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

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

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

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

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

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

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

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

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

definition source
type: AnnotationProperty
definition source: Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition editor: PERSON:Daniel Schober
editor preferred term: definition source
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
has curation status: ready for release

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

data item
type: Class
subclass of: information content entity
definition source: OBO:imported "http://purl.obolibrary.org/obo/iao.owl"
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.

information content entity
type: Class
subclass of: generically_dependent_continuant
definition source: OBO:sourced "OBI:0000142"
definition: an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity

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

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

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

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

obsolete_representation
type: Class
subclass of: ObsoleteClass
definition editor: Albert Goldfain
curator note: creation date: 2009-06-23T10:17:44Z

clinical finding
type: Class
subclass of: data item
definition: A representation that is either the output of a clinical history taking or a physical examination or an image finding, or some combination thereof.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2010-07-19T10:18:02Z

clinical history
type: Class
subclass of: clinical finding
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

clinical picture
type: Class
subclass of: data item
curator note: creation date: 2010-07-19T10:20:20Z
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition: A representation of the clinically significant bodily components and/or bodily processes of a human being that is inferred from the totality of relevant clinical findings.
definition editor: Albert Goldfain

image finding
type: Class
subclass of: clinical finding
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition editor: Albert Goldfain
curator note: creation date: 2009-06-23T10:21:10Z
definition: A representation of an image that supports an inference to an assertion about some quality of a patient.

laboratory finding
type: Class
subclass of: clinical finding
curator note: creation date: 2009-06-23T10:21:58Z
definition: A representation of a quality of a specimen that is the output of a laboratory test and that can support an inference to an assertion about some quality of the patient.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf

preclinical finding
type: Class
subclass of: data item
definition editor: Albert Goldfain
definition: A representation of a quality of a patient that is (1) recorded by a clinician because the quality is hypothesized to be of clinical significance and (2) refers to qualities obtaining in the patient prior to their becoming detectable in a clinical history taking or physical examination.
curator note: creation date: 2009-06-23T10:22:44Z
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf

symptom
type: Class
subclass of: entity
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2010-11-18T11:02:10Z
definition: A quality of a patient that is observed by the patient or a processual entity experienced by the patient, either of which is hypothesized by the patient to be a realization of a disease.
editor note: note: defined class

obsolete_bodily feature of a patient
type: Class
subclass of: ObsoleteClass
definition editor: Albert Goldfain
curator note: creation date: 2009-06-23T11:09:37Z

manifestation of a disease
type: Class
subclass of: quality
curator note: creation date: 2009-06-23T11:12:33Z
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition editor: Albert Goldfain
definition: A quality of a patient that is (a) a deviation from clinical normality that exists in virtue of the realization of a disease and (b) is observable.

phenotype
type: Class
subclass of: quality
curator note: creation date: 2010-07-19T11:13:49Z
definition: A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species.
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition editor: Albert Goldfain

sign
type: Class
subclass of: entity
definition editor: Albert Goldfain
editor note: note: defined class
definition: A quality of a patient, a material entity that is part of a patient, or a processual entity that a patient participates in, any one of which is observed in a physical examination and is deemed by the clinician to be of clinical significance.
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2010-11-18T11:14:36Z

clinical manifestation of a disease
type: Class
subclass of: manifestation of a disease
curator note: creation date: 2009-06-23T11:15:43Z
definition: A manifestation of a disease that is detectable in a clinical history taking or physical examination.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf

preclinical manifestation of a disease
type: Class
subclass of: manifestation of a disease
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition: A manifestation of a disease that exists prior to the time at which it would be detected in a clinical history taking or physical examination, if the patient were to present to a clinician. A realization of a disease that exists prior to its becoming detectable in a clinical history taking or physical examination.
definition editor: Albert Goldfain
curator note: creation date: 2009-06-23T11:16:50Z

clinical phenotype
type: Class
subclass of: phenotype
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition editor: Albert Goldfain
definition: A clinically abnormal phenotype.
curator note: creation date: 2009-06-23T11:18:05Z

disease phenotype
type: Class
subclass of: phenotype
definition: A clinically abnormal phenotype that is characteristic of a single disease.
curator note: creation date: 2009-06-23T11:18:39Z
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf

vital sign
type: Class
subclass of: sign
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition: A physical sign in which a non-zero value is standardly considered to be an indication that the organism is alive.
curator note: creation date: 2009-06-23T11:19:17Z

predisposition to disease of type X
type: Class
subclass of: disposition
definition: A disposition in an organism that constitutes an increased risk of the organism's subsequently developing the disease X.
curator note: creation date: 2009-06-23T11:20:25Z
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf

disease
type: Class
subclass of: disposition
definition editor: Albert Goldfain
curator note: creation date: 2009-06-23T11:21:20Z
definition: A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf

homeostasis
type: Class
subclass of: disposition
curator note: creation date: 2009-06-23T11:22:01Z
definition editor: Albert Goldfain

genetic predisposition to disease of type X
type: Class
subclass of: predisposition to disease of type X
definition: A predisposition to disease of type X whose physical basis is a constitutional abnormality in an organism's genome. This abnormality is the physical basis for the increased risk of acquiring the disease X.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:23:07Z

