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

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

editor preferred label
type: AnnotationProperty
editor preferred label: editor preferred label
editor preferred label: editor preferred term
editor preferred label: editor preferred term~editor preferred label
has curation status: IAO_0000122
definition: The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
label: editor preferred term
label: editor preferred term~editor preferred label

example of usage
type: AnnotationProperty
editor preferred label: example
editor preferred label: example of usage
has curation status: IAO_0000122
definition: A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not
definition: 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.
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
database_cross_reference: IAO:0000112
has_obo_namespace: uberon
id: example_of_usage
is metadata tag: true
shorthand: example_of_usage

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

definition
type: AnnotationProperty
editor preferred label: definition
editor preferred label: textual definition
has curation status: IAO_0000122
definition: English language definitions of what NCI means by the concept. These are limited to 1024 characters. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software.
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.
definition: The official definition.
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.
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
has exact synonym: DEFINITION
label: textual definition

Axiom
annotated source: definition
annotated property: definition
annotated target: The official definition.
database_cross_reference: url:http://purl.obolibrary.org/obo/iao.owl

editor note
type: AnnotationProperty
editor preferred label: 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.
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
definition source: GROUP:OBI:<http://purl.obofoundry.org/obo/obi>
database_cross_reference: IAO:0000116
has_obo_namespace: uberon
id: editor_note
is metadata tag: true
is metadata tag: 1
shorthand: editor_note

definition editor
type: AnnotationProperty
editor preferred label: definition editor
editor preferred label: term editor
has curation status: IAO_0000122
definition: Name of editor entering the definition in the file. The definition editor is a point of contact for information regarding the term. The definition editor may be, but is not always, the author of the definition, which may have been worked upon by several people
definition: 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 http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
editor note: 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
label: term editor

alternative term
type: AnnotationProperty
editor preferred label: alternative label
editor preferred label: alternative term
has curation status: IAO_0000125
definition: A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like.
definition: An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
definition editor: OBO Operations committee
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
comment: Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).
label: alternative label

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

curator note
type: AnnotationProperty
editor preferred label: curator note
has curation status: IAO_0000122
definition: An administrative note of use for a curator but of no use for a user
definition editor: PERSON:Alan Ruttenberg
database_cross_reference: IAO:0000232
has_obo_namespace: uberon
id: curator_notes
is metadata tag: 1
shorthand: curator_notes
label: curator notes

term tracker item
type: AnnotationProperty
editor preferred label: term tracker item
example of usage: the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
has curation status: IAO_0000125
definition: An IRI or similar locator for a request or discussion of an ontology term.
definition editor: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
definition source: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
database_cross_reference: IAO:0000233
has_obo_namespace: uberon
id: term_tracker_item
is metadata tag: true
shorthand: term_tracker_item
comment: The 'tracker item' can associate a tracker with a specific ontology term.

imported from
type: AnnotationProperty
editor preferred label: imported from
has curation status: IAO_0000125
definition: For external terms/classes, the ontology from which the term was imported
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Melanie Courtot
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

OBO foundry unique label
type: AnnotationProperty
editor preferred label: 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 .
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Bjoern Peters
definition editor: PERSON:Chris Mungall
definition editor: PERSON:Melanie Courtot
definition source: GROUP:OBO Foundry <http://obofoundry.org/>

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

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

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

SEPIO_editor_note
type: AnnotationProperty
comment: Used to capture development notes and design decisions or questions. All annotations using this property should be removed before publishing / releasing the ontology to the public (but ideally retained in some place as valuable documentation).

branch class
type: AnnotationProperty
comment: For use in the EMBL-EBI ArrayExpress interface.

created_by
type: AnnotationProperty

has_alternative_id
type: AnnotationProperty

has_broad_synonym
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty
label: has database cross reference

has exact synonym
type: AnnotationProperty
definition: An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.
definition: An alternative label for a given entity such as a commonly used abbreviation or synonym.
definition: Fully qualified synonym, contains the string, term type, source, and an optional source code if appropriate. Each subfield is deliniated to facilitate interpretation by software.
definition: Synonym of the term.
definition editor: http://orcid.org/0000-0001-5208-3432
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/20
has exact synonym: FULL_SYN
has exact synonym: Synonym with Source Data
label: has_exact_synonym

Axiom
annotated source: has exact synonym
annotated property: definition
annotated target: Synonym of the term.
comment: url:http://www.geneontology.org/formats/oboInOwl#hasExactSynonym

has_narrow_synonym
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty
comment: disease_ontology

has_related_synonym
type: AnnotationProperty

id
type: AnnotationProperty
definition: An identifier for an individual entity.

Axiom
annotated source: id
annotated property: definition
annotated target: An identifier for an individual entity.
database_cross_reference: url:http://purl.obolibrary.org/obo/IAO_0020000

in_subset
type: AnnotationProperty

shorthand
type: AnnotationProperty

comment
type: AnnotationProperty

isDefinedBy
type: AnnotationProperty
OBO foundry unique label: is defined by

Axiom
annotated source: isDefinedBy
annotated property: OBO foundry unique label
annotated target: is defined by
comment: This is an experimental annotation

label
type: AnnotationProperty
editor preferred label: label
definition: A human readable name for this class.
comment: A human-readable name for the subject.

Axiom
annotated source: label
annotated property: definition
annotated target: A human readable name for this class.
database_cross_reference: url:http://www.w3.org/2000/01/rdf-schema#label

alternate name
type: AnnotationProperty

derived from
type: AnnotationProperty
python name: derived_from

precedes
type: ObjectProperty
sub property of: temporally related to
editor preferred label: 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

temporally related to
type: ObjectProperty
sub property of: topObjectProperty
has curation status: IAO_0000125
definition editor: https://orcid.org/0000-0002-6601-2165
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.

adult
type: Class
subclass of: human being
subclass of: person
has curation status: External
definition: A person who has reached maturity.
comment: For use in research contexts the minimum age needs to be specified.

identity
type: Class
subclass of: cognitive representation
definition: A cognitive representation of themselves by a person or a group about themselves.
comment: This entity is more than self-identity of an individual as it includes group identity.

self-identity
type: Class
subclass of: identity
definition: An identity that a person has about themselves.
curator note: The term 'self' sounds tautologous but is required to reflect the fact that this is not identity in terms of who you are but how you represent yourself to yourself.
comment: The cognitive representation includes multiple aspects and some of these are social. For example, group memberships, cultural norms. Collective identity as a shared attribute of group is related to this but is separate.

teenager
type: Class
subclass of: human being
subclass of: person
has curation status: External
definition: A person between 13 and 19 years of age.
definition: A person who is between the ages of 13 and 19.

cross over design
type: Class
subclass of: mixed study design
has curation status: External
definition: A mixed study design in which two or more groups experience the same study processes but in a different order.

case-control study design
type: Class
subclass of: non-interventional study design
has curation status: External
definition: A non-interventional study design in which study participants who have been identified as having (case) or not having (control) some characteristic of interest are compared on other characteristics to establish whether these are associated with being a case or control.

non-interventional study design
type: Class
subclass of: study design
has curation status: External
definition: A study design in which study participants are not planned to experience an intervention as a part of the study process.

repeated measure design
type: Class
subclass of: study design
has curation status: External
definition: A study design in which measurements taken on the same study participants at two or more different times in different circumstances are compared.

randomised controlled trial design
type: Class
subclass of: interventional study design
has curation status: External
definition: An interventional study design in which participants are randomly allocated to receive one of two or more interventions or no intervention using a study randomisation process.
alternative term: RCT, randomised controlled trial

mixed study design
type: Class
subclass of: study design
has curation status: External
definition: A study design in which measurements taken on two or more groups of study participants at two or more times are compared allowing differences to be assessed between groups and over time.

interventional study design
type: Class
subclass of: study design
has curation status: External
definition: A study design that includes specification of some intervention as part of the study process.
alternative term: controlled trial, study with at least one comparator group

sequential multiple randomised controlled trial design
type: Class
subclass of: randomised controlled trial design
has curation status: External
definition: A randomised controlled trial design in which participants are randomised to study on more than one occasion during the study.

cluster randomised controlled trial design
type: Class
subclass of: randomised controlled trial design
has curation status: External
definition: A randomised controlled trial design in which pre-existing groups of participants are randomly allocated to intervention arms
alternative term: cRCT, CRT, cluster-randomised controlled intervention trial, cluster-randomised controlled trial

quasi-randomised controlled trial design
type: Class
subclass of: interventional study design
has curation status: External
definition: An interventional study design in which participants are allocated to receive one or two or more interventions or no intervention using a quasi-random process.
alternative term: qRCT, quasi-randomised controlled trial

single-arm intervention design
type: Class
subclass of: interventional study design
has curation status: External
definition: An interventional study design in which all the participants receive the same type of intervention.
alternative term: intervention without comparator group

n-of-1 study design
type: Class
subclass of: repeated measures study design
has curation status: External
definition: A repeated measures study design involving multiple repeated measurements taken in each of two or more conditions facilitating inferential statistical analyses to be undertaken to output statistical parameters from data sets for each individual participant.

wash-out period
type: Class
subclass of: one-dimensional temporal region
has curation status: External
definition: A temporal interval between the end of one intervention and the beginning of another in a cross-over research study

In remission
type: Class
subclass of: health status
has curation status: External
definition: A health status in which the person presents fewer or lower intensity of symptoms compared to their previous symptom presentation, and the current symptoms minimally interfere with their life.

relapsed
type: Class
subclass of: health status
has curation status: External
definition: A health status in which the symptoms of a person suffering from a disorder have reverted from a desired level to an undesired level.

associative learning
type: Class
subclass of: learning
has curation status: Published
definition: Learning that involves changing the strength of association between two or more mental processes.
comment: While associative learning is often defined as learning an association between a stimulus and response, the stimulus has to be perceived. Therefore, associative learning is between perceiving or processing information about a stimulus (a mental process) and one or more other mental processes. The label 'associative learning' is also used for a behaviour change technique (BCT) in the BCT Taxonomy v1 (Michie et al., 2013). The definition for this BCT reads as follows: 'Present a neutral stimulus jointly with a stimulus that already elicits the behavior repeatedly until the neutral stimulus elicits that behavior.' As indicated by the definition, the BCT is the deliberate presentation of a stimulus, whereas the MoA is a learning process that occurs in the brain.

BCI schedule of delivery
type: Class
subclass of: BCI attribute
has curation status: External
definition: A BCI attribute that is its temporal organisation.

number of contact events
type: Class
subclass of: data item
has curation status: External
definition: A data item that is the number of contact events in an intervention temporal part.

regular intervention schedule
type: Class
subclass of: BCI schedule of delivery
has curation status: External
definition: A BCI schedule of delivery in which the frequency and duration of BCI temporal parts are uniform across the course of a BCI or BCI part.

irregular intervention schedule
type: Class
subclass of: BCI schedule of delivery
has curation status: External
definition: A BCI schedule of delivery in which the frequency and duration of contact events differ over the course of a temporal part or BCI.

behaviour change intervention source
type: Class
subclass of: role
example of usage: This includes individual people, groups of people, and organisations.
has curation status: Published
definition: A role played by a person, population or organisation that provides a BCI.
alternative term: BCI source

person source role
type: Class
subclass of: behaviour change intervention source
has curation status: External
definition: A behaviour change intervention source role that inheres in a person.

behaviour change intervention mode of delivery
type: Class
subclass of: process attribute
subclass of: BCI attribute
has curation status: External
has curation status: Published
definition: An attribute of a BCI delivery that is the physical or informational medium through which a BCI is provided.
alternative term: BCI mode of delivery
alternative term: MOD

somatic mode of delivery
type: Class
subclass of: behaviour change intervention mode of delivery
has curation status: External
has curation status: Published
definition: Mode of delivery that involves devices or substances that alter bodily processes or structure.
curator note: Is intended to be disjoint from informational mode of delivery.

ingestion mode of delivery
type: Class
subclass of: somatic mode of delivery
has curation status: External
has curation status: Published
definition: Somatic mode of delivery that involves ingestion of a chemical into the body.

transdermal mode of delivery
type: Class
subclass of: ingestion mode of delivery
has curation status: External
has curation status: Published
definition: Ingestion mode of delivery that involves ingestion of a chemical through the skin.

alimentary mode of delivery
type: Class
subclass of: ingestion mode of delivery
has curation status: External
has curation status: Published
definition: Somatic mode of delivery that involves ingestion of a chemical through the stomach or intestine.

buccal mode of delivery
type: Class
subclass of: ingestion mode of delivery
has curation status: External
has curation status: Published
definition: Ingestion mode of delivery that involves absorption of a chemical through the lining of the buccal cavity.

inhalation mode of delivery
type: Class
subclass of: ingestion mode of delivery
has curation status: External
has curation status: Published
definition: Ingestion mode of delivery that involves absorption of a chemical through the upper airways or lungs by inspiration.

injection mode of delivery
type: Class
subclass of: ingestion mode of delivery
has curation status: External
has curation status: Published
definition: Ingestion mode of delivery that involves a chemical being introduced into body tissue through a hollow needle that punctures the skin.

wearable ingestion mode of delivery
type: Class
subclass of: ingestion mode of delivery
has curation status: External
has curation status: Published
definition: Ingestion mode of delivery that involves a device that is worn on the body.
comment: Includes insulin pump.

behaviour change intervention setting
type: Class
subclass of: object aggregate
example of usage: Includes as parts social setting and physical setting.
has curation status: Published
definition: An aggregate of entities that form the environment in which a BCI is provided.
alternative term: BCI setting

human age
type: Class
subclass of: personal attribute
has curation status: External
definition: A personal attribute that is a time quality inhering in a person by virtue of how long the person has existed.

health status
type: Class
subclass of: personal attribute
has curation status: External
definition: A personal attribute that is the state of an individual's mental or physical condition.

biological sex
type: Class
subclass of: bodily quality
has curation status: External
definition: A bodily quality based on reproductive function or organs.

female biological sex
type: Class
subclass of: biological sex
has curation status: External
definition: A biological sex associated with the ability to produce female gametes.

male biological sex
type: Class
subclass of: biological sex
has curation status: External
definition: A biological sex associated with the ability to produce male gametes.

mean human age
type: Class
subclass of: aggregate human age
has curation status: External
definition: The mean of human age in a population.

medication use status
type: Class
subclass of: health status attribute
has curation status: External
definition: A health status attribute that is having been prescribed the use of one or more drugs to improve, maintain or protect one's health.

behaviour change intervention effect estimate
type: Class
subclass of: behaviour change intervention evaluation finding
example of usage: This includes the following subclasses: 1) BCI effect estimate type -the type of statistic used to represent the difference (e.g. odds ratio, mean difference), 2) BCI effect estimate value – the datum that represents the difference (e.g. 1.35), 3) BCI effect estimate uncertainty type – the type of statistic used to represent the range of uncertainty of the value (e.g. 95% confidence interval see STATO), and 4) the BCI effect estimate uncertainty value - the datum representing the uncertainty (e.g. 1.20-1.55).
has curation status: External
has curation status: Published
definition: A behaviour change intervention evaluation finding that characterises the difference between BCI outcome estimates of two BCI scenarios.
definition: An intervention evaluation finding that characterises the difference between intervention outcome estimates of two intervention scenarios.
alternative term: BCI effect estimate
label: intervention effect estimate

behaviour change intervention evaluation finding
type: Class
subclass of: evaluation finding
has curation status: External
has curation status: Published
definition: An evaluation finding that is the output of a BCI evaluation study.
definition: An evaluation finding that is the output of an intervention evaluation study.
alternative term: BCI evaluation finding
label: intervention evaluation finding

country of intervention
type: Class
subclass of: geographic location
example of usage: Spain
example of usage: United Kingdom
has curation status: External
has curation status: Published
definition: A geographical location of a country where the intervention takes place.

doctor-led primary care facility
type: Class
subclass of: healthcare facility
example of usage: doctor surgery
example of usage: general practitioners surgery
has curation status: External
has curation status: Published
definition: A healthcare facility led by doctors.

care home facility
type: Class
subclass of: healthcare facility
has curation status: External
has curation status: Published
definition: A healthcare facility that is run by a care home organization and is the bearer of a care home function.

community healthcare facility
type: Class
subclass of: healthcare facility
example of usage: polyclinic
has curation status: External
has curation status: Published
definition: A clinic providing healthcare services to people in a certain area

community outpatient clinic facility
type: Class
subclass of: community healthcare facility
has curation status: External
has curation status: Published
definition: A healthcare facility to treat patients in the community without them staying overnight.

dentist facility
type: Class
subclass of: healthcare facility
has curation status: External
has curation status: Published
definition: A healthcare facility where dental healthcare is provided.

educational facility
type: Class
subclass of: facility
has curation status: External
has curation status: Published
definition: A facility in which formal education is provided to a student population.

community facility
type: Class
subclass of: facility
example of usage: recycling centre
example of usage: food bank
has curation status: External
has curation status: Published
definition: A facility used by a group of people living in the same place or having a particular characteristic in common.

retail facility
type: Class
subclass of: facility
example of usage: market
example of usage: shopping centre
example of usage: supermarket
has curation status: External
has curation status: Published
definition: A facility used as an outlet for shopping.

office facility
type: Class
subclass of: facility
has curation status: External
has curation status: Published
definition: A facility of a room, set of rooms, or building used as a place for commercial, professional, or bureaucratic work.

criminal justice facility
type: Class
subclass of: facility
example of usage: prison
has curation status: External
has curation status: Published
definition: A facility where individuals are being reprimanded, detained or imprisoned.

factory facility
type: Class
subclass of: facility
has curation status: External
has curation status: Published
definition: A facility of a building or group of buildings where goods are manufactured or assembled chiefly by machine

military facility
type: Class
subclass of: facility
example of usage: air force
example of usage: navy
example of usage: army
has curation status: External
has curation status: Published
definition: A facility relating to or characteristic of soldiers or armed forces

transportation
type: Class
subclass of: site
has curation status: External
has curation status: Published
definition: Methods of traveling from one place to another.
definition source: NCI Thesaurus OBO Edition

public transportation
type: Class
subclass of: transportation
example of usage: plane
example of usage: train
example of usage: bus
has curation status: External
has curation status: Published
definition: Forms of transportation that run on fixed routes and are available to the public, usually for a set fare
definition source: NCI Thesaurus OBO Edition

private transportation
type: Class
subclass of: transportation
example of usage: bicycle
example of usage: motorbike
example of usage: car
has curation status: External
has curation status: Published
definition: A form of transportation owned by an individual for individual or group use.

mobile intervention venue
type: Class
subclass of: transportation
example of usage: mobile van
has curation status: External
has curation status: Published
definition: A form of transportation delivering interventions in transient locations.

ambulance
type: Class
subclass of: transportation
has curation status: External
has curation status: Published
definition: A form of transporation which can transport patients for health treatment, and in some instances will also provide out-of-hospital healthcare to the patient.

outdoor environment
type: Class
subclass of: site
has curation status: External
has curation status: Published
definition: A site which is an outdoor location outside of a building.

water
type: Class
subclass of: outdoor environment
has curation status: External
has curation status: Published
definition: An outdoor environment set in an expanse of water.

path or pavement
type: Class
subclass of: outdoor environment
has curation status: External
has curation status: Published
definition: An outdoor environment for the passage of persons or cyclists on land

psychiatric facility
type: Class
subclass of: healthcare facility
has curation status: External
has curation status: Published
definition: A place designed and staffed to house and treat individuals that need assistance with mental dysfunctions
definition source: NCI Thesaurus OBO Edition

behaviour change technique
type: Class
subclass of: planned process
has curation status: External
definition: A planned process that is the smallest part of BCI content that is observable, replicable and on its own has the potential to bring about behaviour change.

evaluation finding
type: Class
subclass of: data item
has curation status: Published
definition: A data item that is the output of an intervention evaluation study.

individual human behaviour
type: Class
subclass of: bodily process
example of usage: Also referred to in definitions as human behaviour or just behaviour.
has curation status: Published
definition: A bodily process of a human that involves co-ordinated contraction of striated muscles controlled by the brain.
alternative term: human behaviour
comment: it is concerned with moving skeletal parts to which it is usually attached.' (https://www.collinsdictionary.com/dictionary/english/striped-muscle)
comment: Striated muscles referred to in the definition do not ordinarily involve cardiac muscles. Behaviours are usually in response to an internal or external stimuli. Every behaviour is associated with mental processes, but not every mental process is associated with behaviour. For instance, a verbal communication behaviour will involve mental processes to produce speech. However, mental processes associated with listening can occur without a person performing a behaviour. 'behaviours' can involve a series of activities (e.g., more granular behaviours). 'A 'striated muscle' can defined as 'a type of contractile tissue that is marked by transverse striations

locomotive behaviour
type: Class
subclass of: position-related behaviour
has curation status: External
definition: A position-related behaviour in which muscles are used by a person to move themselves relative to the immediate environment or part of it.

