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
editor preferred term: data about an ontology part
definition: Data about an ontology part is a data item about a part of an ontology, for example a term
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 term: 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

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 term: 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

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

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 term: 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

document
type: Class
subclass of: information content entity
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
editor preferred term: denotator type
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 term: Viruses
imported from: ncbitaxon.owl

Teleostomi
type: Class
subclass of: Gnathostomata <vertebrates>
has db xref: GC_ID:1
has OBO namespace: ncbi_taxonomy

Euteleostomi
type: Class
subclass of: Teleostomi
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: hasExactSynonym
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: hasRelatedSynonym
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: hasRelatedSynonym
annotated target: Boreotheria
has synonym type: synonym

Bacteria
type: Class
subclass of: organism
editor preferred term: Bacteria
alternative term: eubacteria
imported from: ncbitaxon.owl

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: hasRelatedSynonym
annotated target: Homo/Pan/Gorilla group
has synonym type: synonym

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

Eukaryota
type: Class
subclass of: cellular organisms
subclass of: organism
editor preferred term: 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 db xref: PMID:30257078
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: hasExactSynonym
annotated target: eucaryotes
has synonym type: genbank common name

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

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

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

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

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

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

Euarchontoglires
type: Class
subclass of: Boreoeutheria
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: hasRelatedSynonym
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: hasExactSynonym
annotated target: ape
has synonym type: common name

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

Tetrapoda
type: Class
subclass of: Dipnotetrapodomorpha
has db xref: GC_ID:1
has exact synonym: tetrapods
has OBO namespace: ncbi_taxonomy

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

Amniota
type: Class
subclass of: Tetrapoda
has db xref: GC_ID:1
has exact synonym: amniotes
has OBO namespace: ncbi_taxonomy

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

Theria <mammals>
type: Class
subclass of: Mammalia
has db xref: GC_ID:1
has exact synonym: Theria
has OBO namespace: ncbi_taxonomy

Axiom
annotated source: Theria <mammals>
annotated property: hasExactSynonym
annotated target: Theria
has synonym type: scientific name

Opisthokonta
type: Class
subclass of: Eukaryota
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: hasRelatedSynonym
annotated target: Fungi/Metazoa group
has synonym type: synonym

Axiom
annotated source: Opisthokonta
annotated property: hasRelatedSynonym
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: hasExactSynonym
annotated target: metazoans
has synonym type: genbank common name

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

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

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

Bilateria
type: Class
subclass of: Eumetazoa
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: hasExactSynonym
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
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: hasExactSynonym
annotated target: mammals
has synonym type: genbank common name

Axiom
annotated source: Mammalia
annotated property: hasRelatedSynonym
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: hasExactSynonym
annotated target: chordates
has synonym type: genbank common name

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

Vertebrata <vertebrates>
type: Class
subclass of: Craniata <chordates>
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 <vertebrates>
annotated property: hasExactSynonym
annotated target: Vertebrata
has synonym type: scientific name

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

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

Gnathostomata <vertebrates>
type: Class
subclass of: Vertebrata <vertebrates>
has db xref: GC_ID:1
has exact synonym: Gnathostomata
has exact synonym: jawed vertebrates
has OBO namespace: ncbi_taxonomy

Axiom
annotated source: Gnathostomata <vertebrates>
annotated property: hasExactSynonym
annotated target: Gnathostomata
has synonym type: scientific name

Axiom
annotated source: Gnathostomata <vertebrates>
annotated property: hasExactSynonym
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 <chordates>
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 <chordates>
annotated property: hasExactSynonym
annotated target: Craniata
has synonym type: scientific name

Eutheria
type: Class
subclass of: Theria <mammals>
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: hasExactSynonym
annotated target: eutherian mammals
has synonym type: common name

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

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

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

Axiom
annotated source: Eutheria
annotated property: hasRelatedSynonym
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: hasExactSynonym
annotated target: primate
has synonym type: equivalent name

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

Axiom
annotated source: Primates
annotated property: hasRelatedSynonym
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: hasExactSynonym
annotated target: great apes
has synonym type: genbank common name

Axiom
annotated source: Hominidae
annotated property: hasRelatedSynonym
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: hasExactSynonym
annotated target: humans
has synonym type: common name

Homo sapiens
type: Class
subclass of: Homo
has rank: NCBITaxon species
has db xref: GC_ID:1
has exact synonym: human
has exact synonym: man
has OBO namespace: ncbi_taxonomy

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

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

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 term: planned process
example of usage: Injecting mice with a vaccine in order to test its efficacy
has curation status: ready for release
definition: A process 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

