The Biological Collections Ontology
type: Ontology
comment: The Biological Collections Ontology was originally created at the Biocode Commons Hackathon at GSC14. Older versions can be viewed at http://code.google.com/p/biocode-commons/source/browse/#svn%2Ftrunk%2Fontologies%2Fbiocollections. Some of the classes in this ontology may be replaced by existing or newly requested terms from OBI or other ontologies. The Biological Collections Ontology (BCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators.
format: application/rdf+xml
default language: en
language: en
rights: http://creativecommons.org/publicdomain/zero/1.0/
creator: Ramona Walls
creator: John Wieczorek
creator: Barry Smith
creator: Biocode Commons Ontology Hackathon members
version IRI: bco.owl

taxonomic inventory metadata preferred name
type: AnnotationProperty

BCO preferred label
type: AnnotationProperty

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

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

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
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

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

definition editor
type: AnnotationProperty
label: term editor
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.
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: 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
definition editor: PERSON:Daniel Schober
editor preferred term: definition editor
editor preferred term: term editor
has curation status: ready for release

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

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

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

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

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

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

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

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

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

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

term replaced by
type: AnnotationProperty
definition source: Person:Alan Ruttenberg
definition editor: 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

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

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

temporal interpretation
type: AnnotationProperty

never in taxon
type: AnnotationProperty
definition: x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL.
expand assertion to: ?X DisjointWith RO_0002162 some ?Y
example of usage: tooth SubClassOf 'never in taxon' value 'Aves'
definition editor: Chris Mungall
definition source: PMID:17921072
definition source: PMID:20973947

shorthand
type: AnnotationProperty

has role
type: ObjectProperty
definition: The relationship between an independent continuant and a role. Slightly more specific than the parent class bearer of.
comment: This property was originally created in OBI, but in OBI it was deprecated and replaced by BFO:0000087. However, the BFO relation was replaced by has role at some time, which is not yet part of a stable release. Once the BFO role has been tested and released, it may replace this relation.
sub property of: bearer of
domain: independent_continuant
range: role

part of
type: ObjectProperty
type: TransitiveProperty
editor note: Intended meaning: Ambiguous between continuant-parthood and occurrent-parthood. domain: continuant range: continuant time: at some time domain: occurrent range: occurrent time: atemporal
editor note: Parthood as a relation between instances: The primitive instance-level relation p part_of p1 is illustrated in assertions such as: this instance of rhodopsin mediated phototransduction part_of this instance of visual perception. This relation satisfies at least the following standard axioms of mereology: reflexivity (for all p, p part_of p); anti-symmetry (for all p, p1, if p part_of p1 and p1 part_of p then p and p1 are identical); and transitivity (for all p, p1, p2, if p part_of p1 and p1 part_of p2, then p part_of p2). Analogous axioms hold also for parthood as a relation between spatial regions. For parthood as a relation between continuants, these axioms need to be modified to take account of the incorporation of a temporal argument. Thus for example the axiom of transitivity for continuants will assert that if c part_of c1 at t and c1 part_of c2 at t, then also c part_of c2 at t. Parthood as a relation between classes: To define part_of as a relation between classes we again need to distinguish the two cases of continuants and processes, even though the explicit reference to instants of time now falls away. For continuants, we have C part_of C1 if and only if any instance of C at any time is an instance-level part of some instance of C1 at that time, as for example in: cell nucleus part_ of cell.
source: http://www.obofoundry.org/ro/#OBO_REL:part_of
editor preferred term: part of
alternative term: part_of
inverse of: has part
temporal interpretation: axiom holds for all times
sub property of: overlaps

has part
type: ObjectProperty
type: TransitiveProperty
editor note: Intended meaning: Ambiguous between continuant-parthood and occurrent-parthood. domain: continuant range: continuant time: at some time domain: occurrent range: occurrent time: atemporal
editor preferred term: has part
alternative term: has_part
temporal interpretation: axiom holds for all times
sub property of: overlaps

realized in
type: ObjectProperty
editor note: Intended meaning: domain: realizable entity range: processual entity time: atemporal
alternative term: is realized by
editor preferred term: realized in
alternative term: realized_in

realizes
type: ObjectProperty
editor note: Intended meaning: domain: processual entity range: realizable entity time: atemporal
editor preferred term: realizes
inverse of: realized in

