Amanda Hicks
Josh Hanna
Mathias Brochhausen
Matthew Diller
S. Clint Dowland
William R. Hogan
2019-08-03
Ontology for Representing CDM Semantics
2021-11-13
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.
Really of interest to developers only
BFO OWL specification label
BFO OWL specification label
Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
Person:Alan Ruttenberg
Really of interest to developers only
BFO CLIF specification label
BFO CLIF specification label
editor preferred term
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
editor preferred label
editor preferred term
editor preferred term
example of usage
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.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
example of usage
example of usage
in branch
An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.
GROUP:OBI
OBI_0000277
in branch
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
has curation status
definition
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
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.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition
definition
textual definition
editor note
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.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obofoundry.org/obo/obi>
editor note
editor note
term editor
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
20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition editor
definition editor
term editor
term editor
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
alternative term
alternative term
definition source
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
PERSON:Daniel Schober
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition source
definition source
has obsolescence reason
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.
PERSON:Alan Ruttenberg
PERSON:Melanie Courtot
has obsolescence reason
curator note
An administrative note of use for a curator but of no use for a user
PERSON:Alan Ruttenberg
curator note
curator note
curator notes
term tracker item
the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
An IRI or similar locator for a request or discussion of an ontology term.
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
The 'tracker item' can associate a tracker with a specific ontology term.
term tracker item
ontology term requester
The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
The 'term requester' can credit the person, organization or project who request the ontology term.
ontology term requester
is denotator type
Relates an class defined in an ontology, to the type of it's denotator
In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')
Alan Ruttenberg
is denotator type
imported from
For external terms/classes, the ontology from which the term was imported
PERSON:Alan Ruttenberg
PERSON:Melanie Courtot
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
imported from
expand expression to
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)"
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
Chris Mungall
expand expression to
expand assertion to
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)"
A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
Chris Mungall
expand assertion to
first order logic expression
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.
PERSON:Alan Ruttenberg
first order logic expression
antisymmetric property
part_of antisymmetric property xsd:true
Use boolean value xsd:true to indicate that the property is an antisymmetric property
Alan Ruttenberg
antisymmetric property
OBO foundry unique label
An alternative name for a class or property which is unique across the OBO Foundry.
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 .
PERSON:Alan Ruttenberg
PERSON:Bjoern Peters
PERSON:Chris Mungall
PERSON:Melanie Courtot
GROUP:OBO Foundry <http://obofoundry.org/>
OBO foundry unique label
has ID digit count
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"
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)
Person:Alan Ruttenberg
has ID digit count
has ID range allocated
Datatype: idrange:1
Annotations: 'has ID range allocated to': "Chris Mungall"
EquivalentTo: xsd:integer[> 2151 , <= 2300]
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
Person:Alan Ruttenberg
has ID range allocated to
has ID policy for
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"
Relating an ontology used to record id policy to the ontology namespace whose policy it manages
Person:Alan Ruttenberg
has ID policy for
has ID prefix
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"
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.
Person:Alan Ruttenberg
has ID prefix
elucidation
person:Alan Ruttenberg
Person:Barry Smith
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
elucidation
elucidation
has associated axiom(nl)
Person:Alan Ruttenberg
Person:Alan Ruttenberg
An axiom associated with a term expressed using natural language
has associated axiom(nl)
has associated axiom(nl)
has associated axiom(fol)
Person:Alan Ruttenberg
Person:Alan Ruttenberg
An axiom expressed in first order logic using CLIF syntax
has associated axiom(fol)
has associated axiom(fol)
is allocated id range
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"
PERSON:Alan Ruttenberg
Add as annotation triples in the granting ontology
is allocated id range
retired from use as of
relates a class of CRID to the date after which further instances should not be made, according to the central authority
In OWL 2 add AnnotationPropertyRange xsd:dateTimeStamp
Alan Ruttenberg
retired from use as of
has ontology root term
Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root.
Nicolas Matentzoglu
has ontology root term
may be identical to
A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged.
David Osumi-Sutherland
#40
VFB
Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance.
may be identical to
scheduled for obsoletion on or after
Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date.
Chris Mungall, Jie Zheng
https://github.com/geneontology/go-ontology/issues/15532
https://github.com/information-artifact-ontology/ontology-metadata/issues/32
GO ontology
scheduled for obsoletion on or after
has axiom id
Person:Alan Ruttenberg
Person:Alan Ruttenberg
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
has axiom label
instance unique identifier
An annotation to be applied to individuals only. Value is a GUID/UUID for use in a referent tracking system.
IUI
term replaced by
Use on obsolete terms, relating the term to another term that can be used as a substitute
Person:Alan Ruttenberg
Person:Alan Ruttenberg
Add as annotation triples in the granting ontology
term replaced by
has_MedDRA_id
The PUMS serial number assigned to a housing unit, which is only unique within each state, and which explicitly links the housing unit record with person records in PUMS data.
U.S. Census PUMS serial number
ISO 639-1 code
William R. Hogan
ISO 639-1 assigns two-character identifiers to individual human languages. This annotation property is for use in annotating OWL2 individuals in OMRSE that represent languages with their appropriate ISO 639-1 code that designates them in that standard system.
ISO 639-1 code
ISO 639-2/B code
William R. Hogan
ISO 639-2/B assigns three-character identifiers to individual human languages. This annotation property is for use in annotating OWL2 individuals in OMRSE that represent languages with their appropriate ISO 639-2/B ('B' is for "bibliographic applications") code that designates them in that standard system.
ISO 639-2/B code
ISO 639-2/T code
William R. Hogan
ISO 639-2/T assigns three-character identifiers to individual human languages. This annotation property is for use in annotating OWL2 individuals in OMRSE that represent languages with their appropriate ISO 639-2/T ('T' is for "terminology applications") code that designates them in that standard system.
ISO 639-2/T code
ISO 639-3 code
William R. Hogan
ISO 639-3 assigns three-character identifiers to individual human languages. This annotation property is for use in annotating OWL2 individuals in OMRSE that represent languages with their appropriate ISO 639-3 code that designates them in that standard system.
ISO 639-3 code
Mathias Brochhausen
OOSTT user-centered description
A verbatim excerpt—such as a definition, comment, or description—from the PCORnet Common Data Model.
PCORnet CDM comment
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.
temporal interpretation
https://oborel.github.io/obo-relations/temporal-semantics/
tooth SubClassOf 'never in taxon' value 'Aves'
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.
Chris Mungall
?X DisjointWith RO_0002162 some ?Y
never in taxon
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.
non-overlapping with
shares no parts with
Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y)
mutually spatially disjoint with
https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern
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.
taxonomic class assertion
present_in_taxon
defined by inverse
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.
logical macro assertion
https://github.com/oborel/obo-relations/wiki/ShortcutRelations
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.
annotation property cardinality
A logical macro assertion whose domain is an IRI for a class
The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL
logical macro assertion on a class
A logical macro assertion whose domain is an IRI for a property
logical macro assertion on a property
Used to annotate object properties to describe a logical meta-property or characteristic of the object property.
logical macro assertion on an object property
logical macro assertion on an annotation property
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.
dispositional interpretation
'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton'
A is has_no_connections_with B if there are no parts of A or B that have a connection with the other.
shares no connection with
Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y))
has no connections with
inherited annotation property
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)
curator guidance link
brain always_present_in_taxon 'Vertebrata'
forelimb always_present_in_taxon Euarchontoglires
S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S
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.
never lost in
always present in taxon
This properties were created originally for the annotation of developmental or life cycle stages, such as for example Carnegie Stage 20 in humans.
temporal logical macro assertion on a class
measurement property has unit
has start time value
has end time value
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.
start, days post fertilization
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.
end, days post fertilization
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.
start, years post birth
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
end, years post birth
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.
start, months post birth
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
end, months post birth
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.
month of gestation
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
has developmental stage marker
Count of number of days intervening between the start of the stage and the time of coitum.
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)
start, days post coitum
Count of number of days intervening between the end of the stage and the time of coitum.
end, days post coitum
start, weeks post birth
end, weeks post birth
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
is asymmetric relational form of process class
https://github.com/oborel/obo-relations/wiki/InteractionRelations
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
is symmetric relational form of process class
https://github.com/oborel/obo-relations/wiki/InteractionRelations
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
is relational form of process class
https://github.com/oborel/obo-relations/wiki/InteractionRelations
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
The general property hierarchy is:
"directly P" SubPropertyOf "P"
Transitive(P)
Where we have an annotation assertion
"directly P" "is direct form of" "P"
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'
Chris Mungall
is direct form of
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
Chris Mungall
is indirect form of
logical macro assertion on an axiom
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
is a defining property chain axiom
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.
is a defining property chain axiom where second argument is reflexive
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.
is relational form of a class
A shortcut relationship that holds between two entities based on their identity criteria
logical macro assertion involving identity
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.
in approximate one to one relationship with
x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y
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"
is approximately equivalent to
'anterior end of organism' is-opposite-of 'posterior end of organism'
'increase in temperature' is-opposite-of 'decrease in temperature'
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).
is opposite of
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).
is indistinguishable from
evidential logical macro assertion on an axiom
A relationship between a sentence and an instance of a piece of evidence in which the evidence supports the axiom
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.
axiom has evidence
A relationship between a sentence and an instance of a piece of evidence in which the evidence contradicts the axiom
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.
axiom contradicted by evidence
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.
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.
If it is necessary to make the context explicit, an axiom annotation can be added to the annotation assertion
is representative IRI for equivalence set
OWLAPI Reasoner documentation for representativeElement, which follows a similar idea, but selects an arbitrary member
Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be "+", "-" or "0"
cjm
2018-03-13T23:59:29Z
is directional form of
cjm
2018-03-14T00:03:16Z
is positive form of
cjm
2018-03-14T00:03:24Z
is negative form of
part-of is homeomorphic for independent continuants.
R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C.
cjm
2018-10-21T19:46:34Z
R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C.
is homeomorphic for
external_definition
axiom_lost_from_external_ontology
homology_notes
has_relational_adjective
taxon_notes
function_notes
structure_notes
development_notes
external_ontology_notes
fma_set_term
Unique Apollo Label
eco subset
contributor
subset_property
has_alternative_id
has_broad_synonym
database_cross_reference
has_exact_synonym
has_narrow_synonym
has_obo_format_version
has_obo_namespace
has_related_synonym
has_scope
has_synonym_type
in_subset
shorthand
is defined by
is defined by
This is an experimental annotation
label
see also
depicted by
is part of
my brain is part of my body (continuant parthood, two material entities)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)
a core relation that holds between a part and its whole
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.
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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
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
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'.
part_of
part of
http://www.obofoundry.org/ro/#OBO_REL:part_of
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
a core relation that holds between a whole and its part
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.
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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
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
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'.
has_part
has part
realized in
this disease is realized in this disease course
this fragility is realized in this shattering
this investigator role is realized in this investigation
is realized by
realized_in
http://purl.obolibrary.org/obo/ro.owl
[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])
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
realized in
realizes
this disease course realizes this disease
this investigation realizes this investigator role
this shattering realizes this fragility
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])
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
realizes
accidentally included in BFO 1.2 proposal
- should have been BFO_0000062
obsolete preceded by
true
preceded by
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.
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.
is preceded by
preceded_by
http://www.obofoundry.org/ro/#OBO_REL:preceded_by
preceded by
precedes
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.
precedes
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
occurs_in
unfolds in
unfolds_in
Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
occurs in
site of
[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
Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
contains process
exists-at
existsAt
BFO2 Reference: entity
BFO2 Reference: temporal region
b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002])
exists at
o-has-part
hasOccurrentPart
[copied from inverse property 'part of occurrent'] Mary’s 5th birthday occurrent_part_of Mary’s life
[copied from inverse property 'part of occurrent'] The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football.
[copied from inverse property 'part of occurrent'] the first set of the tennis match occurrent_part_of the tennis match.
b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])
[copied from inverse property 'part of occurrent'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
[copied from inverse property 'part of occurrent'] BFO2 Reference: occurrent
http://purl.obolibrary.org/obo/vo.owl
[copied from inverse property 'part of occurrent'] b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002])
(iff (hasOccurrentPart a b) (occurrentPartOf b a)) // axiom label in BFO2 CLIF: [007-001]
has occurrent part
o-has-ppart
hasProperOccurrentPart
[copied from inverse property 'proper part of occurrent'] b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001])
b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001
http://purl.obolibrary.org/obo/vo.owl
has proper occurrent part
has-t-part
[copied from inverse property 'temporal part of'] the 4th year of your life is a temporal part of your life\. The first quarter of a game of football is a temporal part of the whole game\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\ The 4th year of your life is a temporal part of your life
[copied from inverse property 'temporal part of'] the process boundary which separates the 3rd and 4th years of your life.
[copied from inverse property 'temporal part of'] your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating
[copied from inverse property 'temporal part of'] b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001])
[copied from inverse property 'temporal part of'] b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003])
http://purl.obolibrary.org/obo/vo.owl
has temporal part
o-part-of
occurrentPartOf
Mary’s 5th birthday occurrent_part_of Mary’s life
The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football.
the first set of the tennis match occurrent_part_of the tennis match.
[copied from inverse property 'has occurrent part'] b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])
BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
BFO2 Reference: occurrent
http://purl.obolibrary.org/obo/vo.owl
b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002])
occurrent_part_of is antisymmetric. (axiom label in BFO2 Reference: [123-001])
occurrent_part_of is reflexive (every occurrent entity is an occurrent_part_of itself). (axiom label in BFO2 Reference: [113-002])
occurrent_part_of is transitive. (axiom label in BFO2 Reference: [112-001])
occurrent_part_of satisfies unique product. (axiom label in BFO2 Reference: [125-001])
occurrent_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [124-001])
(forall (x y t) (if (and (occurrentPartOf x y t) (not (= x y))) (exists (z) (and (occurrentPartOf z y t) (not (exists (w) (and (occurrentPartOf w x t) (occurrentPartOf w z t)))))))) // axiom label in BFO2 CLIF: [124-001]
(forall (x y t) (if (and (occurrentPartOf x y t) (occurrentPartOf y x t)) (= x y))) // axiom label in BFO2 CLIF: [123-001]
(forall (x y t) (if (exists (v) (and (occurrentPartOf v x t) (occurrentPartOf v y t))) (exists (z) (forall (u w) (iff (iff (occurrentPartOf w u t) (and (occurrentPartOf w x t) (occurrentPartOf w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [125-001]
(forall (x y z) (if (and (occurrentPartOf x y) (occurrentPartOf y z)) (occurrentPartOf x z))) // axiom label in BFO2 CLIF: [112-001]
(forall (x) (if (Occurrent x) (occurrentPartOf x x))) // axiom label in BFO2 CLIF: [113-002]
part of occurrent
o-ppart-of
properOccurrentPartOf
[copied from inverse property 'has proper occurrent part'] b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001
b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001])
(iff (properOccurrentPartOf a b) (and (occurrentPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [005-001]
proper part of occurrent
t-part-of
temporalPartOf
the 4th year of your life is a temporal part of your life\. The first quarter of a game of football is a temporal part of the whole game\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\ The 4th year of your life is a temporal part of your life
the process boundary which separates the 3rd and 4th years of your life.
your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating
b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001])
b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003])
http://purl.obolibrary.org/obo/vo.owl
if b proper_temporal_part_of c, then there is some d which is a proper_temporal_part_of c and which shares no parts with b. (axiom label in BFO2 Reference: [117-002])
(forall (x y) (if (properTemporalPartOf x y) (exists (z) (and (properTemporalPartOf z y) (not (exists (w) (and (temporalPartOf w x) (temporalPartOf w z)))))))) // axiom label in BFO2 CLIF: [117-002]
(iff (properTemporalPartOf a b) (and (temporalPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [116-001]
(iff (temporalPartOf a b) (and (occurrentPartOf a b) (exists (t) (and (TemporalRegion t) (occupiesSpatioTemporalRegion a t))) (forall (c t_1) (if (and (Occurrent c) (occupiesSpatioTemporalRegion c t_1) (occurrentPartOf t_1 r)) (iff (occurrentPartOf c a) (occurrentPartOf c b)))))) // axiom label in BFO2 CLIF: [078-003]
temporal part of
spans
occupiesTemporalRegion
p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001])
occupies temporal region
span-of
spanOf
[copied from inverse property 'occupies temporal region'] p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001])
has temporal occupant
during-which-exists
[copied from inverse property 'exists at'] BFO2 Reference: entity
[copied from inverse property 'exists at'] BFO2 Reference: temporal region
[copied from inverse property 'exists at'] b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002])
during which exists
http://purl.obolibrary.org/obo/bfo/2020/bfo.owl
144-BFO
history of
(Elucidation) b history of c if c is a material entity and b is a history that is the unique history of c
This life is the history of this organism.
history of
http://purl.obolibrary.org/obo/bfo/2020/bfo.owl
145-BFO
has history
b has history c =Def c history of b
This organism has history this life.
has history
has measurement unit label
The process of creation is, for example, writing down on paper the name of a friend by deliberately creating a certain pattern using ink.
Here the ink + paper is the independent continuant and the carrier is the pattern in the ink.
c = pattern in the ink
b = paper + ink
r = friend
c specifically denotes r =def
r is a portion of reality
& c is a particular quality
& c depends specifically on some independent continuant b
& b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly.
Marked means there is a changed or additional quality of the bearer - the quality is the information carrier.
Case 1
Memory trace as mark created when reading some description of some friend. The trace can denote.
Case 2
Pattern of ink arrayed on paper as mark when writing down a friend's name
Case 3
Pattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file.
8/6/2009 Alan Ruttenberg: The suggestions is to deprecate specific and generically denotes in favor of a single denote relationship that corresponds to the generic sense
see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote
Alan Ruttenberg
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
obsolete_specifically denotes
true
This document is about information artifacts and their representations
A (currently) primitive relation that relates an information artifact to an entity.
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.
person:Alan Ruttenberg
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
is about
An information artifact IA mentions an entity E exactly when it has a component/part that denotes E
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)
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
PERSON: Jonathan Rees
Person: Alan Ruttenberg
mentions
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.
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
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
person:Alan Ruttenberg
Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
denotes
see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote
obsolete_materially denotes
true
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
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
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.
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.
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.
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.
Alan Ruttenberg
is quality measurement of
obsolete_describes
true
obsolete_represents
true
inverse of the relation 'denotes'
Person: Jie Zheng, Chris Stoeckert, Mike Conlon
denoted by
relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point
has coordinate unit label
relates a process to a time-measurement-datum that represents the duration of the process
Person:Alan Ruttenberg
is duration of
inverse of the relation of is quality measurement of
2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship
Person:Alan Ruttenberg
is quality measured as
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.
Person:Alan Ruttenberg
Person:Bjoern Peters
is quality specification of
inverse of the relation of is quality specification of
2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship
Person:Alan Ruttenberg
Person:Bjoern Peters
quality is specified as
relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken
Alan Ruttenberg
has time stamp
relates a time stamped measurement datum to the measurement datum that was measured
Alan Ruttenberg
has measurement datum
x designates y, if for any given group of language users, x is an information content entity, is about y, and represents y in a linguistic context..
Mathias Brochhausen
obsolete_designates
true
x is_borrowed_reference_for y, if x is a proper name that is used to refer to one individual among a specific group after the dubbing process took place.
Mathias Brochhausen
is_borrowed_reference_to
x is_fixed_reference_for y, if x is an utterance or graphemes concretized as writing quality inhering in some independent continuant that is used to single out one individual and refer to the latter among a specific group after the.
Mathias Brochhausen
is_fixing_reference_to
p1 is designated by p2, if p2 is an information content entity that represents p1 in a linguistic context.
Mathias Brochhausen
is designated by
d socio-legally revokes s if s participates in d and at the end of d s no longer exists.
It is important to note that this going out of existence of s is complete and unlike the going out of existence for material entities which basically always are transformed into something else. After the declaration nothing is left of the socio-legal generically dependent continuant in question.
Mathias Brochhausen
legally revokes
d socio-legally transfers l if l participates in d and d has specified input (concretization of l)1 and specified output (concretization of l)2, where (concretization of l)1 and (concretization of l)2 are not identical.
Mathias Brochhausen
obsolete_legally transfers
true
has_specified_input
has_specified_input
see is_input_of example_of_usage
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.
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.
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
PERSON: Larry Hunter
PERSON: Melanie Coutot
has_specified_input
is_specified_input_of
some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
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.
Alan Ruttenberg
PERSON:Bjoern Peters
is_specified_input_of
has_specified_output
has_specified_output
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.
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
PERSON: Larry Hunter
PERSON: Melanie Courtot
has_specified_output
is_specified_output_of
is_specified_output_of
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.
Alan Ruttenberg
PERSON:Bjoern Peters
is_specified_output_of
is_specified_output_of
is member of organization
Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization.
2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a population
JZ: Discussed on May 7, 2012 OBI dev call. Bjoern points out that we need to allow for organizations to be members of organizations. And agreed by the other OBI developers. So, human and organization were specified in 'Domains'. The textual definition was updated based on it.
Person:Alan Ruttenberg
Person:Helen Parkinson
Person:Alan Ruttenberg
Person:Helen Parkinson
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
is member of organization
has organization member
Relating an organization to a legal person or organization.
See tracker:
https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_id=177891&atid=886178
Person: Jie Zheng
has organization member
Mathias Brochhausen
This is a primitive relation. This relation is the foundation to the owners right to have the owned entity at his/her full disposal.
owns
a administrates b if c owns b and some rights and obligations grounded in the owning relation regarding b are transferred from c to a.
Mathias Brochhausen
Mathias Brochhausen
A definition of "tranfers" object property can be found in d-acts: http:purl.obolibrary.org/iao/d-acts.owl
administrates
a is owned by b if b has complete power over a. All rights and obligations of ownership are grounded in this (primitive) relation. The claims and obligations of ownership can be partially transferred to a third party by the owner, b.
Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204.
is owned by
BFO relation takes precedence.
We anticipate BFO 2.0 including and defining this relation. When it does, we will obsolete this property and declare it equivalent to the BFO 2.0 relation.
is-aggregate-of
obsolete is-aggregate-of
true
true
At the instance level, this relation is the named inverse of is-aggregate-of.
At the type level, however, not so.
We expect BFO 2.0 to have this relation as well, and we will obsolete this property and declare it equivalent to BFO's version when BFO 2.0 comes out.
obsolete is-component-of-aggregate
true
is administered by
is enrolled in school
is admitted to hospital
provides service
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
Inverse of characteristic_of
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
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.
bearer_of
is bearer of
bearer of
bearer_of
has characteristic
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
participates in
has participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
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.
has_participant
http://www.obofoundry.org/ro/#OBO_REL:has_participant
has participant
has_participant
is concretized as
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).
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).
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.
http://purl.obolibrary.org/obo/obi.owl
is concretized as
concretizes
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).
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).