physical performance behaviour
type: Class
subclass of: individual human behaviour
has curation status: External
definition: An individual human behaviour that involves maintenance or improvement of flexibility, strength, balance or cardiovascular fitness.

avoidance behaviour
type: Class
subclass of: experience-related behaviour
has curation status: External
definition: An individual human behaviour that involves taking defensive action in order to avoid stimuli judged as aversive by the person.

individual human behaviour pattern
type: Class
subclass of: uniform process aggregate
has curation status: Published
definition: A uniform process aggregate whose member parts are behaviours of the same type and in the same person.
alternative term: behaviour pattern
curator note: - For any x and y in P where x does not equal y, if x occupies_spatiotemporal_region s, then y occupies_spatiotemporal_region t and s does not equal t
curator note: - s is instance_of human being
curator note: - For any pi in P, pi is instance_of X
curator note: - For any pi in P, s is participant_in pi
curator note: - X is subtype_of behaviour
curator note: - P is the set {p1, ... pn} of process aggregate member parts of b
curator note: b is a behaviour pattern means: - b is instance_of uniform process aggregate
comment: The term 'pattern' is used to refer to several processes (individual human behaviours) of the same type being repeated overtime. This class is intended to include behaviours that can usefully be characterised in terms of frequency and pattern of enactment with a temporal start and end of the series. This means that the series can be terminated (e.g. stopping smoking), interrupted (e.g. abstaining from alcohol consumption for a month), and changed in frequency (e.g. cutting down on snacks).

process aggregate
type: Class
subclass of: occurrent
has curation status: Published
definition: An occurrent consisting exactly of a plurality of processes that are process_aggregate_member_parts_of that occurrent for all times at which it exists.
curator note: Process aggregate extends BFO in the same way that object aggregate extends its coverage of material entities. It is required to be able to classify occurrents such as behaviour patterns that are repeated occurrences of classes of process that have properties such as average frequency of occurrence (not to be confused with frequency as a process profile) and temporal patterning of occurrences.

walking
type: Class
subclass of: locomotive behaviour
has curation status: External
definition: A locomotive behaviour that involves moving at a regular pace by lifting and setting down each foot in turn, never having both feet off the ground at once.

intervention
type: Class
subclass of: planned process
has curation status: External
definition: A planned process that has the aim of influencing an outcome.

intervention evaluation study
type: Class
subclass of: research study
has curation status: External
definition: A research study that aims to assess attributes of an intervention with regards to their positive or negative value.

intervention outcome
type: Class
subclass of: process
has curation status: External
definition: A process that is influenced by an intervention.

process attribute
type: Class
subclass of: process profile
example of usage: This is intended to provide a user-friendly way of representing the way in which processes are manifest. This is somewhat similar to, but not the same as, the class 'specifically dependent continuant' in Basic Formal Ontology which provides a way of representing features of material entities such as age and size. It is formally equivalent to process profile in Basic Formal Ontology.
has curation status: Published
definition: A process profile that is an attribute of a process.

learning
type: Class
subclass of: mental process
has curation status: Published
definition: A mental process in which a lasting mental or behavioural change occurs as the result of experience.
comment: The class 'learning' from the Gene Ontology was not reused but adapted for the Mechanism of Action (MoA) Ontology, as the Gene Ontology only focuses on learning adaptive behaviours in order to be relevant to all organisms.

uniform process aggregate
type: Class
subclass of: process aggregate
has curation status: Published
definition: A process aggregate whose member parts are of the same type.
curator note: u is a uniform process aggregate means: • u instance_of process aggregate • P is the set {p1,…pn} of process aggregate member parts of u • X is some descendant of process • Each of {p1,…pn} in P is instance_of X

personal attribute
type: Class
subclass of: specifically dependent continuant
has curation status: Published
definition: A specifically dependent continuant that inheres in a person.
comment: Attributes included under this header are age, immigration, social and economic conditions.

BCI attribute
type: Class
subclass of: process attribute
has curation status: Published
definition: A process attribute whose bearer is a behaviour change intervention.
alternative term: behaviour change intervention attribute

belief about quality of life
type: Class
subclass of: belief
has curation status: External
has curation status: Published
definition: A belief about one's position in life in relation to one's goals, expectations, standards and concerns.

position-related behaviour
type: Class
subclass of: individual human behaviour
has curation status: Published
definition: An individual human behaviour that relates to the enactor's posture or location.

experience-related behaviour
type: Class
subclass of: individual human behaviour
has curation status: External
has curation status: Published
definition: An individual human behaviour that relates to some subjective experience of the behaving person.

dataset creating
type: Class
subclass of: planned process
editor preferred label: creating a data set
definition: A planned process that has a data set as its specified output.
definition editor: William R. Hogan
alternative term: data set creation
alternative term: dataset creation

entity
type: Class
BFO OWL specification label: entity
BFO CLIF specification label: Entity
editor preferred label: entity
example of usage: Julius Caesar
example of usage: Verdi’s Requiem
example of usage: the Second World War
example of usage: your body mass index
definition: An entity is anything that exists or has existed or will exist.
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
imported from: bfo.owl
imported from: dron.owl
imported from: envo.owl
imported from: iao.owl
imported from: ico.owl
imported from: mondo.owl
imported from: oae.owl
imported from: obi.owl
imported from: obib.owl
imported from: ogms.owl
imported from: omrse.owl
elucidation: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
database_cross_reference: https://www.wikidata.org/wiki/Q35120
alternate name: entities
derived from: entitātem @la

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
IAO_0010000: 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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/001-001

continuant
type: Class
subclass of: entity
subclass of: Thing
BFO OWL specification label: continuant
BFO CLIF specification label: Continuant
editor preferred label: continuant
definition: An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
editor note: BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
editor note: Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
imported from: bfo.owl
imported from: dron.owl
imported from: envo.owl
imported from: iao.owl
imported from: oae.owl
imported from: obi.owl
imported from: obib.owl
imported from: ogms.owl
imported from: omrse.owl
imported from: pato.owl
imported from: ro.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: 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])
IAO_0010000: 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])
IAO_0010000: 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])
IAO_0010000: 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]
IAO_0010000: 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]
IAO_0010000: 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]
IAO_0010000: 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]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/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
IAO_0010000: 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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/008-002

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

Axiom
annotated source: occurrent
annotated property: editor note
annotated target: Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
IAO_0010000: 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.
IAO_0010000: 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])
IAO_0010000: 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])
IAO_0010000: 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])
IAO_0010000: 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]
IAO_0010000: 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]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/079-001

independent continuant
type: Class
subclass of: continuant
BFO OWL specification label: ic
BFO CLIF specification label: IndependentContinuant
example of usage: a chair
example of usage: a heart
example of usage: a leg
example of usage: a molecule
example of usage: a spatial region
example of usage: an atom
example of usage: an orchestra.
example of usage: an organism
example of usage: the bottom right portion of a human torso
example of usage: the interior of your mouth
definition: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
definition: b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
OBO foundry unique label: anatomical entity (BFO)
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]
comment: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.

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])
IAO_0010000: 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])
IAO_0010000: 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])
IAO_0010000: 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]
IAO_0010000: 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]
IAO_0010000: 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]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/017-002

spatial region
type: Class
subclass of: immaterial entity
BFO OWL specification label: s-region
BFO CLIF specification label: SpatialRegion
has curation status: Proposed
definition: A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R.
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.
IAO_0010000: 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])
IAO_0010000: 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])
IAO_0010000: 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]
IAO_0010000: 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]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/035-001

temporal region
type: Class
subclass of: occurrent
BFO OWL specification label: t-region
BFO CLIF specification label: TemporalRegion
editor note: Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional
elucidation: A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])
has associated axiom(nl): All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
has associated axiom(nl): Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
has associated axiom(fol): (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
has associated axiom(fol): (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
has associated axiom(fol): (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]

Axiom
annotated source: temporal region
annotated property: editor note
annotated target: Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/0000003
comment: per discussion with Barry Smith

Axiom
annotated source: temporal region
annotated property: elucidation
annotated target: A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/100-001

Axiom
annotated source: temporal region
annotated property: has associated axiom(nl)
annotated target: All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/101-001

Axiom
annotated source: temporal region
annotated property: has associated axiom(nl)
annotated target: Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/119-002

Axiom
annotated source: temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/119-002

Axiom
annotated source: temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/101-001

Axiom
annotated source: temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/100-001

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

Axiom
annotated source: process
annotated property: definition
annotated target: p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
IAO_0010000: 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]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/083-003

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

Axiom
annotated source: disposition
annotated property: elucidation
annotated target: b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/062-002

Axiom
annotated source: disposition
annotated property: has associated axiom(nl)
annotated target: If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/063-002

Axiom
annotated source: disposition
annotated property: has associated axiom(fol)
annotated target: (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/063-002

Axiom
annotated source: disposition
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/062-002

realizable entity
type: Class
subclass of: specifically dependent continuant
BFO OWL specification label: realizable
BFO CLIF specification label: RealizableEntity
example of usage: the disposition of this piece of metal to conduct electricity.
example of usage: the disposition of your blood to coagulate
example of usage: the function of your reproductive organs
example of usage: the role of being a doctor
example of usage: the role of this boundary to delineate where Utah and Colorado meet
definition: A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
imported from: dron.owl
imported from: envo.owl
imported from: obi.owl
imported from: obib.owl
imported from: ogms.owl
imported from: omrse.owl
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])
IAO_0010000: 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])
IAO_0010000: 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]
IAO_0010000: 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]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/058-002

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

Axiom
annotated source: quality
annotated property: elucidation
annotated target: a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/055-001

Axiom
annotated source: quality
annotated property: has associated axiom(nl)
annotated target: If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/105-001

Axiom
annotated source: quality
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/055-001

Axiom
annotated source: quality
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/105-001

specifically dependent continuant
type: Class
subclass of: continuant
BFO OWL specification label: sdc
BFO CLIF specification label: SpecificallyDependentContinuant
editor preferred label: 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: bfo.owl
imported from: dron.owl
imported from: envo.owl
imported from: oae.owl
imported from: obi.owl
imported from: obib.owl
imported from: ogms.owl
imported from: omrse.owl
imported from: pato.owl
imported from: ro.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])
IAO_0010000: 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])
IAO_0010000: 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.
IAO_0010000: 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]
IAO_0010000: 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]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/050-003

role
type: Class
subclass of: realizable entity
BFO OWL specification label: role
BFO CLIF specification label: Role
example of usage: John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
example of usage: the priest role
example of usage: the role of a boundary to demarcate two neighboring administrative territories
example of usage: the role of a building in serving as a military target
example of usage: the role of a stone in marking a property boundary
example of usage: the role of subject in a clinical trial
example of usage: the student role
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])
IAO_0010000: 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]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/061-001

fiat object
type: Class
subclass of: material entity
BFO OWL specification label: fiat-object
BFO OWL specification label: fiat-object-part
BFO CLIF specification label: FiatObjectPart
example of usage: or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29
example of usage: the FMA:regional parts of an intact human body.
example of usage: the Western hemisphere of the Earth
example of usage: the division of the brain into regions
example of usage: the division of the planet into hemispheres
example of usage: the dorsal and ventral surfaces of the body
example of usage: the upper and lower lobes of the left lung
editor note: BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions
elucidation: b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])
has associated axiom(fol): (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004]
label: fiat object part

Axiom
annotated source: fiat object
annotated property: elucidation
annotated target: b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/027-004

Axiom
annotated source: fiat object
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/027-004

object aggregate
type: Class
subclass of: material entity
BFO OWL specification label: object-aggregate
BFO CLIF specification label: ObjectAggregate
example of usage: a collection of cells in a blood biobank.
example of usage: a swarm of bees is an aggregate of members who are linked together through natural bonds
example of usage: a symphony orchestra
example of usage: an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)
example of usage: defined by fiat: the aggregate of members of an organization
example of usage: defined through physical attachment: the aggregate of atoms in a lump of granite
example of usage: defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
example of usage: defined via attributive delimitations such as: the patients in this hospital
example of usage: the aggregate of bearings in a constant velocity axle joint
example of usage: the aggregate of blood cells in your body
example of usage: the nitrogen atoms in the atmosphere
example of usage: the restaurants in Palo Alto
example of usage: your collection of Meissen ceramic plates.
has curation status: External
definition: 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.
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
IAO_0010000: 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
IAO_0010000: 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.
IAO_0010000: 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])
IAO_0010000: 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]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/025-004

site
type: Class
subclass of: immaterial entity
BFO OWL specification label: site
BFO CLIF specification label: Site
example of usage: Manhattan Canyon)
example of usage: a hole in the interior of a portion of cheese
example of usage: a rabbit hole
example of usage: an air traffic control region defined in the airspace above an airport
example of usage: the Grand Canyon
example of usage: the Piazza San Marco
example of usage: the cockpit of an aircraft
example of usage: the hold of a ship
example of usage: the interior of a kangaroo pouch
example of usage: the interior of the trunk of your car
example of usage: the interior of your bedroom
example of usage: the interior of your office
example of usage: the interior of your refrigerator
example of usage: the lumen of your gut
example of usage: your left nostril (a fiat part – the opening – of your left nasal cavity)
has curation status: External
definition: A three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof.
definition source: Basic Formal Ontology
elucidation: b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])
has associated axiom(fol): (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]

Axiom
annotated source: site
annotated property: elucidation
annotated target: b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/034-002

Axiom
annotated source: site
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/034-002

object
type: Class
subclass of: material entity
has_obo_namespace: bfo
id: BFO:0000030

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

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])
IAO_0010000: 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]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/074-001

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

Axiom
annotated source: function
annotated property: elucidation
annotated target: A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/064-001

Axiom
annotated source: function
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/064-001

one-dimensional temporal region
type: Class
subclass of: temporal region
has curation status: External
definition: A one-dimensional temporal region is a temporal region that is extended.

material entity
type: Class
subclass of: independent continuant
subclass of: Thing
BFO OWL specification label: material
BFO CLIF specification label: MaterialEntity
editor preferred label: 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
has curation status: External
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: cl.owl
imported from: ido.owl
imported from: uberon.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]
has_obo_namespace: bfo
id: BFO:0000040

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])
IAO_0010000: 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])
IAO_0010000: 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])
IAO_0010000: 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]
IAO_0010000: 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]
IAO_0010000: 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]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/020-002

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

process profile
type: Class
subclass of: process
BFO OWL specification label: process-profile
BFO CLIF specification label: ProcessProfile
example of usage: On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels
example of usage: One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance.
example of usage: The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on.
definition: b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])
elucidation: b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])
has associated axiom(fol): (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005]
has associated axiom(fol): (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]

Axiom
annotated source: process profile
annotated property: definition
annotated target: b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/093-002

Axiom
annotated source: process profile
annotated property: elucidation
annotated target: b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/094-005

Axiom
annotated source: process profile
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/094-005

Axiom
annotated source: process profile
annotated property: has associated axiom(fol)
annotated target: (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/093-002

lipid
type: Class
subclass of: organic molecular entity
definition: 'Lipids' is a loosely defined term for substances of biological origin that are soluble in nonpolar solvents. They consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids.
has_alternative_id: CHEBI:14517
has_alternative_id: CHEBI:25054
has_alternative_id: CHEBI:6486
has_obo_namespace: chebi_ontology
id: CHEBI:18059
in_subset: 3 STAR

ulotaront
type: Class
subclass of: thienopyran
subclass of: secondary amino compound
has curation status: External
definition: A member of the class of thienopyrans that is 4,7-dihydro-5H-thieno[2,3-c]pyran substituted by a (methylamino)methyl at position 7S. It is a trace amine-associated receptor 1 and serotonin 5-HT1A receptors agonist that has demonstrated efficacy in the treatment of patients with schizophrenia.
alternative term: SEP-363856, SEP-856, SEP363856, SEP 363856, SEP 856, SEP856
has_obo_namespace: chebi_ontology
id: CHEBI:228346
in_subset: 3 STAR

molecular entity
type: Class
subclass of: chemical entity
definition: Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
has_obo_namespace: chebi_ontology
id: CHEBI:23367
in_subset: 3 STAR

Axiom
annotated source: molecular entity
annotated property: definition
annotated target: Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
database_cross_reference: fake:2

chemical entity
type: Class
subclass of: object
subclass of: Thing
definition: A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.
has_obo_namespace: chebi_ontology
id: CHEBI:24431
in_subset: 3 STAR

organic heterocyclic compound
type: Class
subclass of: heteroorganic entity
subclass of: organic cyclic compound
subclass of: heterocyclic compound
definition: A cyclic compound having as ring members atoms of carbon and at least of one other element.
has_obo_namespace: chebi_ontology
id: CHEBI:24532
in_subset: 3 STAR

molecule
type: Class
subclass of: polyatomic entity
definition: Any polyatomic entity that is an electrically neutral entity consisting of more than one atom.
has_obo_namespace: chebi_ontology
id: CHEBI:25367
in_subset: 3 STAR

oxygen molecular entity
type: Class
subclass of: chalcogen molecular entity
has_obo_namespace: chebi_ontology
id: CHEBI:25806
in_subset: 3 STAR

sulfur molecular entity
type: Class
subclass of: chalcogen molecular entity
has_obo_namespace: chebi_ontology
id: CHEBI:26835
in_subset: 3 STAR

organic heterobicyclic compound
type: Class
subclass of: heterobicyclic compound
subclass of: organic heteropolycyclic compound
has_obo_namespace: chebi_ontology
id: CHEBI:27171
in_subset: 3 STAR

organosulfur compound
type: Class
subclass of: sulfur molecular entity
subclass of: organochalcogen compound
definition: An organosulfur compound is a compound containing at least one carbon-sulfur bond.
has_alternative_id: CHEBI:23010
has_alternative_id: CHEBI:25714
has_obo_namespace: chebi_ontology
id: CHEBI:33261
in_subset: 3 STAR

heteroorganic entity
type: Class
subclass of: organic molecular entity
definition: A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms.
has_obo_namespace: chebi_ontology
id: CHEBI:33285
in_subset: 3 STAR

pnictogen molecular entity
type: Class
subclass of: p-block molecular entity
definition: A p-block molecular entity containing any pnictogen.
has_obo_namespace: chebi_ontology
id: CHEBI:33302
in_subset: 3 STAR

chalcogen molecular entity
type: Class
subclass of: p-block molecular entity
definition: Any p-block molecular entity containing a chalcogen.
has_obo_namespace: chebi_ontology
id: CHEBI:33304
in_subset: 3 STAR

main group molecular entity
type: Class
subclass of: molecular entity
definition: A molecular entity containing one or more atoms from any of groups 1, 2, 13, 14, 15, 16, 17, and 18 of the periodic table.
has_obo_namespace: chebi_ontology
id: CHEBI:33579
in_subset: 3 STAR

carbon group molecular entity
type: Class
subclass of: p-block molecular entity
has_obo_namespace: chebi_ontology
id: CHEBI:33582
in_subset: 3 STAR

cyclic compound
type: Class
subclass of: molecule
definition: Any molecule that consists of a series of atoms joined together to form a ring.
has_obo_namespace: chebi_ontology
id: CHEBI:33595
in_subset: 3 STAR

polycyclic compound
type: Class
subclass of: cyclic compound
has_obo_namespace: chebi_ontology
id: CHEBI:33635
in_subset: 3 STAR

bicyclic compound
type: Class
subclass of: cyclic compound
definition: A molecule that features two fused rings.
has_obo_namespace: chebi_ontology
id: CHEBI:33636
in_subset: 3 STAR

heteropolycyclic compound
type: Class
subclass of: polycyclic compound
subclass of: heterocyclic compound
definition: A polycyclic compound in which at least one of the rings contains at least one non-carbon atom.
has_obo_namespace: chebi_ontology
id: CHEBI:33671
in_subset: 3 STAR

heterobicyclic compound
type: Class
subclass of: bicyclic compound
subclass of: heterocyclic compound
definition: A bicyclic compound in which at least one of the rings contains at least one skeletal heteroatom.
has_obo_namespace: chebi_ontology
id: CHEBI:33672
in_subset: 3 STAR

p-block molecular entity
type: Class
subclass of: main group molecular entity
definition: A main group molecular entity that contains one or more atoms of a p-block element.
has_obo_namespace: chebi_ontology
id: CHEBI:33675
in_subset: 3 STAR

organic cyclic compound
type: Class
subclass of: cyclic compound
subclass of: organic molecule
definition: Any organic molecule that consists of atoms connected in the form of a ring.
has_obo_namespace: chebi_ontology
id: CHEBI:33832
in_subset: 3 STAR

steroid
type: Class
subclass of: lipid
subclass of: organic polycyclic compound
definition: Any of naturally occurring compounds and synthetic analogues, based on the cyclopenta[a]phenanthrene carbon skeleton, partially or completely hydrogenated; there are usually methyl groups at C-10 and C-13, and often an alkyl group at C-17. By extension, one or more bond scissions, ring expansions and/or ring contractions of the skeleton may have occurred. Natural steroids are derived biogenetically from squalene which is a triterpene.
has_alternative_id: CHEBI:13687
has_alternative_id: CHEBI:26768
has_alternative_id: CHEBI:9263
has_obo_namespace: chebi_ontology
id: CHEBI:35341
in_subset: 3 STAR

organonitrogen compound
type: Class
subclass of: heteroorganic entity
subclass of: nitrogen molecular entity
definition: Any heteroorganic entity containing at least one carbon-nitrogen bond.
has_obo_namespace: chebi_ontology
id: CHEBI:35352
in_subset: 3 STAR

antidepressant
type: Class
subclass of: psychotropic drug
has curation status: External
definition: A mood-stimulating drug used primarily in the treatment of affective disorders and related conditions.

