merged MIABIS and UPenn Biobank ontology
type: Ontology
contributor: William R. Hogan
contributor: Alice Nzinga
contributor: Roxana Merino-Martinez
contributor: Jie Zheng
contributor: Maria Anderberg
contributor: Mathias Brochhausen
contributor: Chris Stoeckert
Source: MIABIS_v2_accepted and UPenn Biobank ontology
contributor: Martin N. Fransson
contributor: Mikael Eriksson
contributor: Jan-Eric Litton
contributor: Sanela Kjellqvist
contributor: Loreana Norlin
version info: development version

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

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

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

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

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

term editor
type: AnnotationProperty
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 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
term editor: PERSON:Daniel Schober
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>
term 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>
term 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
term editor: PERSON:Alan Ruttenberg
term 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
term editor: PERSON:Alan Ruttenberg
editor preferred term: curator note
has curation status: ready for release

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>
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Melanie Courtot
editor preferred term: imported from
has curation status: pending final vetting

expand expression to
type: AnnotationProperty
term 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.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
editor preferred term: expand expression to

elucidation
type: AnnotationProperty

has associated axiom(nl)
type: AnnotationProperty

has associated axiom(fol)
type: AnnotationProperty

has axiom label
type: AnnotationProperty

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

ISA alternative term
type: AnnotationProperty
editor note: Requested by Alejandra Gonzalez-Beltran https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178
editor preferred term: ISA alternative term
term editor: Person: Philippe Rocca-Serra
term editor: Person: Alejandra Gonzalez-Beltran
definition source: ISA tools project (http://isa-tools.org)
definition: An alternative term used by the ISA tools project (http://isa-tools.org).
sub property of: alternative term
has curation status: ready for release

NIAID GSCID-BRC alternative term
type: AnnotationProperty
definition: An alternative term used by the National Institute of Allergy and Infectious Diseases (NIAID) Genomic Sequencing Centers for Infectious Diseases (GSCID) and Bioinformatics Resource Centers (BRC).
editor preferred term: NIAID GSCID-BRC alternative term
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: NIAID GSCID-BRC metadata working group
sub property of: alternative term
has curation status: ready for release

IEDB alternative term
type: AnnotationProperty
definition: An alternative term used by the IEDB.
definition source: IEDB
editor preferred term: IEDB alternative term
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
sub property of: alternative term
has curation status: ready for release

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

logical macro assertion
type: AnnotationProperty
definition: An assertion that holds between two classes that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL.

logical macro assertion on a property
type: AnnotationProperty
definition: A logical macro assertion whose domain is an IRI for a property
sub property of: logical macro assertion

logical macro assertion on an object property
type: AnnotationProperty
sub property of: logical macro assertion on a property

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

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

label
type: AnnotationProperty

part of
type: ObjectProperty
type: TransitiveProperty
editor note: Ambiguous between continuant-parthood and occurrent-parthood
editor preferred term: is part of
alternative term: part_of
inverse of: has part
temporal interpretation: axiom holds for all times
imported from: ro.owl

has part
type: ObjectProperty
type: TransitiveProperty
editor note: Ambiguous between continuant-parthood and occurrent-parthood
editor preferred term: has part
alternative term: has_part
temporal interpretation: axiom holds for all times
imported from: ro.owl

realized in
type: ObjectProperty
elucidation: [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
BFO OWL specification label: realized-in
BFO CLIF specification label: realizedIn
has associated axiom(fol): (forall (x y z t) (if (and (RealizableEntity x) (Process y) (realizesAt y x t) (bearerOfAt z x t)) (hasParticipantAt y z t))) // axiom label in BFO2 CLIF: [106-002]
has associated axiom(nl): if a realizable entity b is realized in a process p, then p stands in the has_participant relation to the bearer of b. (axiom label in BFO2 Reference: [106-002])
alternative term: is realized by
editor preferred term: realized in
alternative term: realized_in
range: process
imported from: bfo.owl
imported from: ro.owl

realizes
type: ObjectProperty
has associated axiom(fol): (forall (x y t) (if (realizesAt x y t) (and (Process x) (or (Disposition y) (Role y)) (exists (z) (and (MaterialEntity z) (hasParticipantAt x z t) (bearerOfAt z y t)))))) // axiom label in BFO2 CLIF: [059-003]
BFO CLIF specification label: realizes
BFO OWL specification label: realizes
editor preferred term: realizes
elucidation: to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
domain: process
range: realizable entity
inverse of: realized in
imported from: bfo.owl
imported from: ro.owl

concretized by at some time
type: ObjectProperty
BFO OWL specification label: concretized-by_st
example of usage: [copied from inverse property 'concretizes at some time'] you may concretize a poem as a pattern of memory traces in your head
elucidation: [copied from inverse property 'concretizes at some time'] b concretizes c at t means: b is a specifically dependent continuant & c is a generically dependent continuant & for some independent continuant that is not a spatial region d, b s-depends_on d at t & c g-depends on d at t & if c migrates from bearer d to another bearer e than a copy of b will be created in e. (axiom label in BFO2 Reference: [075-002])
example of usage: [copied from inverse property 'concretizes at some time'] You may concretize a piece of software by installing it in your computer
editor note: [copied from inverse property 'concretizes at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'concretizes at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'concretizes@en'(x,y,t)
example of usage: [copied from inverse property 'concretizes at some time'] You may concretize a recipe that you find in a cookbook by turning it into a plan which exists as a realizable dependent continuant in your head.
range: specifically dependent continuant
imported from: bfo.owl

concretizes at some time
type: ObjectProperty
BFO CLIF specification label: concretizesAt
has associated axiom(fol): (forall (x y t) (if (genericallyDependsOnAt x y t) (exists (z) (and (concretizesAt z x t) (specificallyDependsOnAt z y t))))) // axiom label in BFO2 CLIF: [076-001]
has associated axiom(fol): (forall (x y t) (if (concretizesAt x y t) (and (SpecificallyDependentContinuant x) (GenericallyDependentContinuant y) (exists (z) (and (IndependentContinuant z) (specificallyDependsOnAt x z t) (genericallyDependsOnAt y z t)))))) // axiom label in BFO2 CLIF: [075-002]
editor note: Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'concretizes at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'concretizes@en'(x,y,t)
BFO OWL specification label: concretizes_st
example of usage: You may concretize a piece of software by installing it in your computer
example of usage: You may concretize a recipe that you find in a cookbook by turning it into a plan which exists as a realizable dependent continuant in your head.
elucidation: b concretizes c at t means: b is a specifically dependent continuant & c is a generically dependent continuant & for some independent continuant that is not a spatial region d, b s-depends_on d at t & c g-depends on d at t & if c migrates from bearer d to another bearer e than a copy of b will be created in e. (axiom label in BFO2 Reference: [075-002])
has associated axiom(nl): if b g-depends on c at some time t, then there is some d, such that d concretizes b at t and d s-depends_on c at t. (axiom label in BFO2 Reference: [076-001])
example of usage: you may concretize a poem as a pattern of memory traces in your head
range: generically dependent continuant
inverse of: concretized by at some time
imported from: bfo.owl

contains process
type: ObjectProperty
BFO OWL specification label: contains-process
BFO CLIF specification label: containsProcess
definition: [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t [XXX-001
imported from: bfo.owl
domain: Class
  union of: site
  union of: material entity
range: Class
  union of: process
  union of: process boundary

specifically depends on at all times
type: ObjectProperty
has associated axiom(fol): (forall (x y t) (if (and (Entity x) (or (continuantPartOfAt y x t) (continuantPartOfAt x y t) (occurrentPartOf x y) (occurrentPartOf y x))) (not (specificallyDependsOnAt x y t)))) // axiom label in BFO2 CLIF: [013-002]
has associated axiom(fol): (forall (x y z t) (if (and (specificallyDependsOnAt x y t) (specificallyDependsOnAt y z t)) (specificallyDependsOnAt x z t))) // axiom label in BFO2 CLIF: [054-002]
example of usage: A pain s-depends_on the organism that is experiencing the pain
has associated axiom(nl): If occurrent b s-depends_on some independent continuant c at t, then b s-depends_on c at every time at which b exists. (axiom label in BFO2 Reference: [015-002])
BFO CLIF specification label: specificallyDependsOn
has associated axiom(fol): (forall (x y t) (if (and (Occurrent x) (IndependentContinuant y) (specificallyDependsOnAt x y t)) (forall (t_1) (if (existsAt x t_1) (specificallyDependsOnAt x y t_1))))) // axiom label in BFO2 CLIF: [015-002]
editor note: BFO 2 Reference: An entity – for example an act of communication or a game of football – can s-depends_on more than one entity. Complex phenomena for example in the psychological and social realms (such as inferring, commanding and requesting) or in the realm of multi-organismal biological processes (such as infection and resistance), will involve multiple families of dependence relations, involving both continuants and occurrents [1, 4, 28
BFO OWL specification label: s-depends-on_at
editor note: BFO2 Reference: specifically dependent continuant\; process; process boundary
has associated axiom(fol): (forall (x) (if (exists (y t) (specificallyDependsOnAt x y t)) (not (MaterialEntity x)))) // axiom label in BFO2 CLIF: [052-001]
editor note: Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'specifically depends on at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'specifically depends on@en(x,y,t)'.
has associated axiom(fol): (forall (x y t) (if (specificallyDependsOnAt x y t) (exists (z) (and (IndependentContinuant z) (not (SpatialRegion z)) (specificallyDependsOnAt x z t))))) // axiom label in BFO2 CLIF: [136-001]
editor note: BFO 2 Reference: S-dependence is just one type of dependence among many; it is what, in the literature, is referred to as ‘existential dependence’ [87, 46, 65, 20
editor note: BFO 2 Reference: the relation of s-depends_on does not in every case require simultaneous existence of its relata. Note the difference between such cases and the cases of continuant universals defined historically: the act of answering depends existentially on the prior act of questioning; the human being who was baptized or who answered a question does not himself depend existentially on the prior act of baptism or answering. He would still exist even if these acts had never taken place.
has associated axiom(nl): If b is s-depends_on something at some time, then b is not a material entity. (axiom label in BFO2 Reference: [052-001])
has associated axiom(nl): If b s-depends_on something at t, then there is some c, which is an independent continuant and not a spatial region, such that b s-depends_on c at t. (axiom label in BFO2 Reference: [136-001])
elucidation: To say that b s-depends_on a at t is to say that b and c do not share common parts & b is of its nature such that it cannot exist unless c exists & b is not a boundary of c and b is not a site of which c is the host [64
example of usage: a gait s-depends_on the walking object. (All at some specific time.)
example of usage: a shape s-depends_on the shaped object
has associated axiom(nl): an entity does not s-depend_on any of its (continuant or occurrent) parts or on anything it is part of. (axiom label in BFO2 Reference: [013-002])
has associated axiom(nl): if b s-depends_on c at t & c s-depends_on d at t then b s-depends_on d at t. (axiom label in BFO2 Reference: [054-002])
example of usage: one-sided s-dependence of a dependent continuant on an independent continuant: an instance of headache s-depends_on some head
example of usage: one-sided s-dependence of a dependent continuant on an independent continuant: an instance of temperature s-depends_on some organism
example of usage: one-sided s-dependence of a process on something: a process of cell death s-depends_on a cell
example of usage: one-sided s-dependence of a process on something: an instance of seeing (a relational process) s-depends_on some organism and on some seen entity, which may be an occurrent or a continuant
example of usage: one-sided s-dependence of one occurrent on another: a process of answering a question is dependent on a prior process of asking a question
example of usage: one-sided s-dependence of one occurrent on another: a process of obeying a command is dependent on a prior process of issuing a command
example of usage: one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of hitting a ball with a cricket bat
example of usage: one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of paying cash to a merchant in exchange for a bag of figs
example of usage: reciprocal s-dependence between occurrents: a process of buying and the associated process of selling
example of usage: reciprocal s-dependence between occurrents: a process of increasing the volume of a portion of gas while temperature remains constant and the associated process of decreasing the pressure exerted by the gas
example of usage: reciprocal s-dependence between occurrents: in a game of chess the process of playing with the white pieces is mutually dependent on the process of playing with the black pieces
example of usage: the one-sided dependence of an occurrent on an independent continuant: football match on the players, the ground, the ball
example of usage: the one-sided dependence of an occurrent on an independent continuant: handwave on a hand
example of usage: the three-sided reciprocal s-dependence of the hue, saturation and brightness of a color [45
example of usage: the three-sided reciprocal s-dependence of the pitch, timbre and volume of a tone [45
example of usage: the two-sided reciprocal s-dependence of the roles of husband and wife [20
sub property of: specifically depends on at some time
imported from: bfo.owl

function of at all times
type: ObjectProperty
editor note: Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'function of at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'function of@en(x,y,t)'.
BFO OWL specification label: f-of_at
has associated axiom(fol): (iff (functionOf a b t) (and (Function a) (inheresInAt a b t))) // axiom label in BFO2 CLIF: [067-001]
BFO CLIF specification label: functionOfAt
definition: a function_of b at t =Def. a is a function and a inheres_in b at t. (axiom label in BFO2 Reference: [067-001])
imported from: bfo.owl

occupies spatial region at some time
type: ObjectProperty
BFO CLIF specification label: occupiesSpatialRegionAt
has associated axiom(fol): (forall (r t) (if (Region r) (occupiesSpatialRegionAt r r t))) // axiom label in BFO2 CLIF: [042-002]
BFO OWL specification label: located-at-r_st
editor note: BFO2 Reference: spatial region
has associated axiom(fol): (forall (x r t) (if (occupiesSpatialRegionAt x r t) (and (SpatialRegion r) (IndependentContinuant x)))) // axiom label in BFO2 CLIF: [041-002]
has associated axiom(fol): (forall (x y r_1 t) (if (and (occupiesSpatialRegionAt x r_1 t) (continuantPartOfAt y x t)) (exists (r_2) (and (continuantPartOfAt r_2 r_1 t) (occupiesSpatialRegionAt y r_2 t))))) // axiom label in BFO2 CLIF: [043-001]
editor note: Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t)
editor note: BFO2 Reference: independent continuant
elucidation: b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002])
has associated axiom(nl): every region r is occupies_spatial_region r at all times. (axiom label in BFO2 Reference: [042-002])
has associated axiom(nl): if b occupies_spatial_region r at t & b continuant_part_of b at t, then there is some r which is continuant_part_of r at t such that b occupies_spatial_region r at t. (axiom label in BFO2 Reference: [043-001])
domain: independent continuant
range: spatial region
inverse of: has spatial occupant at some time
imported from: bfo.owl

has function at some time
type: ObjectProperty
BFO CLIF specification label: hasFunctionAt
has associated axiom(fol): (iff (hasFunctionAt a b t) (functionOf b a t)) // axiom label in BFO2 CLIF: [070-001]
editor note: Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'has function at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has function@en'(x,y,t)
definition: a has_function b at t =Def. b function_of a at t. (axiom label in BFO2 Reference: [070-001])
BFO OWL specification label: has-f_st
range: function
imported from: bfo.owl

exists at
type: ObjectProperty
BFO OWL specification label: exists-at
BFO CLIF specification label: existsAt
editor note: BFO2 Reference: entity
editor note: BFO2 Reference: temporal region
elucidation: b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002])
range: temporal region
inverse of: during which exists
imported from: bfo.owl

has continuant part at all times
type: ObjectProperty
type: TransitiveProperty
BFO CLIF specification label: hasContinuantPartAt
has associated axiom(fol): (iff (hasContinuantPartAt a b t) (continuantPartOfAt b a t)) // axiom label in BFO2 CLIF: [006-001]
BFO OWL specification label: c-has-part_at
definition: [copied from inverse property 'part of continuant at all times that whole exists'] forall(t) exists_at(y,t) -> exists_at(x,t) and 'part of continuant'(x,y,t)
editor note: [copied from inverse property 'part of continuant at all times that whole exists'] This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'has continuant part at all times'
editor note: Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has continuant part at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has continuant part@en(x,y,t)'.
definition: b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001])
sub property of: has continuant part at some time
imported from: bfo.owl

has occurrent part
type: ObjectProperty
type: TransitiveProperty
example of usage: [copied from inverse property 'part of occurrent'] Mary’s 5th birthday occurrent_part_of Mary’s life
example of usage: [copied from inverse property 'part of occurrent'] the first set of the tennis match occurrent_part_of the tennis match.
editor note: [copied from inverse property 'part of occurrent'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
has associated axiom(fol): (iff (hasOccurrentPart a b) (occurrentPartOf b a)) // axiom label in BFO2 CLIF: [007-001]
editor note: [copied from inverse property 'part of occurrent'] BFO2 Reference: occurrent
BFO OWL specification label: o-has-part
BFO CLIF specification label: hasOccurrentPart
elucidation: [copied from inverse property 'part of occurrent'] b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002])
example of usage: [copied from inverse property 'part of occurrent'] The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football.
definition: b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])
range: occurrent
imported from: bfo.owl

has proper occurrent part
type: ObjectProperty
type: TransitiveProperty
definition: [copied from inverse property 'proper part of occurrent'] b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001])
BFO CLIF specification label: hasProperOccurrentPart
BFO OWL specification label: o-has-ppart
definition: b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001
range: occurrent
sub property of: has occurrent part
imported from: bfo.owl

has temporal part
type: ObjectProperty
type: TransitiveProperty
example of usage: [copied from inverse property 'temporal part of'] the 4th year of your life is a temporal part of your life\. The first quarter of a game of football is a temporal part of the whole game\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\ The 4th year of your life is a temporal part of your life
example of usage: [copied from inverse property 'temporal part of'] the process boundary which separates the 3rd and 4th years of your life.
example of usage: [copied from inverse property 'temporal part of'] your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating
definition: [copied from inverse property 'temporal part of'] b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001])
BFO OWL specification label: has-t-part
definition: [copied from inverse property 'temporal part of'] b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003])
range: occurrent
domain: occurrent
sub property of: has occurrent part
imported from: bfo.owl

has spatial occupant at some time
type: ObjectProperty
BFO OWL specification label: r-location-of_st
editor note: [copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: independent continuant
elucidation: [copied from inverse property 'occupies spatial region at some time'] b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002])
editor note: [copied from inverse property 'occupies spatial region at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t)
editor note: [copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: spatial region
range: independent continuant
domain: spatial region
imported from: bfo.owl

has specific dependent at some time
type: ObjectProperty
example of usage: [copied from inverse property 'specifically depends on at some time'] reciprocal s-dependence between occurrents: a process of increasing the volume of a portion of gas while temperature remains constant and the associated process of decreasing the pressure exerted by the gas
example of usage: [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of hitting a ball with a cricket bat
example of usage: [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of paying cash to a merchant in exchange for a bag of figs
example of usage: [copied from inverse property 'specifically depends on at some time'] the one-sided dependence of an occurrent on an independent continuant: football match on the players, the ground, the ball
BFO OWL specification label: has-s-dep_st
editor note: [copied from inverse property 'specifically depends on at some time'] BFO 2 Reference: S-dependence is just one type of dependence among many; it is what, in the literature, is referred to as ‘existential dependence’ [87, 46, 65, 20
example of usage: [copied from inverse property 'specifically depends on at some time'] a shape s-depends_on the shaped object
example of usage: [copied from inverse property 'specifically depends on at some time'] the three-sided reciprocal s-dependence of the hue, saturation and brightness of a color [45
example of usage: [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a dependent continuant on an independent continuant: an instance of headache s-depends_on some head
example of usage: [copied from inverse property 'specifically depends on at some time'] the three-sided reciprocal s-dependence of the pitch, timbre and volume of a tone [45
example of usage: [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a process on something: an instance of seeing (a relational process) s-depends_on some organism and on some seen entity, which may be an occurrent or a continuant
example of usage: [copied from inverse property 'specifically depends on at some time'] a gait s-depends_on the walking object. (All at some specific time.)
elucidation: [copied from inverse property 'specifically depends on at some time'] To say that b s-depends_on a at t is to say that b and c do not share common parts & b is of its nature such that it cannot exist unless c exists & b is not a boundary of c and b is not a site of which c is the host [64
editor note: [copied from inverse property 'specifically depends on at some time'] BFO 2 Reference: the relation of s-depends_on does not in every case require simultaneous existence of its relata. Note the difference between such cases and the cases of continuant universals defined historically: the act of answering depends existentially on the prior act of questioning; the human being who was baptized or who answered a question does not himself depend existentially on the prior act of baptism or answering. He would still exist even if these acts had never taken place.
example of usage: [copied from inverse property 'specifically depends on at some time'] reciprocal s-dependence between occurrents: in a game of chess the process of playing with the white pieces is mutually dependent on the process of playing with the black pieces
editor note: [copied from inverse property 'specifically depends on at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'specifically depends on at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'specifically depends on@en'(x,y,t)
example of usage: [copied from inverse property 'specifically depends on at some time'] reciprocal s-dependence between occurrents: a process of buying and the associated process of selling
example of usage: [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on another: a process of answering a question is dependent on a prior process of asking a question
example of usage: [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on another: a process of obeying a command is dependent on a prior process of issuing a command
editor note: [copied from inverse property 'specifically depends on at some time'] BFO 2 Reference: An entity – for example an act of communication or a game of football – can s-depends_on more than one entity. Complex phenomena for example in the psychological and social realms (such as inferring, commanding and requesting) or in the realm of multi-organismal biological processes (such as infection and resistance), will involve multiple families of dependence relations, involving both continuants and occurrents [1, 4, 28
example of usage: [copied from inverse property 'specifically depends on at some time'] the one-sided dependence of an occurrent on an independent continuant: handwave on a hand
example of usage: [copied from inverse property 'specifically depends on at some time'] A pain s-depends_on the organism that is experiencing the pain
example of usage: [copied from inverse property 'specifically depends on at some time'] the two-sided reciprocal s-dependence of the roles of husband and wife [20
example of usage: [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a process on something: a process of cell death s-depends_on a cell
editor note: [copied from inverse property 'specifically depends on at some time'] BFO2 Reference: specifically dependent continuant\; process; process boundary
example of usage: [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a dependent continuant on an independent continuant: an instance of temperature s-depends_on some organism
imported from: bfo.owl
range: Class
  union of: process
  union of: specifically dependent continuant
domain: Class
  union of: process
  union of: specifically dependent continuant
  union of: Class
    intersection of: independent continuant
    intersection of: Class
      complement of: spatial region

has spatiotemporal occupant
type: ObjectProperty
BFO OWL specification label: occupied-by
editor note: [copied from inverse property 'occupies spatiotemporal region'] BFO 2 Reference: The occupies_spatiotemporal_region and occupies_temporal_region relations are the counterpart, on the occurrent side, of the relation occupies_spatial_region.
elucidation: [copied from inverse property 'occupies spatiotemporal region'] p occupies_spatiotemporal_region s. This is a primitive relation between an occurrent p and the spatiotemporal region s which is its spatiotemporal extent. (axiom label in BFO2 Reference: [082-003])
range: occurrent
domain: spatiotemporal region
imported from: bfo.owl

occupies spatiotemporal region
type: ObjectProperty
BFO OWL specification label: occupies
editor note: BFO 2 Reference: The occupies_spatiotemporal_region and occupies_temporal_region relations are the counterpart, on the occurrent side, of the relation occupies_spatial_region.
BFO CLIF specification label: occupiesSpatiotemporalRegion
elucidation: p occupies_spatiotemporal_region s. This is a primitive relation between an occurrent p and the spatiotemporal region s which is its spatiotemporal extent. (axiom label in BFO2 Reference: [082-003])
range: spatiotemporal region
inverse of: has spatiotemporal occupant
imported from: bfo.owl

part of occurrent
type: ObjectProperty
type: TransitiveProperty
definition: [copied from inverse property 'has occurrent part'] b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])
editor note: BFO2 Reference: occurrent
has associated axiom(fol): (forall (x) (if (Occurrent x) (occurrentPartOf x x))) // axiom label in BFO2 CLIF: [113-002]
has associated axiom(fol): (forall (x y t) (if (and (occurrentPartOf x y t) (occurrentPartOf y x t)) (= x y))) // axiom label in BFO2 CLIF: [123-001]
BFO CLIF specification label: occurrentPartOf
has associated axiom(fol): (forall (x y z) (if (and (occurrentPartOf x y) (occurrentPartOf y z)) (occurrentPartOf x z))) // axiom label in BFO2 CLIF: [112-001]
BFO OWL specification label: o-part-of
has associated axiom(fol): (forall (x y t) (if (exists (v) (and (occurrentPartOf v x t) (occurrentPartOf v y t))) (exists (z) (forall (u w) (iff (iff (occurrentPartOf w u t) (and (occurrentPartOf w x t) (occurrentPartOf w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [125-001]
has associated axiom(fol): (forall (x y t) (if (and (occurrentPartOf x y t) (not (= x y))) (exists (z) (and (occurrentPartOf z y t) (not (exists (w) (and (occurrentPartOf w x t) (occurrentPartOf w z t)))))))) // axiom label in BFO2 CLIF: [124-001]
editor note: BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
example of usage: Mary’s 5th birthday occurrent_part_of Mary’s life
example of usage: The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football.
elucidation: b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002])
has associated axiom(nl): occurrent_part_of is antisymmetric. (axiom label in BFO2 Reference: [123-001])
has associated axiom(nl): occurrent_part_of is reflexive (every occurrent entity is an occurrent_part_of itself). (axiom label in BFO2 Reference: [113-002])
has associated axiom(nl): occurrent_part_of is transitive. (axiom label in BFO2 Reference: [112-001])
has associated axiom(nl): occurrent_part_of satisfies unique product. (axiom label in BFO2 Reference: [125-001])
has associated axiom(nl): occurrent_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [124-001])
example of usage: the first set of the tennis match occurrent_part_of the tennis match.
range: occurrent
inverse of: has occurrent part
imported from: bfo.owl

temporal part of
type: ObjectProperty
type: TransitiveProperty
BFO OWL specification label: t-part-of
has associated axiom(fol): (iff (temporalPartOf a b) (and (occurrentPartOf a b) (exists (t) (and (TemporalRegion t) (occupiesSpatioTemporalRegion a t))) (forall (c t_1) (if (and (Occurrent c) (occupiesSpatioTemporalRegion c t_1) (occurrentPartOf t_1 r)) (iff (occurrentPartOf c a) (occurrentPartOf c b)))))) // axiom label in BFO2 CLIF: [078-003]
has associated axiom(fol): (iff (properTemporalPartOf a b) (and (temporalPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [116-001]
has associated axiom(nl): if b proper_temporal_part_of c, then there is some d which is a proper_temporal_part_of c and which shares no parts with b. (axiom label in BFO2 Reference: [117-002])
BFO CLIF specification label: temporalPartOf
has associated axiom(fol): (forall (x y) (if (properTemporalPartOf x y) (exists (z) (and (properTemporalPartOf z y) (not (exists (w) (and (temporalPartOf w x) (temporalPartOf w z)))))))) // axiom label in BFO2 CLIF: [117-002]
definition: b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001])
definition: b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003])
example of usage: the 4th year of your life is a temporal part of your life\. The first quarter of a game of football is a temporal part of the whole game\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\ The 4th year of your life is a temporal part of your life
example of usage: the process boundary which separates the 3rd and 4th years of your life.
example of usage: your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating
range: occurrent
inverse of: has temporal part
sub property of: part of occurrent
imported from: bfo.owl

projects onto spatial region at some time
type: ObjectProperty
BFO OWL specification label: st-projects-onto-s_st
range: spatial region
domain: spatiotemporal region
inverse of: spatial projection of spatiotemporal at some time
imported from: bfo.owl

spatial projection of spatiotemporal at some time
type: ObjectProperty
BFO OWL specification label: s-projection-of-st_st
domain: spatial region
range: spatiotemporal region
imported from: bfo.owl

projects onto temporal region
type: ObjectProperty
BFO OWL specification label: st-projects-onto-t
range: temporal region
sub property of: exists at
inverse of: temporal projection of spatiotemporal
imported from: bfo.owl

temporal projection of spatiotemporal
type: ObjectProperty
BFO OWL specification label: t-projection-of-st
range: spatiotemporal region
sub property of: during which exists
imported from: bfo.owl

occupies temporal region
type: ObjectProperty
BFO CLIF specification label: occupiesTemporalRegion
BFO OWL specification label: spans
elucidation: p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001])
range: temporal region
sub property of: exists at
inverse of: has temporal occupant
imported from: bfo.owl

has temporal occupant
type: ObjectProperty
elucidation: [copied from inverse property 'occupies temporal region'] p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001])
BFO CLIF specification label: spanOf
BFO OWL specification label: span-of
range: occurrent
imported from: bfo.owl

during which exists
type: ObjectProperty
BFO OWL specification label: during-which-exists
elucidation: [copied from inverse property 'exists at'] b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002])
editor note: [copied from inverse property 'exists at'] BFO2 Reference: entity
editor note: [copied from inverse property 'exists at'] BFO2 Reference: temporal region
range: entity
imported from: bfo.owl

participates in at all times
type: ObjectProperty
BFO CLIF specification label: participatesInAt
BFO OWL specification label: participates-in_at
sub property of: has specific dependent at all times
imported from: bfo.owl

has specific dependent at all times
type: ObjectProperty
BFO OWL specification label: has-s-dep_at
sub property of: has specific dependent at some time
imported from: bfo.owl

