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

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

DUO_preferred_label
type: AnnotationProperty

editor preferred term
type: AnnotationProperty
editor preferred term: editor preferred term
has curation status: IAO_0000122
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 of usage
has curation status: IAO_0000122
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
type: AnnotationProperty
editor preferred term: definition
has curation status: IAO_0000122
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>

editor note
type: AnnotationProperty
editor preferred term: editor note
has curation status: IAO_0000122
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.obofoundry.org/obo/obi>

term editor
type: AnnotationProperty
editor preferred term: term editor
has curation status: IAO_0000122
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: IAO_0000125
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: IAO_0000122
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: IAO_0000122
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: IAO_0000125
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
editor preferred term: ontology term requester
has curation status: IAO_0000125
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: IAO_0000125
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: IAO_0000125
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
editor preferred term: has ID digit count
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
editor preferred term: has ID range allocated
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
editor preferred term: has ID policy for
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
editor preferred term: has ID prefix
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: 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
comment: Add as annotation triples in the granting ontology

retired from use as of
type: AnnotationProperty
editor preferred term: retired from use as of
definition: relates a class of CRID to the date after which further instances should not be made, according to the central authority
editor note: In OWL 2 add AnnotationPropertyRange xsd:dateTimeStamp
term editor: Alan Ruttenberg

has ontology root term
type: AnnotationProperty
editor preferred term: has ontology root term
definition: Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root.
term editor: Nicolas Matentzoglu

may be identical to
type: AnnotationProperty
editor preferred term: may be identical to
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
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
editor preferred term: scheduled for obsoletion on or after
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: IAO_0000125
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
comment: Add as annotation triples in the granting ontology

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

data use permission
type: Class
definition: A data item that is used to indicate consent permissions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used.
alternative term: consent code
id: DUO:0000001

no restriction
type: Class
subclass of: data use permission
definition: This data use permission indicates there is no restriction on use.
id: DUO:0000004
shorthand: NRES
comment: 20180907, Meeting Moran Melanie: This is to be thought about more carefully - what is the intent when using 'no restriction' as usually users still need to be researchers.
comment: Note: the NRES alternative term may be confusing as in the UK it also stands for National Research Ethics Service

population origins or ancestry research prohibited
type: Class
subclass of: data use modifier
definition: This data use modifier indicates use for purposes of population, origin, or ancestry research is prohibited.
id: DUO:0000044
shorthand: NPOA

health or medical or biomedical research
type: Class
subclass of: general research use
definition: This data use permission indicates that use is allowed for health/medical/biomedical purposes; does not include the study of population origins or ancestry.
id: DUO:0000006
shorthand: HMB

disease specific research
type: Class
subclass of: health or medical or biomedical research
definition: This data use permission indicates that use is allowed provided it is related to the specified disease.
id: DUO:0000007
shorthand: DS
comment: This term should be coupled with a term describing a disease from an ontology to specify the disease the restriction applies to. DUO recommends MONDO be used, to provide the basis for automated evaluation. For more information see https://github.com/EBISPOT/DUO/blob/master/MONDO_Overview.md Other resources, such as the Disease Ontology, HPO, SNOMED-CT or others, can also be used. When those other resources are being used, this may require an extra mapping step to leverage automated matching algorithms.

population origins or ancestry research only
type: Class
subclass of: data use permission
definition: This data use permission indicates that use of the data is limited to the study of population origins or ancestry.
alternative term: population origins/ancestry research
id: DUO:0000011
shorthand: POA

research specific restrictions
type: Class
subclass of: data use modifier
definition: This data use modifier indicates that use is limited to studies of a certain research type.
id: DUO:0000012
shorthand: RS

no general methods research
type: Class
subclass of: data use modifier
definition: This data use modifier indicates that use does not allow methods development research (e.g., development of software or algorithms).
id: DUO:0000015
shorthand: NMDS

genetic studies only
type: Class
subclass of: data use modifier
definition: This data use modifier indicates that use is limited to genetic studies only (i.e., studies that include genotype research alone or both genotype and phenotype research, but not phenotype research exclusively)
id: DUO:0000016
shorthand: GSO

data use modifier
type: Class
definition: Data use modifiers indicate additional conditions for use.
id: DUO:0000017

not for profit, non commercial use only
type: Class
subclass of: data use modifier
definition: This data use modifier indicates that use of the data is limited to not-for-profit organizations and not-for-profit use, non-commercial use.
id: DUO:0000018
shorthand: NPUNCU

publication required
type: Class
subclass of: data use modifier
definition: This data use modifier indicates that requestor agrees to make results of studies using the data available to the larger scientific community.
id: DUO:0000019
shorthand: PUB

collaboration required
type: Class
subclass of: data use modifier
definition: This data use modifier indicates that the requestor must agree to collaboration with the primary study investigator(s).
id: DUO:0000020
shorthand: COL
comment: This could be coupled with a string describing the primary study investigator(s).

ethics approval required
type: Class
subclass of: data use modifier
definition: This data use modifier indicates that the requestor must provide documentation of local IRB/ERB approval.
id: DUO:0000021
shorthand: IRB

geographical restriction
type: Class
subclass of: data use modifier
definition: This data use modifier indicates that use is limited to within a specific geographic region.
id: DUO:0000022
shorthand: GS
comment: This should be coupled with an ontology term describing the geographical location the restriction applies to.