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 term: 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: characteristic of
  some values from: material entity
subclass of: Restriction
  on property: realized in
  all values from: assay
editor preferred term: 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
editor preferred term: 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
OBI_0001847: study assay
OBI_9991118: any method

culture medium
type: Class
subclass of: processed material
editor preferred term: culture medium
example of usage: A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008
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
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: processed material
subclass of: Restriction
  on property: has_specified_input
  all values from: material entity
editor preferred term: 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: characteristic of
  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 term: 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 term: 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 term: 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 term: 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)
OBI_0001847: study protocol

reverse transcriptase
type: Class
subclass of: material entity
editor preferred term: 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

assay objective
type: Class
subclass of: objective specification
editor preferred term: 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

measure function
type: Class
subclass of: function
subclass of: Restriction
  on property: function of
  some values from: processed material
editor preferred term: 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 separation objective
type: Class
equivalent class: Class
  union of: portioning objective
  union of: separation into different composition objective
subclass of: objective specification
editor preferred term: 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

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 term: 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

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: specimen
subclass of: Material Sample
subclass of: Restriction
  on property: is_specified_output_of
  some values from: collecting specimen from organism
subclass of: Restriction
  on property: has role
  some values from: material sample role
subclass of: Restriction
  on property: derives from
  some values from: material anatomical entity
editor preferred term: 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 term: 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 term: 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 term: 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

material sample role
type: Class
subclass of: specimen role
editor preferred term: 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
subclass of: specimen collection process
editor preferred term: 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 maintenance objective
type: Class
subclass of: objective specification
editor preferred term: 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: characteristic of
    some values from: deoxyribonucleic acid
subclass of: region
subclass of: Restriction
  on property: is concretized as
  some values from: Restriction
    on property: characteristic of
    some values from: deoxyribonucleic acid
editor preferred term: 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
subclass of: processed material
editor preferred term: 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

primary structure of RNA molecule
type: Class
equivalent class: Restriction
  on property: is concretized as
  some values from: Restriction
    on property: characteristic of
    some values from: ribonucleic acid
subclass of: region
subclass of: Restriction
  on property: is concretized as
  some values from: Restriction
    on property: characteristic of
    some values from: ribonucleic acid
editor preferred term: 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

sequence data
type: Class
subclass of: data item
subclass of: Restriction
  on property: has value specification
  some values from: value specification
editor preferred term: 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

nucleic acid extract
type: Class
subclass of: processed material
subclass of: specimen
subclass of: Material Sample
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 term: 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
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: 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
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: 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

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 term: 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 term: 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

value specification
type: Class
subclass of: information content entity
editor preferred term: 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

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 term: 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

lymphocyte assay
type: Class
subclass of: assay
editor preferred term: lymphocyte assay
has curation status: FossilSpecimen
definition: A cytometry assay that measures the abundance and/or characteristics of lymphocytes
term editor: James A. Overton, ORCID:0000-0001-5139-5572
definition source: OBI

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 term: 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 term: 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 term: 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 term: 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.

DNA sequencer
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: 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 term: 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

maintaining cell culture
type: Class
subclass of: planned process
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
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
editor preferred term: 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 term: '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
subclass of: assay
editor preferred term: 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: material processing
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
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: separation into different composition objective
editor preferred term: 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

collection of organisms
type: Class
equivalent class: Class
  intersection of: object aggregate
  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
subclass of: Restriction
  on property: has member
  all 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.

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: ecologically related to
  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: https://orcid.org/0000-0002-2999-0103
definition source: WEB: http://en.wikipedia.org/wiki/Household

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.

pair of interacting organisms
type: Class
equivalent class: Class
  intersection of: collection of organisms
  intersection of: Restriction
    on property: has member
    qualified cardinality: 2
    on class: organism or virus or viroid
subclass of: collection of organisms
definition: A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other.

protein
type: Class
subclass of: macromolecule
editor preferred term: 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, and any derivatives thereof.
imported from: pr.owl

region
type: Class
subclass of: generically dependent continuant
editor preferred term: 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 term: material anatomical entity
definition: Anatomical entity that has mass.
imported from: uberon.owl

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

obsolete zooarcheological specimen
type: Class
subclass of: Obsolete Class
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
has obsolescence reason: incorrect identifier format, replaced
comment: This class was deprecated because the ID format is wrong. It is replaced by http://purl.obolibrary.org/obo/BCO_0000080
deprecated: true

obsolete archeobotanical specimen
type: Class
subclass of: Obsolete Class
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
has obsolescence reason: incorrect identifier format, replaced
comment: This class was deprecated because the ID format is wrong. It is replaced by http://purl.obolibrary.org/obo/BCO_0000081.
deprecated: true

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.