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.
http://purl.obolibrary.org/obo/obi.owl
concretizes
this catalysis function is a function of this enzyme
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
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.
function_of
is function of
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
function of
this red color is a quality of this apple
a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
A quality inheres in its bearer at all times for which the quality exists.
is quality of
quality_of
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
quality of
this investigator role is a role of this person
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
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.
is role of
role_of
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
role of
this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
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.
has_function
has function
this apple has quality this red color
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
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.
has_quality
has quality
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
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.
has_role
has role
a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
has disposition
inverse of has disposition
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
disposition of
this cell derives from this parent cell (cell division)
this nucleus derives from this parent nucleus (nuclear division)
a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
derives_from
This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations.
derives from
this parent cell derives into this cell (cell division)
this parent nucleus derives into this nucleus (nuclear division)
a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.
derives_into
derives into
is location of
my head is the location of my brain
this cage is the location of this rat
a relation between two independent continuants, the location and the target, in which the target is entirely within the location
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
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
location_of
location of
contained in
Containment is location not involving parthood, and arises only where some immaterial continuant is involved.
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):
Intended meaning:
domain: material entity
range: spatial region or site (immaterial continuant)
contained_in
contained in
contains
contains
penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)
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 allergic trigger for
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.
is autoimmune trigger for
penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)
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 allergic trigger
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.
has autoimmune trigger
located in
my brain is located in my head
this rat is located in this cage
a relation between two independent continuants, the target and the location, in which the target is entirely within the location
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
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
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
located_in
http://www.obofoundry.org/ro/#OBO_REL:located_in
located in
This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.
This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.
the surface of my skin is a 2D boundary of my body
a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity
A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
2D_boundary_of
boundary of
is 2D boundary of
is boundary of
2D boundary of
my body has 2D boundary the surface of my skin
a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity
A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
David Osumi-Sutherland
has boundary
has_2D_boundary
has 2D boundary
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
David Osumi-Sutherland
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.
bounding layer of
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.
Note from NCEAS meeting: consider changing primary label
David Osumi-Sutherland
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.
coincident with
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).
David Osumi-Sutherland
regulates in other organism
A relationship that holds between a process that regulates a transport process and the entity transported by that process.
David Osumi-Sutherland
regulates transport of
A part of relation that applies only between occurents.
occurent part of
A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.
dos
2017-05-24T09:30:46Z
has regulatory component activity
A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.
dos
2017-05-24T09:31:01Z
By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.
has negative regulatory component activity
A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.
dos
2017-05-24T09:31:17Z
By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.
has positive regulatory component activity
dos
2017-05-24T09:36:08Z
A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity.
has necessary component activity
dos
2017-05-24T09:44:33Z
A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.
has component activity
w 'has process component' p if p and w are processes, 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.
dos
2017-05-24T09:49:21Z
has component process
A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function.
dos
2017-07-19T17:30:36Z
has ligand
A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization.
dos
2017-07-20T17:19:37Z
occurs across
dos
2017-09-17T13:52:24Z
Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
directly regulated by
Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
GOC:dos
Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
dos
2017-09-17T13:52:38Z
directly negatively regulated by
Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
GOC:dos
Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
dos
2017-09-17T13:52:47Z
directly positively regulated by
Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
GOC:dos
A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
dos
2017-09-22T14:14:36Z
This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.
has effector activity
A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
GOC:dos
A relationship that holds between two images, A and B, where:
A depicts X;
B depicts Y;
X and Y are both of type T'
C is a 2 layer image consiting of layers A and B;
A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.
Note: A and B may be 2D or 3D.
Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.
2017-12-07T12:58:06Z
in register with
dos
A relationship that holds between two images, A and B, where:
A depicts X;
B depicts Y;
X and Y are both of type T'
C is a 2 layer image consiting of layers A and B;
A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.
Note: A and B may be 2D or 3D.
Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.
GOC:dos
David Osumi-Sutherland
<=
Primitive instance level timing relation between events
before or simultaneous with
David Osumi-Sutherland
t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)
simultaneous with
David Osumi-Sutherland
t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)
before
David Osumi-Sutherland
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.
during which ends
David Osumi-Sutherland
di
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.
encompasses
David Osumi-Sutherland
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
ends after
David Osumi-Sutherland
starts_at_end_of
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately preceded by
David Osumi-Sutherland
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.
during which starts
David Osumi-Sutherland
starts before
David Osumi-Sutherland
ends_at_start_of
meets
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
immediately precedes
David Osumi-Sutherland
io
X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))
starts during
David Osumi-Sutherland
d
during
X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))
happens during
David Osumi-Sutherland
o
overlaps
X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y).
ends during
x overlaps y if and only if there exists some z such that x has part z and z part of y
http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
overlaps
true
X continuous_with Y if and only if X and Y share a fiat boundary.
David Osumi-Sutherland
connected to
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)
continuous with
FMA:85972
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
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
proper overlaps
(forall (?x ?y)
(iff
(proper_overlaps ?x ?y)
(and
(overlaps ?x ?y)
(not (part_of ?x ?y))
(not (part_of ?y ?x)))))
partially overlaps
A is spatially_disjoint_from B if and only if they have no parts in common
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.
Chris Mungall
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
BFO_0000051 exactly 0 (BFO_0000050 some ?Y)
spatially disjoint from
https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern
a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
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
connected to
https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern
https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern
The M8 connects Glasgow and Edinburgh
a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
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.
connects
https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern
https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern
Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy.
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
supplies
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.
The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
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.
has component
inverse of has phenotype
Chris Mungall
phenotype of
every HOTAIR lncRNA is the gene product of some HOXC gene
every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene
x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y
Chris Mungall
has gene product
process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2.
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
Chris Mungall
David Hill
Tanya Berardini
GO
Regulation precludes parthood; the regulatory process may not be within the regulated process.
regulates (processual)
false
regulates
Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
Chris Mungall
negatively regulates (process to process)
negatively regulates
Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
Chris Mungall
positively regulates (process to process)
positively regulates
'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair'))
heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation')
x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation.
Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from)
TODO: add homeomorphy axiom
This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants.
Chris Mungall
has prototype
mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
osteoclast SubClassOf 'capable of' some 'bone resorption'
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.
Chris Mungall
has function realized in
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)".
RO_0000053 some (RO_0000054 only ?Y)
capable of
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.
Chris Mungall
has function in
RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))
capable of part of
true
OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role
x actively participates in y if and only if x participates in y and x realizes some active role
Chris Mungall
agent in
Obsoleted as the inverse property was obsoleted.
actively participates in
obsolete actively participates in
true
'heart development' has active participant some Shh protein
x has participant y if and only if x realizes some active role that inheres in y
This may be obsoleted and replaced by the original 'has agent' relation
Chris Mungall
has agent
http://purl.obolibrary.org/obo/ro.owl
has active participant
obsolete has active participant
true
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
Chris Mungall
surrounded by
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.
The epidermis layer of a vertebrate is adjacent to the dermis.
The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies.
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.
x adjacent to y if and only if x and y share a boundary.
This relation acts as a join point with BSPO
Chris Mungall
adjacent to
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.
inverse of surrounded by
Chris Mungall
surrounds
Chris Mungall
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.
https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1
https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporally related to
inverse of starts with
Chris Mungall
Allen
starts
Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
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.
Chris Mungall
started by
starts with
inverse of ends with
Chris Mungall
ends
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.
Chris Mungall
finished by
ends with
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
Chris Mungall
starts with process that occurs in
has start location
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
Chris Mungall
ends with process that occurs in
has end location
p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
Chris Mungall
consumes
has input
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.
Chris Mungall
produces
has output
A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event.
ExO:0000001
has exposure receptor
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.
ExO:0000000
has exposure stressor
A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor
ExO:0000055
has exposure route
A broad relationship between an exposure event or process and the course takes from the source to the target.
http://purl.obolibrary.org/obo/ExO_0000004
has exposure transport path
Any relationship between an exposure event or process and any other entity.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes.
related via exposure to
Any portion of roundup 'has active ingredient' some glyphosate
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 active substance
has active pharmaceutical ingredient
has active ingredient
inverse of has active ingredient
active ingredient in'
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.
connecting branch of
inverse of connecting branch of
has connecting branch
A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.
c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.
acts upstream of
A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.
c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.
affects
acts upstream of or within
Inverse of 'is substance that treats'
cjm
is treated by substance
cjm
cjm
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, positive effect
cjm
cjm
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
causally upstream of, negative effect
A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event.
Austin Meier
Chris Mungall
Marie Angelique Laporte
cjm
2017-06-05T17:35:04Z
has exposure stimulus
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.
Because part_of is transitive, inheres in is a sub-relation of inheres in part of
Chris Mungall
inheres in part of
true
A mereological relationship or a topological relationship
Chris Mungall
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
mereotopologically related to
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)
a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO].
Chris Mungall
http://www.geneontology.org/GO.annotation.conventions.shtml#colocalizes_with
In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]
Gene Ontology Consortium
colocalizes with
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.
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.
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
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.
Chris Mungall
http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to
In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology.
contributes to
a particular instances of akt-2 enables some instance of protein kinase activity
Chris Mungall
catalyzes
executes
has
is catalyzing
is executing
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.
This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time.
enables
A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
Chris Mungall
This is a grouping relation that collects relations used for the purpose of connecting structure and function
functionally related to
this relation holds between c and p when c is part of some c', and c' is capable of p.
Chris Mungall
false
part of structure that is capable of
true
c involved_in p if and only if c enables some process p', and p' is part of p
Chris Mungall
actively involved in
enables part of
involved in
every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid
p regulates levels of c if p regulates some amount (PATO:0000070) of c
Chris Mungall
regulates levels of (process to entity)
regulates levels of
inverse of enables
Chris Mungall
enabled by
inverse of regulates
Chris Mungall
regulated by (processual)
regulated by
inverse of negatively regulates
Chris Mungall
negatively regulated by
inverse of positively regulates
Chris Mungall
positively regulated by
A relationship that holds via some process of localization
Chris Mungall
Do not use this relation directly. It is a grouping relation.
related via localization to
This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination.
Chris Mungall
has target start location
This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l.
Chris Mungall
has target end location
Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l
Chris Mungall
results in transport along
Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m.
Chris Mungall
results in transport across
'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)
Chris Mungall
results in transport to from or in
An organism that is a member of a population of organisms
is member of is a mereological relation between a item and a collection.
is member of
member part of
SIO
member of
has member is a mereological relation between a collection and an item.
SIO
has member
inverse of has input
Chris Mungall
input of
inverse of has output
Chris Mungall
output of
Chris Mungall
formed as result of
Chris Mungall
http://neurolex.org/wiki/Property:DendriteLocation
has dendrite location
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.
Chris Mungall
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships
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)
in branching relationship with
https://github.com/obophenotype/uberon/issues/170
Deschutes River tributary_of Columbia River
inferior epigastric vein tributary_of external iliac vein
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.
Chris Mungall
drains into
drains to
tributary channel of
http://en.wikipedia.org/wiki/Tributary
http://www.medindia.net/glossary/venous_tributary.htm
This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)
tributary of
http://en.wikipedia.org/wiki/Tributary
Deschutes River distributary_of Little Lava Lake
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
Chris Mungall
branch of
distributary channel of
http://en.wikipedia.org/wiki/Distributary
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
distributary of
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.
Chris Mungall
anastomoses with
anabranch of
A lump of clay and a statue
x spatially_coextensive_with y if and inly if x and y have the same location
Chris Mungall
This relation is added for formal completeness. It is unlikely to be used in many practical scenarios
spatially coextensive with
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
Chris Mungall
branching part of
FMA:85994
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.
Chris Mungall
main stem of
x proper_distributary_of y iff x distributary_of y and x does not flow back into y
Chris Mungall
proper distributary of
x proper_tributary_of y iff x tributary_of y and x does not originate from y
Chris Mungall
proper tributary of
'protein catabolic process' SubClassOf has_direct_input some protein
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.
Chris Mungall
directly consumes
This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'
has direct input
Chris Mungall
Likely to be obsoleted. See:
https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit
obsolete has indirect input
true
translation SubClassOf has_direct_output some protein
p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c.
Chris Mungall
directly produces
obsolete has direct output
true
Chris Mungall
Likely to be obsoleted. See:
https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit
obsolete has indirect output
true
inverse of upstream of
Chris Mungall
causally downstream of
Chris Mungall
immediately causally downstream of
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
Chris Mungall
directly positively regulates
directly activates (process to process)
directly activates
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
Chris Mungall
indirectly positively regulates
indirectly activates
Chris Mungall
directly negatively regulates
directly inhibits (process to process)
directly inhibits
Chris Mungall
indirectly negatively regulates
indirectly inhibits
This relation groups causal relations between material entities and causal relations between processes
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 yield a cross-product of different relation types.
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causally related to
p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain
Chris Mungall
causally upstream of
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.
Chris Mungall
immediately causally upstream of
p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c
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
Chris Mungall
directly provides input for (process to process)
directly provides input for
transitive form of directly_provides_input_for
Chris Mungall
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')
transitively provides input for (process to process)
transitively provides input for
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.
We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
Chris Mungall
influences (processual)
affects
causally upstream of or within
false
Chris Mungall
This is an exploratory relation
differs in
https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions
Chris Mungall
differs in attribute of
Chris Mungall
differs in attribute
inverse of causally upstream of or within
Chris Mungall
causally downstream of or within
c involved in regulation of p if c is involved in some p' and p' regulates some p
Chris Mungall
involved in regulation of
c involved in regulation of p if c is involved in some p' and p' positively regulates some p
Chris Mungall
involved in positive regulation of
c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
Chris Mungall
involved in negative regulation of
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
OWL does not allow defining object properties via a Union
Chris Mungall
involved in or reguates
involved in or involved in regulation of
A protein that enables activity in a cytosol.
c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
Chris Mungall
executes activity in
enables activity in
is active in
true
c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
GOC:cjm
GOC:dos
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.
Chris Mungall
contributes to morphology of
A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
Considering relabeling as 'pairwise interacts with'
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.
Chris Mungall
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.
in pairwise interaction with
interacts with
http://purl.obolibrary.org/obo/MI_0914
https://github.com/oborel/obo-relations/wiki/InteractionRelations
An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.
Chris Mungall
binds
molecularly binds with
molecularly interacts with
http://purl.obolibrary.org/obo/MI_0915
An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts.
Chris Mungall
interacts with on organism level
biotically interacts with
http://eol.org/schema/terms/interactsWith
Porifiera attaches to substrate
A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored.
Chris Mungall
semibiotically interacts with
participates in a abiotic-biotic interaction with
Axiomatization to GO to be added later
Chris Mungall
An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.
phosphorylates
Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.
The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.
A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.
Chris Mungall
Vasundra Touré
molecularly controls
activity directly regulates activity of
directly regulates activity of
Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B.
For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
Chris Mungall
Vasundra Touré
directly inhibits
inhibits
molecularly decreases activity of
activity directly negatively regulates activity of
directly negatively regulates activity of
Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B.
For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
Chris Mungall
Vasundra Touré
activates
directly activates
molecularly increases activity of
activity directly positively regulates activity of
directly positively regulates activity of
Chris Mungall
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
partner in
Chris Mungall
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.
subject participant in
Chris Mungall
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.
target participant in
Chris Mungall
This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.
helper property (not for use in curation)
Chris Mungall
is symbiosis
Chris Mungall
is commensalism
Chris Mungall
is mutualism
Chris Mungall
is parasitism
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.
Chris Mungall
is evidence for
'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'
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.
Chris Mungall
composed primarily of
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.
Chris Mungall
has part that occurs in
true
Chris Mungall
is kinase activity
Chris Mungall
is ubiquitination
See notes for inverse relation
Chris Mungall
receives input from
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.
Chris Mungall
sends output to
A relationship between a material entity and a process where the material entity has some causal role that influences the process
causal agent in process
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.
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causal relation between processes
Chris Mungall
depends on
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
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.
Chris Mungall
towards
'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate
p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c
Chris Mungall
has intermediate product
has intermediate
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
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causal relation between entities
causal relation between material entities
A coral reef environment is determined by a particular coral reef
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.
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
Chris Mungall
determined by (system to material entity)
Chris Mungall
Pier Buttigieg
determined by
inverse of determined by
Chris Mungall
determines (material entity to system)
determines
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.
Chris Mungall
determined by part of
x is transcribed from y if and only if x is synthesized from template y
Chris Mungall
http://www.ncbi.nlm.nih.gov/pubmed/20226267
transcribed from
A relation that holds between two entities that have the property of being sequences or having sequences.
Chris Mungall
http://www.ncbi.nlm.nih.gov/pubmed/20226267
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect.
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.
sequentially related to
Every UTR is adjacent to a CDS of the same transcript
Two consecutive DNA residues are sequentially adjacent
Two exons on a processed transcript that were previously connected by an intron are adjacent
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
Chris Mungall
http://www.ncbi.nlm.nih.gov/pubmed/20226267
sequentially adjacent to
Every CDS has as a start sequence the start codon for that transcript
x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence
Chris Mungall
started by
http://www.ncbi.nlm.nih.gov/pubmed/20226267
has start sequence
inverse of has start sequence
Chris Mungall
starts
http://www.ncbi.nlm.nih.gov/pubmed/20226267
is start sequence of
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)
x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence
Chris Mungall
ended by
http://www.ncbi.nlm.nih.gov/pubmed/20226267
has end sequence
inverse of has end sequence
Chris Mungall
ends
http://www.ncbi.nlm.nih.gov/pubmed/20226267
is end sequence of
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.
In the SO paper, this was defined as an instance-type relation
Chris Mungall
http://www.ncbi.nlm.nih.gov/pubmed/20226267
is consecutive sequence of
Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence.
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
Chris Mungall
is sequentially aligned with
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)
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
Chris Mungall
bounds sequence of
inverse of bounds sequence of
Chris Mungall
is bound by sequence of
x has subsequence y iff all of the sequence parts of x are sequence parts of y
Chris Mungall
contains
http://www.ncbi.nlm.nih.gov/pubmed/20226267
has subsequence
inverse of has subsequence
Chris Mungall
contained by
is subsequence of
x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y.
Chris Mungall
overlaps sequence of
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.
Chris Mungall
disconnected from
does not overlap sequence of
inverse of downstream of sequence of
Chris Mungall
is upstream of sequence of
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.
Chris Mungall
is downstream of sequence of
A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript
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
Chris Mungall
is immediately downstream of sequence of
A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript
inverse of immediately downstream of
Chris Mungall
is immediately upstream of sequence of
inverse of is evidence for
Chris Mungall
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.
has evidence
Chris Mungall
causally influenced by (entity-centric)
causally influenced by (material entity to material entity)
causally influenced by
Chris Mungall
interaction relation helper property
https://github.com/oborel/obo-relations/wiki/InteractionRelations
Chris Mungall
molecular interaction relation helper property
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
The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).
Chris Mungall
Vasundra Touré
causally influences (entity-centric)
causally influences (material entity to material entity)
causally influences
inverse of branching part of
Chris Mungall
has branching part
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.
Chris Mungall
UBERON:cjm
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.
conduit for
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.
Chris Mungall
GOC:cjm
lumen of
s is luminal space of x iff s is lumen_of x and s is an immaterial entity
Chris Mungall
luminal space of
A relation that holds between an attribute or a qualifier and another attribute.
Chris Mungall
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.
has modifier
Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
Chris Mungall
directly regulates (processual)
directly regulates
gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
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
Chris Mungall
has part structure that is capable of
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 breakdown of
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 catabolism of
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.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
Chris Mungall
causal relation between material entity and a process
pyrethroid -> growth
Holds between c and p if and only if c is capable of some activity a, and a regulates p.
capable of regulating
Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
capable of negatively regulating
renin -> arteriolar smooth muscle contraction
Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
capable of positively regulating
pazopanib -> pathological angiogenesis
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.
treats
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.
capable of inhibiting or preventing pathological process
treats
Usage of the term 'treats' applies when we believe there to be a an inhibitory relationship
benzene -> cancer [CHEBI]
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.
causes disease
capable of upregulating or causing pathological process
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.
treats
is substance that treats
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.
May be ceded to OBI
is marker for
Inverse of 'causal agent in process'
process has causal agent
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.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
obsolete related via dependence to
true
A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.
Groups both positive and negative correlation
correlated with
An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support.
A relationship between a piece of evidence and an entity that plays a role in supporting that evidence.
In the Gene Ontology association model, this corresponds to the With/From field
is evidence with support from
Inverse of is-model-of
has model
Do not use this relation directly. It is a grouping relation.
related via evidence or inference to
Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2.
directly positively regulates (process to process)
directly positively regulates
Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2.
directly negatively regulates (process to process)
directly negatively regulates
a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.
Melissa Haendel
Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue.
produces
a produced_by b iff some process that occurs_in b has_output a.
Melissa Haendel
produced by
Holds between protein a (a transcription factor) and DNA element b if and only if a diminishes the process of transcription of b.
Logical axioms to be added after the relevant branch of GO is MIREOTed in
represses expression of
Holds between protein a (a transcription factor) and DNA element b if and only if a activates the process of transcription of b.
Logical axioms to be added after the relevant branch of GO is MIREOTed in
increases expression of
Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity.
To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader?
Matthew Brush
The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest.
is model of
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'.
A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition.
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'.
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.
Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions.
causes or contributes to condition
A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition.
causes condition
A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition.
contributes to condition
A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual.
contributes to expressivity of condition
contributes to severity of condition
A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population.
contributes to penetrance of condition
contributes to frequency of condition
A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition.
is preventative for condition
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.
Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions.
ameliorates condition
A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship.
correlated with condition
A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition.
exacerbates condition
A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity.
condition ameliorated by
A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity.
condition exacerbated by
Do not use this relation directly. It is intended as a grouping for a more specific relations
cjm
2017-11-05T02:38:20Z
condition has genetic basis in
cjm
2017-11-05T02:45:20Z
has material basis in gain of function germline mutation in
cjm
2017-11-05T02:45:37Z
has material basis in loss of function germline mutation in
cjm
2017-11-05T02:45:54Z
has material basis in germline mutation in
cjm
2017-11-05T02:46:07Z
has material basis in somatic mutation in
cjm
2017-11-05T02:46:26Z
has major susceptibility factor
cjm
2017-11-05T02:46:57Z
has partial material basis in germline mutation in
p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c.
cjm
2018-12-13T11:26:17Z
has primary input or output
p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.
cjm
2018-12-13T11:26:32Z
has primary output
p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.
GOC:cjm
GOC:dph
GOC:kva
GOC:pt
PMID:27812932
p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.
cjm
2018-12-13T11:26:56Z
has primary input
p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.