central nervous system drug
type: Class
subclass of: function
has curation status: External
definition: A class of drugs producing both physiological and psychological effects through a variety of mechanisms involving the central nervous system.
has_obo_namespace: chebi_ontology
id: CHEBI:35470
in_subset: 3 STAR

psychotropic drug
type: Class
subclass of: central nervous system drug
definition: A loosely defined grouping of drugs that have effects on psychological function.
has_obo_namespace: chebi_ontology
id: CHEBI:35471
in_subset: 3 STAR

tranquilizing drug
type: Class
subclass of: psychotropic drug
subclass of: central nervous system depressant
definition: A traditional grouping of drugs said to have a soothing or calming effect on mood, thought or behaviour.
has_obo_namespace: chebi_ontology
id: CHEBI:35473
in_subset: 3 STAR

antipsychotic agent
type: Class
subclass of: tranquilizing drug
has curation status: External
definition: An agent that controls agitated psychotic behaviour, alleviate acute psychotic states, reduce psychotic symptoms, and exert a quieting effect.

central nervous system depressant
type: Class
subclass of: central nervous system drug
definition: A loosely defined group of drugs that tend to reduce the activity of the central nervous system.
has_obo_namespace: chebi_ontology
id: CHEBI:35488
in_subset: 3 STAR

polyatomic entity
type: Class
subclass of: molecular entity
definition: Any molecular entity consisting of more than one atom.
has_obo_namespace: chebi_ontology
id: CHEBI:36357
in_subset: 3 STAR

organochalcogen compound
type: Class
subclass of: heteroorganic entity
subclass of: chalcogen molecular entity
definition: An organochalcogen compound is a compound containing at least one carbon-chalcogen bond.
has_obo_namespace: chebi_ontology
id: CHEBI:36962
in_subset: 3 STAR

organooxygen compound
type: Class
subclass of: oxygen molecular entity
subclass of: organochalcogen compound
definition: An organochalcogen compound containing at least one carbon-oxygen bond.
has_obo_namespace: chebi_ontology
id: CHEBI:36963
in_subset: 3 STAR

oxacycle
type: Class
subclass of: organic heterocyclic compound
subclass of: organooxygen compound
definition: Any organic heterocyclic compound containing at least one ring oxygen atom.
has_obo_namespace: chebi_ontology
id: CHEBI:38104
in_subset: 3 STAR

organosulfur heterocyclic compound
type: Class
subclass of: organic heterocyclic compound
subclass of: organosulfur compound
has_obo_namespace: chebi_ontology
id: CHEBI:38106
in_subset: 3 STAR

organic heteropolycyclic compound
type: Class
subclass of: organic heterocyclic compound
subclass of: heteropolycyclic compound
has_alternative_id: CHEBI:25429
has_alternative_id: CHEBI:38075
has_obo_namespace: chebi_ontology
id: CHEBI:38166
in_subset: 3 STAR

very-low-density lipoprotein cholesterol
type: Class
subclass of: lipoprotein cholesterol
has curation status: External
definition: Cholesterol esters and free cholesterol which are contained in or bound to very low density lipoproteins (VLDL).
has_obo_namespace: chebi_ontology
id: CHEBI:47773
in_subset: 3 STAR

low-density lipoprotein cholesterol
type: Class
subclass of: lipoprotein cholesterol
has curation status: External
definition: Cholesterol esters and free cholesterol which are contained in or bound to low-density lipoproteins (LDL).
alternative term: LDL cholesterol
has_obo_namespace: chebi_ontology
id: CHEBI:47774
in_subset: 3 STAR

high-density lipoprotein cholesterol
type: Class
subclass of: lipoprotein cholesterol
has curation status: External
definition: Cholesterol esters and free cholesterol which are contained in or bound to high-density lipoproteins (HDL).
alternative term: HDL cholesterol
has_obo_namespace: chebi_ontology
id: CHEBI:47775
in_subset: 3 STAR

thienopyran
type: Class
subclass of: organic heterobicyclic compound
subclass of: oxacycle
subclass of: organosulfur heterocyclic compound
has_obo_namespace: chebi_ontology
id: CHEBI:48910
in_subset: 3 STAR

organic amino compound
type: Class
subclass of: molecular entity
subclass of: organonitrogen compound
subclass of: organic molecular entity
definition: A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by organyl groups.
has_obo_namespace: chebi_ontology
id: CHEBI:50047
in_subset: 3 STAR

cholestanoid
type: Class
subclass of: steroid
definition: Any steroid based on a cholestane skeleton and its derivatives.
has_obo_namespace: chebi_ontology
id: CHEBI:50401
in_subset: 3 STAR

lipoprotein cholesterol
type: Class
subclass of: cholestanoid
definition: Cholesterol esters and free cholesterol which are contained in or bound to lipoproteins.
has_obo_namespace: chebi_ontology
id: CHEBI:50404
in_subset: 3 STAR

organic molecular entity
type: Class
subclass of: carbon group molecular entity
definition: Any molecular entity that contains carbon.
has_alternative_id: CHEBI:25700
has_alternative_id: CHEBI:33244
has_obo_namespace: chebi_ontology
id: CHEBI:50860
in_subset: 3 STAR

secondary amino compound
type: Class
subclass of: organic amino compound
definition: A compound formally derived from ammonia by replacing two hydrogen atoms by organyl groups.
has_obo_namespace: chebi_ontology
id: CHEBI:50995
in_subset: 3 STAR

nitrogen molecular entity
type: Class
subclass of: pnictogen molecular entity
has_alternative_id: CHEBI:25556
has_alternative_id: CHEBI:7594
has_obo_namespace: chebi_ontology
id: CHEBI:51143
in_subset: 3 STAR

organic polycyclic compound
type: Class
subclass of: polycyclic compound
subclass of: organic cyclic compound
has_obo_namespace: chebi_ontology
id: CHEBI:51958
in_subset: 3 STAR

heterocyclic compound
type: Class
subclass of: cyclic compound
definition: A cyclic compound having as ring members atoms of at least two different elements.
has_obo_namespace: chebi_ontology
id: CHEBI:5686
in_subset: 3 STAR

chemical substance
type: Class
subclass of: chemical entity
definition: A chemical substance is a portion of matter of constant composition, composed of molecular entities of the same type or of different types.
has_obo_namespace: chebi_ontology
id: CHEBI:59999
in_subset: 3 STAR

mixture
type: Class
subclass of: chemical substance
definition: A mixture is a chemical substance composed of multiple molecules, at least two of which are of a different kind.
has_obo_namespace: chebi_ontology
id: CHEBI:60004
in_subset: 3 STAR

diastereoisomeric mixture
type: Class
subclass of: mixture
definition: A mixture composed of two or more diastereoisomers (stereoisomers not related as mirror images).
has_obo_namespace: chebi_ontology
id: CHEBI:60915
in_subset: 3 STAR

organic molecule
type: Class
subclass of: molecule
subclass of: organic molecular entity
definition: Any molecule that consists of at least one carbon atom as part of the electrically neutral entity.
has_obo_namespace: chebi_ontology
id: CHEBI:72695
in_subset: 3 STAR

ractopamine
type: Class
subclass of: diastereoisomeric mixture
has curation status: External
definition: A diastereoisomeric mixture of approximately equal amounts of all four possible diastereoisomers of 4-(1-hydroxy-2-{[4-(4-hydroxyphenyl)butan-2-yl]amino}ethyl)phenol.
definition: A diastereoisomeric mixture of approximately equal amounts of all four possible diastereoisomers of 4-(1-hydroxy-2-{[4-(4-hydroxyphenyl)butan-2-yl]amino}ethyl)phenol. A beta-adrenergic agonist, it is used (generally as the hydrochloride salt) as a feed additive for use in pigs and other livestock to promote protein deposition, resulting in leaner meat. The R,R diastereoisomer, butopamine, is responsible for most of the leanness-enhancing effects. While use of ractopamine has been banned in over 120 countries including throughout the EU, in the US it used in an estimated 80% of all beef, pork and turkey production.
alternative term: ( -)-all-rac-p-hydroxy-alpha-({[3-(p-hydroxyphenyl)-1-methylpropyl]amino}methyl)benzyl alcohol, ractopamine, ractopamina, ractopaminum
has_obo_namespace: chebi_ontology
id: CHEBI:82644
in_subset: 3 STAR

clinical measurement
type: Class
subclass of: planned process
has curation status: External
definition: A quantitative or qualitative value which is the result of an act of assessing a morphological or physiological state or property in a single individual or sample or a group of individuals or samples, based on direct observation or experimental manipulation.
has_obo_namespace: clinical_measurement_ontology
id: CMO:0000000

Axiom
annotated source: clinical measurement
annotated property: definition
annotated target: A quantitative or qualitative value which is the result of an act of assessing a morphological or physiological state or property in a single individual or sample or a group of individuals or samples, based on direct observation or experimental manipulation.
database_cross_reference: American_Heritage:The_American_Heritage_Dictionary_of_the_English_Language--4th_Ed

cardiovascular measurement
type: Class
subclass of: clinical measurement
definition: Any value resulting from the quantification of a morphological or physiological parameter pertaining to the heart and/or blood vessels.
database_cross_reference: EFO:0004298
database_cross_reference: EFO:0006919
has exact synonym: cardiovascular measurement
has_narrow_synonym: cardiovascular event measurement
has_obo_namespace: clinical_measurement_ontology
id: CMO:0000001

Axiom
annotated source: cardiovascular measurement
annotated property: definition
annotated target: Any value resulting from the quantification of a morphological or physiological parameter pertaining to the heart and/or blood vessels.
database_cross_reference: American_Heritage:The_American_Heritage_Dictionary_of_the_English_Language--4th_Ed
database_cross_reference: Dorland:Dorlands_Illustrated_Medical_Dictionary--31st_Ed
database_cross_reference: ISBN:978-1416049982

heart electrical conduction measurement
type: Class
subclass of: heart measurement
definition: Any measurement of components of the electrical conduction system of the heart.The electrical conduction system of the heart transmits signals generated usually by the sinoatrial node to cause contraction of the heart muscle.
created_by: mshimoyama
creation date: 2010-06-17T10:36:15Z
database_cross_reference: EFO:0007885
has_narrow_synonym: JT interval
has_obo_namespace: clinical_measurement_ontology
id: CMO:0000230

QTC interval
type: Class
subclass of: heart electrical conduction measurement
has curation status: External
definition: QT interval corrected for heart rate calculated by the QT interval divided by the square root of the interval from one QRS complex to the onset of the next QRS complex measured in seconds.
created_by: mshimoyama
creation date: 2010-06-17T12:40:52Z
has_obo_namespace: clinical_measurement_ontology
id: CMO:0000269

Axiom
annotated source: QTC interval
annotated property: definition
annotated target: QT interval corrected for heart rate calculated by the QT interval divided by the square root of the interval from one QRS complex to the onset of the next QRS complex measured in seconds.
database_cross_reference: http://en.wikipedia.org

organ measurement
type: Class
subclass of: clinical measurement
definition: Any measurement of a structural part of a system of the body that is composed of tissues and cells that enable it to perform a particular function.
created_by: JSmith
creation date: 2012-02-15T05:00:53Z
has_obo_namespace: clinical_measurement_ontology
id: CMO:0000669

Axiom
annotated source: organ measurement
annotated property: definition
annotated target: Any measurement of a structural part of a system of the body that is composed of tissues and cells that enable it to perform a particular function.
database_cross_reference: Mosby:Mosbys_Medical_Dictionary--8th_Ed

heart measurement
type: Class
subclass of: cardiovascular measurement
subclass of: organ measurement
created_by: JSmith
creation date: 2012-02-15T05:06:19Z
has_obo_namespace: clinical_measurement_ontology
id: CMO:0000670
comment: This is not the same term as the original "heart measurement". That term is now "heart morphological measurement".

planned process
type: Class
equivalent class: planned process
subclass of: process
definition: A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification.

geographic feature
type: Class
subclass of: astronomical body part
definition: An astrononmical body part which delimited by physical discontinuities with its surroundings.
database_cross_reference: https://en.wikipedia.org/wiki/Geographic_feature
has exact synonym: macroscopic spatial feature
in_subset: envoPolar
comment: This class is being depopulated and will be filled only with inferred subclasses. Please do not use this for direct annotation, favouring instead a more descriptive subclass.

anthropogenic geographic feature
type: Class
subclass of: geographic feature
definition: An anthropogenic geographic feature is a geographic feature resulting from the influence of human beings on nature.
database_cross_reference: FTT:78
database_cross_reference: TGN:50001
has_related_synonym: man-made feature
has_related_synonym: manmade feature

Axiom
annotated source: anthropogenic geographic feature
annotated property: definition
annotated target: An anthropogenic geographic feature is a geographic feature resulting from the influence of human beings on nature.
database_cross_reference: ORCID:0000-0002-4366-3088

transport feature
type: Class
subclass of: human construction
definition: A construction which enables the movement of humans, their animals or their vehicles.
database_cross_reference: FTT:83

Axiom
annotated source: transport feature
annotated property: definition
annotated target: A construction which enables the movement of humans, their animals or their vehicles.
database_cross_reference: MA:ma

road
type: Class
subclass of: outdoor environment
subclass of: constructed pavement
has curation status: External
definition: An open way for the passage of vehicles, persons, or animals on land
definition: An open way for the passage of vehicles, persons, or animals on land.
database_cross_reference: EcoLexicon:road
database_cross_reference: FTT:1058
database_cross_reference: FTT:1183
database_cross_reference: FTT:1185
database_cross_reference: FTT:1187
database_cross_reference: FTT:431
database_cross_reference: FTT:443
database_cross_reference: FTT:646
database_cross_reference: FTT:798
database_cross_reference: FTT:884
database_cross_reference: Geonames:R
database_cross_reference: Geonames:R.RD
database_cross_reference: Geonames:R.ST
database_cross_reference: LTER:475
database_cross_reference: SWEETRealm:Highway
database_cross_reference: TGN:53151
database_cross_reference: TGN:53153
database_cross_reference: TGN:53154
database_cross_reference: TGN:53157
database_cross_reference: https://en.wikipedia.org/wiki/Road
has_narrow_synonym: board walk
has_narrow_synonym: caravan route
has_narrow_synonym: causeway
has_narrow_synonym: drive
has_narrow_synonym: highway
has_narrow_synonym: intersection
has_narrow_synonym: parkway
has_narrow_synonym: road bend
has_narrow_synonym: road junction
has_narrow_synonym: traffic circle
has_related_synonym: accessway
has_related_synonym: alley
has_related_synonym: avenue
has_related_synonym: boulevard
has_related_synonym: cart track
has_related_synonym: drove
has_related_synonym: farm lane
has_related_synonym: freeway
has_related_synonym: lane
has_related_synonym: roadway
has_related_synonym: street
has_related_synonym: thorofare
has_related_synonym: thoroughfare
has_related_synonym: thruway
has_related_synonym: turnpike

Axiom
annotated source: road
annotated property: has_narrow_synonym
annotated target: highway
database_cross_reference: USGS:SDTS

Axiom
annotated source: road
annotated property: has_narrow_synonym
annotated target: intersection
database_cross_reference: ADL:FTT

Axiom
annotated source: road
annotated property: has_narrow_synonym
annotated target: parkway
database_cross_reference: ADL:FTT

Axiom
annotated source: road
annotated property: has_narrow_synonym
annotated target: parkway
database_cross_reference: Getty:TGN

Axiom
annotated source: road
annotated property: has_narrow_synonym
annotated target: road bend
database_cross_reference: ADL:FTT

Axiom
annotated source: road
annotated property: has_narrow_synonym
annotated target: road junction
database_cross_reference: ADL:FTT

Axiom
annotated source: road
annotated property: has_narrow_synonym
annotated target: traffic circle
database_cross_reference: ADL:FTT

Axiom
annotated source: road
annotated property: has_related_synonym
annotated target: accessway
database_cross_reference: USGS:SDTS

Axiom
annotated source: road
annotated property: has_related_synonym
annotated target: alley
database_cross_reference: USGS:SDTS

Axiom
annotated source: road
annotated property: has_related_synonym
annotated target: avenue
database_cross_reference: USGS:SDTS

Axiom
annotated source: road
annotated property: has_related_synonym
annotated target: boulevard
database_cross_reference: USGS:SDTS

Axiom
annotated source: road
annotated property: has_related_synonym
annotated target: cart track
database_cross_reference: USGS:SDTS

Axiom
annotated source: road
annotated property: has_related_synonym
annotated target: drove
database_cross_reference: ADL:FTT

Axiom
annotated source: road
annotated property: has_related_synonym
annotated target: farm lane
database_cross_reference: USGS:SDTS

Axiom
annotated source: road
annotated property: has_related_synonym
annotated target: freeway
database_cross_reference: USGS:SDTS

Axiom
annotated source: road
annotated property: has_related_synonym
annotated target: roadway
database_cross_reference: ADL:FTT

Axiom
annotated source: road
annotated property: has_related_synonym
annotated target: street
database_cross_reference: ADL:FTT

Axiom
annotated source: road
annotated property: has_related_synonym
annotated target: street
database_cross_reference: Geonames:feature

Axiom
annotated source: road
annotated property: has_related_synonym
annotated target: street
database_cross_reference: Getty:TGN

Axiom
annotated source: road
annotated property: has_related_synonym
annotated target: street
database_cross_reference: USGS:SDTS

Axiom
annotated source: road
annotated property: has_related_synonym
annotated target: thorofare
database_cross_reference: USGS:SDTS

Axiom
annotated source: road
annotated property: has_related_synonym
annotated target: thoroughfare
database_cross_reference: USGS:SDTS

Axiom
annotated source: road
annotated property: has_related_synonym
annotated target: thruway
database_cross_reference: USGS:SDTS

Axiom
annotated source: road
annotated property: has_related_synonym
annotated target: turnpike
database_cross_reference: USGS:SDTS

Axiom
annotated source: road
annotated property: definition
annotated target: An open way for the passage of vehicles, persons, or animals on land.
database_cross_reference: USGS:SDTS

Axiom
annotated source: road
annotated property: has_narrow_synonym
annotated target: board walk
database_cross_reference: USGS:SDTS

Axiom
annotated source: road
annotated property: has_narrow_synonym
annotated target: caravan route
database_cross_reference: ADL:FTT

Axiom
annotated source: road
annotated property: has_narrow_synonym
annotated target: causeway
database_cross_reference: ADL:FTT

Axiom
annotated source: road
annotated property: has_narrow_synonym
annotated target: drive
database_cross_reference: ADL:FTT

Axiom
annotated source: road
annotated property: has_narrow_synonym
annotated target: highway
database_cross_reference: ADL:FTT

Axiom
annotated source: road
annotated property: has_narrow_synonym
annotated target: highway
database_cross_reference: Getty:TGN

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

Axiom
annotated source: human construction
annotated property: definition
annotated target: A construction that has been assembled by deliberate human effort.
database_cross_reference: MA:ma

beach
type: Class
subclass of: outdoor environment
subclass of: surface landform
has curation status: External
definition: A landform consisting of loose rock particles such as sand, gravel, shingle, pebbles, cobble, or even shell fragments along the shoreline of a body of wate
definition: A landform consisting of loose rock particles such as sand, gravel, shingle, pebbles, cobble, or even shell fragments along the shoreline of a body of water.
database_cross_reference: EcoLexicon:beach
database_cross_reference: EcoLexicon:to_beach
database_cross_reference: FTT:237
database_cross_reference: FTT:239
database_cross_reference: Geonames:T.BCH
database_cross_reference: Geonames:T.BCHS
database_cross_reference: SWEETRealm:Beach
database_cross_reference: TGN:21482
database_cross_reference: https://en.wikipedia.org/wiki/Beach
has exact synonym: Beach
has_narrow_synonym: beach berm
has_narrow_synonym: lagoon beach
has_related_synonym: beach
has_related_synonym: beaches
has_related_synonym: foreshore flats
has_related_synonym: rivage
has_related_synonym: strand

