Hypertension Ontology For Clinical Data
type: Ontology
creator: Mark A. Miller
creation date: 2019-05-20
creator: Amanda Hicks
creator: Chris Stoeckert
creator: Danielle Mowery

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

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

has measurement unit label
type: AnnotationProperty
range: measurement unit label
type: ObjectProperty
sub property of: has_part
type: FunctionalProperty
domain: measurement datum

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

example of usage
type: AnnotationProperty
editor preferred label: example
editor preferred label: example of usage
definition: A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not
definition: A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

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

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

definition
type: AnnotationProperty
editor preferred label: definition
editor preferred label: textual definition
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.
editor note: 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
label: textual definition

editor note
type: AnnotationProperty
editor preferred label: editor note
definition: An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obfoundry.org/obo/obi>

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

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

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

mentions
type: AnnotationProperty
range: entity
type: ObjectProperty
sub property of: is about
definition: An information artifact IA mentions an entity E exactly when it has a component/part that denotes E
editor note: 7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation "mentions" in it's (logical) definition
editor note: 7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity)
definition editor: Person: Alan Ruttenberg
definition editor: PERSON: Jonathan Rees

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

curator note
type: AnnotationProperty
editor preferred label: curator note
definition: An administrative note of use for a curator but of no use for a user
definition editor: PERSON:Alan Ruttenberg

term tracker item
type: AnnotationProperty
editor preferred label: term tracker item
example of usage: the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
definition: An IRI or similar locator for a request or discussion of an ontology term.
definition editor: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
definition source: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
comment: The 'tracker item' can associate a tracker with a specific ontology term.

ontology term requester
type: AnnotationProperty
definition: The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
definition editor: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
definition source: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
comment: The 'term requester' can credit the person, organization or project who request the ontology term.

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

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

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

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

first order logic expression
type: AnnotationProperty
editor preferred label: first order logic expression
definition: An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property.
definition editor: PERSON:Alan Ruttenberg
sub property of: logical macro assertion on an object property

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

obo foundry unique label
type: AnnotationProperty
editor preferred label: OBO foundry unique label
definition: An alternative name for a class or property which is unique across the OBO Foundry.
editor note: The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Bjoern Peters
definition editor: PERSON:Chris Mungall
definition editor: PERSON:Melanie Courtot
definition source: GROUP:OBO Foundry <http://obofoundry.org/>
label: OBO foundry unique label

has ID digit count
type: AnnotationProperty
example of usage: Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"
definition: Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits)
definition editor: Person:Alan Ruttenberg

has ID range allocated to
type: AnnotationProperty
example of usage: Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300]
definition: Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms
definition editor: Person:Alan Ruttenberg

has ID policy for
type: AnnotationProperty
example of usage: Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"
definition: Relating an ontology used to record id policy to the ontology namespace whose policy it manages
definition editor: Person:Alan Ruttenberg

has ID prefix
type: AnnotationProperty
example of usage: Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"
definition: Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created.
definition editor: Person:Alan Ruttenberg

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

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

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

is allocated id range
type: AnnotationProperty
editor preferred label: is allocated id range
definition: Add as annotation triples in the granting ontology
definition: Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999"
definition editor: PERSON:Alan Ruttenberg

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

has axiom label
type: AnnotationProperty
editor preferred label: has axiom id
definition editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI

term replaced by
type: AnnotationProperty
editor preferred label: term replaced by
definition: Add as annotation triples in the granting ontology
definition: Use on obsolete terms, relating the term to another term that can be used as a substitute
definition editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg

has material basis in
type: AnnotationProperty
type: ObjectProperty
imported from: doid.owl

is_specified_input_of
type: AnnotationProperty
range: planned process
type: ObjectProperty
domain: entity
domain: continuant

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

bearer of
type: AnnotationProperty
range: specifically dependent continuant
type: ObjectProperty
domain: independent continuant
alternative term: is bearer of
definition: a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
editor preferred label: bearer of
imported from: cl.owl
example of usage: this vase is bearer of this fragility
alternative term: bearer_of
imported from: hp.owl
example of usage: this apple is bearer of this red color
editor note: A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.

has_quality
type: AnnotationProperty
range: quality
type: ObjectProperty
sub property of: bearer of
domain: independent continuant
label: has quality
example of usage: this apple has quality this red color
is transitive: false
shorthand: has_quality
alternative term: has_quality
imported from: pr.owl
definition: a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
has_obo_namespace: protein
database_cross_reference: RO:0000086
id: has_quality
editor note: A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.

disposition of
type: AnnotationProperty
range: independent continuant
type: ObjectProperty
sub property of: inheres in
domain: disposition
definition: inverse of has disposition
in_subset: defined by inverse

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

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

mutually spatially disjoint with
type: AnnotationProperty
definition: A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B.
alternative term: non-overlapping with
alternative term: shares no parts with
definition source: http://www.ncbi.nlm.nih.gov/pubmed/22293552
expand assertion to: Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y)
sub property of: logical macro assertion on a class

taxonomic class assertion
type: AnnotationProperty
definition: An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon.
sub property of: logical macro assertion on a class

ambiguous for taxon
type: AnnotationProperty
definition: S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg]
sub property of: taxonomic class assertion

dubious for taxon
type: AnnotationProperty
definition: S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T.
definition editor: https://orcid.org/0000-0002-6601-2165
definition source: http://www.ncbi.nlm.nih.gov/pubmed/22293552
comment: This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost
sub property of: taxonomic class assertion

present in taxon
type: AnnotationProperty
definition: S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S
definition editor: https://orcid.org/0000-0002-6601-2165
definition source: http://www.ncbi.nlm.nih.gov/pubmed/22293552
sub property of: taxonomic class assertion

defined by inverse
type: AnnotationProperty
sub property of: subset_property

logical macro assertion
type: AnnotationProperty
definition: An assertion that involves at least one OWL object 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.

annotation property cardinality
type: AnnotationProperty
definition: An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N.
sub property of: logical macro assertion on an annotation property
range: nonNegativeInteger

logical macro assertion on a class
type: AnnotationProperty
definition: A logical macro assertion whose domain is an IRI for a class
editor note: The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL
sub property of: logical macro assertion

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

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

dispositional interpretation
type: AnnotationProperty
definition: An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one.
sub property of: logical macro assertion on an object property

has no connections with
type: AnnotationProperty
example of usage: 'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton'
definition: A is has_no_connections_with B if there are no parts of A or B that have a connection with the other.
alternative term: shares no connection with
expand assertion to: Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y))
sub property of: logical macro assertion on a class

inherited annotation property
type: AnnotationProperty

curator guidance link
type: AnnotationProperty
definition: Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of)
sub property of: inherited annotation property

always present in taxon
type: AnnotationProperty
example of usage: brain always_present_in_taxon 'Vertebrata'
example of usage: forelimb always_present_in_taxon Euarchontoglires
definition: S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S
editor note: This is a very strong relation. Often we will not have enough evidence to know for sure that there are no species within a lineage that lack the structure - loss is common in evolution. However, there are some statements we can make with confidence - no vertebrate lineage could persist without a brain or a heart. All primates are limbed.
alternative term: never lost in
sub property of: present in taxon

temporal logical macro assertion on a class
type: AnnotationProperty
curator note: This properties were created originally for the annotation of developmental or life cycle stages, such as for example Carnegie Stage 20 in humans.
sub property of: logical macro assertion on a class

measurement property has unit
type: AnnotationProperty
sub property of: logical macro assertion on an annotation property

has start time value
type: AnnotationProperty
sub property of: temporal logical macro assertion on a class

has end time value
type: AnnotationProperty
sub property of: temporal logical macro assertion on a class

start, days post fertilization
type: AnnotationProperty
definition: Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property.
sub property of: has start time value

end, days post fertilization
type: AnnotationProperty
definition: Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property.
sub property of: has end time value

start, years post birth
type: AnnotationProperty
definition: Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1.
sub property of: has start time value

end, years post birth
type: AnnotationProperty
definition: Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2
sub property of: has end time value

start, months post birth
type: AnnotationProperty
definition: Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1.
sub property of: has start time value

end, months post birth
type: AnnotationProperty
definition: Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2
sub property of: has end time value

month of gestation
type: AnnotationProperty
definition: Defines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. Thus if month_of_gestation=3, then the stage is 2 month in.
sub property of: temporal logical macro assertion on a class

has developmental stage marker
type: AnnotationProperty
definition: A relationship between a stage class and an anatomical structure or developmental process class, in which the stage is characterized by the appearance of the structure or the occurrence of the biological process
sub property of: temporal logical macro assertion on a class

start, days post coitum
type: AnnotationProperty
definition: Count of number of days intervening between the start of the stage and the time of coitum.
curator note: For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum)
sub property of: has start time value

end, days post coitum
type: AnnotationProperty
definition: Count of number of days intervening between the end of the stage and the time of coitum.
sub property of: has end time value

start, weeks post birth
type: AnnotationProperty
sub property of: has start time value

end, weeks post birth
type: AnnotationProperty
sub property of: has end time value

is asymmetric relational form of process class
type: AnnotationProperty
definition: If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x subject-partner-in p, y object-partner-in p
sub property of: is relational form of process class

is symmetric relational form of process class
type: AnnotationProperty
definition: If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p
sub property of: is relational form of process class

is relational form of process class
type: AnnotationProperty
definition: R is the relational form of a process if and only if either (1) R is the symmetric relational form of a process or (2) R is the asymmetric relational form of a process
sub property of: is relational form of a class

is direct form of
type: AnnotationProperty
definition: relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y
editor note: The general property hierarchy is: "directly P" SubPropertyOf "P" Transitive(P) Where we have an annotation assertion "directly P" "is direct form of" "P"
logical macro assertion on an annotation property: If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q'
creator: Chris Mungall
sub property of: logical macro assertion on an object property

is indirect form of
type: AnnotationProperty
definition: relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y
creator: Chris Mungall
sub property of: logical macro assertion on an object property

logical macro assertion on an axiom
type: AnnotationProperty
sub property of: logical macro assertion

is a defining property chain axiom
type: AnnotationProperty
definition: If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL
sub property of: logical macro assertion on an axiom

is a defining property chain axiom where second argument is reflexive
type: AnnotationProperty
definition: If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.
sub property of: is a defining property chain axiom

is relational form of a class
type: AnnotationProperty
definition: An annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis.
sub property of: logical macro assertion on an object property

logical macro assertion involving identity
type: AnnotationProperty
definition: A shortcut relationship that holds between two entities based on their identity criteria
sub property of: logical macro assertion

in approximate one to one relationship with
type: AnnotationProperty
definition: A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds.
sub property of: logical macro assertion involving identity

is approximately equivalent to
type: AnnotationProperty
definition: x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y
curator note: The precise meaning of this property is dependent upon some contexts. It is intended to group multiple possible formalisms. Possibilities include a probabilistic interpretation, for example, Pr(x=y) > 0.95. Other possibilities include reified statements of belief, for example, "Database D states that x=y"
sub property of: in approximate one to one relationship with

is opposite of
type: AnnotationProperty
example of usage: 'anterior end of organism' is-opposite-of 'posterior end of organism'
example of usage: 'increase in temperature' is-opposite-of 'decrease in temperature'
definition: x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x).
sub property of: in approximate one to one relationship with

is indistinguishable from
type: AnnotationProperty
definition: x is indistinguishable from y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x).
sub property of: is approximately equivalent to

evidential logical macro assertion on an axiom
type: AnnotationProperty
sub property of: logical macro assertion on an axiom

axiom has evidence
type: AnnotationProperty
definition: A relationship between a sentence and an instance of a piece of evidence in which the evidence supports the axiom
curator note: This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual.
sub property of: evidential logical macro assertion on an axiom

axiom contradicted by evidence
type: AnnotationProperty
definition: A relationship between a sentence and an instance of a piece of evidence in which the evidence contradicts the axiom
curator note: This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual.
sub property of: evidential logical macro assertion on an axiom

is representative IRI for equivalence set
type: AnnotationProperty
example of usage: In the context of a particular project, the IRI with CURIE NCBIGene:64327 (which in this example denotes a class) is considered to be representative. This means that if we have equivalent classes with IRIs OMIM:605522, ENSEMBL:ENSG00000105983, HGNC:13243 forming an equivalence set, the NCBIGene is considered the representative member IRI. Depending on the policies of the project, the classes may be merged, or the NCBIGene IRI may be chosen as the default in a user interface context.
definition: this property relates an IRI to the xsd boolean value "True" if the IRI is intended to be the representative IRI for a collection of classes that are mutually equivalent.
curator note: If it is necessary to make the context explicit, an axiom annotation can be added to the annotation assertion
see also: OWLAPI Reasoner documentation for representativeElement, which follows a similar idea, but selects an arbitrary member
sub property of: logical macro assertion involving identity

has_rank
type: AnnotationProperty
definition: A metadata relation between a class and its taxonomic rank (eg species, family)
has_obo_namespace: ncbi_taxonomy
comment: This is an abstract class for use with the NCBI taxonomy to name the depth of the node within the tree. The link between the node term and the rank is only visible if you are using an obo 1.3 aware browser/editor; otherwise this can be ignored

eco subset
type: AnnotationProperty
sub property of: subset_property

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

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

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

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

Description
type: AnnotationProperty
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.
comment: An account of the content of the resource.

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

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

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

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

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

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

Source
type: AnnotationProperty
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.
comment: A reference to a resource from which the present resource is derived.

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

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

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

subset_property
type: AnnotationProperty

has_alternative_id
type: AnnotationProperty

has_broad_synonym
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

has_narrow_synonym
type: AnnotationProperty

has_obo_format_version
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

in_subset
type: AnnotationProperty

shorthand
type: AnnotationProperty

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

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

label
type: AnnotationProperty
editor preferred label: label

part of
type: ObjectProperty
sub property of: overlaps
inverse of: has_part
type: TransitiveProperty
domain: entity
range: entity
editor preferred label: is part of
example of usage: my brain is part of my body (continuant parthood, two material entities)
example of usage: my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
example of usage: this day is part of this year (occurrent parthood)
definition: a core relation that holds between a part and its whole
editor note: Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
editor note: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
editor note: Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
alternative term: part_of
imported from: cl.owl
imported from: hp.owl
database_cross_reference: BFO:0000050
has_obo_namespace: human_stages_ontology
id: part_of
shorthand: part_of

has_part
type: ObjectProperty
sub property of: overlaps
editor preferred label: has part
example of usage: my body has part my brain (continuant parthood, two material entities)
example of usage: my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
example of usage: this year has part this day (occurrent parthood)
definition: a core relation that holds between a whole and its part
editor note: Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
editor note: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
editor note: Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
alternative term: has_part
imported from: cl.owl
imported from: hp.owl
imported from: pr.owl
database_cross_reference: BFO:0000051
has_obo_namespace: protein
id: has_part
shorthand: has_part
label: has part

inheres in at all times
type: ObjectProperty
sub property of: inheres in

realized in
type: ObjectProperty
inverse of: realizes
domain: realizable entity
range: process
editor preferred label: realized in
example of usage: this disease is realized in this disease course
example of usage: this fragility is realized in this shattering
example of usage: this investigator role is realized in this investigation
alternative term: is realized by
alternative term: realized_in
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])
comment: Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process

realizes
type: ObjectProperty
domain: process
range: realizable entity
editor preferred label: realizes
example of usage: this disease course realizes this disease
example of usage: this investigation realizes this investigator role
example of usage: this shattering realizes this fragility
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])
comment: Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process

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

precedes
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
domain: occurrent
range: occurrent
property chain axiom: part of
property chain axiom: happens during
editor preferred label: precedes
definition: x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
in_subset: eco subset

occurs in
type: ObjectProperty
inverse of: contains process
domain: occurrent
domain: process
range: independent continuant
range: Class
  union of: material entity
  union of: immaterial entity
property chain axiom: part of
editor preferred label: occurs in
definition: 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
alternative term: occurs_in
alternative term: unfolds in
alternative term: unfolds_in
imported from: hp.owl
database_cross_reference: BFO:0000066
id: occurs_in
shorthand: occurs_in
comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant

contains process
type: ObjectProperty
editor preferred label: site of
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
imported from: hp.owl
comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant

feature gives rise to disease
type: ObjectProperty
inverse of: disease arises from feature

is about
type: ObjectProperty
domain: information content entity
range: entity
example of usage: This document is about information artifacts and their representations
definition: is_about is a (currently) primitive relation that relates an information artifact to an entity.
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 editor: person:Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy

denotes
type: ObjectProperty
sub property of: is about
domain: information content entity
range: entity
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: 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
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
definition editor: person:Alan Ruttenberg
definition source: Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan

is quality measurement of
type: ObjectProperty
sub property of: is about
inverse of: is quality measured as
domain: measurement datum
range: quality
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
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
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.
definition editor: Alan Ruttenberg

has coordinate unit label
type: ObjectProperty
sub property of: has_part
type: FunctionalProperty
domain: cartesian spatial coordinate datum
range: length unit
comment: relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point

is duration of
type: ObjectProperty
sub property of: is about
domain: time measurement datum
range: process
definition: relates a process to a time-measurement-datum that represents the duration of the process
definition editor: Person:Alan Ruttenberg

is quality measured as
type: ObjectProperty
domain: quality
range: measurement datum
definition: inverse of the relation of is quality measurement of
editor note: 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship
definition editor: Person:Alan Ruttenberg

is quality specification of
type: ObjectProperty
sub property of: is about
inverse of: quality is specified as
domain: data item
definition: a relation between a data item and a quality of a material entity where the material entity is the specified output of a material transformation which achieves an objective specification that indicates the intended value of the specified quality.
definition editor: Person:Alan Ruttenberg
definition editor: Person:Bjoern Peters

quality is specified as
type: ObjectProperty
range: data item
definition: inverse of the relation of is quality specification of
editor note: 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship
definition editor: Person:Alan Ruttenberg
definition editor: Person:Bjoern Peters

has time stamp
type: ObjectProperty
sub property of: has_part
type: FunctionalProperty
domain: time stamped measurement datum
range: time measurement datum
definition: relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken
definition editor: Alan Ruttenberg

has measurement datum
type: ObjectProperty
sub property of: has_part
domain: time stamped measurement datum
range: Class
  intersection of: measurement datum
  intersection of: Class
    complement of: time measurement datum
definition: relates a time stamped measurement datum to the measurement datum that was measured
definition editor: Alan Ruttenberg

has_specified_input
type: ObjectProperty
sub property of: has participant
inverse of: is_specified_input_of
domain: planned process
range: continuant
editor preferred label: has_specified_input
example of usage: see is_input_of example_of_usage
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.
editor note: 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Larry Hunter
definition editor: PERSON: Melanie Coutot

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

has value specification
type: ObjectProperty

inheres in
type: ObjectProperty
sub property of: inheres in part of
sub property of: depends on
inverse of: bearer of
type: FunctionalProperty
domain: specifically dependent continuant
range: independent continuant
editor preferred label: inheres in
example of usage: this fragility inheres in this vase
example of usage: this red color inheres in this apple
definition: a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
editor note: A dependent inheres in its bearer at all times for which the dependent exists.
alternative term: inheres_in
imported from: hp.owl
database_cross_reference: RO:0000052
id: inheres_in
shorthand: inheres_in

participates in
type: ObjectProperty
inverse of: has participant
domain: continuant
range: occurrent
editor preferred label: participates in
example of usage: this blood clot participates in this blood coagulation
example of usage: this input material (or this output material) participates in this process
example of usage: this investigator participates in this investigation
definition: a relation between a continuant and a process, in which the continuant is somehow involved in the process
alternative term: participates_in

has participant
type: ObjectProperty
domain: occurrent
range: continuant
property chain axiom: has_part
property chain axiom: realizes
property chain axiom: inheres in
editor preferred label: has participant
example of usage: this blood coagulation has participant this blood clot
example of usage: this investigation has participant this investigator
example of usage: this process has participant this input material (or this output material)
definition: a relation between a process and a continuant, in which the continuant is somehow involved in the process
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.
alternative term: has_participant
Source: http://www.obofoundry.org/ro/#OBO_REL:has_participant

is concretized as
type: ObjectProperty
inverse of: concretizes
domain: generically dependent continuant
range: specifically dependent continuant
example of usage: A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
example of usage: An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
definition: A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.

concretizes
type: ObjectProperty
domain: specifically dependent continuant
range: generically dependent continuant
example of usage: A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
example of usage: An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
definition: A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.

function of
type: ObjectProperty
sub property of: inheres in
inverse of: has function
domain: function
range: independent continuant
example of usage: this catalysis function is a function of this enzyme
definition: a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
editor note: A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
alternative term: function_of
alternative term: is function of

quality of
type: ObjectProperty
sub property of: inheres in
inverse of: has_quality
range: independent continuant
example of usage: this red color is a quality of this apple
definition: a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
editor note: A quality inheres in its bearer at all times for which the quality exists.
alternative term: is quality of
alternative term: quality_of

role of
type: ObjectProperty
sub property of: inheres in
inverse of: has role
domain: role
range: independent continuant
example of usage: this investigator role is a role of this person
definition: a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
editor note: A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
alternative term: is role of
alternative term: role_of

has function
type: ObjectProperty
sub property of: bearer of
domain: independent continuant
range: function
example of usage: this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
definition: a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
editor note: A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
alternative term: has_function

has role
type: ObjectProperty
sub property of: bearer of
domain: independent continuant
range: role
example of usage: this person has role this investigator role (more colloquially: this person has this role of investigator)
definition: a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
editor note: A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
alternative term: has_role

has disposition
type: ObjectProperty
sub property of: bearer of
inverse of: disposition of
domain: independent continuant
range: disposition
definition: a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence

location of
type: ObjectProperty
inverse of: located in
type: TransitiveProperty
domain: independent continuant
range: independent continuant
editor preferred label: is location of
example of usage: my head is the location of my brain
example of usage: this cage is the location of this rat
definition: a relation between two independent continuants, the location and the target, in which the target is entirely within the location
editor note: Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
alternative term: location_of

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

contains
type: ObjectProperty
editor preferred label: contains
in_subset: eco subset

is allergic trigger for
type: ObjectProperty
sub property of: causes or contributes to condition
inverse of: has allergic trigger
domain: material entity
example of usage: penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)
definition: A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.

is autoimmune trigger for
type: ObjectProperty
sub property of: causes or contributes to condition
inverse of: has autoimmune trigger
domain: material entity
definition: A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.

has allergic trigger
type: ObjectProperty
sub property of: causes or contributes to condition
range: material entity
example of usage: penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)
definition: A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.

has autoimmune trigger
type: ObjectProperty
sub property of: causes or contributes to condition
range: material entity
definition: A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.

located in
type: ObjectProperty
type: TransitiveProperty
domain: independent continuant
range: independent continuant
editor preferred label: located in
example of usage: my brain is located in my head
example of usage: this rat is located in this cage
definition: a relation between two independent continuants, the target and the location, in which the target is entirely within the location
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 note: Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
alternative term: located_in
imported from: doid.owl
Source: http://www.obofoundry.org/ro/#OBO_REL:located_in

2D boundary of
type: ObjectProperty
sub property of: mereotopologically related to
inverse of: has 2D boundary
domain: immaterial entity
range: material entity
example of usage: the surface of my skin is a 2D boundary of my body
definition: a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity
editor note: A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
editor note: Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
alternative term: 2D_boundary_of
alternative term: boundary of
alternative term: is 2D boundary of
alternative term: is boundary of

has 2D boundary
type: ObjectProperty
sub property of: mereotopologically related to
domain: material entity
range: immaterial entity
example of usage: my body has 2D boundary the surface of my skin
definition: a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity
editor note: A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
editor note: Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
definition editor: David Osumi-Sutherland
alternative term: has boundary
alternative term: has_2D_boundary

tracheates
type: ObjectProperty
sub property of: contained in
definition: The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to).
definition editor: David Osumi-Sutherland

has synaptic terminal of
type: ObjectProperty
sub property of: overlaps
inverse of: has synaptic terminal in
definition editor: David Osumi-Sutherland

bounding layer of
type: ObjectProperty
sub property of: part of
domain: Class
  intersection of: material entity
  intersection of: Restriction
    on property: bearer of
    some values from: laminar
range: material entity
definition: X outer_layer_of Y iff: . X :continuant that bearer_of some PATO:laminar . X part_of Y . exists Z :surface . X has_boundary Z . Z boundary_of Y has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000
definition editor: David Osumi-Sutherland
in_subset: eco subset
comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane.

coincident with
type: ObjectProperty
sub property of: mereotopologically related to
domain: Class
  intersection of: continuant
  intersection of: Restriction
    on property: bearer of
    some values from: linear
range: Class
  intersection of: continuant
  intersection of: Restriction
    on property: bearer of
    some values from: linear
definition: A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other.
editor note: Note from NCEAS meeting: consider changing primary label
definition editor: David Osumi-Sutherland
in_subset: eco subset
comment: Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence.

regulates in other organism
type: ObjectProperty
sub property of: causally upstream of or within
domain: process
range: process
definition: x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2).
definition editor: David Osumi-Sutherland

occurent part of
type: ObjectProperty
sub property of: part of
sub property of: causally upstream of or within
domain: occurrent
range: occurrent
definition: A part of relation that applies only between occurents.

before or simultaneous with
type: ObjectProperty
sub property of: temporally related to
definition editor: David Osumi-Sutherland
alternative term: <=
in_subset: eco subset
comment: Primitive instance level timing relation between events

simultaneous with
type: ObjectProperty
sub property of: before or simultaneous with
type: TransitiveProperty
definition editor: David Osumi-Sutherland
in_subset: eco subset
comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)

before
type: ObjectProperty
sub property of: before or simultaneous with
type: TransitiveProperty
definition editor: David Osumi-Sutherland
in_subset: eco subset
comment: t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)

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

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

ends after
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
property chain axiom: ends during
property chain axiom: preceded by
definition editor: David Osumi-Sutherland
in_subset: eco subset
comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)

immediately preceded by
type: ObjectProperty
sub property of: preceded by
inverse of: immediately precedes
property chain axiom: starts with
property chain axiom: ends with
definition editor: David Osumi-Sutherland
alternative term: starts_at_end_of
comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)

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

starts before
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
definition editor: David Osumi-Sutherland
in_subset: eco subset

immediately precedes
type: ObjectProperty
sub property of: precedes
property chain axiom: ends with
property chain axiom: starts with
definition editor: David Osumi-Sutherland
alternative term: ends_at_start_of
alternative term: meets
is direct form of: precedes
in_subset: eco subset
comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)

starts during
type: ObjectProperty
sub property of: temporally related to
domain: occurrent
range: occurrent
definition editor: David Osumi-Sutherland
alternative term: io
in_subset: eco subset
comment: X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))

happens during
type: ObjectProperty
sub property of: ends during
type: TransitiveProperty
definition editor: David Osumi-Sutherland
alternative term: d
alternative term: during
in_subset: eco subset
comment: X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))

ends during
type: ObjectProperty
sub property of: temporally related to
definition editor: David Osumi-Sutherland
alternative term: o
alternative term: overlaps
in_subset: eco subset
comment: X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y).

has soma location
type: ObjectProperty
sub property of: overlaps
property chain axiom: part of
definition: Relation between a neuron and an anatomical structure that its soma is part of.
definition editor: David Osumi-Sutherland
expand expression to: <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)

fasciculates with
type: ObjectProperty
sub property of: overlaps
inverse of: has fasciculating neuron projection
definition: relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.
definition editor: David Osumi-Sutherland
alternative term: fasciculates with
first order logic expression: (forall (?x ?y) (iff (fasciculates_with ?x ?y) (exists (?nps ?npbs) (and ("neuron ; CL_0000540" ?x) ("neuron projection bundle ; CARO_0001001" ?y) ("neuron projection segment ; CARO_0001502" ?nps) ("neuron projection bundle segment ; CARO_0001500' " ?npbs) (part_of ?npbs ?y) (part_of ?nps ?x) (part_of ?nps ?npbs) (forall (?npbss) (if (and ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) (part_of ?npbss ?npbs) ) (overlaps ?nps ?npbss) ))))))
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

axon synapses in
type: ObjectProperty
sub property of: has presynaptic terminal in
inverse of: has postsynaptic terminal in
property chain axiom: part of
definition: Relation between a neuron and some structure its axon forms (chemical) synapses in.
definition editor: Chris Mungall
definition editor: David Osumi-Sutherland
expand expression to: <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)))
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

has plasma membrane part
type: ObjectProperty
sub property of: has_part
example of usage: Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]
definition: Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part.
definition editor: Alexander Diehl
definition editor: Chris Mungall
definition editor: Lindsay Cowell
definition source: http://www.ncbi.nlm.nih.gov/pubmed/19243617
imported from: cl.owl
expand expression to: <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)

has postsynaptic terminal in
type: ObjectProperty
sub property of: has synaptic terminal in
property chain axiom: part of
definition: Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input.
definition editor: Chris Mungall
definition editor: David Osumi-Sutherland
alternative term: synapsed in
expand expression to: http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

has presynaptic terminal in
type: ObjectProperty
sub property of: has synaptic terminal in
property chain axiom: part of
definition: Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input.
alternative term: synapses in
expand expression to: <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

dendrite synapsed in
type: ObjectProperty
sub property of: has postsynaptic terminal in
property chain axiom: part of
definition: Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input.
definition editor: Chris Mungall
definition editor: David Osumi-Sutherland
expand expression to: <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030425> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( http://purl.obolibrary.org/obo/GO_0042734 and <http://purl.obolibrary.org/obo/BFO_0000050> some ( <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)))
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

has synaptic terminal in
type: ObjectProperty
sub property of: overlaps
property chain axiom: part of
definition: A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input.
definition editor: David Osumi-Sutherland
alternative term: has synapse in
expand expression to: <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

overlaps
type: ObjectProperty
sub property of: mereotopologically related to
property chain axiom: part of
property chain axiom: has_part
definition: x overlaps y if and only if there exists some z such that x has part z and z part of y
imported from: cl.owl
imported from: hp.owl
expand expression to: http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
in_subset: ro-eco
in_subset: eco subset

Axiom
annotated source: overlaps
annotated property: propertyChainAxiom
annotated target: has_part
annotated target: part of
RO_0002582: true

has fasciculating neuron projection
type: ObjectProperty
sub property of: overlaps
definition: The relation between a neuron projection bundle and a neuron projection that is fasciculated with it.
definition editor: David Osumi-Sutherland
alternative term: has fasciculating component
first order logic expression: (forall (?x ?y) (iff (has_fasciculating_neuron_projection ?x ?y) (exists (?nps ?npbs) (and ("neuron projection bundle ; CARO_0001001" ?x) ("neuron projection ; GO0043005" ?y) ("neuron projection segment ; CARO_0001502" ?nps) ("neuron projection bundle segment ; CARO_0001500" ?npbs) (part_of ?nps ?y) (part_of ?npbs ?x) (part_of ?nps ?npbs) (forall (?npbss) (if (and ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) (part_of ?npbss ?npbs) ) (overlaps ?nps ?npbss) ))))))
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

continuous with
type: ObjectProperty
sub property of: mereotopologically related to
domain: independent continuant
range: independent continuant
definition: X continuous_with Y if and only if X and Y share a fiat boundary.
definition editor: David Osumi-Sutherland
alternative term: connected to
curator note: The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)

partially overlaps
type: ObjectProperty
sub property of: overlaps
definition: x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x
editor note: We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom
alternative term: proper overlaps
first order logic expression: (forall (?x ?y) (iff (proper_overlaps ?x ?y) (and (overlaps ?x ?y) (not (part_of ?x ?y)) (not (part_of ?y ?x)))))
in_subset: eco subset

spatially disjoint from
type: ObjectProperty
sub property of: mereotopologically related to
definition: A is spatially_disjoint_from B if and only if they have no parts in common
editor note: There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom.
definition editor: Chris Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/22293552
curator note: Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy
expand expression to: BFO_0000051 exactly 0 (BFO_0000050 some ?Y)
in_subset: eco subset

connected to
type: ObjectProperty
sub property of: mereotopologically related to
domain: Restriction
  on property: part of
  some values from: system
range: Restriction
  on property: part of
  some values from: system
property chain axiom:
  inverse of: connects
property chain axiom: connects
example of usage: a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
definition: a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b
definition source: http://www.ncbi.nlm.nih.gov/pubmed/22293552

connects
type: ObjectProperty
sub property of: mereotopologically related to
domain: independent continuant
range: Restriction
  on property: part of
  some values from: system
example of usage: The M8 connects Glasgow and Edinburgh
example of usage: a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
definition: c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system.
definition source: http://www.ncbi.nlm.nih.gov/pubmed/22293552

supplies
type: ObjectProperty
sub property of: connected to
definition: Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy.
editor note: Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20064205

drains
type: ObjectProperty
sub property of: connected to
definition: Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure.
editor note: Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20064205

has component
type: ObjectProperty
sub property of: has_part
definition: w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
editor note: The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
curator note: For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
in_subset: eco subset

has phenotype
type: ObjectProperty
sub property of: topObjectProperty
inverse of: phenotype of
domain: biological entity
range: phenotype
definition: A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype).
definition editor: Chris Mungall
imported from: doid.owl
in_subset: eco subset

phenotype of
type: ObjectProperty
sub property of: topObjectProperty
type: FunctionalProperty
domain: phenotype
range: biological entity
definition: inverse of has phenotype
definition editor: Chris Mungall
in_subset: defined by inverse
in_subset: eco subset

regulates
type: ObjectProperty
sub property of: causally upstream of
inverse of: regulated by
type: TransitiveProperty
domain: process
range: process
property chain axiom: ends with
property chain axiom: directly regulates
definition: x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y
editor note: We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit
definition editor: Chris Mungall
definition editor: David Hill
definition editor: Tanya Berardini
definition source: causal-relations
definition source: GO
curator note: Regulation precludes parthood; the regulatory process may not be within the regulated process.
obo foundry unique label: regulates (processual)
elucidation: false

negatively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, negative effect
inverse of: negatively regulated by
property chain axiom: ends with
definition: x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y
definition editor: Chris Mungall
definition source: causal-relations
obo foundry unique label: negatively regulates (process to process)

positively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, positive effect
inverse of: positively regulated by
property chain axiom: negatively regulates
property chain axiom: ends with
definition: x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y
definition editor: Chris Mungall
definition source: causal-relations
obo foundry unique label: positively regulates (process to process)

capable of
type: ObjectProperty
sub property of: capable of part of
domain: independent continuant
domain: material entity
range: process
example of usage: mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
example of usage: osteoclast SubClassOf 'capable of' some 'bone resorption'
definition: A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
definition editor: Chris Mungall
alternative term: has function realized in
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20123131
definition source: http://www.ncbi.nlm.nih.gov/pubmed/21208450
curator note: For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
imported from: cl.owl
expand expression to: RO_0000053 some (RO_0000054 only ?Y)
in_subset: eco subset

capable of part of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal agent in
domain: material entity
range: process
property chain axiom: capable of
property chain axiom: part of
definition: c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
definition editor: Chris Mungall
alternative term: has function in
imported from: cl.owl
expand expression to: RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))

Axiom
annotated source: capable of part of
annotated property: propertyChainAxiom
annotated target: capable of
annotated target: part of
RO_0002582: true

actively participates in
type: ObjectProperty
sub property of: participates in
inverse of: has active participant
definition: x actively participates in y if and only if x participates in y and x realizes some active role
definition editor: Chris Mungall
alternative term: agent in

has active participant
type: ObjectProperty
sub property of: has participant
example of usage: 'heart development' has active participant some Shh protein
definition: x has participant y if and only if x realizes some active role that inheres in y
editor note: This may be obsoleted and replaced by the original 'has agent' relation
definition editor: Chris Mungall
alternative term: has agent
in_subset: eco subset

surrounded by
type: ObjectProperty
sub property of: adjacent to
inverse of: surrounds
definition: x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x
definition editor: Chris Mungall

adjacent to
type: ObjectProperty
sub property of: spatially disjoint from
domain: independent continuant
range: independent continuant
example of usage: A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
example of usage: The epidermis layer of a vertebrate is adjacent to the dermis.
example of usage: The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies.
example of usage: The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used.
definition: x adjacent to y if and only if x and y share a boundary.
editor note: This relation acts as a join point with BSPO
definition editor: Chris Mungall

Axiom
annotated source: adjacent to
annotated property: example of usage
annotated target: A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.

surrounds
type: ObjectProperty
sub property of: adjacent to
definition: inverse of surrounded by
definition editor: Chris Mungall
in_subset: defined by inverse

temporally related to
type: ObjectProperty
domain: occurrent
range: occurrent
definition editor: Chris Mungall
definition source: Allen's interval algebra
curator note: Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
Source: https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit
in_subset: eco subset
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.

starts
type: ObjectProperty
sub property of: part of
sub property of: temporally related to
inverse of: starts with
definition: inverse of starts with
definition editor: Chris Mungall
definition source: Allen
in_subset: eco subset

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

ends
type: ObjectProperty
sub property of: part of
sub property of: temporally related to
inverse of: ends with
definition: inverse of ends with
definition editor: Chris Mungall
in_subset: eco subset

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

has start location
type: ObjectProperty
sub property of: has part that occurs in
domain: process
range: independent continuant
property chain axiom: starts with
property chain axiom: occurs in
definition: x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y
definition editor: Chris Mungall
alternative term: starts with process that occurs in
in_subset: eco subset

has end location
type: ObjectProperty
sub property of: has part that occurs in
domain: process
range: independent continuant
property chain axiom: ends with
property chain axiom: occurs in
definition: x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y
definition editor: Chris Mungall
alternative term: ends with process that occurs in
in_subset: eco subset

has input
type: ObjectProperty
sub property of: has participant
inverse of: input of
property chain axiom: starts with
definition: p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p.
definition editor: Chris Mungall
alternative term: consumes
in_subset: eco subset

has output
type: ObjectProperty
sub property of: has participant
inverse of: output of
property chain axiom: ends with
definition: p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p.
definition editor: Chris Mungall
alternative term: produces
in_subset: eco subset

has exposure receptor
type: ObjectProperty
sub property of: related via exposure to
definition: A broad relationship between an exposure event or process and any entity (e.g., a human, human population, or a human organ) that interacts with an exposure stressor during the exposure event
definition source: ExO:0000001

has exposure stressor
type: ObjectProperty
sub property of: related via exposure to
definition: A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event.
definition source: ExO:0000000

has exposure route
type: ObjectProperty
sub property of: related via exposure to
definition: A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor
definition source: ExO:0000055

has exposure transport path
type: ObjectProperty
sub property of: related via exposure to
definition: A broad relationship between an exposure event or process and a the material an agent takes from the source to the target.