GOC:cjm
GOC:dph
GOC:kva
GOC:pt
PMID:27812932
Do not use this relation directly. It is intended as a grouping for a more specific relations
cjm
2017-11-05T02:53:08Z
is genetic basis for condition
Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet].
cjm
2017-11-05T02:55:51Z
is causal gain of function germline mutation of in
Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet].
cjm
2017-11-05T02:56:06Z
is causal loss of function germline mutation of in
Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet].
cjm
2017-11-05T02:56:40Z
is causal germline mutation in
Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet].
cjm
2017-11-05T02:57:07Z
is causal somatic mutation in
Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet].
cjm
2017-11-05T02:57:43Z
is causal susceptibility factor for
Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet].
cjm
2017-11-05T02:58:43Z
is causal germline mutation partially giving rise to
cjm
2017-11-05T03:20:01Z
realizable has basis in
cjm
2017-11-05T03:20:29Z
is basis for realizable
cjm
2017-11-05T03:26:47Z
disease has basis in
A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process.
disease has basis in disruption of (disease to process)
cjm
2017-11-05T03:37:52Z
disease has basis in disruption of
A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M.
cjm
2017-12-26T19:45:49Z
realized in response to stimulus
A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease.
cjm
2017-12-26T19:50:53Z
disease has feature
Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.
cjm
2018-01-25T23:20:13Z
enables subfunction
cjm
2018-01-26T23:49:30Z
acts upstream of or within, positive effect
cjm
2018-01-26T23:49:51Z
acts upstream of or within, negative effect
c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive
cjm
2018-01-26T23:53:14Z
acts upstream of, positive effect
c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative
cjm
2018-01-26T23:53:22Z
acts upstream of, negative effect
cjm
2018-03-13T23:55:05Z
causally upstream of or within, negative effect
cjm
2018-03-13T23:55:19Z
causally upstream of or within, positive effect
DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information.
DEPRECATED inheres in
true
DEPRECATED bearer of
true
muffin 'has substance added' some 'baking soda'
"has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time.
The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients.
Damion Dooley
has substance added
'egg white' 'has substance removed' some 'egg yolk'
"has substance removed" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time.
Damion Dooley
has substance removed
sardines 'immersed in' some 'oil and mustard'
"immersed in" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance.
Damion Dooley
immersed in
bread 'has primary substance added' some 'flour'
'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance.
Damion Dooley
has primary substance added
A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions.
An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)
Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph.
r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r.
Austin Meier
Chris Mungall
David Osumi-Sutherland
Marie Angelique Laporte
Austin Meier
Chris Mungall
David Osumi-Sutherland
Marie Angelique Laporte
triggered by process
realized in response to
https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit
triggered by process
RO:cjm
Genetic information generically depend on molecules of DNA.
The novel *War and Peace* generically depends on this copy of the novel.
The pattern shared by chess boards generically depends on any chess board.
The score of a symphony g-depends on a copy of the score.
This pdf file generically depends on this server.
A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*.
[072-ISO]
g-depends on
generically depends on
Molecules of DNA are carriers of genetic information.
This copy of *War and Peace* is carrier of the novel written by Tolstoy.
This hard drive is carrier of these data items.
*b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*
[072-ISO]
is carrier of
The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.
Vasundra Touré
regulates activity of
Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.
ECO:0000041
SO:similar_to
sameness
similar to
correspondence
resemblance
in similarity relationship with
Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.
BGEE:curator
correspondence
Similarity that results from common evolutionary origin.
homologous to
This broad definition encompasses all the working definitions proposed so far in the literature.
in homology relationship with
Similarity that results from common evolutionary origin.
Similarity that results from independent evolution.
homoplasous to
analogy
in homoplasy relationship with
Similarity that results from independent evolution.
Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes.
ECO:0000075
homocracous to
Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues.
in homocracy relationship with
Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes.
Homoplasy that involves different underlying mechanisms or structures.
analogy
Convergence usually implies a notion of adaptation.
in convergence relationship with
Homoplasy that involves different underlying mechanisms or structures.
Homoplasy that involves homologous underlying mechanisms or structures.
parallel evolution
Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage.
in parallelism relationship with
Homoplasy that involves homologous underlying mechanisms or structures.
Homology that is defined by similarity with regard to selected structural parameters.
ECO:0000071
MI:2163
structural homologous to
idealistic homology
in structural homology relationship with
Homology that is defined by similarity with regard to selected structural parameters.
ISBN:0123195837
Homology that is defined by common descent.
homology
ECO:0000080
RO_proposed_relation:homologous_to
SO:0000330
SO:0000853
SO:0000857
SO:homologous_to
TAO:homologous_to
cladistic homology
historical homologous to
phylogenetic homology
taxic homology
true homology
in historical homology relationship with
Homology that is defined by common descent.
ISBN:0123195837
Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype.
ECO:0000067
biological homologous to
transformational homology
Applicable only to morphology. A certain degree of ambiguity is accepted between biological homology and parallelism.
in biological homology relationship with
Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype.
Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage.
atavism
rudiment
reversion
in reversal relationship with
Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage.
Structural homology that is detected by similarity in content and organization between chromosomes.
MeSH:Synteny
SO:0000860
SO:0005858
syntenic homologous to
synteny
in syntenic homology relationship with
Structural homology that is detected by similarity in content and organization between chromosomes.
MeSH:Synteny
Historical homology that involves genes that diverged after a duplication event.
SO:0000854
SO:0000859
SO:paralogous_to
paralogous to
in paralogy relationship with
Historical homology that involves genes that diverged after a duplication event.
Paralogy that involves sets of syntenic blocks.
syntenic paralogous to
duplicon
paralogon
in syntenic paralogy relationship with
Paralogy that involves sets of syntenic blocks.
DOI:10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y
Syntenic homology that involves chromosomes of different species.
syntenic orthologous to
in syntenic orthology relationship with
Syntenic homology that involves chromosomes of different species.
Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous.
fractional homology
partial homologous to
segmental homology
mixed homology
modular homology
partial correspondence
percent homology
in partial homology relationship with
Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous.
ISBN:0123195837
ISBN:978-0471984931
Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence.
MeSH:Structural_Homology,_Protein
protein structural homologous to
in protein structural homology relationship with
Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence.
Structural homology that involves a pseudogenic feature and its functional ancestor.
pseudogene
SO:non_functional_homolog_of
non functional homologous to
in non functional homology relationship with
Structural homology that involves a pseudogenic feature and its functional ancestor.
SO:non_functional_homolog_of
Historical homology that involves genes that diverged after a speciation event.
ECO:00000060
SO:0000855
SO:0000858
SO:orthologous_to
orthologous to
The term is sometimes also used for anatomical structures.
in orthology relationship with
Historical homology that involves genes that diverged after a speciation event.
Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor.
xenologous to
The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis).
in xenology relationship with
Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor.
Historical homology that involves two members sharing no other homologs in the lineages considered.
1 to 1 homologous to
1:1 homology
one-to-one homology
in 1 to 1 homology relationship with
Historical homology that involves two members sharing no other homologs in the lineages considered.
BGEE:curator
Orthology that involves two genes that did not experience any duplication after the speciation event that created them.
1 to 1 orthologous to
1:1 orthology
one-to-one orthology
in 1 to 1 orthology relationship with
Orthology that involves two genes that did not experience any duplication after the speciation event that created them.
Paralogy that results from a whole genome duplication event.
ohnologous to
homoeology
in ohnology relationship with
Paralogy that results from a whole genome duplication event.
Paralogy that results from a lineage-specific duplication subsequent to a given speciation event.
in-paralogous to
inparalogy
symparalogy
in in-paralogy relationship with
Paralogy that results from a lineage-specific duplication subsequent to a given speciation event.
Paralogy that results from a duplication preceding a given speciation event.
alloparalogy
out-paralogous to
outparalogy
in out-paralogy relationship with
Paralogy that results from a duplication preceding a given speciation event.
1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A.
pro-orthologous to
in pro-orthology relationship with
1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A.
1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B.
semi-orthologous to
The converse of pro-orthologous.
in semi-orthology relationship with
1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B.
Iterative homology that involves structures arranged along the main body axis.
serial homologous to
homonomy
in serial homology relationship with
Iterative homology that involves structures arranged along the main body axis.
Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures.
heterochronous homologous to
heterochrony
in heterochronous homology relationship with
Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures.
ISBN:978-0674639416
Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles.
juvenification
pedomorphosis
in paedomorphorsis relationship with
Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles.
ISBN:978-0674639416
Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits.
in peramorphosis relationship with
Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits.
Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage.
in progenesis relationship with
Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage.
ISBN:978-0674639416
Paedomorphosis that is produced by a retardation of somatic development.
juvenilization
neotenous to
in neoteny relationship with
Paedomorphosis that is produced by a retardation of somatic development.
ISBN:978-0674639416
Convergence that results from co-evolution usually involving an evolutionary arms race.
mimicrous to
in mimicry relationship with
Convergence that results from co-evolution usually involving an evolutionary arms race.
Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other.
1 to many orthologous to
1:many orthology
one-to-many orthology
co-orthology
many to 1 orthology
in 1 to many orthology relationship with
Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other.
Historical homology that involves two members of a larger set of homologs.
many to many homologous to
many-to-many homology
many:many homology
in many to many homology relationship with
Historical homology that involves two members of a larger set of homologs.
Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species.
1 to many homologous to
one-to-many homology
1:many homology
in 1 to many homology relationship with
Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species.
BGEE:curator
Historical homology that is based on recent shared ancestry, characterizing a monophyletic group.
apomorphous to
synapomorphy
in apomorphy relationship with
Historical homology that is based on recent shared ancestry, characterizing a monophyletic group.
ISBN:978-0252068140
Historical homology that is based on distant shared ancestry.
plesiomorphous to
symplesiomorphy
This term is usually contrasted to apomorphy.
in plesiomorphy relationship with
Historical homology that is based on distant shared ancestry.
ISBN:978-0252068140
Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution.
deep genetic homology
deep homologous to
generative homology
homoiology
Used for structures in distantly related taxa.
in deep homology relationship with
Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution.
Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree.
hemiplasous to
in hemiplasy relationship with
Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree.
Historical homology that involves not recombining and subsequently differentiated sex chromosomes.
gametologous to
in gametology relationship with
Historical homology that involves not recombining and subsequently differentiated sex chromosomes.
Historical homology that involves the chromosomes able to pair (synapse) during meiosis.
MeSH:Chromosome_Pairing
chromosomal homologous to
in chromosomal homology relationship with
Historical homology that involves the chromosomes able to pair (synapse) during meiosis.
ISBN:0195307615
Orthology that involves two genes that experienced duplications more recent than the species split that created them.
many to many orthologous to
many-to-many orthology
many:many orthology
trans-orthology
co-orthology
trans-homology
in many to many orthology relationship with
Orthology that involves two genes that experienced duplications more recent than the species split that created them.
Paralogy that involves genes from the same species.
within-species paralogous to
in within-species paralogy relationship with
Paralogy that involves genes from the same species.
Paralogy that involves genes from different species.
between-species paralogous to
The genes have diverged before a speciation event.
in between-species paralogy relationship with
Paralogy that involves genes from different species.
Paedomorphosis that is produced by delayed growth of immature structures into the adult form.
post-displacement
in postdisplacement relationship with
Paedomorphosis that is produced by delayed growth of immature structures into the adult form.
Peramorphosis that is produced by a delay in the offset of development.
in hypermorphosis relationship with
Peramorphosis that is produced by a delay in the offset of development.
ISBN:978-0674639416
Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species.
synologous to
in synology relationship with
Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species.
Orthology that involves functional equivalent genes with retention of the ancestral function.
ECO:0000080
isoorthologous to
in isoorthology relationship with
Orthology that involves functional equivalent genes with retention of the ancestral function.
Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment.
tandem paralogous to
iterative paralogy
serial paralogy
in tandem paralogy relationship with
Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment.
ISBN:978-0878932665
Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character).
apomorphic tendency
cryptic homology
latent homologous to
underlying synapomorphy
homoiology
homoplastic tendency
re-awakening
Used for structures in closely related taxa.
in latent homology relationship with
Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character).
ISBN:0199141118
Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual.
generative homology
syngenous to
Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes.
in syngeny relationship with
Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual.
DOI:10.1002/1521-1878(200009)22:9<846::AID-BIES10>3.0.CO;2-R
Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss.
1:1 paralogy
apparent 1:1 orthology
apparent orthologous to
pseudoorthology
The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss.
in apparent orthology relationship with
Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss.
Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer.
pseudoparalogous to
These genes may come out as paralogs in a single-genome analysis.
in pseudoparalogy relationship with
Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer.
Historical homology that involves functional equivalent genes with retention of the ancestral function.
equivalogous to
This may include examples of orthology, paralogy and xenology.
in equivalogy relationship with
Historical homology that involves functional equivalent genes with retention of the ancestral function.
Historical homology that involves orthologous pairs of interacting molecules in different organisms.
interologous to
in interology relationship with
Historical homology that involves orthologous pairs of interacting molecules in different organisms.
Similarity that is characterized by interchangeability in function.
functional similarity
in functional equivalence relationship with
Similarity that is characterized by interchangeability in function.
Biological homology that involves parts of the same organism.
iterative homologous to
in iterative homology relationship with
Biological homology that involves parts of the same organism.
Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome.
duplicate xenology
multiple xenology
paraxenologous to
in paraxenology relationship with
Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome.
Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution.
plerologous to
This phenomenon is usually due to gene conversion process.
in plerology relationship with
Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution.
Structural homology that involves structures with the same or similar relative positions.
homotopous to
Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use.
in homotopy relationship with
Structural homology that involves structures with the same or similar relative positions.
ISBN:0123195837
Biological homology that involves an ectopic structure and the normally positioned structure.
heterotopy
in homeosis relationship with
Biological homology that involves an ectopic structure and the normally positioned structure.
Synology that results from allopolyploidy.
homoeologous to
On a long term, it is hard to distinguish allopolyploidy from whole genome duplication.
in homoeology relationship with
Synology that results from allopolyploidy.
Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure.
axis paramorphism
in paramorphism relationship with
Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure.
Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms.
regulogous to
in regulogy relationship with
Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms.
has measurement value
has x coordinate value
has z coordinate value
has y coordinate value
The only valid string values for this property are ISO 8601 formatted date strings in extended form. It is allowable specify only the year, e.g. '2016' but only when the 1D temporal region references the entire year. Ditto for month, e.g. 2016-04 is acceptable but only if it references the entire interval of that month.
date
time
time of day
0
100
Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population.
2018-05-22T16:43:28Z
This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses.
has increased age-specific mortality rate
dos
Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population.
PMID:24138933
Wikipedia:Infant_mortality
obsolete International Classification of Diseases
true
my filling in an immigration form, a judge's signing and stamping a court order
A deontic declaration creating or revoking a deontic role by lawfully manipulating (signing, stamping, publishing) a document.
Mathias Brochhausen
obsolete_deontic document act
true
A planned process that has specified output a software product and that involves the creation of source code.
Mathias Brochhausen
William R. Hogan
http://en.wikipedia.org/wiki/Software_development
A planned process resulting in a software product involving the creation of source code.
software development
A measurement datum that is the output of counting.
Mathias Brochhausen
A measurement datum that is the output of counting.
count
The planned process of finding the number of elements in a finite set of objects.
Mathias Brochhausen
http://en.wikipedia.org/wiki/Counting
The planned process of finding the number of elements in a finite set of objects.
counting
A name of temporal region that specifies a time span on a specified time scale by giving a start time and a duration.
Mathias Brochhausen
http://purl.obolibrary.org/obo/apollo_sv/v4.1.1./apollo_sv.owl
An information content entity that specifies a time span on a specified time scale by giving a start time and a duration.
TimeSpanCategoryDefinition
name of temporal interval
A name of temporal region that designates a temporal boundary
Matthew Diller
William R. Hogan
http://purl.obolibrary.org/obo/apollo_sv/v4.1.1./apollo_sv.owl
An information content entity that designates a temporal boundary
RealTimePointCategoryDefinition
name of a temporal boundary
http://purl.obolibrary.org/obo/apollo_sv/v4.1.1./apollo_sv.owl
name of temporal region
A name of a temporal region that is systematized according to a particular calendar system, such as the Gregorian calendar.
Matthew Diller
William R. Hogan
http://purl.obolibrary.org/obo/apollo_sv/v4.1.1./apollo_sv.owl
A name of a temporal region that is systematized according to a particular calendar system, such as the Gregorian calendar.
date
date
A behavior of one or more organisms that is characterized by the displacement from one geographic region to some target geographic region, and is the realization of either a biological function or (a concretization of) an objective specification.
Matthew Diller
William R. Hogan
A behavior of one or more organisms that is characterized by the displacement from one geographic region to some target geographic region, and is the realization of either a biological function or (a concretization of) an objective specification.
geographical migration of organism
software source code version control repository
A document that comprises at least one source code module and provenance data about who contributed the set of files making up the module(s), and optionally comprises also multiple versions of files with detailed change history about who committed files and when, a license for the software, readme files, documentation, executables, etc.
William R. Hogan
Refers to the stuff that lives on GitHub, not to GitHub or the git software on which it is based
source code repository
process of compiling software
A planned process that converts human-written or curated software into a machine-executable or interpretable set of instructions.
William R. Hogan
It's compiling "software" (scare quotes) and not "source code" because you can compile Java bytecode to machine code, and Java bytecode is not technically "source code". Compiling source code would be a subclass of this class (as would compiling Java bytecode, etc.).
Source code can be automatically generated to some extent, but we're assuming humans still curate it minimally. Also, in the case of Java and its JVM, it's machine interpretable instructions, not directly executable. Ditto for other languages with intermediate form like Java byte code.
compiling software
A geographical migration of an organism belonging to the species Homo sapiens.
Matthew Diller
William R. Hogan
human travel
creating a data set
A planned process that has a data set as its specified output.
William R. Hogan
data set creation
dataset creation
dataset creating
entity
Entity
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
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
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
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
entity
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
per discussion with Barry Smith
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
continuant
Continuant
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.
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
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
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])
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])
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])
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])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
continuant
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
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])
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])
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])
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])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
occurrent
Occurrent
An entity that has temporal parts and that happens, unfolds or develops through time.
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
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.
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.
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.
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])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
occurrent
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.
per discussion with Barry Smith
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.
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])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
ic
IndependentContinuant
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
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])
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])
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])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(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]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
independent continuant
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])
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])
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])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(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]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities.
obsolete dependent continuant
true
s-region
SpatialRegion
BFO 2 Reference: Spatial regions do not participate in processes.
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.
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])
All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
spatial region
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.
per discussion with Barry Smith
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])
All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
t-region
TemporalRegion
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
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])
All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
temporal region
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
per discussion with Barry Smith
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])
All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
2d-s-region
TwoDimensionalSpatialRegion
an infinitely thin plane in space.
the surface of a sphere-shaped part of space
A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]
two-dimensional spatial region
A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]
st-region
SpatiotemporalRegion
the spatiotemporal region occupied by a human life
the spatiotemporal region occupied by a process of cellular meiosis.
the spatiotemporal region occupied by the development of a cancer tumor
A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
Every spatiotemporal region occupies_spatiotemporal_region itself.
Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
spatiotemporal region
A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
process
Process
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
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])
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)
(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]
process
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])
(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]
disposition
Disposition
an atom of element X has the disposition to decay to an atom of element Y
certain people have a predisposition to colon cancer
children are innately disposed to categorize objects in certain ways.
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
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.
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])
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])
(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]
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
disposition
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])
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])
(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]
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
realizable
RealizableEntity
the disposition of this piece of metal to conduct electricity.
the disposition of your blood to coagulate
the function of your reproductive organs
the role of being a doctor
the role of this boundary to delineate where Utah and Colorado meet
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.
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])
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(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]
(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]
realizable entity
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])
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(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]
(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]
0d-s-region
ZeroDimensionalSpatialRegion
A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]
zero-dimensional spatial region
A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]
quality
Quality
the ambient temperature of this portion of air
the color of a tomato
the length of the circumference of your waist
the mass of this piece of gold.
the shape of your nose
the shape of your nostril
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])
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])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(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]
quality
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])
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])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(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]
sdc
SpecificallyDependentContinuant
specifically dependent continuant
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
of one-sided specifically dependent continuants: the mass of this tomato
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.
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the role of being a doctor
the shape of this hole.
the smell of this portion of mozzarella
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.
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])
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])
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.
(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]
specifically dependent continuant
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])
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.
per discussion with Barry Smith
(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]
role
Role
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.
the priest role
the role of a boundary to demarcate two neighboring administrative territories
the role of a building in serving as a military target
the role of a stone in marking a property boundary
the role of subject in a clinical trial
the student role
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.
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.
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])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
role
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])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
fiat-object-part
FiatObjectPart
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
the FMA:regional parts of an intact human body.
the Western hemisphere of the Earth
the division of the brain into regions
the division of the planet into hemispheres
the dorsal and ventral surfaces of the body
the upper and lower lobes of the left lung
BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions
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])
(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]
fiat object part
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])
(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]
1d-s-region
OneDimensionalSpatialRegion
an edge of a cube-shaped portion of space.
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])
(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]
one-dimensional spatial region
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])
(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]
object-aggregate
ObjectAggregate
a collection of cells in a blood biobank.
a swarm of bees is an aggregate of members who are linked together through natural bonds
a symphony orchestra
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)
defined by fiat: the aggregate of members of an organization
defined through physical attachment: the aggregate of atoms in a lump of granite
defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
defined via attributive delimitations such as: the patients in this hospital
the aggregate of bearings in a constant velocity axle joint
the aggregate of blood cells in your body
the nitrogen atoms in the atmosphere
the restaurants in Palo Alto
your collection of Meissen ceramic plates.
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
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).
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.
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])
(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]
object aggregate
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
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.
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])
(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]
3d-s-region
ThreeDimensionalSpatialRegion
a cube-shaped region of space
a sphere-shaped region of space,
A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
three-dimensional spatial region
A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
site
Site
Manhattan Canyon)
a hole in the interior of a portion of cheese
a rabbit hole
an air traffic control region defined in the airspace above an airport
the Grand Canyon
the Piazza San Marco
the cockpit of an aircraft
the hold of a ship
the interior of a kangaroo pouch
the interior of the trunk of your car
the interior of your bedroom
the interior of your office
the interior of your refrigerator
the lumen of your gut
your left nostril (a fiat part – the opening – of your left nasal cavity)
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])
(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
site
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])
(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
object
Object
atom
cell
cells and organisms
engineered artifacts
grain of sand
molecule
organelle
organism
planet
solid portions of matter
star
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.
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).
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
BFO 2 Reference: an object is a maximal causally unified material entity
BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74
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])
object
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])
gdc
GenericallyDependentContinuant
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.
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
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.
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])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
generically dependent continuant
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])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
function
Function
the function of a hammer to drive in nails
the function of a heart pacemaker to regulate the beating of a heart through electricity
the function of amylase in saliva to break down starch into sugar
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.
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])
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
function
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])
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
p-boundary
ProcessBoundary
the boundary between the 2nd and 3rd year of your life.
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])
Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]
process boundary
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])
Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]
1d-t-region
OneDimensionalTemporalRegion
the temporal region during which a process occurs.
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).
A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
one-dimensional temporal region
A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
material
MaterialEntity
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
the undetached arm of a human being
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
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
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.
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.
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])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(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]
(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]
material entity
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])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(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]
(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]
cf-boundary
ContinuantFiatBoundary
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])
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.
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
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.
Every continuant fiat boundary is located at some spatial region at every time at which it exists
(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]
continuant fiat boundary
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])
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.