Dataset
type: Class
type: NamedIndividual
deprecated: True
comment: The category of information pertaining to a logical set of records.

Event
type: Class
subclass of: process
type: NamedIndividual
BCO preferred label: event
example of usage: A specimen collection process. A camera trap image capture. A marine trawl.
comment: An action that occurs at some location during some time.

Event Attribute
type: Class
type: NamedIndividual
deprecated: True
comment: Container class for information about attributes related to a given sampling event.

Event Measurement
type: Class
type: NamedIndividual
comment: The category of information pertaining to measurements associated with an event.
deprecated: True

Fossil Specimen
type: Class
subclass of: Preserved Specimen
type: NamedIndividual
comment: A preserved specimen that is a fossil.
BCO preferred label: fossil specimen
example of usage: A body fossil. A coprolite. A gastrolith. An ichnofossil. A piece of a petrified tree.

Geological Context
type: Class
type: NamedIndividual
comment: Geological information, such as stratigraphy, that qualifies a region or place.
BCO preferred label: geological context
example of usage: A lithostratigraphic layer.
has curation status: uncurated

Human Observation
type: Class
subclass of: data item
type: NamedIndividual
comment: An output of a human observation process.
BCO preferred label: human observation
example of usage: Evidence of an Occurrence taken from field notes or literature. A record of an Occurrence without physical evidence nor evidence captured with a machine.

Identification
type: Class
subclass of: taxonomic identification process
type: NamedIndividual
BCO preferred label: identification
has curation status: pending final vetting
comment: A taxonomic determination (e.g., the assignment to a taxon).
example of usage: A subspecies determination of an organism.

Living Specimen
type: Class
subclass of: specimen
subclass of: Material Sample
type: NamedIndividual
BCO preferred label: living specimen
example of usage: A living plant in a botanical garden. A living animal in a zoo.
comment: A specimen that is alive.

Machine Observation
type: Class
subclass of: data item
type: NamedIndividual
example of usage: A photograph. A video. An audio recording. A remote sensing image. A Occurrence record based on telemetry.
BCO preferred label: machine observation
comment: An output of a machine observation process.

Material Citation
type: Class
type: NamedIndividual
comment: A reference to or citation of one, a part of, or multiple specimens in scholarly publications.
example of usage: A citation of a physical specimen from a scientific collection in a taxonomic treatment in a scientific publication. A citation of a group of physical specimens, such as paratypes in a taxonomic treatment in a scientific publication. An occurrence mentioned in a field note book.
description: This class constitutes a new value for the controlled vocabulary in the recommendations for basisOfRecord. When importing Darwin Core Archives of literature-based datasets to GBIF, the basisOfRecord should be changed from “Occurrence”, "PreservedSpecimen" or "Literature" to “MaterialCitation”.

Material Sample
type: Class
subclass of: specimen
type: NamedIndividual
BCO preferred label: specimen
comment: A physical result of a sampling (or subsampling) event. In biological collections, the material sample is typically collected, and either preserved or destructively processed.
example of usage: A whole organism preserved in a collection. A part of an organism isolated for some purpose. A soil sample. A marine microbial sample.

Measurement or Fact
type: Class
subclass of: Obsolete Class
type: NamedIndividual
example of usage: The weight of an organism in grams. The number of placental scars. Surface water temperature in Celsius.
deprecated: true
has obsolescence reason: This term was not deprecated from the dwc terms vocabulary, merely from the dwcterms ontology, because it is not needed here.
comment: A measurement of or fact about an rdfs:Resource (http://www.w3.org/2000/01/rdf-schema#Resource).
description: Resources can be thought of as identifiable records or instances of classes and may include, but need not be limited to dwc:Occurrence, dwc:Organism, dwc:MaterialSample, dwc:Event, dwc:Location, dwc:GeologicalContext, dwc:Identification, or dwc:Taxon.

Occurrence
type: Class
type: NamedIndividual
example of usage: A wolf pack on the shore of Kluane Lake in 1988. A virus in a plant leaf in the New York Botanical Garden at 15:29 on 2014-10-23. A fungus in Central Park in the summer of 1929.
comment: An existence of an Organism (sensu http://rs.tdwg.org/dwc/terms/Organism) at a particular place at a particular time.
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.
BCO preferred label: occurrence

Occurrence Measurement
type: Class
type: NamedIndividual
comment: The category of information pertaining to measurements accociated with an occurrence.
deprecated: True

Organism
type: Class
subclass of: organismal entity
type: NamedIndividual
BCO preferred label: organism
description: Instances of the dwc:Organism class are intended to facilitate linking one or more dwc:Identification instances to one or more dwc: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.
comment: A particular organism or defined group of organisms considered to be taxonomically homogeneous.
example of usage: A specific bird. A specific wolf pack. A specific instance of a bacterial culture.