acquired genetic disease
type: Class
subclass of: disease
definition: A disease whose physical basis is an acquired genetic disorder.
curator note: creation date: 2009-06-23T11:24:05Z
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition editor: Albert Goldfain

constitutional genetic disease
type: Class
subclass of: disease
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:24:59Z
definition: A disease whose physical basis is a constitutional genetic disorder.
definition editor: Albert Goldfain

obsolete_infectious disease
type: Class
subclass of: ObsoleteClass
definition: A disease whose physical basis is an infectious disorder.
curator note: creation date: 2009-06-23T11:25:51Z
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition editor: Albert Goldfain

abnormal homeostasis
type: Class
subclass of: homeostasis
definition: Homeostasis that is clinically abnormal for an organism of a given type and age in a given environment.
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:26:44Z
definition editor: Albert Goldfain

normal homeostasis
type: Class
subclass of: homeostasis
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition editor: Albert Goldfain
definition: Homeostasis of a type that is not clinically abnormal.
curator note: creation date: 2009-06-23T11:27:28Z

configuration
type: Class
subclass of: quality
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:36:24Z
definition editor: Albert Goldfain
definition: A quality which is an spatial arrangement or distribution of a(n) independent continuant(s) across a Three Dimensional Region.

pathological physical configuration
type: Class
subclass of: configuration
definition: A configuration which deviates in some way from a canonical configuration for a particular organism.
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition editor: Albert Goldfain
curator note: creation date: 2009-06-23T11:36:58Z

disorder
type: Class
subclass of: material_entity
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition editor: Albert Goldfain
definition: A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease.
curator note: creation date: 2009-06-23T11:39:44Z

epigenetic disorder
type: Class
subclass of: disorder
definition editor: Albert Goldfain
curator note: creation date: 2009-06-23T11:40:27Z
definition: A disorder whose etiology involves (1) a modification to the patient's genomic DNA which leads to alterations in the normal expression pattern of the genome, but is (2) not a change in the nucleotide sequence.
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf

genetic disorder
type: Class
subclass of: disorder
curator note: creation date: 2009-06-23T11:41:14Z
definition editor: Albert Goldfain
definition: A disorder whose etiology involves an abnormality in the nucleotide sequence of an organism's genome.
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf

obsolete_infectious disorder
type: Class
subclass of: ObsoleteClass
curator note: creation date: 2009-06-23T11:41:45Z
definition: A disorder whose etiology includes the presence of a pathogenic organism within a host organism or an abnormal imbalance in the normal resident organismal flora.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf

obsolete_secondary infection
type: Class
subclass of: ObsoleteClass
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition: A disorder consisting in the presence of a pathogenic organism within a host organism that occurs due to the disposition established by a prior infection with a pathogenic organism of a different kind.
curator note: creation date: 2009-06-23T11:42:20Z
definition editor: Albert Goldfain

acquired genetic disorder
type: Class
subclass of: genetic disorder
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition: A genetic disorder acquired by a single cell in an organism that leads to a population of cells within the organism bearing the disorder.
definition editor: Albert Goldfain
curator note: creation date: 2009-06-23T11:43:09Z

constitutional genetic disorder
type: Class
subclass of: genetic disorder
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition: A genetic disorder inherited during conception that is part of all cells in the organism.
definition editor: Albert Goldfain
curator note: creation date: 2009-06-23T11:43:44Z

obsolete_standardized clinical process
type: Class
subclass of: ObsoleteClass
definition: A fiat process part which involves the execution of a standardized protocol for measuring qualities of a patient.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:47:06Z

clinical history taking
type: Class
subclass of: processual_entity
definition: An interview in which a clinician elicits a clinical history from a patient or from a third party who is reporting on behalf of the patient.
curator note: creation date: 2009-06-23T11:49:16Z
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition editor: Albert Goldfain

laboratory test
type: Class
subclass of: processual_entity
definition: A measurement assay that has as input a patient-derived specimen, and as output a result that represents a quality of the specimen.
curator note: creation date: 2009-06-23T11:49:49Z
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition editor: Albert Goldfain

physical examination
type: Class
subclass of: processual_entity
curator note: creation date: 2010-07-19T11:50:18Z
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition: A sequence of acts of observing and measuring qualities of a patient performed by a clinician; measurements may occur with and without elicitation.
definition editor: Albert Goldfain

etiological process
type: Class
subclass of: processual_entity
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:53:07Z
definition editor: Albert Goldfain
definition: A process in an organism that leads to a subsequent disorder.

bodily process
type: Class
subclass of: processual_entity
curator note: creation date: 2009-06-23T11:53:49Z
definition editor: Albert Goldfain

pathological bodily process
type: Class
subclass of: bodily process
curator note: creation date: 2009-06-23T11:54:29Z
definition: A bodily process that is clinically abnormal.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf

disease course
type: Class
subclass of: processual_entity
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition editor: Albert Goldfain
curator note: creation date: 2009-06-23T11:55:44Z
definition: The totality of all processes through which a given disease instance is realized.