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

precedes
type: ObjectProperty
type: TransitiveProperty
editor note: Intended meaning: domain: occurrent range: occurrent time: atemporal
editor preferred term: precedes
sub property of: temporally related to

occurs in
type: ObjectProperty
alternative term: Intended meaning: domain: occurrent range: independent continuant time: atemporal
editor preferred term: occurs in
alternative term: occurs_in
alternative term: unfolds in
alternative term: unfolds_in
inverse of: contains process
property chain axiom: part of

contains process
type: ObjectProperty
editor preferred term: site of

is about
type: ObjectProperty
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
example of usage: This document is about information artifacts and their representations
definition: is_about is a (currently) primitive relation that relates an information artifact to an entity.
definition editor: person:Alan Ruttenberg
has curation status: pending final vetting
imported from: iao.owl

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

is_specified_output_of
type: ObjectProperty
definition editor: PERSON:Bjoern Peters
editor preferred term: is_specified_output_of
definition: A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
definition editor: Alan Ruttenberg
range: planned process
sub property of: output of
imported from: obi.owl

inheres in
type: ObjectProperty
editor note: Intended meaning: domain: specifically dependent continuant range: independent continuant time: at all times A specifically dependent continuant A inheres in its independent continuant B at all times during which A exists.
editor preferred term: inheres in
alternative term: inheres_in
temporal interpretation: axiom holds for all times

bearer of
type: ObjectProperty
editor note: Intended meaning: domain: independent continuant range: specifically dependent continuant time: at some time
editor preferred term: bearer of
alternative term: bearer_of
alternative term: is bearer of
inverse of: inheres in
temporal interpretation: axiom holds for all times

participates in
type: ObjectProperty
editor note: Intended meaning: domain: continuant and (not spatial region) range: processual entity time: at some time
editor preferred term: participates in
alternative term: participates_in

has participant
type: ObjectProperty
editor preferred term: has participant
alternative term: has_participant
source: http://www.obofoundry.org/ro/#OBO_REL:has_participant
editor note: Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
editor note: Intended meaning: domain: processual entity range: continuant and (not spatial region) time: at some time
inverse of: participates in

derives from
type: ObjectProperty
comment: See also BFO_0001009
has curation status: pending final vetting
sub property of: topObjectProperty

derives into
type: ObjectProperty
has curation status: pending final vetting
inverse of: derives from
sub property of: topObjectProperty

location of
type: ObjectProperty
type: TransitiveProperty
editor preferred term: location of
alternative term: location_of
temporal interpretation: axiom holds for all times

contained in
type: ObjectProperty
editor note: Containment is location not involving parthood, and arises only where some immaterial continuant is involved.
editor note: Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):
editor note: Intended meaning: domain: material entity range: spatial region or site (immaterial continuant)
editor preferred term: contained in
alternative term: contained_in
inverse of: contains
temporal interpretation: axiom holds for all times

contains
type: ObjectProperty
editor note: Intended meaning: domain: spatial region or site (immaterial continuant) range: material entity
editor preferred term: contains
temporal interpretation: axiom holds for all times

located in
type: ObjectProperty
type: TransitiveProperty
editor note: Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
source: http://www.obofoundry.org/ro/#OBO_REL:located_in
editor preferred term: located in
alternative term: located_in
inverse of: location of
temporal interpretation: axiom holds for all times

before_or_simultaneous_with
type: ObjectProperty
alternative term: <=
comment: Primitive instance level timing relation between events
sub property of: temporally related to

simultaneous_with
type: ObjectProperty
type: TransitiveProperty
comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)
sub property of: before_or_simultaneous_with

before
type: ObjectProperty
type: TransitiveProperty
comment: t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)
sub property of: before_or_simultaneous_with

during_which_ends
type: ObjectProperty
comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
inverse of: ends_during
sub property of: temporally related to

encompasses
type: ObjectProperty
type: TransitiveProperty
alternative term: di
comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
sub property of: during_which_starts
inverse of: happens_during

ends_after
type: ObjectProperty
type: TransitiveProperty
comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
sub property of: temporally related to
property chain axiom: ends_during
property chain axiom: preceded by