related via exposure to
type: ObjectProperty
sub property of: causally related to
domain: process

has active ingredient
type: ObjectProperty
sub property of: has_part
inverse of: active ingredient in'
example of usage: Any portion of roundup 'has active ingredient' some glyphosate
definition: A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance.
has_exact_synonym: has active substance
has_related_synonym: has active pharmaceutical ingredient

active ingredient in'
type: ObjectProperty
sub property of: part of
definition: inverse of has active ingredient
in_subset: defined by inverse

connecting branch of
type: ObjectProperty
sub property of: in branching relationship with
inverse of: has connecting branch
definition: b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t.

has connecting branch
type: ObjectProperty
sub property of: in branching relationship with
definition: inverse of connecting branch of
in_subset: defined by inverse

has biological role
type: ObjectProperty
sub property of: has role
definition: c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)

has application role
type: ObjectProperty
sub property of: has role
definition: c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)

has chemical role
type: ObjectProperty
sub property of: has role
definition: c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)

acts upstream of
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of
definition: c involved in regulation of p if c enables 'p' and p' causally upstream of p

acts upstream of or within
type: ObjectProperty
sub property of: causal agent in
property chain axiom: enables
property chain axiom: causally upstream of or within
definition: c acts upstream of or within p if c is enables 'p' and p' causally upstream of or within p
has_related_synonym: affects

is treated by substance
type: ObjectProperty
sub property of: causally related to
inverse of: is substance that treats
definition: Inverse of 'is substance that treats'
creator: cjm
in_subset: defined by inverse

causally upstream of, positive effect
type: ObjectProperty
sub property of: causally upstream of
creator: cjm
comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y

causally upstream of, negative effect
type: ObjectProperty
sub property of: causally upstream of
creator: cjm
comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y

inheres in part of
type: ObjectProperty
sub property of: depends on
domain: specifically dependent continuant
range: Class
  intersection of: independent continuant
  intersection of: Restriction
    on property: part of
    some values from: entity
property chain axiom: inheres in
property chain axiom: part of
definition: q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w.
editor note: Because part_of is transitive, inheres in is a sub-relation of inheres in part of
definition editor: Chris Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20064205
imported from: hp.owl
database_cross_reference: RO:0002314
id: inheres_in_part_of
shorthand: inheres_in_part_of

Axiom
annotated source: inheres in part of
annotated property: propertyChainAxiom
annotated target: inheres in
annotated target: part of
RO_0002582: true

mereotopologically related to
type: ObjectProperty
definition: A mereological relationship or a topological relationship
definition editor: Chris Mungall
curator note: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
imported from: cl.owl
imported from: hp.owl

colocalizes with
type: ObjectProperty
sub property of: mereotopologically related to
domain: material entity
range: material entity
example of usage: Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)
definition: a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO].
definition editor: Chris Mungall
definition source: http://www.geneontology.org/GO.annotation.conventions.shtml#colocalizes_with
curator note: In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]
creator: Gene Ontology Consortium

contributes to
type: ObjectProperty
sub property of: capable of part of
sub property of: part of structure that is capable of
example of usage: ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity.
example of usage: Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity.
example of usage: eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex
editor note: We would like to say if and only if exists c', p' c part_of c' and c' capable_of p and c capable_of p' and p' part_of p then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction.
definition editor: Chris Mungall
definition source: http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to
curator note: In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology.

enables
type: ObjectProperty
sub property of: capable of
inverse of: enabled by
example of usage: a particular instances of akt-2 enables some instance of protein kinase activity
definition editor: Chris Mungall
alternative term: catalyzes
alternative term: executes
alternative term: has
alternative term: is catalyzing
alternative term: is executing
curator note: This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
curator note: This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time.

functionally related to
type: ObjectProperty
definition editor: Chris Mungall
curator note: This is a grouping relation that collects relations used for the purpose of connecting structure and function
imported from: cl.owl

part of structure that is capable of
type: ObjectProperty
sub property of: functionally related to
property chain axiom: part of
property chain axiom: capable of
definition: this relation holds between c and p when c is part of some c', and c' is capable of p.
definition editor: Chris Mungall
alternative term: false

Axiom
annotated source: part of structure that is capable of
annotated property: propertyChainAxiom
annotated target: part of
annotated target: capable of
is a defining property chain axiom: true

involved in
type: ObjectProperty
sub property of: involved in or involved in regulation of
property chain axiom: enables
property chain axiom: part of
definition: c involved_in p if and only if c enables some process p', and p' is part of p
definition editor: Chris Mungall
alternative term: actively involved in
alternative term: enables part of

regulates levels of
type: ObjectProperty
sub property of: functionally related to
example of usage: every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid
definition: p regulates levels of c if p regulates some amount (PATO:0000070) of c
definition editor: Chris Mungall
definition source: causal-relations
obo foundry unique label: regulates levels of (process to entity)

enabled by
type: ObjectProperty
sub property of: functionally related to
sub property of:
  inverse of: capable of
definition: inverse of enables
definition editor: Chris Mungall

regulated by
type: ObjectProperty
sub property of: causally downstream of or within
type: TransitiveProperty
domain: process
range: process
definition: inverse of regulates
definition editor: Chris Mungall
obo foundry unique label: regulated by (processual)
in_subset: defined by inverse

negatively regulated by
type: ObjectProperty
sub property of: regulated by
definition: inverse of negatively regulates
definition editor: Chris Mungall
in_subset: defined by inverse

positively regulated by
type: ObjectProperty
sub property of: regulated by
definition: inverse of positively regulates
definition editor: Chris Mungall
in_subset: defined by inverse

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

has member
type: ObjectProperty
sub property of: has_part
type: IrreflexiveProperty
definition: has member is a mereological relation between a collection and an item.
definition source: SIO

input of
type: ObjectProperty
sub property of: participates in
sub property of: functionally related to
definition: inverse of has input
definition editor: Chris Mungall
in_subset: defined by inverse
in_subset: eco subset

output of
type: ObjectProperty
sub property of: participates in
sub property of: functionally related to
definition: inverse of has output
definition editor: Chris Mungall
in_subset: defined by inverse
in_subset: eco subset

formed as result of
type: ObjectProperty
sub property of: output of
definition editor: Chris Mungall

has dendrite location
type: ObjectProperty
sub property of: overlaps
definition editor: Chris Mungall
Source: http://neurolex.org/wiki/Property:DendriteLocation

in branching relationship with
type: ObjectProperty
sub property of: part of
sub property of: mereotopologically related to
domain: material entity
range: material entity
definition: A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network.
definition editor: Chris Mungall
curator note: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships
curator note: This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)

tributary of
type: ObjectProperty
sub property of: in branching relationship with
example of usage: Deschutes River tributary_of Columbia River
example of usage: inferior epigastric vein tributary_of external iliac vein
definition: x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein.
definition editor: Chris Mungall
alternative term: drains into
alternative term: drains to
alternative term: tributary channel of
definition source: http://en.wikipedia.org/wiki/Tributary
definition source: http://www.medindia.net/glossary/venous_tributary.htm
curator note: This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)
in_subset: eco subset

distributary of
type: ObjectProperty
sub property of: in branching relationship with
example of usage: Deschutes River distributary_of Little Lava Lake
definition: x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x
definition editor: Chris Mungall
alternative term: branch of
alternative term: distributary channel of
definition source: http://en.wikipedia.org/wiki/Distributary
in_subset: eco subset
comment: This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes

anabranch of
type: ObjectProperty
sub property of: distributary of
sub property of:
  inverse of: tributary of
property disjoint with: proper distributary of
property disjoint with: proper tributary of
definition: x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y.
definition editor: Chris Mungall
alternative term: anastomoses with
in_subset: eco subset

spatially coextensive with
type: ObjectProperty
sub property of: overlaps
property chain axiom: located in
property chain axiom:
  inverse of: located in
example of usage: A lump of clay and a statue
definition: x spatially_coextensive_with y if and inly if x and y have the same location
definition editor: Chris Mungall
curator note: This relation is added for formal completeness. It is unlikely to be used in many practical scenarios

branching part of
type: ObjectProperty
sub property of: part of
sub property of: in branching relationship with
inverse of: has branching part
range: Restriction
  on property: bearer of
  some values from: branched
property chain axiom: distributary of
property chain axiom: main stem of
definition: x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y
definition editor: Chris Mungall
in_subset: eco subset

main stem of
type: ObjectProperty
sub property of: in branching relationship with
definition: x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path.
definition editor: Chris Mungall
in_subset: eco subset

proper distributary of
type: ObjectProperty
sub property of: distributary of
definition: x proper_distributary_of y iff x distributary_of y and x does not flow back into y
definition editor: Chris Mungall
in_subset: eco subset

proper tributary of
type: ObjectProperty
sub property of: tributary of
definition: x proper_tributary_of y iff x tributary_of y and x does not originate from y
definition editor: Chris Mungall
in_subset: eco subset

has direct input
type: ObjectProperty
sub property of: has input
property chain axiom: starts with
example of usage: 'protein catabolic process' SubClassOf has_direct_input some protein
definition: p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p.
definition editor: Chris Mungall
alternative term: directly consumes
curator note: This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'

obsolete has indirect output
type: ObjectProperty
sub property of: has output
definition editor: Chris Mungall
comment: Likely to be obsoleted. See: https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit
deprecated: true

causally downstream of
type: ObjectProperty
sub property of: preceded by
sub property of: causally downstream of or within
inverse of: causally upstream of
definition: inverse of upstream of
definition editor: Chris Mungall

immediately causally downstream of
type: ObjectProperty
sub property of: immediately preceded by
sub property of: causally downstream of
inverse of: immediately causally upstream of
definition editor: Chris Mungall

directly activates
type: ObjectProperty
sub property of: directly positively regulates
definition: p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q
definition editor: Chris Mungall
alternative term: directly positively regulates
definition source: causal-relations
obo foundry unique label: directly activates (process to process)

indirectly activates
type: ObjectProperty
sub property of: positively regulates
type: TransitiveProperty
property chain axiom: directly activates
property chain axiom: indirectly inhibits
definition: p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q
definition editor: Chris Mungall
alternative term: indirectly positively regulates
is indirect form of: positively regulates

directly inhibits
type: ObjectProperty
sub property of: directly negatively regulates
definition editor: Chris Mungall
alternative term: directly negatively regulates
definition source: causal-relations
obo foundry unique label: directly inhibits (process to process)

indirectly inhibits
type: ObjectProperty
sub property of: negatively regulates
type: TransitiveProperty
property chain axiom: directly inhibits
definition editor: Chris Mungall
alternative term: indirectly negatively regulates
is indirect form of: negatively regulates

causally related to
type: ObjectProperty
sub property of: related via dependence to
domain: Class
  union of: process
  union of: material entity
range: Class
  union of: process
  union of: material entity
definition: This relation groups causal relations between material entities and causal relations between processes
editor note: This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yiel…
definition editor: Chris Mungall
curator note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
imported from: cl.owl

causally upstream of
type: ObjectProperty
sub property of: precedes
sub property of: causally upstream of or within
type: TransitiveProperty
definition: p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain
definition editor: Chris Mungall

immediately causally upstream of
type: ObjectProperty
sub property of: immediately precedes
sub property of: causally upstream of
definition: p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q.
definition editor: Chris Mungall
is direct form of: causally upstream of

directly provides input for
type: ObjectProperty
sub property of: immediately causally upstream of
sub property of: transitively provides input for
definition: p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c
editor note: This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit
definition editor: Chris Mungall
definition source: causal-relations
obo foundry unique label: directly provides input for (process to process)

transitively provides input for
type: ObjectProperty
sub property of: causally upstream of
type: TransitiveProperty
domain: process
range: process
definition: transitive form of directly_provides_input_for
definition editor: Chris Mungall
curator note: This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'directly provides input for' (which may later be relabeled simply to 'provides input for')
obo foundry unique label: transitively provides input for (process to process)

causally upstream of or within
type: ObjectProperty
sub property of: causal relation between processes
inverse of: causally downstream of or within
type: TransitiveProperty
definition: p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.
editor note: We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
definition editor: Chris Mungall
alternative term: influences (processual)
has_related_synonym: affects

causally downstream of or within
type: ObjectProperty
sub property of: causal relation between processes
type: TransitiveProperty
definition: inverse of causally upstream of or within
definition editor: Chris Mungall
definition source: causal-relations
in_subset: defined by inverse

involved in regulation of
type: ObjectProperty
sub property of: acts upstream of
sub property of: involved in or involved in regulation of
property chain axiom: enables
property chain axiom: regulates
property chain axiom: involved in
definition: c involved in regulation of p if c is involved in some 'p' and p' regulates some p
definition editor: Chris Mungall

involved in positive regulation of
type: ObjectProperty
sub property of: involved in regulation of
property chain axiom: enables
property chain axiom: positively regulates
property chain axiom: involved in
definition editor: Chris Mungall

involved in negative regulation of
type: ObjectProperty
sub property of: involved in regulation of
property chain axiom: enables
property chain axiom: negatively regulates
property chain axiom: involved in
definition editor: Chris Mungall

involved in or involved in regulation of
type: ObjectProperty
sub property of: acts upstream of or within
sub property of: functionally related to
sub property of: causal agent in
definition: c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
definition editor: Chris Mungall
alternative term: involved in or reguates

enables activity in
type: ObjectProperty
sub property of: functionally related to
property chain axiom: enables
property chain axiom: occurs in
example of usage: A protein that enables activity in a cytosol.
definition: c executes activity in d if and only if c enables p and p occurs_in d
definition editor: Chris Mungall
alternative term: executes activity in

Axiom
annotated source: enables activity in
annotated property: propertyChainAxiom
annotated target: enables
annotated target: occurs in
is a defining property chain axiom: true

contributes to morphology of
type: ObjectProperty
sub property of: overlaps
definition: p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm.
definition editor: Chris Mungall

interacts with
type: ObjectProperty
type: SymmetricProperty
domain: material entity
range: material entity
definition: A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
editor note: Considering relabeling as 'pairwise interacts with'
editor note: This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
definition editor: Chris Mungall
curator note: Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.
has_exact_synonym: in pairwise interaction with
in_subset: eco subset

molecularly controls
type: ObjectProperty
sub property of: causally influences
property chain axiom: enables
property chain axiom: regulates
property chain axiom: enabled by
definition: Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b
definition editor: Chris Mungall

molecularly decreases activity of
type: ObjectProperty
sub property of: molecularly controls
property chain axiom: enables
property chain axiom: directly inhibits
property chain axiom: enabled by
definition: Holds between molecules a and b if and only if a executes a process that directly diminishes a process executed by b.
definition editor: Chris Mungall
alternative term: inhibits

molecularly increases activity of
type: ObjectProperty
sub property of: molecularly controls
property chain axiom: enables
property chain axiom: directly activates
property chain axiom: enabled by
definition: Holds between molecules a and b if and only if a executes a process that directly activates a process executed by b.
definition editor: Chris Mungall
alternative term: activates

has symptom
type: ObjectProperty
sub property of: has phenotype
definition: A relation that holds between a disease or an organism and a phenotype
definition editor: Chris Mungall

partner in
type: ObjectProperty
sub property of: participates in
definition editor: Chris Mungall
curator note: Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target

subject participant in
type: ObjectProperty
sub property of: partner in
definition editor: Chris Mungall
curator note: Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed.

target participant in
type: ObjectProperty
sub property of: partner in
definition editor: Chris Mungall
curator note: Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed.

is evidence for
type: ObjectProperty
sub property of: related via evidence or inference to
inverse of: has evidence
definition: A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and the a supports either the existence of b, or the truth value of b.
definition editor: Chris Mungall
in_subset: eco subset

composed primarily of
type: ObjectProperty
sub property of: has_part
example of usage: 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'
definition: x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y.
definition editor: Chris Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/22293552
in_subset: eco subset

has part that occurs in
type: ObjectProperty
domain: occurrent
range: independent continuant
property chain axiom: has_part
property chain axiom: occurs in
definition: p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.
definition editor: Chris Mungall
in_subset: eco subset

Axiom
annotated source: has part that occurs in
annotated property: propertyChainAxiom
annotated target: has_part
annotated target: occurs in
is a defining property chain axiom: true

receives input from
type: ObjectProperty
sub property of: connected to
inverse of: sends output to
editor note: See notes for inverse relation
definition editor: Chris Mungall

sends output to
type: ObjectProperty
sub property of: connected to
editor note: This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in.
definition editor: Chris Mungall

causal agent in
type: ObjectProperty
sub property of: causal relation between material entity and a process
inverse of: has causal agent
domain: material entity
range: process
definition: A relationship between a material entity and a process where the material entity has some causal role that influences the process
definition source: causal-relations
imported from: cl.owl

causal relation between processes
type: ObjectProperty
sub property of: causally related to
domain: occurrent
range: occurrent
definition: p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.
definition editor: Chris Mungall
definition source: causal-relations
curator note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

depends on
type: ObjectProperty
definition editor: Chris Mungall
imported from: hp.owl
label: depends_on

towards
type: ObjectProperty
sub property of: depends on
definition: q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2
editor note: This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C.
definition editor: Chris Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20064205

has intermediate
type: ObjectProperty
sub property of: has participant
example of usage: 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate
definition: p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c
definition editor: Chris Mungall
alternative term: has intermediate product
in_subset: eco subset

causal relation between material entities
type: ObjectProperty
sub property of: causally related to
domain: material entity
range: material entity
editor note: The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
definition editor: Chris Mungall
definition source: causal-relations
curator note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

determined by
type: ObjectProperty
sub property of: part of
sub property of: determined by part of
sub property of: causally influenced by
inverse of: determines
domain: system
range: material entity
example of usage: A coral reef environment is determined by a particular coral reef
definition: s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s.
editor note: The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future
definition editor: Chris Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/24330602
obo foundry unique label: determined by (system to material entity)
creator: Chris Mungall
creator: Pier Buttigieg
in_subset: eco subset

determines
type: ObjectProperty
sub property of: causally influences
definition: inverse of determined by
definition editor: Chris Mungall
obo foundry unique label: determines (material entity to system)
in_subset: defined by inverse
in_subset: eco subset

determined by part of
type: ObjectProperty
sub property of: overlaps
sub property of: causal relation between material entities
domain: system
range: material entity
property chain axiom: determined by
property chain axiom: part of
definition: s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w.
definition editor: Chris Mungall
in_subset: eco subset

Axiom
annotated source: determined by part of
annotated property: propertyChainAxiom
annotated target: determined by
annotated target: part of
RO_0002582: true

sequentially related to
type: ObjectProperty
definition: A relation that holds between two entities that have the property of being sequences or having sequences.
definition editor: Chris Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20226267
curator note: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect.
curator note: The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene.
cites as authority: 006650.abstract

sequentially adjacent to
type: ObjectProperty
sub property of: does not overlap sequence of
example of usage: Every UTR is adjacent to a CDS of the same transcript
example of usage: Two consecutive DNA residues are sequentially adjacent
example of usage: Two exons on a processed transcript that were previously connected by an intron are adjacent
definition: x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y
definition editor: Chris Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract

has start sequence
type: ObjectProperty
sub property of: has subsequence
inverse of: is start sequence of
type: TransitiveProperty
example of usage: Every CDS has as a start sequence the start codon for that transcript
definition: x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence
definition editor: Chris Mungall
alternative term: started by
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract

is start sequence of
type: ObjectProperty
sub property of: is subsequence of
type: TransitiveProperty
definition: inverse of has start sequence
definition editor: Chris Mungall
alternative term: starts
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract
in_subset: defined by inverse

has end sequence
type: ObjectProperty
sub property of: has subsequence
inverse of: is end sequence of
type: TransitiveProperty
example of usage: Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)
definition: x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence
definition editor: Chris Mungall
alternative term: ended by
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract

is end sequence of
type: ObjectProperty
sub property of: is subsequence of
type: TransitiveProperty
definition: inverse of has end sequence
definition editor: Chris Mungall
alternative term: ends
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract
in_subset: defined by inverse

is consecutive sequence of
type: ObjectProperty
sub property of: has subsequence
definition: x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y.
editor note: In the SO paper, this was defined as an instance-type relation
definition editor: Chris Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract

is sequentially aligned with
type: ObjectProperty
sub property of: sequentially related to
type: SymmetricProperty
example of usage: Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence.
definition: x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering
definition editor: Chris Mungall
cites as authority: 006650.abstract

bounds sequence of
type: ObjectProperty
sub property of: sequentially related to
inverse of: is bound by sequence of
type: TransitiveProperty
example of usage: The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)
definition: x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y
definition editor: Chris Mungall
cites as authority: 006650.abstract

is bound by sequence of
type: ObjectProperty
sub property of: sequentially related to
type: TransitiveProperty
definition: inverse of bounds sequence of
definition editor: Chris Mungall
cites as authority: 006650.abstract
in_subset: defined by inverse

has subsequence
type: ObjectProperty
sub property of: has_part
sub property of: bounds sequence of
sub property of: overlaps sequence of
inverse of: is subsequence of
type: TransitiveProperty
definition: x has subsequence y iff all of the sequence parts of x are sequence parts of y
definition editor: Chris Mungall
alternative term: contains
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract

is subsequence of
type: ObjectProperty
sub property of: part of
sub property of: is bound by sequence of
sub property of: overlaps sequence of
type: TransitiveProperty
definition: inverse of has subsequence
definition editor: Chris Mungall
alternative term: contained by
cites as authority: 006650.abstract
in_subset: defined by inverse

overlaps sequence of
type: ObjectProperty
sub property of: overlaps
sub property of: sequentially related to
type: SymmetricProperty
property chain axiom: has subsequence
property chain axiom: is subsequence of
definition: x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y.
definition editor: Chris Mungall
cites as authority: 006650.abstract

does not overlap sequence of
type: ObjectProperty
sub property of: sequentially related to
type: SymmetricProperty
definition: x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y.
definition editor: Chris Mungall
alternative term: disconnected from
cites as authority: 006650.abstract

is upstream of sequence of
type: ObjectProperty
sub property of: does not overlap sequence of
type: TransitiveProperty
definition: inverse of downstream of sequence of
definition editor: Chris Mungall
cites as authority: 006650.abstract

is downstream of sequence of
type: ObjectProperty
sub property of: does not overlap sequence of
type: TransitiveProperty
definition: x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y.
definition editor: Chris Mungall
cites as authority: 006650.abstract

is immediately downstream of sequence of
type: ObjectProperty
sub property of: sequentially adjacent to
sub property of: is downstream of sequence of
example of usage: A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript
definition: x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y
definition editor: Chris Mungall
is direct form of: is downstream of sequence of
cites as authority: 006650.abstract

is immediately upstream of sequence of
type: ObjectProperty
sub property of: sequentially adjacent to
sub property of: is upstream of sequence of
example of usage: A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript
definition: inverse of immediately downstream of
definition editor: Chris Mungall
cites as authority: 006650.abstract

has skeleton
type: ObjectProperty
sub property of: has_part
inverse of: skeleton of
example of usage: Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'
definition: A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision.
definition editor: Chris Mungall
alternative term: has supporting framework
curator note: The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell).

has evidence
type: ObjectProperty
sub property of: related via evidence or inference to
definition: inverse of is evidence for
definition editor: Chris Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/25052702
in_subset: defined by inverse
in_subset: eco subset
comment: x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x.

causally influenced by
type: ObjectProperty
sub property of: causal relation between material entities
inverse of: causally influences
definition editor: Chris Mungall
definition source: causal-relations
obo foundry unique label: causally influenced by (material entity to material entity)

results in movement of
type: ObjectProperty
sub property of: has participant
domain: locomotion
definition: Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c
definition editor: Chris Mungall

causally influences
type: ObjectProperty
sub property of: causal relation between material entities
property chain axiom: enables
property chain axiom: causally upstream of
property chain axiom: has input
property chain axiom: enabled by
definition: Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b
definition editor: Chris Mungall
definition source: causal-relations
obo foundry unique label: causally influences (material entity to material entity)

has branching part
type: ObjectProperty
sub property of: in branching relationship with
definition: inverse of branching part of
definition editor: Chris Mungall
in_subset: defined by inverse
in_subset: eco subset

conduit for
type: ObjectProperty
sub property of: overlaps
domain: material entity
range: material entity
definition: x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x.
definition editor: Chris Mungall
definition source: UBERON:cjm
curator note: This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through.
in_subset: eco subset

lumen of
type: ObjectProperty
sub property of: part of
range: material entity
definition: x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull.
definition editor: Chris Mungall
definition source: GOC:cjm
in_subset: eco subset

luminal space of
type: ObjectProperty
sub property of: lumen of
domain: immaterial entity
definition: s is luminal space of x iff s is lumen_of x and s is an immaterial entity
definition editor: Chris Mungall
in_subset: eco subset

has modifier
type: ObjectProperty
definition: A relation that holds between an attribute or a qualifier and another attribute.
definition editor: Chris Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20064205
curator note: This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are.
imported from: hp.owl
database_cross_reference: RO:0002180
id: qualifier
in_subset: ro-eco
in_subset: eco subset
shorthand: qualifier
comment: placeholder relation to indicate normality/abnormality.

skeleton of
type: ObjectProperty
sub property of: part of
definition: inverse of has skeleton
definition editor: Chris Mungall
in_subset: defined by inverse

directly regulates
type: ObjectProperty
sub property of: regulates
sub property of: immediately causally upstream of
definition: p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p
definition editor: Chris Mungall
definition source: causal-relations
obo foundry unique label: directly regulates (processual)
is direct form of: regulates

has part structure that is capable of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal relation between material entity and a process
property chain axiom: has_part
property chain axiom: capable of
example of usage: gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
definition: s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p
definition editor: Chris Mungall

results in breakdown of
type: ObjectProperty
sub property of: has input
definition: p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p

results in catabolism of
type: ObjectProperty
sub property of: results in breakdown of
definition: p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released.

results in disassembly of
type: ObjectProperty
sub property of: results in breakdown of
sub property of: results in organization of

results in remodeling of
type: ObjectProperty
sub property of: has input
sub property of: results in organization of

results in organization of
type: ObjectProperty
sub property of: has participant
definition: p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c

causal relation between material entity and a process
type: ObjectProperty
sub property of: causally related to
domain: material entity
range: process
definition: A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
editor note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
definition editor: Chris Mungall
definition source: causal-relations
imported from: cl.owl

capable of regulating
type: ObjectProperty
sub property of: causal agent in
property chain axiom: capable of
property chain axiom: regulates
example of usage: pyrethroid -> growth
definition: Holds between c and p if and only if c is capable of some activity a, and a regulates p.
definition source: causal-relations

capable of negatively regulating
type: ObjectProperty
sub property of: capable of regulating
property chain axiom: capable of
property chain axiom: negatively regulates
definition: Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
definition source: causal-relations

capable of positively regulating
type: ObjectProperty
sub property of: capable of regulating
property chain axiom: capable of
property chain axiom: positively regulates
example of usage: renin -> arteriolar smooth muscle contraction
definition: Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
definition source: causal-relations

capable of inhibiting or preventing pathological process
type: ObjectProperty
sub property of: capable of negatively regulating
example of usage: pazopanib -> pathological angiogenesis
definition: Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p.
alternative term: treats
definition source: causal-relations
curator note: The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber.

Axiom
annotated source: capable of inhibiting or preventing pathological process
annotated property: alternative term
annotated target: treats
comment: Usage of the term 'treats' applies when we believe there to be a an inhibitory relationship

capable of upregulating or causing pathological process
type: ObjectProperty
sub property of: capable of positively regulating
example of usage: benzene -> cancer [CHEBI]
definition: Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p.
alternative term: causes disease
definition source: causal-relations

is substance that treats
type: ObjectProperty
sub property of: capable of inhibiting or preventing pathological process
definition: c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d.
alternative term: treats
definition source: causal-relations

is marker for
type: ObjectProperty
definition: c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d.
editor note: May be ceded to OBI

has causal agent
type: ObjectProperty
sub property of: causally related to
domain: process
range: material entity
definition: Inverse of 'causal agent in'
definition source: causal-relations
imported from: cl.owl

related via dependence to
type: ObjectProperty
domain: entity
range: entity
definition: A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.
curator note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
imported from: cl.owl

is evidence with support from
type: ObjectProperty
sub property of: related via evidence or inference to
example of usage: An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support.
definition: A relationship between a piece of evidence and an entity that plays a role in supporting that evidence.
comment: In the Gene Ontology association model, this corresponds to the With/From field

related via evidence or inference to
type: ObjectProperty

directly positively regulates
type: ObjectProperty
sub property of: positively regulates
sub property of: directly regulates
definition: p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p
definition source: causal-relations
obo foundry unique label: directly positively regulates (process to process)

directly negatively regulates
type: ObjectProperty
sub property of: negatively regulates
sub property of: directly regulates
definition: p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p
definition source: causal-relations
obo foundry unique label: directly negatively regulates (process to process)

represses expression of
type: ObjectProperty
sub property of: molecularly decreases activity of
definition: Holds between protein a (a transcription factor) and DNA element b if and only if a diminishes the process of transcription of b.
editor note: Logical axioms to be added after the relevant branch of GO is MIREOTed in

increases expression of
type: ObjectProperty
sub property of: molecularly increases activity of
definition: Holds between protein a (a transcription factor) and DNA element b if and only if a activates the process of transcription of b.
editor note: Logical axioms to be added after the relevant branch of GO is MIREOTed in

causes or contributes to condition
type: ObjectProperty
sub property of: causally related to
example of usage: The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'. An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'.
definition: A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some causal or contributing role that influences the condition.
editor note: Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'.
comment: Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. Environments include natural environments or exposures, experimentally applied conditions, or clinical interventions.

causes condition
type: ObjectProperty
sub property of: causes or contributes to condition
definition: A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has a causal role for the condition.

contributes to condition
type: ObjectProperty
sub property of: causes or contributes to condition
definition: A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some contributing role in the manifestation of the condition.

contributes to severity of condition
type: ObjectProperty
sub property of: contributes to condition
definition: A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the severity with which a condition manifests in an individual.
alternative term: contributes to expressivity of condition

contributes to frequency of condition
type: ObjectProperty
sub property of: contributes to condition
definition: A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the frequency of the condition in a population.
alternative term: contributes to penetrance of condition

is preventative for condition
type: ObjectProperty
sub property of: causally related to
definition: A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity prevents or reduces the severity of a condition.
comment: Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. Environments include natural environments or exposures, experimentally applied conditions, or clinical interventions.

correlated with condition
type: ObjectProperty
definition: A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship.

disease arises from feature
type: ObjectProperty
domain: disease
range: Class
  union of: phenotype
  union of: disease
comment: A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature.

has phenotype affecting
type: ObjectProperty
property chain axiom: has_part
property chain axiom: depends on
property chain axiom: part of
imported from: hp.owl

towards
type: ObjectProperty
editor note: AG: Currently the only way to handle relational quality?
comment: relation binding a relational quality or disposition to the relevant type of entity

has measurement value
type: DatatypeProperty
sub property of: topDataProperty
type: FunctionalProperty
domain: scalar measurement datum

has x coordinate value
type: DatatypeProperty
sub property of: topDataProperty
type: FunctionalProperty
domain: cartesian spatial coordinate datum
range: float

has z coordinate value
type: DatatypeProperty
sub property of: topDataProperty
type: FunctionalProperty
domain: cartesian spatial coordinate datum
range: float

has y coordinate value
type: DatatypeProperty
sub property of: topDataProperty
type: FunctionalProperty
domain: cartesian spatial coordinate datum
range: float

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

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

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

continuant
type: Class
subclass of: entity
disjoint with: occurrent
disjoint with: Restriction
  on property: part of
  some values from: occurrent
BFO OWL specification label: continuant
BFO CLIF specification label: Continuant
definition: An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
editor note: BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
editor note: Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
imported from: cl.owl
imported from: hp.owl
elucidation: A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
has associated axiom(nl): if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
has associated axiom(nl): if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
has associated axiom(nl): if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
has associated axiom(fol): (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
has associated axiom(fol): (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

spatiotemporal region
type: Class
subclass of: occurrent
BFO OWL specification label: st-region
BFO CLIF specification label: SpatiotemporalRegion
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
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])
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 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 y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
has associated axiom(fol): (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
has associated axiom(fol): (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]

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

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

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

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

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

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

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

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

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

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

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

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

Axiom
annotated source: process
annotated property: has associated axiom(fol)
annotated target: (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
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
BFO CLIF specification label: Disposition
example of usage: an atom of element X has the disposition to decay to an atom of element Y
example of usage: certain people have a predisposition to colon cancer
example of usage: children are innately disposed to categorize objects in certain ways.
example of usage: the cell wall is disposed to filter chemicals in endocytosis and exocytosis
editor note: BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
elucidation: b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
has associated axiom(nl): If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
has associated axiom(fol): (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
has associated axiom(fol): (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]

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

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

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

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

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

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

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

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

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

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

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

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

quality
type: Class
subclass of: specifically dependent continuant
BFO OWL specification label: quality
BFO CLIF specification label: Quality
example of usage: the ambient temperature of this portion of air
example of usage: the color of a tomato
example of usage: the length of the circumference of your waist
example of usage: the mass of this piece of gold.
example of usage: the shape of your nose
example of usage: the shape of your nostril
imported from: hp.owl
imported from: pr.owl
elucidation: a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
has associated axiom(nl): If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
has associated axiom(fol): (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
has associated axiom(fol): (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
has_obo_namespace: bfo
id: BFO:0000019

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

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

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

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

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

Axiom
annotated source: specifically dependent continuant
annotated property: definition
annotated target: b is a 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/050-003

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

Axiom
annotated source: specifically dependent continuant
annotated property: has associated axiom(fol)
annotated target: (iff (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/050-003

role
type: Class
subclass of: realizable entity
BFO OWL specification label: role
BFO CLIF specification label: Role
example of usage: John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
example of usage: the priest role
example of usage: the role of a boundary to demarcate two neighboring administrative territories
example of usage: the role of a building in serving as a military target
example of usage: the role of a stone in marking a property boundary
example of usage: the role of subject in a clinical trial
example of usage: the student role
definition: A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
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.
imported from: The Ontology of Medically Related Social Entities
elucidation: b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
has associated axiom(fol): (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]

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

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

fiat object part
type: Class
subclass of: material entity
BFO OWL specification label: fiat-object-part
BFO CLIF specification label: FiatObjectPart
example of usage: or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29
example of usage: the FMA:regional parts of an intact human body.
example of usage: the Western hemisphere of the Earth
example of usage: the division of the brain into regions
example of usage: the division of the planet into hemispheres
example of usage: the dorsal and ventral surfaces of the body
example of usage: the upper and lower lobes of the left lung
editor note: BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions
imported from: pr.owl
elucidation: b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])
has associated axiom(fol): (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004]
has_obo_namespace: bfo
id: BFO:0000024

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

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

one-dimensional spatial region
type: Class
subclass of: spatial region
disjoint with: three-dimensional spatial region
BFO OWL specification label: 1d-s-region
BFO CLIF specification label: OneDimensionalSpatialRegion
example of usage: an edge of a cube-shaped portion of space.
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])
has associated axiom(fol): (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]

Axiom
annotated source: one-dimensional spatial region
annotated property: elucidation
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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/038-001

Axiom
annotated source: one-dimensional spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]
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
BFO CLIF specification label: ObjectAggregate
example of usage: a collection of cells in a blood biobank.
example of usage: a swarm of bees is an aggregate of members who are linked together through natural bonds
example of usage: a symphony orchestra
example of usage: an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)
example of usage: defined by fiat: the aggregate of members of an organization
example of usage: defined through physical attachment: the aggregate of atoms in a lump of granite
example of usage: defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
example of usage: defined via attributive delimitations such as: the patients in this hospital
example of usage: the aggregate of bearings in a constant velocity axle joint
example of usage: the aggregate of blood cells in your body
example of usage: the nitrogen atoms in the atmosphere
example of usage: the restaurants in Palo Alto
example of usage: your collection of Meissen ceramic plates.
editor note: An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
editor note: BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee).
definition source: ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
elucidation: b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
has associated axiom(fol): (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]

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

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

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

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

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

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

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

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

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

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

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

object
type: Class
subclass of: material entity
BFO OWL specification label: object
BFO CLIF specification label: Object
example of usage: atom
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
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: 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: an object is a maximal causally unified material entity
editor note: BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74
imported from: hp.owl
imported from: pr.owl
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])
has_obo_namespace: bfo
id: BFO:0000030

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

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

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

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

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

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

process boundary
type: Class
subclass of: occurrent
BFO OWL specification label: p-boundary
BFO CLIF specification label: ProcessBoundary
example of usage: the boundary between the 2nd and 3rd year of your life.
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])
has associated axiom(nl): Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
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(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]

Axiom
annotated source: process boundary
annotated property: definition
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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/084-001

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

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

Axiom
annotated source: process boundary
annotated property: has associated axiom(fol)
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]
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
BFO OWL specification label: 1d-t-region
BFO CLIF specification label: OneDimensionalTemporalRegion
example of usage: the temporal region during which a process occurs.
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).
elucidation: A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
has associated axiom(fol): (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]

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

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

material entity
type: Class
subclass of: independent continuant
disjoint with: immaterial entity
disjoint with: Restriction
  on property: part of
  some values from: immaterial entity
BFO OWL specification label: material
BFO CLIF specification label: MaterialEntity
example of usage: a flame
example of usage: a forest fire
example of usage: a human being
example of usage: a hurricane
example of usage: a photon
example of usage: a puff of smoke
example of usage: a sea wave
example of usage: a tornado
example of usage: an aggregate of human beings.
example of usage: an energy wave
example of usage: an epidemic
example of usage: the undetached arm of a human being
definition: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
editor note: BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
editor note: BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
editor note: BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
imported from: cl.owl
imported from: hp.owl
imported from: pr.owl
elucidation: A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
has associated axiom(nl): Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
has associated axiom(nl): every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
has associated axiom(fol): (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
has associated axiom(fol): (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
has associated axiom(fol): (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
has_obo_namespace: bfo
id: BFO:0000040

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

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

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

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

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

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

continuant fiat boundary
type: Class
subclass of: immaterial entity
BFO OWL specification label: cf-boundary
BFO CLIF specification label: ContinuantFiatBoundary
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])
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: 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
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.
has associated axiom(nl): Every continuant fiat boundary is located at some spatial region at every time at which it exists
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]

Axiom
annotated source: continuant fiat boundary
annotated property: definition
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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/029-001

Axiom
annotated source: continuant fiat boundary
annotated property: editor note
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.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000008