chronic disease course
type: Class
subclass of: disease course
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition: A disease course that (a) does not terminate in a return to normal homeostasis and (b) would, absent intervention, fall within abnormal homeostatic range.
curator note: creation date: 2009-06-23T11:56:26Z
definition editor: Albert Goldfain

progressive disease course
type: Class
subclass of: disease course
curator note: creation date: 2009-06-23T11:57:09Z
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition editor: Albert Goldfain
definition: A disease course that (a) does not terminate in a return to normal homeostasis and (b) would, absent intervention, involve an increasing deviation from homeostasis.

transient disease course
type: Class
subclass of: disease course
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition editor: Albert Goldfain
definition: A disease course that terminates in a return to normal homeostasis.
curator note: creation date: 2009-06-23T11:57:44Z

_undefined primitive term
type: Class
subclass of: entity
definition editor: Albert Goldfain
curator note: creation date: 2009-06-23T11:58:22Z

obsolete_bodily feature
type: Class
subclass of: ObsoleteClass
curator note: creation date: 2009-06-23T11:58:39Z
definition editor: Albert Goldfain

clinically abnormal
type: Class
subclass of: _undefined primitive term
curator note: creation date: 2009-06-23T11:59:24Z
definition editor: Albert Goldfain

physical basis
type: Class
subclass of: _undefined primitive term
curator note: creation date: 2009-06-23T12:00:09Z
definition editor: Albert Goldfain

realization
type: Class
subclass of: _undefined primitive term
curator note: creation date: 2009-06-23T12:00:39Z
definition editor: Albert Goldfain

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

normal value
type: Class
subclass of: generically_dependent_continuant
definition: A value for a quality reported in a lab report and asserted by the testing lab or the kit manufacturer to be normal based on a statistical treatment of values from a reference population.
curator note: creation date: 2009-06-26T10:31:34Z
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf

obsolete_infection
type: Class
subclass of: ObsoleteClass
definition editor: Albert Goldfain
curator note: creation date: 2009-07-08T12:20:49Z

pathological formation
type: Class
subclass of: material_entity
definition editor: Albert Goldfain
definition: TODO: Define, relate to disorder, and place in the OGMS hierarchy.
definition source: http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf
curator note: creation date: 2009-07-13T02:14:59Z

pathological anatomical structure
type: Class
subclass of: material_entity
curator note: creation date: 2009-07-13T02:14:05Z
definition editor: Albert Goldfain
definition: An anatomical structure (FMA) is pathological whenever (1) it has come into being as a result of changes in some pre-existing canonical anatomical structure, (2) through processes other than the expression of the normal complement of genes of an organism of the given type, and (3) is predisposed to have health-related consequences for the organism in question manifested by symptoms and signs.
definition source: http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf

portion of pathological body substance
type: Class
subclass of: material_entity
definition source: http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf
definition editor: Albert Goldfain
curator note: creation date: 2009-07-13T02:15:17Z
definition: TODO: Define, relate to disorder, and place in the OGMS hierarchy.

pathological transformation
type: Class
subclass of: pathological bodily process
curator note: creation date: 2009-07-13T02:17:07Z
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf
definition: A pathological bodily process in which a canonical anatomical structure becomes a pathological anatomical structure.

pathological derivation
type: Class
subclass of: pathological bodily process
curator note: creation date: 2009-07-13T02:17:24Z
definition source: http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf
definition: A pathological bodily process in which matter is reorganized in such a way as to give rise to new pathological formations which take the place of entities existing earlier.
definition editor: Albert Goldfain

pathological invasion
type: Class
subclass of: pathological bodily process
definition editor: Albert Goldfain
curator note: creation date: 2009-07-13T02:17:47Z
definition source: http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf
definition: TODO: Define.

physical examination finding
type: Class
subclass of: clinical finding
definition editor: Albert Goldfain
definition source: http://code.google.com/p/ogms/issues/detail
definition: TODO: Define.
curator note: creation date: 2009-11-24T04:51:11Z

organism population
type: Class
subclass of: object_aggregate
definition: An aggregate of organisms of the same type.
definition source: http://code.google.com/p/ogms/issues/detail
curator note: creation date: 2009-11-24T04:51:11Z
definition editor: Albert Goldfain

pain
type: Class
subclass of: symptom
definition: TODO: Define.
definition source: http://code.google.com/p/ogms/issues/detail
curator note: creation date: 2009-11-24T04:51:11Z
definition editor: Albert Goldfain

syndrome
type: Class
subclass of: quality
definition source: http://code.google.com/p/ogms/issues/detail
definition: A pattern of signs and symptoms that typically co-occur.
curator note: creation date: 2009-11-24T04:51:11Z
definition editor: Albert Goldfain

extended organism
type: Class
subclass of: object_aggregate
definition editor: Albert Goldfain
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 source: http://code.google.com/p/ogms/issues/detail
curator note: creation date: 2010-01-25T04:51:11Z

patient symptom report
type: Class
subclass of: information content entity
definition editor: Albert Goldfain
curator note: creation date: 2010-01-25T04:51:11Z
definition source: http://code.google.com/p/ogms/issues/detail
definition: A communication from a patient about something they perceive as being abnormal about their body or life.