immediately_preceded_by
type: ObjectProperty
comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
alternative term: starts_at_end_of
sub property of: preceded by
inverse of: immediately_precedes

during_which_starts
type: ObjectProperty
comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
inverse of: starts_during
sub property of: temporally related to

starts_before
type: ObjectProperty
type: TransitiveProperty
sub property of: temporally related to

immediately_precedes
type: ObjectProperty
alternative term: meets
comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
alternative term: ends_at_start_of
sub property of: preceded by

starts_during
type: ObjectProperty
comment: X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))
alternative term: io
sub property of: temporally related to

happens_during
type: ObjectProperty
type: TransitiveProperty
comment: X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))
alternative term: during
alternative term: d
sub property of: ends_during

ends_during
type: ObjectProperty
comment: X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y).
alternative term: overlaps
alternative term: o
sub property of: temporally related to

overlaps
type: ObjectProperty
definition: x overlaps y if and only if there exists some z such that x has part z and z part of y
expand expression to: http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
has curation status: pending final vetting
temporal interpretation: axiom holds for all times
sub property of: mereotopologically related to
property chain axiom: part of
property chain axiom: has part

connected to
type: ObjectProperty
definition editor: David Osumi-Sutherland
definition: X connected_to Y if and only if X and Y share a fiat boundary.
curator note: Consider relabeling this to "continuous with" (FMA:85972). The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)
has curation status: pending final vetting
temporal interpretation: axiom holds for all times
sub property of: mereotopologically related to

proper overlaps
type: ObjectProperty
first order logic expression: (forall (?x ?y) (iff (proper_overlaps ?x ?y) (and (overlaps ?x ?y) (not (part_of ?x ?y)) (not (part_of ?y ?x)))))
alternative term: partially overlaps
has curation status: pending final vetting
temporal interpretation: axiom holds for all times
sub property of: overlaps

spatially disjoint from
type: ObjectProperty
definition: A is spatially_disjoint_from B if and only if they have no parts in common
expand expression to: BFO_0000051 exactly 0 (BFO_0000050 some ?Y)
definition editor: Chris Mungall
editor note: There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom.
has curation status: pending final vetting
temporal interpretation: axiom holds for all times
sub property of: mereotopologically related to

has component
type: ObjectProperty
comment: For use in recording has_part with a cardinality constraint.
sub property of: has part
has curation status: pending final vetting
temporal interpretation: axiom holds for all times

actively participates in
type: ObjectProperty
definition: x actively participates in y if and only if x participates in y and x realizes some active role
alternative term: agent in
has curation status: pending final vetting
sub property of: participates in
inverse of: has active participant

has active participant
type: ObjectProperty
definition: x has participant y if and only if x realizes some active role that inheres in y
alternative term: has agent
has curation status: pending final vetting
sub property of: has participant

surrounded by
type: ObjectProperty
definition: x surrounded_by y if and only if x is adjacent to y and for every region r that is adjacent to x, r overlaps y
has curation status: pending final vetting
temporal interpretation: axiom holds for all times
sub property of: adjacent to

adjacent to
type: ObjectProperty
definition: x adjacent to y if and only if x and y share a boundary
comment: TODO: replaced by BFO_0001008
editor note: belongs in BFO?
has curation status: pending final vetting
temporal interpretation: axiom holds for all times
sub property of: spatially disjoint from

surrounds
type: ObjectProperty
has curation status: pending final vetting
temporal interpretation: axiom holds for all times
inverse of: surrounded by
sub property of: adjacent to

temporally related to
type: ObjectProperty
source: https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit
definition source: Allen
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
has curation status: pending final vetting

starts
type: ObjectProperty
definition source: Allen
definition editor: Chris Mungall
definition: inverse of starts with
has curation status: pending final vetting
sub property of: temporally related to

starts with
type: ObjectProperty
type: TransitiveProperty
example of usage: Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
definition: x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
alternative term: started by
has curation status: pending final vetting
sub property of: temporally related to
inverse of: starts

ends
type: ObjectProperty
definition: inverse of ends with
has curation status: pending final vetting
sub property of: temporally related to
inverse of: ends with