Axiom
annotated source: continuant fiat boundary
annotated property: has associated axiom(fol)
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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/029-001

immaterial entity
type: Class
subclass of: independent continuant
disjoint with: Restriction
  on property: has_part
  some values from: material entity
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
imported from: hp.owl

one-dimensional continuant fiat boundary
type: Class
subclass of: continuant fiat boundary
disjoint with: two-dimensional continuant fiat boundary
disjoint with: zero-dimensional continuant fiat boundary
BFO OWL specification label: 1d-cf-boundary
BFO CLIF specification label: OneDimensionalContinuantFiatBoundary
example of usage: The Equator
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
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])
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]

Axiom
annotated source: one-dimensional continuant fiat boundary
annotated property: elucidation
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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/032-001

Axiom
annotated source: one-dimensional continuant fiat boundary
annotated property: has associated axiom(fol)
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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/032-001

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

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

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

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

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

relational quality
type: Class
subclass of: quality
BFO OWL specification label: r-quality
BFO CLIF specification label: RelationalQuality
example of usage: John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
example of usage: 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])
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]

Axiom
annotated source: relational quality
annotated property: definition
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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/057-001

Axiom
annotated source: relational quality
annotated property: has associated axiom(fol)
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]
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
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])
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]

Axiom
annotated source: two-dimensional continuant fiat boundary
annotated property: elucidation
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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/033-001

Axiom
annotated source: two-dimensional continuant fiat boundary
annotated property: has associated axiom(fol)
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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/033-001

zero-dimensional continuant fiat boundary
type: Class
subclass of: continuant fiat boundary
BFO OWL specification label: 0d-cf-boundary
BFO CLIF specification label: ZeroDimensionalContinuantFiatBoundary
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.
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])
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]

Axiom
annotated source: zero-dimensional continuant fiat boundary
annotated property: editor note
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.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000001
comment: requested by Melanie Courtot

Axiom
annotated source: zero-dimensional continuant fiat boundary
annotated property: elucidation
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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/031-001

Axiom
annotated source: zero-dimensional continuant fiat boundary
annotated property: has associated axiom(fol)
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]
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
BFO CLIF specification label: ZeroDimensionalTemporalRegion
example of usage: a temporal region that is occupied by a process boundary
example of usage: right now
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.
alternative term: temporal instant.
elucidation: A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
has associated axiom(fol): (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]

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

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

history
type: Class
subclass of: process
BFO OWL specification label: history
BFO CLIF specification label: History
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])

Axiom
annotated source: history
annotated property: elucidation
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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/138-001

immaterial anatomical entity
type: Class
subclass of: immaterial entity

biological entity
type: Class
subclass of: independent continuant
subclass of: Restriction
  on property: has phenotype
  some values from: phenotype
imported from: hp.owl

disease of metabolism
type: Class
subclass of: disease
definition: A disease that involving errors in metabolic processes of building or degradation of molecules.
imported from: doid.owl
database_cross_reference: ICD10CM:E88.9
database_cross_reference: ICD9CM:277.9
database_cross_reference: MESH:D008659
database_cross_reference: NCI:C3235
database_cross_reference: SNOMEDCT_US_2016_03_01:154733004
database_cross_reference: SNOMEDCT_US_2016_03_01:190961002
database_cross_reference: SNOMEDCT_US_2016_03_01:267456000
database_cross_reference: SNOMEDCT_US_2016_03_01:30390004
database_cross_reference: SNOMEDCT_US_2016_03_01:75934005
database_cross_reference: UMLS_CUI:C0025517
has_exact_synonym: metabolic disease
has_obo_namespace: disease_ontology
id: DOID:0014667
in_subset: DO AGR slim
in_subset: NCIthesaurus

carbohydrate metabolism disease
type: Class
subclass of: acquired metabolic disease
definition: An acquired metabolic disease that is characterized by abnormal carbohydrate metabolism.
imported from: doid.owl
has_obo_namespace: disease_ontology
id: DOID:0050013
in_subset: DO FlyBase slim
in_subset: DO MGI slim

disease by infectious agent
type: Class
subclass of: disease
definition: A disease that is the consequence of the presence of pathogenic microbial agents, including pathogenic viruses, pathogenic bacteria, fungi, protozoa, multicellular parasites, and aberrant proteins known as prions.
imported from: doid.owl
has_alternative_id: DOID:10115
has_alternative_id: DOID:11078
has_alternative_id: DOID:1304
has_alternative_id: DOID:1321
has_alternative_id: DOID:2040
has_alternative_id: DOID:2288
has_alternative_id: DOID:3099
has_alternative_id: DOID:4120
has_alternative_id: DOID:4620
has_alternative_id: DOID:5256
has_alternative_id: DOID:945
has_alternative_id: DOID:95
has_alternative_id: DOID:9532
has_alternative_id: DOID:9696
database_cross_reference: ICD9CM:079.0
database_cross_reference: UMLS_CUI:C0001485
has_exact_synonym: infectious disease
has_obo_namespace: disease_ontology
id: DOID:0050117
in_subset: DO AGR slim
in_subset: DO MGI slim
in_subset: NCIthesaurus

aspiration pneumonia
type: Class
subclass of: bacterial pneumonia
definition: A bacterial pneumonia which is an acute pulmonary inflammatory response that develops after the inhalation of colonized oropharyngeal material containing bacteria. It is seen in individuals with dysphagia and gastric dysmotility. The disease has_symptom tachypnea and has_symptom cough.
imported from: doid.owl
database_cross_reference: ICD10CM:J69.0
database_cross_reference: MESH:D011015
database_cross_reference: SNOMEDCT_US_2016_03_01:422588002
database_cross_reference: SNOMEDCT_US_2016_03_01:47839005
database_cross_reference: UMLS_CUI:C0032290
has_obo_namespace: disease_ontology
id: DOID:0050152

sensory system disease
type: Class
subclass of: nervous system disease
definition: A nervous system disease which is located in a part of the nervous system responsible for processing sensory information that consists of sensory receptors, neural pathways, and parts of the brain involved in sensory perception. Commonly recognized sensory systems are those for vision, hearing, somatic sensation (touch), taste and olfaction (smell).
imported from: doid.owl
has_obo_namespace: disease_ontology
id: DOID:0050155
in_subset: DO FlyBase slim

lower respiratory tract disease
type: Class
subclass of: respiratory system disease
definition: A respiratory system disease which involves the lower respiratory tract.
imported from: doid.owl
database_cross_reference: ICD9CM:478.1
database_cross_reference: ICD9CM:478.19
database_cross_reference: SNOMEDCT_US_2016_03_01:195823002
database_cross_reference: SNOMEDCT_US_2016_03_01:266346007
database_cross_reference: UMLS_CUI:C0029581
has_obo_namespace: disease_ontology
id: DOID:0050161

monogenic disease
type: Class
subclass of: genetic disease
definition: A genetic disease that is the result of one or more abnormal alleles and may be dominant (a single copy of the abnormal allele is sufficient to give rise to the disease), semi-dominant, or recessive (requiring both copies of the gene to have an abnormal allele).
imported from: doid.owl
has_obo_namespace: disease_ontology
id: DOID:0050177

respiratory system cancer
type: Class
subclass of: organ system cancer
definition: An organ system cancer located_in the respiratory system that is characterized by uncontrolled cellular proliferation in the respiratory tract.
imported from: doid.owl
has_obo_namespace: disease_ontology
id: DOID:0050615

reproductive organ benign neoplasm
type: Class
subclass of: organ system benign neoplasm
definition: An organ system benign neoplasm that is located_in reproductive system organs.
imported from: doid.owl
has_obo_namespace: disease_ontology
id: DOID:0050622

organ system cancer
type: Class
subclass of: cancer
definition: A cancer that is classified based on the organ it starts in.
imported from: doid.owl
created by: snadendla
creation date: 2011-06-13T03:28:33Z
database_cross_reference: MESH:D009371
has_obo_namespace: disease_ontology
id: DOID:0050686

cell type cancer
type: Class
subclass of: cancer
definition: A cancer that is classified by the type of cell from which it is derived.
imported from: doid.owl
created by: snadendla
creation date: 2011-06-13T03:28:50Z
has_obo_namespace: disease_ontology
id: DOID:0050687
in_subset: DO MGI slim

cardiomyopathy
type: Class
subclass of: heart disease
definition: A heart disease and a myopathy that is characterized by deterioration of the function of the heart muscle.
imported from: doid.owl
created by: lschriml
creation date: 2012-01-03T02:54:11Z
database_cross_reference: ICD10CM:I42
database_cross_reference: ICD10CM:I42.9
database_cross_reference: ICD10CM:I51.5
database_cross_reference: ICD9CM:425
database_cross_reference: ICD9CM:425.9
database_cross_reference: MESH:D009202
database_cross_reference: NCI:C34830
database_cross_reference: NCI:C53654
database_cross_reference: SNOMEDCT_US_2016_03_01:155351008
database_cross_reference: SNOMEDCT_US_2016_03_01:155353006
database_cross_reference: SNOMEDCT_US_2016_03_01:195035002
database_cross_reference: SNOMEDCT_US_2016_03_01:195037005
database_cross_reference: SNOMEDCT_US_2016_03_01:20072003
database_cross_reference: SNOMEDCT_US_2016_03_01:266244008
database_cross_reference: SNOMEDCT_US_2016_03_01:266301006
database_cross_reference: SNOMEDCT_US_2016_03_01:57809008
database_cross_reference: SNOMEDCT_US_2016_03_01:85898001
database_cross_reference: SNOMEDCT_US_2016_03_01:89461002
database_cross_reference: SNOMEDCT_US_2016_03_01:89600009
database_cross_reference: UMLS_CUI:C0033141
database_cross_reference: UMLS_CUI:C0036529
database_cross_reference: UMLS_CUI:C0878544
has_exact_synonym: Cardiomyopathies
has_obo_namespace: disease_ontology
id: DOID:0050700
in_subset: DO FlyBase slim
comment: MESH:D009202 added from NeuroDevNet [WAK].

autosomal dominant disease
type: Class
subclass of: autosomal genetic disease
definition: An autosomal genetic disease that is characterized by the presence of one disease-associated mutation of a gene which is sufficient to cause the disease.
imported from: doid.owl
created by: lschriml
creation date: 2012-07-24T12:51:47Z
has_obo_namespace: disease_ontology
id: DOID:0050736

autosomal genetic disease
type: Class
subclass of: monogenic disease
definition: A monogenic disease that is has material basis in a mutation in a single gene on one of the non-sex chromosomes.
imported from: doid.owl
created by: lschriml
creation date: 2012-07-24T04:45:53Z
has_obo_namespace: disease_ontology
id: DOID:0050739
in_subset: DO MGI slim

metabolic acidosis
type: Class
subclass of: acquired metabolic disease
definition: An acquired metabolic disease that characterized by excessive production of acid.
imported from: doid.owl
created by: lschriml
creation date: 2013-01-16T01:23:37Z
has_obo_namespace: disease_ontology
id: DOID:0050758

artery disease
type: Class
subclass of: vascular disease
definition: A vascular disease that is located_in an artery.
imported from: doid.owl
created by: lschriml
creation date: 2014-02-12T03:08:35Z
has_obo_namespace: disease_ontology
id: DOID:0050828

glomerulosclerosis
type: Class
subclass of: glomerulonephritis
definition: A glomerulonephritis that is characterized by hardening of the glomerulus in the kidney.
imported from: doid.owl
created by: lschriml
creation date: 2014-04-15T03:40:31Z
has_obo_namespace: disease_ontology
id: DOID:0050851

fibroma
type: Class
subclass of: cell type benign neoplasm
imported from: doid.owl
created by: lschriml
creation date: 2014-06-25T05:14:03Z
has_obo_namespace: disease_ontology
id: DOID:0050871

intrinsic cardiomyopathy
type: Class
subclass of: cardiomyopathy
definition: A cardiomyopathy that is characterized as weakness in the muscle of the heart that is not due to an identifiable external cause.
imported from: doid.owl
has_obo_namespace: disease_ontology
id: DOID:0060036

sexual disorder
type: Class
subclass of: disease of mental health
definition: A disease of mental health that involves the impairment in normal sexual functioning.
imported from: doid.owl
has_obo_namespace: disease_ontology
id: DOID:0060043

benign neoplasm
type: Class
subclass of: disease of cellular proliferation
definition: A disease of cellular proliferation that results in abnormal growths in the body which lack the ability to metastasize.
imported from: doid.owl
created by: lschriml
creation date: 2011-05-11T12:18:41Z
has_obo_namespace: disease_ontology
id: DOID:0060072
in_subset: DO AGR slim
in_subset: DO MGI slim

cell type benign neoplasm
type: Class
subclass of: benign neoplasm
definition: A benign neoplasm that is classified by the type of cell or tissue from which it is derived.
imported from: doid.owl
created by: lschriml
creation date: 2011-07-14T11:59:48Z
has_obo_namespace: disease_ontology
id: DOID:0060084

organ system benign neoplasm
type: Class
subclass of: benign neoplasm
definition: A benign neoplasm that is classified by the organ system from which it is arising from.
imported from: doid.owl
created by: lschriml
creation date: 2011-07-14T12:12:23Z
has_obo_namespace: disease_ontology
id: DOID:0060085
in_subset: DO FlyBase slim

female reproductive organ benign neoplasm
type: Class
subclass of: reproductive organ benign neoplasm
imported from: doid.owl
created by: lschriml
creation date: 2011-07-14T12:20:52Z
has_obo_namespace: disease_ontology
id: DOID:0060086

uterine benign neoplasm
type: Class
subclass of: female reproductive organ benign neoplasm
imported from: doid.owl
created by: lschriml
creation date: 2011-07-15T01:42:11Z
has_alternative_id: DOID:0060113
has_obo_namespace: disease_ontology
id: DOID:0060095

acquired metabolic disease
type: Class
subclass of: disease of metabolism
definition: A disease of metabolism that has _material_basis_in enzyme deficiency or accumulation of enzymes or toxins which interfere with normal function due to an endocrine organ disease, organ malfunction, inadequate intake, dietary deficiency, or malabsorption.
imported from: doid.owl
created by: lschriml
creation date: 2011-08-24T02:53:03Z
has_obo_namespace: disease_ontology
id: DOID:0060158
in_subset: DO MGI slim

cardiac arrest
type: Class
subclass of: congestive heart failure
definition: A congestive heart failure characterized by a sudden stop in effective blood circulation due to the failure of the heart to contract effectively or at all.
imported from: doid.owl
created by: emitraka
creation date: 2015-02-25T15:12:30Z
database_cross_reference: ICD10CM:I46
database_cross_reference: ICD9CM:427.5
database_cross_reference: MESH:D006323
database_cross_reference: NCI:C50479
database_cross_reference: NCI:C50483
database_cross_reference: SNOMEDCT_US_2016_03_01:155372006
database_cross_reference: SNOMEDCT_US_2016_03_01:195085006
database_cross_reference: SNOMEDCT_US_2016_03_01:195090009
database_cross_reference: SNOMEDCT_US_2016_03_01:233926006
database_cross_reference: SNOMEDCT_US_2016_03_01:251189000
database_cross_reference: SNOMEDCT_US_2016_03_01:30298009
database_cross_reference: SNOMEDCT_US_2016_03_01:309810002
database_cross_reference: SNOMEDCT_US_2016_03_01:397829000
database_cross_reference: SNOMEDCT_US_2016_03_01:397912004
database_cross_reference: SNOMEDCT_US_2016_03_01:410429000
database_cross_reference: SNOMEDCT_US_2016_03_01:410430005
database_cross_reference: UMLS_CUI:C0018790
database_cross_reference: UMLS_CUI:C0600228
has_exact_synonym: cardiopulmonary arrest
has_exact_synonym: circulatory arrest
has_obo_namespace: disease_ontology
id: DOID:0060319

left bundle branch hemiblock
type: Class
subclass of: heart conduction disease
imported from: doid.owl
database_cross_reference: ICD10CM:I44.60
database_cross_reference: ICD9CM:426.2
database_cross_reference: SNOMEDCT_US_2016_03_01:195044001
database_cross_reference: SNOMEDCT_US_2016_03_01:195045000
database_cross_reference: SNOMEDCT_US_2016_03_01:266245009
database_cross_reference: SNOMEDCT_US_2016_03_01:4973001
database_cross_reference: UMLS_CUI:C0155702
has_exact_synonym: Left bundle branch [block] or [hemiblock]
has_exact_synonym: Left bundle branch hemiblock (disorder)
has_exact_synonym: Left bundle branch hemiblock NOS (disorder)
has_obo_namespace: disease_ontology
id: DOID:10272

heart conduction disease
type: Class
subclass of: heart disease
definition: A cardiovascular system disease that involves the heart's electrical conduction system.
imported from: doid.owl
database_cross_reference: ICD9CM:426.6
database_cross_reference: SNOMEDCT_US_2016_03_01:195053008
database_cross_reference: SNOMEDCT_US_2016_03_01:195056000
database_cross_reference: UMLS_CUI:C0029630
has_exact_synonym: heart rhythm disease
has_obo_namespace: disease_ontology
id: DOID:10273

bacterial infectious disease
type: Class
equivalent class: Class
  intersection of: disease by infectious agent
  intersection of: Restriction
    on property: has material basis in
    some values from: Bacteria
subclass of: disease by infectious agent
subclass of: Restriction
  on property: BFO_0000113
  some values from: Bacteria
subclass of: Restriction
  on property: has material basis in
  some values from: Bacteria
definition: A disease by infectious agent that results_in infection, has_material_basis_in Bacteria.
imported from: doid.owl
database_cross_reference: ICD10CM:A49
database_cross_reference: ICD10CM:A49.9
database_cross_reference: MESH:D001424
database_cross_reference: MESH:D016905
database_cross_reference: MESH:D016908
database_cross_reference: NCI:C2890
database_cross_reference: SNOMEDCT_US_2016_03_01:154318005
database_cross_reference: SNOMEDCT_US_2016_03_01:186470002
database_cross_reference: SNOMEDCT_US_2016_03_01:187347000
database_cross_reference: SNOMEDCT_US_2016_03_01:266182006
database_cross_reference: SNOMEDCT_US_2016_03_01:266187000
database_cross_reference: SNOMEDCT_US_2016_03_01:301811001
database_cross_reference: SNOMEDCT_US_2016_03_01:87628006
database_cross_reference: UMLS_CUI:C0004623
has_obo_namespace: disease_ontology
id: DOID:104
in_subset: DO FlyBase slim

pre-eclampsia
type: Class
subclass of: hypertension
definition: A hypertension occurring during pregnancy characterized by large amounts of protein in the urine (proteinuria) and edema, usually by the last trimester of pregnancy.
imported from: doid.owl
has_alternative_id: DOID:12684
database_cross_reference: ICD10CM:O14
database_cross_reference: ICD10CM:O14.9
database_cross_reference: ICD10CM:O14.90
database_cross_reference: MESH:D011225
database_cross_reference: NCI:C34943
database_cross_reference: NCI:C85021
database_cross_reference: OMIM:189800
database_cross_reference: OMIM:609402
database_cross_reference: OMIM:609403
database_cross_reference: OMIM:609404
database_cross_reference: OMIM:614592
database_cross_reference: ORDO:275555
database_cross_reference: SNOMEDCT_US_2016_03_01:15394000
database_cross_reference: SNOMEDCT_US_2016_03_01:156106005
database_cross_reference: SNOMEDCT_US_2016_03_01:156109003
database_cross_reference: SNOMEDCT_US_2016_03_01:198972006
database_cross_reference: SNOMEDCT_US_2016_03_01:198979002
database_cross_reference: SNOMEDCT_US_2016_03_01:199011002
database_cross_reference: SNOMEDCT_US_2016_03_01:237280005
database_cross_reference: SNOMEDCT_US_2016_03_01:267306006
database_cross_reference: SNOMEDCT_US_2016_03_01:288201007
database_cross_reference: SNOMEDCT_US_2016_03_01:398254007
database_cross_reference: SNOMEDCT_US_2016_03_01:46764007
database_cross_reference: SNOMEDCT_US_2016_03_01:6758009
database_cross_reference: UMLS_CUI:C0032914
has_exact_synonym: gestational hypertension
has_exact_synonym: hypertension induced by pregnancy
has_exact_synonym: pre-eclamptic toxaemia
has_exact_synonym: preeclampsia
has_exact_synonym: preeclampsia/eclampsia
has_exact_synonym: pregnancy associated hypertension
has_exact_synonym: pregnancy toxemia
has_exact_synonym: proteinuric hypertension of pregnancy
has_exact_synonym: toxaemia of pregnancy
has_obo_namespace: disease_ontology
id: DOID:10591
in_subset: DO rare slim
comment: Xref MGI. OMIM mapping confirmed by DO. [SN].

renal hypertension
type: Class
subclass of: secondary hypertension
imported from: doid.owl
database_cross_reference: MESH:D006977
database_cross_reference: NCI:C3121
database_cross_reference: SNOMEDCT_US_2016_03_01:194775007
database_cross_reference: SNOMEDCT_US_2016_03_01:28119000
database_cross_reference: UMLS_CUI:C0020544
has_obo_namespace: disease_ontology
id: DOID:1073

kidney failure
type: Class
subclass of: kidney disease
definition: A kidney disease characterized by the failure of the kidneys to adequately filter waste products from the blood.
imported from: doid.owl
database_cross_reference: ICD10CM:N19
database_cross_reference: ICD9CM:586
database_cross_reference: MESH:D051437
database_cross_reference: NCI:C4376
database_cross_reference: SNOMEDCT_US_2016_03_01:156092003
database_cross_reference: SNOMEDCT_US_2016_03_01:197656003
database_cross_reference: SNOMEDCT_US_2016_03_01:198524000
database_cross_reference: SNOMEDCT_US_2016_03_01:266553002
database_cross_reference: SNOMEDCT_US_2016_03_01:266616000
database_cross_reference: SNOMEDCT_US_2016_03_01:42399005
database_cross_reference: UMLS_CUI:C0035078
has_exact_synonym: renal failure
has_obo_namespace: disease_ontology
id: DOID:1074
comment: PRISM.

chronic pyelonephritis
type: Class
subclass of: pyelonephritis
imported from: doid.owl
database_cross_reference: ICD10CM:N11
database_cross_reference: ICD10CM:N11.9
database_cross_reference: ICD9CM:590.0
database_cross_reference: NCI:C123216
database_cross_reference: SNOMEDCT_US_2016_03_01:123293005
database_cross_reference: SNOMEDCT_US_2016_03_01:155861006
database_cross_reference: SNOMEDCT_US_2016_03_01:197767009
database_cross_reference: SNOMEDCT_US_2016_03_01:266619007
database_cross_reference: SNOMEDCT_US_2016_03_01:63302006
database_cross_reference: UMLS_CUI:C0085697
has_obo_namespace: disease_ontology
id: DOID:1076

hypertension
type: Class
subclass of: artery disease
subclass of: Restriction
  on property: disease arises from feature
  some values from: Hypertension
definition: An artery disease characterized by chronic elevated blood pressure in the arteries.
imported from: doid.owl
database_cross_reference: EFO:0000537
database_cross_reference: ICD10CM:I10
database_cross_reference: ICD10CM:I10-I15
database_cross_reference: ICD9CM:401-405.99
database_cross_reference: ICD9CM:997.91
database_cross_reference: MESH:D006973
database_cross_reference: NCI:C3117
database_cross_reference: SNOMEDCT_US_2016_03_01:155295004
database_cross_reference: SNOMEDCT_US_2016_03_01:155302005
database_cross_reference: SNOMEDCT_US_2016_03_01:194756002
database_cross_reference: SNOMEDCT_US_2016_03_01:194757006
database_cross_reference: SNOMEDCT_US_2016_03_01:194760004
database_cross_reference: SNOMEDCT_US_2016_03_01:194794002
database_cross_reference: SNOMEDCT_US_2016_03_01:195537001
database_cross_reference: SNOMEDCT_US_2016_03_01:266287006
database_cross_reference: SNOMEDCT_US_2016_03_01:38341003
database_cross_reference: UMLS_CUI:C0020538
has_exact_synonym: HTN
has_exact_synonym: High blood pressure (& [essential hypertension])
has_exact_synonym: hyperpiesia
has_exact_synonym: vascular hypertensive disorder
has_obo_namespace: disease_ontology
has_related_synonym: hypertensive disease
id: DOID:10763

thrombotic thrombocytopenic purpura
type: Class
subclass of: thrombophilia
imported from: doid.owl
database_cross_reference: ICD10CM:M31.1
database_cross_reference: MESH:D011697
database_cross_reference: NCI:C78797
database_cross_reference: SNOMEDCT_US_2016_03_01:155443009
database_cross_reference: SNOMEDCT_US_2016_03_01:195358008
database_cross_reference: SNOMEDCT_US_2016_03_01:195359000
database_cross_reference: SNOMEDCT_US_2016_03_01:360402008
database_cross_reference: SNOMEDCT_US_2016_03_01:78129009
database_cross_reference: UMLS_CUI:C0034155
has_exact_synonym: Moschcowitz's syndrome
has_obo_namespace: disease_ontology
id: DOID:10772

essential hypertension
type: Class
subclass of: hypertension
definition: A hypertension with no known cause. It is the most common type of hypertension.
imported from: doid.owl
database_cross_reference: ICD10CM:I10
database_cross_reference: ICD9CM:401
database_cross_reference: ICD9CM:401.9
database_cross_reference: MESH:C562386
database_cross_reference: NCI:C3478
database_cross_reference: OMIM:145500
database_cross_reference: OMIM:603918
database_cross_reference: OMIM:604329
database_cross_reference: OMIM:607329
database_cross_reference: OMIM:608742
database_cross_reference: OMIM:610261
database_cross_reference: OMIM:610262
database_cross_reference: OMIM:610948
database_cross_reference: OMIM:611014
database_cross_reference: ORDO:243761
database_cross_reference: SNOMEDCT_US_2016_03_01:155296003
database_cross_reference: SNOMEDCT_US_2016_03_01:194757006
database_cross_reference: SNOMEDCT_US_2016_03_01:194760004
database_cross_reference: SNOMEDCT_US_2016_03_01:266228004
database_cross_reference: SNOMEDCT_US_2016_03_01:59621000
database_cross_reference: UMLS_CUI:C0085580
has_exact_synonym: idiopathic hypertension
has_exact_synonym: primary hypertension
has_obo_namespace: disease_ontology
id: DOID:10825
in_subset: DO rare slim
comment: Xref MGI. OMIM mapping confirmed by DO. [SN].

abducens nerve disease
type: Class
subclass of: cranial nerve palsy
imported from: doid.owl
database_cross_reference: ICD10CM:H49.2
database_cross_reference: ICD9CM:378.54
database_cross_reference: MESH:D020434
database_cross_reference: NCI:C27592
database_cross_reference: NCI:C27593
database_cross_reference: OMIM:100200
database_cross_reference: SNOMEDCT_US_2016_03_01:14720007
database_cross_reference: SNOMEDCT_US_2016_03_01:230533001
database_cross_reference: SNOMEDCT_US_2016_03_01:398760006
database_cross_reference: SNOMEDCT_US_2016_03_01:398925009
database_cross_reference: SNOMEDCT_US_2016_03_01:398963001
database_cross_reference: SNOMEDCT_US_2016_03_01:46587002
database_cross_reference: SNOMEDCT_US_2016_03_01:4892003
database_cross_reference: SNOMEDCT_US_2016_03_01:82373004
database_cross_reference: UMLS_CUI:C0271355
has_exact_synonym: Abducens nerve disorder
has_exact_synonym: Abducens nerve weakness
has_exact_synonym: Lateral rectus muscle denervation paresis
has_exact_synonym: Lateral rectus muscle innervation disorder
has_exact_synonym: Sixth cranial nerve disorder, NOS
has_exact_synonym: Sixth nerve palsy (disorder)
has_exact_synonym: Sixth or abducens nerve palsy
has_exact_synonym: VIth nerve Paralysis
has_exact_synonym: VIth nerve disorder
has_exact_synonym: disorder of abducent nerve
has_obo_namespace: disease_ontology
id: DOID:10865

hydrocephalus
type: Class
subclass of: cerebral degeneration
definition: A cerebral degeneration characterized by an abnormal accumulation of cerebrospinal fluid in the ventricles of the brain, leading to progressive enlargement of the head.
imported from: doid.owl
database_cross_reference: ICD10CM:G91
database_cross_reference: ICD10CM:G91.9
database_cross_reference: MESH:D006849
database_cross_reference: NCI:C3111
database_cross_reference: OMIM:123155
database_cross_reference: OMIM:236600
database_cross_reference: OMIM:236635
database_cross_reference: OMIM:307000
database_cross_reference: OMIM:615219
database_cross_reference: ORDO:2182
database_cross_reference: ORDO:2185
database_cross_reference: SNOMEDCT_US_2016_03_01:154995000
database_cross_reference: SNOMEDCT_US_2016_03_01:154997008
database_cross_reference: SNOMEDCT_US_2016_03_01:192807008
database_cross_reference: SNOMEDCT_US_2016_03_01:230745008
database_cross_reference: SNOMEDCT_US_2016_03_01:267687006
database_cross_reference: UMLS_CUI:C0020255
has_exact_synonym: hydrocephalus, X-linked
has_exact_synonym: hydrocephalus, nonsyndromic, autosomal recessive
has_obo_namespace: disease_ontology
id: DOID:10908
in_subset: DO rare slim
comment: Xref MGI. OMIM mapping confirmed by DO. [SN].

tongue disease
type: Class
subclass of: mouth disease
imported from: doid.owl
database_cross_reference: ICD10CM:K14
database_cross_reference: ICD10CM:K14.9
database_cross_reference: ICD9CM:529.9
database_cross_reference: MESH:D014060
database_cross_reference: SNOMEDCT_US_2016_03_01:155533008
database_cross_reference: SNOMEDCT_US_2016_03_01:155665004
database_cross_reference: SNOMEDCT_US_2016_03_01:155667007
database_cross_reference: SNOMEDCT_US_2016_03_01:196595001
database_cross_reference: SNOMEDCT_US_2016_03_01:266496009
database_cross_reference: SNOMEDCT_US_2016_03_01:69244009
database_cross_reference: UMLS_CUI:C0040409
has_obo_namespace: disease_ontology
id: DOID:10944

nephritis
type: Class
subclass of: kidney disease
definition: A kidney disease that is characterized by an inflammation of the kidneys.
imported from: doid.owl
database_cross_reference: ICD10CM:N05
database_cross_reference: ICD10CM:N08
database_cross_reference: MESH:D009393
database_cross_reference: NCI:C26833
database_cross_reference: SNOMEDCT_US_2016_03_01:155853001
database_cross_reference: SNOMEDCT_US_2016_03_01:266615001
database_cross_reference: SNOMEDCT_US_2016_03_01:274107001
database_cross_reference: SNOMEDCT_US_2016_03_01:52845002
database_cross_reference: UMLS_CUI:C0027697
has_obo_namespace: disease_ontology
id: DOID:10952

secondary hypertension
type: Class
subclass of: hypertension
imported from: doid.owl
database_cross_reference: ICD10CM:I15
database_cross_reference: ICD10CM:I15.9
database_cross_reference: ICD9CM:405
database_cross_reference: ICD9CM:405.9
database_cross_reference: NCI:C3657
database_cross_reference: SNOMEDCT_US_2016_03_01:155300002
database_cross_reference: SNOMEDCT_US_2016_03_01:194789002
database_cross_reference: SNOMEDCT_US_2016_03_01:194792003
database_cross_reference: SNOMEDCT_US_2016_03_01:31992008
database_cross_reference: UMLS_CUI:C0155616
has_obo_namespace: disease_ontology
id: DOID:11130

respiratory failure
type: Class
subclass of: lung disease
definition: A lung disease characterized by inadequate gas exchange by the respiratory system.
imported from: doid.owl
has_alternative_id: DOID:11391
has_alternative_id: DOID:11392
has_alternative_id: DOID:11393
database_cross_reference: ICD10CM:J96.0
database_cross_reference: ICD9CM:518.81
database_cross_reference: NCI:C27043
database_cross_reference: SNOMEDCT_US_2016_03_01:65710008
database_cross_reference: UMLS_CUI:C0264490
has_exact_synonym: acute and chronic respiratory failure
has_exact_synonym: acute respiratory Failure
has_exact_synonym: acute-on-chronic respiratory failure
has_exact_synonym: chronic respiratory failure
has_exact_synonym: respiratory insufficiency/failure
has_obo_namespace: disease_ontology
id: DOID:11162

disseminated intravascular coagulation
type: Class
subclass of: thrombophilia
imported from: doid.owl
database_cross_reference: ICD10CM:D65
database_cross_reference: ICD9CM:286.6
database_cross_reference: MESH:D004211
database_cross_reference: NCI:C2992
database_cross_reference: SNOMEDCT_US_2016_03_01:267563002
database_cross_reference: SNOMEDCT_US_2016_03_01:67406007
database_cross_reference: UMLS_CUI:C0012739
has_exact_synonym: DIC
has_exact_synonym: Defibrination syndrome
has_exact_synonym: Diffuse or disseminated intravascular coagulation
has_obo_namespace: disease_ontology
id: DOID:11247

pulmonary edema
type: Class
subclass of: respiratory failure
imported from: doid.owl
has_alternative_id: DOID:13472
database_cross_reference: ICD10CM:J81
database_cross_reference: ICD10CM:J81.1
database_cross_reference: MESH:D011654
database_cross_reference: NCI:C26868
database_cross_reference: SNOMEDCT_US_2016_03_01:19242006
database_cross_reference: SNOMEDCT_US_2016_03_01:196119001
database_cross_reference: SNOMEDCT_US_2016_03_01:266408001
database_cross_reference: UMLS_CUI:C0034063
has_obo_namespace: disease_ontology
id: DOID:11396

heart disease
type: Class
subclass of: cardiovascular system disease
definition: A cardiovascular system disease that involves the heart.
imported from: doid.owl
database_cross_reference: ICD10CM:I51.9
database_cross_reference: ICD9CM:429.9
database_cross_reference: MESH:D006331
database_cross_reference: NCI:C3079
database_cross_reference: SNOMEDCT_US_2016_03_01:155263000
database_cross_reference: SNOMEDCT_US_2016_03_01:194707003
database_cross_reference: SNOMEDCT_US_2016_03_01:195152001
database_cross_reference: SNOMEDCT_US_2016_03_01:266275004
database_cross_reference: SNOMEDCT_US_2016_03_01:266311004
database_cross_reference: SNOMEDCT_US_2016_03_01:56265001
database_cross_reference: UMLS_CUI:C0018799
has_obo_namespace: disease_ontology
id: DOID:114
in_subset: DO FlyBase slim

pyelonephritis
type: Class
subclass of: pyelitis
imported from: doid.owl
database_cross_reference: ICD10CM:N10-N16
database_cross_reference: ICD10CM:N12
database_cross_reference: ICD10CM:N16
database_cross_reference: ICD9CM:590.80
database_cross_reference: MESH:D011704
database_cross_reference: NCI:C34965
database_cross_reference: SNOMEDCT_US_2016_03_01:197779009
database_cross_reference: SNOMEDCT_US_2016_03_01:197784003
database_cross_reference: SNOMEDCT_US_2016_03_01:45816000
database_cross_reference: UMLS_CUI:C0034186
has_obo_namespace: disease_ontology
id: DOID:11400

pseudotumor cerebri
type: Class
subclass of: cerebrovascular disease
subclass of: intracranial hypertension
imported from: doid.owl
database_cross_reference: ICD10CM:G93.2
database_cross_reference: ICD9CM:348.2
database_cross_reference: MESH:D011559
database_cross_reference: NCI:C85035
database_cross_reference: OMIM:243200
database_cross_reference: SNOMEDCT_US_2016_03_01:155052007
database_cross_reference: SNOMEDCT_US_2016_03_01:267701004
database_cross_reference: SNOMEDCT_US_2016_03_01:68267002
database_cross_reference: UMLS_CUI:C0033845
has_exact_synonym: Pseudotumor cerebri
has_exact_synonym: benign intracran. hypt.
has_exact_synonym: benign intracranial hypertension
has_exact_synonym: benign intracranial hypertension (disorder)
has_exact_synonym: idiopathic intracranial hypertension
has_obo_namespace: disease_ontology
id: DOID:11459
comment: OMIM mapping confirmed by DO. [SN].