(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]
immaterial
ImmaterialEntity
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
immaterial entity
1d-cf-boundary
OneDimensionalContinuantFiatBoundary
The Equator
all geopolitical boundaries
all lines of latitude and longitude
the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin.
the median sulcus of your tongue
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])
(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]
one-dimensional continuant fiat boundary
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])
(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]
process-profile
ProcessProfile
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
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.
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.
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])
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])
(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]
(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]
process profile
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])
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])
(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]
(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]
r-quality
RelationalQuality
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.
a marriage bond, an instance of requited love, an obligation between one person and another.
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])
(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]
relational quality
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])
(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]
2d-cf-boundary
TwoDimensionalContinuantFiatBoundary
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])
(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]
two-dimensional continuant fiat boundary
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])
(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]
0d-cf-boundary
ZeroDimensionalContinuantFiatBoundary
the geographic North Pole
the point of origin of some spatial coordinate system.
the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet
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.
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])
(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]
zero-dimensional continuant fiat boundary
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.
requested by Melanie Courtot
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])
(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]
0d-t-region
ZeroDimensionalTemporalRegion
a temporal region that is occupied by a process boundary
right now
the moment at which a child is born
the moment at which a finger is detached in an industrial accident
the moment of death.
temporal instant.
A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
zero-dimensional temporal region
A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
history
History
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])
history
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])
http://purl.obolibrary.org/obo/bfo/2020/bfo.owl
155-BFO
temporal interval
(Elucidation) a temporal interval is a one-dimensional temporal region that is continuous, thus without gaps or breaks
The year 2018.
temporal interval
A one-dimensional temporal region can include as parts not only temporal intervals but also temporal instants separated from other parts by gaps.
http://purl.obolibrary.org/obo/bfo/2020/bfo.owl
209-BFO
temporal instant
(Elucidation) a temporal instant is a zero-dimensional temporal region that has no proper temporal part
The millennium.
temporal instant
An environmental feature that is, or can be, contained and is predominantly composed of one or a few types of stuff.
An object which is large enough to be visible to humans, but small enough that humans can handle the object (i.e. transport it, examine it, etc) in its entirety with little to no technological assistance.
mesoscopic physical object
http://purl.obolibrary.org/obo/envo.owl
MA:ma
This is a legacy class from ENVO's early versions. It will be depopulated and filled in by inference using a PATO quality. Not to be confused with "mesoscopic" as defined in physics, which deals with objects typically between 10e-6 and 10-8 meters in diameter.
https://en.oxforddictionaries.com/definition/mesoscopic
mesoscopic physical object
physical object of mesoscopic geological size
A material entity that has been processed by humans or their technology in any way, including intermediate products as well as final products.
http://purl.obolibrary.org/obo/envo.owl
manufactured good
https://en.wikipedia.org/wiki/Manufactured_product
manufactured product
http://purl.obolibrary.org/obo/envo.owl
ENVO
ENVO:00003075
anthropogenic abiotic mesoscopic feature
http://purl.obolibrary.org/obo/envo.owl
ENVO
ENVO:01000010
abiotic mesoscopic physical object
A system which has the disposition to environ one or more material entities.
http://purl.obolibrary.org/obo/envo.owl
2013-09-23T16:04:08Z
DOI:10.1186/2041-1480-4-43
EcoLexicon:environment
environment
In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised.
environmental system
A vehicle is a mobile machine which transports people or cargo.
http://purl.obolibrary.org/obo/envo.owl
https://en.wikipedia.org/wiki/Vehicle
vehicle
Anatomical cluster
vocal fold
Subdivision of larynx
Heterogeneous cluster
Anatomical structure
Material anatomical entity
molecular process
molecular_function
catalytic activity
The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity.
Wikipedia:Behavior
1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews.
2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis).
behavior
The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity.
GOC:ems
GOC:jl
ISBN:0395448956
PMID:20160973
A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
Wikipedia:Biological_process
Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
biological_process
A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
GOC:pdt
true
kinase activity
transferase activity
transferase activity, transferring phosphorus-containing groups
response to stimulus
conditional specification
A directive information entity that specifies what should happen if the trigger condition is fulfilled.
PlanAndPlannedProcess Branch
OBI branch derived
OBI_0000349
conditional specification
measurement unit label
Examples of measurement unit labels are liters, inches, weight per volume.
A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
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.
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.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
measurement unit label
objective specification
In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
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.
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."
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.
Answers the question, why did you do this experiment?
PERSON: Alan Ruttenberg
PERSON: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
goal specification
OBI Plan and Planned Process/Roles Branch
OBI_0000217
objective specification
narrative object
Examples of narrative objects are reports, journal articles, and patents submission.
A narrative object is an information content entity that is a set of propositions.
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
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
person:Chris Stoeckert
OBI_0000013
group:OBI
narrative object
Pour the contents of flask 1 into flask 2
A directive information entity that describes an action the bearer will take.
Alan Ruttenberg
OBI Plan and Planned Process branch
action specification
obsolete_artifact
true
datum label
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
http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n
GROUP: IAO
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.
datum label
software
Software is a plan specification composed of a series of instructions that can be
interpreted by or directly executed by a processing unit.
see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
PERSON: Chris Stoeckert
PERSON: Melanie Courtot
GROUP: OBI
software
obsolete_digital entity
A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical.
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4
Superclass was 'digitial quality'
person:Chris Stoeckert
OBI_0000261
group:OBI
obsolete2_digital entity
true
journal article
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.
A report that is published in a journal.
PERSON: Alan Ruttenberg
PERSON: Chris Stoeckert
OBI_0000159
group:OBI
journal article
information carrier
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.
A quality of an information bearer that imparts the information content
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'.
2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it.
PERSON: Alan Ruttenberg
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
information carrier
model number
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.
manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers
Person: Alan Ruttenberg
model number
obsolete_material_entity
true
binary digital entity
MS Word document, ZIP file, DICOM file, JPEG file
A binary digital entity is a digital entity that is encoded in a way that is not easily human readable and that contains other than text characters.
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4
Superclass was 'digital entity'
digital_entity
person:Chris Stoeckert
OBI_0000244
group:OBI
obsolete2_binary digital entity
true
The length of a ruler.
a unit of measure is the quality of some material entity compared to which another quality is some multiple of.
Alan Ruttenberg
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
obsolete_unit of measure
true
programming language
R, Perl, Java
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.
person:Alan Ruttenberg
person:Chris Stoeckert
OBI_0000058
group:OBI
programming language
data item
Data items include counts of things, analyte concentrations, and statistical summaries.
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.
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.
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.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
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
PERSON: Alan Ruttenberg
PERSON: Chris Stoeckert
PERSON: Jonathan Rees
data
data item
symbol
a serial number such as "12324X"
a stop sign
a written proper name such as "OBI"
An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
20091104, MC: this needs work and will most probably change
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).
PERSON: James A. Overton
PERSON: Jonathan Rees
based on Oxford English Dictionary
symbol
numeral
A symbol that denotes a number.
PERSON: Jonathan Rees
numeral
information content entity
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
A generically dependent continuant that is about some thing.
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).
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.
PERSON: Chris Stoeckert
OBI_0000142
information content entity
integer numeral
A numeral that denotes an integer
PERSON: Jonathan Rees
integer numeral
1
1
10 feet. 3 ml.
A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
2009-03-16: we decided to keep datum singular in scalar measurement datum, as in
this case we explicitly refer to the singular form
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.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
scalar measurement datum
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
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.
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.
8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
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
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
directive information entity
time trigger
PlanAndPlannedProcess Branch
time trigger
obsolete_study interpretation
A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses
2009-03-16: definition was "A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application."
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.
The obsoleting of narrative object required a modest change in the definition of this term. Circularity with "interpretation... interprets" has been removed, using "about the implications" instead.
Lawrence Hunter
PERSON: Alan Ruttenberg
PERSON: Jennifer Fostel
PERSON: Melanie Courtot
conclusion
OBI_0000005
obsolete_study interpretation
true
dot plot
Dot plot of SSC-H and FSC-H.
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.
person:Allyson Lister
person:Chris Stoeckert
OBI_0000123
group:OBI
dot plot
graph
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.
PERSON: Lawrence Hunter
person:Alan Ruttenberg
person:Allyson Lister
OBI_0000240
group:OBI
graph
text based digital entity
XML file, C++ source code file
A text based digital entity is a digital entity that is encoded so that it only contains text characters.
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4
superclass was 'digital document'
digital_entity
person:Chris Stoeckert
OBI_0000132
group:OBI
obsolete2_text based digital entity
true
rule
example to be added
A rule is an executable which guides, defines, restricts actions.
MSI
PRS
OBI_0500021
PRS
rule
contour plot
Contour plot of SSC-H, FSC-H, and FL1-H.
generically_dependent_continuants
person:Allyson Lister
person:Chris Stoeckert
OBI_0000246
group:Flow Cytometry community
contour plot
report figure
A report figure is a report display element that has some aspect of illustration, but may be a composite of figures, images, and other elements
I prepended the 'report ' to make it clear that we mean parts of reports here. We may want a more generic version of 'figure', in which case this would become a defined class - figure and part_of some report
Replaced by defined version of figure
person:Alan Ruttenberg
person:Allyson Lister
OBI_0000027
group:OBI
obsolete2_report figure
true
algorithm
PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
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.
Philippe Rocca-Serra
PlanAndPlannedProcess Branch
OBI_0000270
adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
algorithm
software interpreter
R program, Perl interpreter, Java virtual machine
A software interpreter is a software application that executes some specified input software.
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
person:Alan Ruttenberg
person:Chris Stoeckert
OBI_0000199
group:OBI
software interpreter
curation status specification
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.
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
PERSON:Bill Bug
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
OBI_0000266
curation status specification
density plot
Density plot of SSC-H and FSC-H.
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.
person:Allyson Lister
person:Chris Stoeckert
OBI_0000179
group:Flow Cytometry community
density plot
report
Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article.
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).
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.
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.
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.
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
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
PERSON: Alan Ruttenberg
PERSON: Chris Stoeckert
PERSON: Melanie Courtot
GROUP: OBI
OBI_0000099
report
report element
A report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page).
2009-03-16: needs some more work (clarify relations).
2009-03-16: was report display element with definition: A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements.
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.
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
Replaced by textual entity and figure
There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text
PERSON: Alan Ruttenberg
PERSON: Allyson Lister
PERSON: Melanie Courtot
GROUP:OBI
OBI_0000001
obsolete_report element
true
binary executable
Binary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions. (derived from Wikipedia, Nov 1, 2007)
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4
superclass was 'digital entity'
person:Jennifer Fostel
OBI_0000222
group:OBI
obsolete2_binary executable
true
source code module
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.
A source code module is a directive information entity that specifies, using a programming language, some algorithm.
person:Alan Ruttenberg
person:Chris Stoeckert
OBI_0000039
group:OBI
source code module
report table
A report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content
2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity table'. Alan restored as there are OBI dependencies and this merits further discussion
person:Alan Ruttenberg
person:Allyson Lister
OBI_0000265
group:OBI
obsolete_report table
true
data format specification
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
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"
PERSON: Alan Ruttenberg
PlanAndPlannedProcess Branch
OBI branch derived
OBI_0000187
data format specification
data set
Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
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.
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
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.
person:Allyson Lister
person:Chris Stoeckert
OBI_0000042
group:OBI
data set
image
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.
person:Alan Ruttenberg
person:Allyson
person:Chris Stoeckert
OBI_0000030
group:OBI
image
data about an ontology part
Data about an ontology part is a data item about a part of an ontology, for example a term
Person:Alan Ruttenberg
data about an ontology part
plan specification
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
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.
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.
2014-03-31: A plan specification can have other parts, such as conditional specifications.
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
Alan Ruttenberg
OBI Plan and Planned Process branch
OBI_0000344
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
plan specification
digital document
A digital document is a digital entity consisting of an electronic file which can be rendered into human-readable form by one or more computational applications. The digital document does not refer to the information content of the document but to an instance of the file.
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4
superclass was 'digial entity'
person:Jennifer Fostel
OBI_0000195
group:OBI
obsolete2_digital document
true
measurement datum
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,}.
A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
2/2/2009 is_specified_output of some assay?
person:Chris Stoeckert
OBI_0000305
group:OBI
measurement datum
_identifier is a container under information content entity for collecting types of terms to indicate a specific instance or clas of what was used or participated in an investigation. Identifiers are borne by a product or its packaging, and can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
Note: everybody agreed that identifier is probably a too general term. We however felt that it would be appropriate to group "identifiying" terms under some kind of umbrella. We therefore propose to use _identifier for that purpose. As per OBI conventions, the _ prefixing identifier indicates that this is a helper class and shouldn't be considered as final.
obsolete_identifier
true
version number
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.
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
GROUP: IAO
version number
serial number
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.
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 :-)
GROUP: IAO
serial number
lot number
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.
GROUP: IAO
batch number
lot number
A settings datum is a datum that denotes some configuration of an instrument.
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.
Alan grouped these in placeholder for the moment. Name by analogy to measurement datum.
setting datum
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4
Need to rework digital entity. Digital quality was suggested by Barry.
obsolete_digital quality
true
conclusion textual entity
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
A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers.
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
2009/10/23 Alan Ruttenberg: We need to work on the definition still
Person:Alan Ruttenberg
conclusion textual entity
material information bearer
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.
a brain
a hard drive
A material entity in which a concretization of an information content entity inheres.
GROUP: IAO
material information bearer
histogram
A histogram is a report graph which is a statistical description of a
distribution in terms of occurrence frequencies of different event classes.
PERSON:Chris Stoeckert
PERSON:James Malone
PERSON:Melanie Courtot
GROUP:OBI
histogram
heatmap
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.
PERSON:Chris Stoeckert
PERSON:James Malone
PERSON:Melanie Courtot
GROUP:OBI
heatmap
Venn diagram
A Venn diagram is a report graph showing all hypothetically possible
logical relations between a finite collection of sets.
PERSON:Chris Stoeckert
PERSON:James Malone
PERSON:Melanie Courtot
WEB: http://en.wikipedia.org/wiki/Venn_diagram
Venn diagram
obsolete_survival curve
A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time.
PERSON:Chris Stoeckert
PERSON:James Malone
PERSON:Melanie Courtot
WEB: http://www.graphpad.com/www/book/survive.htm
obsolete_survival curve
true
dendrogram
Dendrograms are often used in computational biology to
illustrate the clustering of genes.
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.
PERSON:Chris Stoeckert
PERSON:James Malone
PERSON:Melanie Courtot
WEB: http://en.wikipedia.org/wiki/Dendrogram
dendrogram
scatter plot
Comparison of gene expression values in two samples can be displayed in a scatter plot
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.
PERSON:Chris Stoeckert
PERSON:James Malone
PERSON:Melanie Courtot
scattergraph
WEB: http://en.wikipedia.org/wiki/Scatterplot
scatter plot
A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc.
PERSON:Alan Ruttenberg
PERSON:Joanne Luciano
PERSON:Melanie Courtot
WEB: http://en.wiktionary.org/wiki/photograph
photograph
photographic print
A photographic print is a material entity upon which a photograph generically depends.
PERSON:Alan Ruttenberg
PERSON:Melanie Courtot
photographic print
obsolescence reason specification
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.
The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
obsolescence reason specification
textual entity
Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
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.
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.
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.
PERSON: Lawrence Hunter
text
textual entity
citation
Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183.
A textual entity intended to identify a particular publication.
PERSON: Lawrence Hunter
citation
author identification
L. Hunter
A textual entity intended to identify a particular author
PERSON: Lawrence Hunter
author identification
institutional identification
University of Colorado Denver School of Medicine
A textual entity intended to identify a particular institution
PERSON: Lawrence Hunter
institutional identification
caption
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.
A textual entity that describes a figure
PERSON: Lawrence Hunter
caption
document title
Textual characteristics of traditional and Open Access scientific journals are similar
A textual entity that names a document
PERSON: Lawrence Hunter
document title
table
| T F
--+-----
T | T F
F | F F
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
PERSON: Lawrence Hunter
table
table of abbreviations
IAO information artifact ontology
OBI ontology of biomedical investiations
GO gene ontology
A table where the constituent texts are abbreviations and their expansions
PERSON: Lawrence Hunter
table of abbreviations
figure
Any picture, diagram or table
An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
PERSON: Lawrence Hunter
figure
diagram
A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.
A figure that expresses one or more propositions
PERSON: Lawrence Hunter
diagram
document
A journal article, patent application, laboratory notebook, or a book
A collection of information content entities intended to be understood together as a whole
PERSON: Lawrence Hunter
document
publication
journal article, newspaper story, book, etc.
A document that is the output of a publishing process.
PERSON: Chris Stoeckert
PERSON: Jie Zheng
PERSON: Lawrence Hunter
published document
Revisit the term in Octorber 2020. Improve the defintion.
publication
publication about an investigation
Most scientific journal articles
A publication that is about an investigation
PERSON: Lawrence Hunter
scientific publication
publication about an investigation
patent
US Patent 6,449,603
A document that has been accepted by a patent authority
PERSON: Lawrence Hunter
patent
document part
An abstract, introduction, method or results section.
An information content entity that is part of a document.
PERSON: Lawrence Hunter
document part
abstract
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.
A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes.
PERSON: Lawrence Hunter
precis
abstract
introduction to a publication about an investigation
Section labelled 'introduction' of a typical scientific journal article
A part of a publication about an investigation that is about the objective specification (why the investigation is being done)
PERSON: Lawrence Hunter
background
introduction
overview
introduction to a publication about an investigation
methods section
The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article.
A part of a publication about an investigation that is about the study design of the investigation
PERSON: Lawrence Hunter
experimental
experimental methods
experimental procedures
experimental section
method
methodology
methods
methods section
results section
The section labelled 'results' in a typical scientific journal article
A part of a publication about an investigation that is about a study design execution
PERSON: Lawrence Hunter
results
results section
discussion section of a publication about an investigation
A part of a publication about an investigation that is about the study interpretation of the investigation
PERSON: Lawrence Hunter
discussion
discussion section
discussions
discussion section of a publication about an investigation
references section
The list of citations found at the end of a scientific publication, grant proposal or patent application, sometimes called "literature cited" or "bibliography"
A part of a document that has citations as parts
PERSON: Lawrence Hunter
literature cited
reference
reference list
references
references section
author list
Lawrence Hunter and Kevin Brettonel Cohen
A part of a document that enumerates the authors of the document
PERSON: Lawrence Hunter
author list
institution list
The University of Colorado Denver School of Medicine and the University of Colorado Boulder.
A part of a document that has parts that are institution identifications associated with the authors of the document
PERSON: Lawrence Hunter
institution list
author contributions section
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.
A part of a publication that is about the specific contributions of each author
PERSON: Lawrence Hunter
author contributions
authors' contribution
authors' contributions
authors' roles
contributions by the authors
contributorship
author contributions section
acknowledgements section
The authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscript
Part of a publication that is about the contributions of people or institutions other than the authors.
PERSON: Lawrence Hunter
acknowledgement
acknowledgements
acknowledgment
acknowledgments
acknowledgements section
footnote
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.
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.
PERSON: Lawrence Hunter
endnote
footnotes
footnote
supplementary material to a document
A part of a document that is segregated from the rest of the document due to its size
PERSON: Lawrence Hunter
additional file
additional files
additional information
appendix
electronic supplementary material
electronic supplementary materials
supplemental data
supplemental information
supplemental material
supplementary data
supplementary files
supplementary information
supplementary material
supplementary materials
supporting information
supplementary material to a document
table of contents
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).
PERSON: Lawrence Hunter
table of contents
table of figures
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).
PERSON: Lawrence Hunter
table of figures
running title
A shorter version of a document title
PERSON: Lawrence Hunter
running title
copyright section
This work is licensed under a Creative Commons Attribution-Share Alike 3.0 United States License.
A document part that describes legal restrictions on making or distributing copies of the document
PERSON: Lawrence Hunter
copyright section
1
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
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
Alan Ruttenberg
AR notes: We need to discuss whether it should include site.
cartesian spatial coordinate datum
http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617
1
A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region
Alan Ruttenberg
one dimensional cartesian spatial coordinate datum
1
1
A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region
Alan Ruttenberg
two dimensional cartesian spatial coordinate datum
1
1
1
A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region
Alan Ruttenberg
three dimensional cartesian spatial coordinate datum
A scalar measurement datum that is the result of measurement of length quality
Alan Ruttenberg
length measurement datum
denotator type
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.
A denotator type indicates how a term should be interpreted from an ontological perspective.
Alan Ruttenberg
Barry Smith, Werner Ceusters
denotator type
A scalar measurement datum that is the result of measurement of mass quality
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
Person:Alan Ruttenberg
mass measurement datum
hypothesis textual entity
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
A textual entity that expresses an assertion that is intended to be tested.
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
Person:Alan Ruttenberg
hypothesis textual entity
A scalar measurement datum that is the result of measuring a temporal interval
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
Person:Alan Ruttenberg
time measurement datum
A textual entity that is used as directive to deliver something to a person, or organization
2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue https://github.com/information-artifact-ontology/IAO/issues/59
postal address
email address
Alan Ruttenberg 1/3/2012 - Provisional id, see issue at https://github.com/information-artifact-ontology/IAO/issues/130&thanks=130&ts=1325636583
Person:Alan Ruttenberg
Person:Chris Stoeckart
email address
author role
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.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
author role
A planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing
Person:Alan Ruttenberg
data item extraction from journal article
A planned process of making information, such as literature, music, and software etc., available to the public for sale or for free.
Person: Jie Zheng
https://en.wikipedia.org/wiki/Publishing
VEuPathDB
publishing process
A document that is in preparation for submission to be published.
PERSON: Jie Zheng
EFO_0001795 in preparation
VEuPathDB
document in preparation for publication
Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
A planned process in which a document is created or added to by including the specified input in it.
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
Bjoern Peters
wikipedia http://en.wikipedia.org/wiki/Documenting
documenting
line graph
A line graph is a type of graph created by connecting a series of data
points together with a line.
PERSON:Chris Stoeckert
PERSON:Melanie Courtot
line chart
GROUP:OBI
WEB: http://en.wikipedia.org/wiki/Line_chart
line graph
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.
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
2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry.
Person:Alan Ruttenberg
Person:Bjoern Peters
Person:Melanie Courtot
assigning a CRID
assigning a centrally registered identifier
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.
A planned process in which a CRID registry associates an information content entity with a CRID symbol
PERSON:Alan Ruttenberg
associating information with a CRID in the CRID registry
associating information with a centrally registered identifier in its registry
a planned process with the objective to establish a system that allows to refer to specific entities of a certain kind and store information about them, by establishing a CRID registry and plan specifications for the process of 1) assigning a CRID and 2) looking up a CRID.
MC, 20101124: deprecated following discussion at IAO call 20101124. Term was deemed not necessary - no use case for now.
obsolete_establishing a CRID registry
true
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.
A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.