specifically depends on at some time
type: ObjectProperty
BFO OWL specification label: s-depends-on_st
has associated axiom(fol): (forall (x y t) (if (and (Occurrent x) (IndependentContinuant y) (specificallyDependsOnAt x y t)) (forall (t_1) (if (existsAt x t_1) (specificallyDependsOnAt x y t_1))))) // axiom label in BFO2 CLIF: [015-002]
has associated axiom(fol): (forall (x y t) (if (specificallyDependsOnAt x y t) (exists (z) (and (IndependentContinuant z) (not (SpatialRegion z)) (specificallyDependsOnAt x z t))))) // axiom label in BFO2 CLIF: [136-001]
editor note: BFO 2 Reference: An entity – for example an act of communication or a game of football – can s-depends_on more than one entity. Complex phenomena for example in the psychological and social realms (such as inferring, commanding and requesting) or in the realm of multi-organismal biological processes (such as infection and resistance), will involve multiple families of dependence relations, involving both continuants and occurrents [1, 4, 28
editor note: BFO 2 Reference: S-dependence is just one type of dependence among many; it is what, in the literature, is referred to as ‘existential dependence’ [87, 46, 65, 20
editor note: BFO2 Reference: specifically dependent continuant\; process; process boundary
has associated axiom(nl): If b s-depends_on something at t, then there is some c, which is an independent continuant and not a spatial region, such that b s-depends_on c at t. (axiom label in BFO2 Reference: [136-001])
elucidation: To say that b s-depends_on a at t is to say that b and c do not share common parts & b is of its nature such that it cannot exist unless c exists & b is not a boundary of c and b is not a site of which c is the host [64
example of usage: a shape s-depends_on the shaped object
example of usage: one-sided s-dependence of a dependent continuant on an independent continuant: an instance of temperature s-depends_on some organism
example of usage: one-sided s-dependence of one occurrent on another: a process of answering a question is dependent on a prior process of asking a question
BFO CLIF specification label: specificallyDependsOn
has associated axiom(fol): (forall (x y z t) (if (and (specificallyDependsOnAt x y t) (specificallyDependsOnAt y z t)) (specificallyDependsOnAt x z t))) // axiom label in BFO2 CLIF: [054-002]
has associated axiom(fol): (forall (x) (if (exists (y t) (specificallyDependsOnAt x y t)) (not (MaterialEntity x)))) // axiom label in BFO2 CLIF: [052-001]
editor note: Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'specifically depends on at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'specifically depends on@en'(x,y,t)
has associated axiom(fol): (forall (x y t) (if (and (Entity x) (or (continuantPartOfAt y x t) (continuantPartOfAt x y t) (occurrentPartOf x y) (occurrentPartOf y x))) (not (specificallyDependsOnAt x y t)))) // axiom label in BFO2 CLIF: [013-002]
example of usage: A pain s-depends_on the organism that is experiencing the pain
editor note: BFO 2 Reference: the relation of s-depends_on does not in every case require simultaneous existence of its relata. Note the difference between such cases and the cases of continuant universals defined historically: the act of answering depends existentially on the prior act of questioning; the human being who was baptized or who answered a question does not himself depend existentially on the prior act of baptism or answering. He would still exist even if these acts had never taken place.
has associated axiom(nl): If b is s-depends_on something at some time, then b is not a material entity. (axiom label in BFO2 Reference: [052-001])
has associated axiom(nl): If occurrent b s-depends_on some independent continuant c at t, then b s-depends_on c at every time at which b exists. (axiom label in BFO2 Reference: [015-002])
example of usage: a gait s-depends_on the walking object. (All at some specific time.)
has associated axiom(nl): an entity does not s-depend_on any of its (continuant or occurrent) parts or on anything it is part of. (axiom label in BFO2 Reference: [013-002])
has associated axiom(nl): if b s-depends_on c at t & c s-depends_on d at t then b s-depends_on d at t. (axiom label in BFO2 Reference: [054-002])
example of usage: one-sided s-dependence of a dependent continuant on an independent continuant: an instance of headache s-depends_on some head
example of usage: one-sided s-dependence of a process on something: a process of cell death s-depends_on a cell
example of usage: one-sided s-dependence of a process on something: an instance of seeing (a relational process) s-depends_on some organism and on some seen entity, which may be an occurrent or a continuant
example of usage: one-sided s-dependence of one occurrent on another: a process of obeying a command is dependent on a prior process of issuing a command
example of usage: one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of hitting a ball with a cricket bat
example of usage: one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of paying cash to a merchant in exchange for a bag of figs
example of usage: reciprocal s-dependence between occurrents: a process of buying and the associated process of selling
example of usage: reciprocal s-dependence between occurrents: a process of increasing the volume of a portion of gas while temperature remains constant and the associated process of decreasing the pressure exerted by the gas
example of usage: reciprocal s-dependence between occurrents: in a game of chess the process of playing with the white pieces is mutually dependent on the process of playing with the black pieces
example of usage: the one-sided dependence of an occurrent on an independent continuant: football match on the players, the ground, the ball
example of usage: the one-sided dependence of an occurrent on an independent continuant: handwave on a hand
example of usage: the three-sided reciprocal s-dependence of the hue, saturation and brightness of a color [45
example of usage: the three-sided reciprocal s-dependence of the pitch, timbre and volume of a tone [45
example of usage: the two-sided reciprocal s-dependence of the roles of husband and wife [20
inverse of: has specific dependent at some time
imported from: bfo.owl
domain: Class
  union of: process
  union of: specifically dependent continuant
range: Class
  union of: process
  union of: specifically dependent continuant
  union of: Class
    intersection of: independent continuant
    intersection of: Class
      complement of: spatial region

part of continuant at some time
type: ObjectProperty
has associated axiom(fol): (forall (x y t) (if (and (continuantPartOfAt x y t) (not (= x y))) (exists (z) (and (continuantPartOfAt z y t) (not (exists (w) (and (continuantPartOfAt w x t) (continuantPartOfAt w z t)))))))) // axiom label in BFO2 CLIF: [121-001]
has associated axiom(fol): (forall (x y z t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y z t)) (continuantPartOfAt x z t))) // axiom label in BFO2 CLIF: [110-001]
BFO CLIF specification label: continuantPartOfAt
has associated axiom(fol): (forall (x y t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y x t)) (= x y))) // axiom label in BFO2 CLIF: [120-001]
editor note: BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region.
has associated axiom(fol): (forall (x y t) (if (and (continuantPartOfAt x y t) (IndependentContinuant x)) (locatedInAt x y t))) // axiom label in BFO2 CLIF: [047-002]
editor note: BFO2 Reference: continuant
has associated axiom(fol): (forall (x y t) (if (exists (v) (and (continuantPartOfAt v x t) (continuantPartOfAt v y t))) (exists (z) (forall (u w) (iff (iff (continuantPartOfAt w u t) (and (continuantPartOfAt w x t) (continuantPartOfAt w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [122-001]
editor note: [copied from inverse property 'has continuant part at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'has continuant part at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has continuant part@en'(x,y,t)
has associated axiom(fol): (forall (x t) (if (Continuant x) (continuantPartOfAt x x t))) // axiom label in BFO2 CLIF: [111-002]
has associated axiom(fol): (iff (ImmaterialEntity a) (and (IndependentContinuant a) (not (exists (b t) (and (MaterialEntity b) (continuantPartOfAt b a t)))))) // axiom label in BFO2 CLIF: [028-001]
definition: [copied from inverse property 'has continuant part at some time'] b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001])
BFO OWL specification label: c-part-of_st
editor note: Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'part of continuant at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'part of continuant@en'(x,y,t)
editor note: BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001])
editor note: BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
example of usage: Mary’s arm continuant_part_of Mary in the time of her life prior to her operation
elucidation: b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001])
has associated axiom(nl): continuant_part_of is antisymmetric. (axiom label in BFO2 Reference: [120-001])
has associated axiom(nl): continuant_part_of is reflexive (every continuant entity is a continuant_part_of itself). (axiom label in BFO2 Reference: [111-002])
has associated axiom(nl): continuant_part_of is transitive. (axiom label in BFO2 Reference: [110-001])
has associated axiom(nl): continuant_part_of satisfies unique product. (axiom label in BFO2 Reference: [122-001])
has associated axiom(nl): continuant_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [121-001])
has associated axiom(nl): if b continuant_part_of c at t and b is an independent continuant, then b is located_in c at t. (axiom label in BFO2 Reference: [047-002])
example of usage: the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists.
range: continuant
inverse of: has continuant part at some time
imported from: bfo.owl

part of continuant at all times
type: ObjectProperty
type: TransitiveProperty
has associated axiom(fol): (forall (x y t) (if (and (continuantPartOfAt x y t) (IndependentContinuant x)) (locatedInAt x y t))) // axiom label in BFO2 CLIF: [047-002]
has associated axiom(fol): (forall (x y t) (if (and (continuantPartOfAt x y t) (not (= x y))) (exists (z) (and (continuantPartOfAt z y t) (not (exists (w) (and (continuantPartOfAt w x t) (continuantPartOfAt w z t)))))))) // axiom label in BFO2 CLIF: [121-001]
editor note: BFO2 Reference: continuant
BFO CLIF specification label: continuantPartOfAt
BFO OWL specification label: c-part-of_at
editor note: [copied from inverse property 'has continuant part at all times that part exists'] This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'part of continuant at all times'
has associated axiom(fol): (forall (x y z t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y z t)) (continuantPartOfAt x z t))) // axiom label in BFO2 CLIF: [110-001]
has associated axiom(fol): (forall (x y t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y x t)) (= x y))) // axiom label in BFO2 CLIF: [120-001]
editor note: BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001])
definition: [copied from inverse property 'has continuant part at all times that part exists'] forall(t) exists_at(y,t) -> exists_at(x,t) and 'has continuant part'(x,y,t)
editor note: BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region.
editor note: Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'part of continuant@en(x,y,t)'.
has associated axiom(fol): (forall (x y t) (if (exists (v) (and (continuantPartOfAt v x t) (continuantPartOfAt v y t))) (exists (z) (forall (u w) (iff (iff (continuantPartOfAt w u t) (and (continuantPartOfAt w x t) (continuantPartOfAt w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [122-001]
has associated axiom(fol): (forall (x t) (if (Continuant x) (continuantPartOfAt x x t))) // axiom label in BFO2 CLIF: [111-002]
has associated axiom(fol): (iff (ImmaterialEntity a) (and (IndependentContinuant a) (not (exists (b t) (and (MaterialEntity b) (continuantPartOfAt b a t)))))) // axiom label in BFO2 CLIF: [028-001]
editor note: BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
example of usage: Mary’s arm continuant_part_of Mary in the time of her life prior to her operation
elucidation: b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001])
has associated axiom(nl): continuant_part_of is antisymmetric. (axiom label in BFO2 Reference: [120-001])
has associated axiom(nl): continuant_part_of is reflexive (every continuant entity is a continuant_part_of itself). (axiom label in BFO2 Reference: [111-002])
has associated axiom(nl): continuant_part_of is transitive. (axiom label in BFO2 Reference: [110-001])
has associated axiom(nl): continuant_part_of satisfies unique product. (axiom label in BFO2 Reference: [122-001])
has associated axiom(nl): continuant_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [121-001])
has associated axiom(nl): if b continuant_part_of c at t and b is an independent continuant, then b is located_in c at t. (axiom label in BFO2 Reference: [047-002])
example of usage: the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists.
sub property of: part of continuant at some time
imported from: bfo.owl

has continuant part at some time
type: ObjectProperty
BFO OWL specification label: c-has-part_st
editor note: [copied from inverse property 'part of continuant at some time'] BFO2 Reference: continuant
example of usage: [copied from inverse property 'part of continuant at some time'] the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists.
elucidation: [copied from inverse property 'part of continuant at some time'] b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001])
BFO CLIF specification label: hasContinuantPartAt
example of usage: [copied from inverse property 'part of continuant at some time'] Mary’s arm continuant_part_of Mary in the time of her life prior to her operation
editor note: [copied from inverse property 'part of continuant at some time'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
editor note: Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'has continuant part at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has continuant part@en'(x,y,t)
editor note: [copied from inverse property 'part of continuant at some time'] BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001])
editor note: [copied from inverse property 'part of continuant at some time'] BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region.
has associated axiom(fol): (iff (hasContinuantPartAt a b t) (continuantPartOfAt b a t)) // axiom label in BFO2 CLIF: [006-001]
editor note: [copied from inverse property 'part of continuant at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'part of continuant at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'part of continuant@en'(x,y,t)
definition: b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001])
range: continuant
imported from: bfo.owl

history of
type: ObjectProperty
type: FunctionalProperty
type: InverseFunctionalProperty
definition: [copied from inverse property 'has history'] b has_history c iff c history_of b [XXX-001
elucidation: b history_of c if c is a material entity or site and b is a history that is the unique history of cAxiom: if b history_of c and b history_of d then c=d [XXX-001
BFO CLIF specification label: historyOf
BFO OWL specification label: history-of
domain: process
range: material entity
inverse of: has history
imported from: bfo.owl

has history
type: ObjectProperty
type: FunctionalProperty
type: InverseFunctionalProperty
elucidation: [copied from inverse property 'history of'] b history_of c if c is a material entity or site and b is a history that is the unique history of cAxiom: if b history_of c and b history_of d then c=d [XXX-001
BFO CLIF specification label: hasHistory
BFO OWL specification label: has-history
definition: b has_history c iff c history_of b [XXX-001
range: process
domain: material entity
sub property of: contains process
sub property of: participates in at all times
imported from: bfo.owl

part of continuant at all times that whole exists
type: ObjectProperty
type: TransitiveProperty
editor note: This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'has continuant part at all times'
definition: [copied from inverse property 'has continuant part at all times'] b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001])
definition: forall(t) exists_at(y,t) -> exists_at(x,t) and 'part of continuant'(x,y,t)
editor note: [copied from inverse property 'has continuant part at all times'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has continuant part at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has continuant part@en(x,y,t)'.
BFO OWL specification label: c-part-of-object_at
range: continuant
inverse of: has continuant part at all times
sub property of: part of continuant at some time
imported from: bfo.owl

has continuant part at all times that part exists
type: ObjectProperty
type: TransitiveProperty
editor note: [copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region.
editor note: [copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuant
editor note: [copied from inverse property 'part of continuant at all times'] BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001])
editor note: [copied from inverse property 'part of continuant at all times'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
elucidation: [copied from inverse property 'part of continuant at all times'] b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001])
example of usage: [copied from inverse property 'part of continuant at all times'] Mary’s arm continuant_part_of Mary in the time of her life prior to her operation
editor note: This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'part of continuant at all times'
BFO OWL specification label: c-has-part-object_at
editor note: [copied from inverse property 'part of continuant at all times'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'part of continuant@en(x,y,t)'.
example of usage: [copied from inverse property 'part of continuant at all times'] the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists.
definition: forall(t) exists_at(y,t) -> exists_at(x,t) and 'has continuant part'(x,y,t)
range: continuant
inverse of: part of continuant at all times
sub property of: has continuant part at some time
imported from: bfo.owl

has maximum capacity
type: ObjectProperty
definition: A relation that relates a container to a measurement datum that specifies the maximum capacity of the container.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group
range: measurement data item
domain: container

has actual load
type: ObjectProperty
definition: A relation that relates a container to a measurement datum that specifies the actual amount of material in the container.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group
range: measurement data item
domain: container

member of
type: ObjectProperty

has measurement unit label
type: ObjectProperty
type: FunctionalProperty
definition: A relation between a value specification and its unit of measurement.
editor preferred term: has measurement unit label
sub property of: has part
range: measurement unit label

is about
type: ObjectProperty
editor note: 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
example of usage: This document is about information artifacts and their representations
editor preferred term: is about
definition: is_about is a (currently) primitive relation that relates an information artifact to an entity.
term editor: person:Alan Ruttenberg
domain: information content entity
has curation status: pending final vetting

denotes
type: ObjectProperty
editor note: 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r
example of usage: A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named.
definition source: Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
editor preferred term: denotes
definition: denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically
term editor: person:Alan Ruttenberg
sub property of: is about

is quality measurement of
type: ObjectProperty
editor note: 8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later
term editor: Alan Ruttenberg
editor note: From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. -- From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] unit of measure is a quality, e.g. the length of a ruler. [We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] [Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] a represents b means either a denotes b or a describes describe: a describes b means a is about b and a allows an inference of at least one quality of b We have had a long discussion about denotes versus describes.
editor note: From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality.
editor note: From the second meeting on IAO: An attempt at defining assay using Barry's "reliability" wording assay: process and has_input some material entity and has_output some information content entity and which is such that instances of this process type reliably generate outputs that describes the input.
editor note: This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details.
editor preferred term: is quality measurement of
definition: m is a quality measurement of q at t when q is a quality there is a measurement process p that has specified output m, a measurement datum, that is about q
range: quality
domain: measurement data item
sub property of: is about

is duration of
type: ObjectProperty
term editor: Person:Alan Ruttenberg
editor preferred term: is duration of
definition: relates a process to a time-measurement-datum that represents the duration of the process
range: process
has curation status: metadata complete
sub property of: is about
domain: time measurement datum

has time stamp
type: ObjectProperty
type: FunctionalProperty
term editor: Alan Ruttenberg
editor preferred term: has time stamp
definition: relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken
sub property of: has part
has curation status: metadata incomplete
range: time measurement datum
domain: time stamped measurement datum

has measurement datum
type: ObjectProperty
term editor: Alan Ruttenberg
editor preferred term: has measurement datum
definition: relates a time stamped measurement datum to the measurement datum that was measured
sub property of: has part
has curation status: metadata incomplete
domain: time stamped measurement datum
range: Class
  intersection of: measurement data item
  intersection of: Class
    complement of: time measurement datum

designates
type: ObjectProperty
type: AsymmetricProperty
type: IrreflexiveProperty
term editor: Mathias Brochhausen
definition: x designates y, if for any given group of language users, x is an information content entity, is about y, and represents y in a linguistic context..
range: entity
domain: information content entity
inverse of: is designated by

is designated by
type: ObjectProperty
type: AsymmetricProperty
type: IrreflexiveProperty
term editor: Mathias Brochhausen
definition: p1 is designated by p2, if p2 is an information content entity that represents p1 in a linguistic context.

is_supported_by_data
type: ObjectProperty
definition source: Philly 2011 workshop
definition: The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process
example of usage: The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA.
editor preferred term: is_supported_by_data
definition source: OBI
term editor: OBI
range: data item
has curation status: ready for release
domain: conclusion based on data

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

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

is_specified_output_of
type: ObjectProperty
term editor: PERSON:Bjoern Peters
definition: A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
term editor: Alan Ruttenberg
editor preferred term: is_specified_output_of
has curation status: ready for release
range: planned process
sub property of: participates in

achieves_planned_objective
type: ObjectProperty
example of usage: A cell sorting process achieves the objective specification 'material separation objective'
term editor: BP, AR, PPPB branch
definition source: PPPB branch derived
definition: This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.
editor preferred term: achieves_planned_objective
curator note: modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
range: objective specification
has curation status: metadata complete
domain: planned process

has grain
type: ObjectProperty
definition source: PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
editor preferred term: has grain
definition: the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car.
editor note: Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form
term editor: PERSON: Alan Ruttenberg
sub property of: has part
has curation status: metadata complete

objective_achieved_by
type: ObjectProperty
definition: This relation obtains between a a objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
editor preferred term: objective_achieved_by
definition source: OBI
term editor: OBI
domain: objective specification
has curation status: ready for release
range: planned process
inverse of: achieves_planned_objective

is member of organization
type: ObjectProperty
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
editor note: 2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a population
editor note: JZ: Discussed on May 7, 2012 OBI dev call. Bjoern points out that we need to allow for organizations to be members of organizations. And agreed by the other OBI developers. So, human and organization were specified in 'Domains'. The textual definition was updated based on it.
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
definition source: Person:Helen Parkinson
term editor: Person:Helen Parkinson
definition: Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization.
editor preferred term: is member of organization
has curation status: metadata complete
range: organization
domain: Class
  union of: Homo sapiens
  union of: organization

has organization member
type: ObjectProperty
term editor: Person: Jie Zheng
definition: Relating an organization to a legal person or organization.
editor note: See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_id=177891&atid=886178
editor preferred term: has organization member
has curation status: metadata incomplete
domain: organization
inverse of: is member of organization
range: Class
  union of: Homo sapiens
  union of: organization

has value specification
type: ObjectProperty
editor preferred term: has value specification
term editor: PERSON: James A. Overton
definition source: OBI
definition: A relation between an information content entity and a value specification that specifies its value.
sub property of: has part
domain: information content entity
has curation status: metadata complete
range: value specification

owns
type: ObjectProperty
type: AsymmetricProperty
term editor: Mathias Brochhausen
Source: Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204.
elucidation: This is a primitive relation. This relation is the foundation to the owners right to have the owned entity at his/her full disposal.
sub property of: topObjectProperty
domain: Class
  union of: Homo sapiens
  union of: organization
  union of: collection of humans
  union of: aggregate of organizations
range: Class
  union of: material entity
  union of: information content entity

administrates
type: ObjectProperty
type: AsymmetricProperty
comment: A definition of "tranfers" object property can be found in d-acts: http:purl.obolibrary.org/iao/d-acts.owl
term editor: Mathias Brochhausen
definition: a administrates b if c owns b and some rights and obligations grounded in the owning relation regarding b are transferred from c to a.
domain: Class
  union of: Homo sapiens
  union of: organization
  union of: collection of humans
  union of: aggregate of organizations
range: Class
  union of: material entity
  union of: information content entity

is contact information about
type: ObjectProperty
type: AsymmetricProperty
type: IrreflexiveProperty
term editor: Mathias Brochhausen
definition: a is contact information for b, if a is a information content entity, b is a human being or an organization and a identifies a physical location or electronic resource that allows to initiate communication with a.
domain: information content entity
sub property of: is about
range: Class
  union of: Homo sapiens
  union of: organization

is owned by
type: ObjectProperty
type: AsymmetricProperty
definition source: Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204.
definition: a is owned by b if b has complete power over a. All rights and obligations of ownership are grounded in this (primitive) relation. The claims and obligations of ownership can be partially transferred to a third party by the owner, b.
inverse of: owns
range: Class
  union of: Homo sapiens
  union of: organization
  union of: collection of humans
  union of: aggregate of organizations
domain: Class
  union of: material entity
  union of: information content entity

inheres in
type: ObjectProperty
label: inheres in at all times
editor note: BFO2 Reference: specifically dependent continuant
BFO CLIF specification label: inheresInAt
editor note: BFO2 Reference: independent continuant that is not a spatial region
has associated axiom(fol): (iff (inheresInAt a b t) (and (DependentContinuant a) (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))) // axiom label in BFO2 CLIF: [051-002]
editor note: BFO 2 Reference: Inherence is a subrelation of s-depends_on which holds between a dependent continuant and an independent continuant that is not a spatial region. Since dependent continuants cannot migrate from one independent continuant bearer to another, it follows that if b s-depends_on independent continuant c at some time, then b s-depends_on c at all times at which a exists. Inherence is in this sense redundantly time-indexed.For example, consider the particular instance of openness inhering in my mouth at t as I prepare to take a bite out of a donut, followed by a closedness at t+1 when I bite the donut and start chewing. The openness instance is then shortlived, and to say that it s-depends_on my mouth at all times at which this openness exists, means: at all times during this short life. Every time you make a fist, you make a new (instance of the universal) fist. (Every time your hand has the fist-shaped quality, there is created a new instance of the universal fist-shaped quality.)
definition: b inheres_in c at t =Def. b is a dependent continuant & c is an independent continuant that is not a spatial region & b s-depends_on c at t. (axiom label in BFO2 Reference: [051-002])
editor preferred term: inheres in
editor note: Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'inheres in at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'inheres in
BFO OWL specification label: inheres-in_at
alternative term: inheres_in
domain: specifically dependent continuant
sub property of: specifically depends on at all times
temporal interpretation: axiom holds for all times
imported from: bfo.owl
imported from: ro.owl
range: Class
  intersection of: independent continuant
  intersection of: Class
    complement of: spatial region

bearer of
type: ObjectProperty
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
imported from: ro.owl

participates in
type: ObjectProperty
editor preferred term: participates in
alternative term: participates_in
imported from: ro.owl

has participant
type: ObjectProperty
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.
Source: http://www.obofoundry.org/ro/#OBO_REL:has_participant
editor preferred term: has participant
alternative term: has_participant
inverse of: participates in
imported from: ro.owl
property chain axiom: has part
property chain axiom: realizes
property chain axiom: inheres in

role of
type: ObjectProperty
alternative term: is role of
alternative term: role_of
sub property of: inheres in
imported from: ro.owl

has quality
type: ObjectProperty
sub property of: bearer of
imported from: ro.owl

has role
type: ObjectProperty
alternative term: has_role
sub property of: bearer of
inverse of: role of
imported from: ro.owl

derives from
type: ObjectProperty
domain: independent continuant
imported from: ro.owl

location of
type: ObjectProperty
type: TransitiveProperty
editor preferred term: is location of
alternative term: location_of
temporal interpretation: axiom holds for all times
imported from: ro.owl

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

temporal relation
type: ObjectProperty
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
editor note: move to BFO?
definition source: Allen
editor preferred term: temporal relation
range: occurrent
has curation status: pending final vetting

starts
type: ObjectProperty
definition: inverse of starts with
term editor: Chris Mungall
definition source: Allen
editor preferred term: starts
sub property of: part of
has curation status: pending final vetting
sub property of: temporal relation

lacks_part
type: ObjectProperty
has OBO namespace: RO
expand expression to: http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y
imported from: cl.owl

has specified value
type: DatatypeProperty
definition source: OBI
definition: A relation between a value specification and a number that quantifies it.
term editor: PERSON: James A. Overton
editor note: A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning.
editor preferred term: has specified value
has curation status: metadata complete
domain: value specification
range: real

count
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: counting
subclass of: measurement data item
disjoint with: scalar measurement datum
disjoint with: time stamped measurement datum
disjoint with: physiological measurement data
definition: An information content entity that is a representation of counting.
comment: It can be denoted as an arithmetic value or in form of a word, and is usually as a result of a process.

counting
type: Class
equivalent class: Restriction
  on property: has_specified_output
  some values from: count
subclass of: planned process
definition: A planned process that computes the totality of some material entity.

age data by age brackets
type: Class
subclass of: data set
subclass of: Class
  intersection of: data set
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: measurement data item
      intersection of: Restriction
        on property: is about
        some values from: Class
definition: A data set consisting of measurements of age organized in age brackets.

entity
type: Class
BFO CLIF specification label: Entity
editor note: BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
BFO OWL specification label: entity
elucidation: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
editor note: Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
example of usage: Julius Caesar
example of usage: Verdi’s Requiem
example of usage: the Second World War
example of usage: your body mass index

Axiom
annotated target: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
annotated source: entity
annotated property: elucidation
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/001-001

Axiom
annotated target: Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
comment: per discussion with Barry Smith
annotated source: entity
annotated property: editor note
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000004

continuant
type: Class
subclass of: entity
disjoint with: occurrent
has associated axiom(fol): (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
has associated axiom(fol): (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
BFO CLIF specification label: Continuant
BFO OWL specification label: continuant
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
elucidation: A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
editor note: BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
editor note: Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
has associated axiom(nl): if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
has associated axiom(nl): if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
has associated axiom(nl): if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])

Axiom
annotated target: (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
annotated source: continuant
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/008-002

Axiom
annotated target: Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
annotated source: continuant
annotated property: editor note
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000007

Axiom
annotated target: if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
annotated source: continuant
annotated property: has associated axiom(nl)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/011-002

Axiom
annotated target: (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
annotated source: continuant
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/126-001

Axiom
annotated target: if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
annotated source: continuant
annotated property: has associated axiom(nl)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/009-002

Axiom
annotated target: (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
annotated source: continuant
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/009-002

Axiom
annotated target: (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
annotated source: continuant
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/011-002

Axiom
annotated target: if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
annotated source: continuant
annotated property: has associated axiom(nl)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/126-001

Axiom
annotated target: A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
annotated source: continuant
annotated property: elucidation
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/008-002

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

Axiom
annotated target: (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
annotated source: occurrent
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/079-001

Axiom
annotated target: An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
annotated source: occurrent
annotated property: elucidation
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/077-002

Axiom
annotated target: Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
annotated source: occurrent
annotated property: has associated axiom(nl)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/108-001

Axiom
annotated target: (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
annotated source: occurrent
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/108-001

Axiom
annotated target: Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
annotated source: occurrent
annotated property: editor note
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000012

Axiom
comment: per discussion with Barry Smith
annotated target: Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
annotated source: occurrent
annotated property: editor note
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000006

Axiom
annotated target: b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
annotated source: occurrent
annotated property: has associated axiom(nl)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/079-001

independent continuant
type: Class
subclass of: continuant
has associated axiom(fol): (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
has associated axiom(fol): (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
has associated axiom(nl): For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
has associated axiom(nl): For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
BFO OWL specification label: ic
BFO CLIF specification label: IndependentContinuant
has associated axiom(fol): (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
example of usage: a chair
example of usage: a heart
example of usage: a leg
example of usage: a molecule
example of usage: a spatial region
example of usage: an atom
example of usage: an orchestra.
example of usage: an organism
definition: b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
example of usage: the bottom right portion of a human torso
example of usage: the interior of your mouth

Axiom
annotated target: b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
annotated source: independent continuant
annotated property: definition
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/017-002

Axiom
annotated target: (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
annotated source: independent continuant
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/017-002

Axiom
annotated target: For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
annotated source: independent continuant
annotated property: has associated axiom(nl)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/018-002

Axiom
annotated target: For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
annotated source: independent continuant
annotated property: has associated axiom(nl)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/134-001

Axiom
annotated target: (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
annotated source: independent continuant
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/018-002

Axiom
annotated target: (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
annotated source: independent continuant
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/134-001

spatial region
type: Class
subclass of: immaterial entity
has associated axiom(fol): (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
has associated axiom(fol): (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
has associated axiom(nl): All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
BFO OWL specification label: s-region
BFO CLIF specification label: SpatialRegion
elucidation: A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
editor note: BFO 2 Reference: Spatial regions do not participate in processes.
editor note: Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.