congenital malformation
type: Class
subclass of: material_entity
definition source: http://code.google.com/p/ogms/issues/detail
definition: A structurally anomalous part of an organism acquired during fetal development and present at birth (but not necessarily hereditary) which is hypothesized to be harmful for the organism.
definition editor: Albert Goldfain
curator note: creation date: 2010-03-31T04:51:11Z

treatment
type: Class
subclass of: processual_entity
definition source: http://code.google.com/p/ogms/issues/detail
definition editor: Albert Goldfain
curator note: creation date: 2010-03-31T04:51:11Z
definition: A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder

convalescence
type: Class
subclass of: processual_entity
definition: A processual entity during which a patient participating in a disease course gradually returns to participating in a canonical life course.
definition editor: Albert Goldfain
curator note: creation date: 2010-03-31T04:51:11Z
definition source: http://code.google.com/p/ogms/issues/detail

life course
type: Class
subclass of: processual_entity
curator note: creation date: 2010-03-31T04:51:11Z
definition: A processual entity which has as parts all the processes in which a given organism is participant.
definition editor: Albert Goldfain
definition source: http://code.google.com/p/ogms/issues/detail

prognosis
type: Class
subclass of: data item
definition: A hypothesis about the course of a disease.
curator note: creation date: 2010-03-31T12:42:23Z
definition editor: Albert Goldfain
definition source: http://code.google.com/p/ogms/issues/detail

acute disease course
type: Class
subclass of: disease course
curator note: creation date: 2010-07-19T11:57:44Z
definition source: http://code.google.com/p/ogms/wiki/Meeting_notes_20100513
definition editor: Albert Goldfain
definition: a disease course with a rapid onset but typical unfolding of signs and symptoms after this rapid onset.

inflammation process
type: Class
subclass of: processual_entity
definition source: http://code.google.com/p/ogms/wiki/Meeting_notes_20100513
definition: A process which is a response by an organism's tissues that is generally identified by swelling or localized pain
curator note: creation date: 2010-07-19T11:57:44Z
definition editor: Albert Goldfain

health care process
type: Class
subclass of: processual_entity
definition: A social process that has at least one human participant and that includes as parts the treatment, diagnosis, or prevention of disease or injury--or the following of instructions of another human for treatment, diagnosis, or prevention--of a participant in the process
definition editor: Albert Goldfain
curator note: creation date: 2011-02-21T09:57:44Z
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6

health care encounter
type: Class
subclass of: health care process
definition editor: Albert Goldfain
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6
curator note: creation date: 2011-02-21T09:57:44Z
definition: A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role. The health care provider role and patient are realized during the health care encounter

hospitalization
type: Class
subclass of: health care encounter
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6
curator note: creation date: 2011-02-21T09:57:44Z
definition editor: Albert Goldfain
definition: TODO

outpatient encounter
type: Class
subclass of: health care encounter
curator note: creation date: 2011-02-21T09:57:44Z
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6
definition editor: Albert Goldfain
definition: TODO

inpatient encounter
type: Class
subclass of: health care encounter
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6
curator note: creation date: 2011-02-21T09:57:44Z
definition editor: Albert Goldfain
definition: TODO

ED encounter
type: Class
subclass of: health care encounter
definition editor: Albert Goldfain
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6
definition: TODO
curator note: creation date: 2011-02-21T09:57:44Z

injury
type: Class
subclass of: material_entity
definition: A part of an organism that has undergone a change in structural integrity and has a higher chance of dysfunction or causing dysfunction in another structure.
definition editor: Albert Goldfain
curator note: creation date: 2011-09-20T09:57:44Z
editor note: At the scale of organism (as opposed to the cellular scale or the population scale), an injury is typically the result of a catastrophic event. Consider the implications of making 'injury' a subtype of 'disorder'.
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/ca0ad373f27774c5

prophylaxis
type: Class
subclass of: processual_entity
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/e42bde79218ee34e
definition: A planned process that has the objective to reduce the risk of acquiring one or more disorders.
curator note: creation date: 2011-09-20T09:57:44Z
definition editor: Albert Goldfain
editor note: Whether or not 'prophylaxis' and 'treatment' classes are disjoint is an open question.

diagnostic process
type: Class
subclass of: processual_entity
curator note: creation date: 2011-09-20T09:57:44Z
definition: An interpretive process that has as input a clinical picture of a given patient and as output an assertion (diagnostic statement) to the effect that the patient has a disease of such and such a type.
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/2a7008f311fac766/e7de486c94dfd82e
definition editor: Albert Goldfain

entity
type: Class
equivalent class: Class
  union of: continuant
  union of: occurrent

continuant
type: Class
equivalent class: Class
  union of: dependent_continuant
  union of: independent_continuant
  union of: spatial_region
subclass of: entity
disjoint with: occurrent
comment: Definition: An entity [bfo: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.
comment: Examples: a heart, a person, the color of a tomato, the mass of a cloud, a symphony orchestra, the disposition of blood to coagulate, the lawn and atmosphere in front of our building
comment: Synonyms: endurant

dependent_continuant
type: Class
equivalent class: Class
  union of: generically_dependent_continuant
  union of: specifically_dependent_continuant
subclass of: continuant
disjoint with: independent_continuant
disjoint with: spatial_region
comment: Definition: A continuant [snap:Continuant] that is either dependent on one or other independent continuant [snap:IndependentContinuant] bearers or inheres in or is borne by other entities.