Axiom
annotated source: beach
annotated property: definition
annotated target: A landform consisting of loose rock particles such as sand, gravel, shingle, pebbles, cobble, or even shell fragments along the shoreline of a body of water.
database_cross_reference: https://en.wikipedia.org/wiki/Beach

Axiom
annotated source: beach
annotated property: has exact synonym
annotated target: Beach
database_cross_reference: NASA:earthrealm

Axiom
annotated source: beach
annotated property: has_narrow_synonym
annotated target: beach berm
database_cross_reference: USGS:SDTS

Axiom
annotated source: beach
annotated property: has_narrow_synonym
annotated target: lagoon beach
database_cross_reference: USGS:SDTS

Axiom
annotated source: beach
annotated property: has_related_synonym
annotated target: beach
database_cross_reference: Geonames:feature

Axiom
annotated source: beach
annotated property: has_related_synonym
annotated target: beaches
database_cross_reference: Geonames:feature

Axiom
annotated source: beach
annotated property: has_related_synonym
annotated target: foreshore flats
database_cross_reference: USGS:SDTS

Axiom
annotated source: beach
annotated property: has_related_synonym
annotated target: rivage
database_cross_reference: USGS:SDTS

Axiom
annotated source: beach
annotated property: has_related_synonym
annotated target: strand
database_cross_reference: ADL:FTT

Axiom
annotated source: beach
annotated property: has_related_synonym
annotated target: strand
database_cross_reference: USGS:SDTS

grassland
type: Class
subclass of: outdoor environment
subclass of: vegetated area
has curation status: External
definition: An area in which grasses (Graminae) are a significant component of the vegetation
definition: An area in which grasses (Graminae) are a significant component of the vegetation.
has_related_synonym: grazing area
has_related_synonym: herbaceous area
label: grassland area

Axiom
annotated source: grassland
annotated property: definition
annotated target: An area in which grasses (Graminae) are a significant component of the vegetation.
database_cross_reference: https://en.wikipedia.org/wiki/Grassland

Axiom
annotated source: grassland
annotated property: has_related_synonym
annotated target: grazing area
database_cross_reference: Getty:TGN

Axiom
annotated source: grassland
annotated property: has_related_synonym
annotated target: herbaceous area
database_cross_reference: USGS:SDTS

woodland area
type: Class
subclass of: vegetated area
definition: Land having a cover of trees, shrubs, or both.
database_cross_reference: FTT:1083
database_cross_reference: FTT:505
database_cross_reference: FTT:506
database_cross_reference: FTT:719
database_cross_reference: FTT:774
database_cross_reference: Geonames:V.GRVPN
database_cross_reference: LTER:503
database_cross_reference: SWEETRealm:Break
database_cross_reference: SWEETRealm:Scrub
database_cross_reference: TGN:21631
database_cross_reference: TGN:21632
database_cross_reference: TGN:21641
database_cross_reference: https://en.wikipedia.org/wiki/Woodland
has_narrow_synonym: brigalow
has_narrow_synonym: pine grove
has_related_synonym: caatinga
has_related_synonym: chanaral
has_related_synonym: coniferous forest
has_related_synonym: copse
has_related_synonym: deciduous forest
has_related_synonym: equatorial forest
has_related_synonym: equatorial rain forest
has_related_synonym: garique
has_related_synonym: grove
has_related_synonym: jungle
has_related_synonym: mallee scrub
has_related_synonym: monsoon forest
has_related_synonym: moor
has_related_synonym: mott
has_related_synonym: motte
has_related_synonym: mulga
has_related_synonym: mulga scrub
has_related_synonym: rain forest
has_related_synonym: reforested area
has_related_synonym: sagebrush
has_related_synonym: scrub
has_related_synonym: shrub
has_related_synonym: silva
has_related_synonym: stand
has_related_synonym: taiga
has_related_synonym: thicket
has_related_synonym: thorn forest
has_related_synonym: wood
has_related_synonym: wooded area

Axiom
annotated source: woodland area
annotated property: definition
annotated target: Land having a cover of trees, shrubs, or both.
database_cross_reference: USGS:SDTS

Axiom
annotated source: woodland area
annotated property: has_narrow_synonym
annotated target: brigalow
database_cross_reference: USGS:SDTS

Axiom
annotated source: woodland area
annotated property: has_narrow_synonym
annotated target: pine grove
database_cross_reference: Geonames:feature

Axiom
annotated source: woodland area
annotated property: has_related_synonym
annotated target: caatinga
database_cross_reference: USGS:SDTS

Axiom
annotated source: woodland area
annotated property: has_related_synonym
annotated target: chanaral
database_cross_reference: USGS:SDTS

Axiom
annotated source: woodland area
annotated property: has_related_synonym
annotated target: coniferous forest
database_cross_reference: USGS:SDTS

Axiom
annotated source: woodland area
annotated property: has_related_synonym
annotated target: copse
database_cross_reference: USGS:SDTS

Axiom
annotated source: woodland area
annotated property: has_related_synonym
annotated target: deciduous forest
database_cross_reference: USGS:SDTS

Axiom
annotated source: woodland area
annotated property: has_related_synonym
annotated target: equatorial forest
database_cross_reference: USGS:SDTS

Axiom
annotated source: woodland area
annotated property: has_related_synonym
annotated target: equatorial rain forest
database_cross_reference: USGS:SDTS

Axiom
annotated source: woodland area
annotated property: has_related_synonym
annotated target: garique
database_cross_reference: USGS:SDTS

Axiom
annotated source: woodland area
annotated property: has_related_synonym
annotated target: grove
database_cross_reference: ADL:FTT

Axiom
annotated source: woodland area
annotated property: has_related_synonym
annotated target: grove
database_cross_reference: USGS:SDTS

Axiom
annotated source: woodland area
annotated property: has_related_synonym
annotated target: jungle
database_cross_reference: Getty:TGN

Axiom
annotated source: woodland area
annotated property: has_related_synonym
annotated target: jungle
database_cross_reference: USGS:SDTS

Axiom
annotated source: woodland area
annotated property: has_related_synonym
annotated target: mallee scrub
database_cross_reference: USGS:SDTS

Axiom
annotated source: woodland area
annotated property: has_related_synonym
annotated target: monsoon forest
database_cross_reference: USGS:SDTS

Axiom
annotated source: woodland area
annotated property: has_related_synonym
annotated target: moor
database_cross_reference: USGS:SDTS

Axiom
annotated source: woodland area
annotated property: has_related_synonym
annotated target: motte
database_cross_reference: USGS:SDTS

Axiom
annotated source: woodland area
annotated property: has_related_synonym
annotated target: mulga
database_cross_reference: USGS:SDTS

Axiom
annotated source: woodland area
annotated property: has_related_synonym
annotated target: mulga scrub
database_cross_reference: USGS:SDTS

Axiom
annotated source: woodland area
annotated property: has_related_synonym
annotated target: rain forest
database_cross_reference: ADL:FTT

Axiom
annotated source: woodland area
annotated property: has_related_synonym
annotated target: rain forest
database_cross_reference: Getty:TGN

Axiom
annotated source: woodland area
annotated property: has_related_synonym
annotated target: reforested area
database_cross_reference: USGS:SDTS

Axiom
annotated source: woodland area
annotated property: has_related_synonym
annotated target: sagebrush
database_cross_reference: USGS:SDTS

Axiom
annotated source: woodland area
annotated property: has_related_synonym
annotated target: scrub
database_cross_reference: USGS:SDTS

Axiom
annotated source: woodland area
annotated property: has_related_synonym
annotated target: shrub
database_cross_reference: USGS:SDTS

Axiom
annotated source: woodland area
annotated property: has_related_synonym
annotated target: silva
database_cross_reference: USGS:SDTS

Axiom
annotated source: woodland area
annotated property: has_related_synonym
annotated target: stand
database_cross_reference: USGS:SDTS

Axiom
annotated source: woodland area
annotated property: has_related_synonym
annotated target: taiga
database_cross_reference: USGS:SDTS

Axiom
annotated source: woodland area
annotated property: has_related_synonym
annotated target: thicket
database_cross_reference: USGS:SDTS

Axiom
annotated source: woodland area
annotated property: has_related_synonym
annotated target: thorn forest
database_cross_reference: USGS:SDTS

Axiom
annotated source: woodland area
annotated property: has_related_synonym
annotated target: wood
database_cross_reference: Getty:TGN

Axiom
annotated source: woodland area
annotated property: has_related_synonym
annotated target: wooded area
database_cross_reference: USGS:SDTS

forest
type: Class
subclass of: outdoor environment
subclass of: woodland area
has curation status: External
definition: An area with a high density of trees. A small forest may be called a wood
definition: An area with a high density of trees. A small forest may be called a wood.
database_cross_reference: EcoLexicon:forest
database_cross_reference: FTT:258
database_cross_reference: FTT:506
database_cross_reference: FTT:715
database_cross_reference: FTT:717
database_cross_reference: Geonames:V.FRST
database_cross_reference: LTER:2
database_cross_reference: SWEETRealm:Forest
database_cross_reference: TGN:21641
database_cross_reference: TGN:21642
database_cross_reference: TGN:21645
database_cross_reference: https://en.wikipedia.org/wiki/Forest
has_related_synonym: forest
has_related_synonym: wood
comment: The definitions of forest can vary greatly, and different classes will be needed to support the major categories. Tree cover alone is not enough to distinguish between forests and plantations. The international definition proposed by the 2010 FAO Forestry Resource Assessment: "land spanning more than 0.5 ha with trees higher than 5 metres and canopy cover of more than 10 percent, or trees able to reach these thresholds in situ . It does not include land that is predominantly under agricultural or urban land use." - FAO. 2010. Global forest resources assessment 2010, Main report, FAO Forestry Paper 163. Rome.
label: forested area

Axiom
annotated source: forest
annotated property: definition
annotated target: An area with a high density of trees. A small forest may be called a wood.
database_cross_reference: https://en.wikipedia.org/wiki/Forest

Axiom
annotated source: forest
annotated property: has_related_synonym
annotated target: forest
database_cross_reference: Geonames:feature

Axiom
annotated source: forest
annotated property: has_related_synonym
annotated target: wood
database_cross_reference: Getty:TGN

solid astronomical body part
type: Class
subclass of: astronomical body part
subclass of: compound astronomical body part
definition: A part of an astronomical body which is primarily composed of solid material.
database_cross_reference: EcoLexicon:landform
database_cross_reference: EcoLexicon:landforms
database_cross_reference: FTT:754
database_cross_reference: FTT:96
database_cross_reference: SWEETRealm:Landform
database_cross_reference: TGN:21400
database_cross_reference: TGN:21401
has_related_synonym: geological feature
has_related_synonym: landform
has_related_synonym: physiographic feature

Axiom
annotated source: solid astronomical body part
annotated property: definition
annotated target: A part of an astronomical body which is primarily composed of solid material.
database_cross_reference: https://en.wikipedia.org/wiki/Landform

Axiom
annotated source: solid astronomical body part
annotated property: has_related_synonym
annotated target: geological feature
database_cross_reference: ADL:FTT

research facility
type: Class
subclass of: human construction
subclass of: facility
has curation status: External
definition: A facility, permanent or temporary, on land, in air, space or water, where scientific research or measurements can be undertaken
definition: A facility, permanent or temporary, on land, in air, space or water, where scientific research or measurements can be undertaken.

Axiom
annotated source: research facility
annotated property: definition
annotated target: A facility, permanent or temporary, on land, in air, space or water, where scientific research or measurements can be undertaken.
database_cross_reference: MA:ma

park
type: Class
subclass of: outdoor environment
subclass of: anthropogenic geographic feature
has curation status: External
definition: A bounded area of land, or water, usually in its natural or semi-natural (landscaped) state and set aside for some purpose, usually to do with recreation or conservation
definition: A bounded area of land, or water, usually in its natural or semi-natural (landscaped) state and set aside for some purpose, usually to do with recreation or conservation.

Axiom
annotated source: park
annotated property: definition
annotated target: A bounded area of land, or water, usually in its natural or semi-natural (landscaped) state and set aside for some purpose, usually to do with recreation or conservation.
database_cross_reference: https://en.wikipedia.org/wiki/Park

environmental zone
type: Class
subclass of: fiat object
definition: A site which has its extent determined by the presence or influence of one or more components of an environmental system or the processes occurring therein.
has_related_synonym: environmental area
in_subset: envoPolar
comment: Formerly, this class was an experimental class and a subclass of "environmental feature". It is now aligned to BFO. The class was not obsoleted as the core semantics maintained their stability through its transition.

astronomical body part
type: Class
subclass of: material entity
definition: A material part of an astronomical body.
editor note: Also note that some astronomical body parts (ABPs) may have fiat boundaries: if there's strong debate about where an ABP begins or ends (over and above fuzzy boundaries), with different official classifications setting different thresholds or limits, axiomatise the class with fiat boundaries of the appropriate dimension.
editor note: Note that material entities may have immaterial entities (e.g. sites) as parts.
editor note: This class includes material parts of astronomical bodies. Immaterial parts, such as magnetospheres, are represented as sites under the influence of magnetic fields.Please post countercases in the ENVO tracker for revision of this hierarchy if needed.
in_subset: envoAstro
in_subset: envoPolar
comment: Material parts of astronomical bodies generally have boundaries formed by discontinuities in qualities, composition, or other physical characterisitcs. These boundaries are sometimes sharp, and sometimes diffuse, with different classification systems and communities declaring varying thresholds (e.g. for where a shoreline, forest, or other entity begins and ends). However, some boundaries are declared by fiat - that is, by arbitrary human convention or decree - particularly by regulatory or other authorities and communities of practice. The classes in this hierarchy attempt to offer generalisable definitions that allow multiple classfiication systems to map to and interoperate through. If desired, we can create classes that declare thresholds used by a given authority or community under the more generic ones, annotated with source information.

terrestrial environmental zone
type: Class
subclass of: environmental zone
subclass of: astronomical body part
definition: An environmental zone which is bounded by material parts of a land mass or the atmosphere or space adjacent to it.

constructed pavement
type: Class
subclass of: transport feature
definition: A construction which comprises a durable surface layer overlying a solid surface intended to sustain vehicular or foot traffic.

Axiom
annotated source: constructed pavement
annotated property: definition
annotated target: A construction which comprises a durable surface layer overlying a solid surface intended to sustain vehicular or foot traffic.
database_cross_reference: https://en.wikipedia.org/wiki/Road_surface

vegetated area
type: Class
subclass of: terrestrial environmental zone
definition: A vegetated area is a geographic feature which has ground cover dominated by plant communities.
created_by: ORCID:0000-0002-4366-3088
in_subset: envoPolar

compound astronomical body part
type: Class
subclass of: astronomical body part
definition: A part of an astronomical body which is composed of a continuous medium bearing liquid, gaseous, and solid material in variable quantities.
creator: https://orcid.org/0000-0002-4366-3088
date: 2019-10-17T08:36:00Z

Axiom
annotated source: compound astronomical body part
annotated property: definition
annotated target: A part of an astronomical body which is composed of a continuous medium bearing liquid, gaseous, and solid material in variable quantities.
database_cross_reference: https://en.wikipedia.org/wiki/Landform

construction
type: Class
subclass of: material entity
definition: A material entity which has been assembled through the intentional, instinctual, or deliberately programmed efforts of an organism or machine.
creator: https://orcid.org/0000-0002-4366-3088
date: 2019-10-29T14:50:34Z

surface landform
type: Class
subclass of: landform
definition: A landform which occurs on the surface of an astronomical body.
creator: https://orcid.org/0000-0002-4366-3088
date: 2021-05-15T09:16:23Z
has_related_synonym: geographic feature
comment: The usage of "surface" here aligns with that of planetary surface: in contact with the atmosphere or space. The extent of the "surface" can vary. For rocky planets like Earth, astrogeologists consider the crust as the surface.

landform
type: Class
subclass of: solid astronomical body part
definition: A solid astronomical body part which has been formed from and is composed primarily of the matter of that astronomical body.
creator: https://orcid.org/0000-0002-4366-3088
date: 2021-05-15T09:40:37Z
comment: Landforms may be natural or anthropogenic. This term has often has loose usage when referencing entities which are either subterranean or submerged below water bodies. In some cases, oceans themselves are considered landforms. Here, we have provided subclasses to resolve this ambiguity, but place oceans and other water bodies elsewhere.In later revisions, this hiearchy is likely to be reordered based on the formation processes of the entities within it.

Axiom
annotated source: landform
annotated property: definition
annotated target: A solid astronomical body part which has been formed from and is composed primarily of the matter of that astronomical body.
database_cross_reference: Landform

geographic location
type: Class
subclass of: spatial region
subclass of: Thing
has curation status: External
definition: A reference to a place on the Earth, by its name or by its geographical location
definition: A reference to a place on the Earth, by its name or by its geographical location.
definition source: Gazeteer Ontology
has_alternative_id: GAZ:00000467
has exact synonym: geographic region {alternative name}
has_obo_namespace: GAZ
id: GAZ:00000448
label: geographical location

data item
type: Class
subclass of: information entity
editor preferred label: data item
example of usage: Data items include counts of things, analyte concentrations, and statistical summaries.
has curation status: IAO_0000122
has curation status: IAO_0000125
has curation status: External
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 that reliably tends to produce (approximately) truthful statements.
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
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Jonathan Rees
alternative term: data
imported from: iao.owl
imported from: obi.owl
imported from: ogms.owl

information entity
type: Class
subclass of: generically dependent continuant
subclass of: experimental factor
editor preferred label: information content entity
example of usage: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
has curation status: IAO_0000122
has curation status: External
definition: A generically dependent continuant that is about some thing.
definition: A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc.
definition: An information entity is an entity that represents information about some other entity. For example, a measurement, a clustered data set.
definition: an information content entity is an entity that is generically dependent on some material entity and stands in relation of aboutness to some entity
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.
definition editor: James Malone
definition editor: PERSON: Chris Stoeckert
definition source: OBI_0000142
imported from: iao.owl
imported from: obi.owl
imported from: ogms.owl
array express label: information
EFO URI: http://www.ebi.ac.uk/efo/EFO_0001435
organizational class: true
source definition: an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity
has exact synonym: information content entity
label: information content entity
label: textual entity

directive information entity
type: Class
subclass of: information entity
has curation status: IAO_0000122
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
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters

plan specification
type: Class
subclass of: directive information entity
editor preferred label: plan specification
example of usage: PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
has curation status: IAO_0000122
definition: A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, 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: 2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231.
editor note: Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
definition editor: Alan Ruttenberg
definition editor: Clint Dowland
definition source: OBI Plan and Planned Process branch
definition source: OBI_0000344
comment: 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them

measurement data item
type: Class
subclass of: data item
editor preferred label: measurement datum
example of usage: Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
has curation status: IAO_0000125
has curation status: External
definition: A data item that is a recording of the output of an assay.
definition: A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
editor note: 2/2/2009 is_specified_output of some assay?
definition editor: person:Chris Stoeckert
definition source: OBI_0000305
definition source: group:OBI
imported from: obi.owl
label: measurement datum

textual entity
type: Class
subclass of: information entity
editor preferred label: textual entity
example of usage: Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
has curation status: IAO_0000123
definition: A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc.
editor note: AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc.
editor note: MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities.
definition editor: PERSON: Lawrence Hunter
alternative term: text

citation
type: Class
subclass of: textual entity
editor preferred label: citation
example of usage: Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183.
has curation status: IAO_0000125
definition: A textual entity intended to identify a particular publication.
definition editor: PERSON: Lawrence Hunter

institutional identification
type: Class
subclass of: information entity
has curation status: External
definition: A textual entity intended to identify a particular institution.

written name
type: Class
subclass of: information entity
has curation status: External
definition: A textual entity that denotes a particular in reality.

funding source declaration textual entity
type: Class
subclass of: information entity
has curation status: External
definition: A textual entity documenting the source of funding that supported some study.

related work textual entity
type: Class
subclass of: information entity
has curation status: External
definition: A textual entity that discusses work from other publications and expresses their relevancy to the content of a document.