publication moratorium
type: Class
subclass of: data use modifier
definition: This data use modifier indicates that requestor agrees not to publish results of studies until a specific date.
alternative term: publication embargo
id: DUO:0000024
shorthand: MOR
comment: This should be coupled with a date specified as ISO8601

time limit on use
type: Class
subclass of: data use modifier
definition: This data use modifier indicates that use is approved for a specific number of months.
id: DUO:0000025
shorthand: TS
comment: This should be coupled with an integer value indicating the number of months.

user specific restriction
type: Class
subclass of: data use modifier
definition: This data use modifier indicates that use is limited to use by approved users.
id: DUO:0000026
shorthand: US

project specific restriction
type: Class
subclass of: data use modifier
definition: This data use modifier indicates that use is limited to use within an approved project.
id: DUO:0000027
shorthand: PS

institution specific restriction
type: Class
subclass of: data use modifier
definition: This data use modifier indicates that use is limited to use within an approved institution.
id: DUO:0000028
shorthand: IS

return to database or resource
type: Class
subclass of: data use modifier
definition: This data use modifier indicates that the requestor must return derived/enriched data to the database/resource.
id: DUO:0000029
shorthand: RTN

method development
type: Class
subclass of: investigation
DUO_preferred_label: method development
definition: An investigation concerning development of methods, algorithms, software or analytical tools.
curator note: This definition is a placeholder as a result of meetings at ICBO2018.
id: DUO:0000031

population research
type: Class
subclass of: investigation
DUO_preferred_label: population research
definition: An investigation concerning a specific population group.
curator note: This definition is a placeholder as a result of meetings at ICBO2018.
id: DUO:0000032
comment: Should be paired with the an ontology term representing this population (e.g., xxx).

ancestry research
type: Class
subclass of: investigation
DUO_preferred_label: ancestry research
definition: An investigation concerning ancestry or population origins.
curator note: This definition is a placeholder as a result of meetings at ICBO2018.
id: DUO:0000033

age category research
type: Class
subclass of: investigation
DUO_preferred_label: age category research
definition: An investigation concerning specific age categories.
curator note: This definition is a placeholder as a result of meetings at ICBO2018.
id: DUO:0000034
comment: Should be paired with the an ontology term representing this population (e.g., xxx).

gender category research
type: Class
subclass of: investigation
DUO_preferred_label: gender category research
definition: An investigation concerning specific gender categories.
curator note: This definition is a placeholder as a result of meetings at ICBO2018.
id: DUO:0000035
comment: Should be paired with the an ontology term representing this population (e.g., xxx).

research control
type: Class
subclass of: investigation
DUO_preferred_label: research control
definition: An investigation concerning use of data as reference or control material.
curator note: This definition is a placeholder as a result of meetings at ICBO2018.
id: DUO:0000036

biomedical research
type: Class
subclass of: investigation
DUO_preferred_label: biomedical research
definition: An investigation concerning health, medical, or biomedical research.
curator note: This definition is a placeholder as a result of meetings at ICBO2018.
id: DUO:0000037

genetic research
type: Class
subclass of: biomedical research
DUO_preferred_label: genetic research
definition: Biomedical research concerning genetics (i.e., the study of genes, genetic variations and heredity).
curator note: This definition is a placeholder as a result of meetings at ICBO2018.
id: DUO:0000038

drug development research
type: Class
subclass of: biomedical research
DUO_preferred_label: drug development research
definition: Biomedical research concerning drug development.
curator note: This definition is a placeholder as a result of meetings at ICBO2018.
id: DUO:0000039

disease category research
type: Class
subclass of: biomedical research
DUO_preferred_label: disease category research
definition: Biomedical research research concerning specific disease/s
curator note: This definition is a placeholder as a result of meetings at ICBO2018.
id: DUO:0000040

general research use
type: Class
subclass of: data use permission
definition: This data use permission indicates that use is allowed for general research use for any research purpose.
id: DUO:0000042
shorthand: GRU
comment: This includes but is not limited to: health/medical/biomedical purposes, fundamental biology research, the study of population origins or ancestry, statistical methods and algorithms development, and social-sciences research.

clinical care use
type: Class
subclass of: data use modifier
definition: This data use modifier indicates that use is allowed for clinical use and care.
id: DUO:0000043
shorthand: CC
comment: Clinical Care is defined as Health care or services provided at home, in a healthcare facility or hospital. Data may be used for clinical decision making.

not for profit organisation use only
type: Class
subclass of: not for profit, non commercial use only
definition: This data use modifier indicates that use of the data is limited to not-for-profit organizations.
id: DUO:0000045
shorthand: NPU

non-commercial use only
type: Class
subclass of: not for profit, non commercial use only
definition: This data use modifier indicates that use of the data is limited to not-for-profit use.
id: DUO:0000046
shorthand: NCU
comment: This indicates that data can be used by commercial organisations for research purposes, but not commercial purposes.

investigation
type: Class
editor preferred term: investigation
definition: a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
imported from: obi.owl