PERSON: Alan Ruttenberg
PERSON: Bill Hogan
PERSON: Bjoern Peters
PERSON: Melanie Courtot
CRID symbol
Original proposal from Bjoern, discussions at IAO calls
centrally registered identifier symbol
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.
An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs.
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').
Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation.
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.
PERSON: Alan Ruttenberg
PERSON: Bill Hogan
PERSON: Bjoern Peters
PERSON: Melanie Courtot
CRID
Original proposal from Bjoern, discussions at IAO calls
centrally registered identifier
PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles.
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.
PERSON: Alan Ruttenberg
PERSON: Bill Hogan
PERSON: Bjoern Peters
PERSON: Melanie Courtot
CRID registry
Original proposal from Bjoern, discussions at IAO calls
centrally registered identifier registry
Going to the PubMed website and entering a PubMed ID in order to retrieve the Pubmed information associated with that ID.
A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol
PERSON: Alan Ruttenberg
PERSON: Bill Hogan
PERSON: Bjoern Peters
PERSON: Melanie Courtot
looking up a CRID
looking up a centrally registered identifier
time stamped measurement datum
pmid:20604925 - time-lapse live cell microscopy
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.
Alan Ruttenberg
experimental time series
time sampled measurement data set
written name
"Bill Clinton"
"The Eiffel Tower"
"United States of America"
A textual entity that denotes a particular in reality.
PERSON: Bill Hogan
https://github.com/information-artifact-ontology/IAO/issues/114
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.
written name
A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task.
PERSON: Melanie Courtot
PERSON: Michel Dumontier
https://github.com/information-artifact-ontology/IAO/issues/80
software method
A software module is software composed of a collection of software methods.
PERSON: Melanei Courtot
PERSON: Michel Dumontier
https://github.com/information-artifact-ontology/IAO/issues/80
software module
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.
PERSON: Melanie Courtot
PERSON: Michel Dumontier
https://github.com/information-artifact-ontology/IAO/issues/80
software library
A software application is software that can be directly executed by some processing unit.
PERSON: Melanie Courtot
PERSON: Michel Dumontier
https://github.com/information-artifact-ontology/IAO/issues/80
software application
A software script is software whose instructions can be executed using a software interpreter.
PERSON: Melanie Courtot
PERSON: Michel Dumontier
https://github.com/information-artifact-ontology/IAO/issues/80
software script
abbreviation textual entity
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.
A textual entity listing abbreviations and their expansions that are used in a document.
PERSON: Bill Baumgartner
abbreviation textual entity
abbreviations section
The section labelled 'abbreviations' in a typical scientific journal article.
A part of a document where abbreviations and their long-forms used within the document are listed.
PERSON: Bill Baumgartner
abbreviation and acronyms
abbreviation list
abbreviations
abbreviations and acronyms
abbreviations list
abbreviations used
definitions for abbreviations
list of abbreviations
list of abbreviations used
non-standard abbreviations
nonstandard abbreviations
nonstandard abbreviations and acronyms
abbreviations section
author information section
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/)
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.
PERSON: Bill Baumgartner
author information
authors’ information
biographies
contributor information
author information section
author information textual entity
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.
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.
PERSON: Bill Baumgartner
author information textual entity
author summary section
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/)
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.
PERSON: Bill Baumgartner
author summary
summary
synopsis
Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines)
author summary section
author summary textual entity
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.
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).
PERSON: Bill Baumgartner
Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines).
author summary textual entity
availability section
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/).
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.
PERSON: Bill Baumgartner
availability
availability of data
data archiving
data availability
data availability statement
data sharing statement
availability section
availability textual entity
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
A textual entity expressing the location of a resource, e.g. software, or the manner in which a resource can be obtained.
PERSON: Bill Baumgartner
availability textual entity
case report section
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/)
A part of a document about the medical history of a specific patient as it relates to the topic of the document.
PERSON: Bill Baumgartner
case presentation
case report
case report section
case report textual entity
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.
A textual entity that expresses a detailed account of a portion of the medical history for a specific patient.
PERSON: Bill Baumgartner
case report textual entity
conclusion section
The section labelled 'conclusion' in a typical scientific journal article.
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.
PERSON: Bill Baumgartner
concluding remarks
conclusion
conclusions
findings
summary
conclusion section
conflict of interest section
The section labelled 'conflict of interest statement' in a typical scientific journal article.
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.
PERSON: Bill Baumgartner
authors' disclosures of potential conflicts of interest
competing financial interests
competing interests
conflict of interest
conflict of interest statement
conflict of interests
conflicts of interest
declaration of competing interest
declaration of competing interests
declaration of interest
declaration of interests
disclosure of conflict of interest
disclosure of potential conflicts of interest
duality of interest
statement of interest
conflict of interest section
conflict of interest statement
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/)]
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.
PERSON: Bill Baumgartner
conflict of interest textual entity
consent section
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/)
A part of a document about the consent process that was used to enroll patients in a study.
PERSON: Bill Baumgartner
consent
consent section
consent textual entity
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.
A textual entity that documents the consenting process used to enroll patients in a study.
PERSON: Bill Baumgartner
consent textual entity
ethical approval section
The section labelled 'ethical approval' in a typical scientific journal article.
A part of a document about the governance body responsible for approving the work discussed in a document on an ethical basis.
PERSON: Bill Baumgartner
ethical approval
ethical requirements
ethics
ethics statement
ethical approval section
ethical approval textual entity
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.
A textual entity that documents the ethical approval of some study design.
PERSON: Bill Baumgartner
ethical approval textual entity
figures section
The section labelled 'figures' in a typical scientific journal article.
A part of a document that contains one or more figures.
PERSON: Bill Baumgartner
figures
figures section
funding source declaration section
The section labelled 'funding' in a typical scientific journal article.
A part of a document used to detail information regarding the source of funding used in support of the generation of the document content.
PERSON: Bill Baumgartner
financial support
funding
funding information
funding sources
funding statement
funding/support
grants
role of the funding source
source of funding
sources of funding
study funding
funding source declaration section
funding souce declaration textual entity
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.
A textual entity documenting the source of funding that supported some study.
PERSON: Bill Baumgartner
funding source declaration textual entity
future directions section
The section labelled 'future directions' in a typical scientific journal article.
A part of a document detailing extensions of the described work that may be implemented at some future point in time.
PERSON: Bill Baumgartner
future challenges
future considerations
future developments
future directions
future outlook
future perspectives
future plans
future prospects
future research
future research directions
future studies
future work
outlook
future directions section
future directions textual entity
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.
A textual entity expressing ideas regarding future work relevant to work described in a document that could be done.
PERSON: Bill Baumgartner
future directions textual entity
genome announcement section
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/)
A document part announcing the publication of a novel draft genome sequence.
PERSON: Bill Baumgartner
genome announcement
genome announcement section
genome announcement textual entity
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).
A textual entity that describes the generation and public release of a novel, draft genome sequence.
PERSON: Bill Baumgartner
genome announcement textual entity
keyword textual entity
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.
A textual entity listing keywords indicating the major theme(s) of a document.
PERSON: Bill Baumgartner
keyword textual entity
keywords section
The section labelled 'keywords' in a typical scientific journal article.
A part of a document where keywords selected by the author to categorize the major theme(s) of a document are listed.
PERSON: Bill Baumgartner
keywords
keywords section
study limitations section
The section labelled 'limitations' in a typical scientific journal article.
A part of a document about biases or short comings related to the study design and execution.
PERSON: Bill Baumgartner
limitations
study limitations
Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html)
study limitations section
study limitations textual entity
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.
A textual entity addressing a shortcoming or bias of a study design or execution.
PERSON: Bill Baumgartner
Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html)
study limitations textual entity
materials section
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/)
A part of a document about the materials required to reproduce the content of the document.
PERSON: Bill Baumgartner
materials
materials section
notes section
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/):
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.
PERSON: Bill Baumgartner
notes
notes section
patients section
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/)
A part of a document about the patients that participated in a study.
PERSON: Bill Baumgartner
patients section
patients textual entity
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.
A textual entity expressing information regarding the patients used in a study.
PERSON: Bill Baumgartner
patients textual entity
pre-publication history section
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/)
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.
PERSON: Bill Baumgartner
notice of republication
pre-publication history
pre-publication history section
pre-publication history textual entity
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
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.
PERSON: Bill Baumgartner
pre-publication history textual entity
related work section
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/)
A part of a document about work in other publications that is relevant to the content of the document.
PERSON: Bill Baumgartner
related literature
related work
related work section
related work textual entity
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).
A textual entity that discusses work from other publications and expresses their relevancy to the content of a document.
PERSON: Bill Baumgartner
related work textual entity
requirements section
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/).
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.
PERSON: Bill Baumgartner
requirements
requirements section
requirements textual entity
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
A textual entity that expresses the requirements necessary to use a resource, e.g. software.
PERSON: Bill Baumgartner
requirements textual entity
statistical analysis textual entity
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.
A textual entity documenting statistical analysis tools and techniques employed.
PERSON: Bill Baumgartner
statistical analysis textual entity
statistical analysis section
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/)
A part of the document used to describe the statistical methodologies employed in the work presented in the document.
PERSON: Bill Baumgartner
statistical analysis
statistical analysis section
tables section
The section labelled 'tables' in a typical scientific journal article.
A part of a document that contains one or more tables.
PERSON: Bill Baumgartner
tables
tables section
An identifier that denotes some postal delivery route, some aggregate of postal delivery routes or a geographical region and was created for the purpose of sorting and delivering mail.
Mathias Brochhausen
postal code
A plan specification that if realized, is realized by the delivery of mail to some facility or mailbox within some geographical region.
Mathias Brochhausen
Postal delivery route
A postal code that is used in the United States for the purpose of sorting and delivering mail, and that denotes some postal delivery route or some aggregate of postal delivery routes.
Mathias Brochhausen
ZIP code
zone improvement plan code
database extract, transform, and load process
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.
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
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.
PERSON:Alan Ruttenberg
ETL
WEB:https://en.wikipedia.org/wiki/Extract,_transform,_load
database extract, transform, and load process
descriptive data section
A document part that lists and defines data variables, describes data characteristics (e.g. missing data information) and any assumptions and simplifications made.
PERSON: Chen Yang
PERSON: Jie Zheng
https://www.equator-network.org/reporting-guidelines/prisma/
ONE ontology
descriptive data section
additional results section
A results section that reports analyses other than main results of the study (e.g. subgroups analyses, adjusted analyses, sensitivity analyses, etc.)
PERSON: Chen Yang
PERSON: Jie Zheng
https://www.equator-network.org/reporting-guidelines/consort/
https://www.equator-network.org/reporting-guidelines/prisma/
https://www.equator-network.org/reporting-guidelines/strobe/
ONE ontology
additional results section
research participants section
A document part that describes human subject(s) that participated in a study (e.g. inclusion & exclusion criteria, recruitment methods, reasons for non-participation, grouping and randomisation, methods of follow-up, etc.).
PERSON: Chen Yang
PERSON: Jie Zheng
https://www.equator-network.org/reporting-guidelines/consort/
https://www.equator-network.org/reporting-guidelines/prisma/
https://www.equator-network.org/reporting-guidelines/strobe-nut/
ONE ontology
research participants section
measurement methods section
A methods section that describes details of data assessment methods (data measurement).
PERSON: Chen Yang
PERSON: Jie Zheng
https://www.equator-network.org/reporting-guidelines/strobe/
ONE ontology
measurement methods section
research settings section
A document part that describes the physical/social/cultural conditions around a research trial.
PERSON: Chen Yang
PERSON: Jie Zheng
https://www.ncbi.nlm.nih.gov/books/NBK262175/
ONE ontology
research settings section
study bias section
A study limitations section that describes systematic error introduced into sampling or testing by selecting or encouraging one outcome or answer over others.
PERSON: Chen Yang
PERSON: Jie Zheng
DOI: 10.1097/PRS.0b013e3181de24bc
ONE ontology
study bias section
graphical abstract
An abstract that is pictorial summary of the main findings described in the document.
PERSON: Jie Zheng
PERSON: Tim Beck
visual abstract
https://www.elsevier.com/authors/journal-authors/graphical-abstract
Biomedical literature NLP project
graphical abstract
identifier
An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.
Mathias Brochhausen
proper name
Mathias Brochhausen
Sep 29, 2016: The current definition has been amended from the previous version: "A proper name is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity." to more accuratly reflect the necessary and sufficient condition on the class. (MB)
identifier
alphabetic letters, Chinese characters, numerical digits, punctuation marks, and the individual symbols of any of the world's writing systems
A grapheme is an information content entity that is a fundamental unit in a written language.
http://en.wikipedia.org/wiki/Grapheme
Mathias Brochhausen
grapheme
An utterance is an information content entity that is a complete unit of speech in spoken language.
Mathias Brochhausen
Wikipedia: http://en.wikipedia.org/wiki/Utterance
Mathias Brochhausen
utterance
An attributive collection of qualities inhering in energy when transported through a medium in a wave.
Mathias Brochhausen
mechanical wave quality
is a quality that is the concretization of graphemes and inheres in a material object.
Mathias Brochhausen
Mathias Brochhausen
writing quality
pieces of paper, tables, walls, floors, driveways, highway signs, computer screens, skin, tablets of clay, rocks, sheets of metal (license plates), sheets of papyrus, etc. clouds of smoke in skywriting,
is a material information bearer that bears the concretization of graphemes.
Mathias Brochhausen
Mathias Brochhausen
writing bearer
portion of energy
Energy that is transported in a sound wave.
Mathias Brochhausen
sound energy
Sound energy bearing the concretization of an utterance and being the output of an uttering process.
utterance energy
Oscillating is a processual that shows repetitive variation, typically in time, of some measured quality about a central value (often a point of equilibrium) or between two or more different states.
http://en.wikipedia.org/wiki/Oscillation
Mathias Brochhausen
oscillating
A dubbing process is a planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity.
Mathias Brochhausen
Mathias Brochhausen
dubbing process
is a planned process of making speech sounds which may or may not have an actual language involved.
Mathias Brochhausen
http://en.wiktionary.org/wiki/utter
Mathias Brochhausen
utterance process
A personal name is a proper name identifying an individual person.
Mathias Brochhausen
http://en.wikipedia.org/wiki/Personal_name
Personal names "today usually comprises a given name bestowed at birth or at a young age plus a surname. It is nearly universal for a human to have a name; except in rare cases, for example feral children growing up in isolation, or infants orphaned by natural disaster for whom no written record survives.[citation needed] The Convention on the Rights of the Child specifies that a child has the right from birth to a name. Certain isolated tribes, such as the Machiguenga of the Amazon, also lack personal names." (http://en.wikipedia.org/wiki/Personal_name)
Sep 29, 2016: The comment that including the wikipedia definition of personal name is not to be interpreted in a way that restricts this class to only contain strings of letters. A numerical or alphanumerical identifier that denotes a human is being is a personal name, too. (MB)
personal name
A given name, in Western contexts often referred to as a first name, is a personal name that specifies and differentiates between members of a group of individuals, especially in a family, all of whose members usually share the same family name (surname). A given name is purposefully given, usually by a child's parents at or near birth, in contrast to an inherited one such as a family name
Mathias Brochhausen
http://en.wikipedia.org/wiki/Given_name
given name
A family name (in Western contexts often referred to as a surname or last name) is typically a part of a person's name which has been passed, according to law or custom, from one or both parents to their children.
Mathias Brochhausen
http://en.wikipedia.org/wiki/Family_name
family name
A document that is a collection of identifiers that has been created to identify and annotate core ideas of a specified domain, and where the intention of its creators is that the identifiers have a one-to-one correspondence with entities in reality outside the aggregate.
Mathias Brochhausen
code system
codeset
coding system
controlled vocabulary
Clint Dowland
Matt Diller
Sarah Bost
William R. Hogan
Does not imply absence vs. presence of any taxonomy.
Does not imply that identifiers denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities (e.g., SNOMED and even various OBO ontologies have identifiers that identify entities in all three categories).
Each identifier is often (but not necessarily) associated with a text string—variously called a “description,” “name,” “title,” or “label”—that helps humans reach the target of denotation.
When there is no such string, it is almost always because the identifiers take the form of human language words. For example, a “sex” or “gender” code set could have identifiers “MALE” and “FEMALE,” or even “M” and “F” (by convention, we understand what these mean).
For National Drug Codes (NDCs) and similar code sets, there doesn’t even have to be a single, fully-concretized copy somewhere (for example, for NDCs there is no centralized database or repository where they all live as one instance of concretization of code set). The code set can be “distributively” concretized. This seems like an unusual exception, but it also likely applies to Universal Product Codes (UPCs) and their follow on Global Trade Item Numbers (GTINs).
For each given domain, there can potentially exist multiple code sets. The multiplicity of code sets is partially due to the different specific purposes of those code sets.
Many code sets are created for a specific purpose in addition to merely identifying and annotating core ideas of a specified domain.
The identifiers do not denote each other.
code set
A document that denotes some identity and is concretized by the bearer of some credential role.
Amanda Hicks
identity document
A documented identity is the aggregate of all data items about an entity. Notice that a documented identity is not itself a document since a document is intended to be understood as a whole and data items about an individual are usually scattered across different documents.
Amanda Hicks
is an aggregate of ICEs also an ICE? yes
Is part_of the appropriate relation to use for data items and documented identities?
documented identity
I order a beer and the bartender authenticates my age by looking at my DOB on my driver's license. I sign into my email account, and the system authenticates my permission to read the email by checking the password I enter against my password listed in the database.
Authentication is the act of checking or verifying an identity claim (that is either tacit or explicit).
Amanda Hicks
authentication
A role that inheres in a concretization of an identity document and is realized by an authentication process.
Amanda Hicks
credential role
obligor role
Sam's obligor role realized by him taking Nigel to lunch after promising to do so; Sarah's obligor role realized by paying the purchase price to Layla after signing the contract specifying that she is buying a piece of land from Layla.
A role that is the specified output of an obligation generating social act and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements.
Mathias Brochhausen
Sarah Bost
obligor role
obligee role
Nigel's obligee role realized by Sam taking him out for lunch after Sam so promised; Layla's obligee role realized by receiving the money after signing a contract in which Sarah obtained a piece of land in exchange for a specified sum of money.
A role that is the specified output of an obligation generating social act and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements.
Mathias Brochhausen
Sarah Bost
obligee role
Tammy's owner role with regards to the house on 234 Evergreen Terrace; Walter's owner role with regards to the intellectual property on his movie script
A role in a human social process that is based on a social act and whose bearer exercises exclusive control over a property, where this control is permitted by one or more deontic roles, which are parts of the owner role.
Mathias Brochhausen
OBIB/ICO community
https://github.com/d-acts/d-acts/issues/29
owner role
obsolete_claim
true
my filling in an immigration form, a judge's signing and stamping a court order
A deontic declaration creating or revoking a deontic role by lawfully manipulating (signing, stamping, publishing) a document.
Mathias Brochhausen
deontic document act
my filling in an immigration form, a judge's signing and stamping a court order
A social act creating, revoking or transferring a socio-legal generically dependent continuant or a role by validating (signing, stamping, publishing) a document.
Mathias Brochhausen
obsolete_document act
true
Colonel Klink giving Sergeant Schultz an order, Jake promising Jill to take her to the junior prom
A planned process that is carried out by a conscious being or an organization, and is self-generated, directed towards another conscious being or an aggregate of conscious beings, an organization or an aggregate of organizations, and that is in need of being perceived.
Mathias Brochhausen
The phrase "in need of being perceived" does not imply that only planned processes that are in fact perceived can be social acts. Reinach clarifies that by exemplifying these matters for commands: "The command is according to its essence in need of being heard (vernehmungsbedürtig". It can of course happen that commands are given without being heard. Then they fail to fulfil their purpose. They are like thrown spears which fall to the ground without hitting their target." (A. Reinach: The Apriori Foundations of the Civil Law." Edited by J. Crosby, Heusenstamm: ontos Verlag, 2012).
Reinach clearly does not imply that a command that does not fulfill its prupose would not be a command.
Thanks to W.R. Hogan for finding the Reinach quote.
social act
the claim of a piece of land, the obligation to pay rent to the owner of a rental property
Socio-legal generically dependent continuants are generically dependent continuants that come into existence through social acts and that if they get concretized are concretized as realizable entities.
Mathias Brochhausen
obsolete_socio-legal generically dependent continuant
true
deontic declaration
my consenting verbally to buy a used TV set for $ 500, John Robie's taking of Mrs. Steven's jewels, Jane Doe's revoking of informed consent over the phone, John Doe signing an employment contract.
A social act that brings about, transfers or revokes a socio-legal generically dependent continuant or brings about or transforms a role. Declarations do not depend on words spoken or written, but sometimes are merely actions, for instance the signing of a document.
Mathias Brochhausen
declaration
status function declaration
obsolete_deontic declaration
true
A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements.
Mathias Brochhausen
obsolete obligee role
true
A document that is intended to be the specified input in a document act. It has a plan specification as a part that specifies the intended socio-legal entities that are created through the document (objective specification) and the way in which the document act is to be performed (by signing, by stamping, etc.) (action specification).
Mathias Brochhausen
document act input document
A role that inheres in an agent and which is externally grounded in the normative expectations that other agents within a social context have concerning how that agent should behave.
Mathias Brochhausen
Neil Otte
deontic role
A social act that creates or revokes a deontic role.
Mathias Brochhausen
deontic declaration
obsolete_obligation
true
The role borne by a human being, an organization or an aggregate of either of both that is realized by being the active participant in a declaration.
Mathias Brochhausen
obsolete_declaration executive role
true
the role borne by the US Citizen and Immigration Service realized by providing the template form for entering the US as a non-resident alien, the role of a guideline committee in putting together a clinical guideline
The role of a human being or an aggregate of human beings preparing the initial document to undergo a document act, thus creating a socio-legal generically dependent continuant.
Mathias Brochhausen
not that the "template" does not need to be a template at all. It can be a document that is getting stamped and signed and by these acts creating some socio-legal generically dependent continuants.
obsolete_document template creator role
true
The role of a human being or an aggregate of human beings concretizing a claim.
Mathias Brochhausen
obsolete_claimant role
true
The role of a human being or an aggregate of human beings concretizing an obligation.
Mathias Brochhausen
obsolete_obligator role
true
me as a bearer of a spouse role, which participates in a document act, John Doe as bearer of a debtor role, which participates in a document act
The human being or organization or aggregate of any of the aforementioned that is the bearer of a concretization of a socio-legal generically dependent continuant brought about by or transferred in a specific document act.
Mathias Brochhausen
obsolete_declaration target
true
The role of the U.S. Citizenship and Immigration Service realized by the creation of an immigration form that is being filled in, the role of a national professional association realized by the creation of a clinical guideline that is to be certified
A role that inheres in a human being or organization or aggregate of any of the aforementioned that prepares a document that is the specified input to a document act and is the input document of a document act.
Mathias Brochhausen
document act template creator role
A role inhering in a human being or an organization or an aggregate of any of the aforementioned that is realized by the bearer being the agent in a declaration.