mental functioning related anatomical structure
type: Class
subclass of: fiat object
has curation status: External
definition: An anatomical structure in which there inheres the disposition to be the agent of a mental process.
definition source: http://www.jbiomedsem.com/content/1/1/10

human being
type: Class
subclass of: extended organism
definition: An extended organism that is a member of the species Homo sapiens.
alternative term: person
label: person

mental process
type: Class
subclass of: bodily process
has curation status: External
definition: A bodily process that occurs in the brain, and that can of itself be conscious, or can give rise to a process that can of itself be conscious or can give rise to behaviour.
comment: A 'mental process' is a subclass of 'bodily process', as mental processes occur within the body, specifically involving the brain.
comment: A bodily process which brings into being, sustains or modifies a cognitive representation or a behavior inducing state.
comment: Examples include thinking, feeling pain, remembering and emotion as occurrent experiences.
comment: Mental processes can vary in the degree to which they involve consciousness. A 'mental process' is a subclass of 'bodily process', as mental processes occur within the body, specifically involving the brain.
comment: Mental processes can varying in the degree to which they involve consciousness.
see also: GO:0050890, cognition, defined as `The operation of the mind by which an organism becomes aware of objects of thought or perception; it includes the mental activities associated with thinking, learning, and memory.'

representation
type: Class
subclass of: specifically dependent continuant
definition: A dependent continuant which is about a portion of reality.
definition source: http://www.jbiomedsem.com/content/1/1/10

cognitive representation
type: Class
subclass of: representation
definition: A representation which specifically depends on an anatomical structure in the cognitive system of an organism.
definition source: http://www.jbiomedsem.com/content/1/1/10

bodily disposition
type: Class
subclass of: disposition
has curation status: External
definition: A bodily disposition is a disposition that inheres in some extended organism. Examples are: my disposition to catch a cold when exposed to a virus, my ability to speak the English language.
definition: A disposition that inheres in some extended organism.
alternative term: personal disposition
comment: Bodily disposition includes features that can be used in a specific context, such as a person's strength, but not a person's weight. A person has a specific weight independent of the circumstances they are in.
comment: Extended organism refers to an organism and its microbiome (e.g., the bacteria that live in one's digestive system) Bodily disposition would include features, such as a person's strength (which can be used in a specific context), but not weight. A person would have a certain weight independent of most circumstances they are in.
comment: Extended organism refers to an organism and its microbiome (e.g., the bacteria that live in one's digestive system).

mental disposition
type: Class
subclass of: bodily disposition
has curation status: External
definition: A bodily disposition that is realized in a mental process.
definition: A mental disposition is a bodily disposition that is realized in a mental process.
comment: 'Mental disposition' is a subclass of 'bodily disposition', as mental dispositions occur in the body.
comment: Mental disposition' is a subclass of 'bodily disposition', as mental dispositions occur in the body.

belief
type: Class
subclass of: mental disposition
has curation status: External
definition: A mental disposition to represent a proposition to be true.
comment: Judging is a mental process that brings a belief into existence. Judging differently may also bring that belief out of existence. An act of believing is just thinking about a belief. Beliefs typically cause us to behave in ways that are characteristic with the content of that belief. However, this is not a necessary feature for the existence of the belief.

bodily quality
type: Class
subclass of: quality
definition: A bodily quality is a quality that inheres in some extended organism.

measurement scale
type: Class
subclass of: information entity
has curation status: External
definition: An information content entity that represents a type of scale on which a variable is measured, including nominal, ordinal, interval, ratio.

power calculation
type: Class
subclass of: data transformation
has curation status: External
definition: A data transformation that is used to calculate the power of a statistical analysis.

confidence interval
type: Class
subclass of: quantitative confidence value
has curation status: External
definition: A quantitative confidence value that refers to an interval give values within which there is a high probability (95 percent by convention) that the true population value can be found.

standard deviation
type: Class
subclass of: quantitative confidence value
has curation status: External
definition: A quantitative confidence value that measures the variability of data around the mean.
definition editor: Yongqun He
definition source: WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms

derived data from statistical analysis
type: Class
subclass of: data item
subclass of: transformed data item
definition: A data item that is derived from a statistical data analysis.
definition editor: Jie Zheng, Yongqun He, Marcy Harris, Asiyah Yu Lin
alternative term: statistic
definition source: WEB: http://en.wikipedia.org/wiki/Statistic
definition source: WEB: http://www.ask.com/question/what-is-numerical-data

derived data from inferential statistical analysis
type: Class
subclass of: data item
subclass of: derived data from statistical analysis
definition: A data item that is derived from an inferential statistical data analysis.
definition editor: Jie Zheng, Yongqun He
alternative term: inferential statistic
definition source: WEB: http://psc.dss.ucdavis.edu/sommerb/sommerdemo/stat_inf/intro.htm
definition source: WEB: http://www.ask.com/question/what-is-numerical-data

95% confidence interval
type: Class
subclass of: confidence interval
has curation status: External
definition: A confidence interval with 95 percent probability that the true population value can be found.

transformed data item
type: Class
subclass of: data item
definition: A data item that is produced as the output of a data transformation.
definition editor: Person: Jie Zheng, Oliver He

planned process
type: Class
subclass of: process
subclass of: planned process
subclass of: Activity
editor preferred label: planned process
example of usage: Injecting mice with a vaccine in order to test its efficacy
has curation status: IAO_0000122
has curation status: Proposed
definition: A process that realizes a plan which is the concretization of a plan specification.
definition: A processual entity that realizes a plan which is the concretization of a plan specification.
editor note: 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
editor note: We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
definition 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
label: completely executed planned process

quantitative confidence value
type: Class
subclass of: data item
subclass of: derived data from inferential statistical analysis
editor preferred label: quantitative confidence value
has curation status: IAO_0000125
definition: A data item which is used to indicate the degree of uncertainty about a measurement.
definition editor: person:Chris Stoeckert
definition source: group:OBI
imported from: obi.owl

p-value
type: Class
subclass of: quantitative confidence value
has curation status: External
definition: A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.

standard error
type: Class
subclass of: quantitative confidence value
has curation status: External
definition: A quantitative confidence value which is the standard deviations of the sample in a frequency distribution, obtained by dividing the standard deviation by the total number of cases in the frequency distribution.

center value
type: Class
subclass of: data item
has curation status: External
definition: A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data.

average value
type: Class
subclass of: data item
has curation status: External
definition: A data item that is produced as the output of an averaging data transformation and represents the average value of the input data.

dose
type: Class
subclass of: measurement data item
has curation status: External
definition: A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses.

selection criterion
type: Class
subclass of: directive information entity
editor preferred label: selection criterion
example of usage: rats should be aged between 6 and 8 weeks and weight between 180-250grams
has curation status: IAO_0000122
definition: A directive information entity which defines and states a principle of standard by which selection process may take place.
definition editor: Person: Philippe Rocca-Serra
alternative term: selection rule
definition source: OBI discussion summarized under the following tracker item : http://sourceforge.net/p/obi/obi-terms/678/

data transformation
type: Class
subclass of: planned process
editor preferred label: data transformation
example of usage: The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
has curation status: IAO_0000122
definition: A planned process that produces output data from input data.
definition editor: Elisabetta Manduchi
definition editor: Helen Parkinson
definition editor: James Malone
definition editor: Melanie Courtot
definition editor: Philippe Rocca-Serra
definition editor: Richard Scheuermann
definition editor: Ryan Brinkman
definition editor: Tina Hernandez-Boussard
alternative term: data analysis
alternative term: data processing
definition source: Branch editors
imported from: obi.owl

arithmetic mean calculation
type: Class
subclass of: dataset creating
subclass of: averaging data transformation
subclass of: center calculation data transformation
subclass of: descriptive statistical calculation data transformation
editor preferred label: arithmetic mean calculation
has curation status: IAO_0000120
definition: An arithmetic mean calculation is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment.
definition editor: James Malone
definition editor: Monnie McGee
definition editor: Philippe Rocca-Serra
definition source: PERSON: James Malone
definition source: PERSON: Monnie McGee
curator note: From Monnie's file comments - need to add moment_calculation and center_calculation roles but they don't exist yet - (editor note added by James Jan 2008)

averaging data transformation
type: Class
subclass of: data transformation
editor preferred label: averaging data transformation
has curation status: IAO_0000123
definition: An averaging data transformation is a data transformation that has objective averaging.
definition editor: James Malone
definition source: PERSON: James Malone

center calculation data transformation
type: Class
subclass of: data transformation
editor preferred label: center calculation data transformation
has curation status: IAO_0000123
definition: A center calculation data transformation is a data transformation that has objective of center calculation.
definition editor: James Malone
definition source: PERSON: James Malone

descriptive statistical calculation data transformation
type: Class
subclass of: data transformation
editor preferred label: descriptive statistical calculation data transformation
has curation status: IAO_0000122
definition: A descriptive statistical calculation data transformation is a data transformation that has objective descriptive statistical calculation and which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability.
definition editor: James Malone
definition source: PERSON: James Malone

study design
type: Class
subclass of: plan specification
has curation status: External
definition: A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.

parallel group design
type: Class
subclass of: study design
has curation status: External
definition: A parallel group design or independent measure design is a study design which uses unique experimental unit each experimental group, in other word no two individuals are shared between experimental groups, hence also known as parallel group design.

eligibility criterion
type: Class
subclass of: selection criterion
editor preferred label: eligibility criterion
example of usage: PMID: 17579629 -Eligibility criteria included: untreated ED-SCLC; age >/=70 and performance status 0-2, or age <70 and PS 3.
has curation status: IAO_0000122
definition: an eligibility criterion (rule) is_a selection criterion which defines and states the requirements (positive or negative) for an entity to be considered as suitable for a given task or participation in a process.
definition editor: Person: Philippe Rocca-Serra
alternative term: eligibility rule
definition source: Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group

inclusion criterion
type: Class
subclass of: eligibility criterion
editor preferred label: inclusion criterion
example of usage: PMID: 23979341-The major inclusion criterion was patients in whom severe cerebral embolism was diagnosed at age 75 or younger (more than 9 in the NIHSS score on day 7 after the onset of stroke) .
has curation status: IAO_0000125
has curation status: External
definition: An eligibility criterion which defines and states a condition which, if met, makes an entity suitable for a given task or participation in a given process.
definition: an inclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity suitable for a given task or participation in a given process. For instance, in a study protocol, inclusion criteria indicate the conditions that prospective subjects MUST meet to be eligible for participation in a study.
definition editor: Person: Philippe Rocca-Serra
alternative term: inclusion condition
alternative term: inclusion rule
definition source: Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group

exclusion criterion
type: Class
subclass of: eligibility criterion
editor preferred label: exclusion rule
example of usage: PMID: 17600285-Exclusion criteria included the use of any topical ophthalmic or topical oral medication and/or history of ocular or oral surgery within the past six months.
has curation status: IAO_0000125
has curation status: External
definition: An eligibility criterion which defines and states a condition which, if met, makes an entity unsuitable for a given task or participation in a given process.
definition: an exclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity unsuitable for a given task or participation in a given process. For instance, in a study protocol, exclusion criteria indicate the conditions that prospective subjects SHOULD NOT meet to be eligible for participation in a study
definition editor: Person: Philippe Rocca-Serra
definition source: Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group

clinical history
type: Class
subclass of: clinical data item
definition: A series of statements representing health-relevant qualities of a patient and of a patient's family.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2010-07-19T10:18:59Z

symptom
type: Class
subclass of: process
has curation status: External
definition: A process experienced by the patient, which can only be experienced by the patient, that is hypothesized to be clinically relevant.
editor note: note: defined class
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2010-11-18T11:02:10Z Updated: 2020-07-06

bodily process
type: Class
subclass of: process
has curation status: External
definition: A process in which at least one bodily component of an organism participates.
definition: A process in which at least one bodily component of an organsim participates.
definition editor: Albert Goldfain
definition source: http://www.jbiomedsem.com/content/1/1/10
curator note: creation date: 2009-06-23T11:53:49Z
comment: From OGMS: http://purl.obolibrary.org/obo/OGMS_0000060
comment: The phrase 'bodily component of an organism’ in the definition refers to ‘a part of the body’.

pathological bodily process
type: Class
subclass of: bodily process
has curation status: External
definition: A bodily process that is clinically abnormal.

diagnosis
type: Class
subclass of: data item
subclass of: clinical data item
has curation status: External
definition: The representation of a conclusion of a diagnostic process.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T12:42:23Z
imported from: ogms.owl

extended organism
type: Class
subclass of: material entity
definition: An object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism.
definition editor: Albert Goldfain
definition source: http://code.google.com/p/ogms/issues/detail
curator note: creation date: 2010-01-25T04:51:11Z
comment: From OGMS: http://purl.obolibrary.org/obo/OGMS_0000087

health care process
type: Class
subclass of: planned process
definition: A planned process with the objective to improve the health status of a patient that directly involves the treatment, diagnosis, or prevention of disease or injury of a patient
definition editor: Albert Goldfain Sagar Jain
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6
curator note: creation date: 2011-02-21T09:57:44Z editor date: 2017-04-18

clinical data item
type: Class
subclass of: data item
has curation status: External
definition: A data item that is about a patient and is the specified output of a health care process assay or diagnostic process
definition: A data item that is about a patient and is the specified output of a health care process assay or diagnostic process.
curator note: creation date: 2018-11-27

comorbidity
type: Class
subclass of: diagnosis
has curation status: External
definition: A diagnosis that is the outcome of a diagnostic process targeting a second or additional health problem.
definition editor: Alice Nzinga
definition editor: Mathias Brochhausen
alternative term: secondary infection, nosocomial infection
definition source: amended from http://en.wikipedia.org/wiki/Comorbidity
comment: It is argued that Comorbidity occurs due to a disposition established by a prior infection with a pathogenic organism of a different kind.
comment: Relation between person and diagnosis needs to be specified

architectural structure
type: Class
subclass of: material entity
definition: A material entity that is a human made strcuture with firm connection between its foundation and the ground.
definition editor: Mathias Brochhausen
definition source: http://de.wikipedia.org/wiki/Bauwerk
comment: "Building" is a subclass of this.
comment: This type of entity is referred to as "Bauwerk" or "Bauliche Anlage".

facility
type: Class
subclass of: site
subclass of: architectural structure
has curation status: External
definition: An architectural structure that bears some function.
definition editor: Mathias Brochhausen
definition source: Ontology of Medically Related Social Entities

hospital facility
type: Class
subclass of: healthcare facility
has curation status: External
definition: A facility that is run by a hospital organization, such as emergency departments, outpatient clinics and rehabilitation and is the bearer of a hospital function
definition: A health care facility that bears the function to provide acute and intensive healthcare services and that is run by a hospital organization and is the bearer of a hospital function.
definition editor: Mathias Brochhausen
definition editor: William Hogan

healthcare facility
type: Class
subclass of: facility
has curation status: External
definition: A facility that’s administered by a health care organisation for the purpose of providing health care to a patient population
definition editor: A facility bearing the function to provide healthcare and that is administered by a health care organization for the purpose of providing health care to a patient or patient population.
definition editor: William Hogan
definition source: Ontology of Medically Related Social Entities
label: health care facility

hospice facility
type: Class
subclass of: healthcare facility
has curation status: External
definition: A health care facility that bears a function to provide healthcare to the sick or terminally ill
definition editor: Amanda Hicks
definition editor: Emma Norris
definition editor: William Hogan
definition source: Human Behaviour Change Project

rehabilitation facility
type: Class
subclass of: healthcare facility
subclass of: community living health care facility
has curation status: External
definition: A facility to assist in physical or addiction recovery
definition editor: Amanda Hicks
definition editor: Emma Norris
definition editor: William Hogan
definition source: Human Behaviour Change Project

community living health care facility
type: Class
subclass of: healthcare facility
definition: a health care facility that also bears a residence function and thus one in which the patients are also residents of the facility

residential facility
type: Class
subclass of: facility
editor preferred label: residential facility
has curation status: External
definition: A facility that has at least one housing unit as part in which a person or persons live
definition editor: Emma Norris
definition editor: William Hogan
definition source: Modified version of definition provided by Human Behaviour Change Project

status
type: Class
subclass of: realizable entity
definition editor: Oliver He, Edison Ong

study status
type: Class
subclass of: status
has curation status: External
definition: The current stage of a clinical study and whether it is or will be open for enrollment
definition: The current stage of a clinical study and whether it is or will be open for enrolment.
definition editor: Oliver He
definition source: https://clinicaltrials.gov/ct2/help/glossary/recruitment-status

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

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

weight
type: Class
subclass of: force
has curation status: External
definition: A physical quality inhering in a bearer that has mass near a gravitational body.

physical quality
type: Class
subclass of: physical object quality
definition: A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
has_alternative_id: PATO:0002079
database_cross_reference: Wikipedia:Physical_property
has exact synonym: relational physical quality
has_obo_namespace: quality
id: PATO:0001018
in_subset: attribute slim

Axiom
annotated source: physical quality
annotated property: definition
annotated target: A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
database_cross_reference: PATOC:GVG

force
type: Class
subclass of: physical quality
definition: A physical quality inhering in a bearer by virtue of the bearer's rate of change of momentum.
has exact synonym: force amplitude
has_obo_namespace: quality
id: PATO:0001035
in_subset: attribute slim
in_subset: scalar slim

Axiom
annotated source: force
annotated property: definition
annotated target: A physical quality inhering in a bearer by virtue of the bearer's rate of change of momentum.
database_cross_reference: thesaurus.maths:thesaurus.maths

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

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

pharmacy facility
type: Class
subclass of: healthcare facility
has curation status: External
definition: A health care facility whose function is to store, prepare, dispense, and monitor the usage of pharmaceutical drugs among patients in a given area or encountered in a given health care provider organization
definition: A health care facility whose function is to store, prepare, dispense, and monitor the usage of pharmaceutical drugs among patients in a given area or encountered in a given health care provider organization.
definition: Un établissement de santé qui a pour fonction d'entreposer, préparer, distribuer et surveiller l'utilisation des médicaments parmi les patients d'une zone géographique donnée ou suivis dans une organisation de soin donnée. @fr
label: établissement de pharmacologie @fr

protein
type: Class
subclass of: amino acid chain
subclass of: protein-containing molecular entity
definition: An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.
has exact synonym: natural protein
has_narrow_synonym: native protein
has_obo_namespace: protein
id: PR:000000001
comment: The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB].

Axiom
annotated source: protein
annotated property: definition
annotated target: An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.
database_cross_reference: PRO:DAN
database_cross_reference: PRO:WCB

Axiom
annotated source: protein
annotated property: has exact synonym
annotated target: natural protein
database_cross_reference: PRO:DAN

Axiom
annotated source: protein
annotated property: has_narrow_synonym
annotated target: native protein
database_cross_reference: IEDB:BP

rhodopsin-like G-protein coupled receptor
type: Class
subclass of: G-protein coupled receptor
definition: A G-protein coupled receptor that contains the 7 transmembrane receptor (rhodopsin family) domain (Pfam:PF00001), which includes 7 transmembrane helices (TMI-TM7) with 3 intracellular loops (IL1-IL3) and 3 extracellular loops (EL1-EL3) between the helices. The amino-terminal region is extracellular and the carboxyl-terminal region is intracellular. Rhodopsin-like G-protein coupled receptors (GPCRs) are unique among the several classes of GPCRs in that most have a very short amino-terminal segment and several characteristic sequence motifs, particularly NSxxNPxxY in TM7 and D/E-R-Y/F between TM3 and loop IL2. Most bind their ligands within a cavity between the TM regions.
database_cross_reference: IUPHAR:GPCRListForward?class=A
database_cross_reference: PIRSF:PIRSF800006
has exact synonym: class 1 G-protein coupled receptor
has exact synonym: class A G-protein coupled receptor
has exact synonym: fam:rhodopsin
has_obo_namespace: protein
id: PR:000001094
comment: Category=family. Classification based on GRAFS system. [PMID:12761335]

Axiom
annotated source: rhodopsin-like G-protein coupled receptor
annotated property: definition
annotated target: A G-protein coupled receptor that contains the 7 transmembrane receptor (rhodopsin family) domain (Pfam:PF00001), which includes 7 transmembrane helices (TMI-TM7) with 3 intracellular loops (IL1-IL3) and 3 extracellular loops (EL1-EL3) between the helices. The amino-terminal region is extracellular and the carboxyl-terminal region is intracellular. Rhodopsin-like G-protein coupled receptors (GPCRs) are unique among the several classes of GPCRs in that most have a very short amino-terminal segment and several characteristic sequence motifs, particularly NSxxNPxxY in TM7 and D/E-R-Y/F between TM3 and loop IL2. Most bind their ligands within a cavity between the TM regions.
database_cross_reference: PMID:12761335
database_cross_reference: PRO:DAN
database_cross_reference: PRO:WCB

Axiom
annotated source: rhodopsin-like G-protein coupled receptor
annotated property: has exact synonym
annotated target: class 1 G-protein coupled receptor
database_cross_reference: PMID:15914470

Axiom
annotated source: rhodopsin-like G-protein coupled receptor
annotated property: has exact synonym
annotated target: class A G-protein coupled receptor
database_cross_reference: IUPHAR:GPCRListForward?class=A

Axiom
annotated source: rhodopsin-like G-protein coupled receptor
annotated property: has exact synonym
annotated target: fam:rhodopsin
database_cross_reference: PRO:DAN
has synonym type: PRO-short-label

trace amine receptor
type: Class
subclass of: rhodopsin-like G-protein coupled receptor
has curation status: External
definition: A rhodopsin-like G-protein coupled receptor that is related to trace amine-associated receptor 1 (TAAR1) and characterized by the sequence motif NSxxNPxx[YH]xxx[YF]xWF overlapping TM7.
definition: A rhodopsin-like G-protein coupled receptor that is related to trace amine-associated receptor 1 (TAAR1) and characterized by the sequence motif NSxxNPxx[YH]xxx[YF]xWF overlapping TM7. Trace amines are biogenic amines present in very low levels in mammalian tissues. Their physiological roles in mammals are poorly understood. Some of them are neurotransmitters in invertebrates. Ligands are currently known for only two TAARs, TAAR1 in human, rat, and mouse, and TAAR4 in rat.
alternative term: trace-amine-associated receptor, trace amine associated receptor
database_cross_reference: IUPHARfam:64
database_cross_reference: PIRSF:PIRSF038555
has exact synonym: TAAR
has_obo_namespace: protein
has_related_synonym: trace amine-associated receptor
has_related_synonym: trace-amine-associated receptor
id: PR:000001558
comment: Category=family.