autonomic nervous system disease
type: Class
subclass of: peripheral nervous system disease
imported from: doid.owl
database_cross_reference: ICD9CM:337.1
database_cross_reference: UMLS_CUI:C0154691
has_exact_synonym: autonomic nervous system disorder
has_obo_namespace: disease_ontology
id: DOID:11465

mitral valve insufficiency
type: Class
subclass of: mitral valve disease
imported from: doid.owl
has_alternative_id: DOID:11737
has_alternative_id: DOID:13947
database_cross_reference: ICD10CM:Q23.3
database_cross_reference: ICD9CM:396.3
database_cross_reference: ICD9CM:746.6
database_cross_reference: MESH:D008944
database_cross_reference: NCI:C50852
database_cross_reference: NCI:C50888
database_cross_reference: SNOMEDCT_US_2016_03_01:194736003
database_cross_reference: SNOMEDCT_US_2016_03_01:194977007
database_cross_reference: SNOMEDCT_US_2016_03_01:233857005
database_cross_reference: SNOMEDCT_US_2016_03_01:29928006
database_cross_reference: SNOMEDCT_US_2016_03_01:48724000
database_cross_reference: UMLS_CUI:C0026266
database_cross_reference: UMLS_CUI:C0158619
database_cross_reference: UMLS_CUI:C0264774
has_exact_synonym: Congenital insufficiency of mitral valve (disorder)
has_exact_synonym: Mitral valve incompetence
has_exact_synonym: congenital mitral insufficiency
has_exact_synonym: congenital mitral regurgitation
has_exact_synonym: mitral regurgitation
has_obo_namespace: disease_ontology
id: DOID:11502

hypertensive heart disease
type: Class
subclass of: heart disease
definition: A heart disease that is caused by high blood pressure.
imported from: doid.owl
database_cross_reference: ICD10CM:I11
database_cross_reference: ICD10CM:I11.9
database_cross_reference: ICD9CM:402
database_cross_reference: ICD9CM:402.9
database_cross_reference: SNOMEDCT_US_2016_03_01:155297007
database_cross_reference: SNOMEDCT_US_2016_03_01:194769003
database_cross_reference: SNOMEDCT_US_2016_03_01:194772005
database_cross_reference: SNOMEDCT_US_2016_03_01:64715009
database_cross_reference: UMLS_CUI:C0152105
has_obo_namespace: disease_ontology
id: DOID:11516

hypertensive retinopathy
type: Class
subclass of: retinal disease
imported from: doid.owl
database_cross_reference: ICD10CM:H35.03
database_cross_reference: ICD9CM:362.11
database_cross_reference: MESH:D058437
database_cross_reference: NCI:C3514
database_cross_reference: SNOMEDCT_US_2016_03_01:155108001
database_cross_reference: SNOMEDCT_US_2016_03_01:193356005
database_cross_reference: SNOMEDCT_US_2016_03_01:193358006
database_cross_reference: SNOMEDCT_US_2016_03_01:421731000
database_cross_reference: SNOMEDCT_US_2016_03_01:422001004
database_cross_reference: SNOMEDCT_US_2016_03_01:6962006
database_cross_reference: UMLS_CUI:C0152132
has_obo_namespace: disease_ontology
id: DOID:11561

nephrosclerosis
type: Class
subclass of: renal hypertension
imported from: doid.owl
database_cross_reference: ICD10CM:I12
database_cross_reference: ICD10CM:N26.9
database_cross_reference: ICD9CM:587
database_cross_reference: MESH:D009400
database_cross_reference: SNOMEDCT_US_2016_03_01:194773000
database_cross_reference: SNOMEDCT_US_2016_03_01:197658002
database_cross_reference: SNOMEDCT_US_2016_03_01:197662008
database_cross_reference: SNOMEDCT_US_2016_03_01:32916005
database_cross_reference: UMLS_CUI:C0027719
has_exact_synonym: renal sclerosis
has_obo_namespace: disease_ontology
id: DOID:11664

familial hyperlipidemia
type: Class
subclass of: lipid metabolism disorder
imported from: doid.owl
has_alternative_id: DOID:3147
database_cross_reference: ICD10CM:E78.5
database_cross_reference: MESH:D006949
database_cross_reference: MESH:D006951
database_cross_reference: NCI:C34707
database_cross_reference: NCI:C34709
database_cross_reference: SNOMEDCT_US_2016_03_01:154739000
database_cross_reference: SNOMEDCT_US_2016_03_01:154743001
database_cross_reference: SNOMEDCT_US_2016_03_01:190782002
database_cross_reference: SNOMEDCT_US_2016_03_01:267499005
database_cross_reference: SNOMEDCT_US_2016_03_01:3744001
database_cross_reference: SNOMEDCT_US_2016_03_01:55822004
database_cross_reference: UMLS_CUI:C0020473
database_cross_reference: UMLS_CUI:C0020476
has_exact_synonym: familial hyperlipoproteinemia
has_exact_synonym: hyperlipemia
has_obo_namespace: disease_ontology
has_related_synonym: hyperlipidaemia
id: DOID:1168

peripheral nervous system neoplasm
type: Class
subclass of: nervous system cancer
definition: A nervous system cancer that is located_in the peripheral nervous system.
imported from: doid.owl
has_alternative_id: DOID:3194
database_cross_reference: MESH:D010524
database_cross_reference: MESH:D018317
database_cross_reference: NCI:C3321
database_cross_reference: NCI:C4972
database_cross_reference: SNOMEDCT_US_2016_03_01:115242003
database_cross_reference: SNOMEDCT_US_2016_03_01:126980002
database_cross_reference: SNOMEDCT_US_2016_03_01:134214003
database_cross_reference: SNOMEDCT_US_2016_03_01:189946005
database_cross_reference: SNOMEDCT_US_2016_03_01:189953001
database_cross_reference: UMLS_CUI:C0031118
database_cross_reference: UMLS_CUI:C0206727
has_exact_synonym: neoplasm of peripheral nerve (disorder)
has_exact_synonym: nerve sheath neoplasm
has_exact_synonym: nerve sheath tumors
has_exact_synonym: tumor of PNS
has_obo_namespace: disease_ontology
id: DOID:1192
in_subset: TopNodes DOcancerslim

oligohydramnios
type: Class
subclass of: placenta disease
definition: A placenta disease that is characterized by a deficiency of amniotic fluid sometimes resulting in an embryonic defect through adherence between embryo and amnion.
imported from: doid.owl
has_alternative_id: DOID:12595
has_alternative_id: DOID:12596
database_cross_reference: ICD10CM:O41.0
database_cross_reference: ICD10CM:O41.00
database_cross_reference: ICD9CM:658.0
database_cross_reference: MESH:D016104
database_cross_reference: NCI:C92839
database_cross_reference: SNOMEDCT_US_2016_03_01:156190009
database_cross_reference: SNOMEDCT_US_2016_03_01:157051001
database_cross_reference: SNOMEDCT_US_2016_03_01:199652007
database_cross_reference: SNOMEDCT_US_2016_03_01:199656005
database_cross_reference: SNOMEDCT_US_2016_03_01:59566000
database_cross_reference: UMLS_CUI:C0079924
has_exact_synonym: Oligohydramnios - delivered
has_exact_synonym: antepartum oligohydramnios
has_exact_synonym: delivered oligohydramnios
has_obo_namespace: disease_ontology
id: DOID:12215

bronchopneumonia
type: Class
subclass of: pneumonia
definition: A pneumonia involving inflammation of lungs that begins in the terminal bronchioles, which become clogged with thick mucus that forms consolidated patches in adjacent lobules. It is caused by bacteria and viruses.
imported from: doid.owl
database_cross_reference: ICD10CM:J18.0
database_cross_reference: ICD9CM:485
database_cross_reference: MESH:D001996
database_cross_reference: NCI:C26710
database_cross_reference: SNOMEDCT_US_2016_03_01:155551009
database_cross_reference: SNOMEDCT_US_2016_03_01:195914001
database_cross_reference: SNOMEDCT_US_2016_03_01:266352008
database_cross_reference: SNOMEDCT_US_2016_03_01:396285007
database_cross_reference: SNOMEDCT_US_2016_03_01:67814005
database_cross_reference: UMLS_CUI:C0006285
has_exact_synonym: Chest infection - unspecified bronchopneumonia
has_exact_synonym: bronchial pneumonia
has_exact_synonym: lobular pneumonia
has_obo_namespace: disease_ontology
id: DOID:12375

blood coagulation disease
type: Class
subclass of: hematopoietic system disease
imported from: doid.owl
has_alternative_id: DOID:13997
has_alternative_id: DOID:9474
database_cross_reference: ICD10CM:D68.9
database_cross_reference: ICD9CM:286
database_cross_reference: MESH:D001778
database_cross_reference: NCI:C2902
database_cross_reference: SNOMEDCT_US_2016_03_01:127073005
database_cross_reference: SNOMEDCT_US_2016_03_01:154815003
database_cross_reference: SNOMEDCT_US_2016_03_01:191303002
database_cross_reference: SNOMEDCT_US_2016_03_01:267562007
database_cross_reference: SNOMEDCT_US_2016_03_01:362970003
database_cross_reference: SNOMEDCT_US_2016_03_01:64779008
database_cross_reference: UMLS_CUI:C0005779
has_exact_synonym: postpartum coagulation defect
has_exact_synonym: postpartum coagulation defect with delivery
has_obo_namespace: disease_ontology
id: DOID:1247

retinal ischemia
type: Class
subclass of: retinal disease
imported from: doid.owl
database_cross_reference: ICD10CM:H35.82
database_cross_reference: ICD9CM:362.84
database_cross_reference: SNOMEDCT_US_2016_03_01:193427006
database_cross_reference: SNOMEDCT_US_2016_03_01:26468004
database_cross_reference: UMLS_CUI:C0162291
has_obo_namespace: disease_ontology
id: DOID:12510

cardiovascular system disease
type: Class
subclass of: disease of anatomical entity
definition: A disease of anatomical entity which occurs in the blood, heart, blood vessels or the lymphatic system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells or lymph to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis.
imported from: doid.owl
has_alternative_id: DOID:73
database_cross_reference: ICD9CM:429.2
database_cross_reference: MESH:D002318
database_cross_reference: NCI:C2931
database_cross_reference: SNOMEDCT_US_2016_03_01:155263000
database_cross_reference: SNOMEDCT_US_2016_03_01:194707003
database_cross_reference: SNOMEDCT_US_2016_03_01:195139006
database_cross_reference: SNOMEDCT_US_2016_03_01:195594006
database_cross_reference: SNOMEDCT_US_2016_03_01:266275004
database_cross_reference: SNOMEDCT_US_2016_03_01:266336005
database_cross_reference: SNOMEDCT_US_2016_03_01:49601007
database_cross_reference: UMLS_CUI:C0007222
has_exact_synonym: disease of subdivision of hemolymphoid system
has_obo_namespace: disease_ontology
id: DOID:1287
in_subset: DO AGR slim
in_subset: DO MGI slim

dilated cardiomyopathy
type: Class
subclass of: intrinsic cardiomyopathy
definition: An intrinsic cardiomyopathy that is characterized by an an enlarged heart and damage to the myocardium causing the heart to pump blood inefficiently.
imported from: doid.owl
database_cross_reference: EFO:0000407
database_cross_reference: ICD10CM:I42.0
database_cross_reference: KEGG:05414
database_cross_reference: MESH:D002311
database_cross_reference: NCI:C84673
database_cross_reference: OMIM:PS115200
database_cross_reference: ORDO:217604
database_cross_reference: SNOMEDCT_US_2016_03_01:195018001
database_cross_reference: SNOMEDCT_US_2016_03_01:195021004
database_cross_reference: SNOMEDCT_US_2016_03_01:389995008
database_cross_reference: SNOMEDCT_US_2016_03_01:399020009
database_cross_reference: SNOMEDCT_US_2016_03_01:74368002
database_cross_reference: UMLS_CUI:C0007193
has_exact_synonym: primary dilated cardiomyopathy
has_obo_namespace: disease_ontology
has_related_synonym: Congestive cardiomyopathy
has_related_synonym: Familial dilated cardiomyopathy
has_related_synonym: Idiopathic dilation cardiomyopathy
id: DOID:12930
in_subset: DO FlyBase slim
in_subset: DO rare slim
comment: Xref MGI. OMIM mapping confirmed by DO. [LS].

branch retinal artery occlusion
type: Class
subclass of: retinal artery occlusion
imported from: doid.owl
database_cross_reference: ICD10CM:H34.23
database_cross_reference: ICD9CM:362.32
database_cross_reference: MESH:D015356
database_cross_reference: NCI:C34436
database_cross_reference: SNOMEDCT_US_2016_03_01:50821009
database_cross_reference: UMLS_CUI:C0006123
has_exact_synonym: Arterial retinal branch occlusion (disorder)
has_exact_synonym: Retinal Arterial Branch Occlusion
has_exact_synonym: Retinal arterial branch occlusion
has_obo_namespace: disease_ontology
id: DOID:13094

focal segmental glomerulosclerosis
type: Class
subclass of: glomerulosclerosis
imported from: doid.owl
has_alternative_id: DOID:3945
database_cross_reference: EFO:0004236
database_cross_reference: MESH:D005923
database_cross_reference: NCI:C37308
database_cross_reference: OMIM:PS603278
database_cross_reference: SNOMEDCT_US_2016_03_01:236403004
database_cross_reference: SNOMEDCT_US_2016_03_01:25821008
database_cross_reference: UMLS_CUI:C0017668
has_exact_synonym: FGS (focal glomerular sclerosis)
has_exact_synonym: FSGS
has_exact_synonym: focal glomerular sclerosis
has_exact_synonym: focal glomerulosclerosis
has_obo_namespace: disease_ontology
id: DOID:1312
comment: Xref MGI. OMIM mapping confirmed by DO. [SN].

acute cystitis
type: Class
subclass of: cystitis
definition: A cystitis characterized by a sudden onset or severe symptoms.
imported from: doid.owl
database_cross_reference: ICD10CM:N30.0
database_cross_reference: ICD9CM:595.0
database_cross_reference: NCI:C26934
database_cross_reference: SNOMEDCT_US_2016_03_01:155883005
database_cross_reference: SNOMEDCT_US_2016_03_01:197833009
database_cross_reference: SNOMEDCT_US_2016_03_01:266628008
database_cross_reference: SNOMEDCT_US_2016_03_01:68226007
database_cross_reference: UMLS_CUI:C0149523
has_exact_synonym: urinary tract infection
has_obo_namespace: disease_ontology
id: DOID:13148

uterine fibroid
type: Class
subclass of: fibroma
subclass of: uterine benign neoplasm
definition: A uterine benign neoplasm derived from the smooth muscle layer of the uterus.
imported from: doid.owl
database_cross_reference: EFO:0000731
database_cross_reference: ICD10CM:D25
database_cross_reference: ICD10CM:D25.9
database_cross_reference: ICD9CM:218
database_cross_reference: ICD9CM:218.9
database_cross_reference: MESH:D007889
database_cross_reference: NCI:C3434
database_cross_reference: OMIM:150699
database_cross_reference: SNOMEDCT_US_2016_03_01:146801000119103
database_cross_reference: SNOMEDCT_US_2016_03_01:154616000
database_cross_reference: SNOMEDCT_US_2016_03_01:189106003
database_cross_reference: SNOMEDCT_US_2016_03_01:44598004
database_cross_reference: SNOMEDCT_US_2016_03_01:95315005
database_cross_reference: UMLS_CUI:C0042133
has_exact_synonym: Plexiform leiomyoma
has_exact_synonym: UTERUS FIBROMA
has_exact_synonym: leiomyoma of Corpus Uteri
has_exact_synonym: uterine leiomyoma
has_obo_namespace: disease_ontology
id: DOID:13223
comment: OMIM mapping confirmed by DO. [LS].

lung cancer
type: Class
subclass of: respiratory system cancer
subclass of: lung disease
definition: A respiratory system cancer that is located_in the lung.
imported from: doid.owl
has_alternative_id: DOID:13075
has_alternative_id: DOID:1322
has_alternative_id: DOID:9881
database_cross_reference: ICD10CM:C34.1
database_cross_reference: ICD10CM:C34.2
database_cross_reference: ICD10CM:C34.3
database_cross_reference: ICD9CM:162.3
database_cross_reference: ICD9CM:162.4
database_cross_reference: ICD9CM:162.5
database_cross_reference: ICD9CM:162.8
database_cross_reference: OMIM:211980
database_cross_reference: OMIM:608935
database_cross_reference: OMIM:612571
database_cross_reference: OMIM:612593
database_cross_reference: OMIM:614210
database_cross_reference: SNOMEDCT_US_2016_03_01:187860004
database_cross_reference: SNOMEDCT_US_2016_03_01:187863002
database_cross_reference: SNOMEDCT_US_2016_03_01:187864008
database_cross_reference: SNOMEDCT_US_2016_03_01:187867001
database_cross_reference: SNOMEDCT_US_2016_03_01:187868006
database_cross_reference: SNOMEDCT_US_2016_03_01:187871003
database_cross_reference: SNOMEDCT_US_2016_03_01:187874006
database_cross_reference: SNOMEDCT_US_2016_03_01:269464000
database_cross_reference: UMLS_CUI:C0024624
database_cross_reference: UMLS_CUI:C0153491
database_cross_reference: UMLS_CUI:C0153492
database_cross_reference: UMLS_CUI:C0153493
has_obo_namespace: disease_ontology
has_related_synonym: lung neoplasm
id: DOID:1324
in_subset: TopNodes DOcancerslim

obstructive hydrocephalus
type: Class
subclass of: hydrocephalus
imported from: doid.owl
database_cross_reference: ICD10CM:G91.1
database_cross_reference: ICD9CM:331.4
database_cross_reference: MESH:D006849
database_cross_reference: NCI:C116347
database_cross_reference: SNOMEDCT_US_2016_03_01:230746009
database_cross_reference: SNOMEDCT_US_2016_03_01:82346000
database_cross_reference: UMLS_CUI:C0549423
has_obo_namespace: disease_ontology
id: DOID:14159

cerebral degeneration
type: Class
subclass of: brain disease
imported from: doid.owl
database_cross_reference: ICD9CM:331.9
database_cross_reference: SNOMEDCT_US_2016_03_01:154994001
database_cross_reference: SNOMEDCT_US_2016_03_01:154998003
database_cross_reference: SNOMEDCT_US_2016_03_01:192824002
database_cross_reference: SNOMEDCT_US_2016_03_01:267579001
database_cross_reference: SNOMEDCT_US_2016_03_01:267686002
database_cross_reference: SNOMEDCT_US_2016_03_01:267688001
database_cross_reference: SNOMEDCT_US_2016_03_01:418143002
database_cross_reference: SNOMEDCT_US_2016_03_01:52522001
database_cross_reference: SNOMEDCT_US_2016_03_01:73768007
database_cross_reference: UMLS_CUI:C0154671
has_exact_synonym: Brain degeneration
has_obo_namespace: disease_ontology
id: DOID:1443

disease of cellular proliferation
type: Class
subclass of: disease
definition: A disease that is characterized by abnormally rapid cell division.
imported from: doid.owl
has_alternative_id: DOID:0000818
has_exact_synonym: cell process disease
has_exact_synonym: neoplasm
has_obo_namespace: disease_ontology
id: DOID:14566
in_subset: DO FlyBase slim

eye and adnexa disease
type: Class
subclass of: sensory system disease
definition: A sensory system disease that is located_in the eye or the adnexa of the eye.
imported from: doid.owl
database_cross_reference: ICD10CM:H35.00
database_cross_reference: ICD9CM:362.10
database_cross_reference: SNOMEDCT_US_2016_03_01:193355009
database_cross_reference: SNOMEDCT_US_2016_03_01:31411005
database_cross_reference: SNOMEDCT_US_2016_03_01:42873008
database_cross_reference: UMLS_CUI:C0004608
has_obo_namespace: disease_ontology
id: DOID:1492

reproductive system disease
type: Class
subclass of: disease of anatomical entity
definition: A disease of anatomical entity that is located_in reproductive system organs.
imported from: doid.owl
has_alternative_id: DOID:6309
database_cross_reference: NCI:C27613
database_cross_reference: UMLS_CUI:C1335037
has_exact_synonym: genital system disease
has_obo_namespace: disease_ontology
id: DOID:15
in_subset: DO AGR slim
in_subset: DO MGI slim

disease of mental health
type: Class
subclass of: disease
definition: A disease that involves a psychological or behavioral pattern generally associated with subjective distress or disability that occurs in an individual, and which are not a part of normal development or culture.
imported from: doid.owl
database_cross_reference: ICD10CM:F99
database_cross_reference: ICD10CM:F99-F99
database_cross_reference: MESH:D001523
database_cross_reference: NCI:C2893
database_cross_reference: SNOMEDCT_US_2016_03_01:154843007
database_cross_reference: SNOMEDCT_US_2016_03_01:154971002
database_cross_reference: SNOMEDCT_US_2016_03_01:154972009
database_cross_reference: SNOMEDCT_US_2016_03_01:154980002
database_cross_reference: SNOMEDCT_US_2016_03_01:192637001
database_cross_reference: SNOMEDCT_US_2016_03_01:192639003
database_cross_reference: SNOMEDCT_US_2016_03_01:74732009
database_cross_reference: UMLS_CUI:C0004936
has_obo_namespace: disease_ontology
id: DOID:150
in_subset: DO AGR slim
in_subset: DO MGI slim

pleural disease
type: Class
subclass of: lower respiratory tract disease
definition: A thoracic disease which may involve inflammation of pleura, collection of air within the pleural cavity, abnormal collection of pleural fluid, abnormal growths on the pleura (pleural tumor) and pleural plaques. The main causes of pleural diseases including pleural effusions are congestive heart failure, malignancy, parapneumonic infections and pulmonary embolism.
imported from: doid.owl
has_alternative_id: DOID:1531
database_cross_reference: MESH:D010995
database_cross_reference: NCI:C26859
database_cross_reference: SNOMEDCT_US_2016_03_01:88075009
database_cross_reference: UMLS_CUI:C0032226
has_exact_synonym: disorder of pleura
has_exact_synonym: non-neoplastic pleural disease
has_obo_namespace: disease_ontology
id: DOID:1532

respiratory system disease
type: Class
subclass of: disease of anatomical entity
definition: A disease of anatomical entity that located_in the respiratory system which extends from the nasal sinuses to the diaphragm.
imported from: doid.owl
has_alternative_id: DOID:3226
database_cross_reference: ICD10CM:J96-J99
database_cross_reference: ICD10CM:J98
database_cross_reference: ICD9CM:510-519.99
database_cross_reference: ICD9CM:519
database_cross_reference: SNOMEDCT_US_2016_03_01:155603009
database_cross_reference: SNOMEDCT_US_2016_03_01:196057004
database_cross_reference: SNOMEDCT_US_2016_03_01:196184000
database_cross_reference: SNOMEDCT_US_2016_03_01:196255004
database_cross_reference: SNOMEDCT_US_2016_03_01:266373008
database_cross_reference: UMLS_CUI:C0029582
has_obo_namespace: disease_ontology
id: DOID:1579
in_subset: DO AGR slim
in_subset: DO MGI slim

thrombocytopenia
type: Class
subclass of: blood platelet disease
definition: A blood platelet disease characterized by low a platelet count in the blood.
imported from: doid.owl
database_cross_reference: ICD10CM:D69.6
database_cross_reference: ICD9CM:287.5
database_cross_reference: MESH:D013921
database_cross_reference: NCI:C3408
database_cross_reference: OMIM:188000
database_cross_reference: OMIM:273900
database_cross_reference: OMIM:300367
database_cross_reference: OMIM:313900
database_cross_reference: OMIM:612004
database_cross_reference: ORDO:852
database_cross_reference: SNOMEDCT_US_2016_03_01:142969008
database_cross_reference: SNOMEDCT_US_2016_03_01:154827000
database_cross_reference: SNOMEDCT_US_2016_03_01:165556002
database_cross_reference: SNOMEDCT_US_2016_03_01:191326009
database_cross_reference: SNOMEDCT_US_2016_03_01:302215000
database_cross_reference: SNOMEDCT_US_2016_03_01:415116008
database_cross_reference: SNOMEDCT_US_2016_03_01:70786006
database_cross_reference: UMLS_CUI:C0040034
has_obo_namespace: disease_ontology
id: DOID:1588
in_subset: DO rare slim
comment: Xref MGI.

renovascular hypertension
type: Class
subclass of: renal hypertension
imported from: doid.owl
database_cross_reference: ICD10CM:I15.0
database_cross_reference: MESH:D006978
database_cross_reference: NCI:C85044
database_cross_reference: SNOMEDCT_US_2016_03_01:123799005
database_cross_reference: SNOMEDCT_US_2016_03_01:194790006
database_cross_reference: UMLS_CUI:C0020545
has_exact_synonym: Renovascular hypertension (disorder)
has_obo_namespace: disease_ontology
id: DOID:1591

cancer
type: Class
subclass of: disease of cellular proliferation
definition: A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis.
imported from: doid.owl
database_cross_reference: ICD10CM:C80
database_cross_reference: ICD10CM:C80.1
database_cross_reference: ICD9CM:199
database_cross_reference: MESH:D009369
database_cross_reference: NCI:C9305
database_cross_reference: SNOMEDCT_US_2016_03_01:154432008
database_cross_reference: SNOMEDCT_US_2016_03_01:154433003
database_cross_reference: SNOMEDCT_US_2016_03_01:154577008
database_cross_reference: SNOMEDCT_US_2016_03_01:187597000
database_cross_reference: SNOMEDCT_US_2016_03_01:188475001
database_cross_reference: SNOMEDCT_US_2016_03_01:188482002
database_cross_reference: SNOMEDCT_US_2016_03_01:190150006
database_cross_reference: SNOMEDCT_US_2016_03_01:269513004
database_cross_reference: SNOMEDCT_US_2016_03_01:269623003
database_cross_reference: SNOMEDCT_US_2016_03_01:269626006
database_cross_reference: SNOMEDCT_US_2016_03_01:269634000
database_cross_reference: SNOMEDCT_US_2016_03_01:363346000
database_cross_reference: SNOMEDCT_US_2016_03_01:38807002
database_cross_reference: UMLS_CUI:C0006826
has_exact_synonym: malignant neoplasm
has_exact_synonym: malignant tumor
has_exact_synonym: primary cancer
has_obo_namespace: disease_ontology
id: DOID:162
in_subset: DO AGR slim
in_subset: DO FlyBase slim
comment: Updating out dated UMLS CUI.

pneumothorax
type: Class
subclass of: pleural disease
imported from: doid.owl
database_cross_reference: ICD10CM:J93.1
database_cross_reference: SNOMEDCT_US_2016_03_01:196103008
database_cross_reference: SNOMEDCT_US_2016_03_01:196105001
database_cross_reference: SNOMEDCT_US_2016_03_01:196251008
database_cross_reference: SNOMEDCT_US_2016_03_01:266367007
database_cross_reference: UMLS_CUI:C0029850
has_obo_namespace: disease_ontology
id: DOID:1673

cystitis
type: Class
subclass of: bladder disease
imported from: doid.owl
database_cross_reference: ICD10CM:N30
database_cross_reference: ICD10CM:N30.9
database_cross_reference: ICD9CM:595
database_cross_reference: ICD9CM:595.9
database_cross_reference: MESH:D003556
database_cross_reference: NCI:C26738
database_cross_reference: SNOMEDCT_US_2016_03_01:155882000
database_cross_reference: SNOMEDCT_US_2016_03_01:155885003
database_cross_reference: SNOMEDCT_US_2016_03_01:197857009
database_cross_reference: SNOMEDCT_US_2016_03_01:266629000
database_cross_reference: SNOMEDCT_US_2016_03_01:38822007
database_cross_reference: UMLS_CUI:C0010692
has_obo_namespace: disease_ontology
id: DOID:1679

retinal vascular occlusion
type: Class
subclass of: peripheral vascular disease
imported from: doid.owl
database_cross_reference: ICD10CM:H34
database_cross_reference: ICD10CM:H34.9
database_cross_reference: ICD9CM:362.3
database_cross_reference: ICD9CM:362.30
database_cross_reference: NCI:C34980
database_cross_reference: SNOMEDCT_US_2016_03_01:155111000
database_cross_reference: SNOMEDCT_US_2016_03_01:193373007
database_cross_reference: SNOMEDCT_US_2016_03_01:193380009
database_cross_reference: SNOMEDCT_US_2016_03_01:267717005
database_cross_reference: SNOMEDCT_US_2016_03_01:73757007
database_cross_reference: UMLS_CUI:C0035326
has_exact_synonym: Retinal vasc. occlusion
has_exact_synonym: Retinal vascular Occlusion
has_exact_synonym: Retinal vascular occlusion (disorder)
has_exact_synonym: Retinal vascular occlusion NOS (disorder)
has_exact_synonym: Retinal vascular occlusion, unspecified
has_exact_synonym: Unspecified retinal vascular occlusion (disorder)
has_obo_namespace: disease_ontology
id: DOID:1729

vascular disease
type: Class
subclass of: cardiovascular system disease
definition: A cardiovascular system disease that primarily affects the blood vessels which includes the arteries, veins and capillaries that carry blood to and from the heart.
imported from: doid.owl
has_alternative_id: DOID:0000405
has_alternative_id: DOID:2403
has_alternative_id: DOID:2869
has_alternative_id: DOID:324
has_alternative_id: DOID:325
has_alternative_id: DOID:45
database_cross_reference: ICD10CM:I72.9
database_cross_reference: ICD9CM:442.9
database_cross_reference: MESH:D000783
database_cross_reference: MESH:D014652
database_cross_reference: MESH:D020758
database_cross_reference: MESH:D020760
database_cross_reference: NCI:C26693
database_cross_reference: NCI:C35117
database_cross_reference: SNOMEDCT_US_2016_03_01:134342004
database_cross_reference: SNOMEDCT_US_2016_03_01:155425005
database_cross_reference: SNOMEDCT_US_2016_03_01:155428007
database_cross_reference: SNOMEDCT_US_2016_03_01:195292009
database_cross_reference: SNOMEDCT_US_2016_03_01:27550009
database_cross_reference: SNOMEDCT_US_2016_03_01:362727005
database_cross_reference: SNOMEDCT_US_2016_03_01:371029002
database_cross_reference: SNOMEDCT_US_2016_03_01:432119003
database_cross_reference: SNOMEDCT_US_2016_03_01:85659009
database_cross_reference: UMLS_CUI:C0002940
database_cross_reference: UMLS_CUI:C0042373
database_cross_reference: UMLS_CUI:C0752127
database_cross_reference: UMLS_CUI:C0752130
has_exact_synonym: vascular tissue disease
has_obo_namespace: disease_ontology
id: DOID:178

urinary system disease
type: Class
subclass of: disease of anatomical entity
definition: A disease of anatomical entity that is located_in kidney, ureter, bladder and urethra.
imported from: doid.owl
has_alternative_id: DOID:579
database_cross_reference: NCI:C27599
database_cross_reference: UMLS_CUI:C1335051
has_exact_synonym: Non-neoplastic urinary tract disease
has_exact_synonym: urinary tract disease
has_obo_namespace: disease_ontology
id: DOID:18
in_subset: DO AGR slim
in_subset: DO MGI slim

impotence
type: Class
subclass of: sexual dysfunction
imported from: doid.owl
database_cross_reference: EFO:0004234
has_exact_synonym: Sexual impotence (finding)
has_exact_synonym: erectile dysfunction
has_obo_namespace: disease_ontology
id: DOID:1875

sexual dysfunction
type: Class
subclass of: sexual disorder
imported from: doid.owl
database_cross_reference: ICD10CM:F52.9
database_cross_reference: ICD10CM:R37
database_cross_reference: MESH:D012735
database_cross_reference: NCI:C3347
database_cross_reference: SNOMEDCT_US_2016_03_01:225723003
database_cross_reference: SNOMEDCT_US_2016_03_01:231532002
database_cross_reference: SNOMEDCT_US_2016_03_01:39894007
database_cross_reference: SNOMEDCT_US_2016_03_01:56925008
database_cross_reference: SNOMEDCT_US_2016_03_01:65655009
database_cross_reference: UMLS_CUI:C0549622
has_obo_namespace: disease_ontology
id: DOID:1876

hyperuricemia
type: Class
subclass of: acquired metabolic disease
definition: An acquired metabolic disease that has_material_basis_in an abnormally high level of uric acid in the blood.
imported from: doid.owl
database_cross_reference: MESH:D033461
database_cross_reference: NCI:C3961
database_cross_reference: SNOMEDCT_US_2016_03_01:144021008
database_cross_reference: SNOMEDCT_US_2016_03_01:166733000
database_cross_reference: SNOMEDCT_US_2016_03_01:237857006
database_cross_reference: SNOMEDCT_US_2016_03_01:271198001
database_cross_reference: SNOMEDCT_US_2016_03_01:35885006
database_cross_reference: UMLS_CUI:C0740394
has_exact_synonym: (Blood urate raized) or (hyperuricemia)
has_exact_synonym: uricacidemia
has_obo_namespace: disease_ontology
id: DOID:1920

atherosclerosis
type: Class
subclass of: arteriosclerotic cardiovascular disease
imported from: doid.owl
database_cross_reference: EFO:0003914
database_cross_reference: ICD10CM:I25.1
database_cross_reference: ICD10CM:I70
database_cross_reference: ICD9CM:440
database_cross_reference: MESH:D050197
database_cross_reference: NCI:C35768
database_cross_reference: NCI:C35771
database_cross_reference: SNOMEDCT_US_2016_03_01:155382007
database_cross_reference: SNOMEDCT_US_2016_03_01:155414001
database_cross_reference: SNOMEDCT_US_2016_03_01:194848007
database_cross_reference: SNOMEDCT_US_2016_03_01:195251000
database_cross_reference: SNOMEDCT_US_2016_03_01:266318005
database_cross_reference: SNOMEDCT_US_2016_03_01:38716007
database_cross_reference: UMLS_CUI:C0004153
has_obo_namespace: disease_ontology
id: DOID:1936

hemorrhagic disease
type: Class
subclass of: blood coagulation disease
imported from: doid.owl
database_cross_reference: ICD10CM:D69.9
database_cross_reference: ICD9CM:287.9
database_cross_reference: MESH:D006474
database_cross_reference: SNOMEDCT_US_2016_03_01:191327000
database_cross_reference: SNOMEDCT_US_2016_03_01:191331006
database_cross_reference: SNOMEDCT_US_2016_03_01:191437009
database_cross_reference: SNOMEDCT_US_2016_03_01:268884000
database_cross_reference: UMLS_CUI:C0019087
has_exact_synonym: Hemorrhagic diathesis
has_exact_synonym: Hemorrhagic disease
has_obo_namespace: disease_ontology
id: DOID:2213

blood platelet disease
type: Class
subclass of: hemorrhagic disease
imported from: doid.owl
database_cross_reference: MESH:D001791
database_cross_reference: SNOMEDCT_US_2016_03_01:22716005
database_cross_reference: UMLS_CUI:C0005818
has_exact_synonym: Thrombocytopathy
has_exact_synonym: platelet disorder
has_obo_namespace: disease_ontology
id: DOID:2218

transient cerebral ischemia
type: Class
subclass of: brain ischemia
imported from: doid.owl
has_alternative_id: DOID:2315
database_cross_reference: ICD10CM:G45.9
database_cross_reference: ICD9CM:435.8
database_cross_reference: MESH:D002546
database_cross_reference: NCI:C50781
database_cross_reference: SNOMEDCT_US_2016_03_01:155404005
database_cross_reference: SNOMEDCT_US_2016_03_01:195196001
database_cross_reference: SNOMEDCT_US_2016_03_01:195207009
database_cross_reference: SNOMEDCT_US_2016_03_01:266257000
database_cross_reference: SNOMEDCT_US_2016_03_01:266314007
database_cross_reference: SNOMEDCT_US_2016_03_01:313242003
database_cross_reference: SNOMEDCT_US_2016_03_01:38609002
database_cross_reference: UMLS_CUI:C0007787
database_cross_reference: UMLS_CUI:C0155728
has_exact_synonym: TIA
has_exact_synonym: TIA - Transient ischaemic attack
has_exact_synonym: TRANSIENT ISCHEMIC ATTACK
has_exact_synonym: Transient cerebral ischaemia
has_exact_synonym: Transient cerebral ischaemia NOS
has_exact_synonym: Transient cerebral ischemia (disorder) [Ambiguous]
has_exact_synonym: Transient ischemic attacks (disorder)
has_exact_synonym: transient ischemic attack
has_obo_namespace: disease_ontology
id: DOID:224

female reproductive system disease
type: Class
subclass of: reproductive system disease
definition: A reproductive system disease that impairs the ability to reproduce and is located in the uterus, vagina, cervix, ovaries or fallopian tubes.
imported from: doid.owl
database_cross_reference: ICD9CM:629.9
database_cross_reference: MESH:D005831
database_cross_reference: SNOMEDCT_US_2016_03_01:156032001
database_cross_reference: SNOMEDCT_US_2016_03_01:156066005
database_cross_reference: SNOMEDCT_US_2016_03_01:198486002
database_cross_reference: SNOMEDCT_US_2016_03_01:244938009
database_cross_reference: SNOMEDCT_US_2016_03_01:266680004
database_cross_reference: SNOMEDCT_US_2016_03_01:310789003
database_cross_reference: SNOMEDCT_US_2016_03_01:38233001
database_cross_reference: UMLS_CUI:C0017411
has_obo_namespace: disease_ontology
id: DOID:229

brain ischemia
type: Class
subclass of: ischemia
imported from: doid.owl
database_cross_reference: MESH:D002545
database_cross_reference: SNOMEDCT_US_2016_03_01:11890005
database_cross_reference: SNOMEDCT_US_2016_03_01:193049009
database_cross_reference: SNOMEDCT_US_2016_03_01:389100007
database_cross_reference: UMLS_CUI:C0007786
has_exact_synonym: Ischaemic encephalopathy
has_exact_synonym: Ischemic encephalopathy (disorder)
has_obo_namespace: disease_ontology
id: DOID:2316

arteriosclerotic cardiovascular disease
type: Class
subclass of: arteriosclerosis
imported from: doid.owl
database_cross_reference: ICD10CM:I25.1
database_cross_reference: ICD10CM:I70
database_cross_reference: ICD9CM:440
database_cross_reference: MESH:D050197
database_cross_reference: NCI:C34403
database_cross_reference: NCI:C35768
database_cross_reference: NCI:C35771
database_cross_reference: SNOMEDCT_US_2016_03_01:155382007
database_cross_reference: SNOMEDCT_US_2016_03_01:155414001
database_cross_reference: SNOMEDCT_US_2016_03_01:194848007
database_cross_reference: SNOMEDCT_US_2016_03_01:195121002
database_cross_reference: SNOMEDCT_US_2016_03_01:195251000
database_cross_reference: SNOMEDCT_US_2016_03_01:266318005
database_cross_reference: SNOMEDCT_US_2016_03_01:38716007
database_cross_reference: SNOMEDCT_US_2016_03_01:39468009
database_cross_reference: UMLS_CUI:C0004153
database_cross_reference: UMLS_CUI:C3665365
has_exact_synonym: Arteriosclerotic Cardiovascular disease
has_exact_synonym: Arteriosclerotic cardiovascular disease
has_exact_synonym: Arteriosclerotic cardiovascular disease, NOS
has_exact_synonym: Atherosclerotic Cardiovascular disease
has_exact_synonym: Atherosclerotic cardiovascular disease
has_exact_synonym: Cardiovascular arteriosclerosis unspecified (disorder)
has_obo_namespace: disease_ontology
id: DOID:2348

arteriosclerosis
type: Class
subclass of: artery disease
definition: An artery disease that is characterized by a thickening and hardening of arterial walls in the arteries.
imported from: doid.owl
database_cross_reference: CSP:0571-2299
database_cross_reference: ICD10CM:I70
database_cross_reference: MESH:D001161
database_cross_reference: NCI:C34398
database_cross_reference: SNOMEDCT_US_2016_03_01:107671003
database_cross_reference: SNOMEDCT_US_2016_03_01:155414001
database_cross_reference: SNOMEDCT_US_2016_03_01:155418003
database_cross_reference: SNOMEDCT_US_2016_03_01:195251000
database_cross_reference: SNOMEDCT_US_2016_03_01:195257001
database_cross_reference: SNOMEDCT_US_2016_03_01:266318005
database_cross_reference: SNOMEDCT_US_2016_03_01:28960008
database_cross_reference: SNOMEDCT_US_2016_03_01:72092001
database_cross_reference: UMLS_CUI:C0003850
has_exact_synonym: Arteriosclerosis (morphologic abnormality)
has_exact_synonym: Arteriosclerosis NOS
has_exact_synonym: Arteriosclerotic vascular disease (disorder)
has_exact_synonym: Arteriosclerotic vascular disease NOS
has_obo_namespace: disease_ontology
id: DOID:2349

anemia
type: Class
subclass of: hematopoietic system disease
definition: A hematopoietic system disease that is characterized by a decrease in the normal number of red blood cells.
imported from: doid.owl
database_cross_reference: EFO:0004272
database_cross_reference: ICD10CM:D64.9
database_cross_reference: ICD9CM:285.9
database_cross_reference: MESH:D000740
database_cross_reference: NCI:C2869
database_cross_reference: SNOMEDCT_US_2016_03_01:154786001
database_cross_reference: SNOMEDCT_US_2016_03_01:154812000
database_cross_reference: SNOMEDCT_US_2016_03_01:191277004
database_cross_reference: SNOMEDCT_US_2016_03_01:267531008
database_cross_reference: SNOMEDCT_US_2016_03_01:271737000
database_cross_reference: SNOMEDCT_US_2016_03_01:64593003
database_cross_reference: UMLS_CUI:C0002871
has_exact_synonym: anaemia
has_obo_namespace: disease_ontology
id: DOID:2355
comment: PRISM.