disposition
type: Class
subclass of: realizable_entity
disjoint with: function
disjoint with: role
comment: Definition: A realizable entity [snap:RealizableEntity] that essentially causes a specific process or transformation in the object [snap:Object] in which it inheres, under specific circumstances and in conjunction with the laws of nature. A general formula for dispositions is: X (object [snap:Object] has the disposition D to (transform, initiate a process) R under conditions C.
comment: Examples: the disposition of vegetables to decay when not refrigerated, the disposition of a vase to brake if dropped, the disposition of blood to coagulate, the disposition of a patient with a weakened immune system to contract disease, the disposition of metal to conduct electricity.

fiat_object_part
type: Class
subclass of: material_entity
disjoint with: object
disjoint with: object_aggregate
disjoint with: object_boundary
disjoint with: site
comment: Definition: A material entity [snap:MaterialEntity] that is part of an object [snap:Object] but is not demarcated by any physical discontinuities.
comment: Examples: upper and lower lobes of the left lung, the dorsal and ventral surfaces of the body, the east side of Saarbruecken, the lower right portion of a human torso
comment: Synonyms: fiat substance part

function
type: Class
subclass of: realizable_entity
disjoint with: role
comment: Definition: A realizable entity [snap:RealizableEntity] the manifestation of which is an essentially end-directed activity of a continuant [snap:Continuant] entity in virtue of that continuant [snap:Continuant] entity being a specific kind of entity in the kind or kinds of contexts that it is made for.
comment: Examples: the function of a birth canal to enable transport, the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc., the function of reproduction in the transmission of genetic material, the digestive function of the stomach to nutriate the body, the function of a hammer to drive in nails, the function of a computer program to compute mathematical equations, the function of an automobile to provide transportation, the function of a judge in a court of law

generically_dependent_continuant
type: Class
subclass of: dependent_continuant
disjoint with: specifically_dependent_continuant
comment: Definition: A continuant [snap:Continuant] that is dependent on one or other independent continuant [snap:IndependentContinuant] bearers. For every instance of A requires some instance of (an independent continuant [snap:IndependentContinuant] type) B but which instance of B serves can change from time to time.
comment: Examples: a certain PDF file that exists in different and in several hard drives

independent_continuant
type: Class
equivalent class: Class
  union of: material_entity
  union of: object_boundary
  union of: site
subclass of: continuant
disjoint with: spatial_region
comment: Definition: A continuant [snap:Continuant] that is a bearer of quality [snap:Quality] and realizable entity [snap:RealizableEntity] entities, in which other entities inhere and which itself cannot inhere in anything.
comment: Examples: an organism, a heart, a leg, a person, a symphony orchestra, a chair, the bottom right portion of a human torso, the lawn and atmosphere in front of our building
comment: Synonyms: substantial entity

material_entity
type: Class
equivalent class: Class
  union of: fiat_object_part
  union of: object
  union of: object_aggregate
subclass of: independent_continuant
disjoint with: object_boundary
disjoint with: site
comment: Definition: An independent continuant [snap:IndependentContinuant] that is spatially extended whose identity is independent of that of other entities and can be maintained through time. Note: Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology.
comment: Examples: collection of random bacteria, a chair, dorsal surface of the body

object
type: Class
subclass of: material_entity
disjoint with: object_aggregate
disjoint with: object_boundary
disjoint with: site
comment: Definition: A material entity [snap:MaterialEntity] that is spatially extended, maximally self-connected and self-contained (the parts of a substance are not separated from each other by spatial gaps) and possesses an internal unity. The identity of substantial object [snap:Object] entities is independent of that of other entities and can be maintained through time.
comment: Examples: an organism, a heart, a chair, a lung, an apple
comment: Synonyms: substance

object_aggregate
type: Class
subclass of: material_entity
disjoint with: object_boundary
disjoint with: site
comment: Definition: A material entity [snap:MaterialEntity] that is a mereological sum of separate object [snap:Object] entities and possesses non-connected boundaries.
comment: Examples: a heap of stones, a group of commuters on the subway, a collection of random bacteria, a flock of geese, the patients in a hospital
comment: Synonyms: substance aggregate

object_boundary
type: Class
subclass of: independent_continuant
disjoint with: site
comment: Comment: Boundaries are theoretically difficult entities to account for, however the intuitive notion of a physical boundary as a surface of some sort (whether inside or outside of a thing) will generally serve as a good guide for the use of this universal.
comment: Definition: An independent continuant [snap:IndependentContinuant] that is a lower dimensional part of a spatial entity, normally a closed two-dimensional surface. Boundaries are those privileged parts of object [snap:Object] entities that exist at exactly the point where the object [snap:Object] is separated off from the rest of the existing entities in the world.
comment: Examples: the surface of the skin, the surface of the earth, the surface of the interior of the stomach, the outer surface of a cell or cell wall
comment: Synonyms: substance boundary

one_dimensional_region
type: Class
subclass of: spatial_region
disjoint with: three_dimensional_region
disjoint with: two_dimensional_region
disjoint with: zero_dimensional_region
comment: Definition: A spatial region [snap:SpatialRegion] with one dimension.
comment: Examples: the part of space that is a line stretching from one end of absolute space to the other, an edge of a cube-shaped part of space