Axiom
annotated source: trace amine receptor
annotated property: definition
annotated target: A rhodopsin-like G-protein coupled receptor that is related to trace amine-associated receptor 1 (TAAR1) and characterized by the sequence motif NSxxNPxx[YH]xxx[YF]xWF overlapping TM7. Trace amines are biogenic amines present in very low levels in mammalian tissues. Their physiological roles in mammals are poorly understood. Some of them are neurotransmitters in invertebrates. Ligands are currently known for only two TAARs, TAAR1 in human, rat, and mouse, and TAAR4 in rat.
database_cross_reference: PMID:11459929
database_cross_reference: PMID:15718104
database_cross_reference: PMID:16584120
database_cross_reference: PMID:17088868
database_cross_reference: PRO:WCB

trace amine-associated receptor 1-4
type: Class
subclass of: trace amine receptor
definition: A trace amine receptor that is a member of a subfamily comprising TAAR1, TAAR2, TAAR3P and TAAR4.
has_obo_namespace: protein
id: PR:000001678
comment: Category=family.

Axiom
annotated source: trace amine-associated receptor 1-4
annotated property: definition
annotated target: A trace amine receptor that is a member of a subfamily comprising TAAR1, TAAR2, TAAR3P and TAAR4.
database_cross_reference: PMID:15718104
database_cross_reference: PRO:WCB

trace amine-associated receptor 1
type: Class
subclass of: trace amine-associated receptor 1-4
has curation status: External
definition: A trace amine-associated receptor 1-4 that is a translation product of the human TAAR1 gene or a 1:1 ortholog thereof.
definition: A trace amine-associated receptor 1-4 that is a translation product of the human TAAR1 gene or a 1:1 ortholog thereof. The preferred ligands of the human protein are trace amines, including beta-phenylethylamine, p-tyramine, octopamine and tryptamine. It is unresponsive to amines such as epinephrine and histamine and only partially activated by dopamine and serotonine.
alternative term: TRAR1, TAAR1, TAR1, TA1
database_cross_reference: IUPHARobj:364
has exact synonym: TAAR1
has exact synonym: TaR-1
has exact synonym: trace amine receptor 1
has_obo_namespace: protein
has_related_synonym: TA1
has_related_synonym: TAR1
has_related_synonym: TRAR1
id: PR:000001711
comment: Category=gene.

Axiom
annotated source: trace amine-associated receptor 1
annotated property: definition
annotated target: A trace amine-associated receptor 1-4 that is a translation product of the human TAAR1 gene or a 1:1 ortholog thereof. The preferred ligands of the human protein are trace amines, including beta-phenylethylamine, p-tyramine, octopamine and tryptamine. It is unresponsive to amines such as epinephrine and histamine and only partially activated by dopamine and serotonine.
database_cross_reference: PRO:WCB
database_cross_reference: UniProtKB:Q96RJ0

Axiom
annotated source: trace amine-associated receptor 1
annotated property: has exact synonym
annotated target: TAAR1
database_cross_reference: PRO:DNx
has synonym type: PRO-short-label

Axiom
annotated source: trace amine-associated receptor 1
annotated property: has_related_synonym
annotated target: TA1
has synonym type: Gene-based

Axiom
annotated source: trace amine-associated receptor 1
annotated property: has_related_synonym
annotated target: TAR1
has synonym type: Gene-based

Axiom
annotated source: trace amine-associated receptor 1
annotated property: has_related_synonym
annotated target: TRAR1
has synonym type: Gene-based

amino acid chain
type: Class
subclass of: organic amino compound
definition: An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds.
has_narrow_synonym: peptide
has_narrow_synonym: polypeptide
has_obo_namespace: protein
id: PR:000018263
comment: Category=polymer.

Axiom
annotated source: amino acid chain
annotated property: definition
annotated target: An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds.
database_cross_reference: PRO:DAN
database_cross_reference: PRO:JSG

Axiom
annotated source: amino acid chain
annotated property: has_narrow_synonym
annotated target: peptide
database_cross_reference: PRO:DAN

Axiom
annotated source: amino acid chain
annotated property: has_narrow_synonym
annotated target: polypeptide
database_cross_reference: PRO:DAN

G-protein coupled receptor
type: Class
subclass of: protein
definition: A protein that has G protein-coupled receptor (GPCR) activity. Each GPCR consists of a single polypeptide with an extracellular N-terminus, an intracellular C-terminus and seven hydrophobic transmembrane domains (TM1-TM7) linked by three extracellular loops (ECL1-ECL3) and three intracellular loops (ICL1-ICL3). GPCRs function as part of a heterotrimeric complex to transmit an extracellular signal across the membrane by activating an associated G-protein via the exchange of GDP for GTP on the alpha subunit.
has_broad_synonym: 7TM receptor
has_broad_synonym: seven-transmembrane receptor
database_cross_reference: IUPHARfam:694
has exact synonym: fam:GPCR
has_obo_namespace: protein
id: PR:000030035
comment: Category=family. Classification based on GRAFS system. [PMID:12761335]

Axiom
annotated source: G-protein coupled receptor
annotated property: definition
annotated target: A protein that has G protein-coupled receptor (GPCR) activity. Each GPCR consists of a single polypeptide with an extracellular N-terminus, an intracellular C-terminus and seven hydrophobic transmembrane domains (TM1-TM7) linked by three extracellular loops (ECL1-ECL3) and three intracellular loops (ICL1-ICL3). GPCRs function as part of a heterotrimeric complex to transmit an extracellular signal across the membrane by activating an associated G-protein via the exchange of GDP for GTP on the alpha subunit.
database_cross_reference: IUPHARfam:694
database_cross_reference: PRO:DAN
database_cross_reference: Wikipedia:GPCR

Axiom
annotated source: G-protein coupled receptor
annotated property: has_broad_synonym
annotated target: 7TM receptor
database_cross_reference: IUPHARfam:694

Axiom
annotated source: G-protein coupled receptor
annotated property: has_broad_synonym
annotated target: seven-transmembrane receptor
database_cross_reference: IUPHARfam:694

Axiom
annotated source: G-protein coupled receptor
annotated property: has exact synonym
annotated target: fam:GPCR
database_cross_reference: PRO:DAN
has synonym type: PRO-short-label

protein-containing molecular entity
type: Class
subclass of: molecular entity
definition: A molecular entity that minimally consists of a protein.
has_narrow_synonym: protein
has_narrow_synonym: protein aggregate
has_narrow_synonym: protein complex
has_narrow_synonym: protein-containing complex
has_obo_namespace: protein
id: PR:000064867
comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565).

Axiom
annotated source: protein-containing molecular entity
annotated property: definition
annotated target: A molecular entity that minimally consists of a protein.
database_cross_reference: PRO:DAN

Axiom
annotated source: protein-containing molecular entity
annotated property: has_narrow_synonym
annotated target: protein
database_cross_reference: PRO:DAN

Axiom
annotated source: protein-containing molecular entity
annotated property: has_narrow_synonym
annotated target: protein aggregate
database_cross_reference: PRO:DAN

Axiom
annotated source: protein-containing molecular entity
annotated property: has_narrow_synonym
annotated target: protein complex
database_cross_reference: PRO:DAN

Axiom
annotated source: protein-containing molecular entity
annotated property: has_narrow_synonym
annotated target: protein-containing complex
database_cross_reference: PRO:DAN

research activity
type: Class
subclass of: planned process
definition: A planned process executed in the performance of scientific research wherein systematic investigations are performed to establish facts and reach new conclusions about phenomena in the world.
comment: Data generation process are typically experimental studies or observations, but can include any process generating information used to evaluate a claim. This is an organizational class that groups more specific types of such processes that are most commonly used in generating data used as evidence to support claims. These processes produce informational artifacts such as measured data values, derived statistical calculations and confidence measures, or statements representing summaries or conclusions drawn from such data.

research study
type: Class
subclass of: research activity
definition: A planned process that executes some study design or protocol to generate scientific data that is interpreted to test or generate a hypothesis.
SEPIO_editor_note: Explore the classification of study types here as a possibility to implement in SEPIO. https://mcw.libguides.com/evidencebased/studies Useful because these map to the strength of the evidence each might provide.
comment: A research study is considered broadly to be any scientific activity aimed at answering a research question. Studies can be simple or complex, depending on the scope of the question being explored and the extent of resources deployed in doing so. They may include a full research investigation, a set of experiments, or a single experiment or assay. Regardless, that act of summarizing any results as a finding statement is considered part of the study.
comment: A research study is considered broadly to be any scientific activity aimed at answering a research question. Studies can be simple or complex, depending on the scope of the question being explored and the extent of resources deployed in doing so. They may include a full research investigation, a set of related experiments, or a single experiment or assay. Regardless, that act of summarizing any results as a finding statement is considered part of the study. 'Study' here is broadly considered to include any defined activity performed to address a scientific question or generate a scientific hypothesis. It covers scientific inquiry at different scales of complexity, from a single assay, experiment or observation, to a complex research investigation addressing a broader scientific question. Studies can be based on a broad range of methods, including in silico algorithms, in vitro or in vivo experimentation on model systems, clinical studies on human subjects, or curation and analysis of existing knowledge, e.g. from publications, datasets, or knowledegbases, to derive novel insight.

minimum value
type: Class
subclass of: measurement data item
has curation status: IAO_0000122
has curation status: External
definition: A data item which denotes the smallest value found in a dataset or resulting from a calculation.
definition: a minimum value is a data item which denotes the smallest value found in a dataset or resulting from a calculation.
definition editor: Alejandra Gonzalez-Beltran
definition editor: Orlaith Burke
definition editor: Philippe Rocca-Serra
definition source: STATO

maximum value
type: Class
subclass of: measurement data item
has curation status: IAO_0000122
has curation status: External
definition: A data item which denotes the largest value found in a dataset or resulting from a calculation.
definition: maximum value is a data item which denotes the largest value found in a dataset or resulting from a calculation.
definition editor: Alejandra Gonzalez-Beltran
definition editor: Orlaith Burke
definition editor: Philippe Rocca-Serra
definition source: STATO

ratio
type: Class
subclass of: data item
has curation status: IAO_0000125
definition: A ratio is a data item which is formed with two numbers r and s is written r/s, where r is the numerator and s is the denominator. The ratio of r to s is equivalent to the quotient r/s.
editor note: review formal definition as both numerator and denominator should be of the same type, not just some data item
definition editor: Alejandra Gonzalez-Beltran
definition editor: Orlaith Burke
definition editor: Philippe Rocca-Serra
definition source: adapted from Wolfram Alpha: https://www.wolframalpha.com/share/clip?f=d41d8cd98f00b204e9800998ecf8427efdcsig76g7

prevalence
type: Class
subclass of: ratio
has curation status: IAO_0000122
definition: prevalence is a ratio formed by the number of subjects diagnosed with a disease divided by the total population size.
definition editor: Philippe Rocca-Serra
definition source: adapted from: https://www.health.ny.gov/diseases/chronic/basicstat.htm

experimental factor
type: Class
subclass of: generically dependent continuant
subclass of: Thing
has curation status: External
definition: An experimental factor in Array Express which are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This upper level class is really used to give a root class from which applications can rely on and not be tied to upper ontology classses which do change.
definition editor: Helen Parkinson
definition editor: James Malone
definition editor: Jie Zheng
definition editor: Tomasz Adamusiak
organizational class: true
created_by: Helen Parkinson
created_by: James Malone
created_by: Tomasz Adamusiak
database_cross_reference: MO:10
has exact synonym: ExperimentalFactor
comment: Concept naming convention is lower case natural naming with spaces, when necessary captials should be used, for example disease factor, HIV, breast carcinoma, Ewing's sarcoma

measurement
type: Class
subclass of: information entity
definition: A measurement is an information entity that is a recording of the output of a measurement such as produced by an instrument.
definition editor: James Malone
definition editor: Jie Zheng
definition editor: Tomasz Adamusiak
branch class: true
database_cross_reference: MO:144
database_cross_reference: NCIt:C25209
database_cross_reference: NIFSTD:sao279801585
database_cross_reference: SNOMEDCT:122869004

cardiovascular measurement
type: Class
subclass of: measurement
definition: A cardiovascular measurement is a measurement of some part of the cardiovascular system and is typically used in the process of disease diagnosis in human patients.
definition editor: Dani Welter
gwas trait: true
database_cross_reference: MeSH:D003935
database_cross_reference: SNOMEDCT:113021009
has exact synonym: Diagnostic Techniques, Cardiovascular
has exact synonym: cardiovascular diagnostic technique

glucose measurement
type: Class
subclass of: measurement
subclass of: diabetes mellitus biomarker
has curation status: External
definition: Is any quantification of glucose.
definition editor: Helen Parkinson
gwas trait: true
database_cross_reference: ICD10:R73
database_cross_reference: NCIt:C105585
database_cross_reference: SNOMEDCT:36048009
has exact synonym: glucose level

hematological measurement
type: Class
subclass of: measurement
definition: A measurement quantifying some blood cell, or component.
definition editor: Helen Parkinson
gwas trait: true

hemoglobin measurement
type: Class
subclass of: hematological measurement
subclass of: protein measurement
definition: Hemoglobin measurement is a measure of the quantity of the metallo protein hemoglobin in blood often used in the diagnosis of anaemia.
definition: hemoglobin levels
definition editor: Helen Parkinson
gwas trait: true
database_cross_reference: NCIt:C64848
has exact synonym: Hb
has exact synonym: haemoglobin measurement
has exact synonym: hemoglobin count

lipid measurement
type: Class
subclass of: measurement
subclass of: lipid or lipoprotein measurement
definition: A measure of circulating lipid
definition editor: Helen Parkinson
gwas trait: true
database_cross_reference: NCIt:C74949

triglyceride measurement
type: Class
subclass of: lipid measurement
has curation status: External
definition: A triglyceride measurement is a quantification of triglycerides in some body fluid, used as a biomarker for cardiovascular disease.
definition editor: Helen Parkinson
gwas trait: true
database_cross_reference: NCIt:C64812
has exact synonym: triglyceride levels

HbA1c measurement
type: Class
subclass of: measurement
subclass of: glucose measurement
subclass of: hemoglobin measurement
subclass of: glycoprotein measurement
has curation status: External
definition: A quantification of glycated A1c hemoglobin in blood used as an index for blood glucose level over several months.
editor note: Glycated hemoglobin is preferred over glycosylated hemoglobin to reflect the correct (non-enyzmatic) process. Early literature often used glycosylated as it was unclear which process was involved until further research was performed. The terms are still sometimes used interchangeably in English language literature. (See https://en.wikipedia.org/wiki/Glycated_hemoglobin)
definition editor: Helen Parkinson
definition editor: Zoe May Pendlington
gwas trait: true
database_cross_reference: NCIt:C64849
has exact synonym: A1C measurement
has exact synonym: A1c measurement
has exact synonym: Glycosylated Hemoglobin
has exact synonym: Glycosylated Hemoglobin Measurement
has exact synonym: HBA1C
has exact synonym: HbA1c levels
has exact synonym: Hemoglobin A1C
has exact synonym: glycated hemoglobin levels
has exact synonym: glycosylated Haemoglobin A level
has exact synonym: glycosylated Hemoglobin A level

glycoprotein measurement
type: Class
subclass of: measurement
subclass of: protein measurement
definition: Is the quantification of some glycoprotein.
definition editor: Helen Parkinson
gwas trait: true

total cholesterol measurement
type: Class
subclass of: lipid measurement
subclass of: lipoprotein measurement
has curation status: External
definition: A total cholesterol measurement is the quantification of cholesterol in blood, total cholesterol is defined as the sum of HDL, LDL, and VLDL.
definition editor: Helen Parkinson
gwas trait: true
database_cross_reference: SNOMEDCT:121868005
has exact synonym: cholesterol, total
has exact synonym: total cholesterol levels

low density lipoprotein cholesterol measurement
type: Class
subclass of: lipid measurement
subclass of: lipoprotein measurement
subclass of: cardiovascular disease biomarker measurement
has curation status: External
definition: The measurement of LDL cholesterol in blood used as a risk indicator for heart disease.
definition editor: Helen Parkinson
gwas trait: true
database_cross_reference: NCIt:C105588
database_cross_reference: SNOMEDCT:113079009
has exact synonym: LDL measurement

high density lipoprotein cholesterol measurement
type: Class
subclass of: lipid measurement
subclass of: lipoprotein measurement
has curation status: External
definition: The measurement of HDL cholesterol in blood used as a risk indicator for heart disease.
gwas trait: true
database_cross_reference: MedDRA:10020060
database_cross_reference: NCIt:C105587
database_cross_reference: SNOMEDCT:28036006
has exact synonym: HDL measurement

hormone measurement
type: Class
subclass of: measurement
definition: The determination of the amount of hormone present in a sample.
gwas trait: true
database_cross_reference: NCIt:C74742
database_cross_reference: SNOMEDCT:122445005

lipoprotein measurement
type: Class
subclass of: measurement
subclass of: protein measurement
subclass of: lipid or lipoprotein measurement
definition: Is the quantification of some lipoprotein
definition editor: Helen Parkinson
gwas trait: true

protein measurement
type: Class
subclass of: measurement
definition: Is a quantification of some protein, typically obtained from an individual with the intention of using the measurement in some diagnostic process.
definition: This is a general class for any measurement of a protein. Do not annotate to this class, request a more specific child term.
definition editor: Helen Parkinson
gwas trait: true
database_cross_reference: SNOMEDCT:74040009
has exact synonym: protein levels

lipid or lipoprotein measurement
type: Class
subclass of: measurement
definition: quantification of some lipid or lipoprotein
definition editor: Dani Welter
gwas trait: true

cardiovascular disease biomarker measurement
type: Class
subclass of: measurement
subclass of: cardiovascular measurement
definition: cardiovascular disease biomarkers, such as ST2 cardiac biomarker and C-reactive protein, are used as indicators for cardiovascular disease and as predictors for therapeutic responses
definition editor: Dani Welter
gwas trait: true

diabetes mellitus biomarker
type: Class
subclass of: measurement
definition editor: Helen Parkinson
definition editor: The quantification of a biomarker used in the diagnosis or management of diabetes mellitus
gwas trait: true

prolactin measurement
type: Class
subclass of: hormone measurement
has curation status: External
definition: Quantification of prolactin in a sample.
definition: quantification of prolactin in a sample
definition editor: Dani Welter
gwas trait: true

Activity
type: Class
subclass of: process
definition: An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities.

dose of pharmacological substance
type: Class
subclass of: dose
has curation status: Proposed
definition: Dose of pharmacological substance delivered to an individual.

drug name
type: Class
subclass of: written name
has curation status: Proposed
definition: A written name intended to identify a particular drug.

frequency of pharmacological substance dose
type: Class
subclass of: data item
has curation status: Proposed
definition: A data item that is about the number of times a dose of pharmacological substance is delivered during an intervention.

intervention arm name
type: Class
subclass of: written name
has curation status: Proposed
definition: A written name intended to identify a particular intervention arm.

intervention duration
type: Class
subclass of: one-dimensional temporal region
has curation status: Proposed
definition: A temporal interval between the start and end of an intervention.

maximum dose of pharmacological substance
type: Class
subclass of: maximum value
has curation status: Proposed
definition: A maximum value of the dose of pharmacological substance delivered to individuals in a group.

average dose of pharmacological substance
type: Class
subclass of: average value
has curation status: Proposed
definition: A average value of dose of pharmacological substance delivered to individuals in a group.

minimum dose of pharmacological substance
type: Class
subclass of: minimum value
has curation status: Proposed
definition: A minimum value of the dose of pharmacological substance delivered to individuals in a group.

placebo intervention
type: Class
subclass of: intervention
has curation status: Proposed
definition: An intervention that has the same or similar appearance and delivery to another intervention but is intended not to have the active content of that intervention.