renal artery disease
type: Class
subclass of: artery disease
imported from: doid.owl
database_cross_reference: ICD9CM:593.81
database_cross_reference: NCI:C35338
database_cross_reference: SNOMEDCT_US_2016_03_01:16934004
database_cross_reference: SNOMEDCT_US_2016_03_01:197814004
database_cross_reference: SNOMEDCT_US_2016_03_01:266559003
database_cross_reference: UMLS_CUI:C0268790
has_exact_synonym: renal vascular disease
has_exact_synonym: vascular disorder of kidney
has_obo_namespace: disease_ontology
id: DOID:2388

protein S deficiency
type: Class
subclass of: thrombophilia
subclass of: blood protein disease
imported from: doid.owl
database_cross_reference: ICD10CM:D68.59
database_cross_reference: MESH:D018455
database_cross_reference: NCI:C99026
database_cross_reference: SNOMEDCT_US_2016_03_01:1563006
database_cross_reference: UMLS_CUI:C0242666
has_exact_synonym: Protein S deficiency
has_exact_synonym: Protein S deficiency disease (disorder)
has_obo_namespace: disease_ontology
id: DOID:2451

thrombophilia
type: Class
subclass of: blood coagulation disease
imported from: doid.owl
database_cross_reference: ICD10CM:D68.59
database_cross_reference: MESH:D019851
database_cross_reference: NCI:C84479
database_cross_reference: OMIM:188050
database_cross_reference: OMIM:614486
database_cross_reference: SNOMEDCT_US_2016_03_01:191302007
database_cross_reference: SNOMEDCT_US_2016_03_01:234467004
database_cross_reference: SNOMEDCT_US_2016_03_01:76612001
database_cross_reference: UMLS_CUI:C0398623
has_exact_synonym: hypercoagulability state
has_obo_namespace: disease_ontology
id: DOID:2452
comment: OMIM mapping confirmed by DO. [LS].

nephrosis
type: Class
subclass of: kidney disease
imported from: doid.owl
database_cross_reference: MESH:D009401
database_cross_reference: SNOMEDCT_US_2016_03_01:90708001
database_cross_reference: UMLS_CUI:C0027720
has_obo_namespace: disease_ontology
id: DOID:2527

bilirubin metabolic disorder
type: Class
subclass of: inherited metabolic disorder
definition: An inherited metabolic disorder that involves elevated levels of bilirubin resulting from disruption of bilirubin metabolism.
imported from: doid.owl
has_alternative_id: DOID:2740
database_cross_reference: MESH:D006932
database_cross_reference: MESH:D006933
database_cross_reference: NCI:C84761
database_cross_reference: SNOMEDCT_US_2016_03_01:143932000
database_cross_reference: SNOMEDCT_US_2016_03_01:14783006
database_cross_reference: SNOMEDCT_US_2016_03_01:154770008
database_cross_reference: SNOMEDCT_US_2016_03_01:166612004
database_cross_reference: SNOMEDCT_US_2016_03_01:20505009
database_cross_reference: SNOMEDCT_US_2016_03_01:235904007
database_cross_reference: SNOMEDCT_US_2016_03_01:267509000
database_cross_reference: UMLS_CUI:C0020433
database_cross_reference: UMLS_CUI:C0020435
has_exact_synonym: hereditary hyperbilirubinemia
has_exact_synonym: hyperbilirubinemia
has_obo_namespace: disease_ontology
has_related_synonym: hyperbilirubinaemia
id: DOID:2741

pyelitis
type: Class
subclass of: kidney disease
imported from: doid.owl
database_cross_reference: ICD10CM:N12
database_cross_reference: MESH:D011702
database_cross_reference: NCI:C34964
database_cross_reference: SNOMEDCT_US_2016_03_01:197780007
database_cross_reference: SNOMEDCT_US_2016_03_01:27174002
database_cross_reference: UMLS_CUI:C0034183
has_obo_namespace: disease_ontology
id: DOID:2744

cerebellar disease
type: Class
subclass of: brain disease
imported from: doid.owl
database_cross_reference: MESH:D002526
database_cross_reference: SNOMEDCT_US_2016_03_01:155010002
database_cross_reference: SNOMEDCT_US_2016_03_01:192867005
database_cross_reference: SNOMEDCT_US_2016_03_01:223176004
database_cross_reference: SNOMEDCT_US_2016_03_01:224186005
database_cross_reference: SNOMEDCT_US_2016_03_01:267691001
database_cross_reference: SNOMEDCT_US_2016_03_01:307361005
database_cross_reference: SNOMEDCT_US_2016_03_01:49784007
database_cross_reference: UMLS_CUI:C0007760
has_obo_namespace: disease_ontology
id: DOID:2786

glomerulonephritis
type: Class
subclass of: nephritis
definition: A nephritis that causes inflammation of the glomeruli located_in kidney.
imported from: doid.owl
database_cross_reference: ICD10CM:N05
database_cross_reference: ICD10CM:N08
database_cross_reference: MESH:D005921
database_cross_reference: NCI:C26784
database_cross_reference: SNOMEDCT_US_2016_03_01:197648001
database_cross_reference: SNOMEDCT_US_2016_03_01:36171008
database_cross_reference: UMLS_CUI:C0017658
has_obo_namespace: disease_ontology
id: DOID:2921

anuria
type: Class
subclass of: kidney disease
imported from: doid.owl
database_cross_reference: MESH:D001002
database_cross_reference: NCI:C114699
database_cross_reference: SNOMEDCT_US_2016_03_01:139460001
database_cross_reference: SNOMEDCT_US_2016_03_01:158479000
database_cross_reference: SNOMEDCT_US_2016_03_01:207182009
database_cross_reference: SNOMEDCT_US_2016_03_01:2472002
database_cross_reference: UMLS_CUI:C0003460
has_exact_synonym: Suppression of urinary secretion
has_obo_namespace: disease_ontology
id: DOID:2983

IgA glomerulonephritis
type: Class
subclass of: glomerulonephritis
definition: A glomerulonephritis characterized by build up of IgA antibody in the glomerulus.
imported from: doid.owl
database_cross_reference: EFO:0004194
database_cross_reference: MESH:D005922
database_cross_reference: NCI:C34643
database_cross_reference: NCI:C35280
database_cross_reference: OMIM:161950
database_cross_reference: SNOMEDCT_US_2016_03_01:236407003
database_cross_reference: SNOMEDCT_US_2016_03_01:68779003
database_cross_reference: UMLS_CUI:C0017661
has_exact_synonym: Berger's IgA or IgG nephropathy
has_exact_synonym: Focal Glomerulonephritis
has_exact_synonym: IGA glomerulonephritis
has_exact_synonym: IgA nephropathy
has_exact_synonym: primary IgA nephropathy
has_exact_synonym: segmental glomerulonephritis
has_obo_namespace: disease_ontology
id: DOID:2986
comment: OMIM mapping confirmed by DO. [SN].

substance abuse
type: Class
subclass of: substance-related disorder
definition: A substance-related disorder that involves a maladaptive pattern of substance use leading to significant impairment in functioning.
imported from: doid.owl
database_cross_reference: MESH:D019966
database_cross_reference: NCI:C16522
database_cross_reference: SNOMEDCT_US_2016_03_01:26416006
database_cross_reference: UMLS_CUI:C0013146
has_obo_namespace: disease_ontology
id: DOID:302

acute kidney failure
type: Class
subclass of: kidney failure
imported from: doid.owl
has_obo_namespace: disease_ontology
id: DOID:3021

substance-related disorder
type: Class
subclass of: disease of mental health
definition: A disease of mental health involving the abuse or dependence on a substance that is ingested in order to produce a high, alter one's senses, or otherwise affect functioning.
imported from: doid.owl
database_cross_reference: MESH:D019966
database_cross_reference: NCI:C92203
database_cross_reference: UMLS_CUI:C0236969
has_obo_namespace: disease_ontology
id: DOID:303

carcinoma
type: Class
subclass of: cell type cancer
definition: A cell type cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells.
imported from: doid.owl
has_alternative_id: DOID:2428
has_alternative_id: DOID:6570
database_cross_reference: CSP:2000-1867
database_cross_reference: MESH:D002277
database_cross_reference: MESH:D009375
database_cross_reference: NCI:C2916
database_cross_reference: NCI:C3709
database_cross_reference: SNOMEDCT_US_2016_03_01:118285006
database_cross_reference: SNOMEDCT_US_2016_03_01:134207000
database_cross_reference: SNOMEDCT_US_2016_03_01:154433003
database_cross_reference: SNOMEDCT_US_2016_03_01:188083002
database_cross_reference: SNOMEDCT_US_2016_03_01:189546004
database_cross_reference: SNOMEDCT_US_2016_03_01:189549006
database_cross_reference: SNOMEDCT_US_2016_03_01:189559007
database_cross_reference: SNOMEDCT_US_2016_03_01:269513004
database_cross_reference: SNOMEDCT_US_2016_03_01:68453008
database_cross_reference: SNOMEDCT_US_2016_03_01:71298006
database_cross_reference: UMLS_CUI:C0007097
database_cross_reference: UMLS_CUI:C0553707
database_cross_reference: UMLS_CUI:C1368683
has_exact_synonym: epithelioma
has_exact_synonym: malignant Epithelioma
has_obo_namespace: disease_ontology
id: DOID:305
in_subset: DO FlyBase slim
in_subset: DO cancer slim

nervous system cancer
type: Class
subclass of: organ system cancer
definition: An organ system cancer located_in the nervous system that affects the central or peripheral nervous system.
imported from: doid.owl
has_alternative_id: DOID:1193
has_alternative_id: DOID:3195
has_alternative_id: DOID:4695
database_cross_reference: ICD9CM:192
database_cross_reference: ICD9CM:192.9
database_cross_reference: MESH:D009380
database_cross_reference: NCI:C35562
database_cross_reference: SNOMEDCT_US_2016_03_01:188306000
database_cross_reference: UMLS_CUI:C0027665
database_cross_reference: UMLS_CUI:C0153643
database_cross_reference: UMLS_CUI:C1334956
has_exact_synonym: malignant neoplasm of nervous system
has_exact_synonym: neoplasm of nervous system (disorder)
has_exact_synonym: nervous system neoplasm
has_exact_synonym: neural neoplasm
has_exact_synonym: neural tumor
has_exact_synonym: tumor of the nervous system
has_obo_namespace: disease_ontology
id: DOID:3093
in_subset: DO MGI slim

gastrointestinal system cancer
type: Class
subclass of: organ system cancer
subclass of: gastrointestinal system disease
definition: An organ system cancer located_in gastrointestinal tract that is manifested in organs of the gastrointestinal system.
imported from: doid.owl
has_alternative_id: DOID:4945
has_alternative_id: DOID:8377
database_cross_reference: ICD10CM:C26.9
database_cross_reference: ICD9CM:239.0
database_cross_reference: MESH:D004067
database_cross_reference: MESH:D005770
database_cross_reference: NCI:C3052
database_cross_reference: NCI:C4890
database_cross_reference: SNOMEDCT_US_2016_03_01:126768004
database_cross_reference: SNOMEDCT_US_2016_03_01:128348002
database_cross_reference: SNOMEDCT_US_2016_03_01:128415001
database_cross_reference: SNOMEDCT_US_2016_03_01:189527000
database_cross_reference: SNOMEDCT_US_2016_03_01:276806006
database_cross_reference: SNOMEDCT_US_2016_03_01:367543008
database_cross_reference: SNOMEDCT_US_2016_03_01:428905002
database_cross_reference: SNOMEDCT_US_2016_03_01:93811007
database_cross_reference: UMLS_CUI:C0012243
database_cross_reference: UMLS_CUI:C0017185
database_cross_reference: UMLS_CUI:C0685938
has_exact_synonym: GI tumor
has_exact_synonym: digestive system cancer
has_exact_synonym: gastrointestinal tract cancer
has_obo_namespace: disease_ontology
id: DOID:3119
in_subset: DO FlyBase slim
in_subset: DO MGI slim
in_subset: TopNodes DOcancerslim

lipid metabolism disorder
type: Class
subclass of: inherited metabolic disorder
definition: An inherited metabolic disorder that involves the creation and degradation of lipids.
imported from: doid.owl
database_cross_reference: MESH:D008052
database_cross_reference: UMLS_CUI:C0023772
has_exact_synonym: dyslipidemia
has_exact_synonym: fatty acid metabolism disorder
has_obo_namespace: disease_ontology
id: DOID:3146
in_subset: DO FlyBase slim

peripheral nerve sheath neoplasm
type: Class
subclass of: peripheral nervous system neoplasm
definition: A peripheral nervous system neoplasm that is located_in the connective tissue surrounding nerves.
imported from: doid.owl
database_cross_reference: MESH:D018317
database_cross_reference: UMLS_CUI:C0751689
has_exact_synonym: neoplasm of the nerve Sheath
has_exact_synonym: nerve sheath tumour
has_obo_namespace: disease_ontology
id: DOID:3193
in_subset: DO cancer slim

ischemia
type: Class
subclass of: vascular disease
definition: A vascular disease that is characterized by a restriction in blood supply to tissues.
imported from: doid.owl
database_cross_reference: MESH:D007511
database_cross_reference: MESH:D054058
database_cross_reference: NCI:C34738
database_cross_reference: SNOMEDCT_US_2016_03_01:52674009
database_cross_reference: UMLS_CUI:C0022116
has_obo_namespace: disease_ontology
id: DOID:326

central nervous system disease
type: Class
subclass of: nervous system disease
definition: A nervous system disease that affects either the spinal cord (myelopathy) or brain (encephalopathy) of the central nervous system.
imported from: doid.owl
database_cross_reference: ICD10CM:G96.9
database_cross_reference: MESH:D002493
database_cross_reference: NCI:C2934
database_cross_reference: SNOMEDCT_US_2016_03_01:138748005
database_cross_reference: SNOMEDCT_US_2016_03_01:154981003
database_cross_reference: SNOMEDCT_US_2016_03_01:155049004
database_cross_reference: SNOMEDCT_US_2016_03_01:155059003
database_cross_reference: SNOMEDCT_US_2016_03_01:192641002
database_cross_reference: SNOMEDCT_US_2016_03_01:193076009
database_cross_reference: SNOMEDCT_US_2016_03_01:194566008
database_cross_reference: SNOMEDCT_US_2016_03_01:23853001
database_cross_reference: SNOMEDCT_US_2016_03_01:267144009
database_cross_reference: SNOMEDCT_US_2016_03_01:267679005
database_cross_reference: SNOMEDCT_US_2016_03_01:267700003
database_cross_reference: SNOMEDCT_US_2016_03_01:267702006
database_cross_reference: SNOMEDCT_US_2016_03_01:275539005
database_cross_reference: UMLS_CUI:C0007682
has_obo_namespace: disease_ontology
id: DOID:331

coronary artery disease
type: Class
subclass of: artery disease
definition: An artery disease that is characterized by plaque building up along the inner walls of the arteries of the heart resulting in a narrowing of the arteries and a reduced blood supply to the cardiac muscles.
imported from: doid.owl
has_alternative_id: DOID:10506
has_alternative_id: DOID:3363
has_alternative_id: DOID:3394
has_alternative_id: DOID:9420
database_cross_reference: EFO:0001645
database_cross_reference: ICD10CM:I20-I25
database_cross_reference: ICD10CM:I25
database_cross_reference: ICD10CM:I25.1
database_cross_reference: ICD10CM:I25.10
database_cross_reference: ICD10CM:I25.9
database_cross_reference: ICD10CM:K76.1
database_cross_reference: ICD9CM:410-414.99
database_cross_reference: ICD9CM:414.0
database_cross_reference: ICD9CM:414.9
database_cross_reference: MESH:D003324
database_cross_reference: MESH:D003327
database_cross_reference: MESH:D017202
database_cross_reference: NCI:C35505
database_cross_reference: NCI:C50625
database_cross_reference: OMIM:300464
database_cross_reference: OMIM:607339
database_cross_reference: OMIM:608316
database_cross_reference: OMIM:608318
database_cross_reference: OMIM:608320
database_cross_reference: OMIM:610947
database_cross_reference: OMIM:611139
database_cross_reference: OMIM:612030
database_cross_reference: OMIM:614293
database_cross_reference: SNOMEDCT_US_2016_03_01:155303000
database_cross_reference: SNOMEDCT_US_2016_03_01:155315001
database_cross_reference: SNOMEDCT_US_2016_03_01:155316000
database_cross_reference: SNOMEDCT_US_2016_03_01:155318004
database_cross_reference: SNOMEDCT_US_2016_03_01:155322009
database_cross_reference: SNOMEDCT_US_2016_03_01:194795001
database_cross_reference: SNOMEDCT_US_2016_03_01:194841001
database_cross_reference: SNOMEDCT_US_2016_03_01:194852007
database_cross_reference: SNOMEDCT_US_2016_03_01:194878003
database_cross_reference: SNOMEDCT_US_2016_03_01:195540001
database_cross_reference: SNOMEDCT_US_2016_03_01:233822007
database_cross_reference: SNOMEDCT_US_2016_03_01:2610009
database_cross_reference: SNOMEDCT_US_2016_03_01:266231003
database_cross_reference: SNOMEDCT_US_2016_03_01:266290000
database_cross_reference: SNOMEDCT_US_2016_03_01:266291001
database_cross_reference: SNOMEDCT_US_2016_03_01:271430002
database_cross_reference: SNOMEDCT_US_2016_03_01:32598000
database_cross_reference: SNOMEDCT_US_2016_03_01:413838009
database_cross_reference: SNOMEDCT_US_2016_03_01:413844008
database_cross_reference: SNOMEDCT_US_2016_03_01:414545008
database_cross_reference: SNOMEDCT_US_2016_03_01:414795007
database_cross_reference: SNOMEDCT_US_2016_03_01:41702007
database_cross_reference: SNOMEDCT_US_2016_03_01:443502000
database_cross_reference: SNOMEDCT_US_2016_03_01:53741008
database_cross_reference: SNOMEDCT_US_2016_03_01:84537008
database_cross_reference: UMLS_CUI:C0010054
database_cross_reference: UMLS_CUI:C0010068
database_cross_reference: UMLS_CUI:C0151744
database_cross_reference: UMLS_CUI:C0264694
has_exact_synonym: CHD (coronary heart disease)
has_exact_synonym: Coronary disease
has_exact_synonym: coronary arteriosclerosis
has_exact_synonym: coronary heart disease
has_obo_namespace: disease_ontology
id: DOID:3393
comment: Xref MGI.

peripheral vascular disease
type: Class
subclass of: vascular disease
definition: A vascular disease that is characterized by obstruction of larger arteries not within the coronary, aortic arch vasculature, or brain.
imported from: doid.owl
has_alternative_id: DOID:2868
database_cross_reference: ICD9CM:443.81
database_cross_reference: MESH:D001157
database_cross_reference: MESH:D016481
database_cross_reference: SNOMEDCT_US_2016_03_01:195624006
database_cross_reference: SNOMEDCT_US_2016_03_01:2929001
database_cross_reference: UMLS_CUI:C0003838
database_cross_reference: UMLS_CUI:C0031115
has_exact_synonym: arterial occlusive disease
has_obo_namespace: disease_ontology
id: DOID:341

uterine disease
type: Class
subclass of: female reproductive system disease
definition: A female reproductive system disease that is located_in the uterus.
imported from: doid.owl
database_cross_reference: ICD10CM:N85.9
database_cross_reference: ICD9CM:621.9
database_cross_reference: MESH:D014591
database_cross_reference: NCI:C26907
database_cross_reference: SNOMEDCT_US_2016_03_01:12337004
database_cross_reference: SNOMEDCT_US_2016_03_01:156004005
database_cross_reference: SNOMEDCT_US_2016_03_01:156009000
database_cross_reference: SNOMEDCT_US_2016_03_01:198335006
database_cross_reference: SNOMEDCT_US_2016_03_01:237068005
database_cross_reference: UMLS_CUI:C0042131
has_obo_namespace: disease_ontology
id: DOID:345

bladder disease
type: Class
subclass of: urinary system disease
definition: A urinary system disease that is located_in the bladder.
imported from: doid.owl
database_cross_reference: ICD10CM:N32.9
database_cross_reference: ICD9CM:596.9
database_cross_reference: MESH:D001745
database_cross_reference: NCI:C2900
database_cross_reference: SNOMEDCT_US_2016_03_01:155886002
database_cross_reference: SNOMEDCT_US_2016_03_01:155890000
database_cross_reference: SNOMEDCT_US_2016_03_01:197897007
database_cross_reference: SNOMEDCT_US_2016_03_01:266630005
database_cross_reference: SNOMEDCT_US_2016_03_01:42643001
database_cross_reference: UMLS_CUI:C0005686
has_exact_synonym: Urinary Bladder Disease
has_obo_namespace: disease_ontology
id: DOID:365

cranial nerve palsy
type: Class
subclass of: cranial nerve disease
imported from: doid.owl
database_cross_reference: MESH:D003389
database_cross_reference: NCI:C26941
database_cross_reference: SNOMEDCT_US_2016_03_01:73013002
database_cross_reference: UMLS_CUI:C0151311
has_exact_synonym: Cranial nerve Paralysis
has_exact_synonym: Cranial nerve palsy
has_obo_namespace: disease_ontology
id: DOID:3817

lung carcinoma
type: Class
subclass of: lung cancer
subclass of: carcinoma
definition: A lung cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells and is located_in the lungs and has_symptom cough and has_symptom chest discomfort or pain and has_symptom weight loss and has_symptom hemoptysis.
imported from: doid.owl
database_cross_reference: EFO:0001071
database_cross_reference: ICD10CM:C34.90
database_cross_reference: NCI:C4878
database_cross_reference: SNOMEDCT_US_2016_03_01:154485001
database_cross_reference: SNOMEDCT_US_2016_03_01:187875007
database_cross_reference: SNOMEDCT_US_2016_03_01:269561006
database_cross_reference: UMLS_CUI:C0684249
has_exact_synonym: cancer of lung
has_obo_namespace: disease_ontology
has_related_synonym: carcinoma of lung
id: DOID:3905
in_subset: DO cancer slim
comment: OMIM mapping confirmed by DO. [SN].

non-small cell lung carcinoma
type: Class
subclass of: lung carcinoma
definition: A lung carcinoma that is characterized as any type of epithelial lung cancer other than small cell lung carcinoma.
imported from: doid.owl
database_cross_reference: EFO:0003060
database_cross_reference: ICD10CM:C34
database_cross_reference: KEGG:05223
database_cross_reference: MESH:D002289
database_cross_reference: NCI:C2926
database_cross_reference: SNOMEDCT_US_2016_03_01:254637007
database_cross_reference: UMLS_CUI:C0007131
has_exact_synonym: NSCLC
has_exact_synonym: Non-small cell lung cancer
has_obo_namespace: disease_ontology
id: DOID:3908
in_subset: DO cancer slim

mouth disease
type: Class
subclass of: gastrointestinal system disease
definition: A gastrointestinal system disease that is located_in the mouth.
imported from: doid.owl
database_cross_reference: MESH:D009059
database_cross_reference: NCI:C27641
database_cross_reference: NCI:C3240
database_cross_reference: SNOMEDCT_US_2016_03_01:118938008
database_cross_reference: SNOMEDCT_US_2016_03_01:155630004
database_cross_reference: SNOMEDCT_US_2016_03_01:266484002
database_cross_reference: UMLS_CUI:C0026636
has_obo_namespace: disease_ontology
id: DOID:403

heart valve disease
type: Class
subclass of: heart disease
definition: A heart disease involving one or more of the four valves of the heart (the aortic and mitral valves on the left and the pulmonary and tricuspid valves on the right).
imported from: doid.owl
has_alternative_id: DOID:989
database_cross_reference: MESH:D006349
database_cross_reference: MESH:D016127
database_cross_reference: NCI:C45525
database_cross_reference: SNOMEDCT_US_2016_03_01:195013005
database_cross_reference: SNOMEDCT_US_2016_03_01:368009
database_cross_reference: SNOMEDCT_US_2016_03_01:398995000
database_cross_reference: UMLS_CUI:C0018824
database_cross_reference: UMLS_CUI:C0079485
has_exact_synonym: Valvular heart disease
has_obo_namespace: disease_ontology
id: DOID:4079

glucose metabolism disease
type: Class
subclass of: carbohydrate metabolism disease
imported from: doid.owl
database_cross_reference: MESH:D044882
database_cross_reference: NCI:C53655
database_cross_reference: SNOMEDCT_US_2016_03_01:126877002
database_cross_reference: UMLS_CUI:C1257958
has_exact_synonym: disorder of glucose metabolism (disorder)
has_obo_namespace: disease_ontology
id: DOID:4194

large cell carcinoma
type: Class
subclass of: carcinoma
definition: A carcinoma that is composed of large, monotonous rounded or overtly polygonal-shaped cells with abundant cytoplasm.
imported from: doid.owl
database_cross_reference: MESH:D018287
database_cross_reference: NCI:C3780
database_cross_reference: SNOMEDCT_US_2016_03_01:189551005
database_cross_reference: SNOMEDCT_US_2016_03_01:22687000
database_cross_reference: UMLS_CUI:C0206704
has_obo_namespace: disease_ontology
id: DOID:4552

lung large cell carcinoma
type: Class
subclass of: non-small cell lung carcinoma
subclass of: large cell carcinoma
imported from: doid.owl
database_cross_reference: NCI:C4450
database_cross_reference: SNOMEDCT_US_2016_03_01:254629004
database_cross_reference: UMLS_CUI:C0345958
has_exact_synonym: large cell carcinoma of lung (disorder)
has_exact_synonym: large cell lung carcinoma
has_obo_namespace: disease_ontology
id: DOID:4556
in_subset: DO cancer slim

aortic disease
type: Class
subclass of: artery disease
definition: An artery disease that is characterized by degeneration of the cells composing the aortic wall.
imported from: doid.owl
database_cross_reference: MESH:D001018
database_cross_reference: NCI:C101253
database_cross_reference: SNOMEDCT_US_2016_03_01:47040006
database_cross_reference: UMLS_CUI:C0003493
has_exact_synonym: aortic disorder
has_exact_synonym: disorder of the aorta (disorder)
has_obo_namespace: disease_ontology
id: DOID:520

pneumonia
type: Class
subclass of: lung disease
definition: A lung disease that involves lung parenchyma or alveolar inflammation and abnormal alveolar filling with fluid (consolidation and exudation). It results from a variety of causes including infection with bacteria, viruses, fungi or parasites, and chemical or physical injury to the lungs. It is accompanied by fever, chills, cough, and difficulty in breathing.
imported from: doid.owl
has_alternative_id: DOID:10509
has_alternative_id: DOID:11742
has_alternative_id: DOID:5871
database_cross_reference: MESH:D011014
database_cross_reference: NCI:C3333
database_cross_reference: SNOMEDCT_US_2016_03_01:155548002
database_cross_reference: SNOMEDCT_US_2016_03_01:155552002
database_cross_reference: SNOMEDCT_US_2016_03_01:155558003
database_cross_reference: SNOMEDCT_US_2016_03_01:233604007
database_cross_reference: SNOMEDCT_US_2016_03_01:266391003
database_cross_reference: SNOMEDCT_US_2016_03_01:274103002
database_cross_reference: SNOMEDCT_US_2016_03_01:60363000
database_cross_reference: UMLS_CUI:C0032285
has_exact_synonym: acute pneumonia
has_obo_namespace: disease_ontology
id: DOID:552

kidney disease
type: Class
subclass of: urinary system disease
definition: A urinary system disease that is located_in the kidney.
imported from: doid.owl
database_cross_reference: EFO:0003086
database_cross_reference: ICD10CM:N08
database_cross_reference: ICD10CM:N28.9
database_cross_reference: MESH:D007674
database_cross_reference: NCI:C3149
database_cross_reference: NCI:C34843
database_cross_reference: SNOMEDCT_US_2016_03_01:155871008
database_cross_reference: SNOMEDCT_US_2016_03_01:266612003
database_cross_reference: SNOMEDCT_US_2016_03_01:266624005
database_cross_reference: SNOMEDCT_US_2016_03_01:266627003
database_cross_reference: SNOMEDCT_US_2016_03_01:274108006
database_cross_reference: SNOMEDCT_US_2016_03_01:90708001
database_cross_reference: UMLS_CUI:C0022658
has_exact_synonym: nephropathy
has_obo_namespace: disease_ontology
id: DOID:557
in_subset: DO FlyBase slim

eye disease
type: Class
subclass of: eye and adnexa disease
definition: An eye and adnexa disease that is located_in the eye.
imported from: doid.owl
has_alternative_id: DOID:2933
database_cross_reference: ICD10CM:H44
database_cross_reference: ICD10CM:H44.9
database_cross_reference: ICD9CM:360
database_cross_reference: ICD9CM:360.9
database_cross_reference: ICD9CM:379.90
database_cross_reference: MESH:D005128
database_cross_reference: NCI:C26767
database_cross_reference: SNOMEDCT_US_2016_03_01:111509007
database_cross_reference: SNOMEDCT_US_2016_03_01:155101007
database_cross_reference: SNOMEDCT_US_2016_03_01:155198005
database_cross_reference: SNOMEDCT_US_2016_03_01:193265001
database_cross_reference: SNOMEDCT_US_2016_03_01:193266000
database_cross_reference: SNOMEDCT_US_2016_03_01:193316008
database_cross_reference: SNOMEDCT_US_2016_03_01:194183009
database_cross_reference: SNOMEDCT_US_2016_03_01:264555006
database_cross_reference: SNOMEDCT_US_2016_03_01:366261005
database_cross_reference: SNOMEDCT_US_2016_03_01:371405004
database_cross_reference: SNOMEDCT_US_2016_03_01:371409005
database_cross_reference: SNOMEDCT_US_2016_03_01:79517001
database_cross_reference: UMLS_CUI:C0015397
has_obo_namespace: disease_ontology
id: DOID:5614
in_subset: DO FlyBase slim

cranial nerve disease
type: Class
subclass of: neuropathy
definition: A neuropathy that is located_in one of the twelve cranial nerves.
imported from: doid.owl
database_cross_reference: ICD10CM:G52.9
database_cross_reference: ICD9CM:352.9
database_cross_reference: MESH:D003389
database_cross_reference: NCI:C26733
database_cross_reference: SNOMEDCT_US_2016_03_01:193104009
database_cross_reference: SNOMEDCT_US_2016_03_01:267598004
database_cross_reference: SNOMEDCT_US_2016_03_01:267709002
database_cross_reference: SNOMEDCT_US_2016_03_01:276379008
database_cross_reference: SNOMEDCT_US_2016_03_01:73013002
database_cross_reference: UMLS_CUI:C0010266
has_exact_synonym: Cranial nerve disorder
has_exact_synonym: disorder of cranial nerve
has_obo_namespace: disease_ontology
id: DOID:5656

retinal disease
type: Class
subclass of: eye disease
definition: An eye disease that is located_in the retina.
imported from: doid.owl
database_cross_reference: ICD10CM:H35.9
database_cross_reference: ICD9CM:362.9
database_cross_reference: MESH:D012164
database_cross_reference: NCI:C26875
database_cross_reference: NCI:C62601
database_cross_reference: SNOMEDCT_US_2016_03_01:193430004
database_cross_reference: SNOMEDCT_US_2016_03_01:267715002
database_cross_reference: SNOMEDCT_US_2016_03_01:29555009
database_cross_reference: SNOMEDCT_US_2016_03_01:35426003
database_cross_reference: SNOMEDCT_US_2016_03_01:399625000
database_cross_reference: UMLS_CUI:C0035309
has_obo_namespace: disease_ontology
id: DOID:5679

peripheral nervous system disease
type: Class
subclass of: nervous system disease
definition: A nervous system disease that affects the peripheral nervous system.
imported from: doid.owl
has_alternative_id: DOID:13069
database_cross_reference: ICD10CM:G64
database_cross_reference: ICD9CM:350-359.99
database_cross_reference: MESH:D010523
database_cross_reference: NCI:C119734
database_cross_reference: NCI:C27580
database_cross_reference: NCI:C27587
database_cross_reference: SNOMEDCT_US_2016_03_01:155064004
database_cross_reference: SNOMEDCT_US_2016_03_01:155080009
database_cross_reference: SNOMEDCT_US_2016_03_01:155100008
database_cross_reference: SNOMEDCT_US_2016_03_01:193088006
database_cross_reference: SNOMEDCT_US_2016_03_01:193264002
database_cross_reference: SNOMEDCT_US_2016_03_01:264554005
database_cross_reference: SNOMEDCT_US_2016_03_01:267706009
database_cross_reference: SNOMEDCT_US_2016_03_01:302226006
database_cross_reference: SNOMEDCT_US_2016_03_01:42658009
database_cross_reference: UMLS_CUI:C0031117
database_cross_reference: UMLS_CUI:C1335029
has_obo_namespace: disease_ontology
has_related_synonym: peripheral nerve disease
has_related_synonym: peripheral neuropathy
id: DOID:574
in_subset: DO MGI slim

proteinuria
type: Class
subclass of: kidney disease
imported from: doid.owl
database_cross_reference: ICD10CM:R80
database_cross_reference: ICD10CM:R80.9
database_cross_reference: ICD9CM:791.0
database_cross_reference: MESH:D011507
database_cross_reference: NCI:C38012
database_cross_reference: SNOMEDCT_US_2016_03_01:144515004
database_cross_reference: SNOMEDCT_US_2016_03_01:158565005
database_cross_reference: SNOMEDCT_US_2016_03_01:158568007
database_cross_reference: SNOMEDCT_US_2016_03_01:167279003
database_cross_reference: SNOMEDCT_US_2016_03_01:207310001
database_cross_reference: SNOMEDCT_US_2016_03_01:207315006
database_cross_reference: SNOMEDCT_US_2016_03_01:232691000
database_cross_reference: SNOMEDCT_US_2016_03_01:236719005
database_cross_reference: SNOMEDCT_US_2016_03_01:29738008
database_cross_reference: UMLS_CUI:C0033687
has_obo_namespace: disease_ontology
id: DOID:576

hemolytic anemia
type: Class
subclass of: normocytic anemia
imported from: doid.owl
database_cross_reference: ICD10CM:D55-D59
database_cross_reference: MESH:D000743
database_cross_reference: NCI:C34376
database_cross_reference: OMIM:266120
database_cross_reference: OMIM:612631
database_cross_reference: SNOMEDCT_US_2016_03_01:191231008
database_cross_reference: SNOMEDCT_US_2016_03_01:191416001
database_cross_reference: SNOMEDCT_US_2016_03_01:61261009
database_cross_reference: UMLS_CUI:C0002878
has_exact_synonym: ANEMIA HEMOLYTIC
has_obo_namespace: disease_ontology
id: DOID:583
comment: OMIM mapping confirmed by DO. [SN]. OMIM mapping by NeuroDevNet. [LS].

myocardial infarction
type: Class
subclass of: coronary artery disease
definition: A coronary artery disease characterized by myocardial cell death (myocardial necrosis) due to prolonged ischaemia.
imported from: doid.owl
database_cross_reference: EFO:0000612
database_cross_reference: ICD10CM:I21
database_cross_reference: ICD10CM:I22
database_cross_reference: MESH:D009203
database_cross_reference: NCI:C27996
database_cross_reference: OMIM:608557
database_cross_reference: SNOMEDCT_US_2016_03_01:155304006
database_cross_reference: SNOMEDCT_US_2016_03_01:194796000
database_cross_reference: SNOMEDCT_US_2016_03_01:22298006
database_cross_reference: SNOMEDCT_US_2016_03_01:233824008
database_cross_reference: SNOMEDCT_US_2016_03_01:266288001
database_cross_reference: SNOMEDCT_US_2016_03_01:66514008
database_cross_reference: UMLS_CUI:C0027051
has_exact_synonym: Myocardial infarct
has_exact_synonym: heart attack
has_obo_namespace: disease_ontology
id: DOID:5844
comment: Xref MGI.