Preserved Specimen
type: Class
subclass of: specimen
subclass of: Material Sample
type: NamedIndividual
example of usage: A plant on an herbarium sheet. A cataloged lot of fish in a jar.
comment: A specimen that has been preserved.
BCO preferred label: preserved specimen

Resource Relationship
type: Class
subclass of: Obsolete Class
type: NamedIndividual
description: Resources can be thought of as identifiable records or instances of classes and may include, but need not be limited to dwc:Occurrence, dwc:Organism, dwc:MaterialSample, dwc:Event, dwc:Location, dwc:GeologicalContext, dwc:Identification, or dwc:Taxon.
comment: A relationship of one rdfs:Resource (http://www.w3.org/2000/01/rdf-schema#Resource) to another.
deprecated: true
example of usage: An instance of an Organism is the mother of another instance of an Organism. A uniquely identified Occurrence represents the same Occurrence as another uniquely identified Occurrence. A MaterialSample is a subsample of another MaterialSample.
has obsolescence reason: This term was not deprecated from the dwc terms vocabulary, merely from the dwcterms ontology, because it is not needed here.

Sample
type: Class
type: NamedIndividual
deprecated: True
comment: Container class for information about the results of a sampling event (specimen, observation, etc.)

Sample Attribute
type: Class
type: NamedIndividual
deprecated: True
comment: Container class for information about attributes related to a given sample.

Sampling Event
type: Class
type: NamedIndividual
deprecated: True
comment: Container class for information about the conditions and methods of acquisition of samples.

Sampling Location
type: Class
type: NamedIndividual
comment: Container class for information about the location where a sampling event occurred.
deprecated: True

Taxon
type: Class
subclass of: collection of organisms
type: NamedIndividual
example of usage: The genus Truncorotaloides as published by Brönnimann et al. in 1953 in the Journal of Paleontology Vol. 27(6) p. 817-820.
comment: A group of organisms (sensu http://purl.obolibrary.org/obo/OBI_0100026) considered by taxonomists to form a homogeneous unit.
BCO preferred label: taxon

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

incorrect identifier format, replaced
type: NamedIndividual
type: curation status specification
comment: false

example to be eventually removed
type: NamedIndividual
type: curation status specification
editor preferred term: example to be eventually removed

failed exploratory term
type: Thing
type: NamedIndividual
type: obsolescence reason specification
editor preferred term: failed exploratory term
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: Thing
type: NamedIndividual
type: curation status specification
editor preferred term: metadata complete
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: Thing
type: NamedIndividual
type: curation status specification
editor preferred term: organizational term
definition: Term created to ease viewing/sort terms for development purpose, and will not be included in a release
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: Thing
type: NamedIndividual
type: curation status specification
editor preferred term: ready for release
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: Thing
type: NamedIndividual
type: curation status specification
editor preferred term: metadata incomplete
definition: Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.

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

pending final vetting
type: Thing
type: NamedIndividual
type: curation status specification
editor preferred term: pending final vetting
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: Thing
type: NamedIndividual
type: obsolescence reason specification
editor preferred term: placeholder removed

terms merged
type: NamedIndividual
type: obsolescence reason specification
editor preferred term: terms merged
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 preferred term: term imported
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 preferred term: term split
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.

universal
type: NamedIndividual
type: denotator type
editor preferred term: universal
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
editor preferred term: defined class
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
editor preferred term: named class expression
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
editor preferred term: to be replaced with external ontology term
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
editor preferred term: requires discussion
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

obsolete_the supplier role of Affymetrix
type: Thing
type: NamedIndividual
editor preferred term: obsolete_the supplier role of Affymetrix
has curation status: metadata incomplete
has obsolescence reason: failed exploratory term
deprecated: true

obsolete_the manufacturer role of Agilent
type: Thing
type: NamedIndividual
editor preferred term: obsolete_the manufacturer role of Agilent
has curation status: metadata incomplete
has obsolescence reason: failed exploratory term
deprecated: true

obsolete_manufacturer role of Bruker Daltonics
type: Thing
type: NamedIndividual
editor preferred term: obsolete_manufacturer role of Bruker Daltonics
has curation status: metadata incomplete
has obsolescence reason: failed exploratory term
deprecated: true