Abnormal Involuntary Movement Scale data item
type: Class
subclass of: measurement data item
has curation status: Proposed
definition: A measurement data item that is the recording of the output of the Abnormal Involuntary Movement Scale.
alternative term: AIMS score
definition source: Guy, W. (1976). ECDEU assessment manual for psychopharmacology. US Department of Health, Education, and Welfare, Public Health Service, Alcohol, Drug Abuse, and Mental Health Administration, National Institute of Mental Health, Psychopharmacology Research Branch, Division of Extramural Research Programs.
curator note: A measure for 'dyskinesias' and 'dyskinesias following an intervention'

Anxiety and depression subscale of Positive and Negative Syndrome Scale data item
type: Class
subclass of: Positive and Negative Syndrome Scale data item
has curation status: Proposed
definition: Positive and Negative Syndrome Scale data item that is the recording of the output of the subscale about affective psychotic disorder symptoms.
alternative term: PANSS Depression/Anxiety score
definition source: https://academic.oup.com/schizophreniabulletin/article/13/2/261/1919795
curator note: A measure for 'affective psychotic disorder symptom severity'

Anxiety subscale of Positive and Negative Syndrome Scale data item
type: Class
subclass of: Positive and Negative Syndrome Scale data item
has curation status: Proposed
definition: Positive and Negative Syndrome Scale data item that is the recording of the output of the subscale about anxiety symptoms.
alternative term: PANSS anxiety score
definition source: https://academic.oup.com/schizophreniabulletin/article/13/2/261/1919795
curator note: A measure for 'affective psychotic disorder symptom severity'

Barnes Akathisia Rating Scale data item
type: Class
subclass of: measurement data item
has curation status: Proposed
definition: A measurement data item that is the recording of the output of the Barnes Akathisia Rating Scale.
alternative term: BARS score
definition source: https://www.cambridge.org/core/journals/the-british-journal-of-psychiatry/article/abs/rating-scale-for-druginduced-akathisia/77334A34A80E801C6297640C63701866
curator note: A measure for 'akathisia' and 'akathisia following an intervention'

Brief Negative Symptom Scale data item
type: Class
subclass of: measurement data item
has curation status: Proposed
definition: A measurement data item that is the recording of the output of the Brief Negative Symptom Scale.
alternative term: BNSS score
definition source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3044634/
curator note: A measure for 'negative psychotic disorder symptom severity'

Brief Psychiatric Rating Scale data item
type: Class
subclass of: measurement data item
has curation status: Proposed
definition: A measurement data item that is the recording of the output of the Brief Psychiatric Rating Scale.
alternative term: BPRS score
definition source: https://journals.sagepub.com/doi/abs/10.2466/pr0.1962.10.3.799
curator note: A measure for 'psychotic disorder symptom severity'

Clinical Global Impression data item
type: Class
subclass of: measurement data item
has curation status: Proposed
definition: A measurement data item that is the recording of the output of the Clinical Global Impression scale.
alternative term: CGI score
definition source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2880930/

Clinical Global Impression – Improvement data item
type: Class
subclass of: Clinical Global Impression data item
has curation status: Proposed
definition: Clinical Global Impression data item about the improvement in a person's condition.
alternative term: CGI-I score
definition source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2880930/
curator note: A measure for 'human functioning'

Clinical Global Impressions - Severity data item
type: Class
subclass of: Clinical Global Impression data item
has curation status: Proposed
definition: Clinical Global Impression data item about the severity of a disorder.
alternative term: CGI-S score
definition source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2880930/
curator note: A measure for 'human functioning'

Columbia-Suicide Severity Rating Scale data item
type: Class
subclass of: measurement data item
has curation status: Proposed
definition: A measurement data item that is the recording of the output of the Columbia-Suicide Severity Rating Scale.
alternative term: C-SSRS score
definition source: https://ajp.psychiatryonline.org/doi/full/10.1176/appi.ajp.2011.10111704

Columbia-Suicide Severity Rating Scale ideation data item
type: Class
subclass of: Columbia-Suicide Severity Rating Scale data item
has curation status: Proposed
definition: Columbia-Suicide Severity Rating Scale data item about suicidal ideation.
alternative term: C-SSRS suicide ideation score
definition source: https://ajp.psychiatryonline.org/doi/full/10.1176/appi.ajp.2011.10111704
curator note: A measure for 'suicidal ideation' and 'suicidal ideation following intervention'

Columbia-Suicide Severity Rating Scale suicide attempt data item
type: Class
subclass of: Columbia-Suicide Severity Rating Scale data item
has curation status: Proposed
definition: Columbia-Suicide Severity Rating Scale data item about suicide attempts.
alternative term: C-SSRS suicide attempt data
definition source: https://ajp.psychiatryonline.org/doi/full/10.1176/appi.ajp.2011.10111704
curator note: A measure for 'suicidal attempt' and 'suicidal attempt following intervention'

Depression subscale of Positive and Negative Syndrome Scale data item
type: Class
subclass of: Positive and Negative Syndrome Scale data item
has curation status: Proposed
definition: Positive and Negative Syndrome Scale data item that is the recording of the output of the subscale about depression symptoms.
alternative term: PANSS depression score
definition source: https://academic.oup.com/schizophreniabulletin/article/13/2/261/1919795
curator note: A measure for 'depression symptom severity'

EuroQol five dimensions questionnaire-3 levels data item
type: Class
subclass of: measurement data item
has curation status: Proposed
definition: A measurement data item that is the recording of the output of the EuroQol five dimensions questionnaire-3 levels.
alternative term: EQ-5D-3L score
definition source: https://euroqol.org/information-and-support/euroqol-instruments/eq-5d-3l/
curator note: A measure for 'belief about quality of life'

Montgomery and Asberg Depression Rating Scale data item
type: Class
subclass of: measurement data item
has curation status: Proposed
definition: A measurement data item that is the recording of the output of the Montgomery and Asberg Depression Rating Scale.
alternative term: MADRS score
definition source: https://www.cambridge.org/core/journals/the-british-journal-of-psychiatry/article/abs/new-depression-scale-designed-to-be-sensitive-to-change/94D3798EAE4FD0EF2FC50FF671E9AE5D
curator note: A measure for 'depression symptom severity'

Negative subscale of Positive and Negative Syndrome Scale data item
type: Class
subclass of: Positive and Negative Syndrome Scale data item
has curation status: Proposed
definition: Positive and Negative Syndrome Scale data item that is the recording of the output of the subscale about negative psychotic disorder symptoms.
alternative term: PANSS negative scale score
definition source: https://academic.oup.com/schizophreniabulletin/article/13/2/261/1919795
curator note: A measure for 'negative psychotic disorder symptom severity'

Personal and Social Performance Scale data item
type: Class
subclass of: measurement data item
has curation status: Proposed
definition: A measurement data item that is the recording of the output of the Personal and Social Performance Scale.
alternative term: PSP score
definition source: https://psycnet.apa.org/doiLanding
curator note: A measure for 'human functioning'

Positive and Negative Syndrome Scale data item
type: Class
subclass of: measurement data item
has curation status: Proposed
definition: A measurement data item that is the recording of the output of the Positive and Negative Syndrome Scale.
alternative term: PANSS score
definition source: https://academic.oup.com/schizophreniabulletin/article/13/2/261/1919795

Positive subscale of Positive and Negative Syndrome Scale data item
type: Class
subclass of: Positive and Negative Syndrome Scale data item
has curation status: Proposed
definition: Positive and Negative Syndrome Scale data item that is the recording of the output of the subscale about positive psychotic disorder symptoms.
alternative term: PANSS positive scale score
definition source: https://academic.oup.com/schizophreniabulletin/article/13/2/261/1919795

Scale for Assessment of Positive Symptoms for Parkinson's disease data item
type: Class
subclass of: measurement data item
has curation status: Proposed
definition: A measurement data item that is the recording of the output of the Scale for Assessment of Positive Symptoms for Parkinson's disease.
alternative term: SAPS-PD score
definition source: https://movementdisorders.onlinelibrary.wiley.com/doi/full/10.1002/mds.22575
curator note: A measure for 'positive psychotic disorder symptom severity'

Simpson Angus Scale data item
type: Class
subclass of: measurement data item
has curation status: Proposed
definition: A measurement data item that is the recording of the output of the Simpson Angus Scale data item.
alternative term: SAS score
definition source: https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1600-0447.1970.tb02066.x
curator note: A measure for 'neuroleptic-induced parkinsonism' and 'neuroleptic-induced parkinsonism following an intervention'

The Neuropsychiatric Inventory Huntington's disease data item
type: Class
subclass of: measurement data item
has curation status: Proposed
definition: A measurement data item that is the recording of the output of the Neuropsychiatric Inventory Huntington's disease.
alternative term: NPI-HD score
definition source: https://www.neurology.org/doi/abs/10.1212/wnl.44.12.2308
curator note: A measure for 'psychotic disorder symptom severity'

Unified Parkinson's Disease Rating Scale Part 3 data item
type: Class
subclass of: measurement data item
has curation status: Proposed
definition: A measurement data item that is the recording of the output of the Unified Parkinson's Disease Rating Scale Part 3.
alternative term: UPDRS-III score
definition source: Fahn, S. R. L. E. (1987). Unified Parkinson's disease rating scale. Recent developments in Parkinson's disease, 153-163.
curator note: A measure for 'drug-induced movement disorder' and 'drug-induced movement disorder following an intervention'

University of California, San Diego Performance-Based Skills Assessment-Brief
type: Class
subclass of: measurement data item
has curation status: Proposed
definition: A measurement data item that is the recording of the output of the University of California, San Diego Performance-Based Skills Assessment-Brief.
alternative term: UPSA-B score
definition source: https://academic.oup.com/schizophreniabulletin/article/33/6/1364/1900584
curator note: A measure for 'human functioning'

adverse change in HbA1c measurement
type: Class
subclass of: adverse change in a bodily measurement parameter
has curation status: Proposed
definition: An adverse change in a bodily measurement parameter relating to HbA1c measurement.

adverse change in a bodily measurement parameter
type: Class
subclass of: adverse event following an intervention
has curation status: Proposed
definition: An adverse event associated with a change in a person's bodily meeasurement parameters.
definition source: Based on http://purl.obolibrary.org/obo/OAE_0000581

adverse change in body mass index
type: Class
subclass of: adverse change in a bodily measurement parameter
has curation status: Proposed
definition: An adverse change in a bodily measurement parameter relating to the body mass index.

adverse change in body weight
type: Class
subclass of: adverse change in a bodily measurement parameter
has curation status: Proposed
definition: An adverse change in a bodily measurement parameter relating to body weight.

adverse change in glucose measurement
type: Class
subclass of: adverse change in a bodily measurement parameter
has curation status: Proposed
definition: An adverse change in a bodily measurement parameter relating to glucose measurement.

adverse change in high density lipoprotein cholesterol measurement
type: Class
subclass of: adverse change in a bodily measurement parameter
has curation status: Proposed
definition: An adverse change in a bodily measurement parameter relating to the high density lipoprotein cholesterol measurement.

adverse change in low density lipoprotein cholesterol measurement
type: Class
subclass of: adverse change in a bodily measurement parameter
has curation status: Proposed
definition: An adverse change in a bodily measurement parameter relating to the low density lipoprotein cholesterol measurement.

adverse change in prolactin measurement
type: Class
subclass of: adverse change in a bodily measurement parameter
has curation status: Proposed
definition: An adverse change in a bodily measurement parameter relating to prolactin measurement.

adverse change in prolactin measurement of females
type: Class
subclass of: adverse change in prolactin measurement
has curation status: Proposed
definition: An adverse change in prolactin measurement in people with female gender.

adverse change in prolactin measurement of males
type: Class
subclass of: adverse change in prolactin measurement
has curation status: Proposed
definition: An adverse change in prolactin measurement in people with male gender.

adverse change in total cholesterol measurement
type: Class
subclass of: adverse change in a bodily measurement parameter
has curation status: Proposed
definition: An adverse change in a bodily measurement parameter relating to the total cholesterol measurement.

adverse change in triglyceride measurement
type: Class
subclass of: adverse change in a bodily measurement parameter
has curation status: Proposed
definition: An adverse change in a bodily measurement parameter relating to triglyceride measurement.

adverse event following an intervention
type: Class
subclass of: pathological bodily process
has curation status: Proposed
definition: A pathological bodily process that occurs after the intervention delivery starts.

affective psychotic disorder symptom
type: Class
subclass of: psychotic disorder symptom
has curation status: Proposed
definition: A psychotic disorder symptom is characterized by a person experiencing depression, anxiety or low moods.

affective psychotic disorder symptom severity
type: Class
subclass of: symptom severity
has curation status: Proposed
definition: Symptom severity that is associated with an affective psychotic disorder symptom.

akathisia following pharmacological intervention
type: Class
subclass of: drug-induced movement disorder following intervention
has curation status: Proposed
definition: A drug-induced movement disorder following intervention that involves feeling restlessness, increased urges to move and reduced capability to suppress such urges.
definition source: Based on https://www.ncbi.nlm.nih.gov/books/NBK519543/

belief about drug safety
type: Class
subclass of: belief about drug-related adverse events
has curation status: Proposed
definition: A belief about the degree to which a drug results in harm to a person.
definition source: Based on Alshammari, T. M. (2016). Drug safety: The concept, inception and its importance in patients’ health. Saudi Pharmaceutical Journal, 24(4), 405-412.

belief about drug-related adverse events
type: Class
subclass of: belief
has curation status: Proposed
definition: A belief about about the negative effects of a drug on a person.

belief about intervention acceptability
type: Class
subclass of: belief
has curation status: Proposed
definition: A belief about whether the delivered intervention is appropriate based on anticipated or experienced responses to the intervention.
definition source: Based on Sekhon, M., Cartwright, M., and Francis, J. J. (2017). Acceptability of healthcare interventions: an overview of reviews and development of a theoretical framework. BMC health services research, 17(1), 1-13.

belief about tolerability of drug
type: Class
subclass of: belief about drug-related adverse events
has curation status: Proposed
definition: A belief about the degree to which a drug results in unpleasant or bothersome bodily reactions.
definition source: Based on Stanulović, V., Hodolic, M., Mitsikostas, D. D., and Papadopoulos, D. (2022). Drug tolerability: how much ambiguity can be tolerated? A systematic review of the assessment of tolerability in clinical studies. British Journal of Clinical Pharmacology, 88(2), 551-565.

body mass index
type: Class
subclass of: data item
has curation status: Proposed
definition: A data item that is derived by dividing the body weight be the square of the body height.
definition source: Based on Nuttall F. Q. (2015). Body Mass Index: Obesity, BMI, and Health: A Critical Review. Nutrition today, 50(3), 117–128. https://doi.org/10.1097/NT.0000000000000092

body weight
type: Class
subclass of: weight
has curation status: Proposed
definition: Weight of an organism.

death due to accidents following an intervention
type: Class
subclass of: death following an intervention
has curation status: Proposed
definition: A death following an intervention that involves a participant dying as a result of an accident.

death due to natural causes following an intervention
type: Class
subclass of: death following an intervention
has curation status: Proposed
definition: A death following an intervention that results from an illness or its complications or an internal bodily malfunction that is not directly caused by external events.
definition source: Based on https://en.wikipedia.org/wiki/Manner_of_death

death following an intervention
type: Class
subclass of: serious adverse event following an intervention
has curation status: Proposed
definition: A serious adverse event following an intervention that has an outcome of death.

depression symptom
type: Class
subclass of: symptom
has curation status: Proposed
definition: A symptom that is related to a depression diagnosis.
alternative term: depressive symptom

depression symptom severity
type: Class
subclass of: symptom severity
has curation status: Proposed
definition: Symptom severity that is associated with a depression symptom.
definition: Symptom severity that is associated with a depression symtom.

drug-induced movement disorder following intervention
type: Class
subclass of: adverse event following an intervention
has curation status: Proposed
definition: An adverse event following a pharmacological intervention that involves reduced abilities to control movements.
alternative term: extrapyramidal symptom following intervention
definition source: Based on https://www.ncbi.nlm.nih.gov/books/NBK534115/

dyskinesias following an intervention
type: Class
subclass of: adverse event following an intervention
has curation status: Proposed
definition: An adverse event following an intervention that involves dyskinesias.

homicide following an intervention
type: Class
subclass of: death following an intervention
has curation status: Proposed
definition: A death following an intervention that involves a participant being intentionally killed by another person.

hospitalization
type: Class
subclass of: health care process
has curation status: Proposed
definition: A health care process that involves a person being admitted to a hospital.

human functioning
type: Class
subclass of: bodily disposition
has curation status: Proposed
definition: A bodily disposition to realise processes that influence a person's life quality.

negative psychotic disorder symptom
type: Class
subclass of: psychotic disorder symptom
has curation status: Proposed
definition: A psychotic disorder symptom that is characterized by the absence or decrease in ability or motivation to initiate plans, speak, express emotion of find pleasure.
definition source: Based on https://www.psychiatry.org/patients-families/schizophrenia/what-is-schizophrenia

negative psychotic disorder symptom severity
type: Class
subclass of: psychotic disorder symptom severity
has curation status: Proposed
definition: Psychotic disorder symptom severity that is associated with negative psychotic disorder symptoms.

neuroleptic-induced parkinsonism following intervention
type: Class
subclass of: drug-induced movement disorder following intervention
has curation status: Proposed
definition: A drug-induced movement disorder following intervention that involves experiencing slowness of movement, tremors and rigidity.
definition source: Based on https://link.springer.com/article/10.1007/s007020100006

number of participant drop-out due to adverse events
type: Class
subclass of: number of participant drop-out from intervention
has curation status: Proposed
definition: Number of participant drop-out from the intervention as a result the participants experiencing some adverse event.

number of participant drop-out due to inefficacy
type: Class
subclass of: number of participant drop-out from intervention
has curation status: Proposed
definition: Number of participant drop-out from the intervention as a result of the intervention failing to produce the desired effect.

number of participant drop-out due to side-effects
type: Class
subclass of: number of participant drop-out due to adverse events
has curation status: Proposed
definition: Number of participant drop-out due to adverse events that are experienced following the intervention.

number of participant drop-out from intervention
type: Class
subclass of: number of intervention participants
has curation status: Proposed
definition: Number of intervention participants who discontinue participating in an intervention.

positive intervention outcome
type: Class
subclass of: intervention outcome
has curation status: Proposed
definition: An intervention outcome that is positively influenced by the intervention.

positive psychotic disorder symptom
type: Class
subclass of: psychotic disorder symptom
has curation status: Proposed
definition: A psychotic disorder symptom that is characterized by the presence of hallucinations, delusions, or disorganised thoughts or behaviours.
definition source: Based on https://www.psychiatry.org/patients-families/schizophrenia/what-is-schizophrenia

positive psychotic disorder symptom severity
type: Class
subclass of: psychotic disorder symptom severity
has curation status: Proposed
definition: Psychotic disorder symptom severity that is associated with positive psychotic disorder symptoms.
curator note: A measure for 'positive psychotic disorder symptom severity'

psychotic disorder symptom severity
type: Class
subclass of: psychotic disorder symptom
has curation status: Proposed
definition: Symptom severity that is associated with a psychotic disorder symptom.

serious adverse event following an intervention
type: Class
subclass of: adverse event following an intervention
has curation status: Proposed
definition: An adverse event following an intervention that results in death, a life-threatening event, a persistent or significant disability or a birth defect or requires hospitalisation or extends hospitalisation.
definition source: Based on http://purl.obolibrary.org/obo/OAE_0000631

serious psychological adverse event following an intervention
type: Class
subclass of: serious adverse event following an intervention
has curation status: Proposed
definition: A serious adverse event following an intervention that is associated with multiple, persistent or salient negative mental processes.

serious somatic adverse event following an intervention
type: Class
subclass of: serious adverse event following an intervention
has curation status: Proposed
definition: A serious adverse event following an intervention that is associated with multiple, persistent or salient physical symptoms.

suicidal ideation following intervention
type: Class
subclass of: adverse event following an intervention
has curation status: Proposed
definition: An adverse event following an intervention that involves thoughts about suicide.
definition source: Based on http://purl.obolibrary.org/obo/OAE_0001432

suicide attempt following intervention
type: Class
subclass of: adverse event following an intervention
has curation status: Proposed
definition: An adverse event following an intervention that involves at least one attempted suicide.
definition source: Based on http://purl.obolibrary.org/obo/OAE_0001433

suicide following an intervention
type: Class
subclass of: death following an intervention
has curation status: Proposed
definition: A death following an intervention that involves a participant intentionally ending their own life.