Mathias Brochhausen
declaration performer role
deontic declaration performer role
The human being or organization or aggregate of any of the aforementioned that is the bearer of a concretization of a socio-legal generically dependent continuant brought about by or transferred in a specific document act.
Mathias Brochhausen
obsoleted_document act target
true
a judge's role of signing a court order
A role inhering in a human being or an organization or an aggregate of any of the aforementioned that is realized by the bearer being the agent in a document act.
Mathias Brochhausen
document act performer role
A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements.
Sarah Bost
obsolete_obligee role
true
A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements.
Sarah Bost
obsolete_obligor role
true
A social act that postulates a socio-legal fact for a specified group of people or organizations.
Mathias Brochhausen
enactment
standing declaration
A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements.
John Judkins
Mathias Brochhausen
obsolete obligor role
true
ontology module
I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it.
ontology file
This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology.
ontology module
base ontology module
An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies.
base ontology module
editors ontology module
An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users.
source ontology module
editors ontology module
main release ontology module
An ontology module that is intended to be the primary release product and the one consumed by the majority of tools.
TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module
main release ontology module
bridge ontology module
An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module.
bridge ontology module
import ontology module
A subset ontology module that is intended to be imported from another ontology.
TODO: add axioms that indicate this is the output of a module extraction process.
import file
import ontology module
subset ontology module
An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms.
ontology slim
subset ontology
subset ontology module
curation subset ontology module
A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation.
curation subset ontology module
analysis ontology module
An ontology module that is intended for usage in analysis or discovery applications.
analysis subset ontology module
single layer ontology module
A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint.
ribbon subset
single layer subset ontology module
exclusion subset ontology module
A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes.
antislim
exclusion subset ontology module
external import ontology module
An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach.
external import
external import ontology module
species subset ontology module
A subset ontology that is crafted to either include or exclude a taxonomic grouping of species.
taxon subset
species subset ontology module
reasoned ontology module
An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available.
reasoned ontology module
generated ontology module
An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV.
TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process
generated ontology module
template generated ontology module
An ontology module that is automatically generated from a template specification and fillers for slots in that template.
template generated ontology module
taxonomic bridge ontology module
taxonomic bridge ontology module
ontology module subsetted by expressivity
ontology module subsetted by expressivity
obo basic subset ontology module
A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools.
Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses).
An ontology is OBO Basic if and only if it has the following characteristics:
DAG
Unidirectional
No Dangling Clauses
Fully Asserted
Fully Labeled
No equivalence axioms
Singly labeled edges
No qualifier lists
No disjointness axioms
No owl-axioms header
No imports
obo basic subset ontology module
ontology module subsetted by OWL profile
ontology module subsetted by OWL profile
EL++ ontology module
EL++ ontology module
Homo sapiens
human being
Homo sapiens
obsolete Systematized Nomenclature of Medicine
true
medical intervention is a planned process that has the goal of diagnosing, preventing or relieving illness or injury.
The act of intervening, interfering or interceding with the intent of modifying the outcome. In medicine, an intervention is usually undertaken to help treat or cure a condition. For example, "Acupuncture as a therapeutic intervention is widely practiced in the United States,"
Reference:
http://www.medterms.com/script/main/art.asp?articlekey=34214 . Some interventions can be used for diagnosis.
YH
WEB: http://wiki.answers.com/Q/What_is_medical_intervention
medical intervention
Surgery is a medical procedure that uses operative manual and instrumental techniques on a patient to investigate and/or treat a pathological condition such as disease or injury, to help improve bodily function or appearance. The key difference between a surgery and a general procedure is the need for an incision. Making an incision, or cutting into the skin to gain access to the body’s deeper tissues or organs, is a defining characteristic of surgery.
YH, SS
surgical procedure
WEB: http://en.wikipedia.org/wiki/Surgery
WEB: http://www.wisegeekhealth.com/what-is-the-difference-between-a-surgery-and-a-procedure.htm
10042609
surgery
a medical intervention that refers to any series of pre-defined steps that should be followed to achieve a desired result.
YH, SS
WEB: http://www.wisegeekhealth.com/what-is-the-difference-between-a-surgery-and-a-procedure.htm
medical procedure
planned process
planned process
Injecting mice with a vaccine in order to test its efficacy
A process that realizes a plan which is the concretization of a plan specification.
A processual entity that realizes a plan which is the concretization of a plan specification.
'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some
objectives is a planned process.
Bjoern Peters
branch derived
6/11/9: Edited at workshop. Used to include: is initiated by an agent
This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
planned process
investigation
a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
investigation
organization
PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based:
1) there are organization_member_roles (president, treasurer, branch
editor), with individual persons as bearers
2) there are organization_roles (employer, owner, vendor, patent holder)
3) an organization has a charter / rules / bylaws, which specify what roles
there are, how they should be realized, and how to modify the
charter/rules/bylaws themselves.
It is debatable what the organization itself is (some kind of dependent
continuant or an aggregate of people). This also determines who/what the
bearer of organization_roles' are. My personal favorite is still to define
organization as a kind of 'legal entity', but thinking it through leads to
all kinds of questions that are clearly outside the scope of OBI.
Interestingly enough, it does not seem to matter much where we place
organization itself, as long as we can subclass it (University, Corporation,
Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO,
W3C, University of Oklahoma), and have it play roles.
This leads to my proposal: We define organization through the statements 1 -
3 above, but without an 'is a' statement for now. We can leave it in its
current place in the is_a hierarchy (material entity) or move it up to
'continuant'. We leave further clarifications to BFO, and close this issue
for now.
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
PERSON: Philippe Rocca-Serra
PERSON: Susanna Sansone
GROUP: OBI
organization
study design execution
a planned process that carries out a study design
study design execution
organism
animal
fungus
plant
virus
A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
13-02-2009:
OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus.
This issue is outside the scope of OBI.
GROUP: OBI Biomaterial Branch
WEB: http://en.wikipedia.org/wiki/Organism
organism
data transformation
The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
A planned process that produces output data from input data.
Elisabetta Manduchi
Helen Parkinson
James Malone
Melanie Courtot
Philippe Rocca-Serra
Richard Scheuermann
Ryan Brinkman
Tina Hernandez-Boussard
data analysis
data processing
Branch editors
data transformation
study design
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.
study design
dialysis
the use of a dialysis bag of select pore size to remove salt from collagen isolated from mouse cartilage
a protocol application that uses diffusion through a semi-permeable membrane to separate an input material into two fractions of different composition
PERSON:Kevin Clancy
OBI branch derived
dialysis
A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
Albert Goldfain
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
creation date: 2009-06-23T11:21:20Z
https://github.com/OGMS/ogms/releases/tag/v2019-04-30
disease
The representation of a conclusion of a diagnostic process.
Albert Goldfain
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
creation date: 2009-06-23T12:42:23Z
https://github.com/OGMS/ogms/releases/tag/v2019-04-30
diagnosis
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
Albert Goldfain
Sagar Jain
http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6
creation date: 2011-02-21T09:57:44Z
editor date: 2017-04-18
https://github.com/OGMS/ogms/releases/tag/v2019-04-30
health care process
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
Albert Goldfain
http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6
creation date: 2011-02-21T09:57:44Z
health care encounter
TODO
Albert Goldfain
http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6
creation date: 2011-02-21T09:57:44Z
https://github.com/OGMS/ogms/releases/tag/v2019-04-30
outpatient encounter
TODO
Albert Goldfain
http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6
creation date: 2011-02-21T09:57:44Z
https://github.com/OGMS/ogms/releases/tag/v2019-04-30
inpatient encounter
A disorder that involves some structural damage that is immediately caused by a catastrophic external force.
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.
Albert Goldfain
Sagar Jain
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
creation date: 2011-09-20T09:57:44Z
edited date: 30 SEPT 2015
injury
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).
Albert Goldfain
http://groups.google.com/group/ogms-discuss/browse_thread/thread/2a7008f311fac766/e7de486c94dfd82e
creation date: 2011-09-20T09:57:44Z
https://github.com/OGMS/ogms/releases/tag/v2019-04-30
diagnostic process
a data item that is about a patient and is the specified output of a health care process assay or diagnostic process
creation date: 2018-11-27
https://github.com/OGMS/ogms/releases/tag/v2019-04-30
clinical data item
A data item that contains the outcome of a survey.
Alice Nzinga
Mathias Brochhausen
survey data
A plan specification that is realized by process of gathering information (e.g. by asking questions).
Alice Nzinga
Mathias Brochhausen
survey plan specification
A planned process that realizes the concretization of a survey to generate an output(survey data.)
survey execution
Social Security Number(SSN) is a Centrally Registered IDentifier that is a nine-digit number issued to U.S. citizens, permanent residents, and temporary (working) residents under section 205(c) of the Social Security Act, codified as 42 U.S.C. § 405(c). The number is issued to an individual by the Social Security Administration, an independent agency of the United States government. Its primary purpose is to track individuals for Social Security purposes.
SSN
http://en.wikipedia.org/wiki/Social_Security_number
Cheng Chen(cxchen1@ualr.edu)
social security number
A social role inhering in a human being.
Mathias Brochhausen
William R. Hogan
human social role
party to a legal entity
party to a legal proceeding
party to a legal agreement
party to a marriage contract
party to a power of attorney
A human social role borne by a human being being realized in behaviour which is considered socially appropriate for individuals of a specific sex in the context of a specific culture.
Mathias Brochhausen
http://en.wikipedia.org/wiki/Gender_role
gender role
A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the male sex in the context of the culture in question.
Mathias Brochhausen
male gender
male gender role
A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the female sex in the context of the culture in question.
Mathias Brochhausen
female gender
female gender role
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.
William R. Hogan
health care role
Mathias Brochhausen
human health care role
A role borne by an organism and that is realized by presenting to a health care provider in a clinical encounter.
Amanda Hicks
Mathias Brochhausen
patient
CAFE domain expert working group.
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.
patient role
A human health care role inhering in an organization or human being that is realized by a process of providing health care services to an organism.
Mathias Brochhausen
William R. Hogan
health care provider role
A health care role borne by a human being and realized by promoting, maintaining or restoring human health through the study, diagnosis, and treatment of disease, injury and other physical and mental impairments.
Mathias Brochhausen
physician
http://en.wikipedia.org/wiki/Physician
physician role
A health care role borne by a human being and realized by the care of individuals, families, and communities so they may attain, maintain, or recover optimal health and quality of life.
Mathias Brochhausen
nurse
based on: http://en.wikipedia.org/wiki/Nursing
nurse role
A role that inheres in an organization and that is realized by the providing of services in a health care encounter.
Mathias Brochhausen
Amanda Hicks
health care provider organization role
person health care provider role
2
A health care provider organization role that inheres in an organization consisting of two or more physicians.
Amanda Hicks
physician practice
A role borne by an organization and realized by providing healthcare services by healthcare professionals of multiple different disciplines of medicine and enabling stationary treatment.
Mathias Brochhausen
hospital
obsolete_hospital role
true
A health care provider organization role that inheres in an organization that is comprised of other organizations.
Amanda Hicks
integrated delivery network
An object aggregate of objectual organisms.
http://purl.obolibrary.org/obo/omrse.owl
Any arbitrary collection of organisms. They need not be of the same taxonomic class.
aggregate of objectual organisms
An object aggregate all of whose components are human beings.
http://purl.obolibrary.org/obo/omrse.owl
collection of humans
A role inhering in an entity realized by social interactions in human society.
Mathias Brochhausen
http://purl.obolibrary.org/obo/omrse.owl
Previous definition: A role played by an entity in human social processes.
role in human social processes
A role in human social processes that inheres in an organization.
William R. Hogan
Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist.
Ditto for its current descendants.
organization social role
A role in human social processes that inheres in an organism.
William R. Hogan
Mathias Brochhausen
Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist.
Ditto for its current descendants.
Includes animals as well as humans. For example, pet, assistance animal, animal grown for food, work animal, domesticated animal, K-9, etc. Human roles include gender role, party to legal entities, health care provider roles like doctor, nurse, etc.
Previous definition: A role in human social processes played by an organism.
organism social role
An organization social role that, if realized, is realized by either a health care process or an ancillary health care process
Previous definition: An organization social role played by an organization in health care processes.
organization health care role
An organization that governs the people living in a particular geographical region or aggregate of geographical regions. The geographical region it governs can change over time (such as the westward expansion of the United States and the addition of Hawaii).
William R. Hogan
geopolitical organization
obsolete geopolitical organization
true
geopoli organization
obsolete geopoli organization
true
A patient role that inheres in a human being.
human patient role
A subnational entity that is the primary organizational member of a nation, is subject to the full set of laws of the nation, enjoys all the privileges established under the laws of the nation, is not a member of any other geopolitical entity, and itself governs a part of the geographical region governed by the nation.
major administrative subdivision
example: Northern Ireland
obsolete major administrative subdivision
true
A subnational entity that does not possess full political independence or sovereignty as a sovereign state, but remains politically outside of the controlling state and controls a geographical region that is outside the controlling state's integral region.
geopolitical dependency
Typically, the common feature is that the dependency does not conduct foreign affairs, and relegates this authority to the sovereign state. BUt otherwise, it is largely or completely autonomous relative to the administrative subdivisions. Examples include Puerto Rico (U.S.), Guam (U.S.), Greenland (Denmark), French Polynesia (France), and Falkland Islands (United Kingdom).
obsolete geopolitical dependency
true
2
An aggregate of organizations that have some feature in common, but is not itself an organization.
An object aggregate that is not itself an organization and whose members are only organizations that have some feature in common
William R. Hogan
William R. Hogan
Amanda Hicks
http://purl.obolibrary.org/obo/omrse.owl
It is often convenient to group organizations together that otherwise might not even interact with one another.
aggregate of organizations
An aggregate of sovereign states that share some feature in common, but is not an organization nor necessarily the outcome of some treaty among them.
An aggregate of geopoli organizations that is not itself a sovereign state and whose members are only sovereign states that have some feature in common
William R. Hogan
aggregate of sovereign states
obsolete aggregate of sovereign states
true
An object aggregate that is not itself a geopolitical organization and whose members are only geopolitical organizations that have some feature in common
Amanda Hicks
William R. Hogan
aggregate of geopoli organizations
obsolete aggregate of geopoli organizations
true
An aggregate of geopoli organizations that is not itself a geopolitical dependency and whose members are only geopolitical dependencies that have some feature in common.
Amanda Hicks
aggregate of dependencies
obsolete aggregate of dependencies
true
An aggregate of geopoli organizations that is not itself a major administrative subdivision and whose members are only major administrative subdivisions that have some feature in common
Amanda Hicks
aggregate of major administrative subdivisions
obsolete aggregate of major administrative subdivisions
true
A role borne by a human individual or by a collection of humans regarded as possessing rights and duties enforeable at law.
Mathias Brochhausen
Malcolm N. Shaw: International Law. Cambridge University Press, Cambridge, 2008.
We are aware of the fact that Wikipedia's definition differs from ours by saying that "Legal personality (...) is the characteristic of a non-living entity regarded by law to have the status of personhood" (http://en.wikipedia.org/wiki/Legal_personality)
However, Shaw explicates:
"In any legal system, certain entities, whether they be individuals or companies, will be regarded as possessing rights and duties enforceable at law. Thus an individual may prosecute or be prosecuted for assault and a company can sue for breach of contract. They are able to do this because the law recognises them as 'legal persons' possessing the capacity to have and to maintain certain rights, and being subject to perform specific duties. (...) In municipal law individuals, limited companies and public corporations are recognized as each possessing a distinct legal personality, the terms of which are circumscribed by the relevant legislation" (Shaw MN: International Law. Sixth Edition. Cambridge University Press, Cambridge, 2008). We hold that Shaw's position is ontological more prolific since it not only allows to explain how groups of individuals become recognized as unities at law, but also how different individuals can hold different legal personality roles (always against the context of one legal system). The latter will proof useful when dealing with the representing comatous patients or minorsat law in ontologies.
legal person role
A role that inheres in an organism and is realized by habitually smoking tobacco products.
smoker role
intravenous drug user
an intergovernmental organization that has at least three member states, that has activies in at least three states, and that is unified by some formal intergovernmental agreement
Amanda Hicks
intergovernmental organization
"IGOs are organizations whose memebers include at lesat three states, that have activities in several states, and whose members are held together by a formal intergovernmental agreement ... These organizations range in size from three members (North American Free Trade Argreement [NAFTA]) to more than 190 memembers (Universal Postal Union (UPU)]. Memebers may come from primarily one georgraphic regioni (Oragnaization of American States [OAS]) or from all geographic regions (World Bank). although soem IGOs are designed to achieve a single purpose (Organization of Petroleum exporting countries [OPEC]), others have been developed for multiple tasks (United Nations [UN}). ... IGOs are recognized subjects of international law with separate standing fromt heir member states." Karns and Mingst I(2004) p. 7
Katrina Donovan
examples:
North American Free Trade Argreement [NAFTA] , Universal Postal Union [UPU], Oragnaization of American States [OAS], World Bank), Organization of Petroleum exporting countries [OPEC] United Nations [UN[, The World Trade Organization [WTO], The World Health Organization [WHO], UNICEF
obsolete intergovernmental organization
true
a geopolitical organization that is voluntary and private, whose members are individual persons or organizations that come together to acheive a common purpose.
nongovernmental organizations
NGOs are private voluntary organizations whose members are individuals or associations that come together to acheive a common purpose. Some organizations are formed to advocate a particular cause such as human rights, peace, or envirnomental projetion. Others are established to provide services such as disaster relief, humantarian aid in war-torn socieities, or development assistance. ... National level groups are often called interest or pressure groups, and many of them are now linked to counterpart groups in other countries through transnational networks or federations. International NGOs, like IGOs, may draw their members from one region or several regions, and they may have very specific functions or be multi-functional.
Karns and Mingst (2004) p. 10f.
Katrina Donovan
Examples:
Internaltion Federation of Red Cross and Red Crescent Societies, Oxfam, CARE, Doctors Without Borders, World Wildlife Fund, Transparency International, Human Rights Watch, Amnesty International, and Save the Children.
obsolete nongovernmental organization
true
Amanda Hicks
private governance organizations
"Although the very meaning of the term is controversial, it involves authoritative decsionmaking in areas that once were part of national legal frameworks, the government, the sovereign state, or the public sector."
Karns and Mingst (2004) p. 14.
Katrina Donovan
Examples: private bond-rating agencies such as Moody's Investors Service, International Chamber of Commerce, Worldwide Responsible Apparel Manufacturing Principles, Forest Stewardship
obsolete private governance organizations
true
An organization that governs the people living in a particular geographical region or aggregate of geographical regions. The geographical region it governs can change over time (such as the westward expansion of the United States and the addition of Hawaii).
Note: this definition was taken over from "geopolitical organization".
Amanda Hicks
governmental organization
IMPORTANT: The label "geopolitical organization" was previously used for OMRSE_00000044 (governmental organization). "geopoli organization" is a label for a new and different class.
obsolete governmental organization
true
A governmental organization with a defined territory on which it exercises internal and external sovereignty, a permanent population, a government, and the capacity to enter into relations with other sovereign states.
William R. Hogan
nation
nation state
sovereign state
http://en.wikipedia.org/wiki/Sovereign_state
Per Wikipedia, the word 'nation' does not always refer to soverign states. For example, the "nation of Islam".
obsolete sovereign state
true
a governmental organization that has a local, regional, or territorial government that recognizes a sovereign state as its higher political authority
Amanda Hicks
William R. Hogan
subnational entity
obsolete subnational entity
true
Amanda Hicks
supranational entity
e.g., the EU
obsolete supranational entity
true
material entity role
organism role
Homo sapiens role
organization role
A function inhering in a material entity that, if realized, is realized by the material entity being the site at which inpatient and outpatient healthcare is provided to a patient population.
Mathias Brochhausen
hospital function
A function inhering in a material entity that, if realized, is realized by that material entity being the site at which formal education is provided to a student population.
Mathias Brochhausen
school function
A healthcare provider role that inheres in an organization and is realized by providing inpatient and outpatient care.
Mathias Brochhausen
hospital role
An organization social role that inheres in an organization and is realized by providing formal education to students.
Mathias Brochhausen
school role
An organization that is the bearer of a hospital role.
Mathias Brochhausen
hospital organization
An organization that is the bearer of a school role.
Mathias Brochhausen
school organization
A human social role that, if realized, is realized by the process of formal education that the bearer undergoes.
Mathias Brochhausen
student role
Mathias Brochhausen
nursery school role
Mathias Brochhausen
primary school role
A material entity that is a human made strcuture with firm connection between its foundation and the ground.
Mathias Brochhausen
http://de.wikipedia.org/wiki/Bauwerk
"Building" is a subclass of this.
This type of entity is referred to as "Bauwerk" or "Bauliche Anlage".
architectural structure
An architectural structure that bears some function.
Mathias Brochhausen
facility
09/09/2017
A health care facility that bears the function to provide acute and intensive healthcare services and that is run by a hospital organization and is the bearer of a hospital function.
Mathias Brochhausen
William Hogan
hospital facility
A facility that is run by a school organization and is the bearer of a school function.
Mathias Brochhausen
school facility
Mathias Brochhausen
secondary school role
A trauma patient role that inheres in a homo sapiens who is under the age of 15 years.
Amanda Hicks
pediatric trauma patient
The following definition for 'pediatric trauma patient' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015.
"A trauma patient who is under the age of 15 years."
pediatric trauma patient role
A patient role that inheres an organism suffering one or more injuries.
Amanda Hicks
injured patient
The following definition for 'injured patient' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015.
A patient suffering one or more injuries.
injured patient role
A patient role that inheres in an organism suffering a thermal, electrical, chemical or radiation burn.
Amanda Hicks
The following definition for 'burn patient' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015.
A patient suffering a thermal, electrical, chemical or radiation burn.
burn patient
burn patient role
A physician role that is created by training and certification in rehabilitation/physical medicine and that is realized by the provision of or supervising of the provision of rehabilitation or physical therapy to a patient.
Amanda Hicks
physiatrist
The following definition for 'physiatrist' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015.
A physician with training and certification in rehabilitation/physical medicine.
Definition updated May 5, 2016. Original definitions was, a health care role borne by a human being and realized by training and certification in rehabilitation medicine.
physiatrist role
A patient role that inheres in an organism with some non-superficial traumatic injury. The role is realized by admision to a hospital, transfer from one hospital to another for the purpose of trauma care, or has death as a result of the traumatic injury.
Amanda Hicks
trauma patient
The following definition for 'trauma patient' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015.
A patient sustaining an injury who has been admitted to the hospital, transferred from one hospital to another for the purpose of trauma care, or has died as a result of the traumatic injury.
trauma patient role
1
A material entity that has as parts one or more sites large enough to contain humans, has as part one or more material entities that separates it from other sites, and bears a residence function.
Amanda Hicks
https://github.com/ufbmi/OMRSE/wiki/Housing-unit-and-Household
Housing units are individuated by their residence functions.
housing unit
A function that inheres in a material entity and, if realized, is realized by protecting persons and their possessions from weather and by some person or group of persons habitually sleeping in at least one site that is contained by that material entity.