Axiom
annotated target: (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
annotated source: spatial region
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/036-001

Axiom
annotated target: (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
annotated source: spatial region
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/035-001

Axiom
annotated target: All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
annotated source: spatial region
annotated property: has associated axiom(nl)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/036-001

Axiom
comment: per discussion with Barry Smith
annotated target: Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
annotated source: spatial region
annotated property: editor note
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000002

Axiom
annotated target: A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
annotated source: spatial region
annotated property: elucidation
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/035-001

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

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

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

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

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

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

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

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

two-dimensional spatial region
type: Class
subclass of: spatial region
BFO OWL specification label: 2d-s-region
has associated axiom(fol): (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]
BFO CLIF specification label: TwoDimensionalSpatialRegion
elucidation: A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
example of usage: an infinitely thin plane in space.
example of usage: the surface of a sphere-shaped part of space

Axiom
annotated target: A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
annotated source: two-dimensional spatial region
annotated property: elucidation
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/039-001

Axiom
annotated target: (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]
annotated source: two-dimensional spatial region
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/039-001

spatiotemporal region
type: Class
subclass of: occurrent
has associated axiom(fol): (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
has associated axiom(fol): (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
has associated axiom(fol): (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
has associated axiom(fol): (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
BFO CLIF specification label: SpatiotemporalRegion
BFO OWL specification label: st-region
has associated axiom(fol): (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
elucidation: A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
has associated axiom(nl): All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
has associated axiom(nl): Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
has associated axiom(nl): Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
has associated axiom(nl): Every spatiotemporal region occupies_spatiotemporal_region itself.
has associated axiom(nl): Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
example of usage: the spatiotemporal region occupied by a human life
example of usage: the spatiotemporal region occupied by a process of cellular meiosis.
example of usage: the spatiotemporal region occupied by the development of a cancer tumor

Axiom
annotated target: (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/099-001

Axiom
annotated target: (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/095-001

Axiom
annotated target: Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
annotated source: spatiotemporal region
annotated property: has associated axiom(nl)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/099-001

Axiom
annotated target: Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
annotated source: spatiotemporal region
annotated property: has associated axiom(nl)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/107-002

Axiom
annotated target: All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
annotated source: spatiotemporal region
annotated property: has associated axiom(nl)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/096-001

Axiom
annotated target: A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
annotated source: spatiotemporal region
annotated property: elucidation
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/095-001

Axiom
annotated target: (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/098-001

Axiom
annotated target: (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/107-002

Axiom
annotated target: Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
annotated source: spatiotemporal region
annotated property: has associated axiom(nl)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/098-001

Axiom
annotated target: (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/096-001

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

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

Axiom
annotated target: (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
annotated source: process
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/083-003

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

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

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

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

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

realizable entity
type: Class
subclass of: specifically dependent continuant
disjoint with: quality
has associated axiom(fol): (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
has associated axiom(fol): (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
BFO CLIF specification label: RealizableEntity
has associated axiom(nl): All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
elucidation: To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
BFO OWL specification label: realizable
example of usage: the disposition of this piece of metal to conduct electricity.
example of usage: the disposition of your blood to coagulate
example of usage: the function of your reproductive organs
example of usage: the role of being a doctor
example of usage: the role of this boundary to delineate where Utah and Colorado meet

Axiom
annotated target: (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
annotated source: realizable entity
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/058-002

Axiom
annotated target: To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
annotated source: realizable entity
annotated property: elucidation
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/058-002

Axiom
annotated target: All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
annotated source: realizable entity
annotated property: has associated axiom(nl)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/060-002

Axiom
annotated target: (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
annotated source: realizable entity
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/060-002

zero-dimensional spatial region
type: Class
subclass of: spatial region
BFO CLIF specification label: ZeroDimensionalSpatialRegion
has associated axiom(fol): (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]
BFO OWL specification label: 0d-s-region
elucidation: A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])

Axiom
annotated target: (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]
annotated source: zero-dimensional spatial region
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/037-001

Axiom
annotated target: A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
annotated source: zero-dimensional spatial region
annotated property: elucidation
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/037-001

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

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

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

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

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

specifically dependent continuant
type: Class
subclass of: continuant
has associated axiom(fol): (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]
example of usage: Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
editor note: Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
BFO CLIF specification label: SpecificallyDependentContinuant
has associated axiom(fol): (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
definition: b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
definition: b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
example of usage: of one-sided specifically dependent continuants: the mass of this tomato
example of usage: of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
BFO OWL specification label: sdc
example of usage: the disposition of this fish to decay
example of usage: the function of this heart: to pump blood
example of usage: the mutual dependence of proton donors and acceptors in chemical reactions [79
example of usage: the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
example of usage: the pink color of a medium rare piece of grilled filet mignon at its center
example of usage: the role of being a doctor
example of usage: the shape of this hole.
example of usage: the smell of this portion of mozzarella

Axiom
annotated target: b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
annotated source: specifically dependent continuant
annotated property: definition
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/050-003

Axiom
annotated target: (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]
annotated source: specifically dependent continuant
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/131-004

Axiom
comment: per discussion with Barry Smith
annotated target: Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
annotated source: specifically dependent continuant
annotated property: editor note
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000005

Axiom
annotated target: b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
annotated source: specifically dependent continuant
annotated property: definition
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/131-004

Axiom
annotated target: (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
annotated source: specifically dependent continuant
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/050-003

role
type: Class
subclass of: realizable entity
editor note: BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
BFO OWL specification label: role
has associated axiom(fol): (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
example of usage: John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
BFO CLIF specification label: Role
elucidation: b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
example of usage: the priest role
example of usage: the role of a boundary to demarcate two neighboring administrative territories
example of usage: the role of a building in serving as a military target
example of usage: the role of a stone in marking a property boundary
example of usage: the role of subject in a clinical trial
example of usage: the student role

Axiom
annotated target: (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
annotated source: role
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/061-001

Axiom
annotated target: b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
annotated source: role
annotated property: elucidation
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/061-001

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

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

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

one-dimensional spatial region
type: Class
subclass of: spatial region
has associated axiom(fol): (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]
BFO CLIF specification label: OneDimensionalSpatialRegion
BFO OWL specification label: 1d-s-region
elucidation: A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])
example of usage: an edge of a cube-shaped portion of space.

Axiom
annotated target: A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])
annotated source: one-dimensional spatial region
annotated property: elucidation
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/038-001

Axiom
annotated target: (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]
annotated source: one-dimensional spatial region
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/038-001

object aggregate
type: Class
subclass of: material entity
BFO OWL specification label: object-aggregate
definition source: ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
has associated axiom(fol): (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]
BFO CLIF specification label: ObjectAggregate
editor note: An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
editor note: BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee).
example of usage: a collection of cells in a blood biobank.
example of usage: a swarm of bees is an aggregate of members who are linked together through natural bonds
example of usage: a symphony orchestra
example of usage: an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)
elucidation: b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
example of usage: defined by fiat: the aggregate of members of an organization
example of usage: defined through physical attachment: the aggregate of atoms in a lump of granite
example of usage: defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
example of usage: defined via attributive delimitations such as: the patients in this hospital
example of usage: the aggregate of bearings in a constant velocity axle joint
example of usage: the aggregate of blood cells in your body
example of usage: the nitrogen atoms in the atmosphere
example of usage: the restaurants in Palo Alto
example of usage: your collection of Meissen ceramic plates.

Axiom
annotated target: An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
annotated source: object aggregate
annotated property: editor note
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000301

Axiom
annotated target: (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]
annotated source: object aggregate
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/025-004

Axiom
annotated target: An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
annotated source: object aggregate
annotated property: editor note
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000011

Axiom
annotated target: ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
annotated source: object aggregate
annotated property: definition source
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000300

Axiom
annotated target: b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
annotated source: object aggregate
annotated property: elucidation
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/025-004

three-dimensional spatial region
type: Class
subclass of: spatial region
has associated axiom(fol): (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
BFO OWL specification label: 3d-s-region
BFO CLIF specification label: ThreeDimensionalSpatialRegion
elucidation: A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
example of usage: a cube-shaped region of space
example of usage: a sphere-shaped region of space,

Axiom
annotated target: A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
annotated source: three-dimensional spatial region
annotated property: elucidation
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/040-001

Axiom
annotated target: (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
annotated source: three-dimensional spatial region
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/040-001

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

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

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

object
type: Class
subclass of: material entity
editor note: BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47
editor note: BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74
BFO CLIF specification label: Object
BFO OWL specification label: object
editor note: BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting.
editor note: BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below).
editor note: BFO 2 Reference: an object is a maximal causally unified material entity
example of usage: atom
elucidation: b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])
example of usage: cell
example of usage: cells and organisms
example of usage: engineered artifacts
example of usage: grain of sand
example of usage: molecule
example of usage: organelle
example of usage: organism
example of usage: planet
example of usage: solid portions of matter
example of usage: star

Axiom
annotated target: b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])
annotated source: object
annotated property: elucidation
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/024-001

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

Axiom
annotated target: b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
annotated source: generically dependent continuant
annotated property: definition
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/074-001

Axiom
annotated target: (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
annotated source: generically dependent continuant
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/074-001

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

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

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

process boundary
type: Class
subclass of: occurrent
BFO CLIF specification label: ProcessBoundary
BFO OWL specification label: p-boundary
has associated axiom(fol): (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]
has associated axiom(fol): (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
has associated axiom(nl): Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
definition: p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])
example of usage: the boundary between the 2nd and 3rd year of your life.

Axiom
annotated target: (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
annotated source: process boundary
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/085-002

Axiom
annotated target: Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
annotated source: process boundary
annotated property: has associated axiom(nl)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/085-002

Axiom
annotated target: p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])
annotated source: process boundary
annotated property: definition
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/084-001

Axiom
annotated target: (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]
annotated source: process boundary
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/084-001

one-dimensional temporal region
type: Class
subclass of: temporal region
disjoint with: zero-dimensional temporal region
has associated axiom(fol): (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
BFO OWL specification label: 1d-t-region
elucidation: A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
editor note: BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks).
BFO CLIF specification label: OneDimensionalTemporalRegion
example of usage: the temporal region during which a process occurs.

Axiom
annotated target: A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
annotated source: one-dimensional temporal region
annotated property: elucidation
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/103-001

Axiom
annotated target: (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
annotated source: one-dimensional temporal region
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/103-001

material entity
type: Class
subclass of: independent continuant
disjoint with: immaterial entity
has associated axiom(fol): (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
BFO OWL specification label: material
BFO CLIF specification label: MaterialEntity
has associated axiom(fol): (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
has associated axiom(fol): (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
elucidation: A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
editor note: BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
editor note: BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
editor note: BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
has associated axiom(nl): Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
example of usage: a flame
example of usage: a forest fire
example of usage: a human being
example of usage: a hurricane
example of usage: a photon
example of usage: a puff of smoke
example of usage: a sea wave
example of usage: a tornado
example of usage: an aggregate of human beings.
example of usage: an energy wave
example of usage: an epidemic
has associated axiom(nl): every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
example of usage: the undetached arm of a human being

Axiom
annotated target: (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
annotated source: material entity
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/019-002

Axiom
annotated target: Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
annotated source: material entity
annotated property: has associated axiom(nl)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/020-002

Axiom
annotated target: every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
annotated source: material entity
annotated property: has associated axiom(nl)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/021-002

Axiom
annotated target: (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
annotated source: material entity
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/021-002

Axiom
annotated target: A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
annotated source: material entity
annotated property: elucidation
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/019-002

Axiom
annotated target: (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
annotated source: material entity
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/020-002

continuant fiat boundary
type: Class
subclass of: immaterial entity
has associated axiom(fol): (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001]
editor note: BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions.
editor note: Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions.
BFO CLIF specification label: ContinuantFiatBoundary
has associated axiom(nl): Every continuant fiat boundary is located at some spatial region at every time at which it exists
BFO OWL specification label: cf-boundary
editor note: BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29
definition: b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])

Axiom
annotated target: b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])
annotated source: continuant fiat boundary
annotated property: definition
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/029-001

Axiom
annotated target: (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001]
annotated source: continuant fiat boundary
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/029-001

Axiom
annotated target: Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions.
annotated source: continuant fiat boundary
annotated property: editor note
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000008

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

one-dimensional continuant fiat boundary
type: Class
subclass of: continuant fiat boundary
BFO CLIF specification label: OneDimensionalContinuantFiatBoundary
has associated axiom(fol): (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]
BFO OWL specification label: 1d-cf-boundary
example of usage: The Equator
elucidation: a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])
example of usage: all geopolitical boundaries
example of usage: all lines of latitude and longitude
example of usage: the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin.
example of usage: the median sulcus of your tongue

Axiom
annotated target: a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])
annotated source: one-dimensional continuant fiat boundary
annotated property: elucidation
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/032-001

Axiom
annotated target: (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]
annotated source: one-dimensional continuant fiat boundary
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/032-001

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

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

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

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

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

relational quality
type: Class
subclass of: quality
has associated axiom(fol): (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001]
example of usage: John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
BFO CLIF specification label: RelationalQuality
example of usage: a marriage bond, an instance of love, an obligation between one person and another.
definition: b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])
BFO OWL specification label: r-quality

Axiom
annotated target: (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001]
annotated source: relational quality
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/057-001

Axiom
annotated target: b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])
annotated source: relational quality
annotated property: definition
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/057-001

two-dimensional continuant fiat boundary
type: Class
subclass of: continuant fiat boundary
BFO OWL specification label: 2d-cf-boundary
BFO CLIF specification label: TwoDimensionalContinuantFiatBoundary
has associated axiom(fol): (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]
elucidation: a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])

Axiom
annotated target: a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])
annotated source: two-dimensional continuant fiat boundary
annotated property: elucidation
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/033-001

Axiom
annotated target: (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]
annotated source: two-dimensional continuant fiat boundary
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/033-001

zero-dimensional continuant fiat boundary
type: Class
subclass of: continuant fiat boundary
has associated axiom(fol): (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]
BFO OWL specification label: 0d-cf-boundary
BFO CLIF specification label: ZeroDimensionalContinuantFiatBoundary
elucidation: a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])
example of usage: the geographic North Pole
example of usage: the point of origin of some spatial coordinate system.
example of usage: the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet
editor note: zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona.

Axiom
comment: requested by Melanie Courtot
annotated target: zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona.
annotated source: zero-dimensional continuant fiat boundary
annotated property: editor note
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000001

Axiom
annotated target: a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])
annotated source: zero-dimensional continuant fiat boundary
annotated property: elucidation
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/031-001

Axiom
annotated target: (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]
annotated source: zero-dimensional continuant fiat boundary
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/031-001

zero-dimensional temporal region
type: Class
subclass of: temporal region
BFO OWL specification label: 0d-t-region
has associated axiom(fol): (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
elucidation: A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
BFO CLIF specification label: ZeroDimensionalTemporalRegion
example of usage: a temporal region that is occupied by a process boundary
example of usage: right now
alternative term: temporal instant.
example of usage: the moment at which a child is born
example of usage: the moment at which a finger is detached in an industrial accident
example of usage: the moment of death.

Axiom
annotated target: A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
annotated source: zero-dimensional temporal region
annotated property: elucidation
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/102-001

Axiom
annotated target: (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
annotated source: zero-dimensional temporal region
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/102-001

history
type: Class
subclass of: process
elucidation: A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])
BFO CLIF specification label: History
BFO OWL specification label: history

Axiom
annotated target: A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])
annotated source: history
annotated property: elucidation
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/138-001

freezer shelf
type: Class
subclass of: device
subclass of: Restriction
  on property: has function at some time
  some values from: solid support function
definition: A device that is part of a freezer and consists of a solid horizontal surface to keep material in the freezer on a flat surface.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

discarding
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: located in
      some values from: trash container
definition: A planned process that gets rid of a material that is no longer useful or desirable.
definition source: Penn Group
term editor: Person: Jie Zheng, Chris Stoeckert

human subject recuiter role
type: Class
subclass of: worker role
definition: A worker role of recruiting human subjects to partcipate in a clinical investigation in which data about human subject is collected.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

cryovial box
type: Class
subclass of: device
subclass of: Restriction
  on property: has function at some time
  some values from: contain function
definition: A device that is intended to hold cryovials.
definition source: Penn Group
term editor: Person: Jie Zheng, Chris Stoeckert

trash container
type: Class
subclass of: device
subclass of: Restriction
  on property: has function at some time
  some values from: contain function
definition: A container that is used for discarded material.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

freezer rack
type: Class
subclass of: device
subclass of: Restriction
  on property: has function at some time
  some values from: solid support function
definition: A device that is part of a freezer for keeping material in the freezer in a defined position and prevents movement.
definition source: Penn Group
term editor: Person: Jie Zheng, Chris Stoeckert

blood spot card box
type: Class
subclass of: device
subclass of: Restriction
  on property: has function at some time
  some values from: contain function
definition: A device that is designed to contain blood spot cards.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

data confirm questionnaire
type: Class
subclass of: questionnaire
definition: A questionnaire that comprises a set of questions about patient, such as height, weight, race, biological sex, clinical history, etc., which will be filled by a recruiter based on an Electronic Medical Record (EMR).
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

form filling
type: Class
subclass of: document editing
definition: A document editing process in which one or more fields in a form are filled with related information, such as when answering a questionnare.
definition source: Penn Group
term editor: Person: Jie Zheng, Chris Stoeckert

filled patient questionnaire
type: Class
subclass of: patient questionnaire
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: form filling
    intersection of: Restriction
      on property: has_specified_input
      some values from: patient questionnaire
    intersection of: Restriction
      on property: has participant
      some values from: Class
        intersection of: Homo sapiens
        intersection of: Restriction
definition: A patient questionnaire which has been filled out by a patient.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

patient questionnaire
type: Class
subclass of: questionnaire
definition: A questionnaire that comprises a set of questions about a patient, such as height, weight, race, biological sex, clinical history, etc., which will be filled by the human subject.
definition source: Penn Group
term editor: Person: Jie Zheng, Chris Stoeckert

collection packet with specimen and information material
type: Class
subclass of: collection packet with specimen
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: bearer of
      some values from: Restriction
        on property: concretizes at some time
        some values from: Class
definition: A collection packet which contains a container with a specimen and a form filled with information about the collected specimen and specimen source.
definition source: Penn Group
term editor: Person: Jie Zheng, Chris Stoeckert

blood additive role
type: Class
subclass of: material to be added role
definition: A material to be added role that is born by a chemical entity which is added into a blood collection containter to optimize specific blood component(s) preservation and/or separation.
definition source: Penn Group
term editor: Person: Jie Zheng, Chris Stoeckert

lab technician role
type: Class
subclass of: worker role
definition: A worker role that performs the practical hands-on work in laboratories and is realized during study design execution.
definition source: Penn Group
term editor: Person: Jie Zheng, Chris Stoeckert

collection packet with specimen
type: Class
subclass of: collection packet
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: specimen
    intersection of: Restriction
      on property: located in
      some values from: container
definition: A collection packet which contains a container with a specimen.
definition source: Penn Group
term editor: Person: Jie Zheng, Chris Stoeckert

collection packet with empty container
type: Class
subclass of: collection packet
subclass of: Restriction
  on property: lacks_part
  some values from: material information bearer
subclass of: Restriction
  on property: lacks_part
  some values from: specimen
definition: A collection packet which contains an empty container that will be used for holding a specimen.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

filled data confirm questionnaire
type: Class
subclass of: data confirm questionnaire
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: form filling
    intersection of: Restriction
      on property: has_specified_input
      some values from: data confirm questionnaire
    intersection of: Restriction
      on property: has participant
      some values from: Class
        intersection of: Homo sapiens
        intersection of: Restriction
definition: A data confirm questionnaire which has been filled out by a human subject recruiter.
definition source: Penn Group
term editor: Person: Jie Zheng, Chris Stoeckert

collection packet
type: Class
subclass of: material entity
subclass of: Restriction
  on property: has part
  some values from: container
definition: A material entity used for specimen collection. It can contain a container to hold a specimen and material (e.g. paper) carrying information about the specimen and the specimen source (e.g. patient).
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

blood spot card
type: Class
subclass of: device
subclass of: Restriction
  on property: has function at some time
  some values from: solid support function
subclass of: Restriction
  on property: has function at some time
  some values from: contain function
definition: A device that is designed to collect, ship and store blood specimens in an easy and inexpensive way.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

cryovial
type: Class
subclass of: test tube
definition: A test tube that designed to store materials at very low temperatures.
definition source: Penn Group
term editor: Person: Jie Zheng, Chris Stoeckert

vacutainer
type: Class
subclass of: test tube
definition: A test tube which is either a sterile glass or plastic tube with a closure that is evacuated to create a vacuum inside the tube facilitating the draw of a predetermined volume of liquid. Most commonly used to draw a blood sample directly from the vein, these also are used to collect urine samples. Vacutainer tube may contain additives designed to stabilize and preserve the specimen prior to analytical testing.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: http://en.wikipedia.org/wiki/Vacutainer

specimen receiving
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: collection packet
    intersection of: Restriction
      on property: located in
      some values from: Laboratory
definition: A planned process for receiving specimens such as into a laboratory.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

adding specimen into a container
type: Class
subclass of: adding a material entity into a target
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: specimen
    intersection of: Restriction
      on property: has role
      some values from: material to be added role
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: container
        intersection of: Restriction
definition: An adding a material entity into a target process where a collected specimen is added to a specimen container. (note, not used for other specimen process that produce new specimens)
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

blood spotting
type: Class
subclass of: adding specimen into a container
subclass of: Restriction
  on property: has participant
  some values from: blood spot card
subclass of: Restriction
  on property: has_specified_input
  some values from: blood specimen
definition: An adding specimen into a container process that spots the blood from an organism on the blood spot card.
definition source: Penn Group
term editor: Person: Jie Zheng, Chris Stoeckert

buffy coat specimen
type: Class
subclass of: processed specimen
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: centrifugation
    intersection of: Restriction
      on property: has_specified_input
      some values from: blood specimen
definition: A processed specimen which is the output of a density gradient centrifugation of an anticoagulated blood specimen that contains most of the white blood cells and platelets.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: http://en.wikipedia.org/wiki/Buffy_coat

blood specimen on blood spot card
type: Class
subclass of: blood specimen
subclass of: Restriction
  on property: located in
  some values from: blood spot card
subclass of: Restriction
  on property: is_specified_output_of
  some values from: blood spotting
definition: A blood specimen that is located on a blood spot card.
term editor: Person: Jie Zheng, Chris Stoeckert
comment: A specimen that located in a blood spot card via blood spotting process.
definition source: Penn Group

collection packet with empty container and unfilled information material
type: Class
subclass of: collection packet
subclass of: Restriction
  on property: lacks_part
  some values from: specimen
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: bearer of
      some values from: Restriction
        on property: concretizes at some time
        some values from: information content entity
definition: A collection packet which contains a container without a specimen and an unfilled form that will be used to fill in information about specimen to be collected.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

duration time of smoking regularly
type: Class
subclass of: duration time of smoking
definition: A duration time of smoking about how long a person has been smoking regularly. (better to have criteria of regularly mean, such as smoke everyday)
definition source: Penn Group
term editor: Person: Jie Zheng, Chris Stoeckert

average daily use of cigarette datum
type: Class
subclass of: data item
subclass of: Restriction
  on property: is_specified_output_of
  some values from: averaging data transformation
definition: An average value of use of cigarettes per day.
definition source: Penn Group
term editor: Person: Jie Zheng, Chris Stoeckert

nicotine patch
type: Class
subclass of: processed material
subclass of: Restriction
  on property: has part
  some values from: nicotine
definition: A processed material that contains nicotine in the form of a transdermal patch which releases nicotine into the body through the skin. It is commonly used as an aid in nicotine replacement therapy (NRT), a process for smoking cessation.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: http://en.wikipedia.org/wiki/Nicotine_patch

cigarette
type: Class
subclass of: processed material
subclass of: Restriction
  on property: derives from
  some values from: tobacco
subclass of: Restriction
  on property: has part
  some values from: nicotine
definition: A processed material which is a small cylinder of finely cut tobacco leaves rolled in thin paper for smoking.
definition source: http://en.wikipedia.org/wiki/Cigarette
term editor: Person: Jie Zheng, Chris Stoeckert

nicotine gum or lozenge
type: Class
subclass of: processed material
subclass of: Restriction
  on property: has part
  some values from: nicotine
definition: A processed material contains nicotine in a form of a chewing gum or a candy-like tablet. It delivers nicotine to the body via absorption by the tissues of the mouth. It is commonly used as an aid in nicotine replacement therapy (NRT), a process for smoking cessation.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: http://en.wikipedia.org/wiki/Nicotine_gum

cigar
type: Class
subclass of: processed material
subclass of: Restriction
  on property: has part
  some values from: nicotine
subclass of: Restriction
  on property: derives from
  some values from: tobacco
definition: A processed material which is a tightly-rolled bundle of dried and fermented tobacco that is ignited so that its smoke may be drawn into the mouth.
definition source: http://en.wikipedia.org/wiki/Cigar
term editor: Person: Jie Zheng, Chris Stoeckert

chewing tobacco
type: Class
subclass of: processed material
subclass of: Restriction
  on property: derives from
  some values from: tobacco
definition: A processed material which is a kind of smokeless tobacco product consumed by placing a portion of the tobacco between the cheek and gum or upper lip teeth and chewing.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: http://en.wikipedia.org/wiki/Chewing_tobacco

nicotine material
type: Class
equivalent class: Class
  intersection of: processed material
  intersection of: Restriction
    on property: has part
    some values from: nicotine
definition: A processed material that contains nicotine.
term editor: Person: Jie Zheng, Chris Stoeckert
alternative term: nicotine product
definition source: Penn Group

smoking pipe
type: Class
subclass of: device
subclass of: Restriction
  on property: has function at some time
  some values from: contain function
definition: A device made to allow the user to inhale or taste smoke or vapor derived from the burning or vaporization of some substance.
definition source: http://en.wikipedia.org/wiki/Smoking_pipe
term editor: Person: Jie Zheng, Chris Stoeckert

nicotine e-cigarette
type: Class
subclass of: processed material
subclass of: Restriction
  on property: has part
  some values from: nicotine
definition: A processed material that vaporizes a liquid solution containing nicotine and simulates tobacco smoking by producing an aerosol that resembles smoke.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: http://en.wikipedia.org/wiki/Electronic_cigarette

smoking start date
type: Class
subclass of: time measurement datum
subclass of: Restriction
  on property: is about
  some values from: smoking behavior
definition: A time measurement datum which is the start date of a smoking behavior.
definition source: Penn Group
term editor: Person: Jie Zheng, Chris Stoeckert

pipe smoking behavior
type: Class
subclass of: smoking behavior
subclass of: Restriction
  on property: has_specified_input
  some values from: pipe tobacco
subclass of: Restriction
  on property: has participant
  some values from: smoking pipe
definition: A smoking behavior that uses a smoking pipe to inhale or taste tobacco material.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

duration time of smoking
type: Class
subclass of: time measurement datum
subclass of: Restriction
  on property: is duration of
  some values from: smoking behavior
definition: A time measurement datum about how long a person has been smoking.
definition source: Penn Group
term editor: Person: Jie Zheng, Chris Stoeckert

smoking end date
type: Class
subclass of: time measurement datum
subclass of: Restriction
  on property: is about
  some values from: smoking behavior
definition: A time measurement datum which is the end date of a smoking behavior.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

pipe tobacco
type: Class
subclass of: processed material
subclass of: Restriction
  on property: derives from
  some values from: tobacco
definition: A processed material which is made from tobacco for smoking tobacco using a pipe.
definition source: Penn Group
term editor: Person: Jie Zheng, Chris Stoeckert

tobacco
type: Class
subclass of: Eukaryota
definition: A Eukaryota that is within the genus Nicotiana of the Solanaceae (nightshade) family.
definition source: Penn Group
term editor: Person: Jie Zheng, Chris Stoeckert

tobacco material
type: Class
equivalent class: Class
  intersection of: processed material
  intersection of: Restriction
    on property: derives from
    some values from: tobacco
definition: A processed material that is made from tobacco. Typically, tobacco material is meant to be used as a source of nicotine as tobacco contains a higher concentration of nicotine than most other plants.
term editor: Person: Jie Zheng, Chris Stoeckert
alternative term: tobacco product
definition source: Penn Group

portion of organism substance
type: Class
subclass of: gross anatomical part
definition: Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.
editor preferred term: portion of organism substance
imported from: caro.owl

gross anatomical part
type: Class
subclass of: material entity
definition: Anatomical structure that is part of a multicellular organism and is at the gross anatomical level, e.g. above the level of a cell. Included are portions of organism substances such as blood, multi-cell-part structures such as axon tracts, acellular anatomical structures such as hair, and organism subdivisions such as head. Excluded is the whole organism and more granular parts of the organism, such as atoms, molecules, macromolecular complexes and cells.
editor preferred term: gross anatomical part
imported from: caro.owl

formaldehyde
type: Class
subclass of: molecular entity
definition: The simplest aldehyde.
imported from: chebi.owl

deoxyribonucleic acid
type: Class
subclass of: nucleic acid
definition: High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
editor preferred term: deoxyribonucleic acid
imported from: chebi.owl

nicotine
type: Class
subclass of: molecular entity
definition: An N-alkylpyrrolidine that consists of N-methylpyrrolidine bearing a pyridin-3-yl substituent at position 2.
editor preferred term: nicotine
imported from: chebi.owl

molecular entity
type: Class
subclass of: material entity
definition: Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
editor preferred term: molecular entity
editor note: We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well
imported from: chebi.owl

nucleic acid
type: Class
subclass of: macromolecule
definition: A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
editor preferred term: nucleic acid
imported from: chebi.owl

ribonucleic acid
type: Class
subclass of: nucleic acid
definition: High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
editor preferred term: ribonucleic acid
imported from: chebi.owl

macromolecule
type: Class
subclass of: molecular entity
definition: A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
editor preferred term: macromolecule
alternative term: polymer
imported from: chebi.owl

ethylenediaminetetraacetic acid
type: Class
subclass of: molecular entity
subclass of: Restriction
  on property: has role
  some values from: blood additive role
definition: A polyamino carboxylic acid that has formula C10H16N2O8.
editor preferred term: ethylenediaminetetraacetic acid
imported from: chebi.owl

sodium citrate
type: Class
subclass of: molecular entity
subclass of: Restriction
  on property: has role
  some values from: blood additive role
definition: The trisodium salt of citric acid.
editor preferred term: sodium citrate
imported from: chebi.owl

cell
type: Class
subclass of: material entity
definition: A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
editor preferred term: cell
example of usage: PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .."
imported from: cl.owl

cultured cell
type: Class
subclass of: experimentally modified cell in vitro
subclass of: Class
  union of: Restriction
    on property: is_specified_output_of
    some values from: establishing cell culture
  union of: Restriction
    on property: derives from
    some values from: Restriction
      on property: is_specified_output_of
      some values from: establishing cell culture
definition: A cell in vitro that is or has been maintained or propagated as part of a cell culture.
editor preferred term: cultured cell
imported from: cl.owl

experimentally modified cell in vitro
type: Class
subclass of: cell
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: material processing
definition: A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.
editor preferred term: experimentally modified cell in vitro
imported from: cl.owl

freezer
type: Class
subclass of: device
subclass of: Restriction
  on property: has function at some time
  some values from: contain function
subclass of: Restriction
  on property: has part
  some values from: freezer shelf
subclass of: Restriction
  on property: has part
  some values from: freezer rack
definition: An instrument that consists of a thermally insulated compartment, cabinet, or room in which a subfreezing temperature is maintained for the rapid freezing and storing of perishable items.
editor preferred term: freezer
imported from: ero.owl

geographical location
type: Class
subclass of: site
definition: A reference to a place on the Earth, by its name or by its geographical location.
editor preferred term: geographical location
imported from: gaz.owl

subnational entity
type: Class
equivalent class: Class
  intersection of: governmental organization
  intersection of: Restriction
    on property: member of
    on class: sovereign state
    qualified cardinality: 1
subclass of: governmental organization
term editor: Amanda Hicks
term editor: William R. Hogan
definition: a governmental organization that has a local, regional, or territorial government that recognizes a sovereign state as its higher political authority

geopolitical dependency
type: Class
subclass of: subnational entity
definition: A subnational entity that does not possess full political independence or sovereignty as a sovereign state, but remains politically outside of the controlling state and controls a geographical region that is outside the controlling state's integral region.
term editor: Amanda Hicks
comment: Typically, the common feature is that the dependency does not conduct foreign affairs, and relegates this authority to the sovereign state. But otherwise, it is largely or completely autonomous relative to the administrative subdivisions. Examples include Puerto Rico (U.S.), Guam (U.S.), Greenland (Denmark), French Polynesia (France), and Falkland Islands (United Kingdom).
term editor: William R. Hogan

geographical entity
type: Class
subclass of: object
imported from: http://purl.obolibrary.org/obo/geo.owl

geographical region
type: Class
subclass of: geographical entity
imported from: http://purl.obolibrary.org/obo/geo.owl

sovereign state
type: Class
subclass of: governmental organization
definition: A governmental organization with a defined territory on which it exercises internal and external sovereignty, a permanent population, a government, and the capacity to enter into relations with other sovereign states.
comment: Per Wikipedia, the word 'nation' does not always refer to soverign states. For example, the "nation of Islam".
term editor: William R. Hogan
definition source: http://en.wikipedia.org/wiki/Sovereign_state
alternative term: nation
alternative term: nation state

governmental organization
type: Class
subclass of: organization
term editor: Amanda Hicks
definition: An organization that governs the people living in a particular geographical region or aggregate of geographical regions. The geographical region it governs can change over time (such as the westward expansion of the United States and the addition of Hawaii). Note: this definition was taken over from "geopolitical organization".
comment: IMPORTANT: The label "geopolitical organization" was previously used for OMRSE_00000044 (governmental organization). "geopoli organization" is a label for a new and different class.