congestive heart failure
type: Class
subclass of: heart disease
definition: A heart disease that is characterized by any structural or functional cardiac disorder that impairs the ability of the heart to fill with or pump a sufficient amount of blood throughout the body.
imported from: doid.owl
has_alternative_id: DOID:395
database_cross_reference: ICD10CM:I50
database_cross_reference: ICD10CM:I50.9
database_cross_reference: ICD9CM:428
database_cross_reference: ICD9CM:428.0
database_cross_reference: ICD9CM:428.9
database_cross_reference: MESH:D006333
database_cross_reference: NCI:C3080
database_cross_reference: NCI:C50577
database_cross_reference: SNOMEDCT_US_2016_03_01:155374007
database_cross_reference: SNOMEDCT_US_2016_03_01:155375008
database_cross_reference: SNOMEDCT_US_2016_03_01:155377000
database_cross_reference: SNOMEDCT_US_2016_03_01:195108009
database_cross_reference: SNOMEDCT_US_2016_03_01:195117009
database_cross_reference: SNOMEDCT_US_2016_03_01:266248006
database_cross_reference: SNOMEDCT_US_2016_03_01:266308000
database_cross_reference: SNOMEDCT_US_2016_03_01:42343007
database_cross_reference: SNOMEDCT_US_2016_03_01:84114007
database_cross_reference: UMLS_CUI:C0018801
database_cross_reference: UMLS_CUI:C0018802
has_exact_synonym: CHF
has_exact_synonym: Cardiac Failure Congestive
has_exact_synonym: Congestive heart disease
has_exact_synonym: Weak heart
has_obo_namespace: disease_ontology
id: DOID:6000

mitral valve disease
type: Class
subclass of: heart valve disease
imported from: doid.owl
has_alternative_id: DOID:11505
has_alternative_id: DOID:58
has_alternative_id: DOID:59
database_cross_reference: ICD10CM:I05
database_cross_reference: ICD10CM:I05.1
database_cross_reference: ICD10CM:I05.9
database_cross_reference: ICD9CM:394
database_cross_reference: ICD9CM:394.1
database_cross_reference: ICD9CM:424.0
database_cross_reference: NCI:C78446
database_cross_reference: SNOMEDCT_US_2016_03_01:11851006
database_cross_reference: SNOMEDCT_US_2016_03_01:155276006
database_cross_reference: SNOMEDCT_US_2016_03_01:155278007
database_cross_reference: SNOMEDCT_US_2016_03_01:155279004
database_cross_reference: SNOMEDCT_US_2016_03_01:194724009
database_cross_reference: SNOMEDCT_US_2016_03_01:194729004
database_cross_reference: SNOMEDCT_US_2016_03_01:194982000
database_cross_reference: SNOMEDCT_US_2016_03_01:250998008
database_cross_reference: SNOMEDCT_US_2016_03_01:266278002
database_cross_reference: SNOMEDCT_US_2016_03_01:266279005
database_cross_reference: SNOMEDCT_US_2016_03_01:31085000
database_cross_reference: SNOMEDCT_US_2016_03_01:83898004
database_cross_reference: UMLS_CUI:C0026265
database_cross_reference: UMLS_CUI:C0155563
database_cross_reference: UMLS_CUI:C0264765
has_exact_synonym: Mitral RH valve dis.
has_exact_synonym: Rheumatic disease of mitral valve (disorder)
has_exact_synonym: Rheumatic mitral insufficiency
has_exact_synonym: Rheumatic mitral valve changes
has_exact_synonym: Rheumatic mitral valve regurgitation
has_exact_synonym: chronic rheumatic mitral valve (disorder)
has_exact_synonym: disease of mitral valve
has_exact_synonym: rheumatic disease of mitral valve
has_exact_synonym: rheumatic mitral valve incompetence
has_obo_namespace: disease_ontology
id: DOID:61

blood protein disease
type: Class
subclass of: hematopoietic system disease
imported from: doid.owl
database_cross_reference: MESH:D001796
database_cross_reference: UMLS_CUI:C0005830
has_exact_synonym: blood protein disorder
has_obo_namespace: disease_ontology
id: DOID:620

genetic disease
type: Class
subclass of: disease
definition: A disease that has_material_basis_in genetic variations in the human genome.
imported from: doid.owl
database_cross_reference: MESH:D030342
database_cross_reference: NCI:C3101
database_cross_reference: SNOMEDCT_US_2016_03_01:264530000
database_cross_reference: SNOMEDCT_US_2016_03_01:32895009
database_cross_reference: UMLS_CUI:C0019247
has_obo_namespace: disease_ontology
id: DOID:630

inherited metabolic disorder
type: Class
subclass of: disease of metabolism
definition: A disease of metabolism that is characterized by enzyme deficiency or accumulation of enzymes or toxins which interfere with normal function due to inherited enzyme abnormality.
imported from: doid.owl
database_cross_reference: MESH:D008661
database_cross_reference: NCI:C34816
database_cross_reference: SNOMEDCT_US_2016_03_01:363205007
database_cross_reference: SNOMEDCT_US_2016_03_01:86095007
database_cross_reference: UMLS_CUI:C0025521
has_exact_synonym: Inborn Errors of Metabolism
has_exact_synonym: Metabolic hereditary disorder
has_exact_synonym: inborn metabolism disorder
has_obo_namespace: disease_ontology
id: DOID:655
in_subset: DO MGI slim

cerebrovascular disease
type: Class
subclass of: artery disease
definition: An artery disease that is characterized by dysfunction of the blood vessels supplying the brain.
imported from: doid.owl
has_alternative_id: DOID:12214
has_alternative_id: DOID:3455
has_alternative_id: DOID:8231
database_cross_reference: EFO:0000712
database_cross_reference: ICD10CM:I60-I69
database_cross_reference: ICD10CM:I63.9
database_cross_reference: ICD10CM:I67.9
database_cross_reference: ICD9CM:430-438.99
database_cross_reference: ICD9CM:437.9
database_cross_reference: MESH:D002561
database_cross_reference: MESH:D020521
database_cross_reference: NCI:C2938
database_cross_reference: NCI:C3390
database_cross_reference: OMIM:601367
database_cross_reference: SNOMEDCT_US_2016_03_01:155388006
database_cross_reference: SNOMEDCT_US_2016_03_01:155405006
database_cross_reference: SNOMEDCT_US_2016_03_01:155412002
database_cross_reference: SNOMEDCT_US_2016_03_01:195208004
database_cross_reference: SNOMEDCT_US_2016_03_01:195249004
database_cross_reference: SNOMEDCT_US_2016_03_01:195595007
database_cross_reference: SNOMEDCT_US_2016_03_01:230690007
database_cross_reference: SNOMEDCT_US_2016_03_01:266312006
database_cross_reference: SNOMEDCT_US_2016_03_01:266315008
database_cross_reference: SNOMEDCT_US_2016_03_01:270883006
database_cross_reference: SNOMEDCT_US_2016_03_01:313267000
database_cross_reference: SNOMEDCT_US_2016_03_01:62914000
database_cross_reference: SNOMEDCT_US_2016_03_01:82797006
database_cross_reference: UMLS_CUI:C0007820
database_cross_reference: UMLS_CUI:C0038454
has_exact_synonym: CVA (cerebral vascular accident)
has_exact_synonym: Cerebrovascular accident (disorder)
has_exact_synonym: cerebrovascular accident
has_exact_synonym: cerebrovascular disorder
has_exact_synonym: stroke
has_obo_namespace: disease_ontology
id: DOID:6713
comment: OMIM mapping confirmed by DO. [SN].

retinal edema
type: Class
subclass of: retinal disease
imported from: doid.owl
database_cross_reference: ICD10CM:H35.81
database_cross_reference: ICD9CM:362.83
database_cross_reference: MESH:D010211
database_cross_reference: SNOMEDCT_US_2016_03_01:193426002
database_cross_reference: SNOMEDCT_US_2016_03_01:6141006
database_cross_reference: UMLS_CUI:C0242420
has_obo_namespace: disease_ontology
id: DOID:6929

disease of anatomical entity
type: Class
subclass of: disease
definition: A disease that manifests in a defined anatomical structure.
imported from: doid.owl
has_alternative_id: DOID:1
has_alternative_id: DOID:2
has_alternative_id: DOID:5
has_alternative_id: DOID:71
has_alternative_id: DOID:72
has_alternative_id: DOID:8
has_obo_namespace: disease_ontology
id: DOID:7

normocytic anemia
type: Class
subclass of: anemia
imported from: doid.owl
database_cross_reference: NCI:C35142
database_cross_reference: SNOMEDCT_US_2016_03_01:300980002
database_cross_reference: UMLS_CUI:C0085577
has_exact_synonym: ANEMIA NORMOCYTIC
has_exact_synonym: Normocytic anemia (disorder)
has_obo_namespace: disease_ontology
id: DOID:720

hematopoietic system disease
type: Class
subclass of: disease of anatomical entity
definition: An immune system disease that has_material_basis_in hematopoietic cells.
imported from: doid.owl
database_cross_reference: ICD10CM:D75.9
database_cross_reference: ICD9CM:280-289.99
database_cross_reference: ICD9CM:289.9
database_cross_reference: MESH:D006402
database_cross_reference: NCI:C26323
database_cross_reference: SNOMEDCT_US_2016_03_01:154785002
database_cross_reference: SNOMEDCT_US_2016_03_01:154842002
database_cross_reference: SNOMEDCT_US_2016_03_01:191124002
database_cross_reference: SNOMEDCT_US_2016_03_01:191402006
database_cross_reference: SNOMEDCT_US_2016_03_01:191446003
database_cross_reference: SNOMEDCT_US_2016_03_01:267552000
database_cross_reference: SNOMEDCT_US_2016_03_01:267573000
database_cross_reference: SNOMEDCT_US_2016_03_01:34093004
database_cross_reference: UMLS_CUI:C0018939
has_exact_synonym: Blood disease
has_exact_synonym: Blood dyscrasia NOS
has_exact_synonym: DISEASE OF THE BLOOD AND BLOOD-FORMING ORGANS
has_exact_synonym: Hematological disease
has_exact_synonym: blood disorder
has_exact_synonym: disease of hematopoietic system
has_obo_namespace: disease_ontology
id: DOID:74
in_subset: DO AGR slim
in_subset: DO MGI slim

gastrointestinal system disease
type: Class
subclass of: disease of anatomical entity
definition: A disease of anatomical entity that is located_in the gastrointestinal tract.
imported from: doid.owl
has_alternative_id: DOID:27
has_alternative_id: DOID:944
database_cross_reference: ICD10CM:K92.9
database_cross_reference: ICD9CM:520-579.99
database_cross_reference: MESH:D004066
database_cross_reference: SNOMEDCT_US_2016_03_01:155629009
database_cross_reference: SNOMEDCT_US_2016_03_01:155847001
database_cross_reference: SNOMEDCT_US_2016_03_01:197575000
database_cross_reference: SNOMEDCT_US_2016_03_01:266483008
database_cross_reference: SNOMEDCT_US_2016_03_01:53619000
database_cross_reference: UMLS_CUI:C0012242
has_exact_synonym: GIT disease
has_exact_synonym: Gastroenteropathy
has_exact_synonym: alimentary system disease
has_exact_synonym: digestive system disorder
has_exact_synonym: gastrointestinal disease
has_exact_synonym: gastrointestinal disorder
has_obo_namespace: disease_ontology
id: DOID:77
in_subset: DO AGR slim
in_subset: DO MGI slim

placenta disease
type: Class
subclass of: uterine disease
definition: A uterine disease that is located_in the placenta.
imported from: doid.owl
has_alternative_id: DOID:1815
has_alternative_id: DOID:5366
has_alternative_id: DOID:9219
database_cross_reference: ICD10CM:O43
database_cross_reference: ICD10CM:O43.9
database_cross_reference: ICD10CM:O43.90
database_cross_reference: ICD9CM:646.9
database_cross_reference: MESH:D010922
database_cross_reference: MESH:D011248
database_cross_reference: NCI:C26857
database_cross_reference: NCI:C27619
database_cross_reference: NCI:C34941
database_cross_reference: NCI:C35169
database_cross_reference: SNOMEDCT_US_2016_03_01:125586008
database_cross_reference: SNOMEDCT_US_2016_03_01:156069003
database_cross_reference: SNOMEDCT_US_2016_03_01:156097009
database_cross_reference: SNOMEDCT_US_2016_03_01:156123001
database_cross_reference: SNOMEDCT_US_2016_03_01:156131006
database_cross_reference: SNOMEDCT_US_2016_03_01:172422001
database_cross_reference: SNOMEDCT_US_2016_03_01:173300003
database_cross_reference: SNOMEDCT_US_2016_03_01:198881004
database_cross_reference: SNOMEDCT_US_2016_03_01:199152008
database_cross_reference: SNOMEDCT_US_2016_03_01:23288008
database_cross_reference: SNOMEDCT_US_2016_03_01:267293009
database_cross_reference: SNOMEDCT_US_2016_03_01:267311008
database_cross_reference: SNOMEDCT_US_2016_03_01:267314000
database_cross_reference: SNOMEDCT_US_2016_03_01:90821003
database_cross_reference: UMLS_CUI:C0032045
database_cross_reference: UMLS_CUI:C0032962
database_cross_reference: UMLS_CUI:C0151864
database_cross_reference: UMLS_CUI:C1335423
has_obo_namespace: disease_ontology
id: DOID:780

end stage renal failure
type: Class
subclass of: chronic kidney disease
imported from: doid.owl
has_exact_synonym: end stage renal disease
has_obo_namespace: disease_ontology
id: DOID:783

chronic kidney disease
type: Class
subclass of: kidney failure
imported from: doid.owl
database_cross_reference: EFO:0003884
database_cross_reference: ICD10CM:N18.9
database_cross_reference: ICD9CM:585.6
database_cross_reference: MESH:D007676
database_cross_reference: NCI:C9438
database_cross_reference: SNOMEDCT_US_2016_03_01:155856009
database_cross_reference: SNOMEDCT_US_2016_03_01:197654000
database_cross_reference: SNOMEDCT_US_2016_03_01:197655004
database_cross_reference: SNOMEDCT_US_2016_03_01:197755007
database_cross_reference: SNOMEDCT_US_2016_03_01:46177005
database_cross_reference: SNOMEDCT_US_2016_03_01:90688005
database_cross_reference: UMLS_CUI:C0022661
has_exact_synonym: CKD
has_exact_synonym: CRF
has_exact_synonym: chronic kidney failure
has_exact_synonym: chronic renal disease
has_exact_synonym: chronic renal failure syndrome
has_exact_synonym: renal failure - chronic
has_obo_namespace: disease_ontology
id: DOID:784

cocaine abuse
type: Class
subclass of: substance abuse
definition: A substance abuse that involves the recurring use of cocaine despite negative consequences.
imported from: doid.owl
database_cross_reference: ICD10CM:F14.1
database_cross_reference: ICD9CM:305.6
database_cross_reference: ICD9CM:305.60
database_cross_reference: MESH:D019970
database_cross_reference: SNOMEDCT_US_2016_03_01:78267003
database_cross_reference: UMLS_CUI:C0009171
has_obo_namespace: disease_ontology
id: DOID:809

retinal artery occlusion
type: Class
subclass of: retinal vascular occlusion
imported from: doid.owl
database_cross_reference: MESH:D015356
database_cross_reference: NCI:C34978
database_cross_reference: SNOMEDCT_US_2016_03_01:232035005
database_cross_reference: UMLS_CUI:C0035302
has_exact_synonym: Retinal artery occlusion (disorder)
has_obo_namespace: disease_ontology
id: DOID:8483

lung disease
type: Class
subclass of: lower respiratory tract disease
definition: A lower respiratory tract disease in which the function of the lungs is adversely affected by narrowing or blockage of the airways resulting in poor air flow, a loss of elasticity in the lungs that produces a decrease in the total volume of air that the lungs are able to hold, and clotting, scarring, or inflammation of the blood vessels that affect the ability of the lungs to take up oxygen and to release carbon dioxide.
imported from: doid.owl
has_alternative_id: DOID:11894
has_alternative_id: DOID:11895
has_alternative_id: DOID:29
has_alternative_id: DOID:766
database_cross_reference: ICD10CM:J98.4
database_cross_reference: MESH:D008171
database_cross_reference: NCI:C3198
database_cross_reference: SNOMEDCT_US_2016_03_01:196164004
database_cross_reference: SNOMEDCT_US_2016_03_01:19829001
database_cross_reference: SNOMEDCT_US_2016_03_01:266374002
database_cross_reference: UMLS_CUI:C0024115
has_obo_namespace: disease_ontology
id: DOID:850
comment: Updating out dated CUI and removing lung abscess as a synonym.

oral cavity cancer
type: Class
subclass of: gastrointestinal system cancer
definition: A gastrointestinal system cancer that is located_in the oral cavity.
imported from: doid.owl
has_alternative_id: DOID:0050627
has_alternative_id: DOID:8617
has_alternative_id: DOID:9049
has_alternative_id: DOID:9055
database_cross_reference: ICD10CM:C04
database_cross_reference: ICD10CM:C04.0
database_cross_reference: ICD10CM:C04.1
database_cross_reference: ICD10CM:C04.9
database_cross_reference: ICD9CM:144
database_cross_reference: ICD9CM:144.0
database_cross_reference: ICD9CM:144.1
database_cross_reference: ICD9CM:144.9
database_cross_reference: NCI:C9318
database_cross_reference: SNOMEDCT_US_2016_03_01:187652003
database_cross_reference: SNOMEDCT_US_2016_03_01:187653008
database_cross_reference: SNOMEDCT_US_2016_03_01:187656000
database_cross_reference: SNOMEDCT_US_2016_03_01:363385007
database_cross_reference: SNOMEDCT_US_2016_03_01:93672006
database_cross_reference: SNOMEDCT_US_2016_03_01:93802007
database_cross_reference: SNOMEDCT_US_2016_03_01:93860002
database_cross_reference: UMLS_CUI:C0153368
database_cross_reference: UMLS_CUI:C0153369
database_cross_reference: UMLS_CUI:C0496758
has_exact_synonym: malignant neoplasm of anterior portion of floor of mouth
has_exact_synonym: malignant neoplasm of floor of mouth
has_exact_synonym: malignant neoplasm of lateral floor of mouth
has_exact_synonym: malignant neoplasm of lateral portion of floor of mouth
has_exact_synonym: malignant tumor of anterior floor of mouth (disorder)
has_exact_synonym: malignant tumor of lateral floor of mouth (disorder)
has_exact_synonym: malignant tumor of the Floor of the Mouth
has_obo_namespace: disease_ontology
id: DOID:8618
in_subset: TopNodes DOcancerslim

nervous system disease
type: Class
subclass of: disease of anatomical entity
definition: A disease of anatomical entity that is located_in the central nervous system or located_in the peripheral nervous system.
imported from: doid.owl
database_cross_reference: ICD10CM:G00-G99
database_cross_reference: ICD10CM:G98
database_cross_reference: ICD10CM:G98.8
database_cross_reference: ICD9CM:349.9
database_cross_reference: MESH:D009422
database_cross_reference: NCI:C26835
database_cross_reference: SNOMEDCT_US_2016_03_01:118940003
database_cross_reference: SNOMEDCT_US_2016_03_01:154981003
database_cross_reference: SNOMEDCT_US_2016_03_01:155262005
database_cross_reference: SNOMEDCT_US_2016_03_01:192641002
database_cross_reference: SNOMEDCT_US_2016_03_01:267679005
database_cross_reference: SNOMEDCT_US_2016_03_01:286946008
database_cross_reference: UMLS_CUI:C0027765
has_obo_namespace: disease_ontology
id: DOID:863
in_subset: DO AGR slim
in_subset: DO MGI slim

tongue cancer
type: Class
subclass of: tongue disease
subclass of: oral cavity cancer
imported from: doid.owl
has_alternative_id: DOID:8648
has_alternative_id: DOID:8779
has_alternative_id: DOID:8900
has_alternative_id: DOID:8940
has_alternative_id: DOID:8999
has_alternative_id: DOID:9058
has_alternative_id: DOID:9068
has_alternative_id: DOID:9196
database_cross_reference: ICD10CM:C01
database_cross_reference: ICD10CM:C02.0
database_cross_reference: ICD10CM:C02.1
database_cross_reference: ICD10CM:C02.2
database_cross_reference: ICD10CM:C02.4
database_cross_reference: ICD10CM:C02.9
database_cross_reference: ICD9CM:141
database_cross_reference: ICD9CM:141.0
database_cross_reference: ICD9CM:141.1
database_cross_reference: ICD9CM:141.2
database_cross_reference: ICD9CM:141.3
database_cross_reference: ICD9CM:141.5
database_cross_reference: ICD9CM:141.6
database_cross_reference: ICD9CM:141.9
database_cross_reference: MESH:D014062
database_cross_reference: NCI:C3524
database_cross_reference: NCI:C9345
database_cross_reference: SNOMEDCT_US_2016_03_01:187632004
database_cross_reference: SNOMEDCT_US_2016_03_01:187633009
database_cross_reference: SNOMEDCT_US_2016_03_01:187636001
database_cross_reference: SNOMEDCT_US_2016_03_01:187637005
database_cross_reference: SNOMEDCT_US_2016_03_01:187638000
database_cross_reference: SNOMEDCT_US_2016_03_01:187642002
database_cross_reference: SNOMEDCT_US_2016_03_01:187644001
database_cross_reference: SNOMEDCT_US_2016_03_01:187646004
database_cross_reference: SNOMEDCT_US_2016_03_01:363375006
database_cross_reference: SNOMEDCT_US_2016_03_01:363376007
database_cross_reference: SNOMEDCT_US_2016_03_01:363377003
database_cross_reference: SNOMEDCT_US_2016_03_01:371974006
database_cross_reference: SNOMEDCT_US_2016_03_01:93687001
database_cross_reference: SNOMEDCT_US_2016_03_01:93773005
database_cross_reference: SNOMEDCT_US_2016_03_01:93848003
database_cross_reference: SNOMEDCT_US_2016_03_01:93868009
database_cross_reference: SNOMEDCT_US_2016_03_01:94100005
database_cross_reference: SNOMEDCT_US_2016_03_01:94101009
database_cross_reference: SNOMEDCT_US_2016_03_01:94134006
database_cross_reference: UMLS_CUI:C0153349
database_cross_reference: UMLS_CUI:C0153350
database_cross_reference: UMLS_CUI:C0153351
database_cross_reference: UMLS_CUI:C0153356
database_cross_reference: UMLS_CUI:C0474963
database_cross_reference: UMLS_CUI:C0496755
database_cross_reference: UMLS_CUI:C0684333
has_exact_synonym: Tongue neoplasm malignant stage Unspecified
has_exact_synonym: malignant neoplasm of anterior 2/3 of tongue unspecified (disorder)
has_exact_synonym: malignant neoplasm of anterior two-thirds of tongue, part unspecified
has_exact_synonym: malignant neoplasm of base of tongue
has_exact_synonym: malignant neoplasm of border of tongue
has_exact_synonym: malignant neoplasm of dorsal surface of tongue
has_exact_synonym: malignant neoplasm of dorsal tongue NOS
has_exact_synonym: malignant neoplasm of dorsum of tongue NOS (disorder)
has_exact_synonym: malignant neoplasm of fixed part of tongue NOS
has_exact_synonym: malignant neoplasm of fixed part of tongue NOS (disorder)
has_exact_synonym: malignant neoplasm of junctional zone of tongue
has_exact_synonym: malignant neoplasm of lingual tonsil
has_exact_synonym: malignant neoplasm of mobile part of tongue NOS
has_exact_synonym: malignant neoplasm of other sites of tongue
has_exact_synonym: malignant neoplasm of other sites of tongue (disorder)
has_exact_synonym: malignant neoplasm of tip and lateral border of tongue
has_exact_synonym: malignant neoplasm of tip and/or lateral border of tongue
has_exact_synonym: malignant neoplasm of tongue
has_exact_synonym: malignant neoplasm of tongue NOS
has_exact_synonym: malignant neoplasm of tongue NOS (disorder)
has_exact_synonym: malignant neoplasm of tongue, NOS
has_exact_synonym: malignant neoplasm of tongue, tip and lateral border (disorder)
has_exact_synonym: malignant neoplasm of ventral surface of tongue
has_exact_synonym: malignant neoplasm of ventral tongue surface NOS (disorder)
has_exact_synonym: malignant tumor of Posterior Tongue

vein disease
type: Class
subclass of: vascular disease
definition: A vascular disease that is located_in a vein.
imported from: doid.owl
database_cross_reference: ICD10CM:I82
database_cross_reference: ICD9CM:453
database_cross_reference: SNOMEDCT_US_2016_03_01:195435006
database_cross_reference: UMLS_CUI:C0155774
has_obo_namespace: disease_ontology
id: DOID:866

neuropathy
type: Class
subclass of: peripheral nervous system disease
definition: A nervous system disease that is located_in nerves or nerve cells.
imported from: doid.owl
database_cross_reference: ICD10CM:G62.9
database_cross_reference: NCI:C4731
database_cross_reference: SNOMEDCT_US_2016_03_01:193167000
database_cross_reference: SNOMEDCT_US_2016_03_01:264554005
database_cross_reference: SNOMEDCT_US_2016_03_01:277317008
database_cross_reference: SNOMEDCT_US_2016_03_01:277878001
database_cross_reference: SNOMEDCT_US_2016_03_01:386033004
database_cross_reference: SNOMEDCT_US_2016_03_01:42658009
database_cross_reference: UMLS_CUI:C0442874
has_exact_synonym: peripheral neuropathy
has_obo_namespace: disease_ontology
id: DOID:870

neurofibromatosis
type: Class
subclass of: autosomal dominant disease
imported from: doid.owl
has_alternative_id: DOID:14750
has_alternative_id: DOID:8711
has_alternative_id: DOID:9137
database_cross_reference: ICD10CM:Q85.00
database_cross_reference: ICD10CM:Q85.01
database_cross_reference: ICD10CM:Q85.02
database_cross_reference: ICD9CM:237.7
database_cross_reference: ICD9CM:237.70
database_cross_reference: ICD9CM:237.71
database_cross_reference: ICD9CM:237.72
database_cross_reference: MESH:C537392
database_cross_reference: MESH:D009456
database_cross_reference: MESH:D016518
database_cross_reference: MESH:D017253
database_cross_reference: NCI:C3273
database_cross_reference: NCI:C3274
database_cross_reference: NCI:C6727
database_cross_reference: OMIM:101000
database_cross_reference: OMIM:162200
database_cross_reference: OMIM:162210
database_cross_reference: OMIM:162260
database_cross_reference: OMIM:162270
database_cross_reference: ORDO:636
database_cross_reference: ORDO:637
database_cross_reference: ORDO:93921
database_cross_reference: SNOMEDCT_US_2016_03_01:154642000
database_cross_reference: SNOMEDCT_US_2016_03_01:19133005
database_cross_reference: SNOMEDCT_US_2016_03_01:700060008
database_cross_reference: SNOMEDCT_US_2016_03_01:700061007
database_cross_reference: SNOMEDCT_US_2016_03_01:81669005
database_cross_reference: SNOMEDCT_US_2016_03_01:92503002
database_cross_reference: SNOMEDCT_US_2016_03_01:92824003
database_cross_reference: UMLS_CUI:C0027831
database_cross_reference: UMLS_CUI:C0027832
database_cross_reference: UMLS_CUI:C0162678
database_cross_reference: UMLS_CUI:C0220695
has_exact_synonym: Acoustic neurofibromatosis
has_exact_synonym: Neurofibromatosis 1
has_exact_synonym: Recklinghausen's neurofibromatosis
has_exact_synonym: central Neurofibromatosis
has_exact_synonym: neurofibromatosis type 1
has_exact_synonym: neurofibromatosis type 2
has_exact_synonym: neurofibromatosis type 4
has_exact_synonym: neurofibromatosis type IV
has_exact_synonym: peripheral Neurofibromatosis
has_exact_synonym: type IV neurofibromatosis of riccardi
has_exact_synonym: von Reklinghausen disease
has_obo_namespace: disease_ontology
id: DOID:8712
in_subset: DO FlyBase slim
in_subset: DO rare slim
comment: Xref MGI. OMIM mapping confirmed by DO. [SN].

bacterial pneumonia
type: Class
subclass of: pneumonia
definition: A pneumonia involving inflammation of the lungs caused by bacteria.
imported from: doid.owl
has_alternative_id: DOID:13815
database_cross_reference: ICD10CM:J15.9
database_cross_reference: ICD9CM:482.9
database_cross_reference: MESH:D018410
database_cross_reference: NCI:C26704
database_cross_reference: SNOMEDCT_US_2016_03_01:155553007
database_cross_reference: SNOMEDCT_US_2016_03_01:195891009
database_cross_reference: SNOMEDCT_US_2016_03_01:195892002
database_cross_reference: SNOMEDCT_US_2016_03_01:53084003
database_cross_reference: UMLS_CUI:C0004626
has_exact_synonym: Pneumonia due to other gram-negative bacteria
has_exact_synonym: gram-negative pneumonia
has_obo_namespace: disease_ontology
id: DOID:874
in_subset: GOLD

polyp of corpus uteri
type: Class
subclass of: uterine disease
imported from: doid.owl
database_cross_reference: ICD10CM:N84.0
database_cross_reference: ICD9CM:621.0
database_cross_reference: NCI:C3662
database_cross_reference: SNOMEDCT_US_2016_03_01:11314008
database_cross_reference: SNOMEDCT_US_2016_03_01:266659005
database_cross_reference: UMLS_CUI:C0156369
has_exact_synonym: endometrial/uterine polyp
has_exact_synonym: polyp of Endometrium
has_exact_synonym: polyp of corpus uteri
has_exact_synonym: polyp of the Uterus
has_exact_synonym: polyp, uterus
has_obo_namespace: disease_ontology
id: DOID:9042

diabetes mellitus
type: Class
subclass of: glucose metabolism disease
definition: A glucose metabolism disease characterized by chronic hyperglycaemia with disturbances of carbohydrate, fat and protein metabolism resulting from defects in insulin secretion, insulin action, or both.
imported from: doid.owl
database_cross_reference: ICD10CM:E08-E13
database_cross_reference: ICD10CM:E11
database_cross_reference: ICD9CM:250
database_cross_reference: MESH:D003920
database_cross_reference: NCI:C2985
database_cross_reference: SNOMEDCT_US_2016_03_01:154671004
database_cross_reference: SNOMEDCT_US_2016_03_01:191044006
database_cross_reference: SNOMEDCT_US_2016_03_01:267467004
database_cross_reference: SNOMEDCT_US_2016_03_01:73211009
database_cross_reference: UMLS_CUI:C0011849
has_obo_namespace: disease_ontology
id: DOID:9351

type 2 diabetes mellitus
type: Class
subclass of: diabetes mellitus
definition: A diabetes mellitus that involves high blood glucose resulting from cells fail to use insulin properly.
imported from: doid.owl
database_cross_reference: EFO:0001360
database_cross_reference: ICD10CM:E11
database_cross_reference: KEGG:04930
database_cross_reference: MESH:D003924
database_cross_reference: NCI:C26747
database_cross_reference: OMIM:125853
database_cross_reference: OMIM:601283
database_cross_reference: OMIM:601407
database_cross_reference: OMIM:603694
database_cross_reference: OMIM:608036
database_cross_reference: SNOMEDCT_US_2016_03_01:154672006
database_cross_reference: SNOMEDCT_US_2016_03_01:190323008
database_cross_reference: SNOMEDCT_US_2016_03_01:190384004
database_cross_reference: SNOMEDCT_US_2016_03_01:267468009
database_cross_reference: SNOMEDCT_US_2016_03_01:44054006
database_cross_reference: UMLS_CUI:C0011860
has_exact_synonym: NIDDM
has_exact_synonym: non-insulin-dependent diabetes mellitus
has_exact_synonym: type II diabetes mellitus
has_obo_namespace: disease_ontology
id: DOID:9352
in_subset: DO FlyBase slim
comment: Xref MGI. OMIM mapping confirmed by DO. [SN].

brain disease
type: Class
subclass of: central nervous system disease
definition: A central nervous system disease that is located_in the brain.
imported from: doid.owl
has_alternative_id: DOID:8510
database_cross_reference: ICD10CM:G93.40
database_cross_reference: ICD10CM:G93.9
database_cross_reference: ICD9CM:348.3
database_cross_reference: ICD9CM:348.30
database_cross_reference: ICD9CM:348.9
database_cross_reference: MESH:D001927
database_cross_reference: NCI:C26920
database_cross_reference: NCI:C96413
database_cross_reference: SNOMEDCT_US_2016_03_01:155053002
database_cross_reference: SNOMEDCT_US_2016_03_01:193051008
database_cross_reference: SNOMEDCT_US_2016_03_01:193059005
database_cross_reference: SNOMEDCT_US_2016_03_01:76011009
database_cross_reference: SNOMEDCT_US_2016_03_01:81308009
database_cross_reference: UMLS_CUI:C0006111
database_cross_reference: UMLS_CUI:C0085584
has_exact_synonym: encephalopathy
has_obo_namespace: disease_ontology
id: DOID:936

intracranial hypertension
type: Class
subclass of: brain disease
imported from: doid.owl
database_cross_reference: MESH:D019586
database_cross_reference: NCI:C84791
database_cross_reference: SNOMEDCT_US_2016_03_01:155052007
database_cross_reference: SNOMEDCT_US_2016_03_01:267701004
database_cross_reference: SNOMEDCT_US_2016_03_01:271719001
database_cross_reference: SNOMEDCT_US_2016_03_01:28073009
database_cross_reference: UMLS_CUI:C0151740
has_exact_synonym: Raised intracranial pressure
has_obo_namespace: disease_ontology
id: DOID:9428

neurofibroma
type: Class
subclass of: peripheral nerve sheath neoplasm
imported from: doid.owl
database_cross_reference: MESH:D009455
database_cross_reference: NCI:C3272
database_cross_reference: SNOMEDCT_US_2016_03_01:115242003
database_cross_reference: SNOMEDCT_US_2016_03_01:134214003
database_cross_reference: SNOMEDCT_US_2016_03_01:189947001
database_cross_reference: SNOMEDCT_US_2016_03_01:404029005
database_cross_reference: SNOMEDCT_US_2016_03_01:89084002
database_cross_reference: UMLS_CUI:C0027830
has_obo_namespace: disease_ontology
id: DOID:962

biome
type: Class
subclass of: environmental system

environmental system
type: Class
subclass of: system

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

system process
type: Class
subclass of: multicellular organismal process
imported from: cl.owl

circulatory system process
type: Class
subclass of: system process
imported from: cl.owl

response to stress
type: Class
subclass of: response to stimulus
imported from: hp.owl

defense response
type: Class
subclass of: response to stress
imported from: hp.owl

inflammatory response
type: Class
subclass of: defense response
imported from: hp.owl

respiratory gaseous exchange
type: Class
subclass of: multicellular organismal process
imported from: hp.owl

blood coagulation
type: Class
subclass of: hemostasis
subclass of: coagulation
imported from: cl.owl

hemostasis
type: Class
subclass of: regulation of body fluid levels
imported from: cl.owl

behavior
type: Class
subclass of: response to stimulus

feeding behavior
type: Class
subclass of: behavior

blood circulation
type: Class
subclass of: circulatory system process
imported from: cl.owl

biological_process
type: Class
subclass of: process
imported from: cl.owl
imported from: hp.owl

multicellular organismal process
type: Class
subclass of: biological_process
imported from: cl.owl
imported from: hp.owl

developmental process
type: Class
subclass of: biological_process
imported from: cl.owl

growth
type: Class
subclass of: biological_process
imported from: hp.owl

locomotion
type: Class
subclass of: biological_process
imported from: cl.owl

symbiosis, encompassing mutualism through parasitism
type: Class
subclass of: interspecies interaction between organisms

interspecies interaction between organisms
type: Class
subclass of: multi-organism process

coagulation
type: Class
subclass of: multicellular organismal process
imported from: cl.owl

regulation of body fluid levels
type: Class
subclass of: regulation of biological quality
imported from: cl.owl

response to stimulus
type: Class
subclass of: biological_process
imported from: hp.owl

interaction with symbiont
type: Class
subclass of: interspecies interaction between organisms

multi-organism process
type: Class
subclass of: biological_process

multi-organism behavior
type: Class
subclass of: behavior
subclass of: multi-organism process

acquisition of nutrients from other organism during symbiotic interaction
type: Class
subclass of: feeding behavior

acquisition of nutrients from symbiont
type: Class
subclass of: interaction with symbiont
subclass of: multi-organism behavior
subclass of: acquisition of nutrients from other organism during symbiotic interaction

biological regulation
type: Class
subclass of: biological_process
imported from: cl.owl

regulation of biological quality
type: Class
subclass of: biological regulation
imported from: cl.owl

parasitism
type: Class
subclass of: symbiosis, encompassing mutualism through parasitism

mutualism
type: Class
subclass of: symbiosis, encompassing mutualism through parasitism

commensalism
type: Class
subclass of: symbiosis, encompassing mutualism through parasitism