Amanda Hicks
residence function
A human or collection of humans that occupies a housing unit by storing their possessions there and habitually sleeping there thereby participating in the realization of that housing unit's residence function.
Amanda Hicks
Note in OMRSE it is the housing unit, not the people living there, that are the bearers of a "residence function". Note the distinction between being a residence and a resident.
Note that it is not possible in OWL 2, at least that we have yet found, to say that the housing unit in which the process occurs is the same one that is the bearer of the residence function (that the process realizes).
household
A role in human social processes that, if realized, is realized when the bearer provides labor or services in exchange for a wage or salary as specified by some deontic declaration.
Amanda hicks
employee
job role
Amanda Hicks
workplace facility
a function inhering in a material entity that, if realized, is realized by that material entity being the site where the work of some organization is carried out
Amanda Hicks
workplace function
A US Census householder role is a human social role that, if realized, is realized by that person being a member of a household and either owning or renting the housing unit in which that household resides and being designated as the householder. If there is only one member of the household who owns or rents the housing unit, that person is designated the householder by default.
Amanda Hicks
http://www.census.gov/cps/about/cpsdef.html
last accessed on June 30, 2015
US census householder role
A US cenus reference person role is a human social role that inheres in a Homo sapiens who is a member of a household and is realized by other persons in the household being recorded in the US census in relation to that person.
Amanda Hicks
http://www.census.gov/cps/about/cpsdef.html
last accessed June 30, 2015
US Census reference person role
An ethnic identity datum that is the output of an ethnic identification process that uses OMB terminology for ethnicity or terminology that is mapped the OMB ethnicity terms.
Amanda Hicks
OMB ethnic identity information content entity
obsolete OMB ethnic identity datum
true
enrollment end date
A role that concretizes a socio-lega generically dependent continuant
Amanda Hicks
obsolete socio-legal human social role
true
A human social role that is created by a deontic declaration performed by an organization.
Amanda Hicks
human organizational role
human role within an organization
a role in human social processes that is realized when the bearer provides a wage or salary in exchange for some labour or services as specified by some declaration
employer role
age measurement datum
A document that records a legally binding agreement between two or more parties.
A contract is a document that is the specified output of a legally binding document act and records a legally binding agreement between two or more parties.
contract
A contract by which one party secures the other against pecuniary loss by payment of a sum of money if a specified event occurs.
Amanda Hicks
indemnity contract
An indemnity contract that distributes risk among a group of people
Amanda Hicks
insurance policy
A role that inheres in an organism that is able to receive benefits from an insurance policy. The role, if realized, is realized by receiving benefits that are covered by the insurance policy.
Amanda Hicks
insured party role
An organization that secures a group of people against pecuniary loss by payment of a sum of money if a a specified event occurs.
Amanda Hicks
insurance company
An insured party role that inheres in a person who participates in the creation of the insurance contract and is eligible to receive benefits as specified by the insurance contract.
Amanda Hicks
policy holder role
payer role
party to an insurance policy
enrollment start date
A racial identity is an information content entity that is the output of some racial identitification process and is intended to be a truthful statement about the genetic or cultural race of a person. Unlike data items they are not necessilary contributed or acquired by a reliable method.
racial identity information content entity
obsolete racial identity datum
true
racial identification process
An ethnic identity datum is an information content entity that is the output of some ethnic identitification process and is intended to be a truthful statement about the cultural or national heritage of a person. Unlike data items they are not necessilary contributed or acquired by a reliable method.
Amanda Hicks
ethnic identity information content entity
obsolete ethnic identity datum
true
ethnic identification process
A facility bearing the function to provide healthcare and that is administered by a health care organization for the purpose of providing health care to a patient or patient population.
William Hogan
health care facility
A human social role that inheres in a human who is legally eligible to work, is conferred by the U.S. Census Bureau, and is realized by the bearer not working and either making active efforts to find employment in the four weeks prior to the reference week or waiting to be recalled from temporary layoff.
Amanda Hicks
US Census unemployed role
A health care facility that bears a function to provide healthcare to the sick or terminally ill
Amanda Hicks
Emma Norris
William Hogan
Human Behaviour Change Project
hospice facility
Amanda Hicks
skilled nursing facility
A facility to assist in physical or addiction recovery
Amanda Hicks
Emma Norris
William Hogan
Human Behaviour Change Project
rehabilitation facility
A facility that is run by a nursing home organization and is the bearer of a nursing home function.
Amanda Hicks
nursing home facility
A community living health care facility that provides health care services in a home-like setting
Amanda Hicks
William Hogan
residential health care facility
Amanda Hicks
overnight dialysis facility
A health care facility that bears a function to provide low intensity healthcare services to patients on a short-term basis, with patients leaving on the same date as arriving (i.e., without them staying overnight)
Amanda Hicks
Emma Norris
William Hogan
Human Behaviour Change Project
Broadened from treatment to healthcare services generally. "Low intensity" is not defined at the moment, but is needed to differentiate from same-day surgery centers or observation stays in hospitals that last <24 hours. The idea is that few invasive procedures are performed, and the ones that are invasive are not typically much worse than a blood draw. Maybe bone marrow biopsy is as aggressive as it gets. I wonder if hematologists do that on an outpatient basis.
outpatient clinic facility
Amanda Hicks
physician office facility
Amanda Hicks
ambulatory surgery facility
Amanda Hicks
urgent care facility
A health care facility that bears a function to provide emergency healthcare services and the acute care of patients who present without prior appointment, having arrived either by their own means or by ambulance
Amanda Hicks
Emma Norris
William Hogan
Adapted from Human Behaviour Change Project
emergency department facility
urgent care function
Amanda Hicks
ambulatory surgery function
hospice function
emergency department function
physician office function
outpatient clinic function
overnight dialysis function
rehabilitation function
skilled nursing function
residential function
nursing home function
A deontic document act that concludes an inpatient encounter.
Amanda Hicks
discharge process
patient discharge
An OMB ethnic identity datum that indicates the person identified is of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin regardless of race.
Amanda Hicks
OMB Hispanic or Latino identity information content entity
obsolete hispanic or latino identity datum
true
An OMB ethnic identity datum that indicates the person identified is not of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin regardless of race.
Amanda Hicks
OMB not Hispanic or Latino identity information content entity
obsolete not hispanic or latino identity datum
true
A human health care provider role that inheres in a human being that is created by state licensing and that is realized by taking patient histories, performing physical exams, diagnosing illnesses, developing treatment plans, ordering lab tests, prescribing medications, counselling and educating patients, suturing wounds, and assisting in surgery under the supervision of a physician or a surgeon.
US physician assistant role
A physician role that inheres a human being and, if it is realized, is realized either by administering medication for the temporary general or local suppression of sensory or motor nerve function during some health care encounter or by making decisions independently of a supervising physician regarding the adminstration of such medication.
anesthesiologist role
OMB racial identification process
An identity datum is an information content entity that is the output of some identitification process and is intended to be a truthful statement about a person's social identity. Unlike data items they are not necessilary contributed or acquired by a reliable method.
social identity information content entity
Amanda Hicks
obsolete identity datum
true
A gender identity is an information content entity that is the output of some gender identitification process and is intended to be a truthful statement about a person's subjective sense of their gender. Unlike data items they are not necessilary contributed or acquired by a reliable method.
gender identity information content entity
Amanda Hicks
obsolete gender identity datum
true
Amanda Hicks
identification process
gender identification process
a gender identity datum resulting from a gender identification process in which ‘female’ is selected based on the participant's subjective sense of gender
Amanda Hicks
female gender identity information content entity
obsolete female gender identity datum
true
surgeon role
A surgeon role realized by its bearer using performing neurosurgery.
neurosurgeon role
a gender identity datum resulting from a gender identification process in which ‘male’ is selected based on the participant's subjective sense of gender
Amanda Hicks
male gender identity information content entity
obsolete male gender identity datum
true
An information content entity that is about human travel.
https://github.com/ufbmi/OMRSE/issues/79
Jie Zheng
Amanda Hicks
human traveling information
A symbol that denotes a specific household
Jie Zheng
Amanda Hicks
household identifier
A symbol that denotes a family.
Jie Zheng
Amanda Hicks
family identifier
an identity datum that has been asserted by the person whom it is about
Amanda Hicks
obsolete self-identity data item
true
A planned process in which the bearer of an employer role provides wages or salary to the bearer of an employee roll in fullfillment of the arrangements specified in some declaration
employment process
A surgeon role borne by a human being and that, if realized, is realized by its bearer using operative manual and instrumental techniques on preadult patients to investigate and/or treat a pathological condition such as disease or injury, to help improve bodily function or appearance or to repair unwanted ruptured areas.
Amanda Hicks
pediatric surgeon role
a facility that is run by an adult foster home organization and is the bearer of an adult foster home organization
Amanda Hicks
adult foster home facility
adult foster home function
a health care facility that also bears a residence function and thus one in which the patients are also residents of the facility
community living health care facility
registered nurse role
skilled nursing encounter
They include assistance with activities of daily living, assistance with instrumental activities of daily living, medication assistance, and health support
http://ahca.myflorida.com/Medicaid/acs/index.shtml
Amanda Hicks
assistive care encounter
assistance with activities of daily living care encounter
assistance with instrumental activities of daily living encounter
medication assistance care encounter
A facility that is run by an assisted living facility organization and is the bearer of an assisted living facility function.
assisted living facility
assisted living function
temporally located after some acute care encounter
Somehow involves skilled nursing encounters
post-acute health care encounter
acute care encounter
leaving a health care facility after receiving care
obsolete medical advice
true
Note that not all responses to a question asking process are answers. For example, a refusal to answer is not an answer. A refusal to answer is also not a specified output of the question asking process since it does not acheive the objective of asking the question, which is to get an answer.
response to a question asking process
home health care organization
home health care function
home health care encounter
http://purl.obolibrary.org/obo/OMRSE_00000198
questions asking process
true
palliative function
palliative care encounter
hospice organization
health care function
material information bearer of question text plus answer set
true
refusal to answer datum
response to an identity question asking process
identity question asking process
true
http://purl.obolibrary.org/obo/OMRSE_00000199
ethnic identity question asking process
true
http://purl.obolibrary.org/obo/OMRSE_00000200
race identity question asking process
true
answer to identity question
A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the original peoples of North and South America (including Central America), and maintains tribal affiliation or community attachment.
Amanda Hicks
OMB American Indian or Alaska Native identity information content entity
obsolete American Indian or Alaska Native identity datum
true
A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the original peoples of the Far East, Southeast Asia, or the Indian subcontinent.
Amanda Hicks
OMB Asian identity information content entity
obsolete Asian identity datum
true
A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the black racial groups of Africa.
Amanda Hicks
OMB black or African American identity information content entity
obsolete black or African American identity datum
true
A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the original peoples of Hawaii, Guam, Samoa, or other Pacific Islands.
Amanda Hicks
OMB Native Hawaiian or other Pacific Islander identity information content entity
obsolete Native Hawaiian or other Pacific Islander identity datum
true
A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the original peoples of Europe, the Middle East, or North Africa.
Amanda Hicks
OMB white identity information content entity
obsolete white identity datum
true
A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms.
Amanda Hicks
OMB racial identity information content entity
obsolete OMB racial identity datum
true
A role that inheres in an organism and is realized by habitually smoking 10 or more tobacco cigerettes a day or the equivalent in other tobacco products.
heavy smoker role
A role that inheres in an organism and is realized by habitually smoking 1>10 tobacco cigerettes a day or the equivalent in other tobacco products.
light smoker role
answer set
question text
option as member of some answer set
residential facility
A facility that has at least one housing unit as part in which a person or persons live
Emma Norris
William Hogan
Modified version of definition provided by Human Behaviour Change Project
residential facility
A process in which some participant shares some information content entity about some state of that participant with some other participant.
S. Clint Dowland
Mathias Brochhausen
Matthew Diller
William R. Hogan
The term 'participant' in the definition need not refer to a human agent.
communication
A disposition inhering in a material entity that, if realized, is realized by that material entity’s communicating via some linguistic concretization.
S. Clint Dowland
Mathias Brochhausen
Matthew Diller
William R. Hogan
linguistic competence
A disposition inhering in a linguistic community that (i) is a maximal aggregate of communicatively compatible linguistic competences, and (ii) if realized, is realized by any and all realizations of those linguistic competences.
William R. Hogan
Mathias Brochhausen
Matthew Diller
S. Clint Dowland
language
A maximal aggregate of material entities such that each member bears a linguistic competence for the same language.
Matthew Diller
Mathias Brochhausen
S. Clint Dowland
William R. Hogan
linguistic community
A communication in which some participant states a preference for some communicative process to be in a certain language, and that has a concretization of a preferred language information content entity as its specified output.
S. Clint Dowland
Mathias Brochhausen
Matthew Diller
William R. Hogan
expression of preferred language
An information content entity that (i) is about some person, some language, and some linguistic competence; and (ii) conveys the language with which that person prefers to communicate within some given context.
Mathias Brochhausen
Matthew Diller
S. Clint Dowland
William R. Hogan
preferred language information content entity
a communication in which some participant requests of some other participant an information content entity about some portion of reality
S. Clint Dowland
As with the parent class, 'participant' in the definition need not refer to a human agent.
The medium and grammatical form are irrelevant. For example, the request may be written or spoken, and while it may be in the form of a question, it need not be.
information content entity-request process
an information content entity-request process in which some participant requests of some other participant an information content entity that indicates the ethnic identity of that other participant
S. Clint Dowland
information content entity request about ethnic identity
an information content entity-request process in which some participant requests of some other participant an information content entity that indicates the racial identity of that other participant
S. Clint Dowland
information content entity request about racial identity
A deontic document act in which a patient is registered with a health care provider for the purpose of receiving care in an inpatient encounter.
Amanda Hicks
admission process
cancer summary staging
The cancer summary staging performed on patient John Doe's clinical picture.
A planned process of determining the extent to which a cancer disease has developed by growing and spreading throughout an organism.
Mathias Brochhausen
tumor summary staging
cancer summary staging
cancer summary staging code
The cancer summary staging code that is the outcome of the cancer summary staging performed on patient John Doe's clinical picture.
An information content entity that is the specified output of cancer summary staging.
Mathias Brochhausen
tumor summary staging code
cancer summary staging code
An information content entity that is intended to be a truthful statement about some person and whether that person identifies as some particular aspect of social identity—such as a gender, an ethnicity, a race, or a sexual orientation—where the sense of identifying may correspond to either (i) an aspect of one’s cognitive representation of oneself, (ii) how one prefers to be regarded by others within some social context, or (iii) how one chooses to present oneself to others within some social context.
S. Clint Dowland
Amanda Hicks
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
We include (i)-(iii) to acknowledge that there are different senses of "identify" that are relevant here, and that we may not always be sure which sense the person concretizing the social identity information content entity intended. While (i) concerns how one thinks of oneself, (ii) and (iii) are more focused on one's interactions with others. Importantly, some choose not to share with others how they identify in the sense of (i). For example, one can consider oneself to be some certain gender without either wanting others to know or choosing to present oneself in a corresponding way. We distinguish (ii) and (iii) because one can prefer to be regarded some certain way without attempting to present oneself in any corresponding way.
social identity information content entity
A social identity information content entity that is about whether some person identifies as some ethnicity.
S. Clint Dowland
Amanda Hicks
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
Ethnicity is separate from but related to racial identity. It refers more to identifying with a particular culture than with individuals similar in physical appearance. It includes things like Hispanic ethnicity (which spans many nations) and national cultural identities like Irish and ethnic groups within nations such as Catalan and Armenian.
ethnic identity information content entity
An ethnic identity information content entity that uses OMB terminology for ethnicity or terminology that is strictly mapped onto the OMB ethnicity terms.
S. Clint Dowland
Amanda Hicks
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
OMB dichotomizes ethnicity into Hispanic or Latino and Not Hispanic or Latino, and ignores all other forms of ethnicity.
OMB ethnic identity information content entity
An OMB ethnic identity information content entity that is about some person's identifying as Hispanic or Latino, which are intended to mean being of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race.
S. Clint Dowland
Amanda Hicks
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
It comprehends people of Portuguese culture or origin in Brazil.
OMB Hispanic or Latino identity information content entity
An OMB ethnic identity information content entity that is about some person's identifying as neither Hispanic nor Latino, which are intended to mean being of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race.
S. Clint Dowland
Amanda Hicks
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
OMB not Hispanic or Latino identity information content entity
A social identity information content entity that is about whether some person identifies as some gender.
S. Clint Dowland
Amanda Hicks
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
gender identity information content entity
A gender identity information content entity that is about some person's identifying as female in gender.
S. Clint Dowland
Amanda Hicks
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
female gender identity information content entity
A gender identity information content entity that is about some person's identifying as male in gender.
S. Clint Dowland
Amanda Hicks
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
male gender identity information content entity
A gender identity information content entity that is about some person's identifying as non-binary in gender.
S. Clint Dowland
Amanda Hicks
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
non-binary identity information content entity
A social identity information content entity that is about whether some person identifies as some race.
S. Clint Dowland
Amanda Hicks
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
racial identity information content entity
A racial identity information content entity that uses OMB terminology and definitions for race or terminology that is strictly mapped onto the OMB race terms.
S. Clint Dowland
Amanda Hicks
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
OMB racial identity information content entity
An OMB racial identity information content entity that is about some person's identifying as American Indian or Alaska Native, which is intended to mean having origins in any of the original peoples of North and South America (including Central America), and maintains tribal affiliation or community attachment.
S. Clint Dowland
Amanda Hicks
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
This definition corresponds to that used by OMB. It is worth noting that the OMB definition from which this one is derived is problematic, in that it implies that one's race cannot be Native American or Alaskan Native unless one maintains tribal affiliations or community attachment.
OMB American Indian or Alaska Native identity information content entity
An OMB racial identity information content entity that is about some person's identifying as Asian, which is intended to mean having origins in any of the original peoples of the Far East, Southeast Asia, or the Indian subcontinent.
S. Clint Dowland
Amanda Hicks
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
OMB Asian identity information content entity
An OMB racial identity information content entity that is about some person's identifying as black or African American which is intended to mean having origins in any of the black racial groups of Africa.
S. Clint Dowland
Amanda Hicks
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
OMB black or African American identity information content entity
An OMB racial identity information content entity that is about some person's identifying as Native Hawaiian or other Pacific Islander, which is intended to mean having origins in any of the original peoples of Hawaii, Guam, Samoa, or other Pacific Islands.
S. Clint Dowland
Amanda Hicks
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
OMB Native Hawaiian or other Pacific Islander identity information content entity
An OMB racial identity information content entity that is about some person's identifying as white which is intended to mean having origins in any of the original peoples of Europe, the Middle East, or North Africa.
S. Clint Dowland
Amanda Hicks
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
OMB white identity information content entity
A social identity information content entity that is about whether some person identifies as having some sexual orientation.
Amanda Hicks
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
sexual orientation identity information content entity
An information content entity that is about some geographical region, in which a postal delivery route denoted by a particular ZIP code is realized, and that is the specified output of a disclosure of residence.
Matthew Diller
Hansi Zhang
Mathias Brochhausen
S. Clint Dowland
Sarah Bost
William R. Hogan
residence ZIP code information content entity
A social act that creates an information content entity that is about some geographical region in which a human being dwells.
Matthew Diller
Hansi Zhang
Mathias Brochhausen
S. Clint Dowland
Sarah Bost
William R. Hogan
disclosure of residence
A data set whose members are obtained from one or more electronic health records.
Matthew Diller
EHR data set
Alan Ruttenberg
Mathias Brocchausen
S. Clint Dowland
Sarah Bost
William R. Hogan
electronic health record data set
A data set whose members are the specified output of some process of adjudicating health care insurance claims (and whose inputs are at least partly some members of a health care billing data set).
William R. Hogan
Alan Ruttenberg
Mathias Brocchausen
Matthew Diller
S. Clint Dowland
Sarah Bost
It covers prescription claims because pharmacies bill insurance companies for patients’ prescriptions via submitting insurance claims.
The insurance claim is submitted to the insurance company by either the patient or the provider. It is not necessarily always the provider, although in the United States, it typically is.
The outcome of the adjudication of a claim in the claims dataset could be favorable or unfavorable for the healthcare provider, the patient, or both. The idea is just that they’ve been adjudicated, one way or the other (or anything in between if that’s a possibility).
The reason we say billing data are only part of the input is because we are not conflating the insurance claim with the bill. It is our understanding that the provider’s bill of services is either part of the claim or “attached” to it in some manner, but doesn’t constitute the entire claim itself.
The sources of these data are held by insurers or other health plan providers.
health care claim data set
A data set whose members are obtained from billing-related data sources that (i) are generated by a health care organization as a result of internal administrative processes, and (ii) are about services rendered or materials used during some health care encounter.
S. Clint Dowland
Alan Ruttenberg
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
health care billing data set
Recording data in an EHR. Financial tasks for a healthcare organization. Scheduling shifts for health care workers.
A planned process (i) that is neither a health care process nor an ancillary health care process, and (ii) in which some employee of a health care organization manages, or helps to manage, the performance of tasks that realize the functions of that organization.
Matthew Diller
S. Clint Dowland
health care administrative process
A health care administrative process that has as input a diagnosis, and has as output a value indicating that diagnosis is about the condition that prompts the admission process that starts the encounter during which the diagnostic process that outputs that diagnosis begins.
S. Clint Dowland
Matthew Diller
principal diagnosis-assignment process
A health care administrative process that has as input a diagnosis, and has as output a value indicating that diagnosis is about an underlying condition that is distinct from the condition that prompts the admission process that starts the encounter during which the diagnostic process that outputs that diagnosis begins.
S. Clint Dowland
Matthew Diller
secondary diagnosis-assignment process
The Alachua county smoking survey plan specification.
A survey plan specification that aims to collect information about the smoking behavior or lack thereof of a population on a county level. Concretization of a smoking survey plan that is stratified by county.
Mathias Brochhausen
Hansi Zhang
Jiang Bian
Matthew Diller
S. Clint Dowland
Sarah Bost
William R. Hogan
county smoking survey plan specification
The Alachua county smoking survey execution.
A survey execution that realizes the concretization of a smoking survey plan specification that is stratified by county.
Mathias Brochhausen
Hansi Zhang
Jiang Bian
Matthew Diller
S. Clint Dowland
Sarah Bost
William R. Hogan
county smoking survey execution
The Alachua county smoking survey data.
Survey data that is the specified output of a county smoking survey execution.
Mathias Brochhausen
Hansi Zhang
Jiang Bian
Matthew Diller
S. Clint Dowland
Sarah Bost
William R. Hogan
county smoking survey data
Calculating the Alachua County smoking rate from Alachua County smoking data.
A data transformation that has data about the smoking status of a population as its specified input and a percentage or ratio of smokers in that population as a specified output.
Mathias Brochhausen
smoking rate calculation
The Alachua County smoking rate.
A data item that is the specified output of a smoking rate calculation that has data about smoking behavior or lack there of on a county level.