biological_process
type: Class
subclass of: process
definition: Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
editor preferred term: biological_process
imported from: go.owl

conditional specification
type: Class
subclass of: directive information entity
definition source: OBI branch derived
definition source: OBI_0000349
term editor: PlanAndPlannedProcess Branch
definition: a directive information entity that specifies what should happen if the trigger condition is fulfilled
editor preferred term: conditional specification
has curation status: metadata complete

measurement unit label
type: Class
subclass of: data item label
editor note: 2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term.
editor note: 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
definition: A data item label that denotes a unit of measure.
example of usage: Examples of measurement unit labels are liters, inches, weight per volume.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot
editor preferred term: measurement unit label
has curation status: ready for release

objective specification
type: Class
subclass of: directive information entity
editor note: 2013-09-23 OBI call: Simplify definition by removing following part - When the objective specification is part of a plan specification, the concretization of the plan specification is realized in a planned process in which the bearer tries to control the world so that the process endpoint is achieved.
editor note: 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."
editor note: Answers the question, why did you do this experiment?
definition source: OBI Plan and Planned Process/Roles Branch
definition source: OBI_0000217
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Barry Smith
term editor: PERSON: Bjoern Peters
term editor: PERSON: Jennifer Fostel
definition: a directive information entity that describes an intended process endpoint.
editor preferred term: objective specification
example of usage: the objective of a ChIP assay is to identify protein and DNA interaction purpose of a study; support of hypothesis, discovery of new information
has curation status: ready for release

narrative object
type: Class
subclass of: information content entity
editor note: 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion
definition: A narrative object is an information content entity that is a set of propositions.
example of usage: Examples of narrative objects are reports, journal articles, and patents submission.
definition source: OBI_0000013
editor note: agree - DENRIE. Issue(alan) do we only mean text? What about a story told by mime. Does music count? (no) what about an oral report. Regarding definition, saying it is a set of propositions means we loose the idea that wording matters. Maybe adjust saying a narrative object has some relationshop to a set of propositions
definition source: group:OBI
editor preferred term: narrative object
term editor: person:Chris Stoeckert
has curation status: uncurated

action specification
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: has part
  all values from: Class
    complement of: Class
      union of: objective specification
      union of: plan specification
term editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch
example of usage: Pour the contents of flask 1 into flask 2
definition: a directive information entity that describes an action the bearer will take
editor preferred term: action specification
has curation status: ready for release

data item label
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: part of
  some values from: data item
curator note: 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum.
term editor: GROUP: IAO
alternative term: datum label
definition: An information content entity that is part of some data item and is used to partially define the denotation of that data item.
editor preferred term: data item label
editor note: http://www.golovchenko.org/cgi-bin/wnsearch#4n
has curation status: ready for release

information carrier
type: Class
equivalent class: Class
  intersection of: quality
  intersection of: Restriction
    on property: concretizes at some time
    some values from: information content entity
subclass of: quality
editor note: 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'.
definition: A quality of an information bearer that imparts the information content
example of usage: In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case.
term editor: PERSON: Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
editor preferred term: information carrier
has curation status: ready for release

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.
definition: An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method that reliably tends to produce (approximately) truthful statements.
example of usage: Data items include counts of things, analyte concentrations, and statistical summaries.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jonathan Rees
alternative term: data
editor preferred term: data item
has curation status: ready for release

symbol
type: Class
subclass of: information content entity
editor note: 20091104, MC: this needs work and will most probably change
example of usage: A written proper name such as “OBI”; a serial number such as “12324X”; a stop sign.
definition: An information content entity that is a mark or character used as a conventional representation of another entity.
term editor: PERSON: Jonathan Rees
definition source: based on Oxford English Dictionary
editor preferred term: symbol
has curation status: ready for release

numeral
type: Class
subclass of: symbol
definition: A symbol that denotes a number.
term editor: PERSON: Jonathan Rees
editor preferred term: numeral

information content entity
type: Class
subclass of: generically dependent continuant
subclass of: Restriction
  on property: concretized by at some time
  some values from: Class
    intersection of: information carrier
    intersection of: Restriction
      on property: inheres in
      some values from: material information bearer
subclass of: Restriction
  on property: is about
  some values from: entity
example of usage: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
definition source: OBI_0000142
term editor: PERSON: Chris Stoeckert
definition: an information content entity is an entity that is generically dependent on some material entity and stands in relation of aboutness to some entity
editor preferred term: information content entity
editor note: information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
has curation status: ready for release

scalar measurement datum
type: Class
subclass of: measurement data item
subclass of: Restriction
  on property: has value specification
  some values from: scalar value specification
example of usage: 10 feet. 3 ml.
editor note: 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot
editor note: Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.
definition: a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
editor preferred term: scalar measurement datum
has curation status: metadata complete

directive information entity
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is about
  some values from: realizable entity
editor note: 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
editor note: Philly2013 - AR: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.
editor note: 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
definition: An information content entity whose concretizations indicate to their bearer how to realize them in a process.
term editor: PERSON: Alan Ruttenberg
term 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
editor preferred term: directive information entity
has curation status: ready for release

algorithm
type: Class
subclass of: plan specification
definition: A plan specification which describes inputs, output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
definition source: OBI_0000270
example of usage: PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
term editor: Philippe Rocca-Serra
term editor: PlanAndPlannedProcess Branch
definition source: adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
editor preferred term: algorithm
has curation status: ready for release

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
term 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

report
type: Class
subclass of: information content entity
editor note: 2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on something that has completed." Should it be restricted to those things that are completed? For example, a progress report is (usually) about something that definitely has *not* been completed, or may include (only) projections. I think the definition would not suffer if the whole sentence is deleted.
editor note: 2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so.
editor note: 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
editor note: 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion
definition: An information content entity assembled by an author for the purpose of providing information for an audience, and that is meant to provide an accurate account of something that happened.
definition source: GROUP: OBI
definition source: OBI_0000099
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot
term editor: PERSON:Chris Stoeckert
editor note: disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification
example of usage: journal article, patent application, grant progress report, case report (not patient record)
editor preferred term: report
has curation status: ready for release

data format specification
type: Class
subclass of: directive information entity
editor note: 2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes information. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file"
definition: A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file
definition source: OBI branch derived
definition source: OBI_0000187
term editor: PERSON: Alan Ruttenberg
term editor: PlanAndPlannedProcess Branch
editor preferred term: data format specification
has curation status: metadata incomplete

data set
type: Class
subclass of: data item
editor note: 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type
definition: A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
example of usage: Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
definition source: OBI_0000042
editor preferred term: data set
definition source: group:OBI
term editor: person:Allyson Lister
term editor: person:Chris Stoeckert
has curation status: ready for release

image
type: Class
subclass of: figure
definition: An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface.
definition source: OBI_0000030
definition source: group:OBI
editor preferred term: image
term editor: person:Alan Ruttenberg
term editor: person:Allyson
term editor: person:Chris Stoeckert
has curation status: ready for release

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

plan specification
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: has part
  some values from: objective specification
subclass of: Restriction
  on property: has part
  some values from: action specification
comment: 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them
editor note: 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
term editor: Alan Ruttenberg
editor note: Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
definition source: OBI Plan and Planned Process branch
definition source: OBI_0000344
example of usage: To lose weight, go running daily for at least 30 minutes. To isolate plasma from blood, centrifuge tubes at 1100-1300 rpm for 15 minutes.
definition: a directive information entity that, when concretized, is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified.
editor preferred term: plan specification
has curation status: ready for release

measurement data item
type: Class
subclass of: data item
subclass of: Restriction
  on property: has value specification
  some values from: value specification
subclass of: Restriction
  on property: is_specified_output_of
  some values from: assay
editor note: 2/2/2009 is_specified_output of some assay?
definition: A data item that is a recording of the output of an assay.
example of usage: Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
definition source: OBI_0000305
definition source: group:OBI
alternative term: measurement datum
editor preferred term: measurement data item
term editor: person:Chris Stoeckert
has curation status: ready for release

setting datum
type: Class
subclass of: data item
editor note: 2/3/2009 Feedback from OBI This should be a "setting specification". There is a question of whether it is information about a realizable or not. Pro other specification are about realizables. Cons sometimes specifies a quality which is not a realizable.
definition: A settings datum is a datum that denotes some configuration of an instrument.
editor note: Alan grouped these in placeholder for the moment. Name by analogy to measurement datum.
editor preferred term: setting datum
has curation status: uncurated

conclusion textual entity
type: Class
subclass of: textual entity
subclass of: conclusion based on data
subclass of: Restriction
  on property: is_supported_by_data
  some values from: data item
subclass of: Restriction
  on property: is_specified_output_of
  some values from: drawing a conclusion based on data
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
editor note: 2009/10/23 Alan Ruttenberg: We need to work on the definition still
definition: A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers.
term editor: Person:Alan Ruttenberg
editor preferred term: conclusion textual entity
example of usage: that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660
has curation status: metadata complete

material information bearer
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: bearer of
    some values from: Restriction
      on property: concretizes at some time
      some values from: information content entity
subclass of: material entity
definition: A material entity in which a concretization of an information content entity inheres.
example of usage: A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier. Additional examples: a hard drive, a brain.
term editor: GROUP: IAO
editor preferred term: material information bearer
has curation status: ready for release

photograph
type: Class
subclass of: image
definition: A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc.
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Joanne Luciano
term editor: PERSON:Melanie Courtot
definition source: WEB: http://en.wiktionary.org/wiki/photograph
editor preferred term: photograph
has curation status: ready for release

photographic print
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: bearer of
    some values from: Restriction
      on property: concretizes at some time
      some values from: photograph
subclass of: material information bearer
definition: A photographic print is a material entity upon which a photograph generically depends.
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Melanie Courtot
editor preferred term: photographic print
has curation status: pending final vetting

obsolescence reason specification
type: Class
equivalent class: Class
  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
term editor: PERSON: Alan Ruttenberg
term 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

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

figure
type: Class
subclass of: information content entity
definition: An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
example of usage: Any picture, diagram or table
term editor: PERSON: Lawrence Hunter
editor preferred term: figure
has curation status: metadata complete

document
type: Class
subclass of: information content entity
definition: A collection of information content entities intended to be understood together as a whole
example of usage: A journal article, patent application, laboratory notebook, or a book
term editor: PERSON: Lawrence Hunter
editor preferred term: document
has curation status: metadata complete

length measurement datum
type: Class
subclass of: scalar measurement datum
subclass of: Restriction
  on property: is quality measurement of
  some values from: length
definition: A scalar measurement datum that is the result of measurement of length quality
term editor: Alan Ruttenberg
editor preferred term: length measurement datum
has curation status: metadata incomplete

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.
term 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.
editor preferred term: denotator type

mass measurement datum
type: Class
subclass of: measurement data item
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A scalar measurement datum that is the result of measurement of mass quality
term editor: Person:Alan Ruttenberg
editor preferred term: mass measurement datum
has curation status: metadata incomplete

time measurement datum
type: Class
subclass of: scalar measurement datum
subclass of: Class
  intersection of: Restriction
    on property: has measurement unit label
    all values from: time unit
  intersection of: Restriction
    on property: is duration of
    all values from: process
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A scalar measurement datum that is the result of measuring a temporal interval
term editor: Person:Alan Ruttenberg
editor preferred term: time measurement datum
has curation status: metadata incomplete

postal address
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: geographical location
definition: A textual entity that is used as directive to deliver something to a person, or organization
editor note: 2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue http://code.google.com/p/information-artifact-ontology/issues/detail?id=59
editor preferred term: postal address

email address
type: Class
subclass of: information content entity
editor note: Alan Ruttenberg 1/3/2012 - Provisional id, see issue at http://code.google.com/p/information-artifact-ontology/issues/detail?id=130&thanks=130&ts=1325636583
term editor: Person:Alan Ruttenberg
term editor: Person:Chris Stoeckart
editor preferred term: email address
has curation status: metadata incomplete

documenting
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: information content entity
subclass of: Restriction
  on property: has_specified_output
  some values from: report
editor note: 6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape
term editor: Bjoern Peters
example of usage: Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database. Copying the readout from an instrument into a spreadsheet.
definition: a planned process in which input information is used to create or add to a report
editor preferred term: documenting
definition source: wikipedia http://en.wikipedia.org/wiki/Documenting
has curation status: ready for release

CRID
type: Class
subclass of: symbol
subclass of: Restriction
  on property: part of
  some values from: CRID registry
alternative term: centrally registered identifier
definition: A symbol that is sufficient to look up information about the corresponding entity from its CRID (centrally registered identifier) registry.
editor preferred term: CRID
editor note: IAO call, 20101124: 12345 is not a CRID symbol. To be a CRID symbol you need to have some information about the registry within which the CRID is recorded.
definition source: Original proposal from Bjoern, discussions at IAO calls
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bill Hogan
term editor: PERSON: Bjoern Peters
term editor: PERSON: Melanie Courtot
example of usage: PubMed identifier “PMID:12345”
has curation status: ready for release

centrally registered identifier
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: has part
  some values from: CRID
alternative term: Centrally Registered IDentifier (CRID)
editor note: Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation.
definition: An information content entity that consists of a CRID symbol and additional information about which CRID registry it belongs.
example of usage: Entries in a Column of which the header is "Pubmed ID"
editor note: Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered.
definition source: Original proposal from Bjoern, discussions at IAO calls
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bill Hogan
term editor: PERSON: Bjoern Peters
term editor: PERSON: Melanie Courtot
example of usage: PMID:12345
example of usage: The following URL: "http://www.ncbi.nlm.nih.gov/pubmed/19918065"
example of usage: The following sentence contains a CRID: "The article with Pubmed ID: 19918065".
editor preferred term: centrally registered identifier

CRID registry
type: Class
subclass of: data set
definition: A data set that consists of CRIDs (centrally registered identifier) and additional information about their corresponding entities, that were recorded in the dataset through an assigning a centrally registered identifier process.
alternative term: centrally registered identifier registry
editor preferred term: CRID registry
editor note: IAO call, 20101124: PubMed registry is an instance of CRID registry
term editor: PERSON: Bill Hogan
example of usage: PubMed and GenBank both have CRID registries as parts of their database systems.
definition source: Original proposal from Bjoern, discussions at IAO calls
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Melanie Courtot
has curation status: ready for release

time stamped measurement datum
type: Class
subclass of: measurement data item
subclass of: Class
  intersection of: Restriction
    on property: has time stamp
    some values from: time measurement datum
  intersection of: Restriction
    on property: has measurement datum
    some values from: measurement data item
editor preferred term: time stamped measurement datum
has curation status: metadata incomplete

identifier
type: Class
label: proper name
equivalent class: Class
  intersection of: Restriction
    on property: designates
    some values from: entity
  intersection of: Restriction
    on property: is_specified_output_of
    all values from: dubbing process
subclass of: information content entity
definition: A proper name is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.
term editor: Mathias Brochhausen

dubbing process
type: Class
equivalent class: Restriction
  on property: has_specified_output
  some values from: identifier
subclass of: planned process
term editor: Mathias Brochhausen
definition: A dubbing process is a planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity.

personal name
type: Class
equivalent class: Class
  intersection of: identifier
  intersection of: Restriction
    on property: designates
    all values from: Homo sapiens
subclass of: identifier
definition: A personal name is a proper name identifying an individual person.
term editor: Mathias Brochhausen
comment: Personal names "today usually comprises a given name bestowed at birth or at a young age plus a surname. It is nearly universal for a human to have a name; except in rare cases, for example feral children growing up in isolation, or infants orphaned by natural disaster for whom no written record survives.[citation needed] The Convention on the Rights of the Child specifies that a child has the right from birth to a name. Certain isolated tribes, such as the Machiguenga of the Amazon, also lack personal names." (http://en.wikipedia.org/wiki/Personal_name)
definition source: http://en.wikipedia.org/wiki/Personal_name

informed consent form
type: Class
subclass of: document
definition: A document that explains all relevant study information to assist a human subject in understanding the expectations and requirements of participation in a research study. This form document is presented to and signed by the study subject.
editor preferred term: informed consent form
imported from: ico.owl

completely filled informed consent form
type: Class
subclass of: informed consent form
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: form filling
    intersection of: Restriction
      on property: has_specified_input
      some values from: data confirm questionnaire
    intersection of: Restriction
      on property: has participant
      some values from: Class
        intersection of: Homo sapiens
        intersection of: Restriction
    intersection of: Restriction
      on property: has participant
      some values from: Class
        intersection of: Homo sapiens
        intersection of: Restriction
definition: an informed consent form that has been filled with all required contents.
editor preferred term: completely filled informed consent form
imported from: ico.owl

partially filled informed consent form
type: Class
subclass of: informed consent form
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: form filling
    intersection of: Restriction
      on property: has_specified_input
      some values from: data confirm questionnaire
    intersection of: Restriction
      on property: has participant
      some values from: Class
        intersection of: Homo sapiens
        intersection of: Restriction
    intersection of: Restriction
      on property: has participant
      some values from: Class
        intersection of: Homo sapiens
        intersection of: Restriction
definition: an informed consent form that has been partically filled with required contents.
editor preferred term: partially filled informed consent form
imported from: ico.owl

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

Euteleostomi
type: Class
subclass of: Vertebrata <Metazoa>
editor preferred term: Euteleostomi
alternative term: bony vertebrates
imported from: ncbitaxon.owl

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

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

Eukaryota
type: Class
subclass of: organism
editor preferred term: Eukaryota
alternative term: eucaryotes
alternative term: eukaryotes
imported from: ncbitaxon.owl

Euarchontoglires
type: Class
subclass of: Mammalia
editor preferred term: Euarchontoglires
imported from: ncbitaxon.owl

Tetrapoda
type: Class
subclass of: Euteleostomi
editor preferred term: Tetrapoda
alternative term: tetrapods
imported from: ncbitaxon.owl

Amniota
type: Class
subclass of: Tetrapoda
editor preferred term: Amniota
alternative term: amniotes
imported from: ncbitaxon.owl

Opisthokonta
type: Class
subclass of: Eukaryota
editor preferred term: Opisthokonta
imported from: ncbitaxon.owl

Bilateria
type: Class
subclass of: Opisthokonta
editor preferred term: Bilateria
imported from: ncbitaxon.owl

Mammalia
type: Class
subclass of: Amniota
editor preferred term: Mammalia
alternative term: mammals
imported from: ncbitaxon.owl

Vertebrata <Metazoa>
type: Class
subclass of: Bilateria
alternative term: Vertebrata
editor preferred term: Vertebrata <Metazoa>
alternative term: vertebrates
imported from: ncbitaxon.owl

Homo sapiens
type: Class
subclass of: Euarchontoglires
editor preferred term: Homo sapiens
alternative term: human
alternative term: human being
alternative term: man
imported from: ncbitaxon.owl

planned process
type: Class
equivalent class: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes at some time
    some values from: plan specification
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
term editor: Bjoern Peters
example of usage: Injecting mice with a vaccine in order to test its efficacy
editor note: We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
definition 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

biological feature identification objective
type: Class
subclass of: objective specification
definition: Biological_feature_identification_objective is an objective role carried out by the proposition defining the aim of a study designed to examine or characterize a particular biological feature.
term editor: Jennifer Fostel
editor preferred term: biological feature identification objective
has curation status: metadata incomplete

processed material
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: material processing
subclass of: material entity
example of usage: Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
definition: Is a material entity that is created or changed during material processing.
term editor: PERSON: Alan Ruttenberg
editor preferred term: processed material
has curation status: ready for release

investigation
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has part
  some values from: documenting
subclass of: Restriction
  on property: has part
  some values from: drawing a conclusion based on data
subclass of: Restriction
  on property: has part
  some values from: study design execution
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: planning
    intersection of: Restriction
      on property: has_specified_output
      some values from: study design
curator note: Could add specific objective specification
example of usage: Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation
ISA alternative term: study
term editor: Bjoern Peters
curator note: Following OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core editor = PRS
definition source: OBI branch derived
definition: a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
editor preferred term: investigation
has curation status: ready for release
imported from: obi.owl

evaluant role
type: Class
subclass of: role
subclass of: Restriction
  on property: realized in
  all values from: assay
subclass of: Restriction
  on property: inheres in
  some values from: material entity
curator note: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
term editor: GROUP: Role Branch
definition source: OBI
editor note: Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is)
example of usage: When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source.
definition: a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role
editor preferred term: evaluant role
editor note: examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected")
has curation status: ready for release

assay
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: has role
      some values from: evaluant role
subclass of: Restriction
  on property: realizes
  some values from: evaluant role
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: information content entity
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: material entity
        intersection of: Restriction
example of usage: Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
IEDB alternative term: any method
ISA alternative term: study assay
editor note: 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation.
definition: A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
editor preferred term: assay
alternative term: measuring
alternative term: scientific observation
has curation status: ready for release
imported from: obi.owl

culture medium
type: Class
subclass of: processed material
definition: a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.
editor note: changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178 Modification made by JZ.
example of usage: A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008
definition source: OBI
term editor: Person: Jennifer Fostel, Jie Zheng
editor preferred term: culture medium
has curation status: ready for release

reagent role
type: Class
subclass of: role
curator note: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities ("a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction.
definition source: PERSON:Matthew Brush
alternative term: reagent
comment: (copied from ReO) Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance will realize only one of these roles in the execution of a given assay or technique. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique, note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is t…
definition: A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer.
example of usage: Buffer, dye, a catalyst, a solvating agent.
term editor: PERSON:Matthew Brush
editor preferred term: reagent role
has curation status: metadata complete

patient role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: Homo sapiens
alternative term: patient
curator note: CDISC definition: patient. Person under a physician's care for a particular disease or condition. NOTE: A subject in a clinical trial is not necessarily a patient, but a patient in a clinical trial is a subject. See also subject, trial subject, healthy volunteer. Often used interchangeably
term editor: GROUP:Role Branch
definition source: OBI, CDISC
example of usage: a hospitalized person; a person with controlled diabetes; the patient's role http://www.fertilityjourney.com/testingAndDiagnosis/theRightDoctor/thePatientsRole/index.asp?C=55245395146924652778
definition: a role which inheres in a person and is realized by the process of being under the care of a physician or health care provider
editor preferred term: patient role
has curation status: metadata complete

material processing
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: processed material
subclass of: Restriction
  on property: has_specified_output
  all values from: material entity
subclass of: Restriction
  on property: has_specified_input
  all values from: material entity
example of usage: A cell lysis, production of a cloning vector, creating a buffer.
term editor: PERSON: Frank Gibson
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Melanie Courtot
term editor: PERSON: Philippe Rocca Serra
definition: A planned process which results in physical changes in a specified input material
definition source: OBI branch derived
term editor: PERSON: Bjoern Peters
editor preferred term: material processing
alternative term: material transformation
has curation status: ready for release

participant under investigation role
type: Class
subclass of: role
subclass of: Restriction
  on property: realized in
  all values from: study design execution
definition: A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected.
example of usage: Human subjects in a clinical trial, rats in a toxicogenomics study, tissue cutlures subjected to drug tests, fish observed in an ecotoxicology study. Parasite example: people are infected with a parasite which is then extracted; the particpant under investigation could be the parasite, the people, or a population of which the people are members, depending on the nature of the study. Lake example: a lake could realize this role in an investigation that assays pollution levels in samples of water taken from the lake.
definition source: OBI
editor note: A participant can realize both "specimen role" and "participant under investigation role" at the same time. However "participant under investigation role" is distinct from "specimen role", since a specimen could somehow be involved in an investigation without being the thing that is under investigation.
curator note: Following OBI call November 2012,26th: 1. it was decided there was no need for moving the children class and making them siblings of study subject role. 2. it also settles the disambiguation about 'study subject'. This is about the individual participating in the investigation/study, Not the 'topic' (as in 'toxicity study') of the investigation/study This note closes the issue and validates the class definition to be part of the OBI core editor = PRS
term editor: GROUP: Role Branch
editor preferred term: participant under investigation role
has curation status: ready for release

responsible party role
type: Class
subclass of: investigation agent role
alternative term: responsible party
definition source: OBI
term editor: Person: Jennifer Fostel
definition: a study personnel role played by a party who is accountable for the execution of a study component and can make decisions about the conduct of the study
example of usage: he THERAPIST has the ability to print a separate statement for the patient and each responsible party. http://www.beaverlog.com/therapist/ez_support/billing/responsible_party_statements.htm
editor preferred term: responsible party role
has curation status: metadata complete

principal investigator role
type: Class
subclass of: responsible party role
alternative term: principal investigator
curator note: CDISC definition: A person responsible for the conduct of the clinical trial at a trial site. If a trial is conducted by a team of individuals at a trial site, the investigator is the responsible leader of the team and may be called the principal investigator. 2. The individual principal investigator. 2. The individual under whose immediate direction the test article is administered or dispensed to, or used involving, a subject, or, in the event of an investigation conducted by a team of individuals, is See also sponsor-investigator.; Leiter der klinischen Prufung.Under the German Drug Law, the physician who is head of the clinical investigation (CDISC): coordinating investigator (CDISC) (also study coordinator, MUSC); sponsor-investigator. An individual who both initiates and conducts, alone or with others, a clinical trial, and under whose immediate direction the investigational product is administered to, dispensed to, or used by a subject.NOTE: The term does not include any person other than an individual, hence not a corporation, agency (CDISC)
term editor: Person: Jennifer Fostel
definition: a responsible party role played by a person responsible for the overall conduct of a study
editor preferred term: principal investigator role
has curation status: metadata incomplete

specimen role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection
editor note: 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role.
term editor: GROUP: Role Branch
editor note: Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
definition source: OBI
example of usage: liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.
definition: a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation
editor note: blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen.
editor note: parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject.
editor preferred term: specimen role
has curation status: ready for release

worker role
type: Class
subclass of: investigation agent role
editor note: "executes the study plan" includes the suppliers and manufacturers of reagents and other materials used in the study
alternative term: worker
definition source: OBI
term editor: Person:Jennifer Fostel
example of usage: Public sector workers in states that run their own OSHA programs are covered by those states. http://www.osha.gov/as/opa/worker/index.html
definition: a personnel role played by a party who executes a component of the study plan; this can occur before, during, after or outside the study timeline
editor preferred term: worker role
has curation status: metadata complete

filter paper
type: Class
subclass of: material separation device
subclass of: Restriction
  on property: has function at some time
  some values from: filter function
term editor: Frank Gibson
definition: a device manufacture with the intent to provide a porous unsized paper used for filtering.
editor preferred term: filter paper
definition source: sep:00107
has curation status: metadata complete

population
type: Class
subclass of: material entity
editor note: 1/28/2013, BP, on the call it was raised that we may want to switch to an external ontology for all populatin terms: http://code.google.com/p/popcomm-ontology/
term editor: PERSON: Philippe Rocca-Serra
example of usage: PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population.
definition: a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area
definition source: adapted from Oxford English Dictionnary
editor preferred term: population
curator note: rem1: collection somehow always involve a selection process
has curation status: pending final vetting

investigation agent role
type: Class
equivalent class: Class
  intersection of: role
  intersection of: Restriction
    on property: inheres in
    some values from: Restriction
      on property: bearer of
      some values from: Restriction
        on property: concretizes at some time
        some values from: Restriction
subclass of: role
subclass of: Restriction
  on property: realized in
  all values from: investigation
curator note: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
editor note: Implementing a study means carrying out or performing the study and providing reagents or other materials used in the study and other tasks without which the study would not happen.
editor preferred term: investigation agent role
alternative term: investigator
ISA alternative term: study person role
definition: A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing.
term editor: GROUP: Role Branch
editor note: Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable representing investigations run by robot scientists such as ADAM (King et al, Science, 2009)
comment: Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable investigations run by robot scientists such as ADAM (King et al, Science, 2009)
definition source: OBI
example of usage: The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress.
has curation status: ready for release

organization
type: Class
subclass of: material entity
definition source: GROUP: OBI
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Philippe Rocca-Serra
term editor: PERSON: Susanna Sansone
definition: An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
editor note: BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now.
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