ends with
type: ObjectProperty
type: TransitiveProperty
alternative term: finished by
definition: x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
has curation status: pending final vetting
sub property of: temporally related to

has input
type: ObjectProperty
has curation status: pending final vetting
sub property of: has participant

has output
type: ObjectProperty
has curation status: pending final vetting
sub property of: has participant

inheres in part of
type: ObjectProperty
temporal interpretation: axiom holds for all times
property chain axiom: inheres in
property chain axiom: part of

mereotopologically related to
type: ObjectProperty
definition editor: Chris Mungall
definition: A mereological relationship or a topological relationship
temporal interpretation: axiom holds for all times

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

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

input of
type: ObjectProperty
sub property of: participates in
inverse of: has input

output of
type: ObjectProperty
sub property of: participates in
inverse of: has output

formed as result of
type: ObjectProperty
sub property of: output of

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

taxonomic inventory
type: Class
equivalent class: Class
  intersection of: information content entity
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: taxonomic inventory process
subclass of: information content entity
example of usage: The butterflies of Great Britain
definition: An information content entity that is a list of taxa recorded in some geospatially defined area over some stated time period using some method involving some actor.
example of usage: The plants of Yosemite National Park
creator: Taxonomic Inventory Metadata Workshop
example of usage: "The Flora of North America"
source: https://docs.google.com/spreadsheet/ccc
has curation status: pending final vetting

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

open search taxonomic inventory process
type: Class
subclass of: taxonomic inventory process
definition: Search restricted within a larger defined geographic area, but where effort isn't even or complete across the defined region. That is, a planned search restricted to a larger, defined geographic area, but effort isn't evenly distributed throughout the area, nor expected to be a complete and comprehensive accounting of TOI's across the defined region. Temporal duration is typically longer than restricted search-- lasting hours to all day.
example of usage: Individual Christmas Bird Count by some team. Organized field trip to a State Park.
creator: Taxonomic Inventory Metadata Workshop
source: https://docs.google.com/spreadsheet/ccc
taxonomic inventory metadata preferred name: open search
has curation status: uncurated

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

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

adventitious taxonomic inventory process
type: Class
subclass of: taxonomic inventory process
creator: Taxonomic Inventory Metadata Workshop
definition: A taxonomic inventory in which taxon occurrences are recorde as a co-variates of another study and later compiled as a taxonomic inventory.
taxonomic inventory metadata preferred name: adventitious inventory
example of usage: data from ecological studies in which presence of some taxa is recorded to clarify population or community parameters
source: https://docs.google.com/spreadsheet/ccc
has curation status: uncurated

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

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

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

data item
type: Class
subclass of: information content entity
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.
example of usage: Data items include counts of things, analyte concentrations, and statistical summaries.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Jonathan Rees
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.
alternative term: data
editor preferred term: data item
has curation status: pending final vetting
imported from: iao.owl

information content entity
type: Class
subclass of: generically_dependent_continuant
example of usage: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
definition source: OBI_0000142
definition editor: PERSON: Chris Stoeckert
definition: an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity
editor preferred term: information content entity
has curation status: pending final vetting
imported from: iao.owl

directive information entity
type: Class
subclass of: information content entity
editor note: 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
definition: An information content entity whose concretizations indicate to their bearer how to realize them in a process.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
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
has curation status: metadata incomplete
imported from: iao.owl

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.

planned process
type: Class
subclass of: process
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.)
curator note: 6/11/9: Edited at workshop. Used to include: is initiated by an agent
definition editor: Bjoern Peters
example of usage: Injecting mice with a vaccine in order to test its efficacy
definition source: branch derived
definition: A processual entity that realizes a plan which is the concretization of a plan specification.
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)
editor preferred term: planned process
has curation status: ready for release
imported from: obi.owl

assay
type: Class
subclass of: planned process
example of usage: Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
definition: A planned process with the objective to produce information about some evaluant
definition source: OBI branch derived
definition editor: PlanAndPlannedProcess Branch
editor preferred term: assay
alternative term: measuring
alternative term: scientific observation
has curation status: ready for release
imported from: obi.owl