symptom severity
type: Class
subclass of: data item
has curation status: Proposed
definition: A data item that is about the location on the dimension of a symptom.
definition: A data item that is about the severity dimension associated with a symptom.
curator note: A measure for 'psychotic disorder symptom severity'

unnatural dealth due to external factors following an intervention
type: Class
equivalent class: Class
  union of: death due to accidents following an intervention
  union of: homicide following an intervention
subclass of: death following an intervention
has curation status: Proposed
definition: Death following an intervention that involves a homicide or accidents.

advanced age
type: Class
subclass of: person
has curation status: Proposed
definition: A person who is in the latter end of their lifespan.

child
type: Class
subclass of: person
has curation status: Proposed
definition: A person who has not yet reached maturity.

clinical history of psychosis experience
type: Class
subclass of: clinical history
has curation status: Proposed
definition: A clinical history in which there is a history of psychosis experience.

ethnic group membership
type: Class
subclass of: self-identity
has curation status: Proposed
definition: A self-identity as belonging to a group or groups whose members have a common heritage that is real or presumed such as common culture, language, religion, behaviour or biological trait.

female gender
type: Class
subclass of: gender identity
has curation status: Proposed
definition: A gender identity as being female.

first psychosis experience history
type: Class
subclass of: clinical history of psychosis experience
has curation status: Proposed
definition: A clinical history in which there is a history of only one period of psychosis experience.

gender identity
type: Class
subclass of: self-identity
has curation status: Proposed
definition: A self-identity as having a particular gender, which may or may not correspond with sex assigned at birth.

predominant negative psychotic disorder symptom history
type: Class
subclass of: clinical history
has curation status: Proposed
definition: A clinical history in which a person has more negative than psychotic disorder symptoms.

psychosis experience
type: Class
subclass of: symptom
has curation status: Proposed
definition: A symptom that involves a person experiencing delusions, hallucinations, conceptual disorganisation or disorganised speech or behaviour
definition source: https://www.mind.org.uk/information-support/types-of-mental-health-problems/psychosis/about-psychosis/ DSM V
comment: Hallucinatory behaviour is an example of disorganised behaviour

schizophrenia diagnosis
type: Class
subclass of: psychosis diagnosis
has curation status: Proposed
definition: A psychosis diagnosis that involves the conclusion that a person meets pre-set criteria for schizophrenia as a result of a diagnostic process.

standard deviation human age
type: Class
subclass of: standard deviation
has curation status: Proposed
definition: Standard deviation of human age in a population.

treatment-resistant clinical history
type: Class
subclass of: clinical history
has curation status: Proposed
definition: A clinical history in which a person has an inadequate response to at least two adequate rials of antipsychotic drugs.

number of sites
type: Class
subclass of: data item
has curation status: Proposed
definition: A data item that is about the number of sites.

psychiatric inpatient facility
type: Class
subclass of: psychiatric facility
has curation status: Proposed
definition: A psychiatric facility in which patients stay at the facility overnight.

psychiatric outpatient facility
type: Class
subclass of: psychiatric facility
has curation status: Proposed
definition: A psychiatric facility to treat patients without them staying overnight.

study recruitment setting
type: Class
subclass of: object aggregate
has curation status: Proposed
definition: An aggregate of entities that form the environment in which participants are recruited for a study.

author identification
type: Class
subclass of: information entity
has curation status: Proposed
definition: A textual entity intended to identify a particular author.

blinding data analysts of intervention arm
type: Class
subclass of: blinding process
has curation status: Proposed
definition: A blinding process in which the data analysts are not informed about intervention arm assignments until after the data analysis is completed.

blinding intervention source about intervention arm
type: Class
subclass of: blinding process
has curation status: Proposed
definition: A blinding process in which sources deliverying the intervention are not informed about which of two or more interventions they are deliverying until after an endpoint has been reached.

blinding outcome assessor of intervention arm
type: Class
subclass of: blinding process
has curation status: External
definition: A blinding process in which the outcome assessors are not informed about which of two or more interventions they are collecting data about until after an endpoint has been reached.

blinding participant about intervention arm
type: Class
subclass of: blinding process
has curation status: Proposed
definition: A blinding process in which participants are not informed about which of two or more interventions they are to experience until after an endpoint has been reached.

blinding process
type: Class
subclass of: planned process
has curation status: Proposed
definition: A planned process in which information about study arm assignment is withheld from people until they completed their role in the study's data collection or analysis has ended.

cross over randomised controlled trial design
type: Class
subclass of: randomised controlled trial design
has curation status: Proposed
definition: "randomised controlled trial design" AND "cross over design"

n-of-1 randomised controlled trial design
type: Class
equivalent class: Class
  intersection of: randomised controlled trial design
  intersection of: n-of-1 study design
subclass of: randomised controlled trial design
has curation status: External
definition: "randomised controlled trial design" AND "n-of-1 study design"

number of intervention arms
type: Class
subclass of: data item
has curation status: Proposed
definition: A data item that is about the number of intervention groups in a study.

publication from same research project
type: Class
subclass of: related work textual entity
has curation status: Proposed
definition: A related work textual entity that discusses work from other publications done as part of the same research project as the work reported in a document.

pre-registered plan specification source
type: Class
subclass of: citation
has curation status: Proposed
definition: Formal citation for a plan specification of the study published as protocol or trial registration.

publication year textual entity
type: Class
subclass of: information entity
has curation status: Proposed
definition: A textual entity documenting the year in which some study was published.

parallel randomised controlled trial design
type: Class
equivalent class: Class
  intersection of: randomised controlled trial design
  intersection of: parallel group design
subclass of: randomised controlled trial design
has curation status: Proposed
definition: "randomised controlled trial design" AND "parallel group design"

control arm
type: Class
subclass of: study arm
has curation status: Proposed
definition: A study arm designation as a comparator to some intervention arm.

intervention arm
type: Class
subclass of: study arm
has curation status: Proposed
definition: A study arm that is subject to evaluation in an intervention evaluation study.

intervention contact event duration
type: Class
subclass of: one-dimensional temporal region
has curation status: Proposed
definition: A temporal interval between the start and end of an intervention contact event.

intervention content
type: Class
subclass of: planned process
has curation status: Proposed
definition: A planned process that is part of an intervention and is intended to be causally active in influencing its target outcome or outcomes.

no treatment control arm
type: Class
subclass of: control arm
has curation status: Proposed
definition: A control arm designation where there is no intervention.

study arm
type: Class
subclass of: information entity
has curation status: Proposed
definition: An information content entity that is about an intervention scenario and designates it as part of an intervention evaluation study.

treatment as usual control arm
type: Class
subclass of: control arm
has curation status: Proposed
definition: A control arm designation where the same content and delivery is already provided as standard practice.

waitlist control arm
type: Class
subclass of: control arm
has curation status: Proposed
definition: A control arm designation where no intervention prior to the primary outcome follow-up point is delivered but participants in the study arm are informed that they will be entitled to receive an intervention at some time after that point.

anhedonia
type: Class
subclass of: mental disposition
definition: A mental disposition that is realised by experiencing low pleasure or interest in response to various positively valenced stimuli.

anhedonia symptom severity
type: Class
subclass of: symptom severity
definition: Symptom severity that is associated with anhedonia.

heart rate
type: Class
subclass of: data item
definition: A data item about the number of heart contractions within a temporal interval.

lower bound of 95% confidence interval
type: Class
subclass of: quantitative confidence value
definition: A quantitative confidence value that denotes the lower endpoint of a 95% confidence interval and indicates the lowest value within a true parameter is likely to reside within the confidence interval.
definition source: Based on Ross, S. M. (2017). Estimation. Introductory statistics ( p. 329-380). Academic Press.

number of participant drop-out from intervention arm
type: Class
subclass of: number of intervention participants
has curation status: Proposed
definition: Number of intervention participants who discontinue participating in a intervention arm.

reward sensitivity
type: Class
subclass of: bodily disposition
definition: A bodily disposition to detect, pursue, learn from, and derive pleasure from stimuli perceived as positive.
definition source: Goodnight, J. (Ed.) (2018). . (Vols. 1-5). SAGE Publications, Inc., https://doi.org/10.4135/9781506307633

reward-based learning
type: Class
subclass of: associative learning
definition: Associative learning by which information is acquired regarding the positive outcomes of stimuli and behaviours.

reward-prediction error signalling
type: Class
subclass of: mental process
definition: A mental process in which the discrepancy between the predicted and received rewards is signalled.
definition source: Based on Schultz, W. (2022). Dopamine reward prediction error coding. Dialogues in clinical neuroscience. RDoC - https://www.nimh.nih.gov/research/research-funded-by-nimh/rdoc/definitions-of-the-rdoc-domains-and-constructs

temporal reference associated with measurement in intervention
type: Class
subclass of: one-dimensional temporal region
definition: Time point at which a measurement is taken with reference to a temporal part of the intervention evaluation study.

upper bound of 95% confidence interval
type: Class
subclass of: quantitative confidence value
definition: A quantitative confidence value that denotes the upper endpoint of a 95% confidence interval and indicates the highest value within a true parameter is likely to reside within the confidence interval.
definition source: Based on Ross, S. M. (2017). Estimation. Introductory statistics ( p. 329-380). Academic Press.

vo2 max
type: Class
subclass of: data item
has curation status: Proposed
definition: A data item about the maximum capacity of an individual's body to transport and use oxygen during incremental exercise, which reflects the physical fitness of the individual.

anxiety diagnosis severity
type: Class
subclass of: diagnosis severity
has curation status: Proposed
definition: Diagnosis severity relating to an anxiety diagnosis.

anxiety symptom
type: Class
subclass of: symptom
has curation status: Proposed
definition: A symptom that related to a anxiety diagnosis.

anxiety symptom severity
type: Class
subclass of: symptom severity
has curation status: Proposed
definition: Symptom severity that is associated with a anxiety symtom.

autism spectrum disorder diagnosis
type: Class
subclass of: diagnosis
has curation status: Proposed
definition: A diagnosis that involves the conclusion that a person meets pre-set criteria for autism spectrum disorder as a result of a diagnostic process.
alternative term: ASD diagnosis status

autism spectrum disorder diagnosis severity
type: Class
subclass of: diagnosis severity
has curation status: Proposed
definition: Diagnosis severity relating to an autism spectrum disorder diagnosis.
alternative term: ASD severity

depression data item
type: Class
subclass of: measurement data item
has curation status: Proposed
definition: A measurement data item that is the recording of depression symptom severity.

diagnosis severity
type: Class
subclass of: data item
has curation status: Proposed
definition: A data item that is about the severity dimension associated with a diagnosis.
comment: There are different scales for rating severity, which can be indicate differences in severity.

dysthymia diagnosis
type: Class
subclass of: depression diagnosis
has curation status: Proposed
definition: A depression diagnosis that involves the conclusion that a person meets pre-set criteria for dysthymic disorder as a result of a diagnostic process.
alternative term: persistent depressive disorder diagnosis status

insomnia symptom severity
type: Class
subclass of: symptom severity
has curation status: Proposed
definition: Symptom severity that is associated with insomnia.

major depressive disorder diagnosis
type: Class
subclass of: depression diagnosis
has curation status: Proposed
definition: A depression diagnosis that involves the conclusion that a person meets pre-set criteria for major depressive disorder as a result of a diagnostic process.

number of intervention participants
type: Class
subclass of: data item
has curation status: Proposed
definition: A data item that is about the number of participants in an intervention or part of an intervention at a timepoint.

number of participants in intervention arm
type: Class
subclass of: number of intervention participants
has curation status: Proposed
definition: Number of intervention participants who are part of an intervention arm.

number of randomised intervention participants
type: Class
subclass of: number of intervention participants
has curation status: Proposed
definition: Number of intervention participants who were randomly allocated to study arms within an intervention.

post-traumatic stress disorder diagnosis severity
type: Class
subclass of: anxiety diagnosis severity
has curation status: Proposed
definition: Diagnosis severity relating to a post-traumatic stress disorder diagnosis.
alternative term: PTSD severity

post-traumatic stress disorder diagnosis
type: Class
subclass of: diagnosis
has curation status: Proposed
definition: A diagnosis that involves the conclusion that a person meets pre-set criteria for post-traumatic stress disorder as a result of a diagnostic process.
alternative term: PTSD diagnosis status

post-traumatic stress disorder severity measurement item
type: Class
subclass of: measurement data item
has curation status: Proposed
definition: A measurement data item that is the recording of post-traumatic stress disorder severity level.
alternative term: PTSD measurement item

pre-intervention anxiety symptom severity
type: Class
equivalent class: Class
  intersection of: anxiety symptom severity
  intersection of: Restriction
    on property: precedes
    some values from: intervention
subclass of: anxiety symptom severity
has curation status: Proposed
definition: Anxiety symptom severity before the intervention delivery begins.

pre-intervention autism spectrum disorder diagnosis severity
type: Class
equivalent class: Class
  intersection of: autism spectrum disorder diagnosis severity
  intersection of: Restriction
    on property: precedes
    some values from: intervention
subclass of: autism spectrum disorder diagnosis severity
has curation status: Proposed
definition: Autism spectrum diagnosis severity before the intervention delivery begins.
alternative term: baseline ASD severity

pre-intervention depression symptom severity
type: Class
equivalent class: Class
  intersection of: depression symptom severity
  intersection of: Restriction
    on property: precedes
    some values from: intervention
subclass of: depression symptom severity
has curation status: Proposed
definition: Depression symptom severity before an intervention starts.

pre-intervention insomnia severity
type: Class
equivalent class: Class
  intersection of: insomnia symptom severity
  intersection of: Restriction
    on property: precedes
    some values from: intervention
subclass of: insomnia symptom severity
has curation status: Proposed
definition: Insomnia symptom severity before the intervention delivery begins.

pre-intervention personal attribute
type: Class
equivalent class: Class
  intersection of: personal attribute
  intersection of: Restriction
    on property: precedes
    some values from: intervention
subclass of: personal attribute
has curation status: Proposed
definition: Personal attribute before the intervention delivery begins.
alternative term: Baseline clinical variable, baseline variable
definition source: Based on https://dictionary.apa.org/baseline-characteristic

pre-intervention post-traumatic stress disorder diagnosis severity
type: Class
equivalent class: Class
  intersection of: post-traumatic stress disorder diagnosis severity
  intersection of: Restriction
    on property: precedes
    some values from: intervention
subclass of: post-traumatic stress disorder diagnosis severity
has curation status: Proposed
definition: Post-traumatic stress disorder diagnosis severity before the intervention delivery begins.
alternative term: baseline PTSD severity
curator note: Logical definition was: "post-traumatic stress disorder diagnosis severity" precedes "intervention"

pre-intervention substance use severity
type: Class
equivalent class: Class
  intersection of: substance use severity
  intersection of: Restriction
    on property: precedes
    some values from: intervention
subclass of: substance use severity
has curation status: Proposed
definition: Substance use severity before the intervention delivery begins.

prevalence of bipolar disorder diagnosis
type: Class
subclass of: prevalence of diagnosis
has curation status: Proposed
definition: Prevalence of diagnosis for bipolar disorder.

prevalence of diagnosis
type: Class
subclass of: prevalence
has curation status: Proposed
definition: Prevalence of people diagnosed with a specific disorder.

prevalence of major depressive disorder diagnosis
type: Class
subclass of: prevalence of diagnosis
has curation status: Proposed
definition: Prevalence of diagnosis for major depressive disorder.
alternative term: prevalence of unipolar depression disorder diagnosis

substance use severity
type: Class
subclass of: data item
has curation status: Proposed
definition: A data item about the frequency of a substance use behaviour or the amount of psychoactive substance ingested into the body.

intervention setting
type: Class
subclass of: object aggregate
has curation status: External
definition: An aggregate of entities that form the environment in which an intervention is provided.

author email address textual entity
type: Class
subclass of: information entity
definition: A textual entity documenting the email address of an author of a publication.

language of document
type: Class
subclass of: information entity
has curation status: Proposed
definition: An information content entity that is the language used to express the information in a document.

psychotic disorder symptom
type: Class
subclass of: symptom
has curation status: Proposed
definition: A symptom that is related to a psychotic disorder diagnosis.

post-traumatic stress symptom severity
type: Class
subclass of: anxiety symptom severity
has curation status: Proposed
definition: Anxiety symptom severity relating to a post-traumatic stress symptom.
alternative term: PTSD severity

post-traumatic stress symptom
type: Class
subclass of: anxiety symptom
has curation status: Proposed
definition: An anxiety symptom that related to a post-traumatic stress disorder diagnosis.

validity of measurement scale
type: Class
subclass of: specifically dependent continuant
has curation status: Proposed
definition: An attribute of a measurement scale that involves the degree to which the outcomes from the scale represent the intended variable or variables.
definition source: Based on Price, P. (2015). Research methods in psychology, 2nd Canadian Edition. BCcampus.

depression diagnosis
type: Class
subclass of: diagnosis
has curation status: Proposed
definition: A diagnosis that involves the conclusion that a person meets pre-set criteria for depression as a result of a diagnostic process.

daily dose of pharmacological substance
type: Class
subclass of: dose of pharmacological substance
has curation status: Proposed
definition: Dose of pharmacological substance delivered to individuals within each day.

digestive system adverse event following intervention
type: Class
subclass of: adverse event following an intervention
has curation status: Proposed
definition: An adverse event following an intervention that occurs in the digestive system.

dizziness following intervention
type: Class
subclass of: adverse event following an intervention
has curation status: Proposed
definition: An adverse event following an intervention that involves experiencing dizziness.

dry mouth following intervention
type: Class
subclass of: digestive system adverse event following intervention
has curation status: Proposed
definition: A digestive system adverse event following intervention that involves experiencing dry mouth.

headache following intervention
type: Class
subclass of: pain following intervention
has curation status: Proposed
definition: A pain following intervention that has an outcome of headache.

insomnia following intervention
type: Class
subclass of: adverse event following an intervention
has curation status: Proposed
definition: An adverse event following an intervention in which there is an inability to fall asleep or to stay asleep as long as desired.

nausea following intervention
type: Class
subclass of: digestive system adverse event following intervention
has curation status: Proposed
definition: A digestive system adverse event following intervention that has an outcome of nausea, a gastric discomfort associated with the inclination to vomit

pain following intervention
type: Class
subclass of: adverse event following an intervention
has curation status: Proposed
definition: An adverse event following an intervention that has an outcome of pain.

vomiting following intervention
type: Class
subclass of: digestive system adverse event following intervention
has curation status: Proposed
definition: A digestive system adverse event following intervention that has an outcome of vomiting, the retrograde expulsion of gastric contents through the oral cavity.

psychosis diagnosis
type: Class
subclass of: diagnosis
has curation status: Proposed
definition: A diagnosis that involves the conclusion that a person meets pre-set criteria for psychosis as a result of a diagnostic process.

aggregate human age
type: Class
subclass of: data item
has curation status: Proposed
definition: The aggregate of human age in a population.

health status attribute
type: Class
subclass of: personal attribute
has curation status: Proposed
definition: A personal attribute that is the state of an individual's mental or physical condition.

person
type: Class
subclass of: extended organism
has curation status: Proposed
definition: An extended organism that is a member of the species Homo sapiens.

repeated measures study design
type: Class
subclass of: study design
has curation status: Proposed
definition: A study design in which measurements taken on the same study participants at two or more different times in different circumstances are compared.

cardiovascular exercise behaviour
type: Class
subclass of: physical performance behaviour pattern
has curation status: Proposed
definition: Physical performance behaviour pattern that increases heart rate and respiration while using large muscle groups repetitively and rhythmically.
alternative term: cardio training, aerobic exercise, aerobics, endurance exercise, endurance training, cardiovascular exercise

jogging
type: Class
subclass of: locomotive behaviour
has curation status: Proposed
definition: A locomotive behaviour that involves trotting or running at a slow and steady pace.

physical performance behaviour pattern
type: Class
subclass of: individual human behaviour pattern
has curation status: Proposed
definition: An individual human behaviour pattern that involves repeated physical performance behaviour.

resistance training behaviour
type: Class
subclass of: physical performance behaviour pattern
has curation status: Proposed
definition: Physical performance behaviour pattern that uses weight, or other forms of resistance, to induce muscle contraction and build strength, anaerobic endurance, and size of skeletal muscles.
alternative term: resistance training, strength training

running
type: Class
subclass of: locomotive behaviour
has curation status: Proposed
definition: A locomotive behaviour that involves moving at a steady pace and speed with long strides such that there is a phase at which all limbs are above the ground.

bodybuilding behaviour
type: Class
subclass of: individual human behaviour pattern
has curation status: Proposed
definition: Individual human behaviour pattern involving consumption behaviour and physical performance behaviour in order to grow muscles.