DNA extraction
type: Class
subclass of: nucleic acid extraction
subclass of: Restriction
  on property: has_specified_output
  some values from: deoxyribonucleic acid
definition: A DNA extraction is a nucleic acid extraction where the desired output material is DNA.
editor preferred term: DNA extraction
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
has curation status: metadata incomplete

organism feature identification objective
type: Class
subclass of: biological feature identification objective
term editor: Jennifer Fostel
definition: Organism_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the level of the organism, e.g. height, weight, stage of development, stage of life cycle.
editor preferred term: organism feature identification objective
has curation status: metadata incomplete

protocol
type: Class
subclass of: plan specification
ISA alternative term: study protocol
definition: A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.
definition source: OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
example of usage: PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR.
term editor: PlanAndPlannedProcess Branch
editor preferred term: protocol
has curation status: ready for release

adding a material entity into a target
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: adding material objective
subclass of: material combination
subclass of: Restriction
  on property: realizes
  some values from: target of material addition role
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: has role
      some values from: material to be added role
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: material entity
        intersection of: Restriction
subclass of: Restriction
  on property: realizes
  some values from: material to be added role
term editor: BP
editor note: Class was renamed from 'administering substance', as this is commonly used only for additions into organisms.
example of usage: Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water.
definition source: branch derived
editor preferred term: adding a material entity into a target
definition: is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'.
has curation status: ready for release

material to be added role
type: Class
subclass of: role
subclass of: Restriction
  on property: realized in
  all values from: adding a material entity into a target
curator note: 9 March 09 from discussion with PA branch
definition source: OBI
term editor: Role Branch
example of usage: drug added to a buffer contained in a tube; substance injected into an animal;
editor preferred term: material to be added role
definition: material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process
has curation status: metadata complete

drawing a conclusion based on data
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: data item
subclass of: Restriction
  on property: has_specified_output
  some values from: conclusion based on data
definition source: Bjoern Peters
example of usage: Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene.
term editor: PERSON: Bjoern Peters
term editor: PERSON: Jennifer Fostel
definition: A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion
editor preferred term: drawing a conclusion based on data
has curation status: ready for release

planning
type: Class
subclass of: process
subclass of: Class
  intersection of: process
  intersection of: Restriction
    on property: has participant
    some values from: plan specification
editor note: 7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'.
term editor: Bjoern Peters
definition source: Bjoern Peters
definition source: Plans and Planned Processes Branch
example of usage: The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software.
definition: a process of creating or modifying a plan specification
editor preferred term: planning
has curation status: ready for release

histological sample preparation
type: Class
subclass of: material processing
subclass of: specimen collection
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: specimen collection objective
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: Restriction
  on property: has_specified_input
  some values from: organ section
subclass of: Restriction
  on property: has participant
  some values from: microtome
definition source: OBI branch derived
term editor: PERSON:Bjoern Peters
editor preferred term: histological sample preparation
definition: histological sample preparation is the preparation of an input tissue via slicing and labeling to make tissue microstructure of interest visible in a future histology assay
has curation status: pending final vetting

hypothesis driven investigation
type: Class
subclass of: investigation
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
editor preferred term: hypothesis driven investigation
definition: is an investigation with the goal to test one or more hypothesis
has curation status: pending final vetting

hypothesis generating investigation
type: Class
subclass of: investigation
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
editor preferred term: hypothesis generating investigation
definition: is an investigation in which data is generated and analyzed with the purpose of generating new hypothesis
has curation status: pending final vetting

contain function
type: Class
subclass of: function
example of usage: A syringe, a beaker
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
definition: A contain function is a function to constrain a material entities location in space
editor preferred term: contain function
has curation status: ready for release

heat function
type: Class
subclass of: function
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
definition: A heat function is a function that increases the internal kinetic energy of a material
editor preferred term: heat function
has curation status: ready for release

material separation function
type: Class
subclass of: function
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
definition: A material separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality.
editor preferred term: material separation function
has curation status: ready for release

freeze function
type: Class
subclass of: function
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
definition: A freeze function is a function to decrease the internal kinetic energy of a material below the freezing point of that type of material.
editor preferred term: freeze function
has curation status: ready for release

filter function
type: Class
subclass of: material separation function
term editor: Frank Gibson
definition: A filter function is a function to prevent the flow of certain entities based on a quality or qualities of the entity while allowing entities which have different qualities to pass through
editor preferred term: filter function
has curation status: ready for release

mechanical function
type: Class
subclass of: function
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
definition: A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force).
definition source: http://en.wikipedia.org/wiki/Mechanical_work
editor preferred term: mechanical function
has curation status: ready for release

cool function
type: Class
subclass of: function
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
definition: A cool function is a function to decrease the internal kinetic energy of a material below the initial kinetic energy of that type of material.
editor preferred term: cool function
has curation status: ready for release

solid support function
type: Class
subclass of: function
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
example of usage: Taped, glued, pinned, dried or molecularly bonded to a solid support
definition: A solid support function is a function of a device on which an entity is kept in a defined position and prevented in its movement
editor preferred term: solid support function
has curation status: ready for release

environment control function
type: Class
subclass of: function
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
definition: An environmental control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature.
editor preferred term: environment control function
has curation status: ready for release

viral RNA extraction
type: Class
subclass of: RNA extraction
subclass of: Restriction
  on property: has_specified_input
  some values from: Viruses
term editor: Person:Bjoern Peters
example of usage: The AccuPrepTM Viral RNA Extraction Kit is designed for the rapid and convenient extraction of viral RNA from cell-free samples as serum, plasma, CSF, urine, etc - http://www.biokits.com/moreinfos.html?id=2703
definition: The extraction of RNA from an input material that specifically isolates viral RNA
editor preferred term: viral RNA extraction
has curation status: metadata incomplete

extract
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: extraction
definition source: GROUP: OBI Biomatrial Branch
term editor: PERSON: Philippe Rocca-Serra
example of usage: Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923
definition: an extract is a material entity which results from an extraction process
editor preferred term: extract
alternative term: extracted material
has curation status: metadata complete

averaging objective
type: Class
subclass of: data transformation objective
term editor: Elisabetta Manduchi
definition source: PERSON: Elisabetta Manduchi
example of usage: A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment.
definition: An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation.
term editor: James Malone
editor preferred term: averaging objective
has curation status: ready for release

adding material objective
type: Class
subclass of: material combination objective
term editor: BP
example of usage: creating a mouse infected with LCM virus
editor preferred term: adding material objective
definition: is the specification of an objective to add a material into a target material. The adding is asymmetric in the sense that the target material largely retains its identity
has curation status: ready for release

assay objective
type: Class
subclass of: objective specification
term editor: PPPB branch
definition source: PPPB branch
example of usage: the objective to determine the weight of a mouse.
definition: an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role)
editor preferred term: assay objective
has curation status: ready for release

target of material addition role
type: Class
subclass of: role
subclass of: Restriction
  on property: realized in
  all values from: adding a material entity into a target
subclass of: Restriction
  on property: inheres in
  some values from: material entity
editor note: From Branch discussion with BP, AR, MC -- there is a need for the recipient to interact with the administered material. for example, a tooth receiving a filling was not considered to be a target role.
term editor: GROUP: Role Branch
definition source: OBI
example of usage: peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application.
definition: target of material addition role is a role realized by an entity into which a material is added in a material addition process
editor preferred term: target of material addition role
has curation status: metadata complete

measure function
type: Class
subclass of: function
subclass of: Restriction
  on property: realized in
  all values from: Restriction
    on property: has_specified_output
    some values from: measurement data item
subclass of: Restriction
  on property: function of at all times
  some values from: processed material
example of usage: A glucometer measures blood glucose concentration, the glucometer has a measure function.
term editor: PERSON: Daniel Schober
term editor: PERSON: Helen Parkinson
term editor: PERSON: Melanie Courtot
term editor: PERSON:Frank Gibson
definition: Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference.
editor preferred term: measure function
has curation status: ready for release

material transformation objective
type: Class
subclass of: objective specification
definition source: GROUP: OBI PlanAndPlannedProcess Branch
term editor: PERSON: Bjoern Peters
term editor: PERSON: Frank Gibson
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Melanie Courtot
term editor: PERSON: Philippe Rocca-Serra
example of usage: The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.
definition: an objective specifiction that creates an specific output object from input materials.
alternative term: artifact creation objective
editor preferred term: material transformation objective
has curation status: ready for release

study design execution
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: realizes
    some values from: Restriction
      on property: concretizes at some time
      some values from: study design
subclass of: planned process
curator note: 6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation.
definition: a planned process that realizes the concretization of a study design
definition source: branch derived
example of usage: injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design.
editor note: removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired.
editor preferred term: study design execution
has curation status: ready for release
imported from: obi.owl

material separation objective
type: Class
equivalent class: Class
  union of: portioning objective
  union of: separation into different composition objective
subclass of: material transformation objective
definition source: PPPB branch
term editor: PPPB branch
example of usage: The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood.
definition: is an objective to transform a material entity into spatially separated components.
editor preferred term: material separation objective
has curation status: ready for release

data set of features
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: descriptive statistical calculation data transformation
subclass of: data set
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
definition: A data set that is produced as the output of a descriptive statistical calculation data transformation and consists of producing a data set that represents one or more features of interest about the input data set.
editor preferred term: data set of features
has curation status: pending final vetting

urine specimen
type: Class
subclass of: tissue specimen
subclass of: Restriction
  on property: derives from
  some values from: urine
subclass of: Restriction
  on property: has role
  some values from: specimen role
subclass of: Restriction
  on property: is_specified_output_of
  some values from: collecting specimen from organism
editor note: 4/10/2011BP: It seems to me that the editor notes refer to a previous version, and are no longer relevant.
editor note: This could be instead a kind of collection of secreted stuff. Among secreted stuff there is passive, and active. urine is secreted, passiv. lavage is secreted, active
definition: a portion of urine collected from an organism
editor note: are we happy calling collection of urine a material separation?
editor preferred term: urine specimen
has curation status: metadata complete

material combination
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material combination objective
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: material entity
example of usage: Mixing two fluids. Adding salt into water. Injecting a mouse with PBS.
term editor: bp
definition source: bp
editor note: created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes.
definition: is a material processing with the objective to combine two or more material entities as input into a single material entity as output.
editor preferred term: material combination
has curation status: ready for release

blood specimen
type: Class
subclass of: tissue specimen
subclass of: Restriction
  on property: has role
  some values from: specimen role
subclass of: Restriction
  on property: is_specified_output_of
  some values from: collecting specimen from organism
subclass of: Restriction
  on property: derives from
  some values from: blood
definition source: Bjoern Peters
term editor: Bjoern Peters
definition: a material entity derived from a portion of blood collected from an organism
example of usage: blood drawn from a human for glucose assay
editor preferred term: blood specimen
has curation status: ready for release

specimen collection
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: specimen collection objective
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: specimen
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
curator note: 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
curator note: 6/9/09: used at workshop
definition: A planned process with the objective of collecting a specimen.
term editor: Bjoern Peters
editor note: Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
editor preferred term: specimen collection
example of usage: drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation
editor note: Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role.
editor note: Philly2013: The specimen_role for the specimen is created during the specimen collection process.
has curation status: ready for release

sample from organism
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: collecting specimen from organism
  intersection of: Restriction
    on property: has role
    some values from: material sample role
subclass of: material sample
subclass of: tissue specimen
subclass of: Restriction
  on property: derives from
  some values from: gross anatomical part
editor note: 5/29: This is a helper class for now
definition: a material obtained from an organism in order to be a representative of the whole
editor preferred term: sample from organism
editor note: we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about.
has curation status: example to be eventually removed

center value
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: center calculation data transformation
subclass of: data item
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
alternative term: median
definition: A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data.
editor preferred term: center value
has curation status: pending final vetting

portioning objective
type: Class
subclass of: material separation objective
definition: A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material.
example of usage: The objective to obtain multiple aliquots of an enzyme preparation.
editor preferred term: portioning objective
has curation status: metadata incomplete

average value
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: averaging data transformation
subclass of: data item
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
alternative term: arithmetic mean
definition: A data item that is produced as the output of an averaging data transformation and represents the average value of the input data.
editor preferred term: average value
has curation status: pending final vetting

whole organism preparation
type: Class
subclass of: specimen
subclass of: Restriction
  on property: derives from
  some values from: organism
subclass of: Restriction
  on property: is_specified_output_of
  some values from: specimen collection
subclass of: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: specimen role
definition: A material entity which is the output of a process in which one or more whole organisms are prepared in a way to make it easier to study them, and in which the great majority of organismal parts are maintained
editor note: does this include injecting a dye to a patient to be able to visualize parts of his brain? If not, we should state that the components of the organism are substantially re-arranged.
example of usage: putting a mouse in the blender. Not: putting a mouse on a scale
editor preferred term: whole organism preparation
has curation status: metadata incomplete

separation into different composition objective
type: Class
subclass of: material separation objective
definition: A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities).
example of usage: The objective to obtain cells contained in a sample of blood.
editor note: We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives
editor preferred term: separation into different composition objective
has curation status: metadata complete

specimen collection objective
type: Class
subclass of: objective specification
definition: A objective specification to obtain a material entity for potential use as an input during an investigation.
term editor: Bjoern Peters
definition source: Bjoern Peters
example of usage: The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
editor preferred term: specimen collection objective
has curation status: ready for release

material combination objective
type: Class
subclass of: material transformation objective
term editor: PPPB branch
definition source: bp
definition: is an objective to obtain an output material that contains several input materials.
editor preferred term: material combination objective
has curation status: ready for release

material sample role
type: Class
subclass of: specimen role
editor note: 7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off.
definition: A material sample role is a specimen role borne by a material entity that is the output of a material sampling process.
example of usage: a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
editor preferred term: material sample role
has curation status: pending final vetting

material sampling process
type: Class
equivalent class: Class
  intersection of: specimen collection
  intersection of: Restriction
    on property: has_specified_input
    some values from: material entity
  intersection of: Restriction
    on property: has_specified_output
    some values from: material sample
subclass of: specimen collection
definition: A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity
editor preferred term: material sampling process
has curation status: metadata incomplete

material sample
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: material sample role
subclass of: specimen
definition: A material entity that has the material sample role
term editor: OBI: workshop
example of usage: blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
editor preferred term: material sample
ISA alternative term: sample
alternative term: sample population
has curation status: metadata incomplete

study design independent variable
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: part of
  some values from: study design
curator note: 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Chris Stoeckert
definition source: Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables
ISA alternative term: study factor
example of usage: In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, disease status is the independent variable.
editor note: 2/2/2009 Original definition - In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled.
alternative term: independent variable
editor note: In the Philly 2013 workshop the label was chosen to distinguish it from "dependent variable" as used in statistical modelling. See: http://en.wikipedia.org/wiki/Statistical_modeling
definition: a directive information entity that is part of a study design. Independent variables are entities whose values are selected to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled
alternative term: experimental factor
editor preferred term: study design independent variable
has curation status: ready for release

material maintenance objective
type: Class
subclass of: objective specification
definition: An objective specification maintains some or all of the qualities of a material over time.
term editor: PERSON: Bjoern Peters
editor preferred term: material maintenance objective
definition source: PERSON: Bjoern Peters
has curation status: ready for release

informed consent process
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: Homo sapiens
subclass of: Restriction
  on property: has participant
  some values from: Restriction
    on property: has role
    some values from: investigation agent role
editor note: 09/28/2009 Alan Ruttenberg: This is made a subclass of the higher level processual entity in BFO because I don't want to take a stand on whether it is a process aggregate. Analogous to the situation with Material entity.
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A planned process in which a person or their legal representative is informed about key facts about potential risks and benefits of a process and makes a documented decision as to whether the person in question will participate.
term editor: Person:Alan Ruttenberg
definition source: http://clinicaltrials.gov/ct2/info/glossary#informed
editor preferred term: informed consent process
has curation status: ready for release

measurement device
type: Class
equivalent class: Class
  intersection of: device
  intersection of: Restriction
    on property: has function at some time
    some values from: measure function
subclass of: device
definition: A device in which a measure function inheres.
example of usage: A ruler, a microarray scanner, a Geiger counter.
term editor: GROUP:OBI Philly workshop
definition source: OBI
editor preferred term: measurement device
has curation status: ready for release

high molecular weight DNA extract
type: Class
subclass of: DNA extract
example of usage: Extraction of chromosomal DNA from mammalian cells by first isolating nucei
definition source: OBI
term editor: PERSON:Chris Stoeckert
definition: The output of an extraction process in which DNA molecules above a molecular weight cutoff are purified in order to exclude DNA from organellas.
editor preferred term: high molecular weight DNA extract
has curation status: metadata complete

test tube
type: Class
subclass of: container
subclass of: Restriction
  on property: has function at some time
  some values from: contain function
definition: A test tube is a device consisting of a glass or plastic tubing, open at the top, usually with a rounded U-shaped bottom which has the function to contain material
term editor: Bjoern Peters
alternative term: collection tube
definition source: http://en.wikipedia.org/wiki/Test_tube
alternative term: sample tube
editor preferred term: test tube
has curation status: metadata complete

material maintenance
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
subclass of: planned process
definition: a process with that achieves the objective to maintain some or all of the characteristics of an input material over time
editor preferred term: material maintenance
has curation status: metadata incomplete

polyA RNA extraction
type: Class
subclass of: RNA extraction
definition: A RNA extraction process typically involving the use of poly dT oligomers in which the desired output material is polyA RNA.
term editor: Person: Chris Stoeckert
term editor: Person: Jie Zheng
definition source: UPenn Group
editor preferred term: polyA RNA extraction
has curation status: metadata complete

organellar RNA extraction
type: Class
subclass of: RNA extraction
definition: A RNA extraction process in which the desired output material is RNA in the organelle(s).
term editor: Person: Chris Stoeckert
term editor: Person: Jie Zheng
definition source: UPenn Group
editor preferred term: organellar RNA extraction
has curation status: metadata complete

total RNA extraction
type: Class
subclass of: RNA extraction
definition: A RNA extraction process in which total cellular and organelle RNA are extracted.
term editor: Person: Chris Stoeckert
term editor: Person: Jie Zheng
definition source: UPenn Group
editor preferred term: total RNA extraction
has curation status: metadata complete

cytoplasmic RNA extraction
type: Class
subclass of: RNA extraction
definition: A RNA extraction process in which the desired output material is RNA in the cytoplasm.
term editor: Person: Chris Stoeckert
term editor: Person: Jie Zheng
definition source: UPenn Group
editor preferred term: cytoplasmic RNA extraction
has curation status: metadata complete

nuclear RNA extract
type: Class
subclass of: RNA extract
subclass of: Restriction
  on property: is_specified_output_of
  some values from: nuclear RNA extraction
definition: A RNA extract that is the output of an extraction process in which RNA molecules found in the nucleus, including mRNA precursors (pre-mRNA), are extracted.
example of usage: Isolation and purification of nuclear RNA from animal cells using Norgen Bioteck corp. cytoplasmic and nuclear RNA purification kit (http://www.norgenbiotek.com/display-product.php?ID=30)
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition source: UPenn Group
editor preferred term: nuclear RNA extract
has curation status: metadata complete

polyA RNA extract
type: Class
subclass of: RNA extract
subclass of: Restriction
  on property: is_specified_output_of
  some values from: polyA RNA extraction
definition: A RNA extract that is the output of an extraction process in which RNA molecules with poly A tail at its 3’ end are purified.
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
example of usage: Preparation of polyA RNA by cellulose-bound oligo-dT (Aviv, H., Leder, P. 1972. Purification of biologically active globin messenger RNA by chromatography on oligothymidylic acid-cellulose. Proc. Nat. Acad. Sci. USA 69, 1408-1412.)
definition source: UPenn Group
editor preferred term: polyA RNA extract
has curation status: metadata complete

pre-mortem specimen
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: specimen collection
    intersection of: Restriction
      on property: has_specified_input
      some values from: Class
        intersection of: organism
        intersection of: Restriction
subclass of: specimen with pre- or post-mortem status
term editor: Bjoern Peters
definition: a specimen that was taken from a live organism
example of usage: material obtained through a liver biopsy from a human patient
editor preferred term: pre-mortem specimen
definition source: MO_705 premortem
has curation status: metadata complete

cytoplasmic RNA extract
type: Class
subclass of: RNA extract
subclass of: Restriction
  on property: is_specified_output_of
  some values from: cytoplasmic RNA extraction
definition: A RNA extract that is the output of a RNA extraction process in which RNA molecules found in the cytoplasm are extracted.
example of usage: Cytoplasmic RNA extraction from mammalian tissues to create cDNA library (Carninci P, Nakamura M, Sato K, Hayashizaki Y, Brownstein MJ. Cytoplasmic RNA extraction from fresh and frozen mammalian tissues. Biotechniques. 2002;33:306–309.)
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition source: UPenn Group
editor preferred term: cytoplasmic RNA extract
has curation status: metadata complete

RNA extract
type: Class
subclass of: nucleic acid extract
subclass of: Restriction
  on property: is_specified_output_of
  some values from: RNA extraction
subclass of: Restriction
  on property: has grain
  some values from: ribonucleic acid
definition source: Group: UPenn Group
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
editor preferred term: RNA extract
definition: an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen.
has curation status: metadata complete

nuclear RNA extraction
type: Class
subclass of: RNA extraction
definition: A RNA extraction process in which the desired output material is RNA in the nucleus.
term editor: Person: Chris Stoeckert
term editor: Person: Jie Zheng
definition source: UPenn Group
editor preferred term: nuclear RNA extraction
has curation status: metadata complete

total RNA extract
type: Class
subclass of: RNA extract
subclass of: Restriction
  on property: is_specified_output_of
  some values from: total RNA extraction
definition: A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen.
example of usage: Extraction of total RNA from cells with Qiagen mini RNeasy kit.
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition source: UPenn Group
editor preferred term: total RNA extract
has curation status: metadata complete

organellar RNA extract
type: Class
subclass of: RNA extract
subclass of: Restriction
  on property: is_specified_output_of
  some values from: organellar RNA extraction
definition: A RNA extract that is the output of an extraction process in which RNA molecules found in an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus, are extracted.
example of usage: Extraction of organellar RNA from plant cells using organellar RNA binding protein.
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition source: UPenn Group
editor preferred term: organellar RNA extract
has curation status: metadata complete

post mortem specimen
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: specimen collection
    intersection of: Restriction
      on property: has_specified_input
      some values from: Class
        intersection of: organism
        intersection of: Restriction
subclass of: specimen with pre- or post-mortem status
term editor: Bjoern Peters
definition: a specimen that was taken from a dead organism
editor preferred term: post mortem specimen
example of usage: the spleen taken from a dead mouse
definition source: MO_416 postmortem
has curation status: metadata complete

labeled DNA extract
type: Class
subclass of: labeled nucleic acid extract
subclass of: Restriction
  on property: has grain
  some values from: deoxyribonucleic acid
subclass of: Class
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: Class
      intersection of: addition of molecular label
      intersection of: Restriction
        on property: has_specified_input
        some values from: DNA extract
  intersection of: Restriction
    on property: has role
    some values from: specimen role
definition source: Group: OBI group
term editor: Group: OBI group
editor note: Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. Added duirng Mar 1, 2010 dev call
definition: a labeled specimen that is the output of a labeling process and has grain labeled DNA to be able to detect DNA in future experiments.
editor preferred term: labeled DNA extract
has curation status: metadata complete

cloacal specimen
type: Class
subclass of: specimen
subclass of: Restriction
  on property: has role
  some values from: specimen role
definition: A specimen obtained by inserting a swab deeply into the vent of the cloaca of an organism and vigorously swabbing the wall. The swab should be deeply stained with fecal material and is then placed in transport medium.
term editor: PERSON: Melanie Courtot
definition source: WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf
editor preferred term: cloacal specimen
example of usage: type of sample used in the PCIRN influenza network
has curation status: metadata complete

nasopharyngeal aspirate specimen
type: Class
subclass of: specimen
subclass of: Restriction
  on property: has role
  some values from: specimen role
definition: A speciemn which derives from nasopharyngeal mucosa after aspiration.
term editor: PERSON: Melanie Courtot
definition source: WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf
editor preferred term: nasopharyngeal aspirate specimen
example of usage: type of sample used in the PCIRN influenza network
has curation status: metadata complete

freezing storage
type: Class
subclass of: storage
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
subclass of: Class
  intersection of: Restriction
    on property: has_specified_input
    some values from: Class
      intersection of: material entity
      intersection of: Restriction
        on property: has quality
        some values from: frozen
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: material entity
      intersection of: Restriction
        on property: has quality
        some values from: frozen
editor note: 2010/3/3 Alan Ruttenberg: There is a question of whether we should have a separate objective to "prepare for maintenance" 2014/2/3 OBI dev call: "prepare for maintenance" is a separate process. For example, 'freezing' and 'flash freezing' are defined and can be used to produce frozen material for storage. Updated both textual and logical definition. Both input and output material of freezing storage have quality frozen.
definition: A storage process in temperature that maintenance the frozen status of the stored entities.
definition source: OBI
term editor: Person: Alan Ruttenberg, Mathias Brochhausen
example of usage: a fozen pellet used for later assay
editor preferred term: freezing storage
definition source: MO_481 frozen_storage
has curation status: metadata complete

nasal swab specimen
type: Class
subclass of: specimen
subclass of: Restriction
  on property: has role
  some values from: specimen role
definition: A specimen obtained using a cotton swab on a stick, passed up the nostril to obtain a sample of exudate and epithelial debris for microbiological or cellular examination.
term editor: PERSON: Melanie Courtot
definition source: WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf
editor preferred term: nasal swab specimen
example of usage: type of sample used in the PCIRN influenza network
has curation status: metadata complete

labeled RNA extract
type: Class
subclass of: labeled nucleic acid extract
subclass of: Restriction
  on property: has grain
  some values from: ribonucleic acid
subclass of: Class
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: Class
      intersection of: addition of molecular label
      intersection of: Restriction
        on property: has_specified_input
        some values from: RNA extract
  intersection of: Restriction
    on property: has role
    some values from: specimen role
term editor: Group: OBI group
definition source: Group: OBI group
editor note: Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. Added duirng Mar 1, 2010 dev call
definition: a labeled specimen that is the output of a labeling process and has grain labeled RNA to be able to detect RNA in future experiments.
editor preferred term: labeled RNA extract
has curation status: metadata complete

frozen specimen
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: Class
      intersection of: freezing storage
      intersection of: Restriction
        on property: has_specified_input
        some values from: Restriction
  intersection of: Restriction
    on property: has role
    some values from: specimen role
subclass of: specimen with known storage state
definition: A specimen that has been frozen in order to store it.
example of usage: Frozen blood plasma
definition source: MO_610 frozen_sample
term editor: Person:Alan Ruttenberg
editor preferred term: frozen specimen
has curation status: metadata incomplete

labeled specimen
type: Class
equivalent class: Class
  intersection of: specimen
  intersection of: Restriction
    on property: has part
    some values from: molecular label
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: addition of molecular label
subclass of: processed specimen
subclass of: molecular-labeled material
definition: A specimen that has been modified in order to be able to detect it in future experiments
term editor: OBI group
editor note: added during call 3/1/2010
editor preferred term: labeled specimen
has curation status: metadata incomplete

lyophilization storage
type: Class
subclass of: storage
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition: a storage process with input material entity and output freeze dried material for long time storage
comment: can link to freezing-dying equipment, such as freeze-dryer, rotary evaporator, if needed
editor preferred term: lyophilization storage
has curation status: metadata incomplete

material separation device
type: Class
equivalent class: Restriction
  on property: has function at some time
  some values from: material separation function
subclass of: device
definition: A device with a separation function realized in a planed process
example of usage: flow cytometer
editor preferred term: material separation device
has curation status: metadata incomplete

paraffin specimen
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: Class
      intersection of: paraffin storage
      intersection of: Restriction
        on property: has_specified_input
        some values from: Restriction
  intersection of: Restriction
    on property: has role
    some values from: specimen role
subclass of: specimen with known storage state
definition source: MO_990 paraffin_sample
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition: a specimen that is output of a paraffin storage process in which specimen is embedded in paraffin
example of usage: liver tissue embedded in paraffin
editor preferred term: paraffin specimen
has curation status: metadata incomplete

processed specimen
type: Class
equivalent class: Class
  intersection of: processed material
  intersection of: specimen
subclass of: processed material
subclass of: specimen
definition: A specimen that has been intentionally physically modified.
definition source: Bjoern Peters
term editor: Bjoern Peters
editor preferred term: processed specimen
comment: A tissue sample that has been sliced and stained for a histology study.
example of usage: A tissue sample that has been sliced and stained for a histology study. A blood specimen that has been centrifuged to obtain the white blood cells.
has curation status: ready for release

lyophilized specimen
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: Class
      intersection of: lyophilization storage
      intersection of: Restriction
        on property: has_specified_input
        some values from: Restriction
  intersection of: Restriction
    on property: has role
    some values from: specimen role
subclass of: specimen with known storage state
definition source: MO_589 freeze_dried_sample
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition: a specimen that is output of a lyophilization storage process in which specimen is lyophilized for storage.
example of usage: freezing dried DNA
editor preferred term: lyophilized specimen
has curation status: metadata incomplete

container
type: Class
equivalent class: Restriction
  on property: has function at some time
  some values from: contain function
subclass of: device
subclass of: Restriction
  on property: has maximum capacity
  some values from: measurement data item
subclass of: Restriction
  on property: has actual load
  some values from: measurement data item
editor note: 03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?)
definition: A device that can be used to restrict the location of material entities over time
term editor: PERSON: Bjoern Peters
editor preferred term: container
has curation status: metadata incomplete

device
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: material processing
subclass of: Restriction
  on property: has function at some time
  some values from: function
editor note: 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent…
definition: A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
example of usage: A voltmeter is a measurement device which is intended to perform some measure function.
example of usage: An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
definition source: OBI development call 2012-12-17.
term editor: PERSON: Helen Parkinson
editor preferred term: device
alternative term: instrument
has curation status: ready for release

fresh specimen
type: Class
subclass of: specimen with known storage state
definition source: MO_730 fresh_sample
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
example of usage: a liver freshly removed from a rat
definition: a specimen that is output of a specimen creation process used for an investigation without storage.
editor preferred term: fresh specimen
has curation status: metadata incomplete

paraffin storage
type: Class
subclass of: storage
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: gross anatomical part
    union of: organism
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition source: UPenn Group
definition: a storage process with input organism or anatomical entity and paraffin and output material embedded in paraffin for long term storage
comment: need to specify paraffin or wax is one of specified input of the process
editor preferred term: paraffin storage
has curation status: metadata complete

agar stab specimen
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: agar stab storage
    intersection of: Restriction
      on property: has_specified_input
      some values from: Restriction
        on property: has role
        some values from: specimen role
subclass of: specimen with known storage state
definition source: MO_971 agar_stab
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition: a specimen that is output of a process that cell culture inoculated into agar for long term storage.
editor preferred term: agar stab specimen
has curation status: metadata incomplete

questionnaire
type: Class
subclass of: document
editor note: Need to clarify if this is a document or a directive information entity (or what their connection is))
editor preferred term: questionnaire
definition: A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study.
editor note: JT: It plays a role in collecting data that could be fleshed out more; but I'm thinking it is, in itself, an edited document. JZ: based on textual definition of edited document, it can be defined as N&S. I prefer to leave questionnaire as a document now. We can add more restrictions in the future and use that to determine it is an edited document or not.
definition source: Merriam-Webster
term editor: PERSON: Jessica Turner
has curation status: metadata complete

agar stab storage
type: Class
subclass of: storage
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
subclass of: Restriction
  on property: has_specified_input
  some values from: cultured cell population
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition source: UPenn Group
definition: a storage process with input cell culture and agar and output agar stab for long time storage
editor preferred term: agar stab storage
comment: need to specify that agar is one of input for this process
has curation status: metadata complete

nucleic acid extract
type: Class
subclass of: extract
subclass of: processed specimen
subclass of: Class
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: nucleic acid extraction
  intersection of: Restriction
    on property: has role
    some values from: specimen role
subclass of: Restriction
  on property: has grain
  some values from: nucleic acid
definition: An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.
term editor: PERSON: Jie Zheng
definition source: UPenn Group
editor preferred term: nucleic acid extract
has curation status: metadata complete