quality
type: Class
subclass of: specifically_dependent_continuant
disjoint with: realizable_entity
comment: Definition: A specifically dependent continuant [snap:SpecificallyDependentContinuant] that is exhibited if it inheres in an entity or entities at all (a categorical property).
comment: Examples: the color of a tomato, the ambient temperature of air, the circumference of a waist, the shape of a nose, the mass of a piece of gold, the weight of a chimpanzee

realizable_entity
type: Class
subclass of: specifically_dependent_continuant
comment: Comment: If a realizable entity [snap:RealizableEntity] inheres in a continuant [snap:Continuant], this does not imply that it is actually realized.
comment: Definition: A specifically dependent continuant [snap:SpecificallyDependentContinuant] that inheres in continuant [snap: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.
comment: Examples: the role of being a doctor, the function of the reproductive organs, the disposition of blood to coagulate, the disposition of metal to conduct electricity

role
type: Class
subclass of: realizable_entity
comment: Definition: A realizable entity [snap:RealizableEntity] the manifestation of which brings about some result or end that is not essential to a continuant [snap:Continuant] in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant [snap:Continuant] in some kinds of natural, social or institutional contexts.
comment: Examples: the role of a person as a surgeon, the role of a chemical compound in an experiment, the role of a patient relative as defined by a hospital administrative form, the role of a woman as a legal mother in the context of system of laws, the role of a biological grandfather as legal guardian in the context of a system of laws, the role of ingested matter in digestion, the role of a student in a university

site
type: Class
subclass of: independent_continuant
comment: Comment: An instance of Site [snap:Site] is a mixture of independent continuant [snap:IndependentContinuant] entities which act as surrounding environments for other independent continuant [snap:IndependentContinuant] entities, most importantly for instances of object [snap:Object]. A site [snap:Site] is typically made of object [snap:Object] or fiat object part [snap:FiatObjectPart] entities and a surrounding medium in which is found an object [snap:Object] occupying the site [snap:Site]. Independent continuant [snap:IndependentContinuant] entities may be associated with others (which, then, are site [snap:Site] entities) through a relation of "occupation". That relation is connected to, but distinct from, the relation of spatial location. Site [snap:Site] entities are not to be confused with spatial region [snap:SpatialRegion] entities. In BFO, site [snap:Site] allows for a so-called relational view of space which is different from the view corresponding to the class spatial region [snap:SpatialRegion] (see the comment on this class).
comment: Definition: An independent continuant [snap:IndependentContinuant] consisting of a characteristic spatial shape in relation to some arrangement of other continuant [snap:Continuant] entities and of the medium which is enclosed in whole or in part by this characteristic spatial shape. Site [snap:Site] entities are entities that can be occupied by other continuant [snap:Continuant] entities.
comment: Examples: a particular room in a particular hospital, Maria's nostril or her intestines for a variety of bacteria.

spatial_region
type: Class
equivalent class: Class
  union of: one_dimensional_region
  union of: three_dimensional_region
  union of: two_dimensional_region
  union of: zero_dimensional_region
subclass of: continuant
comment: Comment: All instances of continuant [snap:Continuant] are spatial entities, that is, they enter in the relation of (spatial) location with spatial region [snap:SpatialRegion] entities. As a particular case, the exact spatial location of a spatial region [snap:SpatialRegion] is this region itself.
comment: Comment: An instance of spatial region [snap:SpatialRegion] is a part of space. All parts of space are spatial region [snap:SpatialRegion] entities and only spatial region [snap:SpatialRegion] entities are parts of space. Space is the entire extent of the spatial universe, a designated individual, which is thus itself a spatial region [snap:SpatialRegion].
comment: Comment: Space and spatial region [snap:SpatialRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of space is sometimes called "absolutist" or "the container view". In BFO, the class site [snap:Site] allows for a so-called relational view of space, that is to say, a view according to which spatiality is a matter of relative location between entities and not a matter of being tied to space. The bridge between these two views is secured through the fact that while instances of site [snap:Site] are not spatial region [snap:SpatialRegion] entities, they are nevertheless spatial entities.
comment: Definition: A continuant [snap:Continuant] that is neither bearer of quality [snap:Quality] entities nor inheres in any other entities.
comment: Examples: the sum total of all space in the universe, parts of the sum total of all space in the universe

specifically_dependent_continuant
type: Class
equivalent class: Class
  union of: quality
  union of: realizable_entity
subclass of: dependent_continuant
comment: Definition: A continuant [snap: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.
comment: Examples: the mass of a cloud, the smell of mozzarella, the liquidity of blood, the color of a tomato, the disposition of fish to decay, the role of being a doctor, the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc.
comment: Synonyms: property, trope, mode

three_dimensional_region
type: Class
subclass of: spatial_region
disjoint with: two_dimensional_region
disjoint with: zero_dimensional_region
comment: Definition: A spatial region [snap:SpatialRegion] with three dimensions.
comment: Examples: a cube-shaped part of space, a sphere-shaped part of space

two_dimensional_region
type: Class
subclass of: spatial_region
disjoint with: zero_dimensional_region
comment: Definition: A spatial region [snap:SpatialRegion] with two dimensions.
comment: Examples: the surface of a cube-shaped part of space, the surface of a sphere-shaped part of space, the surface of a rectilinear planar figure-shaped part of space

zero_dimensional_region
type: Class
subclass of: spatial_region
comment: Definition: A spatial region [snap:SpatialRegion] with no dimensions.
comment: Examples: a point