Hypertension
type: Class
equivalent class: Restriction
  on property: feature gives rise to disease
  some values from: hypertension
subclass of: elevated blood pressure phenotype
editor preferred label: hypertensive phenotype
definition: The presence of chronic increased pressure in the systemic arterial system.
imported from: hp.owl

diastolic blood pressure measurement datum
type: Class
subclass of: blood pressure measurement datum
subclass of: Restriction
  on property: is about
  some values from: diastolic blood pressure
definition editor: Amanda Hicks
comment: A blood pressure measurement datum that is a quality measure of some diastolic blood pressure

systolic blood pressure measurement datum
type: Class
subclass of: blood pressure measurement datum
subclass of: Restriction
  on property: is about
  some values from: systolic blood pressure
definition: A blood pressure measurement datum that is a quality measure of some systolic blood pressure
definition editor: Amanda Hicks

elevated adult systolic blood pressure measurement datum
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: is about
    some values from: Class
      intersection of: systolic blood pressure
      intersection of: Restriction
        on property: inheres in
        some values from: adult over 18 years of age
  intersection of: Restriction
    on property: has measurement value
    some values from: Datatype
      on datatype: double
      with restrictions:
        min inclusive: 120.0
subclass of: elevated systolic blood pressure measurement datum
comment: A systolic blood pressure measurement datum that is about a blood pressure that inheres in an adult with a measurement value that is equal to or above some specified threshold for adults

documented hypertensive phenotype
type: Class
equivalent class: Restriction
  on property: phenotype of
  some values from: Restriction
    on property: bearer of
    some values from: Class
      intersection of: blood pressure
      intersection of: Restriction
        min qualified cardinality: 2
        on class: Class
subclass of: Hypertension
definition: A phenotype of hypertension that has been documented
creator: Amanda Hicks

adult over 18 years of age
type: Class
equivalent class: Class
  intersection of: Homo sapiens
  intersection of: Restriction
    on property: bearer of
    some values from: Class
      intersection of: age
      intersection of: Restriction
        some values from: adult over 18 years of age measurement datum
subclass of: Homo sapiens
definition editor: Amanda Hicks
comment: A human who is equal to or older than 18 years old

elevated systolic phenotype
type: Class
subclass of: elevated blood pressure phenotype
definition: An elevated blood pressure phenotype of systolic blood pressure that is above some specifed threshold
definition editor: Amanda Hicks

elevated systolic blood pressure measurement datum
type: Class
subclass of: systolic blood pressure measurement datum
subclass of: Restriction
  on property: is about
  some values from: elevated systolic phenotype
definition: Amanda Hicks
comment: A systolic blood pressure measurement datum with a measurement value that is equal to or above some specified threshold

elevated blood pressure phenotype
type: Class
subclass of: phenotype
definition: A phenotype of blood pressure that is above some specified threshold
creator: Amanda Hicks

elevated blood pressure measurement datum
type: Class
equivalent class: Restriction
  on property: has_part
  some values from: Class
    union of: elevated systolic blood pressure measurement datum
    union of: elevated diastolic blood pressure measurement datum
subclass of: blood pressure measurement datum
subclass of: Restriction
  on property: is about
  some values from: elevated blood pressure phenotype
comment: A blood pressure measurement datum with a measurement value that is equal to or above some specified threshold

elevated diastolic phenotype
type: Class
subclass of: elevated blood pressure phenotype
definition: An elevated blood pressure phenotype of diastolic blood pressure that is above some specifed threshold
definition editor: Amanda Hicks

diagnosis of hypertension
type: Class
equivalent class: Class
  intersection of: diagnosis
  intersection of: Restriction
    on property: is about
    some values from: hypertension
subclass of: Class
  intersection of: Restriction
    on property: is about
    some values from: hypertension
  intersection of: Restriction
    on property: is about
    some values from: Hypertension
  intersection of: Restriction
    on property: is about
    some values from: organism
definition: A diagnosis that asserts of some patient that they have a disposition to chronically elevated blood pressure

stage 1 elevated adult systolic blood pressure meaurement datum per ACC 2017 guidelines
type: Class
equivalent class: Class
  intersection of: elevated adult systolic blood pressure measurement datum
  intersection of: Restriction
    on property: has measurement value
    some values from: Datatype
      on datatype: double
      with restrictions:
        min inclusive: 130.0
  intersection of: Restriction
    on property: has measurement value
    some values from: Datatype
      on datatype: double
      with restrictions:
        max inclusive: 139.0
definition: 2017 Guideline for High Blood Pressure in Adults http://www.onlinejacc.org/content/71/19/e127?_ga=2.55616109.754894593.1553089039-383350264.1553089039
definition: An elevated adult diastolic blood pressure measurement datum that is quality measurement of a diastolic blood pressure is equal to above 120 mm Hg and equal to or less than 139 mm Hg
definition editor: Amanda Hicks

elevated diastolic blood pressure measurement datum
type: Class
subclass of: diastolic blood pressure measurement datum
subclass of: Restriction
  on property: is about
  some values from: elevated diastolic phenotype
comment: A diastolic blood pressure measurement datum with a measurement value that is equal to or above some specified threshold

elevated adult diastolic blood pressure measurement datum
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: is about
    some values from: Class
      intersection of: diastolic blood pressure
      intersection of: Restriction
        on property: inheres in
        some values from: adult over 18 years of age
  intersection of: Restriction
    on property: has measurement value
    some values from: Datatype
      on datatype: double
      with restrictions:
        min inclusive: 80.0
subclass of: elevated diastolic blood pressure measurement datum
definition editor: Amanda Hicks
comment: An elevated diastolic blood pressure measurement datum that is quality measurement of a diastolic blood pressure that inheres in an adult with a measurement value that is equal to or above some specified threshold for adults

stage 1 elevated adult diastolic blood pressure measurement datum per 2017 guidelines
type: Class
equivalent class: Class
  intersection of: elevated adult diastolic blood pressure measurement datum
  intersection of: Restriction
    on property: has measurement value
    some values from: Datatype
      on datatype: double
      with restrictions:
        min inclusive: 80.0
  intersection of: Restriction
    on property: has measurement value
    some values from: Datatype
      on datatype: double
      with restrictions:
        max inclusive: 89.0
subclass of: elevated adult diastolic blood pressure measurement datum
definition source: 2017 Guideline for High Blood Pressure in Adults http://www.onlinejacc.org/content/71/19/e127?_ga=2.55616109.754894593.1553089039-383350264.1553089039
creator: An elevated adult diastolic blood pressure measurement datum that is quality measurement of a diastolic blood pressure is equal to above 80 mm Hg and equal to or less than 89 mm Hg

stage 2 elevated adult diastolic blood pressure measurement datum per 2017 guidelines
type: Class
equivalent class: Class
  intersection of: elevated adult diastolic blood pressure measurement datum
  intersection of: Restriction
    on property: has measurement value
    some values from: Datatype
      on datatype: double
      with restrictions:
        min inclusive: 90.0
subclass of: elevated adult diastolic blood pressure measurement datum

stage 2 elevated adult systolic blood pressure meaurement datum per ACC 2017 guidelines
type: Class
equivalent class: Class
  intersection of: elevated adult systolic blood pressure measurement datum
  intersection of: Restriction
    on property: has measurement value
    some values from: Datatype
      on datatype: double
      with restrictions:
        min inclusive: 140.0
subclass of: elevated adult systolic blood pressure measurement datum

elevated adult blood pressure measurement datum per 2017 guidelines
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: Restriction
      on property: has_part
      some values from: diastolic blood pressure measurement datum
    intersection of: Restriction
      on property: has measurement value
      some values from: Datatype
        on datatype: double
  intersection of: Class
    intersection of: Restriction
      on property: has_part
      some values from: elevated adult systolic blood pressure measurement datum
    intersection of: Restriction
      on property: has measurement value
      some values from: Datatype
        on datatype: double
subclass of: elevated blood pressure measurement datum
comment: 120–129 mm Hg and <80 mm Hg

stage 1 adult blood pressure measurement datum per 2017 guidelines
type: Class
equivalent class: Restriction
  on property: has_part
  some values from: Class
    union of: stage 1 elevated adult systolic blood pressure meaurement datum per ACC 2017 guidelines
    union of: stage 1 elevated adult diastolic blood pressure measurement datum per 2017 guidelines
subclass of: elevated blood pressure measurement datum
comment: 130–139 mm Hg or 80–89 mm Hg

stage 2 adult blood pressure measurement datum per 2017 guidelines
type: Class
equivalent class: Restriction
  on property: has_part
  some values from: Class
    union of: stage 2 elevated adult diastolic blood pressure measurement datum per 2017 guidelines
    union of: stage 2 elevated adult systolic blood pressure meaurement datum per ACC 2017 guidelines
subclass of: elevated blood pressure measurement datum

adult over 18 years of age measurement datum
type: Class
equivalent class: Class
  intersection of: age measurement datum
  intersection of: Restriction
    on property: has measurement value
    some values from: Datatype
      on datatype: double
      with restrictions:
        min inclusive: 18.0
definition: An age measurement datum that is about a human being has a measurement value equal to or greater than 18 years
definition editor: Amanda Hicks

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

measurement unit label
type: Class
subclass of: datum label
editor preferred label: measurement unit label
example of usage: Examples of measurement unit labels are liters, inches, weight per volume.
definition: A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
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 editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot

objective specification
type: Class
subclass of: directive information content entity
editor preferred label: objective specification
example of usage: In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
definition: a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect 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: 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that.
editor note: Answers the question, why did you do this experiment?
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Barry Smith
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Jennifer Fostel
alternative term: goal specification
definition source: OBI Plan and Planned Process/Roles Branch
definition source: OBI_0000217

narrative object
type: Class
subclass of: information content entity
editor preferred label: narrative object
example of usage: Examples of narrative objects are reports, journal articles, and patents submission.
definition: A narrative object is an information content entity that is a set of propositions.
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
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 editor: person:Chris Stoeckert
definition source: OBI_0000013
definition source: group:OBI

action specification
type: Class
subclass of: directive information content entity
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
definition editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch

datum label
type: Class
subclass of: information content entity
editor preferred label: datum label
definition: A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
editor note: http://www.golovchenko.org/cgi-bin/wnsearch#4n
definition editor: GROUP: IAO
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.

software
type: Class
subclass of: plan specification
editor preferred label: software
definition: Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit.
editor note: see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Melanie Courtot
definition source: GROUP: OBI

journal article
type: Class
subclass of: report
editor preferred label: journal article
example of usage: Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number.
definition: a report that is published in a journal
definition editor: person:Alan Ruttenberg
definition editor: person:Chris Stoeckert
definition source: OBI_0000159
definition source: group:OBI

information carrier
type: Class
equivalent class: Class
  intersection of: quality
  intersection of: Restriction
    on property: concretizes
    some values from: information content entity
subclass of: quality
editor preferred label: information carrier
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.
definition: A quality of an information bearer that imparts the information content
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'.
editor note: 2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it.
definition editor: PERSON: Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy

model number
type: Class
subclass of: symbol
editor preferred label: model number
definition: A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
editor note: manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers
definition editor: Person: Alan Ruttenberg

programming language
type: Class
subclass of: plan specification
editor preferred label: programming language
example of usage: R, Perl, Java
definition: A language in which source code is written that is intended to be executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it.
definition editor: person:Alan Ruttenberg
definition editor: person:Chris Stoeckert
definition source: OBI_0000058
definition source: group:OBI

data item
type: Class
subclass of: information content entity
editor preferred label: data item
example of usage: Data items include counts of things, analyte concentrations, and statistical summaries.
definition: a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
editor note: 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
editor note: 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
editor note: 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
editor note: 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
editor note: JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Jonathan Rees
alternative term: data

symbol
type: Class
subclass of: information content entity
editor preferred label: symbol
example of usage: a serial number such as "12324X"
example of usage: a stop sign
example of usage: a written proper name such as "OBI"
definition: An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
editor note: 20091104, MC: this needs work and will most probably change
editor note: 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154).
definition editor: PERSON: James A. Overton
definition editor: PERSON: Jonathan Rees
definition source: based on Oxford English Dictionary

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

information content entity
type: Class
subclass of: generically dependent continuant
subclass of: Restriction
  on property: is about
  some values from: entity
editor preferred label: information content entity
example of usage: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
definition: A generically dependent continuant that is about some thing.
definition: An information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity
editor note: 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
editor note: information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
definition editor: PERSON: Chris Stoeckert
definition source: OBI_0000142

integer numeral
type: Class
subclass of: numeral
editor preferred label: integer numeral
definition: a numeral that denotes an integer
definition editor: PERSON: Jonathan Rees

scalar measurement datum
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: has value specification
  some values from: scalar value specification
subclass of: Restriction
  on property: has measurement unit label
  min cardinality: 1
subclass of: Restriction
  on property: has measurement value
  min cardinality: 1
example of usage: 10 feet. 3 ml.
definition: a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
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
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 editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot

directive information content entity
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is about
  some values from: realizable entity
definition: An information content entity whose concretizations indicate to their bearer how to realize them in a process.
editor note: 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
editor note: 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.
editor note: 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
editor note: Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
label: directive information entity

time trigger
type: Class
subclass of: conditional specification
editor preferred label: time trigger
definition: revisit?
definition editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
definition source: OBI_0000331

dot plot
type: Class
subclass of: graph
editor preferred label: dot plot
example of usage: Dot plot of SSC-H and FSC-H.
definition: A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions.
definition editor: person:Allyson Lister
definition editor: person:Chris Stoeckert
definition source: OBI_0000123
definition source: group:OBI

graph
type: Class
subclass of: diagram
editor preferred label: graph
definition: A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way.
definition editor: PERSON: Lawrence Hunter
definition editor: person:Alan Ruttenberg
definition editor: person:Allyson Lister
definition source: OBI_0000240
definition source: group:OBI

rule
type: Class
subclass of: conditional specification
editor preferred label: rule
example of usage: example to be added
definition: a rule is an executable which guides, defines, restricts actions
editor note: MSI
definition editor: PRS
definition source: OBI_0500021
definition source: PRS

contour plot
type: Class
subclass of: graph
editor preferred label: contour plot
example of usage: Contour plot of SSC-H, FSC-H, and FL1-H.
editor note: generically_dependent_continuants
definition editor: person:Allyson Lister
definition editor: person:Chris Stoeckert
definition source: OBI_0000246
definition source: group:Flow Cytometry community

algorithm
type: Class
subclass of: plan specification
editor preferred label: algorithm
example of usage: PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
definition: A plan specification which describes the inputs and 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 editor: Philippe Rocca-Serra
definition editor: PlanAndPlannedProcess Branch
definition source: OBI_0000270
definition source: adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)

software interpreter
type: Class
subclass of: algorithm
editor preferred label: software interpreter
example of usage: R program, Perl interpreter, Java virtual machine
definition: A software interpreter is a software application that executes some specified input software.
editor note: Do we care? Jennifer: Yes, there was a particular version of R that had a bug and it was fixed later. That would imply that we mean specific version of an interpreter. So an instance of this would be a particular version of the interpreter
definition editor: person:Alan Ruttenberg
definition editor: person:Chris Stoeckert
definition source: OBI_0000199
definition source: group:OBI

curation status specification
type: Class
subclass of: data about an ontology part
editor preferred label: curation status specification
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 note: Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
definition editor: PERSON:Bill Bug
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition source: OBI_0000266

density plot
type: Class
subclass of: graph
editor preferred label: density plot
example of usage: Density plot of SSC-H and FSC-H.
definition: A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel.
definition editor: person:Allyson Lister
definition editor: person:Chris Stoeckert
definition source: OBI_0000179
definition source: group:Flow Cytometry community

report
type: Class
subclass of: document
editor preferred label: report
example of usage: Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article.
definition: a document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record)
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
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
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot
definition editor: PERSON:Chris Stoeckert
definition source: GROUP: OBI
definition source: OBI_0000099

source code module
type: Class
subclass of: directive information content entity
editor preferred label: source code module
example of usage: The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script.
definition: A source code module is a directive information entity that specifies, using a programming language, some algorithm.
definition editor: person:Alan Ruttenberg
definition editor: person:Chris Stoeckert
definition source: OBI_0000039
definition source: group:OBI

data format specification
type: Class
subclass of: directive information content entity
editor preferred label: data format specification
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
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 editor: PERSON: Alan Ruttenberg
definition editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
definition source: OBI_0000187

data set
type: Class
subclass of: data item
editor preferred label: data set
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: 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.
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
editor note: 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.
definition editor: person:Allyson Lister
definition editor: person:Chris Stoeckert
definition source: OBI_0000042
definition source: group:OBI

image
type: Class
subclass of: figure
editor preferred label: image
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 editor: person:Alan Ruttenberg
definition editor: person:Allyson
definition editor: person:Chris Stoeckert
definition source: OBI_0000030
definition source: group:OBI

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

plan specification
type: Class
subclass of: directive information content 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
editor preferred label: plan specification
example of usage: PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
definition: A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
editor note: 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
editor note: 2014-03-31: A plan specification can have other parts, such as conditional specifications.
editor note: Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
definition editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch
definition source: OBI_0000344
comment: 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them

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

version number
type: Class
subclass of: symbol
editor preferred label: version number
definition: A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name.
editor note: Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version
definition editor: GROUP: IAO

serial number
type: Class
subclass of: symbol
editor preferred label: serial number
definition: A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
editor note: Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-)
definition editor: GROUP: IAO

lot number
type: Class
subclass of: symbol
editor preferred label: lot number
definition: A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots.
definition editor: GROUP: IAO
alternative term: batch number

setting datum
type: Class
subclass of: data item
definition: A settings datum is a datum that denotes some configuration of an instrument.
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.
editor note: Alan grouped these in placeholder for the moment. Name by analogy to measurement datum.

conclusion textual entity
type: Class
subclass of: textual entity
editor preferred label: 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
definition: A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers.
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 editor: Person:Alan Ruttenberg

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
      some values from: information content entity
subclass of: material entity
editor preferred label: material information bearer
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.
example of usage: a brain
example of usage: a hard drive
definition: A material entity in which a concretization of an information content entity inheres.
definition editor: GROUP: IAO

histogram
type: Class
subclass of: graph
editor preferred label: histogram
definition: A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes.
definition editor: PERSON:Chris Stoeckert
definition editor: PERSON:James Malone
definition editor: PERSON:Melanie Courtot
definition source: GROUP:OBI

heatmap
type: Class
subclass of: graph
editor preferred label: heatmap
definition: A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map.
definition editor: PERSON:Chris Stoeckert
definition editor: PERSON:James Malone
definition editor: PERSON:Melanie Courtot
definition source: GROUP:OBI

Venn diagram
type: Class
subclass of: graph
editor preferred label: Venn diagram
definition: A Venn diagram is a report graph showing all hypothetically possible logical relations between a finite collection of sets.
definition editor: PERSON:Chris Stoeckert
definition editor: PERSON:James Malone
definition editor: PERSON:Melanie Courtot
definition source: WEB: http://en.wikipedia.org/wiki/Venn_diagram

dendrogram
type: Class
subclass of: graph
editor preferred label: dendrogram
example of usage: Dendrograms are often used in computational biology to illustrate the clustering of genes.
definition: A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm.
definition editor: PERSON:Chris Stoeckert
definition editor: PERSON:James Malone
definition editor: PERSON:Melanie Courtot
definition source: WEB: http://en.wikipedia.org/wiki/Dendrogram

scatter plot
type: Class
subclass of: graph
editor preferred label: scatter plot
example of usage: Comparison of gene expression values in two samples can be displayed in a scatter plot
definition: A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis.
definition editor: PERSON:Chris Stoeckert
definition editor: PERSON:James Malone
definition editor: PERSON:Melanie Courtot
alternative term: scattergraph
definition source: WEB: http://en.wikipedia.org/wiki/Scatterplot

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.
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Joanne Luciano
definition editor: PERSON:Melanie Courtot
definition source: WEB: http://en.wiktionary.org/wiki/photograph

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
      some values from: photograph
subclass of: material information bearer
editor preferred label: photographic print
definition: A photographic print is a material entity upon which a photograph generically depends.
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Melanie Courtot

obsolescence reason specification
type: Class
subclass of: data about an ontology part
editor preferred label: obsolescence reason specification
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 note: The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot

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

citation
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: document
editor preferred label: citation
example of usage: Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183.
definition: a textual entity intended to identify a particular publication
definition editor: PERSON: Lawrence Hunter

author identification
type: Class
subclass of: written name
editor preferred label: author identification
example of usage: L. Hunter
definition: A textual entity intended to identify a particular author
definition editor: PERSON: Lawrence Hunter

institutional identification
type: Class
subclass of: textual entity
editor preferred label: institutional identification
example of usage: University of Colorado Denver School of Medicine
definition: A textual entity intended to identify a particular institution
definition editor: PERSON: Lawrence Hunter

caption
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: figure
editor preferred label: caption
example of usage: Figure 1: A system diagram describing the modules of the Hanalyzer. Reading methods (green) take external sources of knowledge (blue) and extract information from them, either by parsing structured data or biomedical language processing to extract information from unstructured data. Reading modules are responsible for tracking the provenance of all knowledge. Reasoning methods (yellow) enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. All knowledge sources, read or reasoned, are assigned a reliability score, and all are combined using that score into a knowledge network (orange) that represents the integration of all sorts of relationship between a pair of genes and a combined reliability score. A data network (also orange) is created from experimental results to be analyzed. The reporting modules (pink) integrate the data and knowledge networks, producing visualizations that can be queried with the associated drill-down tool.
definition: A textual entity that describes a figure
definition editor: PERSON: Lawrence Hunter

document title
type: Class
subclass of: textual entity
editor preferred label: document title
example of usage: Textual characteristics of traditional and Open Access scientific journals are similar
definition: A textual entity that names a document
definition editor: PERSON: Lawrence Hunter

table
type: Class
subclass of: textual entity
editor preferred label: table
example of usage: | T F --+----- T | T F F | F F
definition: A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions
definition editor: PERSON: Lawrence Hunter

table of abbreviations
type: Class
subclass of: table
editor preferred label: table of abbreviations
example of usage: IAO information artifact ontology OBI ontology of biomedical investiations GO gene ontology
definition: A table where the constituent texts are abbreviations and their expansions
definition editor: PERSON: Lawrence Hunter

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

diagram
type: Class
subclass of: figure
editor preferred label: diagram
example of usage: A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.
definition: A figure that expresses one or more propositions
definition editor: PERSON: Lawrence Hunter

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

publication
type: Class
subclass of: document
editor preferred label: publication
example of usage: A journal article or book
definition: A document that has been accepted by a publisher
definition editor: PERSON: Lawrence Hunter

publication about an investigation
type: Class
subclass of: publication
subclass of: Restriction
  on property: is about
  some values from: investigation
editor preferred label: publication about an investigation
example of usage: Most scientific journal articles
definition: A publication that is about an investigation
definition editor: PERSON: Lawrence Hunter
alternative term: scientific publication

patent
type: Class
subclass of: document
editor preferred label: patent
example of usage: US Patent 6,449,603
definition: A document that has been accepted by a patent authority
definition editor: PERSON: Lawrence Hunter

document part
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: part of
  some values from: document
editor preferred label: document part
example of usage: An abstract, introduction, method or results section.
definition: an information content entity that is part of a document
definition editor: PERSON: Lawrence Hunter

abstract
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: document
editor preferred label: abstract
example of usage: The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or biomedical language processing to extract information from unstructured data, and track knowledge provenance. Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data.
definition: A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes.
definition editor: PERSON: Lawrence Hunter

introduction to a publication about an investigation
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: objective specification
editor preferred label: introduction to a publication about an investigation
example of usage: Section labelled 'introduction' of a typical scientific journal article
definition: A part of a publication about an investigation that is about the objective specification (why the investigation is being done)
definition editor: PERSON: Lawrence Hunter
alternative term: background
alternative term: introduction

methods section
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: study design
editor preferred label: methods section
example of usage: The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article.
definition: A part of a publication about an investigation that is about the study design of the investigation
definition editor: PERSON: Lawrence Hunter
alternative term: experimental
alternative term: experimental procedures
alternative term: experimental section
alternative term: methods

results section
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: study design execution
editor preferred label: results section
example of usage: The section labelled 'results' in a typical scientific journal article
definition: A part of a publication about an investigation that is about a study design execution
definition editor: PERSON: Lawrence Hunter
alternative term: results

discussion section of a publication about an investigation
type: Class
subclass of: document part
editor preferred label: discussion section of a publication about an investigation
definition: A part of a publication about an investigation that is about the study interpretation of the investigation
definition editor: PERSON: Lawrence Hunter
alternative term: discussion
alternative term: discussion section

references section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has_part
  some values from: citation
editor preferred label: references section
example of usage: The list of citations found at the end of a scientific publication, grant proposal or patent application, sometimes called "literature cited" or "bibliography"
definition: A part of a document that has citations as parts
definition editor: PERSON: Lawrence Hunter

author list
type: Class
subclass of: document part
subclass of: Restriction
  on property: has_part
  some values from: author identification
editor preferred label: author list
example of usage: Lawrence Hunter and Kevin Brettonel Cohen
definition: part of a document that enumerates the authors of the document
definition editor: PERSON: Lawrence Hunter

institution list
type: Class
subclass of: document part
subclass of: Restriction
  on property: has_part
  some values from: institutional identification
editor preferred label: institution list
example of usage: The University of Colorado Denver School of Medicine and the University of Colorado Boulder.
definition: part of a document that has parts that are institution identifications associated with the authors of the document
definition editor: PERSON: Lawrence Hunter

author contributions section
type: Class
subclass of: document part
editor preferred label: author contributions section
example of usage: LH conceived of the hypothesis, designed the study and contributed to the writing of the manuscript. KBC executed the experiments, analyzed the data, and contributed to the writing of the manuscript.
definition: A part of a publication that is about the specific contributions of each author
definition editor: PERSON: Lawrence Hunter
alternative term: author contributions
alternative term: contributions by the authors

acknowledgements section
type: Class
subclass of: document part
editor preferred label: acknowledgements section
example of usage: The authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscript
definition: Part of a publication that is about the contributions of people or institutions other than the authors.
definition editor: PERSON: Lawrence Hunter
alternative term: acknowledgements
alternative term: acknowledgments

footnote
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: document part
editor preferred label: footnote
example of usage: The referent in the text is usually indicated by a special typographic character such as * or a superscripted number, which is also used to indicate the footnote that refers to that text.
definition: A part of a document that is about a specific other part of the document. Usually footnotes are spatially segregated from the rest of the document.
definition editor: PERSON: Lawrence Hunter
alternative term: endnote

supplementary material to a document
type: Class
subclass of: document part
editor preferred label: supplementary material to a document
definition: part of a document that is segregated from the rest of the document due to its size
definition editor: PERSON: Lawrence Hunter
alternative term: additional information
alternative term: appendix
alternative term: supplemental information
alternative term: supplementary material
alternative term: supporting information

table of contents
type: Class
subclass of: table
editor preferred label: table of contents
definition: A table that relates document parts to specific locations in a document (usually page numbers). This is also a document part (subsumption there should be inferred).
definition editor: PERSON: Lawrence Hunter

table of figures
type: Class
subclass of: table
editor preferred label: table of figures
definition: A table that relates figures in a document to specific locations in that document (usually page numbers). This is also a document part (subsumption there should be inferred).
definition editor: PERSON: Lawrence Hunter

running title
type: Class
subclass of: document title
editor preferred label: running title
definition: A shorter version of a document title
definition editor: PERSON: Lawrence Hunter

copyright section
type: Class
subclass of: document part
editor preferred label: copyright section
example of usage: This work is licensed under a Creative Commons Attribution-Share Alike 3.0 United States License.
definition: A document part that describes legal restrictions on making or distributing copies of the document
definition editor: PERSON: Lawrence Hunter

cartesian spatial coordinate datum
type: Class
subclass of: data item
subclass of: Restriction
  on property: denotes
  some values from: zero-dimensional spatial region
subclass of: Restriction
  on property: has coordinate unit label
  cardinality: 1
definition: A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude
editor note: 2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617
definition editor: Alan Ruttenberg
curator note: AR notes: We need to discuss whether it should include site.

one dimensional cartesian spatial coordinate datum
type: Class
subclass of: cartesian spatial coordinate datum
subclass of: Restriction
  on property: denotes
  some values from: Class
    intersection of: zero-dimensional spatial region
    intersection of: Restriction
      on property: part of
      some values from: one-dimensional spatial region
subclass of: Restriction
  on property: has x coordinate value
  cardinality: 1
definition: A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region
definition editor: Alan Ruttenberg

two dimensional cartesian spatial coordinate datum
type: Class
subclass of: cartesian spatial coordinate datum
subclass of: Restriction
  on property: denotes
  some values from: Class
    intersection of: zero-dimensional spatial region
    intersection of: Restriction
      on property: part of
      some values from: two-dimensional spatial region
subclass of: Restriction
  on property: has x coordinate value
  cardinality: 1
subclass of: Restriction
  on property: has y coordinate value
  cardinality: 1
definition: A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region
definition editor: Alan Ruttenberg

three dimensional cartesian spatial coordinate datum
type: Class
subclass of: cartesian spatial coordinate datum
subclass of: Restriction
  on property: denotes
  some values from: Class
    intersection of: zero-dimensional spatial region
    intersection of: Restriction
      on property: part of
      some values from: three-dimensional spatial region
subclass of: Restriction
  on property: has x coordinate value
  cardinality: 1
subclass of: Restriction
  on property: has z coordinate value
  cardinality: 1
subclass of: Restriction
  on property: has y coordinate value
  cardinality: 1
definition: A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region
definition editor: Alan Ruttenberg

length measurement datum
type: Class
subclass of: scalar measurement datum
subclass of: Restriction
  on property: has measurement unit label
  some values from: length unit
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
definition editor: Alan Ruttenberg

denotator type
type: Class
subclass of: data about an ontology part
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.
definition: A denotator type indicates how a term should be interpreted from an ontological perspective.
definition editor: Alan Ruttenberg
definition source: Barry Smith, Werner Ceusters

mass measurement datum
type: Class
subclass of: scalar measurement datum
subclass of: Class
  intersection of: Restriction
    on property: has measurement unit label
    all values from: mass unit
  intersection of: Restriction
    on property: is quality measurement of
    all values from: mass
definition: A scalar measurement datum that is the result of measurement of mass quality
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition editor: Person:Alan Ruttenberg

hypothesis textual entity
type: Class
subclass of: textual entity
editor preferred label: hypothesis 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
definition: A textual entity that expresses an assertion that is intended to be tested.
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition editor: Person:Alan Ruttenberg

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
definition: A scalar measurement datum that is the result of measuring a temporal interval
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition editor: Person:Alan Ruttenberg

postal address
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: geographic 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 https://github.com/information-artifact-ontology/IAO/issues/59

email address
type: Class
subclass of: information content entity
editor preferred label: email address
editor note: Alan Ruttenberg 1/3/2012 - Provisional id, see issue at https://github.com/information-artifact-ontology/IAO/issues/130&thanks=130&ts=1325636583
definition editor: Person:Alan Ruttenberg
definition editor: Person:Chris Stoeckart

author role
type: Class
subclass of: role
editor preferred label: author role
definition: A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot

data item extraction from journal article
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: journal article
subclass of: Restriction
  on property: has_specified_output
  some values from: data item
definition: a planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing
definition editor: Person:Alan Ruttenberg

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: document
example of usage: Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
definition: a planned process in which a document is created or added to by including the specified input in it.
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
definition editor: Bjoern Peters
definition source: wikipedia http://en.wikipedia.org/wiki/Documenting

line graph
type: Class
subclass of: graph
editor preferred label: line graph
definition: A line graph is a type of graph created by connecting a series of data points together with a line.
definition editor: PERSON:Chris Stoeckert
definition editor: PERSON:Melanie Courtot
alternative term: line chart
definition source: GROUP:OBI
definition source: WEB: http://en.wikipedia.org/wiki/Line_chart

assigning a centrally registered identifier
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: centrally registered identifier symbol
subclass of: Restriction
  on property: has participant
  some values from: centrally registered identifier registry
example of usage: A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned.
definition: a planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity
editor note: 2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry.
definition editor: Person:Alan Ruttenberg
definition editor: Person:Bjoern Peters
definition editor: Person:Melanie Courtot
alternative term: assigning a CRID

associating information with a centrally registered identifier in its registry
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: centrally registered identifier symbol
subclass of: Restriction
  on property: has participant
  some values from: centrally registered identifier registry
example of usage: Articles in Pubmed are reviewed by curators who add MESH terms to the Pubmed records in order to categorize them better and improve the ability to search for them.
definition: A planned process in which a CRID registry associates an information content entity with a CRID symbol
definition editor: PERSON:Alan Ruttenberg
alternative term: associating information with a CRID in the CRID registry

centrally registered identifier symbol
type: Class
subclass of: symbol
subclass of: Restriction
  on property: part of
  some values from: centrally registered identifier
example of usage: The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.
definition: A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bill Hogan
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Melanie Courtot
alternative term: CRID symbol
definition source: Original proposal from Bjoern, discussions at IAO calls

centrally registered identifier
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: has_part
  some values from: centrally registered identifier symbol
subclass of: Restriction
  on property: has_part
  some values from: Restriction
    on property: denotes
    some values from: centrally registered identifier registry
example of usage: The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.
definition: An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs.
editor note: 2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records').
editor note: Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation.
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 editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bill Hogan
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Melanie Courtot
alternative term: CRID
definition source: Original proposal from Bjoern, discussions at IAO calls

centrally registered identifier registry
type: Class
subclass of: data set
example of usage: PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles.
definition: A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bill Hogan
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Melanie Courtot
alternative term: CRID registry
definition source: Original proposal from Bjoern, discussions at IAO calls

looking up a centrally registered identifier
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: centrally registered identifier symbol
subclass of: Restriction
  on property: has_specified_output
  some values from: information content entity
subclass of: Restriction
  on property: has participant
  some values from: centrally registered identifier registry
example of usage: Going to the PubMed website and entering a PubMed ID in order to retrieve the Pubmed information associated with that ID.
definition: A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bill Hogan
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Melanie Courtot
alternative term: looking up a CRID

time stamped measurement datum
type: Class
subclass of: measurement datum
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 datum

time sampled measurement data set
type: Class
subclass of: data set
subclass of: Restriction
  on property: has_part
  some values from: time stamped measurement datum
example of usage: pmid:20604925 - time-lapse live cell microscopy
definition: A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time.
definition editor: Alan Ruttenberg
alternative term: experimental time series

written name
type: Class
subclass of: textual entity
editor preferred label: written name
example of usage: "Bill Clinton"
example of usage: "The Eiffel Tower"
example of usage: "United States of America"
definition: A textual entity that denotes a particular in reality.
definition editor: PERSON: Bill Hogan
definition source: https://github.com/information-artifact-ontology/IAO/issues/114
curator note: The qualifier "written" is to set it apart from spoken names. Also, note the restrictions to particulars. We are not naming universals. We could however, be naming, attributive collections which are particulars, so "All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT" would be a name.

software method
type: Class
subclass of: software
definition: A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task.
definition editor: PERSON: Melanie Courtot
definition editor: PERSON: Michel Dumontier
definition source: https://github.com/information-artifact-ontology/IAO/issues/80

software module
type: Class
subclass of: software
definition: A software module is software composed of a collection of software methods.
definition editor: PERSON: Melanei Courtot
definition editor: PERSON: Michel Dumontier
definition source: https://github.com/information-artifact-ontology/IAO/issues/80

software library
type: Class
subclass of: software
definition: A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application.
definition editor: PERSON: Melanie Courtot
definition editor: PERSON: Michel Dumontier
definition source: https://github.com/information-artifact-ontology/IAO/issues/80

software application
type: Class
subclass of: software
definition: A software application is software that can be directly executed by some processing unit.
definition editor: PERSON: Melanie Courtot
definition editor: PERSON: Michel Dumontier
definition source: https://github.com/information-artifact-ontology/IAO/issues/80

software script
type: Class
subclass of: software
definition: A software script is software whose instructions can be executed using a software interpreter.
definition editor: PERSON: Melanie Courtot
definition editor: PERSON: Michel Dumontier
definition source: https://github.com/information-artifact-ontology/IAO/issues/80

abbreviation textual entity
type: Class
subclass of: textual entity
editor preferred label: abbreviation textual entity
example of usage: From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): BAC: Bacterial artificial chromosome; CR: Calretinin; GFAP: Glial fibrillary acidic protein; MAP: Microtubule-associated protein; MRI: Magnetic resonance imaging; NSC: Neural stem cell; PDA: Patent ductus arteriosus; PMG: Polymicrogyria; PNH: Periventricular nodular heterotopia; VSD: Ventricular septal defect.
definition: A textual entity listing abbreviations and their expansions that are used in a document.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

abbreviations section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has_part
  some values from: abbreviation textual entity
editor preferred label: abbreviations section
example of usage: The section labelled 'abbreviations' in a typical scientific journal article.
definition: A part of a document where abbreviations and their long-forms used within the document are listed.
definition editor: PERSON: Bill Baumgartner
alternative term: abbreviations
alternative term: abbreviations list
alternative term: abbreviations used
alternative term: list of abbreviations
alternative term: list of abbreviations used
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

author information section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has_part
  some values from: author information textual entity
editor preferred label: author information section
example of usage: The section labelled 'author information' in a typical scientific journal article, e.g. in Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/)
definition: A part of a document about the authors that provides biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document.
definition editor: PERSON: Bill Baumgartner
alternative term: author information
alternative term: authors’ information
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

author information textual entity
type: Class
subclass of: textual entity
editor preferred label: author information textual entity
example of usage: From Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/): IT [the author] is the lead paediatrician for ADHD services in East Hertfordshire, UK, where she runs a weekly joint ADHD clinic with the Child and Adolescent psychiatrist and works within an ADHD specialist team. IT also sees children with other neurodisability issues who may have comorbid ADHD, where the presentation may be more complex and challenging to manage. IT has vast experience in managing children with complex ADHD. She has 18 years of experience in paediatrics and also has extensive experience in the use of psychopharmacologic agents in managing children with ADHD.
definition: A textual entity expression information about an author of a document. This information may include biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

author summary section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has_part
  some values from: author summary textual entity
editor preferred label: author summary section
example of usage: The section labelled 'synopsis' in a typical scientific journal article, e.g. in Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/)
definition: A part of a document, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers.
definition editor: PERSON: Bill Baumgartner
alternative term: author summary
alternative term: summary
alternative term: synopsis
definition source: Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines)
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

author summary textual entity
type: Class
subclass of: textual entity
editor preferred label: author summary textual entity
example of usage: From Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/): The search for genetic risk factors for common human diseases often relies on the use of linkage and association studies to establish correlation between genomic markers and disease risk. These studies require additional functional evaluation of candidate genes, including their possible interaction with diet and environment. The number of candidate genes is typically large and the development of appropriate genetic tools in mammalian systems is slow. By contrast, large-scale genetic screens, using widely available genetic tools, are routinely conducted in the fruit fly Drosophila melanogaster. In this study, we used Drosophila to screen candidate genes identified in human genome-wide scans as associated with risk of metabolic abnormalities such as type 2 diabetes. We show that a number of human candidate genes have fly orthologs that play an important role in Drosophila tolerance to high dietary sucrose. We further explored some of the specific metabolic abnormalities that can result when these genes’ activities are reduced in flies, focusing on a gene we call dHHEX (CG7056), the fly ortholog of human HHEX.
definition: A textual entity, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers, e.g as described in the article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines).
definition editor: PERSON: Bill Baumgartner
definition source: Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines).
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

availability section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has_part
  some values from: availability textual entity
editor preferred label: availability section
example of usage: The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/).
definition: A part of a document about a resource described in the document, e.g. software, that describes where and/or how that resource can be obtained.
definition editor: PERSON: Bill Baumgartner
alternative term: availability
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

availability textual entity
type: Class
subclass of: textual entity
editor preferred label: availability textual entity
example of usage: From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): Project home page:http://krux.googlecode.com
definition: A textual entity expressing the location of a resource, e.g. software, or the manner in which a resource can be obtained.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

case report section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has_part
  some values from: case report textual entity
editor preferred label: case report section
example of usage: The section labelled 'case report' in a typical scientific journal article, e.g. in Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/)
definition: A part of a document about the medical history of a specific patient as it relates to the topic of the document.
definition editor: PERSON: Bill Baumgartner
alternative term: case presentation
alternative term: case report
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

case report textual entity
type: Class
subclass of: textual entity
editor preferred label: case report textual entity
example of usage: Excerpt from Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/): The patient is a 50-year-old man. His medical history was not contributory. At the age of 37 years, he complained of persistent fatigue and dyspnoea even for modest efforts and oedema of lower limbs. The patient was examined at the department of internal medicine of the local hospital, and hospitalised with a diagnosis of dilated cardiomyopathy probably consequence of a myocarditis process. Soon after he was transferred to the cardiologic department of the regional hospital, and pharmacologically treated for heart failure and pulmonary hypertension.
definition: A textual entity that expresses a detailed account of a portion of the medical history for a specific patient.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