organization
type: Class
subclass of: material_entity
definition source: GROUP: OBI
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Philippe Rocca-Serra
definition editor: PERSON: Susanna Sansone
definition: An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
example of usage: PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
editor preferred term: organization
has curation status: ready for release
imported from: obi.owl

protocol
type: Class
subclass of: directive information entity
definition source: OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
example of usage: PMID: 18388943.Nat Protoc. 2008;3(4):612-8.Protocol for the induction of arthritis in C57BL/6 mice.
definition editor: PlanAndPlannedProcess Branch
definition: a protocol is a plan specification which has sufficient level of detail and quantitative information to communicate it between domain experts, so that different domain experts will reliably be able to independently reproduce the process.
editor preferred term: protocol
has curation status: ready for release
imported from: obi.owl

sequence data
type: Class
subclass of: data item
definition source: GROUP: OBI
definition editor: Person:Chris Stoeckert
example of usage: example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search.
editor preferred term: sequence data
has curation status: metadata complete
imported from: obi.owl

sequencing assay
type: Class
subclass of: assay
definition source: OBI branch derived
definition editor: PlanAndPlannedProcess Branch
example of usage: The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template
editor note: has_output should be sequence of input; we don't have sequence well defined yet
editor preferred term: sequencing assay
definition: the use of a chemical or biochemical means to infer the sequence of a biomaterial
has curation status: pending final vetting
imported from: obi.owl

evidence role
type: Class
subclass of: role
comment: It might be better to request this term in OBI or IAO.
example of usage: A museum specimen that serves as evidence for a taxonomic identification process bears an evidence role.
definition: A role that is borne by some entity as a result of the entity providing evidence to support an assertion.
has curation status: uncurated

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

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

observing process
type: Class
equivalent class: Class
  intersection of: process
  intersection of: Restriction
    on property: has part
    some values from: selecting process
  intersection of: Restriction
    on property: has input
    some values from: material target of observation
  intersection of: Restriction
    on property: has output
    some values from: information content entity
subclass of: process
example of usage: Observing butterflies during a transect walk.
definition: A process in which a person or machine sees or detects a material entity and selects it as worthy of observation, and which has as output an information content entity about the selected material entity.
creator: Biocode Commons Ontology Hackathon
example of usage: A trip camera capture of an image of a jaguar is an observation, because it is "selected" by the camera as worthy of obsevation simply by virtue of moving in front of the camera.
example of usage: Seeing three pelicans flying overhead on Christmas day.
comment: The information artifact may written or recorded or just be stored in someone's head (specifically depenedent upon that person). In the context of a taxonomic inventory, an observing process may be called a sighting, and is an ad hoc reporting of, typically, a single taxon occurrence, usually motivated by rarity, individual interest in the taxon, or atypicality of circumstances.
taxonomic inventory metadata preferred name: sighting
has curation status: pending final vetting

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

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

printed observational report
type: Class
subclass of: printed report
example of usage: A field notebook.
definition: A printed report that records the outcome of some observing process.
creator: Biocode Commons Ontology Hackathon
has curation status: uncurated

selecting process
type: Class
subclass of: process
subclass of: Restriction
  on property: has input
  some values from: material_entity
definition: A process by which a person or machine decides that a particular material entity as worthy of collection or observation.
creator: Biocode Commons Ontology Hackathon
example of usage: Filtering sea water to extract only organisms smaller than a certain size.
comment: The criteria for selection may be specified in a protocol or may be ad hoc.
example of usage: deciding which branch to collect for a herbarium specimen
has curation status: requires discussion

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

physical extraction process
type: Class
subclass of: process
subclass of: Restriction
  on property: has input
  some values from: material_entity
comment: Considered acquisition in OBI, but that is about taking possession. Physical extraction may involve taking pocession, but it may also just involve extraction of something that is already posessed (e.g. of dna from cells).
example of usage: removing a fish from the ocean with a net
example of usage: picking leaves from a plant
definition: A process that involves removing a material entity from its original site to another site.
example of usage: removing dna from cells
creator: Biocode Commons Ontology Hackathon
has curation status: requires discussion

material sampling process
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has part
  some values from: submitting process
subclass of: Restriction
  on property: has_specified_output
  some values from: material sample
subclass of: Restriction
  on property: has_specified_output
  all values from: material sample
subclass of: Restriction
  on property: has part
  some values from: physical extraction process
subclass of: Restriction
  on property: has part
  some values from: selecting process
definition: A planned process that includes selecting a material entity for study, physically extracting the material entity, and submitting the material entity to some institution for preservation or study.
comment: Consider use of specimen collection from OBI.
creator: Biocode Commons Ontology Hackathon
alternative term: collecting event
example of usage: collecting plant parts for herbarium specimens
example of usage: collecting sea water samples as part of Ocean Sampling Day
has curation status: pending final vetting