obsolete_the manufacturer role of Thermo
type: Thing
type: NamedIndividual
editor preferred term: obsolete_the manufacturer role of Thermo
has curation status: metadata incomplete
has obsolescence reason: failed exploratory term
deprecated: true

obsolete_the manufacturer role of Li-Cor
type: Thing
type: NamedIndividual
editor preferred term: obsolete_the manufacturer role of Li-Cor
has curation status: metadata incomplete
has obsolescence reason: failed exploratory term
deprecated: true

obsolete_the manufacturer role of Roche
type: Thing
type: NamedIndividual
editor preferred term: obsolete_the manufacturer role of Roche
has curation status: metadata incomplete
has obsolescence reason: failed exploratory term
deprecated: true

obsolete_the manufacturer role of Ambion
type: Thing
type: NamedIndividual
editor preferred term: obsolete_the manufacturer role of Ambion
has curation status: metadata incomplete
has obsolescence reason: failed exploratory term
deprecated: true

obsolete_the manufacturer role of BIO-RAD
type: Thing
type: NamedIndividual
editor preferred term: obsolete_the manufacturer role of BIO-RAD
has curation status: metadata incomplete
has obsolescence reason: failed exploratory term
deprecated: true

obsolete_the regulator role of the FDA
type: Thing
type: NamedIndividual
editor preferred term: obsolete_the regulator role of the FDA
has curation status: metadata incomplete
has obsolescence reason: failed exploratory term
deprecated: true

obsolete_the manufacturer role of Illumina
type: Thing
type: NamedIndividual
editor preferred term: obsolete_the manufacturer role of Illumina
has curation status: metadata incomplete
has obsolescence reason: failed exploratory term
deprecated: true

obsolete_the manufacturer role of Helicos
type: Thing
type: NamedIndividual
editor preferred term: obsolete_the manufacturer role of Helicos
has curation status: metadata incomplete
has obsolescence reason: failed exploratory term
deprecated: true

obsolete_manufacturer role of Bruker Corporation
type: Thing
type: NamedIndividual
editor preferred term: obsolete_manufacturer role of Bruker Corporation
has curation status: metadata incomplete
has obsolescence reason: failed exploratory term
deprecated: true

obsolete_the manufacturer role of Waters
type: Thing
type: NamedIndividual
editor preferred term: obsolete_the manufacturer role of Waters
has curation status: metadata incomplete
has obsolescence reason: failed exploratory term
deprecated: true

obsolete_manufacturer role of applied biosystems
type: Thing
type: NamedIndividual
editor preferred term: obsolete_manufacturer role of applied biosystems
has curation status: metadata incomplete
has obsolescence reason: failed exploratory term
deprecated: true

Thermo Fisher Scientific
type: NamedIndividual
type: organization
editor preferred term: 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

obsolete incorrect identifier format, do not use
type: NamedIndividual
has obsolescence reason: incorrect identifier format, replaced
deprecated: true

Darwin Core Type
type: NamedIndividual
type: VocabularyEncodingScheme
comment: The set of classes specified by the Darwin Core Type Vocabulary, used to categorize the nature or genre of the resource.
deprecated: True

Event
deprecated: false
has curation status: requires discussion

dwc_terms status

infer input from direct reg
is rule enabled: true
comment: MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z
type: Imp
body: IndividualPropertyAtom
  property predicate: enables
  argument1: http://purl.obolibrary.org/obo/ro.owl#z
  argument2: http://purl.obolibrary.org/obo/ro.owl#y
body: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: http://purl.obolibrary.org/obo/ro.owl#x
  argument2: http://purl.obolibrary.org/obo/ro.owl#y
body: ClassAtom
  class predicate: molecular_function
  argument1: http://purl.obolibrary.org/obo/ro.owl#x
body: ClassAtom
  class predicate: molecular_function
  argument1: http://purl.obolibrary.org/obo/ro.owl#y
head: IndividualPropertyAtom
  property predicate: has input
  argument1: http://purl.obolibrary.org/obo/ro.owl#x
  argument2: http://purl.obolibrary.org/obo/ro.owl#z

'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
type: Imp
body: IndividualPropertyAtom
  property predicate: overlaps
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: causally downstream of
  argument1: x
  argument2: y
head: ClassAtom
  class predicate: Nothing
  argument1: y
head: ClassAtom
  class predicate: Nothing
  argument1: x

'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
type: Imp
body: IndividualPropertyAtom
  property predicate: overlaps
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: causally upstream of
  argument1: x
  argument2: y
head: ClassAtom
  class predicate: Nothing
  argument1: y
head: ClassAtom
  class predicate: Nothing
  argument1: x