DNA extract
type: Class
subclass of: nucleic acid extract
subclass of: Restriction
  on property: has grain
  some values from: deoxyribonucleic acid
subclass of: Restriction
  on property: is_specified_output_of
  some values from: DNA extraction
editor preferred term: DNA extract
definition source: Group: UPenn group
term editor: Person: Jie Zheng
definition: The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas.
has curation status: metadata complete

labeled nucleic acid extract
type: Class
subclass of: labeled specimen
subclass of: Class
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: Class
      intersection of: addition of molecular label
      intersection of: Restriction
        on property: has_specified_input
        some values from: nucleic acid extract
  intersection of: Restriction
    on property: has role
    some values from: specimen role
subclass of: Restriction
  on property: has grain
  some values from: nucleic acid
definition source: MO_221 labeledExtract
term editor: Person: Jie Zheng
definition: a labeled specimen that is the output of a labeling process and has grain labeled nucleic acid for detection of the nucleic acid in future experiments.
alternative term: labeled extract
ISA alternative term: labeled extract
editor preferred term: labeled nucleic acid extract
has curation status: metadata complete

disease state design
type: Class
subclass of: study design
subclass of: Restriction
  on property: has part
  some values from: organism feature identification objective
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: is about
      some values from: disease
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design in which the pathological condition of a part, organ, or system of an organism is studied. The etiology may be from infection, genetic defect, or environmental stress.
definition source: MO_902 disease_state_design
editor preferred term: disease state design
has curation status: metadata complete

cell specimen
type: Class
subclass of: specimen
subclass of: Restriction
  on property: has grain
  some values from: cell
subclass of: Restriction
  on property: has role
  some values from: specimen role
definition: A specimen primarily composed of cells collected from a multicellular organism or a cell culture
definition source: MO_612 cell
term editor: PERSON: Chris Stoeckert, Jie Zheng
editor preferred term: cell specimen
has curation status: metadata incomplete

specimen with known storage state
type: Class
equivalent class: Class
  union of: fresh specimen
  union of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: storage
subclass of: specimen
definition: A specimen for which it is known whether it has been subjected to storage of a specified type.
definition source: MO_95 BiosourceType
term editor: PERSON: Chris Stoeckert, Jie Zheng
editor preferred term: specimen with known storage state
has curation status: metadata incomplete

tissue specimen
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has role
    some values from: specimen role
  intersection of: Restriction
    on property: derives from
    some values from: gross anatomical part
subclass of: specimen
definition: A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm).
definition source: MO_954 organism_part
term editor: PERSON: Chris Stoeckert, Jie Zheng
editor preferred term: tissue specimen
has curation status: ready for release

specimen with pre- or post-mortem status
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: specimen collection
    intersection of: Restriction
      on property: has_specified_input
      some values from: Class
        intersection of: organism
        intersection of: Restriction
subclass of: specimen
definition: A specimen that has been established to be taken from a live (pre-mortem) or dead (post-mortem) organism.
definition source: MO_84 OrganismStatus
term editor: PERSON: Chris Stoeckert, Jie Zheng
editor note: organizational term, used in description of specimen that is created from known pre- or post-mortem status
editor preferred term: specimen with pre- or post-mortem status
has curation status: metadata complete

specimen collection time measurement datum
type: Class
subclass of: time measurement datum
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: process boundary
    intersection of: Restriction
      on property: starts
      some values from: specimen collection
NIAID GSCID-BRC alternative term: Specimen Collection Date
definition: A time measurement datum that is the measure of the time when the specimens are collected.
Source: NIAID GSCID-BRC
definition source: NIAID GSCID-BRC metadata working group
term editor: Person: Chris Stoeckert, Jie Zheng
alternative term: collection date
editor preferred term: specimen collection time measurement datum
has curation status: metadata complete

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

cell culture
type: Class
subclass of: processed material
subclass of: Restriction
  on property: has part
  some values from: Class
    union of: culture medium
    union of: cell freezing medium
subclass of: Restriction
  on property: has part
  some values from: cultured cell
comment: A cell culture includes the cells in culture, as well as the media and all additives in which the cells are being grown or in which they are stored.
definition: A material entity comprised of cultured cells and the media in which they are being propagated or stored.
term editor: PERSON:Matthew Brush
editor preferred term: cell culture
definition source: OBI-CLO Alignment Working Group (Spring 2013)
has curation status: metadata complete

conclusion based on data
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is_supported_by_data
  some values from: data item
subclass of: Restriction
  on property: is_specified_output_of
  some values from: drawing a conclusion based on data
definition: An information content entity that is inferred from data.
definition source: Group:2013 Philly Workshop group
term editor: Group:2013 Philly Workshop group
editor preferred term: conclusion based on data
editor note: In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate.
example of usage: The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting. The following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. "13 is prime".
has curation status: ready for release

cell freezing medium
type: Class
subclass of: processed material
definition: A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles.
term editor: PERSON: Matthew Brush
editor preferred term: cell freezing medium
has curation status: metadata complete

selection
type: Class
equivalent class: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes at some time
    some values from: selection criterion
subclass of: planned process
definition: A planned process which results in the creation of group of entity from a larger group by the application of predefined criteria.
definition source: OBI
example of usage: PMID: 24023800. In this study, a set of eleven genes (VATP16, 60 S, UQCC, SMD3, EF1?, UBQ, SAND, GAPDH, ACT, PsaB, PTB2) was evaluated to identify reference genes during the first hours of interaction (6, 12, 18 and 24 hpi) between two V. vinifera genotypes and P. viticola. Two analyses were used for the selection of reference genes: direct comparison of susceptible, Trincadeira, and resistant, Regent, V. vinifera cultivars at 0 h, 6, 12, 18 and 24 hours post inoculation with P. viticola (genotype effect); and comparison of each genotype with mock inoculated samples during inoculation time-course (biotic stress effect). Three statistical methods were used, GeNorm, NormFinder, and BestKeeper, allowing to identify UBQ, EF1? and GAPDH as the most stable genes for the genotype effect.
term editor: Person: Philippe Rocca-Serra
editor preferred term: selection
alternative term: selection process
editor note: this term refers to a planned process and therefore is distinct from the notion of 'natural selection', a process covering the operation of natural causes by which those individuals of a species that are best adapted to the environment tend to be preserved and to transmit their characters, while those less adapted die out, so that in the course of generations the degree of adaptation to the environment tends progressively to increase. (as defined by Oxford English Dictionary)
has curation status: ready for release

scalar value specification
type: Class
subclass of: value specification
subclass of: Restriction
  on property: has specified value
  min cardinality: 1
subclass of: Restriction
  on property: has measurement unit label
  min cardinality: 1
editor preferred term: scalar value specification
definition: A value specification that consists of two parts: a numeral and a unit label
term editor: PERSON:Bjoern Peters
has curation status: metadata incomplete

value specification
type: Class
subclass of: information content entity
editor note: This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement.
example of usage: The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
editor preferred term: value specification
term editor: PERSON:Bjoern Peters
definition: An information content entity that specifies a value within a classification scheme or on a quantitative scale.
has curation status: ready for release

molecular-labeled material
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has part
    some values from: molecular label
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: addition of molecular label
subclass of: processed material
term editor: PERSON:Matthew Brush
definition source: OBI developer call, 3-12-12
definition: a material entity that is the specified output of an addition of molecular label process that aims to label some molecular target to allow for its detection in a detection of molecular label assay
editor preferred term: molecular-labeled material
has curation status: pending final vetting

flash freezing
type: Class
subclass of: freezing
definition source: WEB: http://en.wikipedia.org/wiki/Flash_freezing
definition: A freezing process by which material entities are quickly frozen by subjecting them to cryogenic temperatures, or in direct contact with Liquid nitrogen at -320.8F or -196°C.
term editor: Person: Mathias Brochhausen, Jie Zheng
editor preferred term: flash freezing
has curation status: metadata complete

freezing
type: Class
subclass of: planned process
definition: A planned process in which a material entity has it's temperature lowered to below the freezing point in order to bring it to a state in which it can be maintained at this lower temperature in order to preserve some of its qualities.
definition source: Mathias Brochhausen
term editor: Person: Mathias Brochhausen, Jie Zheng
editor preferred term: freezing
has curation status: metadata complete

blood plasma specimen
type: Class
subclass of: processed specimen
subclass of: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: specimen role
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: material component separation
    intersection of: Restriction
      on property: has_specified_input
      some values from: blood specimen
term editor: PERSON: Philippe Rocca-Serra
editor note: 03/21/2010: BP, blood plasma is defined as the output of certain separation processes, so this is in the domain of OBI, not FMA.
term editor: PERSON: Maura Gasparetto
term editor: PERSON: Melanie Courtot
example of usage: PMID: 18217225.Sex Transm Dis. 2008 Jan;35(1):55-60. Review.Human immunodeficiency virus viral load in blood plasma and semen: review and implications of empirical findings.
definition source: WEB: http://en.wikipedia.org/wiki/Blood_plasma
definition: a material entity which corresponds to the liquid component of blood, in which the blood cells are suspended.
editor preferred term: blood plasma specimen
alternative term: plasma
has curation status: metadata complete

blood serum specimen
type: Class
subclass of: processed specimen
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: Class
      union of: filtration
      union of: centrifugation
      union of: dialysis
    intersection of: Restriction
      on property: has_specified_input
      some values from: blood specimen
subclass of: Restriction
  on property: has role
  some values from: specimen role
term editor: PERSON: Philippe Rocca-Serra
definition: A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors.
term editor: PERSON: Maura Gasparetto
term editor: PERSON: Melanie Courtot
example of usage: PMID: 18229666.Adv Med Sci. 2007;52 Suppl 1:204-6.Antioxidant activity of blood serum and saliva in patients with periodontal disease treated due to epilepsy.
definition source: WEB: http://en.wikipedia.org/wiki/Blood_plasma
editor preferred term: blood serum specimen
has curation status: metadata complete

organism
type: Class
equivalent class: Class
  union of: Viruses
  union of: Bacteria
  union of: Archaea
  union of: Eukaryota
subclass of: material entity
editor note: 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
editor note: 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI.
term editor: GROUP: OBI Biomaterial Branch
definition: A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
definition source: WEB: http://en.wikipedia.org/wiki/Organism
example of usage: animal
example of usage: fungus
editor preferred term: organism
example of usage: plant
example of usage: virus
has curation status: ready for release

specimen
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: specimen role
subclass of: material entity
example of usage: Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
editor note: Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
term editor: PERSON: James Malone
term editor: PERSON: Philippe Rocca-Serra
definition: A material entity that has the specimen role.
definition source: GROUP: OBI Biomaterial Branch
editor preferred term: specimen
has curation status: ready for release

cultured cell population
type: Class
subclass of: processed material
subclass of: Restriction
  on property: has grain
  some values from: cultured cell
subclass of: Restriction
  on property: is_specified_output_of
  some values from: maintaining cell culture
subclass of: Restriction
  on property: has grain
  all values from: cultured cell
definition: A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history.
definition source: PERSON:Matthew Brush
term editor: PERSON:Matthew Brush
comment: The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally.
editor preferred term: cultured cell population
editor note: 2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line.
alternative term: cell culture sample
example of usage: A cultured cell population applied in an experiment: "293 cells expressing TrkA were serum-starved for 18 hours and then neurotrophins were added for 10 min before cell harvest." (Lee, Ramee, et al. "Regulation of cell survival by secreted proneurotrophins." Science 294.5548 (2001): 1945-1948). A cultured cell population maintained in vitro: "Rat cortical neurons from 15 day embryos are grown in dissociated cell culture and maintained in vitro for 8–12 weeks" (Dichter, Marc A. "Rat cortical neurons in cell culture: culture methods, cell morphology, electrophysiology, and synapse formation." Brain Research 149.2 (1978): 279-293).
has curation status: metadata complete

organ section
type: Class
subclass of: processed material
subclass of: Restriction
  on property: derives from
  some values from: gross anatomical part
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    union of: histological sample preparation
    union of: collecting specimen from organism
definition source: GROUP: OBI Biomaterial Branch
term editor: PERSON: Philippe Rocca-Serra
example of usage: A liver slice used in a perfusion experiment. Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ section study with long-term functional evaluation. Clin Otolaryngol Allied Sci. 1995 Apr;20(2):145-9. PMID: 7634521
definition: A processed material which derives from an organ and results from a process of dissection or histological sample preparation a portion(formerly an organ section is portion of an organ removed from the context of the organ)
definition source: GROUP: CEBS
term editor: PERSON: Helen Parkinson
editor preferred term: organ section
has curation status: pending final vetting

bronchial alveolar lavage
type: Class
subclass of: specimen
subclass of: Restriction
  on property: has role
  some values from: specimen role
subclass of: Restriction
  on property: is_specified_output_of
  all values from: lavage
alternative term: BAL
definition source: GROUP: IEDB
definition: Group of biomaterials present in the bronchial aveolar space of an organism which are collected through lavage including the reagents used to for the lavage process, organisms, cells, and cellular secretions present in the bronchial aveolar space.
term editor: PERSON: Bjoern Peters
editor preferred term: bronchial alveolar lavage
example of usage: solution containing lung derived T cells, eosinophils, and TNFa.
has curation status: metadata complete

data transformation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: data transformation objective
subclass of: planned process
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes at some time
    some values from: Class
      intersection of: algorithm
      intersection of: Restriction
        on property: has part
        some values from: objective specification
subclass of: Restriction
  on property: has_specified_output
  all values from: data item
subclass of: Restriction
  on property: has_specified_input
  all values from: data item
subclass of: Restriction
  on property: has_specified_input
  some values from: data item
subclass of: Restriction
  on property: has_specified_output
  some values from: data item
term editor: Philippe Rocca-Serra
example of usage: The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
definition: A planned process that produces output data from input data.
definition source: Branch editors
term editor: Elisabetta Manduchi
term editor: Helen Parkinson
term editor: James Malone
term editor: Melanie Courtot
term editor: Richard Scheuermann
term editor: Ryan Brinkman
term editor: Tina Hernandez-Boussard
alternative term: data analysis
alternative term: data processing
editor preferred term: data transformation
has curation status: ready for release

moving average
type: Class
subclass of: averaging data transformation
subclass of: Class
  intersection of: Restriction
    on property: has_specified_output
    some values from: average value
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: averaging objective
term editor: Philippe Rocca-Serra
definition: A moving average is a data transformation in which center calculations, usually mean calculations, are performed on values within a sliding window across the input data set.
term editor: Elisabetta Manduchi
term editor: Helen Parkinson
definition source: PERSON: Elisabetta Manduchi
definition source: PERSON: Helen Parkinson
example of usage: The moving average is often used to handle data from tiling arrays.
editor preferred term: moving average
has curation status: ready for release

descriptive statistical calculation objective
type: Class
subclass of: data transformation objective
definition: A descriptive statistical calculation objective is a data transformation objective which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability.
term editor: Elisabetta Manduchi
term editor: James Malone
term editor: Melanie Courtot
term editor: Monnie McGee
definition source: PERSON: Elisabetta Manduchi
definition source: PERSON: James Malone
definition source: PERSON: Melanie Courtot
definition source: PERSON: Monnie McGee
editor preferred term: descriptive statistical calculation objective
has curation status: ready for release

mean calculation
type: Class
subclass of: averaging data transformation
subclass of: center calculation data transformation
subclass of: descriptive statistical calculation data transformation
subclass of: Class
  intersection of: Restriction
    on property: has_specified_output
    some values from: center value
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: center calculation objective
subclass of: Class
  intersection of: Restriction
    on property: has_specified_output
    some values from: average value
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: averaging objective
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: descriptive statistical calculation objective
term editor: Philippe Rocca-Serra
definition: A mean calculation is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment.
curator note: From Monnie's file comments - need to add moment_calculation and center_calculation roles but they don't exist yet - (editor note added by James Jan 2008)
term editor: James Malone
term editor: Monnie McGee
definition source: PERSON: James Malone
definition source: PERSON: Monnie McGee
editor preferred term: mean calculation
has curation status: metadata complete

data combination
type: Class
subclass of: data transformation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: merging objective
alternative term: data pooling
definition: A data transformation in which individual input data elements and values are merged together into a output set of data elements and values.
term editor: Richard Scheuermann
editor preferred term: data combination
definition source: editor
has curation status: metadata incomplete

data transformation objective
type: Class
subclass of: objective specification
editor note: Modified definition in 2013 Philly OBI workshop
definition: An objective specification to transformation input data into output data
term editor: James Malone
definition source: PERSON: James Malone
editor preferred term: data transformation objective
example of usage: normalize objective
has curation status: ready for release

averaging data transformation
type: Class
equivalent class: Class
  union of: Restriction
    on property: has_specified_output
    some values from: average value
  union of: Restriction
    on property: achieves_planned_objective
    some values from: averaging objective
subclass of: data transformation
term editor: James Malone
definition: An averaging data transformation is a data transformation that has objective averaging.
definition source: PERSON: James Malone
editor preferred term: averaging data transformation
has curation status: metadata incomplete

center calculation objective
type: Class
subclass of: data transformation objective
definition source: PERSON: James Malone
definition: A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set.
example of usage: A mean calculation which has center calculation objective is a data transformation in which the center of the input data is discovered through the calculation of a mean average.
term editor: James Malone
editor preferred term: center calculation objective
has curation status: ready for release

center calculation data transformation
type: Class
equivalent class: Class
  union of: Restriction
    on property: has_specified_output
    some values from: center value
  union of: Restriction
    on property: achieves_planned_objective
    some values from: center calculation objective
subclass of: data transformation
term editor: James Malone
definition: A center calculation data transformation is a data transformation that has objective of center calculation.
definition source: PERSON: James Malone
editor preferred term: center calculation data transformation
has curation status: metadata incomplete

descriptive statistical calculation data transformation
type: Class
equivalent class: Class
  union of: Restriction
    on property: has_specified_output
    some values from: data set of features
  union of: Restriction
    on property: achieves_planned_objective
    some values from: descriptive statistical calculation objective
subclass of: data transformation
definition: A descriptive statistical calculation data transformation is a data transformation that has objective descriptive statistical calculation and which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability.
term editor: James Malone
definition source: PERSON: James Malone
editor preferred term: descriptive statistical calculation data transformation
has curation status: ready for release

merging objective
type: Class
subclass of: data transformation objective
definition source: PERSON: Data Transformation Branch
definition: A merging objective is a data transformation objective in which the data transformation has the aim of performing a union of two or more sets.
term editor: James Malone
alternative term: combining objective
editor preferred term: merging objective
example of usage: merging of columns from two different data sets
has curation status: metadata incomplete

pool of specimens
type: Class
equivalent class: Class
  intersection of: specimen
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: Class
      intersection of: material combination
      intersection of: Restriction
        on property: has_specified_input
        all values from: specimen
subclass of: processed specimen
definition source: GROUP: CEBS
term editor: PERSON: Jennifer Fostel
definition: A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish.
editor note: check with advisors as to how to represent multiple instances of any class? a set of specimens which have been gathered from one or more sample_populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish
editor preferred term: pool of specimens
has curation status: metadata complete

edited document
type: Class
subclass of: document
subclass of: Restriction
  on property: is_specified_output_of
  some values from: document editing
definition: A document which is the output of a document editing process
term editor: Person:Bjoern Peters
term editor: Philippe Rocca-Serra
example of usage: The OBI manuscript is (much) edited imformation
editor preferred term: edited document
has curation status: ready for release

extraction
type: Class
subclass of: material component separation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: separation into different composition objective
definition: A material separation in which a desired component of an input material is separated from the remainder
term editor: Person:Bjoern Peters
term editor: Philippe Rocca-Serra
example of usage: nucleic acid extraction using phenol chloroform
editor note: Current the output of material processing defined as the molecular entity, main component in the output material entity, rather than the material entity that have grain molecular entity. 'nucleic acid extract' is the output of 'nucleic acid extraction' and has grain 'nucleic acid'. However, the output of 'nucleic acid extraction' is 'nucleic acid' rather than 'nucleic acid extract'. We are aware of this issue and will work it out in the future.
editor preferred term: extraction
has curation status: metadata incomplete

filtration
type: Class
subclass of: material component separation
subclass of: Restriction
  on property: has participant
  some values from: filter paper
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: separation into different composition objective
definition source: OBI-Branch: adapted from wikipedia and wordnet
term editor: Philippe Rocca-Serra
example of usage: PMID: 18524968.Filtration of CSF improves isolation of Mycobacteria.J Clin Microbiol. 2008 Jun 4.
editor preferred term: filtration
definition: filtration is a process which separates components suspended in a fluid based on granularity properties relying on a filter device
has curation status: metadata complete

centrifugation
type: Class
subclass of: material component separation
subclass of: Restriction
  on property: has participant
  some values from: centrifuge
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: separation into different composition objective
term editor: Philippe Rocca-Serra
definition source: adapted from http://www.fao.org/DOCREP/003/X3910E/X3910E06.htm
example of usage: PMID: 18428461.Purification of oligodendrocytes and their progenitors using immunomagnetic separation and Percoll gradient centrifugation. Curr Protoc Neurosci. 2001 May;Chapter 3:Unit 3.12.
editor preferred term: centrifugation
definition: centrifugation is a process separating molecules by size or density using centrifugal forces generated by a spinning rotor. G-forces of several hundred thousand times gravity are generated in ultracentrifugation
has curation status: metadata complete

storage
type: Class
subclass of: material maintenance
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
definition source: OBI-Branch
term editor: Philippe Rocca-Serra
definition: A maintenance process by which material entities that are not actively metabolizing are placed in well identified location and possibly under controlled environment in ad-hoc devices/structures in order to preserve and protect them from decay/alteration and maintain availability
example of usage: PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10.
editor preferred term: storage
has curation status: metadata complete

document editing
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: edited document
subclass of: Restriction
  on property: has_specified_input
  some values from: document
term editor: Philippe Rocca-Serra and OBI consortium
definition source: adapted from wikipedia
example of usage: Wax DB, Beilin Y, Hossain S, Lin HM, Reich DL. Manual editing of automatically recorded data in an anesthesia information management system. Anesthesiology. 2008 Nov;109(5):811-5. PMID: 18946292
editor preferred term: document editing
definition: is a planned process with specified input original document and specified output edited document
has curation status: metadata complete

digital curation
type: Class
subclass of: documenting
term editor: Philippe Rocca-Serra
definition source: wikipedia
definition: Digital curation is the process of establishing and developing long term repositories of digital assets for current and future reference by researchers, scientists, and historians, and scholars generally.
example of usage: PMID: 16901087. Supporting the curation of biological databases with reusable text mining.Genome Inform. 2005;16(2):32-44.
editor preferred term: digital curation
has curation status: metadata complete

centrifuge
type: Class
subclass of: measurement device
subclass of: material separation device
subclass of: Restriction
  on property: has function at some time
  some values from: measure function
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: has function at some time
    some values from: contain function
subclass of: Restriction
  on property: has function at some time
  some values from: Class
    intersection of: material separation function
    intersection of: Restriction
      on property: realized in
      all values from: centrifugation
definition: A device with a rapidly rotating container that applies centrifugal force to its contents
term editor: Person: Jennifer Fostel
term editor: Melanie Courtot
term editor: Trish Whetzel
editor preferred term: centrifuge
definition source: http://en.wikipedia.org/wiki/Centrifuge
has curation status: ready for release

microtome
type: Class
subclass of: material separation device
subclass of: Restriction
  on property: has function at some time
  some values from: mechanical function
subclass of: Restriction
  on property: has function at some time
  some values from: material separation function
definition source: PERSON: Daniel Schober
term editor: PERSON: Phillippe Rocca-Serra
definition: A microtome is a mechanical instrument used to cut biological specimens into very thin segments for further treatment (e.g. ISH) and ultimately microscopic or histologic examination. Most microtomes provide cooling facilities (cryo-microtome) and use a steel blade to cut a slice of defined thickness. Some are automatic, and some are driven by hand.
example of usage: PMID: 9974145.Serial sectioning of thick tissue with a novel vibrating blade microtome. Brain Res Brain Res Protoc. 1999 Jan;3(3):302-7.
editor preferred term: microtome
has curation status: pending final vetting

study design
type: Class
subclass of: plan specification
subclass of: Restriction
  on property: has part
  some values from: protocol
definition: A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
editor note: Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available.
term editor: PERSON: Chris Stoeckert
example of usage: a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design.
alternative term: experimental design
curator note: rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol.
editor preferred term: study design
has curation status: ready for release
imported from: obi.owl