conclusion section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has_part
  some values from: conclusion textual entity
editor preferred label: conclusion section
example of usage: The section labelled 'conclusion' in a typical scientific journal article.
definition: A part of a document used to summarize the findings discussed in the document. The conclusion section is typically found near the end of a document.
definition editor: PERSON: Bill Baumgartner
alternative term: concluding remarks
alternative term: conclusion
alternative term: conclusions
alternative term: findings
alternative term: summary
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

conflict of interest section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has_part
  some values from: conflict of interest textual entity
editor preferred label: conflict of interest section
example of usage: The section labelled 'conflict of interest statement' in a typical scientific journal article.
definition: A part of a document used to declare any competing interests regarding the authors and/or funding organization for the work described in the document.
definition editor: PERSON: Bill Baumgartner
alternative term: competing interests
alternative term: conflict of interest
alternative term: conflict of interest statement
alternative term: declaration of competing interests
alternative term: disclosure of potential conflicts of interest
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

conflict of interest textual entity
type: Class
subclass of: textual entity
editor preferred label: conflict of interest statement
example of usage: SD [an author] is a Merck employee and Merck is the sponsor of this study. [Taken from 'Effects of obstructive sleep apnoea risk on postoperative respiratory complications: protocol for a hospital-based registry study' Shin et al. 2016 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4735131/)]
definition: A textual entity that expresses a situation involving one or more of the authors, or the funding source of a document whereby the authors or funding source stand to potentially gain (typically financially) from the results reported in the document.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

consent section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has_part
  some values from: consent textual entity
editor preferred label: consent section
example of usage: The section labelled 'consent' in a typical scientific journal article, e.g. Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/)
definition: A part of a document about the consent process that was used to enroll patients in a study.
definition editor: PERSON: Bill Baumgartner
alternative term: consent
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

consent textual entity
type: Class
subclass of: textual entity
editor preferred label: consent textual entity
example of usage: From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): Written informed consent was obtained from the patient’s parents for publication of this Case report and any accompanying images. A copy of the written consent is available for review by the Editor-in chief of this journal.
definition: A textual entity that documents the consenting process used to enroll patients in a study.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

ethical approval section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has_part
  some values from: ethical approval textual entity
editor preferred label: ethical approval section
example of usage: The section labelled 'ethical approval' in a typical scientific journal article.
definition: A part of a document about the governance body responsible for approving the work discussed in a document on an ethical basis.
definition editor: PERSON: Bill Baumgartner
alternative term: ethical approval
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

ethical approval textual entity
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: study design
editor preferred label: ethical approval textual entity
example of usage: From McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/): The NHS National Research Ethics Service had previously approved the use of these anonymised data for research purposes and this analysis did not require independent review.
definition: A textual entity that documents the ethical approval of some study design.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

figures section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has_part
  some values from: figure
editor preferred label: figures section
example of usage: The section labelled 'figures' in a typical scientific journal article.
definition: A part of a document that contains one or more figures.
definition editor: PERSON: Bill Baumgartner
alternative term: figures
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

funding source declaration section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has_part
  some values from: funding source declaration textual entity
editor preferred label: funding source declaration section
example of usage: The section labelled 'funding' in a typical scientific journal article.
definition: A part of a document used to detail information regarding the source of funding used in support of the generation of the document content.
definition editor: PERSON: Bill Baumgartner
alternative term: funding
alternative term: funding information
alternative term: funding sources
alternative term: funding statement
alternative term: funding/support
alternative term: source of funding
alternative term: sources of funding
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

funding source declaration textual entity
type: Class
subclass of: textual entity
editor preferred label: funding souce declaration textual entity
example of usage: From Stephan et al. Accid Anal Prev. 2011 May; 43(3): 1062–1067. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062852/): This study was supported by the International Collaborative Research Grants Scheme with joint grants from the Wellcome Trust UK (GR071587MA) and the Australian NHMRC (268055). The funding sources played no role in study design, data collection, analysis or interpretation, writing the report, or the decision to submit the paper for publication.
definition: A textual entity documenting the source of funding that supported some study.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

future directions section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has_part
  some values from: future directions textual entity
editor preferred label: future directions section
example of usage: The section labelled 'future directions' in a typical scientific journal article.
definition: A part of a document detailing extensions of the described work that may be implemented at some future point in time.
definition editor: PERSON: Bill Baumgartner
alternative term: future challenges
alternative term: future considerations
alternative term: future developments
alternative term: future directions
alternative term: future outlook
alternative term: future perspectives
alternative term: future plans
alternative term: future prospects
alternative term: future research
alternative term: future research directions
alternative term: future studies
alternative term: future work
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

future directions textual entity
type: Class
subclass of: textual entity
editor preferred label: future directions textual entity
example of usage: Excerpt from Wang and Li. Acta Pharmacol Sin. 2016 Jan; 37(1): 25–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4722976/): In the future, several questions will need to be resolved regarding the physiological assembly of KCNQ channels and their functional implications in complex neural circuits. First, we still lack sufficiently selective inhibitors and activators among the KCNQ family members.
definition: A textual entity expressing ideas regarding future work relevant to work described in a document that could be done.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

genome announcement section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has_part
  some values from: genome announcement textual entity
editor preferred label: genome announcement section
example of usage: The section labelled 'genome announcement' in a typical scientific journal article, e.g. in Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/)
definition: A document part announcing the publication of a novel draft genome sequence.
definition editor: PERSON: Bill Baumgartner
alternative term: genome announcement
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

genome announcement textual entity
type: Class
subclass of: textual entity
editor preferred label: genome announcement textual entity
example of usage: Excerpt from Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/): Here we report the genome sequence of Lactobacillus malefermentans KCTC 3548, which we obtained using a whole-genome shotgun strategy (4) with Roche 454 GS (FLX Titanium) pyrosequencing (257,559 reads totaling ∼89.8 Mb; ∼45-fold coverage of the genome) at the Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB).
definition: A textual entity that describes the generation and public release of a novel, draft genome sequence.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

keyword textual entity
type: Class
subclass of: textual entity
editor preferred label: keyword textual entity
example of usage: From: Fu and Lin. Identification of gene-oriented exon orthology between human and mouse. BMC Genomics. 2012; 13(Suppl 1): S10. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303729/): Exon orthology; alternative splicing; exon duplication; intron-exon structure.
definition: A textual entity listing keywords indicating the major theme(s) of a document.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

keywords section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has_part
  some values from: keyword textual entity
editor preferred label: keywords section
example of usage: The section labelled 'keywords' in a typical scientific journal article.
definition: A part of a document where keywords selected by the author to categorize the major theme(s) of a document are listed.
definition editor: PERSON: Bill Baumgartner
alternative term: keywords
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

study limitations section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has_part
  some values from: study limitations textual entity
subclass of: Restriction
  on property: is about
  some values from: study design
editor preferred label: study limitations section
example of usage: The section labelled 'limitations' in a typical scientific journal article.
definition: A part of a document about biases or short comings related to the study design and execution.
definition editor: PERSON: Bill Baumgartner
alternative term: limitations
alternative term: study limitations
definition source: Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html)
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

study limitations textual entity
type: Class
subclass of: textual entity
editor preferred label: study limitations textual entity
example of usage: Excerpt from the Limitations section of Fermann et al 2015, Acad Emerg Med. 2015 Mar; 22(3): 299–307 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405051/). Owing to the nature of a post hoc study, any significant values must be interpreted with caution. In the current analysis, no multiple testing was conducted and p-values remain unadjusted. Moreover, a selection bias arising from the randomized open-label design of the original EINSTEIN PE study cannot be ruled out.
definition: A textual entity addressing a shortcoming or bias of a study design or execution.
definition editor: PERSON: Bill Baumgartner
definition source: Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html)
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

materials section
type: Class
subclass of: document part
editor preferred label: materials section
example of usage: The section labelled 'materials' in a typical scientific journal article, e.g. Nguyen et al. BMC Bioinformatics. 2010; 11: 279. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889936/)
definition: A part of a document about the materials required to reproduce the content of the document.
definition editor: PERSON: Bill Baumgartner
alternative term: materials
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

notes section
type: Class
subclass of: document part
editor preferred label: notes section
example of usage: The section labelled 'notes' in a typical scientific journal article, e.g. McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/):
definition: A part of a document containing typically short notes about the document itself and/or the authors. Often the notes section contains subsections related to funding, competing interests, ethical approval, etc.
definition editor: PERSON: Bill Baumgartner
alternative term: footnotes
alternative term: notes
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

patients section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has_part
  some values from: patients textual entity
editor preferred label: patients section
example of usage: The section labelled 'patients' in a typical scientific journal article, e.g. in Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/)
definition: A part of a document about the patients that participated in a study.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

patients textual entity
type: Class
subclass of: textual entity
editor preferred label: patients textual entity
example of usage: Excerpt from Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/): Between January 1996 and February 2012, we treated 4 patients with interprosthetic femoral fractures (3 of them women) (Figure 2) using a custom-made interposition device (Waldemar Link GmbH, Hamburg, Germany) (Figure 1). Mean age was 74 (59–86) years. The fractures occurred mean 18 (13–28) years after primary THA and mean 14 (10–17) years after primary TKA. At the latest follow-up, after mean 8 (0.5–16) years, revision surgery with a total femur replacement was required in 1 case due to aseptic loosening. No other complications requiring revision surgery occurred.
definition: A textual entity expressing information regarding the patients used in a study.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

pre-publication history section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has_part
  some values from: pre-publication history textual entity
editor preferred label: pre-publication history section
example of usage: The section labelled 'pre-publication history' in a typical scientific journal article, e.g. in Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/)
definition: A part of the document about the publication history of a document. This section typically details dates of document submission to a journal and dates of any re-submissions as well as reviewer comments and responses to reviewers by the authors.
definition editor: PERSON: Bill Baumgartner
alternative term: notice of republication
alternative term: pre-publication history
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

pre-publication history textual entity
type: Class
subclass of: textual entity
editor preferred label: pre-publication history textual entity
example of usage: From Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/): The pre-publication history for this paper can be accessed here: http://www.biomedcentral.com/1471-2253/13/33/prepub
definition: A textual entity that expresses the pre-publication history (submission dates, reviewer comments, etc) for a document, often including a hyperlink to a web page detailing the information.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

related work section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has_part
  some values from: related work textual entity
editor preferred label: related work section
example of usage: The section labelled 'related work' in a typical scientific journal article, e.g. Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/)
definition: A part of a document about work in other publications that is relevant to the content of the document.
definition editor: PERSON: Bill Baumgartner
alternative term: related literature
alternative term: related work
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

related work textual entity
type: Class
subclass of: textual entity
editor preferred label: related work textual entity
example of usage: Excerpt from Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/): Our work presented here is similar in spirit to our recently developed methodology for data fusion via collective matrix factorization (Žitnik and Zupan, 2015).
definition: A textual entity that discusses work from other publications and expresses their relevancy to the content of a document.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

requirements section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has_part
  some values from: requirements textual entity
editor preferred label: requirements section
example of usage: The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/).
definition: A part of a document about a resource described in the document, e.g. software, that describes the requirements necessary to use the resource, e.g. operating systems, hardware, etc. in the case of a software resource.
definition editor: PERSON: Bill Baumgartner
alternative term: requirements
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

requirements textual entity
type: Class
subclass of: textual entity
editor preferred label: requirements textual entity
example of usage: From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): • Operating systems: Platform independent • Programming language: Matlab, R, Python • Other requirements: None • License: GNU GPL v3 • Any restrictions to use by non-academics: None
definition: A textual entity that expresses the requirements necessary to use a resource, e.g. software.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

statistical analysis textual entity
type: Class
subclass of: textual entity
editor preferred label: statistical analysis textual entity
example of usage: From Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/): Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Stata version 10 for analysis. Continuous variables were summarised as mean (± standard deviation) and median (inter-quartile range), and presented in the tables. Categorical data were analysed using frequency and percentages, and results are presented in frequency tables and bar charts. Test of significance (p-value) was determined using the chi-square test. A p-value of less than 0.05 was considered significant.
definition: A textual entity documenting statistical analysis tools and techniques employed.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

statistical analysis section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has_part
  some values from: statistical analysis textual entity
editor preferred label: statistical analysis section
example of usage: The section labelled 'statistical analysis' in a typical scientific journal article, e.g. Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/)
definition: A part of the document used to describe the statistical methodologies employed in the work presented in the document.
definition editor: PERSON: Bill Baumgartner
alternative term: statistical analysis
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

tables section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has_part
  some values from: table
editor preferred label: tables section
example of usage: The section labelled 'tables' in a typical scientific journal article.
definition: A part of a document that contains one or more tables.
definition editor: PERSON: Bill Baumgartner
alternative term: tables
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

database extract, transform, and load process
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: information content entity
editor preferred label: database extract, transform, and load process
definition: A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second.
editor note: Alan Ruttenberg 12/21/16: Maybe this definition instead: A planned process which takes as input a database and copies concretizations from the first, optionally transforms then copies the result to the second
editor note: Alan Ruttenberg 12/21/16: We don't define database in IAO, currently, as the bare word is ambiguous. Reasonable interpretations of the word might be the material entity, an information structure, an information content entity. However this definition commits, at least, to there being some material thing which bear concretizations of information entities and that there are new concretizations created during the process. We consider the ETL process in terms of information entities rather than the concretizations. No committment is made as to whether the specified output.
definition editor: PERSON:Alan Ruttenberg
alternative term: ETL
definition source: WEB:https://en.wikipedia.org/wiki/Extract,_transform,_load
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/187

cellular organisms
type: Class
equivalent class: organism
subclass of: object
subclass of: Restriction
  on property: has phenotype
  some values from: phenotype
imported from: doid.owl
imported from: hp.owl
imported from: ncbitaxon.owl
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: biota

Bacteria
type: Class
subclass of: cellular organisms
imported from: doid.owl
imported from: ncbitaxon.owl
database_cross_reference: GC_ID:11
database_cross_reference: PMID:10425795
database_cross_reference: PMID:10425796
database_cross_reference: PMID:10425797
database_cross_reference: PMID:10490293
database_cross_reference: PMID:10843050
database_cross_reference: PMID:10939651
database_cross_reference: PMID:10939673
database_cross_reference: PMID:10939677
database_cross_reference: PMID:11211268
database_cross_reference: PMID:11321083
database_cross_reference: PMID:11321113
database_cross_reference: PMID:11411719
database_cross_reference: PMID:11540071
database_cross_reference: PMID:11542017
database_cross_reference: PMID:11542087
database_cross_reference: PMID:11760965
database_cross_reference: PMID:12054223
database_cross_reference: PMID:2112744
database_cross_reference: PMID:270744
database_cross_reference: PMID:8123559
database_cross_reference: PMID:8590690
database_cross_reference: PMID:9103655
database_cross_reference: PMID:9336922
has_exact_synonym: eubacteria
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Monera
has_related_synonym: Procaryotae
has_related_synonym: Prokaryota
has_related_synonym: Prokaryotae
has_related_synonym: bacteria
has_related_synonym: not Bacteria Haeckel 1894
has_related_synonym: prokaryote
has_related_synonym: prokaryotes
label: Bacteria <prokaryote>

Homo sapiens
type: Class
subclass of: cellular organisms
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has_exact_synonym: human
has_exact_synonym: man
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Home sapiens
has_related_synonym: Homo sampiens
has_related_synonym: Homo sapeins
has_related_synonym: Homo sapian
has_related_synonym: Homo sapians
has_related_synonym: Homo sapien
has_related_synonym: Homo sapience
has_related_synonym: Homo sapiense
has_related_synonym: Homo sapients
has_related_synonym: Homo sapines
has_related_synonym: Homo spaiens
has_related_synonym: Homo spiens
has_related_synonym: Humo sapiens

planned process
type: Class
subclass of: process
editor preferred label: planned process
definition: A processual entity that realizes a plan which is the concretization of a plan specification.

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

organization
type: Class
subclass of: material entity

study design execution
type: Class
subclass of: planned process
editor preferred label: study design execution
definition: a planned process that carries out a study design

age measurement datum
type: Class
subclass of: time measurement datum
subclass of: Restriction
  on property: is about
  some values from: age
editor preferred label: age measurement datum
definition: A time measurement datum that is the result of measurement of age of an organism
editor note: note that we are currently defining subtypes of age measurement datum that specify when the age is relative to, e.g. planting, as we don't have adequate temporal predicates yet. life of bearer doesn't imply organism this assay measures time not developmental stage. we recognize that development can take different time periods under different conditions such as media / temperature age as a quality is dubious; we plan to revisit stages in development are currently handled with controlled vocabulary, such as 2-somite stage
definition editor: PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng
definition source: MO_178 Age
curator note: In MageTab file, we use initialTimePoint (a process) + age (a number expected) + TimeUnit (definied in UO, such as year, hour, day, etc.) Now we use the term label indicating the start time point of measuring the age, (number + TimeUnit) are expected instances of the class
curator note: discussed on Nov 15, dev call All subtype will be defined by textual definition now.

scalar value specification
type: Class
subclass of: information content entity

value specification
type: Class
subclass of: information content entity

organism
type: Class
subclass of: material entity

study design
type: Class
subclass of: plan specification
editor preferred label: study design
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.

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

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

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

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

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

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

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

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

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

sign
type: Class
subclass of: entity
editor preferred label: sign
definition: A quality of a patient, a material entity that is part of a patient, or a processual entity that a patient participates in that is observed in a physical examination and is deemed by the clinician to be of clinical significance.
definition: A quality of a patient, a material entity that is part of a patient, or a processual entity that a patient participates in, any one of which is observed in a physical examination and is deemed by the clinician to be of clinical significance.
editor note: note: defined class
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2010-11-18T11:14:36Z
IAO_0000412: ogms.owl

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

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

vital sign
type: Class
subclass of: sign
editor preferred label: vital sign
definition: A physical sign in which a non-zero value is standardly considered to be an indication that the organism is alive.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:19:17Z
IAO_0000412: ogms.owl

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

disease
type: Class
subclass of: disposition
subclass of: Restriction
  on property: realized in
  some values from: disease course
subclass of: Restriction
  on property: BFO_0000113
  some values from: disorder
definition: A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:21:20Z

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

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

acquired genetic disease
type: Class
subclass of: disease
subclass of: Restriction
  on property: BFO_0000113
  some values from: genetic disorder
definition: A disease whose physical basis is an acquired genetic disorder.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:24:05Z

constitutional genetic disease
type: Class
subclass of: disease
subclass of: Restriction
  on property: BFO_0000113
  some values from: constitutional genetic disorder
definition: A disease whose physical basis is a constitutional genetic disorder.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:24:59Z

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

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

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

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

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.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:39:44Z

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

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

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

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

clinical history taking
type: Class
subclass of: health care process assay
definition: A health care process in which a clinician elicits a description of previous sign and symptoms of disease from a patient or from a third party who is reporting on behalf of the patient.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:49:16Z

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

pain
type: Class
subclass of: symptom
definition: A bodily process in an organism S involving two integrated levels: (a) activation of the nociceptive system and associated emotion generating brain components of S, and (b) a simultaneous aversive sensory and emotional experience on the part of S, where (b) is phenomenologically similar to the sort of aversive experience involved in pain with concordant tissue damage.
definition editor: Albert Goldfain
definition source: http://www.referent-tracking.com/RTU/sendfile/
curator note: creation date: 2009-11-24T04:51:11Z

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

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

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

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

treatment
type: Class
subclass of: planned process
definition: A planned process whose completion is hypothesized by a health care provider to eliminate a disorder or to alleviate the signs and symptoms of a disorder.
definition editor: Albert Goldfain
definition source: http://code.google.com/p/ogms/issues/detail
curator note: creation date: 2010-03-31T04:51:11Z

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

life course
type: Class
subclass of: process
definition: A process which has as parts all the processes in which a given organism is participant.
definition editor: Albert Goldfain Richard Scheuermann Sagar Jain
definition source: http://code.google.com/p/ogms/issues/detail
curator note: creation date: 2010-03-31T04:51:11Z EDIT: 10 NOV 2015

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

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

inflammatory process
type: Class
subclass of: bodily process
definition: A bodily process caused by some disorder that results in recruitment of leukocytes into a localized tissue site, typically causing localized pain and swelling.
definition editor: Albert Goldfain Richard Scheuermann Sagar Jain
definition source: http://code.google.com/p/ogms/wiki/Meeting_notes_20100513
curator note: creation date: 2010-07-19T11:57:44Z Updated: 10 NOV 2015

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

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

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

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

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

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

injury
type: Class
subclass of: disorder
definition: A disorder that involves some structural damage that is immediately caused by a catastrophic external force.
editor note: At the scale of organism (as opposed to the cellular scale or the population scale), an injury is typically the result of a catastrophic event. Consider the implications of making 'injury' a subtype of 'disorder'. Note: Adopted subtype of disorder, and injury can occur at the scale of organism down to cellular level.
definition editor: Albert Goldfain Sagar Jain
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/ca0ad373f27774c5 OGMS call adoption- 16 SEPT 2015 https://docs.google.com/document/d/1iiV1-fTS7BUUSzDw3N_Afx42698YWf54-FOTY2NkAxo/edit
curator note: creation date: 2011-09-20T09:57:44Z edited date: 30 SEPT 2015

disease prophylaxis
type: Class
subclass of: planned process
definition: A planned process whose completion is hypothesized by a health care provider to reduce the risk of developing a disorder or the signs and symptoms of a disorder.
editor note: Whether or not 'prophylaxis' and 'treatment' classes are disjoint is an open question.
definition editor: Albert Goldfain
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/e42bde79218ee34e
curator note: creation date: 2011-09-20T09:57:44Z

diagnostic process
type: Class
subclass of: health care process
definition: A health care process that involves the interpretation of a clinical picture from a given patient (input) and the assertion to the effect that the patient has a disease, disorder, or syndrome of a certain type, or none of these (output).
definition editor: Albert Goldfain
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/2a7008f311fac766/e7de486c94dfd82e
curator note: creation date: 2011-09-20T09:57:44Z

relapse
type: Class
subclass of: disease stage
definition: a disease stage which is preceded by a remission and characterized by the return of a manifestation of a disease.
editor note: A pathological bodily process which is part of a disease couse that occurs after an incomplete remission and that is similar to earlier parts of the disease course.
definition editor: Albert Goldfain Richard Scheuermann Sagar Jain
definition source: http://code.google.com/p/ogms/issues/detail
date: 10 NOV 2015

remission
type: Class
subclass of: disease stage
definition: a disease stage which is characterized by the lack of a manifestation of a disease.
editor note: A part of a disease course in which the extent or rate of change of the signs and symptoms of a disorder has decreased.
definition editor: Albert Goldfain Richard Scheuermann Sagar Jain
definition source: http://code.google.com/p/ogms/issues/detail
date: 10 NOV 2015

ancillary health care process
type: Class
subclass of: planned process
definition: A planned process that has the objective to support the objective of a health care process without directly involving the treatment, diagnosis, or prevention of disease or injury of a patient.
date: 2017-04-18
publisher: Sagar Jain

health care process assay
type: Class
subclass of: health care process
definition: A health care process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
date: creation: 16MAY2017
publisher: Sagar Jain

health care process biomaterial transformation
type: Class
subclass of: health care process
definition: A health care process which results in physical changes in a specified input material
date: creation: 16MAY2017
publisher: Sagar Jain

health care process data transformation
type: Class
subclass of: health care process
definition: A health care process that produces output from input data
date: creation: 16MAY2017
publisher: Sagar Jain

human health care role
type: Class
subclass of: role in human social processes
subclass of: Restriction
  on property: realized in
  some values from: health care encounter
definition: A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis.
definition editor: William R. Hogan
alternative term: health care role
imported from: The Ontology of Medically Related Social Entities
comment: Mathias Brochhausen

patient role
type: Class
subclass of: human health care role
subclass of: Restriction
  on property: inheres in
  some values from: organism
definition: A role borne by an organism and that is realized by presenting to a health care provider in a clinical encounter.
definition editor: Amanda Hicks
definition editor: Mathias Brochhausen
alternative term: patient
definition source: CAFE domain expert working group.
imported from: The Ontology of Medically Related Social Entities
comment: In order to avoid the presumption of the formal structures and institutions of Western civilization, bearing a patient role does not entail that the organism presents at an official place of business, with an organization formally and legally registered with various gov't entities, with a person endowed by the gov't with certain certifications.

role in human social processes
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: Class
    union of: organization
    union of: organism
definition: A role inhering in an entity realized by social interactions in human society.
definition editor: Mathias Brochhausen
imported from: The Ontology of Medically Related Social Entities
comment: Previous definition: A role played by an entity in human social processes.

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

intensity
type: Class
subclass of: qualitative
imported from: hp.owl

morphology
type: Class
subclass of: quality
subclass of: physical object quality
imported from: cl.owl
imported from: hp.owl

shape
type: Class
subclass of: morphology
imported from: cl.owl

occurrence
type: Class
subclass of: temporal distribution quality
imported from: hp.owl

qualitative
type: Class
subclass of: quality
imported from: hp.owl

deviation(from_normal)
type: Class
equivalent class: Class
  intersection of: qualitative
  intersection of: Restriction
    on property: has modifier
    some values from: abnormal
subclass of: qualitative
imported from: hp.owl

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

mass
type: Class
subclass of: quality
editor preferred label: mass
definition: A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
imported from: pato.owl

weight
type: Class
subclass of: force
imported from: hp.owl

structure
type: Class
subclass of: morphology

temperature
type: Class
subclass of: quality
definition: A physical quality of the thermal energy of a system.
IAO_0000412: PATO.owl

rate
type: Class
subclass of: physical quality of a process
definition: A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time.
imported from: hp.owl
IAO_0000412: PATO.owl

severe intensity
type: Class
subclass of: intensity
imported from: hp.owl

branched
type: Class
subclass of: branchiness

abnormal
type: Class
subclass of: deviation(from_normal)
imported from: hp.owl

decreased weight
type: Class
subclass of: weight
subclass of: decreased force
imported from: hp.owl

increased rate
type: Class
subclass of: rate
subclass of: increased process quality
imported from: hp.owl

physical quality
type: Class
subclass of: physical object quality
imported from: hp.owl

pressure
type: Class
subclass of: quality
definition: A physical quality that inheres in a bearer by virtue of the bearer's amount of force per unit area it exerts.
IAO_0000412: PATO.owl

force
type: Class
subclass of: physical quality
imported from: hp.owl

linear
type: Class
subclass of: shape

process quality
type: Class
subclass of: quality
imported from: hp.owl

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

physical object quality
type: Class
subclass of: quality
imported from: cl.owl
imported from: hp.owl

functionality
type: Class
subclass of: physical object quality
imported from: hp.owl

progressive
type: Class
subclass of: occurrence
imported from: hp.owl

cylindrical
type: Class
subclass of: convex 3-D shape
imported from: cl.owl

discoid
type: Class
subclass of: cylindrical
imported from: cl.owl

convex 3-D shape
type: Class
subclass of: 3-D shape
imported from: cl.owl

branchiness
type: Class
subclass of: shape

physical quality of a process
type: Class
subclass of: process quality
imported from: hp.owl

laminar
type: Class
subclass of: structure

decreased force
type: Class
subclass of: force
subclass of: decreased object quality
imported from: hp.owl

3-D shape
type: Class
subclass of: shape
imported from: cl.owl

increased quality
type: Class
subclass of: deviation(from_normal)
imported from: hp.owl

decreased quality
type: Class
subclass of: deviation(from_normal)
imported from: hp.owl

decreased object quality
type: Class
subclass of: physical object quality
subclass of: decreased quality
imported from: hp.owl

increased process quality
type: Class
subclass of: process quality
subclass of: increased quality
imported from: hp.owl

temporal distribution quality
type: Class
subclass of: physical quality of a process
imported from: hp.owl

amino acid chain component
type: Class
subclass of: fiat object part
definition: A fiat object part that is either a modified amino-acid residue or an unmodified amino-acid residue.
imported from: pr.owl
has_broad_synonym: amino-acid residue
has_obo_namespace: protein
id: PR:000036907
comment: Category=external. Note: This entity is distinct from CHEBI: "amino-acid residue" in that it includes residues that are technically not part of that class. [PRO:JSG]

system
type: Class
subclass of: material entity
definition: A material entity consisting of multiple components that are causally integrated.
editor note: May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43
definition editor: Chris Mungall
definition source: http://www.jbiomedsem.com/content/4/1/43

length unit
type: Class
subclass of: measurement unit label
editor preferred label: length unit
definition: A unit which is a standard measure of the distance between two points.
imported from: uo.owl

mass unit
type: Class
subclass of: measurement unit label
editor preferred label: mass unit
definition: A unit which is a standard measure of the amount of matter/energy of a physical object.
imported from: uo.owl

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

auscultatory blood pressure measurement process
type: Class
subclass of: noninvasive blood pressure measurement process

auscultatory pulse rate measurement process
type: Class
subclass of: pulse rate measurement process

axillary temperature
type: Class
subclass of: body temperature
definition: The temperature of the axillary fossa.

blood pressure
type: Class
subclass of: vital sign
editor preferred label: blood pressure
definition: The pressure exerted by circulating blood on the walls of blood vessels.
editor note: Unless otherwise specified, a clinical report of a blood pressure is systolic left ventricular pressure over diastolic left ventricular pressure.
definition editor: Albert Goldfain
definition source: http://en.wikipedia.org/wiki/Blood_pressure

blood pressure measurement datum
type: Class
subclass of: scalar measurement datum
subclass of: Restriction
  on property: is about
  some values from: blood pressure

blood pressure measurement process
type: Class
equivalent class: Restriction
  on property: has_specified_output
  some values from: blood pressure measurement datum
subclass of: planned process

body temperature
type: Class
subclass of: vital sign
definition: The temperature of a part of the human body
definition editor: Albert Goldfain

body temperature measurement datum
type: Class
equivalent class: Restriction
  on property: is about
  some values from: body temperature
subclass of: measurement datum

body temperature measurement process
type: Class
equivalent class: Restriction
  on property: has_specified_output
  some values from: body temperature measurement datum
subclass of: planned process

brachial pulse rate
type: Class
subclass of: pulse rate
definition: The pulse rate of the brachial artery.

cardiac cycle phase
type: Class
subclass of: biological_process
editor note: These phases belong in some OBO foundry ontology of cardiac physiology. Should include the subprocesses of systole and diastole as illustrated here http://en.wikipedia.org/wiki/Cardiac_cycle .

carotid pulse rate
type: Class
subclass of: pulse rate
definition: The pulse rate of the carotid artery.

core body temperature
type: Class
subclass of: body temperature

diastole
type: Class
subclass of: cardiac cycle phase
definition: The phase of the cardiac cycle in which the heart fills with blood.

diastolic blood pressure
type: Class
equivalent class: Class
  intersection of: blood pressure
  intersection of: Restriction
    on property: exists during
    some values from: diastole
subclass of: blood pressure
definition: The blood pressure during diastole.

diastolic central venous pressure
type: Class
subclass of: diastolic blood pressure
definition: The diastolic blood pressure in the thoracic vena cava.

diastolic left ventricular pressure
type: Class
subclass of: diastolic blood pressure
definition: The left ventricular pressure during diastole.

diastolic pulmonary artery pressure
type: Class
subclass of: diastolic blood pressure
definition: The pulmonary artery pressure during diastole.

diastolic right ventricular pressure
type: Class
subclass of: diastolic blood pressure
definition: The right ventricular pressure during diastole.

dorsalis pedis pulse rate
type: Class
subclass of: pulse rate
definition: The pulse rate of the dorsalis pedis artery.

facial pulse rate
type: Class
subclass of: pulse rate
definition: The pulse rate of the facial artery.

femoral pulse rate
type: Class
subclass of: pulse rate
definition: The pulse rate of the femoral artery.

invasive blood pressure measurement process
type: Class
subclass of: blood pressure measurement process

noninvasive blood pressure measurement process
type: Class
subclass of: blood pressure measurement process

oral temperature
type: Class
subclass of: body temperature
definition: The temperature of the oral cavity.

oscillometric blood pressure measurement process
type: Class
subclass of: noninvasive blood pressure measurement process

popliteal pulse rate
type: Class
subclass of: pulse rate
definition: The pulse rate of the popliteal artery.

pulse rate
type: Class
subclass of: vital sign
subclass of: rate
definition: The rate at which an artery pulses (i.e., participates in expansion-contraction cycles) as blood passes through it.
definition editor: Albert Goldfain

pulse rate measurement datum
type: Class
equivalent class: Restriction
  on property: is about
  some values from: pulse rate
subclass of: measurement datum

pulse rate measurement process
type: Class
equivalent class: Restriction
  on property: has_specified_output
  some values from: pulse rate measurement datum
subclass of: planned process

radial pulse rate
type: Class
subclass of: pulse rate
definition: The pulse rate of the radial artery.

rectal temperature
type: Class
subclass of: body temperature
definition: The temperature of the lumen of the rectum.

respiratory rate
type: Class
subclass of: vital sign
subclass of: rate
definition: The rate at which an organism breathes.

respiratory rate measurement datum
type: Class
equivalent class: Restriction
  on property: is about
  some values from: respiratory rate
subclass of: measurement datum

respiratory rate measurement process
type: Class
equivalent class: Restriction
  on property: has_specified_output
  some values from: respiratory rate measurement datum
subclass of: planned process

systole
type: Class
subclass of: cardiac cycle phase
definition: The phase of the cardiac cycle in which the heart contracts.

systolic blood pressure
type: Class
equivalent class: Class
  intersection of: blood pressure
  intersection of: Restriction
    on property: exists during
    some values from: systole
subclass of: blood pressure
definition: The blood pressure during systole.

systolic central venous pressure
type: Class
subclass of: systolic blood pressure
definition: The systolic blood pressure in the thoracic vena cava.

systolic left ventricular pressure
type: Class
subclass of: systolic blood pressure
definition: The left ventricular pressure during systole.

systolic pulmonary artery pressure
type: Class
subclass of: systolic blood pressure
definition: The pulmonary artery pressure during systole.

systolic right ventricular pressure
type: Class
subclass of: systolic blood pressure
definition: The right ventricular pressure during systole.

temporal pulse rate
type: Class
subclass of: pulse rate
definition: The pulse rate of the temporal artery.

tibialis posterior pulse rate
type: Class
subclass of: pulse rate
definition: The pulse rate of the tibialis posterior artery.

tympanic temperature
type: Class
subclass of: body temperature
definition: The temperature of the external acoustic tube.

ulnar pulse rate
type: Class
subclass of: pulse rate
definition: The pulse rate of the ulnar artery.

vaginal temperature
type: Class
subclass of: body temperature
definition: The temperature of the lumen of the vagina.

palpatory pulse rate measurement process
type: Class
subclass of: pulse rate measurement process

disease stage
type: Class
subclass of: disease course
editor note: This class should be imported from OBI. https://github.com/OGMS/ogms/issues/105

regulation of temperature
type: Class
subclass of: regulation of biological quality
definition: A homeostatic process in which an organism modulates its internal body temperature.
IAO_0000412: GO.owl

regulation of heart rate
type: Class
subclass of: regulation of biological quality
definition: Any process that modulates the frequency or rate of heart contraction.
IAO_0000412: GO.owl

blood circulation
type: Class
subclass of: process
definition: The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products.
IAO_0000412: GO.owl

regulation of blood pressure
type: Class
subclass of: regulation of biological quality
definition: Any process that modulates the force with which blood travels through the circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure.
IAO_0000412: GO.owl

regulation of biological quality
type: Class
subclass of: process
definition: Any process that modulates the frequency, rate or extent of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc.
IAO_0000412: GO.owl

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

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 source: BFO_0000134
annotated property: elucidation
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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/080-003

Axiom
annotated source: BFO_0000134
annotated property: elucidation
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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/081-003

cl.owl
license: http://creativecommons.org/licenses/by/4.0/
comment: See PMID:15693950, PMID:12799354, PMID:20123131, PMID:21208450; Contact Alexander Diehl, addiehl@buffalo.edu, University at Buffalo.

doid.owl
has_obo_format_version: 1.2
saved-by: lschriml
comment: The Disease Ontology content is available via the Creative Commons Public Domain Dedication CC0 1.0 Universal license (https://creativecommons.org/publicdomain/zero/1.0/).
date: 02:03:2018 14:00
default-namespace: disease_ontology

hp.owl
creator: Sebastian Koehler
comment: Please see license of HPO at http://www.human-phenotype-ontology.org
saved-by: Peter Robinson, Sebastian Koehler, Sandra Doelken, Chris Mungall, Melissa Haendel, Nicole Vasilevsky, Monarch Initiative, et al.
creator: The Human Phenotype Ontology Consortium
creator: The Monarch Initiative
logical-definition-view-relation: has_part
creator: Peter N Robinson
Contributor: Joie Davis
default-namespace: human_phenotype
Contributor: Nicole Vasilevsky
subject: Phenotypic abnormalities encountered in human disease
Rights Management: Peter Robinson, Sebastian Koehler, The Human Phenotype Ontology Consortium, and The Monarch Initiative
license: see http://www.human-phenotype-ontology.org
Contributor: Sandra Doelken
Contributor: Melissa Haendel
Contributor: Mark Engelstad
Contributor: Courtney Hum
Contributor: Chris Mungall

MONDO: Monarch Disease Ontology
source: rarediseases.info.nih.gov
source: ncbitaxon.owl
source: chebi.owl
comment: Includes Ontology(OntologyID(Anonymous-31)) [Axioms: 86367 Logical Axioms: 0]
license: http://creativecommons.org/licenses/by/4.0/
source: ncit.owl
source: hp.owl
description: A semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology.
source: mf.owl
source: go.owl
source: orphanet.owl
source: envo.owl
source: uberon.owl
source: mesh
comment: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/mondo/imports/equivalencies.owl>) VersionIRI(<null>))) [Axioms: 184582 Logical Axioms: 81364]
source: doid.owl
has_obo_format_version: 1.2

ncbitaxon.owl
comment: Autogenerated by OWLTools-NCBIConverter.

pr.owl
default-namespace: protein
license: http://creativecommons.org/licenses/by/4.0/
auto-generated-by: OBO-Edit 2.0
saved-by: ceci
comment: The PRotein Ontology is licensed under CC BY 4.0. Please see http://obofoundry.org/ontology/pr for details.
date: 15:02:2018 08:11
has_obo_format_version: 1.2
comment: Use reasoner in OBO Edit to see the correct hierarchy.

d-acts.owl
is allocated id range: IAO_0021000-IAO_0021999

pno.owl
is allocated id range: IAO_0020000-IAO_0020999

max inclusive: 80.0

max inclusive: 129.0