connected_spatiotemporal_region
type: Class
equivalent class: Class
  union of: spatiotemporal_instant
  union of: spatiotemporal_interval
subclass of: spatiotemporal_region
disjoint with: scattered_spatiotemporal_region
comment: Definition: A spatiotemporal region [span:SpatiotemporalRegion] that has temporal and spatial dimensions such that all points within the spatiotemporal region are mediately or immediately connected to all other points within the same spatiotemporal region [span:SpatiotemporalRegion].
comment: Examples: the spatial and temporal location of an individual organism's life, the spatial and temporal location of the development of a fetus

connected_temporal_region
type: Class
equivalent class: Class
  union of: temporal_instant
  union of: temporal_interval
subclass of: temporal_region
disjoint with: scattered_temporal_region
comment: Definition: A temporal region [span:TemporalRegion] every point of which is mediately or immediately connected with every other point of which.
comment: Examples: the 1970s years, the time from the beginning to the end of a heart attack, the time taken up by cellular meiosis

fiat_process_part
type: Class
subclass of: processual_entity
disjoint with: process
disjoint with: process_aggregate
disjoint with: process_boundary
disjoint with: processual_context
comment: Definition: A processual entity [span:ProcessualEntity] that is part of a process but that does not have bona fide beginnings and endings corresponding to real discontinuities.
comment: Examples: chewing during a meal, the middle part of a rainstorm, the worst part of a heart-attack, the most interesting part of Van Gogh's life

occurrent
type: Class
equivalent class: Class
  union of: processual_entity
  union of: spatiotemporal_region
  union of: temporal_region
subclass of: entity
comment: Definition: An entity [bfo:Entity] that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants.
comment: Examples: the life of an organism, a surgical operation as processual context for a nosocomical infection, the spatiotemporal context occupied by a process of cellular meiosis, the most interesting part of Van Gogh's life, the spatiotemporal region occupied by the development of a cancer tumor
comment: Synonyms: perdurant

process
type: Class
subclass of: processual_entity
disjoint with: process_aggregate
disjoint with: process_boundary
disjoint with: processual_context
comment: Definition: A processual entity [span:ProcessualEntity] that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities.
comment: Examples: the life of an organism, the process of sleeping, the process of cell-division

process_aggregate
type: Class
subclass of: processual_entity
disjoint with: process_boundary
disjoint with: processual_context
comment: Definition: A processual entity [span:ProcessualEntity] that is a mereological sum of process [span:Process] entities and possesses non-connected boundaries.
comment: Examples: the beating of the hearts of each of seven individuals in the room, the playing of each of the members of an orchestra, a process of digestion and a process of thinking taken together

process_boundary
type: Class
subclass of: processual_entity
disjoint with: processual_context
comment: Definition: A processual entity [span:ProcessualEntity] that is the fiat or bona fide instantaneous temporal process boundary.
comment: Examples: birth, death, the forming of a synapse, the onset of REM sleep, the detaching of a finger in an industrial accident, the final separation of two cells at the end of cell-division, the incision at the beginning of a surgery

processual_context
type: Class
subclass of: processual_entity
comment: Comment: An instance of a processual context [span:ProcessualContext] is a mixture of processual entity [span:ProcessualEntity] which stand as surrounding environments for other processual entity [span:ProcessualEntity] entities. The class processual context [span:ProcessualContext] is the analogous among occurrent [span:Occurrent] entities to the class site [snap:Site] among continuant [snap:Continuant] entities.
comment: Definition: An occurrent [span:Occurrent] consisting of a characteristic spatial shape inhering in some arrangement of other occurrent [span:Occurrent] entities. Processual context [span:ProcessualContext] entities are characteristically entities at or in which other occurrent [span:Occurrent] entities can be located or occur.
comment: Examples: The processual context for a given manipulation occurring as part of an experiment is made of processual entities which occur in parallel, are not necessarily all parts of the experiment themselves and may involve continuant [snap:Continuant] entities which are in the spatial vicinity of the participants in the experiment.

processual_entity
type: Class
equivalent class: Class
  union of: fiat_process_part
  union of: process
  union of: process_aggregate
  union of: process_boundary
  union of: processual_context
subclass of: occurrent
disjoint with: spatiotemporal_region
disjoint with: temporal_region
comment: Definition: An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.
comment: Examples: the life of an organism, the process of meiosis, the course of a disease, the flight of a bird

scattered_spatiotemporal_region
type: Class
subclass of: spatiotemporal_region
comment: Definition: A spatiotemporal region [span:SpatiotemporalRegion] that has spatial and temporal dimensions and every spatial and temporal point of which is not connected with every other spatial and temporal point of which.
comment: Examples: the space and time occupied by the individual games of the World Cup, the space and time occupied by the individual liaisons in a romantic affair

scattered_temporal_region
type: Class
subclass of: temporal_region
comment: Definition: A temporal region [span:TemporalRegion] every point of which is not mediately or immediately connected with every other point of which.
comment: Examples: the time occupied by the individual games of the World Cup, the time occupied by the individual liaisons in a romantic affair

spatiotemporal_instant
type: Class
subclass of: connected_spatiotemporal_region
disjoint with: spatiotemporal_interval
comment: Definition: A connected spatiotemporal region [span:ConnectedSpatiotemporalRegion] at a specific moment.
comment: Examples: the spatiotemporal region occupied by a single instantaneous temporal slice (part) of a process