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

human subject enrollment
type: Class
subclass of: selection
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: Class
      intersection of: population
      intersection of: Restriction
        on property: has part
        some values from: Homo sapiens
    intersection of: Restriction
      on property: has role
      some values from: participant under investigation role
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: population
    intersection of: Restriction
      on property: has part
      some values from: Homo sapiens
subclass of: Restriction
  on property: has part
  some values from: informed consent process
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes at some time
    some values from: eligibility criterion
editor note: As with group assignment, should the specified output here be an organism which bears a role
definition: A planned process with the objective to obtain a population of human subjects to participate in an investigation by determining eligibility of subjects and obtaining informed consent.
term editor: Bjoern Peters
definition source: IEDB
curator note: criteria come from plan / clinical trial branch
example of usage: enlisting familiy members of HIV patients into a study
editor preferred term: human subject enrollment
has curation status: ready for release

collecting specimen from organism
type: Class
subclass of: specimen collection
subclass of: Restriction
  on property: has_specified_input
  some values from: organism
subclass of: Restriction
  on property: has_specified_output
  some values from: specimen
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: specimen collection objective
definition source: IEDB
term editor: PERSON:Bjoern Peters
definition: a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation
editor preferred term: collecting specimen from organism
example of usage: taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient
has curation status: ready for release

acquisition
type: Class
subclass of: selection
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    union of: material entity
    union of: information content entity
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes at some time
    some values from: selection criterion
editor note: 5/31/2012 - OBI workshop: This process is not implying ownership of the material / information.
example of usage: Downloading a 3D structure from the PDB. Purchasing antibodies from sigma.
term editor: Bjoern Peters
editor note: Following OBI call November 2012,5th: addition of a restriction to acquisition class to capture the need of having selection criteria Relates to the creation of a class 'selection rule'
definition source: IEDB
curator note: This needs to be fleshed out and logical definitions added that will allow to place the children terms automatically under acquisition
editor preferred term: acquisition
definition: the planned process of gaining possession of a continuant
has curation status: ready for release

material acquisition
type: Class
subclass of: acquisition
subclass of: Restriction
  on property: has_specified_output
  some values from: material entity
editor note: The assumption is that the object already exists in its current state, e.g, an available mouse strain purchased from the Jackson Lab, this is the differentia from specimen creation
alternative term: material procurement
example of usage: Acquiring 50 C57BL/6 mice bred in the animal facility of the institute as a service to investigators. Purchasing 1 mg of peptides synthesized by Mimotopes at 80% purity. Getting a gift of purified CD4+ specific antibodies presented by Stephen Schoenberger at LIAI.
definition: An acquisition in which possession of a material entity is gained.
term editor: Bjoern Peters, Alan Ruttenberg, Helen Parkinson
definition source: IEDB
editor note: This excludes processes that create or change materials, such as material transformations.
editor preferred term: material acquisition
has curation status: ready for release

environmental material collection
type: Class
subclass of: specimen collection
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: specimen collection objective
subclass of: Restriction
  on property: has_specified_output
  some values from: specimen
term editor: Bjoern Peters, Alan Ruttenberg
definition source: IEDB
example of usage: Taking 1 liter of surface ocean water from the San Diego Mission Bay Jetty. Capturing mice living in rural Arkansas
editor preferred term: environmental material collection
definition: environmental_material_collection is an acquisition where an object is taken from an environment and put into a storage container. Roles include, environment, thing collected, container, acquirer.
curator note: the researcher is very interested in the location
has curation status: metadata incomplete

information acquisition
type: Class
subclass of: acquisition
subclass of: Restriction
  on property: has_specified_output
  some values from: information content entity
alternative term: data collection
definition: An acquisition in which possession of information is gained.
term editor: Bjoern Peters
editor note: This excludes processes that create or change information, such as assays and data transformations.
example of usage: Gathering all influenza HA sequences from GenBank, Retrieveing HLA allele frequencies in the North American populations from dbMHC
definition source: OBI branch derived
editor preferred term: information acquisition
has curation status: ready for release

material component separation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material separation objective
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: material entity
term editor: Bjoern Peters
definition source: IEDB
example of usage: Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification
definition: a material processing in which components of an input material become segregated in space
editor preferred term: material component separation
has curation status: ready for release

pooling specimens
type: Class
subclass of: material combination
subclass of: Restriction
  on property: has_specified_input
  min cardinality: 2
subclass of: Restriction
  on property: has_specified_output
  some values from: pool of specimens
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material combination objective
subclass of: Restriction
  on property: has_specified_input
  some values from: specimen
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
example of usage: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=104564; Combining spleens of 20 mice, Combining supernatant from a cell culture obtained at different time points
curator note: like' is one of the things that you should be controling for in a well-designed experiment. The instances of material need to have the same class.
definition: physical combination of several instances of like material
editor preferred term: pooling specimens
alternative term: sample pooling
has curation status: pending final vetting

material portioning
type: Class
subclass of: material component separation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: portioning objective
definition source: OBI branch derived
term editor: PERSON:Bjoern Peters
definition: a material processing in which the input substance is partitioned into a number of portions that are similar in composition.
alternative term: aliquoting
alternative term: apportioning
editor preferred term: material portioning
example of usage: pouring 50 mL aliquots of fetal calf serum into conical tubes from a 500 mL stock
has curation status: metadata incomplete

maintaining cell culture
type: Class
subclass of: material maintenance
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: culture medium
    union of: cell freezing medium
subclass of: Restriction
  on property: has_specified_output
  some values from: cultured cell population
subclass of: Restriction
  on property: has_specified_input
  some values from: cultured cell population
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
example of usage: When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture
definition: a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing
editor preferred term: maintaining cell culture
has curation status: pending final vetting

establishing cell culture
type: Class
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: cell
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: Restriction
  on property: has_specified_input
  some values from: culture medium
subclass of: Restriction
  on property: has_specified_output
  some values from: cultured cell population
definition source: PERSON:Matthew Brush
definition: a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line).
editor preferred term: establishing cell culture
comment: A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms.
term editor: PERSON:Matthew Brush
has curation status: metadata complete

addition of molecular label
type: Class
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: target of material addition
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: Restriction
  on property: has_specified_input
  some values from: molecular label
subclass of: Restriction
  on property: has_specified_output
  some values from: molecular-labeled material
alternative term: labeling
definition source: OBI developer call, 3-12-12
term editor: PERSON:Matthew Brush
example of usage: The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies. The addition of anti-CD8-PE to a population of cells, to label the subpopulation cells that are CD8+.
definition: a material processing technique intended to add a molecular label to some input material entity, to allow detection of the molecular target of this label in a detection of molecular label assay
editor preferred term: addition of molecular label
has curation status: pending final vetting

lavage
type: Class
subclass of: collecting specimen from organism
subclass of: material component separation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material separation objective
definition: A protocol application to separate cells and/or cellular secretions from an anatomical space by the introduction and removal of fluid
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
editor note: This is not washing, in which case the material of interest is not the resulting fluid
editor preferred term: lavage
example of usage: the collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present
has curation status: metadata complete

dialysis
type: Class
subclass of: material component separation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: separation into different composition objective
definition source: OBI branch derived
term editor: PERSON:Kevin Clancy
definition: a protocol application that uses diffusion through a semi-permeable membrane to separate an input material into two fractions of different composition
editor preferred term: dialysis
example of usage: the use of a dialysis bag of select pore size to remove salt from collagen isolated from mouse cartilage
has curation status: pending final vetting

RNA extraction
type: Class
subclass of: nucleic acid extraction
subclass of: Restriction
  on property: has_specified_output
  some values from: ribonucleic acid
definition: A RNA extraction is a nucleic acid extraction where the desired output material is RNA
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
editor preferred term: RNA extraction
curator note: requested by Helen Parkinson for MO
has curation status: pending final vetting

nucleic acid extraction
type: Class
subclass of: extraction
subclass of: Restriction
  on property: has_specified_output
  some values from: nucleic acid
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: sample from organism
    union of: organism
    union of: cultured cell population
definition source: OBI branch derived
example of usage: Phenol / chlorophorm extraction disolvation of protein content folllowed by ethanol precipitation of the nucleic acid fraction over night in the fridge followed by centrifugation to obtain a nucleic acid pellet.
term editor: PlanAndPlannedProcess Branch
definition: a material separation to recover the nucleic acid fraction of an input material
editor preferred term: nucleic acid extraction
curator note: requested by Helen Parkinson for MO. Could be defined class
has curation status: pending final vetting

whole mount tissue
type: Class
subclass of: whole organism preparation
subclass of: processed specimen
subclass of: tissue specimen
subclass of: Restriction
  on property: derives from
  some values from: gross anatomical part
subclass of: Restriction
  on property: is_specified_output_of
  some values from: histological sample preparation
term editor: PERSON: Philippe Rocca-Serra
definition: A whole organism preparation resulting from a histological preparation known as whole mount preparation where the whole specimen is mounted or spread on the microscope (glass) slide
definition source: GROUP: OBI
term editor: PERSON: Helen Parkinson
curator note: PRS:22-02-2008: indicates the need to create a protocol application and distinguish it from this entity
curator note: PRS:22-02-2008: is a material which has output_role during whole mount preparation protocol-application
alternative term: whole mount sample
editor preferred term: whole mount tissue
has curation status: metadata complete

donor
type: Class
subclass of: role
example of usage: A T cell line from a PPD(+) donor.
curator note: Definition modified by HP to deal with the case where an organ may be removed for donation but is not transplanted as intended.
alternative term: donor role
definition: A role which inheres in an organism or part thereof from which any part including cell, organ or tissue is removed with the intention that the donated part will be placed into another organism and/or cultured in vitro.
definition source: IEDB
term editor: IEDB
editor preferred term: donor
has curation status: metadata complete

target of material addition
type: Class
equivalent class: Restriction
  on property: has role
  some values from: target of material addition role
subclass of: material entity
editor note: 10/26/09: This defined class is used as a 'macro' to reduce the size of the IEDB export.
example of usage: A cell culture into which a mixture of peptides is being added.
definition: A material entity into which another is being added in a material combinatino process
definition source: IEDB
editor preferred term: target of material addition
has curation status: ready for release

clinical history
type: Class
subclass of: information content entity
definition: A series of statements representing health-relevant qualities of a patient and of a patient's family.
editor preferred term: clinical history
imported from: ogms.owl

phenotype
type: Class
subclass of: quality
editor preferred term: phenotype
definition: A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species.
imported from: ogms.owl

disease
type: Class
subclass of: disposition
definition: A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
imported from: ogms.owl

disorder
type: Class
subclass of: material entity
definition: A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease.
imported from: ogms.owl

diagnosis
type: Class
subclass of: data item
definition: The representation of a conclusion of a diagnostic process.
imported from: ogms.owl

treatment
type: Class
subclass of: process
definition: A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder
imported from: ogms.owl

diagnostic process
type: Class
subclass of: process
definition: An interpretive process that has as input a clinical picture of a given patient and as output an assertion to the effect that the patient has a disease, disorder, or syndrome of a certain type, or none of these.
imported from: ogms.owl

biobank
type: Class
equivalent class: Class
  intersection of: object aggregate
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: object aggregate
      intersection of: Restriction
        on property: has part
        all values from: Class
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: material information bearer
      intersection of: Restriction
        on property: participates in
        some values from: Class
  intersection of: Restriction
    on property: is owned by
    some values from: biobank organization
subclass of: object aggregate
term editor: Mathias Brochhausen
definition: A biobank is a collections of samples of biological substances (e.g. tissue, blood, DNA) which are linked to data about the samples and their donors. They have a dual nature as collections of samples and data.
definition source: definition derived from the definition of 'human biobank', based on http://www.ethikrat.org/files/der_opinion_human-biobanks.pdf

human biobank
type: Class
subclass of: biobank
definition source: Deutscher Ethikrat: Human biobanks for research. Opinion. Berlin, 2010. http://www.ethikrat.org/files/der_opinion_human-biobanks.pdf
definition: A human biobank is a collections of samples of human body substances (e.g. Tissue, blood, DNA) which are linked to personal data and socio deographic information about the donors of the material. They have a dual nature as collections of samples and data."

settlement part of address of sample collection or study contact
type: Class
equivalent class: Class
  intersection of: settlement part of address
  intersection of: Restriction
    on property: part of
    some values from: Class
      intersection of: postal address
      intersection of: Restriction
        on property: is contact information about
        some values from: Class
subclass of: settlement part of address
term editor: Mathias Brochhausen
alternative term: Sample Collection/Study contact city
definition: The part of a sample collection or study contact's adress denoting a settlement.

biobank proper name
type: Class
equivalent class: Restriction
  on property: designates
  some values from: biobank
subclass of: identifier
term editor: Mathias Brochhausen
definition: An identifier in natural language referring to a biobank.
alternative term: Name of biobank

ISO 3166-1 alpha-2 code
type: Class
subclass of: identifier
subclass of: Restriction
  on property: designates
  some values from: Class
    union of: geopolitical dependency
    union of: sovereign state
definition: An identifier that consists of two letters, is part of the ISO 3166-1, and designates countries, dependent territories, and special areas of geographical interest.
term editor: Mathias Brochhausen
comment: Two-letter country codes defined in ISO 3166-1, part of the ISO 3166 standard published by the International Organization for Standardization (ISO), to designate countries, dependent territories, and special areas of geographical interest.
definition source: http://en.wikipedia.org/wiki/ISO_3166-1_alpha-2

biobank idenfier with ISO 3166-1 alpha-2 code
type: Class
subclass of: biobank proper name
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: ISO 3166-1 alpha-2 code
  intersection of: Restriction
    on property: designates
    some values from: biobank
definition: A biobank identifier that has an ISO 3166-1 alpha-2 code as a part.
alternative term: Biobank ID
term editor: Mathias Brochhausen
comment: Textual string of letters starting with the country code (according to standard ISO1366 alpha2) followed by the underscore “_” and post-fixed by a biobank ID or name specified by its juristic person (nationally specific).

sample collection or study identifier
type: Class
subclass of: Class
  intersection of: identifier
  intersection of: Restriction
    on property: designates
    some values from: Class
      union of: study design execution
      union of: Class
        intersection of: object aggregate
        intersection of: Restriction
term editor: Mathias Brochhausen
definition: A sample collection or study proper name that is centrally registered and unique within one framework.
alternative term: Sample Collection/Study ID

ISO 3166-1 alpha-2 code for sample collection or study contact
type: Class
equivalent class: Class
  intersection of: ISO 3166-1 alpha-2 code
  intersection of: Restriction
    on property: part of
    some values from: Class
      intersection of: postal address
      intersection of: Restriction
        on property: is contact information about
        some values from: Class
subclass of: ISO 3166-1 alpha-2 code
term editor: Mathias Brochhausen
alternative term: Sample Collection/Study contact country
definition: The ISO 3166-1 alpha-2 code that is part of the sample collection or study contact's postal address.

biobank organization
type: Class
equivalent class: Class
  intersection of: organization
  intersection of: Class
    union of: Restriction
      on property: owns
      some values from: biobank
    union of: Restriction
      on property: administrates
      some values from: biobank
  intersection of: Restriction
    on property: bearer of
    some values from: legal person role
subclass of: organization
subclass of: Restriction
  on property: has organization member
  some values from: biobank contact person
definition: An organization bearing legal personality that ownes or adminstrates a biobank.
term editor: Mathias Brochhausen
alternative term: biobank juristic person

contacting
type: Class
subclass of: planned process
definition: Contacting is the process of one human being starting a communication process with another human being. Contacting can be done using all modes of communication used by humans.
term editor: Mathias Brochhausen
definition: A planned process that involves a human being and is intended to initiate a communication with another human being.

contact role
type: Class
subclass of: role in human social processes
subclass of: Restriction
  on property: realized in
  some values from: contacting
subclass of: Restriction
  on property: inheres in
  all values from: Class
    intersection of: Homo sapiens
    intersection of: Restriction
      on property: is member of organization
      some values from: organization
subclass of: Restriction
  on property: realized in
  all values from: contacting
definition: A role borne by a human being that is part of an group of individuals and acts as contact person for the group. This role gets realized by the bearer being a participant in a contacting process.
term editor: Mathias Brochhausen

biobank contact person
type: Class
equivalent class: Class
  intersection of: Homo sapiens
  intersection of: Restriction
    on property: is member of organization
    some values from: biobank organization
  intersection of: Restriction
    on property: bearer of
    some values from: biobank contact role
subclass of: Homo sapiens
definition: A human being that is member of a biobank organization and bears the organization contact role.
term editor: Mathias Brochhausen

name of biobank contact person
type: Class
equivalent class: Restriction
  on property: designates
  some values from: Class
    intersection of: Homo sapiens
    intersection of: Restriction
      on property: is member of organization
      some values from: biobank organization
    intersection of: Restriction
      on property: bearer of
      some values from: biobank contact role
subclass of: personal name
definition: A personal name that designates the person acting as contact for a sample collection or a study.
alternative term: Biobank contact person
term editor: Mathias Brochhausen

email address of biobank contact person
type: Class
equivalent class: Class
  intersection of: email address
  intersection of: Restriction
    on property: is contact information about
    some values from: Class
      intersection of: Homo sapiens
      intersection of: Restriction
        on property: is member of organization
        some values from: biobank organization
      intersection of: Restriction
        on property: bearer of
        some values from: biobank contact role
subclass of: email address
definition: An email address for the purpose of contacting a biobank contact person.
alternative term: Biobank contact email
term editor: Mathias Brochhausen

postal address of biobank contact person
type: Class
equivalent class: Class
  intersection of: postal address
  intersection of: Restriction
    on property: is contact information about
    some values from: biobank contact person
subclass of: postal address
term editor: Mathias Brochhausen
definition: Postal address used as a directive for deliveries to the biobank contact person.

department
type: Class
subclass of: organization
subclass of: Class
  intersection of: Class
    complement of: Restriction
      on property: bearer of
      some values from: legal person role
  intersection of: Restriction
    on property: is member of organization
    some values from: Class
      intersection of: organization
      intersection of: Restriction
        on property: bearer of
        some values from: legal person role
definition: An organization with a specific responsibility that is a part of a larger organization with a specific responsibility.
definition source: http://en.wikipedia.org/wiki/Department

department of biobank contact
type: Class
equivalent class: Class
  intersection of: department
  intersection of: Restriction
    on property: has organization member
    some values from: Class
      intersection of: Homo sapiens
      intersection of: Restriction
        on property: is member of organization
        some values from: biobank organization
      intersection of: Restriction
        on property: bearer of
        some values from: biobank contact role
subclass of: department
definition: A department that has a contact person for a biobank as an organizational member.
term editor: Mathias Brochhausen
alternative term: Biobank contact department

unique resource locator
type: Class
subclass of: centrally registered identifier
definition source: http://en.wikipedia.org/wiki/Uniform_resource_locator
definition: A CRID that constitutes a reference to an Internet resource.
term editor: Mathias Brochhausen
alternative term: uri

biobank's unique resource locator
type: Class
subclass of: unique resource locator
term editor: Mathias Brochhausen
definition: A unique resource locator referring to the homepage of a biobank.
alternative term: Biobank URL

telephone number
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: has part
  all values from: numeral
term editor: Mathias Brochhausen
definition: A telephone number is a textual entity consisting of a sequence of digits used to call from one telephone line to another in a public switched telephone network.
comment: MB: This class should probably be a subclass to CRID. However, the textual definition of CRID right now states that each instance has the CRID identifier as a part. This is not the case for telephone numbers. Therefore, they cannot be subsumed under CRID now. I am looking into changing IAO accordingly. Once that is done, the class ought to be a subclass of CRID.
definition source: http://en.wikipedia.org/wiki/Telephone_number

telephone number of biobank contact
type: Class
equivalent class: Class
  intersection of: telephone number
  intersection of: Restriction
    on property: is contact information about
    some values from: Class
      intersection of: Homo sapiens
      intersection of: Restriction
        on property: is member of organization
        some values from: biobank organization
      intersection of: Restriction
        on property: bearer of
        some values from: biobank contact role
subclass of: telephone number
definition: A telephone number that is contact information about a biobank contact person.
alternative term: Biobank contact phone
term editor: Mathias Brochhausen

post-office box number
type: Class
equivalent class: Class
  intersection of: centrally registered identifier
  intersection of: Restriction
    on property: denotes
    all values from: post-office box
subclass of: centrally registered identifier
term editor: Mathias Brochhausen
definition: A centrally registered identifier denoting a post-office box.

post-office box
type: Class
subclass of: material entity
term editor: Mathias Brochhausen
definition: A post-office box is material entity that is a box on the premises of a post office station and is uniquely addressable.
definition source: http://en.wikipedia.org/wiki/Post-office_box

telephone number of sample collection or study contact
type: Class
equivalent class: Class
  intersection of: telephone number
  intersection of: Restriction
    on property: is contact information about
    some values from: Class
      intersection of: Homo sapiens
      intersection of: Class
        union of: Class
subclass of: telephone number
definition: A telephone number that is contact information about a sample collection or study contact person.
term editor: Mathias Brochhausen
alternative term: Sample Collection/Study contact phone

postal code
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: geographical location
term editor: Mathias Brochhausen
definition: A postal code is a textual entity that is a series of letters and/or digits and is part of a postal address for the purpose of sorting mail.
comment: MB: This class should probably be a subclass to CRID. However, the textual definition of CRID right now states that each instance has the CRID identifier as a part. This is not the case for postal codes. Therefore, they cannot be subsumed under CRID now. I am looking into changing IAO accordingly. Once that is done, the class ought to be a subclass of CRID.
definition source: http://en.wikipedia.org/wiki/Postal_code

postal code of biobank contact
type: Class
equivalent class: Class
  intersection of: postal code
  intersection of: Restriction
    on property: part of
    some values from: Class
      intersection of: postal address
      intersection of: Restriction
        on property: is contact information about
        some values from: Class
subclass of: postal code
alternative term: Biobank contact ZIP
term editor: Mathias Brochhausen
definition: The postal code that is part of the postal address of the biobank contact person.

ISO 3166-1 alpha-2 code for biobank contact person
type: Class
equivalent class: Class
  intersection of: ISO 3166-1 alpha-2 code
  intersection of: Restriction
    on property: part of
    some values from: Class
      intersection of: postal address
      intersection of: Restriction
        on property: is contact information about
        some values from: Class
subclass of: ISO 3166-1 alpha-2 code
term editor: Mathias Brochhausen
alternative term: Biobank country code
definition: The ISO 3166-1 alpha-2 code that is part of the biobank contact person's postal address.

settlement part of address
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: geographical location
definition: A textual entity that is part of a postal address and denotes a human settlement for the purpose of delivering mail.
term editor: Mathias Brochhausen

settlement part of address biobank contact
type: Class
equivalent class: Class
  intersection of: settlement part of address
  intersection of: Restriction
    on property: part of
    some values from: Class
      intersection of: postal address
      intersection of: Restriction
        on property: is contact information about
        some values from: Class
subclass of: settlement part of address
term editor: Mathias Brochhausen
alternative term: Biobank contact city
definition: The part of a biobank contact's adress denoting a settlement.

intra-settlement specification part of address
type: Class
equivalent class: Class
  intersection of: textual entity
  intersection of: Restriction
    on property: part of
    some values from: postal address
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: identifier
      intersection of: Restriction
        on property: designates
        some values from: Class
subclass of: textual entity
definition: A textual entity that is part of a postal address and specifies the location inside the settlement (which is specified by another part of the address). This can be a street name and a house number, or just a number or a post-office box number.
term editor: Mathias Brochhausen

intra-settlement specification part of address of biobank contact
type: Class
equivalent class: Class
  intersection of: intra-settlement specification part of address
  intersection of: Restriction
    on property: part of
    some values from: Class
      intersection of: postal address
      intersection of: Restriction
        on property: is contact information about
        some values from: Class
subclass of: intra-settlement specification part of address
term editor: Mathias Brochhausen
definition: An intra-settlement specification part of address that is part of a biobank contact's postal address.
alternative term: Biobank contact address

hosted study collection
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: object aggregate
    intersection of: Restriction
      on property: has part
      all values from: specimen
  intersection of: Restriction
    on property: part of
    some values from: biobank
  intersection of: Restriction
    on property: participates in
    some values from: study design execution
definition: A object aggregate that consists of specimens, participates in a study and is part of a biobank.
alternative term: Hosted studies
term editor: Mathias Brochhausen

name of hosted study collection
type: Class
equivalent class: Class
  intersection of: identifier
  intersection of: Restriction
    on property: designates
    some values from: hosted study collection
subclass of: identifier
term editor: Mathias Brochhausen
definition: The proper name that designates a hosted study collection.

email address of sample collection or study contact
type: Class
equivalent class: Class
  intersection of: email address
  intersection of: Restriction
    on property: is contact information about
    some values from: Class
      intersection of: Homo sapiens
      intersection of: Class
        union of: Class
subclass of: email address
term editor: Mathias Brochhausen
definition: An email address for the purpose of contacting a sample collection or study contact person.
alternative term: Sample Collection/Study contact email

sample collection or study aim description
type: Class
equivalent class: Class
  intersection of: textual entity
  intersection of: Restriction
    on property: is about
    some values from: Class
      union of: Class
        intersection of: object aggregate
        intersection of: Restriction
      union of: Restriction
        on property: is about
        some values from: Class
subclass of: textual entity
definition: A textual entity describing a study aim or a sample collection.
term editor: Mathias Brochhausen
alternative term: Sample collection or study description

study proper name
type: Class
equivalent class: Class
  intersection of: identifier
  intersection of: Restriction
    on property: designates
    some values from: study design execution
subclass of: identifier
definition: A proper name that designates a study.
term editor: Mathias Brochhausen
alternative term: Study name

name of sample collection responsible or principal investigator
type: Class
equivalent class: Restriction
  on property: designates
  some values from: Class
    intersection of: Homo sapiens
    intersection of: Class
      union of: Class
        intersection of: Restriction
      union of: Class
        intersection of: Restriction
subclass of: personal name
definition: A personal name that designates the human being responsible for a sample collection or the human being being the principal investigator in a study.
term editor: Mathias Brochhausen
alternative term: Sample Collection Responsible / Principal Investigator

name of sample collection or study contact person
type: Class
equivalent class: Restriction
  on property: designates
  some values from: Class
    intersection of: Homo sapiens
    intersection of: Class
      union of: Class
        intersection of: Restriction
      union of: Class
        intersection of: Restriction
subclass of: personal name
term editor: Mathias Brochhausen
definition: A personal name that designates the person acting as contact for a sample collection or a study.
alternative term: Sample Collection/Study contact person

department of sample collection or study contact
type: Class
equivalent class: Class
  intersection of: department
  intersection of: Restriction
    on property: has organization member
    some values from: Class
      intersection of: Homo sapiens
      intersection of: Class
        union of: Class
subclass of: department
definition: Mathias Brochhausen
definition: A department that has a contact person for a sample collection or a study as an organizational member.
alternative term: Sample Collection/Study contact department

street
type: Class
subclass of: material entity
definition: A street is a thoroughfare in a built environment.
term editor: Mathias Brochhausen

intra-settlement specification part of address of sample collection or study contact
type: Class
equivalent class: Class
  intersection of: intra-settlement specification part of address
  intersection of: Restriction
    on property: part of
    some values from: Class
      intersection of: postal address
      intersection of: Restriction
        on property: is contact information about
        some values from: Class
subclass of: intra-settlement specification part of address
definition: An intra-settlement specification part of address that is part of a sample collection or study contact's postal address.
term editor: Mathias Brochhausen
definition: Sample Collection/Study contact address

postal code for sample collection or study contact
type: Class
equivalent class: Class
  intersection of: postal code
  intersection of: Restriction
    on property: part of
    some values from: Class
      intersection of: postal address
      intersection of: Restriction
        on property: is contact information about
        some values from: Class
subclass of: postal code
term editor: Mathias Brochhausen
definition: Postal code that is part of the address of a human being serving as sample collection or study contact.
alternative term: Sample Collection/Study contact ZIP

biobank location ISO 3166-1 alpha-2 code
type: Class
equivalent class: Class
  intersection of: ISO 3166-1 alpha-2 code
  intersection of: Restriction
    on property: designates
    some values from: Class
      intersection of: geographical location
      intersection of: Restriction
        on property: location of
        some values from: biobank
subclass of: ISO 3166-1 alpha-2 code
definition: An ISO 3166-1 alpha-2 code that designates the country a biobank is located in.
term editor: Mathias Brochhausen
alternative term: Biobank country code

CTEP organization identifier
type: Class
subclass of: identifier
subclass of: Restriction
  on property: designates
  some values from: organization
definition: An identifier for an organization that is assigned to that organization by the Cancer Therapy Evaluation Program.
term editor: Mathias Brochhausen

biobank identifier with ISO 3166-1 alpha-2 code and CTEP organization identifier
type: Class
subclass of: biobank idenfier with ISO 3166-1 alpha-2 code
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: ISO 3166-1 alpha-2 code
      intersection of: Class
        intersection of: CTEP organization identifier
        intersection of: Restriction
  intersection of: Restriction
    on property: designates
    some values from: biobank
definition: A biobank identifier that has both an ISO 3166-1 alpha-2 code and a CTEP organization code.
term editor: Mathias Brochhausen

bone marrow specimen
type: Class
subclass of: specimen
comment: Bone marrow contains two types of stem cells: haematopoietic (which can produce blood cells) and stromal (which can produce fat, cartilage and bone).
definition: A specimen that refers to the tissue at the center of large bones which is the place where new blood cells are produced.
definition source: http://www.who.int/transplantation/activities/GlobalGlossaryonDonationTransplantation.pdf
term editor: Alice Nzinga

fixed tissue specimen
type: Class
subclass of: processed specimen
subclass of: Restriction
  on property: is_specified_output_of
  some values from: fixation
definition: A processed specimen that is the output of a fixation process.
term editor: Alice Nzinga
term editor: Mathias Brochhausen

fixed tissue block specimen
type: Class
subclass of: fixed tissue specimen
definition: A fixed tissue specimen that is in block form.

fixed tissue slide specimen
type: Class
subclass of: fixed tissue specimen
definition: A fixed tissue specimen that is placed in a slide.

flash frozen specimen
type: Class
subclass of: frozen specimen
definition: A frozen specimen that has been instantly/quickly frozen by subjecting the specimen to cryogenic temperatures, or in direct contact with liquid nitrogen at -320.8F 0r -196C.
definition source: http://en.wikipedia.org/wiki/Flash_freezing

fresh tissue specimen
type: Class
subclass of: fresh specimen
definition: A fresh specimen that is in a tissue form.

frozen tissue block specimen
type: Class
subclass of: frozen specimen
definition: A frozen specimen is a tissue sample preserved in a block.

frozen tissue slide specimen
type: Class
subclass of: frozen specimen
definition: A frozen specimen that has been sliced from a tissue block into thin layers that are placed on a glass to be examined under a microscope.

microdissected specimen
type: Class
subclass of: specimen
definition: A specimen that has been procured from a histology slide under direct microscopic visualization.
term editor: Alice Nzinga
definition source: http://www.ncbi.nlm.nih.gov/pubmed/11269646

survey data
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  all values from: survey execution
subclass of: data item
definition: A data set that contains the outcome of a survey.
term editor: Alice Nzinga
term editor: Mathias Brochhausen

sampling specimens for biobank
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: object aggregate
      intersection of: Restriction
        on property: part of
        some values from: biobank
      intersection of: Restriction
        on property: has part
        all values from: Class
subclass of: planned process
term editor: Mathias Brochhausen
definition: The process of collecting or selecting an aggregate of specimens into a biobank.

biobank contact role
type: Class
subclass of: contact role
definition: A contact role borne by a member of a biobank organization and realized by serving as the contact for one of its biobanks.
definition: A contact role borne by a member of a sample collection or study organization and realized by serving as the contact for the collection or the study.

sample collection or study contact role
type: Class
subclass of: contact role

sample collection or study contact person
type: Class
equivalent class: Class
  intersection of: Homo sapiens
  intersection of: Class
    union of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: bearer of
        some values from: sample collection or study contact role
    union of: Class
      intersection of: Restriction
        on property: bearer of
        some values from: sample collection or study contact role
      intersection of: Restriction
        on property: participates in
        some values from: study design execution
subclass of: Homo sapiens
definition: A human being acting as bearing the contact role for a sample collection or a study.

study principle investigator or responsible
type: Class
equivalent class: Class
  intersection of: Homo sapiens
  intersection of: Class
    union of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: bearer of
        some values from: responsible party role
    union of: Class
      intersection of: Restriction
        on property: bearer of
        some values from: principal investigator role
      intersection of: Restriction
        on property: participates in
        some values from: study design execution
subclass of: Homo sapiens
definition: The principle investigtor or responsible person for a study or a sample collection.

specimen disease state datum
type: Class
subclass of: data item
subclass of: Restriction
  on property: is about
  some values from: specimen
definition: A data item that indicates the pathological assessment of a specimen.

diseased state specimen datum
type: Class
subclass of: specimen disease state datum
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: specimen
    intersection of: Restriction
      on property: has part
      some values from: disorder
definition: A specimen disease state datum item that specifies that the specimen in question consists of a disorder.