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

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

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

material sample role
type: Class
equivalent class: Class
  intersection of: role
  intersection of: Restriction
    on property: realized in
    some values from: material sampling process
subclass of: role
creator: Biocode Commons Ontology Hackathon
definition: A role that is borne by some material entity and is realized by the material entity being the output of a material sampling process.
comment: This term may be replaced by OBI:specimen role.
example of usage: the role borne by a branch when it becomes a herbarium specimen
has curation status: pending final vetting

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

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

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

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

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

organismal museum collection
type: Class
subclass of: museum collection
definition: A museum collection that has as member part a material sample that was derived from an organism.
creator: Biocode Commons Ontology Hackathon
example of usage: the insect collection at the Smithsonian Institution
has curation status: requires discussion

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

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

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

material sample
type: Class
equivalent class: Class
  intersection of: material_entity
  intersection of: Restriction
    on property: has role
    some values from: material sample role
example of usage: A herbarium or museum specimen.
creator: Biocode Commons Ontology Hackathon
example of usage: A jar of water, the microbes that were filtered from that water, the DNA extracted from those microbes, a subsample of that DNA.
definition: A material entity that has a material sample role. A material entity takes on the material sample role by being the output of a material samping process. That is, is selected for study, collected, and submitted to an institution for preservation or study.
comment: Material sample is already in OBI, but with a slightly different meaning. Consider import of OBI:specimen to replace this term.
has curation status: pending final vetting

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

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

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

taxonomic identification process
type: Class
subclass of: planned process
example of usage: Using BLAST to identify the taxa present in an environmental (metagenomic) sample.
example of usage: Associating a museum specimen with a specific taxonomic concept based on its characters.
example of usage: Using a key to identify a plant in the field.
example of usage: Using DNA barcoding to identify a plant species.
creator: Biocode Commons Ontology Hackathon
definition: A process by which a material sample is associated with a taxon or taxa.
has curation status: pending final vetting

process that yields a material representation of a material entity
type: Class
subclass of: process
creator: Biocode Commons Ontology Hackathon
curator note: Consider term from OBI or IAO.
comment: Includes as output rubbings, casts, photographic prints, audio or video tapes. Needs a better name. Current name is the definition.
has curation status: to be replaced with external ontology term

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

process that yields an information artifact that is a representation of a material entity
type: Class
subclass of: process
creator: Biocode Commons Ontology Hackathon
comment: Includes audio recordings and photographs (which are information artifacts). Needs a better name. Current name is the definition.
curator note: Some instances of term could possibly be replaced by OBI:image acquisition. Maybe request another OBI term for audio recording acquisition.
has curation status: to be replaced with external ontology term

material target of observation role
type: Class
equivalent class: Class
  intersection of: role
  intersection of: Restriction
    on property: realized in
    some values from: observing process
subclass of: role
creator: Biocode Commons Ontology Hackathon
definition: A role that is borne by some material entity and is realized by the material entity being the input of an observing process.
example of usage: the role borne by a bird during a Christmas Bird Count
has curation status: pending final vetting

Obsolete Class
type: Class
subclass of: Thing

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

axiom holds for all times
type: NamedIndividual
definition: ## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally' ## How to interpret (informal) First the "atemporal" FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation

relation has no temporal argument
type: NamedIndividual
definition: ## Elucidation This is used when the first-order logic form of the relation is binary, and takes no temporal argument. ## Example: Class: limb SubClassOf: develops_from some lateral-plate-mesoderm forall t, t2: forall x : instance_of(x,Limb,t) implies exists y : instance_of(y,LPM,t2) develops_from(x,y)