spatiotemporal_interval
type: Class
subclass of: connected_spatiotemporal_region
comment: Definition: A connected spatiotemporal region [span:ConnectedSpatiotemporalRegion] that endures for more than a single moment of time.
comment: Examples: the spatiotemporal region occupied by a process or by a fiat processual part

spatiotemporal_region
type: Class
equivalent class: Class
  union of: connected_spatiotemporal_region
  union of: scattered_spatiotemporal_region
subclass of: occurrent
disjoint with: temporal_region
comment: Comment: All instances of occurrent [span:Occurrent] are spatiotemporal entities, that is, they enter in the relation of (spatiotemporal) location with spatiotemporal region [span:SpatiotemporalRegion] entities. As a particular case, the exact spatiotemporal location of a spatiotemporal region [span:SpatiotemporalRegion] is this region itself.
comment: Comment: An instance of the spatiotemporal region [span:SpatiotemporalRegion] is a part of spacetime. All parts of spacetime are spatiotemporal region [span:SpatiotemporalRegion] entities and only spatiotemporal region [span:SpatiotemporalRegion] entities are parts of spacetime. In particular, neither spatial region [snap:SpatialRegion] entities nor temporal region [span:TemporalRegion] entities are in BFO parts of spacetime. Spacetime is the entire extent of the spatiotemporal universe, a designated individual, which is thus itself a spatiotemporal region [span:SpatiotemporalRegion]. Spacetime is among occurrents the analogous of space among continuant [snap:Continuant] entities.
comment: Comment: Spacetime and spatiotemporal region [span:SpatiotemporalRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of spacetime can be called "absolutist" or "the container view". In BFO, the class processual context [span:ProcessualContext] allows for a so-called relational view of spacetime, that is to say, a view according to which spatiotemporality is a matter of relative location between entities and not a matter of being tied to spacetime. In BFO, the bridge between these two views is secured through the fact that instances of processual context [span:ProcessualContext] are too spatiotemporal entities.
comment: Definition: An occurrent [span:Occurrent] at or in which processual entity [span:ProcessualEntity] entities can be located.
comment: Examples: the spatiotemporal region occupied by a human life, the spatiotemporal region occupied by the development of a cancer tumor, the spatiotemporal context occupied by a process of cellular meiosis

temporal_instant
type: Class
subclass of: connected_temporal_region
disjoint with: temporal_interval
comment: Definition: A connected temporal region [span:ConnectedTemporalRegion] comprising a single moment of time.
comment: Examples: right now, the moment at which a finger is detached in an industrial accident, the moment at which a child is born, the moment of death

temporal_interval
type: Class
subclass of: connected_temporal_region
comment: Definition: A connected temporal region [span:ConnectedTemporalRegion] lasting for more than a single moment of time.
comment: Examples: any continuous temporal duration during which a process occurs

temporal_region
type: Class
equivalent class: Class
  union of: connected_temporal_region
  union of: scattered_temporal_region
subclass of: occurrent
comment: Comment: All instances of occurrent [span:Occurrent] are temporal entities, that is, they enter in the relation of (temporal) location with temporal region [span:TemporalRegion] entities. As a particular case, the exact spatiotemporal location of a temporal region [span:TemporalRegion] is this region itself. Continuant [snap:Continuant] entities are not temporal entities in the technical sense just explained; they are related to time in a different way, not through temporal location but through a relation of existence at a time or during a period of time (see continuant [snap:Continuant].
comment: Comment: An instance of temporal region [span:TemporalRegion] is a part of time. All parts of time are temporal region [span:TemporalRegion] entities and only temporal region [span:TemporalRegion] entities are parts of time. Time is the entire extent of the temporal universe, a designated individual, which is thus a temporal region itself.
comment: Comment: Time and temporal region [span:TemporalRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of time can be called "absolutist" or "the container view" in analogy to what is traditionally the case with space (see spatial region [snap:SpatialRegion].
comment: Definition: An occurrent [span:Occurrent] that is part of time.
comment: Examples: the time it takes to run a marathon, the duration of a surgical procedure, the moment of death

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

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

metadata complete
type: NamedIndividual
type: curation status specification
definition: Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.

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

ready for release
type: NamedIndividual
type: curation status specification
definition: Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."

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

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

pending final vetting
type: NamedIndividual
type: curation status specification
definition: All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the definition editor.

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

placeholder removed
type: NamedIndividual
type: obsolescence reason specification

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

term imported
type: NamedIndividual
type: obsolescence reason specification
editor note: This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.

term split
type: NamedIndividual
type: obsolescence reason specification
editor note: This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.

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

universal
type: NamedIndividual
type: denotator type
definition source: A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
definition editor: Alan Ruttenberg
editor note: Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.

defined class
type: NamedIndividual
type: denotator type
editor note: "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
definition editor: A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
definition editor: Alan Ruttenberg

named class expression
type: NamedIndividual
type: denotator type
definition: A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
definition editor: Alan Ruttenberg
editor note: named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions

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

requires discussion
type: NamedIndividual
type: curation status specification
definition: A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
definition editor: Alan Ruttenberg
definition source: group:OBI