mixed state specimen datum
type: Class
subclass of: specimen disease state datum
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: specimen
    intersection of: Restriction
      on property: has part
      some values from: disorder
    intersection of: Restriction
      on property: has part
      some values from: normal specimen
definition: A specimen disease state datum that specifies that the specimen in question consists of partially normal tissue and a disorder.

normal state specimen datum
type: Class
subclass of: specimen disease state datum
subclass of: Restriction
  on property: is about
  some values from: normal specimen
definition: A specimen disease state datum that specifies that the specimenin questions consists of normal tissue.

obsolote_unknown state specimen data
type: Class
subclass of: Obsolete Class
definition: A specimen disease state data of the procured specimen that is unclear.
comment: This is a temporary state.

fixation
type: Class
subclass of: material processing
definition: A material processing that uses chemical process by which biological tissues are preserved from decay. Fixation terminates any ongoing biochemical reactions and may increase stability of the treated tissues.
comment: The choice of fixation depends on the type of study.
definition source: http://en.wikipedia.org/wiki/Fixation_%28histology%29
definition source: http://sharedresources.fhcrc.org/training/tips-about-fixation-and-formalin

addition of molecular label
type: Class
subclass of: material processing
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: Restriction
  on property: has_specified_output
  some values from: molecular-labeled material
subclass of: Restriction
  on property: has_specified_input
  some values from: molecular label
subclass of: Restriction
  on property: has_specified_input
  some values from: target of material addition
alternative term: labeling
definition source: OBI developer call, 3-12-12
term editor: PERSON: Matthew Brush
example of usage: The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies. The addition of anti-CD8-PE to a population of cells, to label the subpopulation cells that are CD8+.
definition: a material processing technique intended to add a molecular label to some input material entity, to allow detection of the molecular target of this label in a detection of molecular label assay
editor preferred term: addition of molecular label
has curation status: pending final vetting

age interval information
type: Class
subclass of: information content entity
subclass of: Class
  intersection of: information content entity
  intersection of: Restriction
    on property: is about
    some values from: Class
      intersection of: Restriction
        on property: part of
        some values from: data set
      intersection of: Restriction
        on property: is about
        some values from: Class
term editor: Alice Nzinga
definition: An information content entity that is about a data set that has age information and specifies the range of age information in that data set.
comment: Example: age interval is 18-65
term editor: Martin Fransson
term editor: Mathias Brochhausen

average age
type: Class
subclass of: Class
  intersection of: average value
  intersection of: Restriction
    on property: is about
    some values from: Class
      intersection of: Class
        intersection of: measurement data item
        intersection of: Restriction
      intersection of: Restriction
        on property: part of
        some values from: data set
term editor: Alice Nzinga
definition: An average value of age for a certain group of individuals.
term editor: Mathias Brochhausen

patient registry data
type: Class
subclass of: data set
subclass of: Restriction
  on property: is about
  some values from: Homo sapiens
definition: A data set of collected secondary data related to patients with a specific diagnosis, condition, or procedure and plays an important role in post marketing surveillance of pharmaceuticals.
term editor: Alice Nzinga
comment: It can be said to be a formal record of an internationally agreed minimum amount of information about clinical trial.
term editor: Martin Fransson
alternative term: patient register data

obsolete_survey data
type: Class
subclass of: Obsolete Class
definition: A data set that contains additional information about a group of individuals and is gathered through a survey.
term editor: Alice Nzinga
comment: The equivalent class restriction includes data combination since the the output of survey execution is from one participant, while the survey data is the combination of data gathered from multipe participants or multiple executions of the survey.

date of data entry
type: Class
subclass of: data item
subclass of: Class
  intersection of: data item
  intersection of: Restriction
    on property: is about
    some values from: Class
      intersection of: one-dimensional temporal region
      intersection of: Restriction
        on property: has part
        some values from: Class
disjoint with: date of data update
disjoint with: end date of sampling for biobank
disjoint with: start date of sampling for biobank
definition: A data item that indicates the time when data about the sample collection was reported into a database.
term editor: Alice Nzinga
comment: It is denoted by Date in ISO-standard (8601) time format.

date of data update
type: Class
subclass of: data item
subclass of: Class
  intersection of: data item
  intersection of: Restriction
    on property: is about
    some values from: Class
      intersection of: one-dimensional temporal region
      intersection of: Restriction
        on property: has part
        some values from: Class
disjoint with: end date of sampling for biobank
disjoint with: start date of sampling for biobank
definition: A data item that indicates the time when data about the sample collection was last updated in a database.
term editor: Alice Nzinga
comment: It is expressed as a Date in ISO-standard (8601) time format.

end date of sampling for biobank
type: Class
subclass of: data item
subclass of: Class
  intersection of: data item
  intersection of: Restriction
    on property: is about
    some values from: Class
      intersection of: one-dimensional temporal region
      intersection of: Restriction
        on property: has part
        some values from: Restriction
disjoint with: start date of sampling for biobank
definition: A data item that indicates the time when the sampling of specimens for a biobank ended.
term editor: Alice Nzinga
comment: It is denoted by Date in ISO-standard (8601) time format.

start date of sampling for biobank
type: Class
subclass of: data item
subclass of: Class
  intersection of: data item
  intersection of: Restriction
    on property: is about
    some values from: Class
      intersection of: one-dimensional temporal region
      intersection of: Restriction
        on property: has part
        some values from: Restriction
definition: A data item that indicates the time when the sampling of specimens for a biobank started.
term editor: Alice Nzinga
comment: It is denoted by Date in ISO-standard (8601) time format.

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

primary diagnosis
type: Class
subclass of: diagnosis
definition: A diagnosis that is the main reason for the inducement of medical care.
term editor: Alice Nzinga
definition source: Hint: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
alternative term: main diagnosis

count of current sampled human study participant
type: Class
subclass of: count
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: object aggregate
    intersection of: Restriction
      on property: has part
      all values from: Class
        intersection of: Homo sapiens
        intersection of: Restriction
disjoint with: physiological measurement data
definition: A count that is about the aggregate of individuals who have contributed biological specimens in a study.
term editor: Alice Nzinga

count of current total human study participant
type: Class
subclass of: count
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: object aggregate
    intersection of: Restriction
      on property: has part
      all values from: Class
        intersection of: Homo sapiens
        intersection of: Class
disjoint with: physiological measurement data
definition: A count that is about the aggregate of individuals who have been recruited to participate in a study.
term editor: Alice Nzinga

physiological measurement data
type: Class
subclass of: data item
subclass of: Class
  intersection of: data item
  intersection of: Restriction
    on property: is about
    some values from: Class
      union of: disease
      union of: disorder
      union of: treatment
      union of: Class
        intersection of: function
        intersection of: Restriction
definition: A measurement datum that contains the assessment information about the functioning of a major organ system, the extent of disease or disability,as well as the provision and/or response to therapeutic interventions.
term editor: Alice Nzinga
definition source: http://www.improvement.nhs.uk/physiologydiagnostics/documents/WhatisPhysiologicalMeasurement.pdf
comment: Examples: Audiology, Cardiac Physiology, GI Physiology, Neurophysiology, Ophthalmic and Vision Science, Respiratory and Sleep Physiology, Urodynamics, Vascular Technology
term editor: Mathias Brochhausen

storage temperature setting
type: Class
subclass of: setting datum
definition: A setting datum that specifies the temperature inside a container participating in a storage process.
term editor: Alice Nzinga
comment: Examples: -18 °C to -35 °C, -60 °C to -85 °C, Liquid nitrogen, Room temperature etc
term editor: Mathias Brochhausen

omics experiment on specimen
type: Class
subclass of: planned process
subclass of: Class
  intersection of: planned process
  intersection of: Restriction
    on property: realizes
    some values from: Restriction
      on property: concretizes at some time
      some values from: study design
  intersection of: Restriction
    on property: has participant
    some values from: specimen
comment: A tentative procedure that is aimed at discovering some characteristic of a large familiy of cellular molecules, having named by appending suffix "-omics."
term editor: Alice Nzinga
definition: An objective specification that aims at the collective characterization and quantification of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms.
term editor: Mathias Brochhausen
definition: Technologies that measure some characteristic of a large family of cellular molecules, such as genes, proteins, or small metabolites, have been named by appending the suffix "-omics," as in "genomics." Omics refers to the collective technologies used to explore the roles, relationships, and actions of the various types of molecules that make up the cells of an organism.
definition source: http://en.wikipedia.org/wiki/Omics
comment: interrelated experiments.

number of sampled human study participants objective
type: Class
subclass of: objective specification
subclass of: Restriction
  on property: part of
  some values from: study design
disjoint with: number of total human study participant objective
term editor: Alice Nzinga
definition: An objective specification that specifies the number of individuals to participate in a study and provide biological specimens to the study.
term editor: Mathias Brochhausen

number of total human study participant objective
type: Class
subclass of: objective specification
subclass of: Restriction
  on property: part of
  some values from: study design
term editor: Alice Nzinga
definition: An objective specification that specifies the total number of individuals who are planned to participate in study.

case control study design
type: Class
subclass of: study design
disjoint with: cross sectional study design
disjoint with: longitudinal study design
disjoint with: population based study design
disjoint with: quality control study design
disjoint with: twin study design
definition: A study design that compares two groups of subjects; those with the disease or condtion under study and a similar group of subjects who do not have the condition.
term editor: Alice Nzinga

cross sectional study design
type: Class
subclass of: study design
disjoint with: longitudinal study design
disjoint with: population based study design
disjoint with: quality control study design
disjoint with: twin study design
definition: A study design in which all participants or a representative subset of participants are examined at only a single time for characteristics of a interest (e.g. a specific disease).
term editor: Alice Nzinga

longitudinal study design
type: Class
subclass of: study design
disjoint with: population based study design
disjoint with: quality control study design
disjoint with: twin study design
definition: A study design that involves repeated observations of the same entity over time. In the biobank context, longitudinal studies sample a group of people in a given time period, and study them at intervals by the acquisition and analyses of data and/or samples over time.
term editor: Alice Nzinga

cohort study design
type: Class
subclass of: longitudinal study design
disjoint with: panel study design
definition: A longitudinal study that aims to study a case-defined population who presently have a certain condition or recepient of a particular treatment that are followed over time and are compared with a similar group who do not have condition.

panel study design
type: Class
subclass of: longitudinal study design
definition: A longitudinal study that samples a cross-section and studies it at regular intervals.

population based study design
type: Class
subclass of: study design
disjoint with: quality control study design
disjoint with: twin study design
definition: A study design that is multidisciplinary done at the population level or among the population groups, generally to find the cause, incidence or spread of the disease or to see the response to the treatment, nutrition or environment.
term editor: Alice Nzinga

quality control study design
type: Class
subclass of: study design
disjoint with: twin study design
definition: A study design where some aspect of the experiment is quality controlled for the purposes of quality assurance.
term editor: Alice Nzinga

twin study design
type: Class
subclass of: study design
definition: A study design usually in behavior genetics which aids the study of individual differences between genetically identical twins by highlighting the role of environmental and genetic causes on behavior.
term editor: Alice Nzinga

survey plan specification
type: Class
subclass of: plan specification
definition: A plan specification that is realized by process of gathering information (e.g. by asking questions).
term editor: Alice Nzinga
term editor: Mathias Brochhausen

medical record
type: Class
subclass of: document
comment: It is a chronological written account of examination, treatment, medical history or complaints.
term editor: Martin Fransson
definition: A document that contains information representing health-relevant qualities of a patient written in a chronological manner and that is primarily used for patient care in a clinical setting.
comment: It is used interchangeably with health record and medical chart. https://en.wikipedia.org/wiki/Medical_record

sample medical record
type: Class
subclass of: medical record
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: Homo sapiens
    intersection of: Class
      intersection of: Restriction
        on property: has role
        some values from: participant under investigation role
      intersection of: Restriction
        on property: has role
        some values from: donor
definition: A medical record of a specimen donor.
term editor: Alice Nzinga

sample handling summary
type: Class
equivalent class: Restriction
  on property: is about
  some values from: sample handling
subclass of: document
definition: A document that outlines the procedures employed to preserve and protect the material collected during specimen collection as an indication of sample quality.
term editor: Alice Nzinga
comment: It could be argued as to why this class was not created as an 'objective specification'. However, the emphasis here is to 'a briefing of how the specimen in the sample collection have been handled as an indication of specimen quality.'
comment: It could be freeze chain, freze time, SPREC compliant, etc.

age interval information for sampled donors
type: Class
subclass of: age interval information
subclass of: Class
  intersection of: information content entity
  intersection of: Restriction
    on property: is about
    some values from: Restriction
      on property: part of
      some values from: Class
        intersection of: data set
        intersection of: Restriction
term editor: Alice Nzinga
definition: Age interval information that is age information of specimen donors.
definition source: http://www.abta.org/Dictionary/67
alternative term: sampled group age interval

donor patient registry data
type: Class
subclass of: patient registry data
subclass of: Restriction
  on property: is about
  some values from: donor
term editor: Alice Nzinga
definition: Registry data for a patient who participates as a donor in a study.

study subject survey data
type: Class
subclass of: Class
  intersection of: survey data
  intersection of: Restriction
    on property: is about
    some values from: Class
      intersection of: Restriction
        on property: bearer of
        some values from: participant under investigation role
      intersection of: Restriction
        on property: bearer of
        some values from: donor
definition: A survey data for a specimen donor.
term editor: Alice Nzinga
comment: Examples: Individual Disease History, Individual History of Injuries, Medication, Perception of Health, Women's Health, Reproductive History, Familial Disease History, Life Habits/Behaviors, Sociodemographic Characteristics, Socioeconomic Characteristics, Physical Environment, Mental Health, Other.
term editor: Mathias Brochhausen

sample collection data entry
type: Class
subclass of: planned process
definition: A planned process that involves the initial entering of data about sample collection into a database.

sample collection data update
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: date of data update
definition: A planned process which involves editing of specimen collection data into a database after its initial entry.

survey execution
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: realizes
    some values from: Restriction
      on property: concretizes at some time
      some values from: survey plan specification
  intersection of: Restriction
    on property: has_specified_output
    some values from: survey data
subclass of: planned process
definition: A planned process that realizes the concretization of a survey to generate an output(survey data.)

temperature regulating
type: Class
subclass of: planned process
comment: As per placing the term as a planned process, it can be argued that nature does play a role in the final output of the actual temperature.
definition: A planned process that aims to control or maintain the temperature of a material entity to a given or required measurement datum.

comment from tissue procurement
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: Class
    union of: sampling specimens for biobank
    union of: Restriction
      on property: participates in
      some values from: sampling specimens for biobank
comment: A textual entity that states additional information about the specimen or donor that is deemed relevant for the specimen collection process.
definition source: Alice Nzinga

specimen measurement
type: Class
subclass of: measurement data item
subclass of: Class
  intersection of: measurement data item
  intersection of: Restriction
    on property: has part
    some values from: length measurement datum
  intersection of: Restriction
    on property: is about
    some values from: specimen
example of usage: 3mm X 3mm X 3mm
definition: A measurement datum that is the result of measurement of the three dimensions of a specimen.
term editor: Alice Nzinga
term editor: Mathias Brochhausen

date of specimen collection
type: Class
subclass of: data item
subclass of: Class
  intersection of: data item
  intersection of: Restriction
    on property: is about
    some values from: Class
      intersection of: one-dimensional temporal region
      intersection of: Restriction
        on property: has part
        some values from: Class
definition: A data item that indicates the time when the collection of a specimen occurred.
term editor: Alice Nzinga
comment: It is denoted by Date in ISO-standard (8601) time format.
term editor: Mathias Brochhausen
alternative term: date of specimen preparation

specimen meeting specification
type: Class
subclass of: specimen
definition source: All specimens that meet the set parameters to be procured on.
term editor: Mathias Brochhausen
alternative term: adherance to specification

surgical procedure
type: Class
subclass of: planned process
definition: A planned process that uses operative manual and instrumental techniques on a patient to investigate and/or treat a pathological condition such as disease or injury, or to help improve bodily function or appearance.
definition source: http://en.wikipedia.org/wiki/Surgery
example of usage: mastectomy / craniotomy / liver resection e.t.c.

specimen preparation contact
type: Class
subclass of: personal name
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: Homo sapiens
    intersection of: Class
      union of: Restriction
        on property: participates in
        some values from: specimen collection
      union of: Restriction
        on property: participates in
        some values from: material maintenance
    intersection of: Restriction
      on property: bearer of
      some values from: contact role
definition: A personal name that designates the person who prepared the specimen.
term editor: Alice Nzinga

time in formalin measurement
type: Class
subclass of: time measurement datum
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: Class
      union of: one-dimensional temporal region
      union of: zero-dimensional temporal region
    intersection of: Restriction
      on property: has temporal occupant
      some values from: Class
        intersection of: sample handling
        intersection of: Restriction
example of usage: 15min
definition: A time measurement datum that states the duration during which a specimen was submerged in formalin.
term editor: Alice Nzinga

specimen surgical removal
type: Class
subclass of: collecting specimen from organism
definition: A collecting specimen from organism process that involves removing the specimen from an individual through a surgical procedure.

specimen freezing
type: Class
equivalent class: Class
  intersection of: freezing storage
  intersection of: Restriction
    on property: has participant
    some values from: specimen
subclass of: freezing storage
definition: A freezing storage for the specimen.

specimen ID
type: Class
subclass of: identifier
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: CRID
  intersection of: Restriction
    on property: is about
    some values from: specimen
definition: A proper name that identifies a specimen and is usually in form of a label included in the specimen cassette.
term editor: Alice Nzinga
definition source: http://biospecimens.cancer.gov/resources/sops/GTEx_SOPs/II/A/GTEx%20Tissue%20Procurement%20SOP%20%28PR-0004%20v1.2.1%29.pdf

case ID
type: Class
subclass of: identifier
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: Homo sapiens
    intersection of: Restriction
      on property: participates in
      some values from: specimen collection
    intersection of: Restriction
      on property: has role
      some values from: donor
term editor: Alice Nzinga
definition: An identifier that refers to a specimen donor who is participating in specimen collection process for tissue procurement purposes and is usually assigned at the time of donor procurement.
definition source: http://biospecimens.cancer.gov/resources/sops/GTEx_SOPs/II/A/GTEx%20Tissue%20Procurement%20SOP%20%28PR-0004%20v1.2.1%29.pdf

specimen measurement specification
type: Class
subclass of: objective specification
comment: A specification (often abbreviated as spec) may refer to an explicit set of requirements to be satisfied by a material, design, product, or service.
term editor: Alice Nzinga
definition: An directive information entity that states the technical standard measurement set and values that determines if a specimen qualifies for procurement or not.
definition source: http://en.wikipedia.org/wiki/Specification_(technical_standard)

time of specimen freezing
type: Class
subclass of: data item
subclass of: Class
  intersection of: data item
  intersection of: Restriction
    on property: is about
    some values from: Class
      intersection of: one-dimensional temporal region
      intersection of: Restriction
        on property: has temporal occupant
        some values from: specimen freezing
definition: A data item that reports the time when a specimen was frozen.
term editor: Alice Nzinga
term editor: Mathias Brochhausen

time of surgical removal of specimen
type: Class
subclass of: data item
subclass of: Class
  intersection of: data item
  intersection of: Restriction
    on property: is about
    some values from: Class
      intersection of: one-dimensional temporal region
      intersection of: Restriction
        on property: has temporal occupant
        some values from: specimen surgical removal
definition: A data item that reports the time when a specimen was collected by a surgical procedure.
term editor: Alice Nzinga
term editor: Mathias Brochhausen

normal specimen
type: Class
equivalent class: Class
  intersection of: specimen
  intersection of: Class
    complement of: Restriction
      on property: has part
      some values from: disorder
subclass of: specimen
definition: A specimen that is normal.

cerebrospinal fluid specimen
type: Class
subclass of: specimen
comment: Abbreviated as 'CSF'.
definition: A specimen that refers to a portion of a fluid largely secreted by the choroid plexuses of the ventricles of the brain, filling the ventricles and the subarachnoid cavities of the brain and spinal cord, collected from an organism.
term editor: Alice Nzinga
definition source: http://www.ncbi.nlm.nih.gov/books/NBK398/

faeces specimen
type: Class
subclass of: specimen
definition: A specimen that comprises of a portion of faeces collected from an organism.
term editor: Alice Nzinga

saliva specimen
type: Class
subclass of: specimen
definition: A specimen consisting of a portion of saliva collected from an organism.
term editor: Alice Nzinga
comment: It is a clear, tasteless, odorless, slightly acidic (pH 6.8) viscid fluid, secreted from the parotid, sublingual, and submandibular salivary glands and the mucous glands of the oral cavity.

hosting biobank
type: Class
equivalent class: Class
  intersection of: biobank
  intersection of: Restriction
    on property: participates in
    some values from: Class
      intersection of: specimen collection
      intersection of: Restriction
        on property: part of
        some values from: study design execution
subclass of: biobank
definition: A biobank that collects and stores specimen during specimen collection primarily for the purposes of some study.
term editor: Alice Nzinga

specimen donor
type: Class
equivalent class: Class
  intersection of: Homo sapiens
  intersection of: Restriction
    on property: bearer of
    some values from: Class
      intersection of: role
      intersection of: Restriction
        on property: realized in
        some values from: specimen collection
subclass of: Homo sapiens
comment: A Homo sapiens who contributes specimen.
term editor: Alice Nzinga
term editor: Mathias Brochhausen
alternative term: sample donor

sample handling
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Class
    intersection of: Restriction
      on property: has_specified_input
      some values from: Restriction
        on property: is_specified_output_of
        some values from: specimen collection
    intersection of: Restriction
      on property: has_specified_output
      some values from: Class
        intersection of: specimen
        intersection of: Restriction
subclass of: planned process
definition: A planned process of preparing and submitting specimens to storage.
definition source: http://www.exchangenetwork.net/standards/SampleHandling_01_06_2006_Final.pdf
alternative term: specimen handling

start of sampling specimens for biobank
type: Class
subclass of: process boundary
subclass of: Restriction
  on property: part of
  some values from: sampling specimens for biobank
term editor: Mathias Brochhausen
definition: The process boundary marking the beginning of a sampling of specimens into a biobank.

end of sampling specimens for biobank
type: Class
subclass of: process boundary
subclass of: Restriction
  on property: part of
  some values from: sampling specimens for biobank
term editor: Mathias Brochhausen
definition: The process boundary marking the end of a sampling of specimens into a biobank.

collection of humans
type: Class
subclass of: collection of organisms
imported from: omrse.owl

role in human social processes
type: Class
subclass of: role
definition: A role inhering in an entity realized by social interactions in human society.
imported from: omrse.owl

aggregate of organizations
type: Class
subclass of: object aggregate
definition: An object aggregate that is not itself an organization and whose members are only organizations that have some feature in common
imported from: omrse.owl

legal person role
type: Class
subclass of: role in human social processes
definition: A role borne by a human individual or by a collection of humans regarded as possessing rights and duties enforeable at law.
imported from: omrse.owl

age
type: Class
subclass of: quality of a single physical entity
definition: A time quality inhering in a bearer by virtue of how long the bearer has existed.
imported from: pato.owl

biological sex
type: Class
subclass of: quality
subclass of: physical object quality
subclass of: organismal quality
definition: An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved.
editor preferred term: biological sex
imported from: pato.owl

size
type: Class
subclass of: physical object quality
definition: A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude.
editor preferred term: size
imported from: pato.owl

height
type: Class
subclass of: size
definition: A 1-D extent quality inhering in a bearer by virtue of the bearer's vertical dimension of extension.
editor preferred term: height
imported from: pato.owl

length
type: Class
subclass of: quality
editor preferred term: length
definition: A 1-D extent quality which is equal to the distance between two points.
imported from: pato.owl

weight
type: Class
subclass of: physical quality
definition: A physical quality inhering in a bearer that has mass near a gravitational body.
editor preferred term: weight
imported from: pato.owl

temperature
type: Class
subclass of: quality of a single physical entity
definition: A physical quality of the thermal energy of a system.
imported from: pato.owl

female
type: Class
subclass of: biological sex
definition: A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes.
imported from: pato.owl

male
type: Class
subclass of: biological sex
definition: A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes.
imported from: pato.owl

volume
type: Class
subclass of: size
subclass of: quality of a single physical entity
definition: A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies.
editor preferred term: volume
imported from: pato.owl

physical quality
type: Class
subclass of: physical object quality
definition: A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
editor preferred term: physical quality
imported from: pato.owl

pressure
type: Class
subclass of: quality of a single physical entity
definition: A physical quality that inheres in a bearer by virtue of the bearer's amount of force per unit area it exerts.
imported from: pato.owl

quality of a single physical entity
type: Class
subclass of: quality
definition: A physical object quality which inheres in a single-bearer.
editor preferred term: quality of a single physical entity
imported from: pato.owl

physical object quality
type: Class
subclass of: quality
definition: A quality which inheres in a continuant.
editor preferred term: physical object quality
imported from: pato.owl

hermaphrodite
type: Class
subclass of: biological sex
definition: A biological sex quality inhering in an organism or a population with both male and female sexual organs in one individual.
imported from: pato.owl

alive
type: Class
subclass of: quality of a single physical entity
definition: A viability quality inhering in a bearer by virtue of the bearer's condition before death.
editor preferred term: alive
imported from: pato.owl

dead
type: Class
subclass of: quality of a single physical entity
definition: A viability quality inhering in a bearer by virtue of the cessation of the bearer's life.
editor preferred term: dead
imported from: pato.owl

frozen
type: Class
subclass of: physical quality
subclass of: quality of a single physical entity
definition: A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point.
editor preferred term: frozen
imported from: pato.owl

organismal quality
type: Class
subclass of: quality
definition: A quality that inheres in an entire organism or part of an organism.
editor preferred term: organismal quality
imported from: pato.owl

collection of organisms
type: Class
subclass of: object aggregate
definition: A material entity that consists of two or more organisms, viruses, or viroids.
imported from: pco.owl

molecular label role
type: Class
subclass of: role
editor note: MHB (9-29-13): 'molecular label role' imported from the Reagent Ontology and replaced OBI:OBI_0000140 (label role)
definition: a reagent role inhering in a molecular entity intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay.
definition source: OBI developer call, 3-12-12
editor preferred term: molecular label role
alternative term: molecular tracer role
imported from: reo.owl

molecular label
type: Class
equivalent class: Class
  intersection of: molecular entity
  intersection of: Restriction
    on property: has role
    some values from: molecular label role
subclass of: molecular entity
editor preferred term: molecular label
definition: a molecular reagent intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay
definition source: OBI developer call, 3-12-12
alternative term: molecular tracer
imported from: reo.owl

blood
type: Class
subclass of: portion of organism substance
definition: Circulating body substance which consists of blood plasma and hemoglobin-carrying red blood cells. Excludes blood analogues (see UBERON:0000179 haemolymphatic fluid).
editor preferred term: blood
imported from: uberon.owl

urine
type: Class
subclass of: portion of organism substance
definition: Excretion in liquid state processed by the kidney.[FMA]
editor preferred term: urine
imported from: uberon.owl

time unit
type: Class
subclass of: measurement unit label
definition: A unit which is a standard measure of the dimension in which events occur in sequence.
editor preferred term: time unit
imported from: uo.owl

Laboratory
type: Class
subclass of: organization
definition: An organizational unit (as opposed to the physical facility) that performs research, provides services, or processes materials
editor preferred term: Laboratory
imported from: ero.owl

smoking behavior
type: Class
subclass of: biological_process
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: cigarette
    union of: cigar
    union of: pipe tobacco
alternative term: smoking
editor preferred term: smoking behavior
imported from: efo.owl

chewing tobacco behavior
type: Class
subclass of: biological_process
subclass of: Restriction
  on property: has_specified_input
  some values from: chewing tobacco
editor preferred term: chewing tobacco behavior
imported from: efo.owl

Obsolete Class
type: Class
subclass of: Thing
editor preferred term: Obsolete Class

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

failed exploratory term
type: Thing
type: obsolescence reason specification
type: NamedIndividual
term 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
editor preferred term: failed exploratory term

metadata complete
type: Thing
type: curation status specification
type: NamedIndividual
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.
editor preferred term: metadata complete

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

ready for release
type: Thing
type: curation status specification
type: NamedIndividual
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."
editor preferred term: ready for release
has curation status: pending final vetting

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

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

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

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

placeholder removed
type: Thing
type: obsolescence reason specification
type: NamedIndividual
editor preferred term: placeholder removed

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.
editor preferred term: terms merged

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.
editor preferred term: term imported

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.
editor preferred term: term split

universal
type: NamedIndividual
type: denotator type
definition source: A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
term 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.
editor preferred term: universal

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.
term editor: A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
term editor: Alan Ruttenberg
editor preferred term: defined class

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.
term editor: Alan Ruttenberg
editor preferred term: named class expression
editor note: named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions

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

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.
term editor: Alan Ruttenberg
definition source: group:OBI
editor preferred term: requires discussion

axiom holds for all times
type: NamedIndividual

BFO_0000134
elucidation: To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003])
elucidation: To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003])

Axiom
annotated target: To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003])
annotated source: BFO_0000134
annotated property: elucidation
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/081-003

Axiom
annotated target: To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003])
annotated source: BFO_0000134
annotated property: elucidation
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/080-003

bfo-spec-label
definition source: Person:Alan Ruttenberg

Class
intersection of: one-dimensional temporal region
intersection of: Restriction
  on property: has temporal occupant
  on class: history
  qualified cardinality: 1

Class
intersection of: one-dimensional temporal region
intersection of: Restriction
  on property: has temporal occupant
  on class: history
  qualified cardinality: 1

Restriction
on property: is about
some values from: Class
  intersection of: one-dimensional temporal region
  intersection of: Restriction
    on property: has temporal occupant
    on class: history
    qualified cardinality: 1

Restriction
on property: is about
some values from: Class
  intersection of: one-dimensional temporal region
  intersection of: Restriction
    on property: has temporal occupant
    on class: Class
      intersection of: history
      intersection of: Restriction
        on property: history of
        some values from: specimen donor
    qualified cardinality: 1