Mathias Brochhausen
county smoking rate data
Can be about any aspect of employment, such as salary, work location, or employer.
A data item that is about a person's job role and/or its realization.
Matthew Diller
employment data item
Chris Stoeckert
S. Clint. Dowland
William R. Hogan
job role data item
income data item
government assistance health care plan data item
health care plan data item
government assistance income data item
WIC data item
socio-economic data item
non-binary gender identity datum
A gender identity datum resulting from a gender identification process in which ‘non binary’ is selected based on the participant's subjective sense of gender.
Paul Fabry
William Hogan
non-binary gender identity information content entity
Alternatively: A gender identity datum stating that a person's subjective sense of gender is non-binary.)
Examples of usage: ‘Non-binary’, ‘Trigender’, ‘Agender’, ‘Genderfluid’, ‘2’ (intended to refer to a non-binary gender role)
obsolete non-binary gender identity datum
true
educating
A planned process with an active participant who acquires mental representations of information content entities (ICEs), which had no previous mental representation in the cognitive system, and through repeated use or application of these ICEs becomes the bearer of a new instance of some type of capability, and the participant was not previously the bearer of that instance of that type of capability.
William R. Hogan
An act of acquiring new information and repeatedly applying that information to develop a new skill.
An interesting question is whether there must be another participant who is the "educator". Some might object that many people are "self taught". A real case of being self taught is the first person who learned to play a stringed instrument, or to spin a ball on the top of a finger. There was no previous information about that. The ICEs acquired are via one's sensory systems (vision, proprioception, auditory, etc.).
On the other hand, in the case of those who are self-taught by reading books or watching videos, or acquiring some other form of ICEs concretized outside their brain, one argument might be that the author of those ICEs somehow "plays a role" in the education, although they cannot participate in the education process itself (If I read Aristotle, and through repeated application of the information I acquire through doing so, develop the ability to write better ontology definitions, surely Aristotle did not actively participate in my particular education process, although he did influence it in a very real way).
education process
educational objective specification
An objective specification that describes the type of capability or capabilities to be imparted by its realization, which is an educating (education process).
William R. Hogan
An objective specification that describes the new knowledge & skill(s) to be obtained via an education process.
educational objective
educational plan specification
A plan specification with an educational objective specification as part.
William R. Hogan
A plan specification with one or more educational objectives.
Very broad. Covers everything from grade school to high school to college to graduate education, a MOOC, an individual course, a tutorial at a conference, a continuing education course or program, an informed consent video, etc, etc.
educational program
completing a program of eduction
An educating that realizes a concretization of some program of education.
William R. Hogan
Note that parent class 'educating' and referenced class 'program of education' are defined elsewhere in this education module of OMRSE.
This class refers extremely broadly to the successful realization of any program of education: a single course, first grade, MD, PhD, high school, the ninth grade, getting a black belt in karate, getting a master mechanic certification, a bachelor's degree, a masters degree, a graduate certificate, early childhood education program, and even getting a certificate at the end of some week-long workshop, summer camp, a certifcate from a cooking class, an actuarial certification.
completing a program of education
early childhood education program
An educational program whose intended active participant, when a concretization of it is realized, is a human child of age birth to 8 years or a human fetus prior to birth.
William R. Hogan
pre-K education program
prekindergarten education program
preschool education program
https://apps.who.int/iris/bitstream/handle/10665/69729/a91213.pdf?sequence
early childhood education plan specification
primary education plan specification
An education plan specification with one or more primary education objective specifications as parts, and these are the only objective specifications it has as parts.
William R. Hogan
elementary education
In the united states, also called "elementary education"
It can still have action specifications as parts, and possibly other ICEs as parts. That's why we cannot say it has only primary education objectives as parts, and we have to introduce the double negative in the class axiom.
Primary education provides learning and educational activities typically designed to provide students with fundamental skills in reading, writing and mathematics (i.e. literacy and numeracy), and to establish a sound foundation for learning and solid understanding of core areas of knowledge and personal development, preparing for lower secondary education. It aims at learning at a basic level of complexity with little if any specialisation.
primary education program
primary education objective specification
An education objective specification that has a concretization that, when realized, results in the active participant's acquisition and development of fundamental skills in reading, writing and mathematics (i.e. literacy and numeracy).
William R. Hogan
http://uis.unesco.org/en/glossary-term/primary-education-isced-1
By the end of primary education, the student has established a sound foundation for learning and solid understanding of core areas of knowledge and personal development, preparing for lower secondary education. It aims at learning at a basic level of complexity with little if any specialisation.
primary education objective
lower secondary education objective specification
An education objective specification that has a concretization that, when realized, confers to the active participant skills and knowledge in subject areas more specialized than basic reading, writing, and mathematics, with the overall goal of laying the foundation for lifelong learning and human development on which education systems may systematically expand further educational opportunities.
William R. Hogan
http://uis.unesco.org/en/glossary-term/lower-secondary-education-isced-2
Examples of specific subjects could--but are not necessarily required to--include biology, history, science, literature, music, art. Programs at this level are usually organized around a more subject-oriented curriculum, introducing theoretical concepts across a broad range of subjects.
Programmes at ISCED level 2, or ‘lower secondary’ education, are typically designed to build upon the fundamental teaching and learning processes which begin at ISCED level 1. Usually, the educational aim is to lay the foundation for lifelong learning and human development on which education systems may systematically expand further educational opportunities. Programmes at this level are usually organized around a more subject-oriented curriculum, introducing theoretical concepts across a broad range of subjects.
lower secondary education objective
awarding of an academic degree
A deontic document act that has as specified output an academic degree and that confers on recipient of the academic degree the recognition and the claims and obligations that accompany the degree.
William R. Hogan
Different degrees have different claims and obligations associated with them. For example, having a medical degree (either M.D. or D.O.) entitles a person to sit for stage 3 of the US Medical Licensing Exam (otherwise one may not take the exam).
awarding an academic degree
basic education plan specification
An education plan specification that has as part both a primary educational objective specification and a lower secondary educational objective specification.
William R. Hogan
http://uis.unesco.org/en/glossary-term/basic-education
Most nations in the world mandate that children complete at least a basic education program. Some nations go further and include upper secondary education after basic education.
Whole range of educational activities, taking place in various settings, that aim to meet basic learning needs as defined in the World Declaration on Education for All (Jomtien, Thailand, 1990). According to ISCED standard, basic education comprises primary education (first stage of basic education) and lower secondary education (second stage). It also covers a wide variety of non-formal and informal public and private activities intended to meet the basic learning needs of people of all ages.
basic education program
lower secondary education plan specification
An education plan specification with one or more lower secondary education objective specifications as parts, and these are the only objective specifications it has as parts.
William R. Hogan
It can still have action specifications as parts, and possibly other ICEs as parts. That's why we cannot say it has only lower secondary education objectives as parts, and we have to introduce the double negative in the class axiom.
Programmes at ISCED level 2, or ‘lower secondary’ education, are typically designed to build upon the fundamental teaching and learning processes which begin at ISCED level 1. Usually, the educational aim is to lay the foundation for lifelong learning and human development on which education systems may systematically expand further educational opportunities. Programmes at this level are usually organized around a more subject-oriented curriculum, introducing theoretical concepts across a broad range of subjects.
Requires successful completion of a primary education program as a pre-requisite.
lower secondary education program
upper secondary education objective specification
An educational objective specification that has a concretization that, when realized, confers on the active participant skills and knowledge that prepare them for tertiary education, or employment, or both.
William R. Hogan
http://uis.unesco.org/en/glossary-term/upper-secondary-education-isced-3
Programmes at ISCED level 3, or ‘upper secondary’ education, are typically designed to complete secondary education in preparation for tertiary education, or to provide skills relevant to employment, or both. Programmes at this level offer students more varied, specialised and in-depth instruction than programmes at lower secondary education (ISCED level 2). They are more differentiated, with an increased range of options and streams available.
upper secondary education objective
upper secondary education plan specification
An education plan specification with one or more upper secondary education objective specifications as parts, and these are the only objective specifications it has as parts.
William R. Hogan
It can still have action specifications as parts, and possibly other ICEs as parts. That's why we cannot say it has only lower secondary education objectives as parts, and we have to introduce the double negative in the class axiom.
Programmes at ISCED level 3, or ‘upper secondary’ education, are typically designed to complete secondary education in preparation for tertiary education, or to provide skills relevant to employment, or both. Programmes at this level offer students more varied, specialised and in-depth instruction than programmes at lower secondary education (ISCED level 2). They are more differentiated, with an increased range of options and streams available.
Requires successful completion of a lower secondary education program as a pre-requisite.
upper secondary education program
higher education plan specification
William R. Hogan
post-secondary education plan specification
post-secondary education program
Includes college, university, community college, professional schools (MD, RN, PharmD, PT, OT, DDS, dental hygienist, etc.), and so on.
Refers to all higher education beyond secondary education, and thus encompasses ISCED levels 5 and above, which will eventually be subclasses of this one.
Requires successful completion of a secondary education program as a pre-requisite.
higher education program
higher education objective specification
An educational objective specification that has a concretization that, when realized, confers on the active participant skills and knowledge in a specialized discipline, and culminates in the awarding of an academic degree.
William R. Hogan
post-secondary education objective
Refers to all education beyond secondary education that leads to the awarding of an academic degree.
higher education objective
vocational education objective specification
An educational objective specification that has a concretization that, when realized, is realized by a process that confers on the active participant knowledge and skills required to realize a particular type of employee role for a given occupation or trade.
William R. Hogan
http://uis.unesco.org/sites/default/files/documents/international-standard-classification-of-education-isced-2011-en.pdf
Usually the skills are a major focus moreso than in other types of education. For example, auto mechanics, plumbers, and electricians.
vocational education objective
highest level of education socio-economic data item
A socio-economic data item that is about a person and their completion of an education program (and its type), where that education progam is the last one in a sequence (of education programs) that the person has completed, where each education program completed except the last one is a pre-requisite to the education program completed after it.
William R. Hogan
This data item in a typical attribute-value system such as table, XML, JSON takes values like "secondary education", "Associate Degree", "Bachelor Degree", "High School", and so on.
highest level of education data item
vocational education plan specification
An educational plan specification that has a vocational objective specification as part.
William R. Hogan
http://uis.unesco.org/sites/default/files/documents/international-standard-classification-of-education-isced-2011-en.pdf
Vocational education programs are designed for learners to acquire the knowledge, skills and competencies specific to a particular occupation, trade, or class of occupations or trades. Such programs may have work-based components (e.g. apprenticeships, dual-system education programmes). Successful completion of such programs leads to labor market-relevant, vocational qualifications acknowledged as occupationally-oriented by the relevant national authorities and/or the labor market.
vocational education program
kindergarten education plan specification
A primary education plan specification that specifies the competencies and information content entities that should be acquired by students in the first year of primary education in the United States.
William R. Hogan
kindergarten education program
2020-09-02T12:38:43Z
undergraduate higher education plan specification
A higher education plan specification that specifies the awarding of an associates or bachelors degree in the United States or equivalent degrees in other nations, and specifies as a pre-requisite the completion of some secondary education program.
William R. Hogan
undergraduate education program
2020-09-02T12:52:46Z
undergraduate higher education program
graduate higher education plan specification
A higher education plan specification that specifies the awarding of a graduate certificate or degree, and specifies as a pre-requisite the awarding of an undergraduate degree.
graduate education program
2020-09-02T13:01:34Z
Graduate degrees include masters, PhD, MD, PharmD, and other post-graduate professional degrees. To distinguish MS/PhD from the professional ones, subclass this class.
The prerequisite degree is at the bachelors level or equivalent. An associates degree is almost never sufficient for entry into graduate education programs.
graduate higher education program
highest level of education is completion of grades one through six socio-economic data item
A highest level of education socio-economic data item that represents the fact that the highest level of education achieved by an individual in the United States is in the range of first through sixth grade.
William R. Hogan
2020-09-02T13:23:46Z
Note: this broad, very loose level of grouping emerged as an early requirement from the SODA project, funded by a PCORI Methods Grant, at the University of Florida with Dr. Yonghui Wu as PI.
It indicates completion of some to all of primary education in the United States.
highest level of education is grades 1 through 6 data item
highest level of education is completion of grades seven through nine socio-economic data item
A highest level of education socio-economic data item that represents the fact that the highest level of education achieved by an individual in the United States is in the range of seventh (7th) through ninth (9th) grade.
William R. Hogan
2020-09-02T13:27:15Z
Note: this broad, very loose level of grouping emerged as an early requirement from the SODA project, funded by a PCORI Methods Grant, at the University of Florida with Dr. Yonghui Wu as PI.
It indicates completion of some to all of lower secondary education in the United States.
highest level of education is grades 7 through 9 data item
highest level of education is completion of grades ten through twelve socio-economic data item
A highest level of education socio-economic data item that represents the fact that the highest level of education achieved by an individual in the United States is in the range of tenth (10th) through twelfth (12th) grade.
William R. Hogan
2020-09-02T13:27:50Z
Note: this broad, very loose level of grouping emerged as an early requirement from the SODA project, funded by a PCORI Methods Grant, at the University of Florida with Dr. Yonghui Wu as PI.
It indicates completion of some to all of upper secondary education in the United States.
highest level of education is grades 10 through 12 data item
highest level of education is completion of some undergraduate degree socio-economic data item
A highest level of education socio-economic data item that represents the fact that the highest level of education achieved by an individual in the United States is completion of some undergraduate degree.
William R. Hogan
2020-09-02T13:28:27Z
Note: The requirement for this class emerged as an early requirement from the SODA project, funded by a PCORI Methods Grant, at the University of Florida with Dr. Yonghui Wu as PI.
highest level of education is completion of undergraduate degree data item
highest level of education is completion of some graduate degree socio-economic data item
A highest level of education socio-economic data item that represents the fact that the highest level of education achieved by an individual in the United States is completion of some graduate certificate or degree.
William R. Hogan
2020-09-02T13:28:49Z
Note: The requirement for this class emerged as an early requirement from the SODA project, funded by a PCORI Methods Grant, at the University of Florida with Dr. Yonghui Wu as PI.
highest level of education is completion of graduate certificate or degree data item
highest level of education is completion of some vocational education program socio-economic data item
A highest level of education socio-economic data item that represents the fact that the highest level of education achieved by an individual in the United States is completion of some vocational education program.
William R. Hogan
2020-09-02T13:29:28Z
Note: The requirement for this class emerged as an early requirement from the SODA project, funded by a PCORI Methods Grant, at the University of Florida with Dr. Yonghui Wu as PI.
highest level of education is completion of vocaational education program data item
highest level of education is completion of kindergarten socio-economic data item
A highest level of education socio-economic data item that represents the fact that the highest level of education achieved by an individual in the United States is pre-kindergarten.
William R. Hogan
2020-09-02T13:47:38Z
Note: The requirement for this class emerged as an early requirement from the SODA project, funded by a PCORI Methods Grant, at the University of Florida with Dr. Yonghui Wu as PI.
It indicates that a person has completed only early childhood education and nothing more.
highest level of education is completion of kindergarten data item
highest level of education is completion of pre-kindergarten socio-economic data item
A highest level of education socio-economic data item that represents the fact that the highest level of education achieved by an individual in the United States is kindergarten.
William R. Hogan
2020-09-02T13:48:10Z
Note: The requirement for this class emerged as an early requirement from the SODA project, funded by a PCORI Methods Grant, at the University of Florida with Dr. Yonghui Wu as PI.
highest level of education is completion of pre-kindergarten data item
language literacy competence
A disposition borne by a human being that (1) has a linguistic competence as a dispositional part and (2) if realized, is realized by the bearer's achievement of some personal goal.
William R. Hogan
human literacy
linguistic literacy
Jiang Bian
Xi Yang
Yonghui Wu
Other dispositions that it can and likely does have as dispositional parts include cultural competencies, interpersonal competencies, competencies for navigating a society's systems of laws, claims, obligations, deontic declarations, and norms of financial and other economic exchange.
The realization of this disposition by definition realizes the bearer's linguistic competence that is a dispositional part of this disposition. The realization of the linguistic competence would be an occurrent part of the realization of this disposition (and not a temporal part).
Whereas linguistic competence may be afforded to non-human agents, literacy is nearly always considered in the context of human beings.
linguistic literacy competence
A human social role that, if realized, is realized in providing assistance in the activities of daily living of another human being who possesses reduced capability to complete some of these activities alone.
Matthew Diller
John Judkins
S. Clint Dowland
William R. Hogan
caregiver role
A relational quality that inheres within two or more persons related as members of a domestic group, or a number of domestic groups linked through descent from a common ancestor, marriage, or adoption.
http://purl.obolibrary.org/obo/ERO_0002033
John Judkins
S. Clint Dowland
William R. Hogan
We are also intending on including other family arrangements. This is something we are working on.
family relationship
An information content entity that is the specified outcome of and documents the sucessful completion of a tertiary education program.
John Judkins
Mathias Brochhausen
Recognized degree awarded after successful completion of a college or post-graduate porgram.
academic degree
An academic degree awarded by colleges and universities upon completion of a program of study lasting two years.
John Judkins
Mathias Brochhausen
https://en.wikipedia.org/w/index.php?title=Associate_degree&oldid=723897149
Recognition awarded after completion of a specific curriculum from an accredited tertiary education provider that falls between high school and bachelor's degree program.
associate degree
An academic degree awarded by universities upon completion of a course of study demonstrating a mastery or high-order overview of a specific field of study or area of professional practice.[1] Within the area studied, graduates are posited to possess advanced knowledge of a specialized body of theoretical and applied topics; high order skills in analysis, critical evaluation, or professional application; and the ability to solve complex problems and think rigorously and independently.
John Judkins
Mathias Brochhausen
https://en.wikipedia.org/w/index.php?title=Master%27s_degree&oldid=726036185
master's degree
An academic degree awarded by colleges and universities upon completion of a course of study lasting three to seven years.
John Judkins
Mathias Brochhausen
https://en.wikipedia.org/w/index.php?title=Bachelor%27s_degree&oldid=725713923
bachelor's degree
An academic degree in the science and principles of nursing, granted by an accredited tertiary education provider after the successful completion of a bachelor's of nursing program.
John Judkins
Mathias Brochhausen
https://en.wikipedia.org/w/index.php?title=Bachelor_of_Science_in_Nursing&oldid=725962822
bachelor's of nursing degree
An academic degree in the science and principles of nursing, granted by an accredited tertiary education provider after the successful completion of a master's of nursing program.
John Judkins
Mathias Brochhausen
An advanced academic degree in the principles and practices of nursing, with a focus on administration, education, or advanced nursing practice, granted by an accredited college or university after the successful completion of a master's of nursing program.
master's in the science of nursing degree
a diagnosis that is about some patient and that is the specified output of a diagnostic process that occurs before or during the admission of that patient
Amanda Hicks
S. Clint Dowland
PCORnet CDM 4.1
admitting diagnosis
Amanda Hicks
'PCORnet racial identity information content entity'
A racial identity that is the output of a racial identification process that uses the PCORnet CDM race or terminology. PCORnet CDM claims to use the OMB racial classification, but the crucial difference is that PCORnet CDM requires persons to identify with only one category whereas the OMB allows for multiple racial identities as outputs of an identification process.
obsolete PCORnet racial identity datum
true
Amanda Hicks
'PCORnet American Indian or Alaska Native identity information content entity'
obsolete PCORnet American Indian or Alaska Native identity datum
true
Amanda Hicks
'PCORnet Asian identity information content entity'
obsolete PCORnet Asian identity datum
true
Amanda Hicks
'PCORnet black or African American identity information content entity'
obsolete PCORnet black or African American identity datum
obsolete PCORnet item
true
obsolete PCORnet CDM item identifier
true
obsolete PCORnet item
true
Amanda Hicks
'PCORnet Native Hawaiian or other Pacific Islander identity information content entity'
obsolete PCORnet Native Hawaiian or other Pacific Islander identity datum
true
Amanda Hicks
'PCORnet white identity information content entity'
obsolete PCORnet white identity datum
true
Amanda Hicks
'PCORnet multiple race identity information content entity'
obsolete PCORnet multiple race identity datum
true
Amanda Hicks
'PCORnet Hispanic identity information content entity'
From PCORnet CDM "A person of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race."
obsolete PCORnet Hispanic identity datum
true
Amanda Hicks
'PCORnet non-Hispanic identity information content entity'
obsolete PCORnet not Hispanic identity datum
true
Amanda Hicks
'PCORnet ethnic identity information content entity'
obsolete PCORnet ethnic identity datum
true
A centrally registered identifier that denotes a person in a PCORnet data mart and is used to link across tables. This identifier is not necessarily unique within PCORnet.
Amanda Hicks
PCORnet patient identifier
a social act in which a patient is registered with a health care provider for the purposes of recieving care in an inpatient encounter
Amanda Hicks
'admission process'
http://purl.obolibrary.org/obo/OMRSE_00000201
obsolete admission process
true
a diagnosis that is about some patient and that is the specified output of a diagnostic process that occurs before or simultaneously with the discharge of that patient
Amanda Hicks
S. Clint Dowland
PCORnet CDM 4.1
discharge diagnosis
a diagnosis that is about some patient and that is the specified output of a diagnostic process that occurs during an outpatient encounter
Amanda Hicks
S. Clint Dowland
PCORnet CDM 4.1
final diagnosis
a diagnosis that is about some patient and that is the specified output of a diagnostic process that occurs during an inpatient encounter, after admission, and before discharge of that patient
Amanda Hicks
S. Clint Dowland
PCORnet CDM 4.1
interim diagnosis
PCORnet racial identification process
'PCORnet sexual orientation identity information content entity'
obsolete PCORnet sexual orientation identity datum
true
An outpatient encounter that occurs in an outpatient clinic, physician
office, ambulatory surgery facility, urgent care
facilitu, or a hospital encounters and
that does not occur in an emergency department facillity.
Amanda Hicks
PCORnet CDM 4.1
Includes visits at outpatient clinics, physician
offices, same day/ambulatory surgery centers, urgent care
facilities, and other same-day ambulatory hospital encounters, but
excludes emergency department encounters
ambulatory visit
A health care encounter that occurs in an emergency department facillity and realizes the health care provider role of an organization and the emergency department function of the facility.
Amanda Hicks
PCORnet CDM 4.1
Includes ED encounters that become inpatient stays (in which case inpatient stays would be a separate encounter). Excludes urgent care facility visits. ED claims should be pulled before hospitalization claims to ensure that ED with subsequent admission won't be rolled up in the hospital event. Does not include observation stays, where known.
deprecated emergency department encounter
true
Amanda Hicks
'sexual orientation identity information content entity'
A sexual orientation identity datum sis an information content entity that is the output of some sexual orientation identitification process and is intended to be a truthful statement about the subjective feelings of sexual attration, emotional attraction, and romantic attatchments of the person. Unlike data items they are not necessilary contributed or acquired by a reliable method.
obsolete sexual orientation identity datum
true
'PCORnet asexual identity information content entity'
obsolete PCORnet asexual identity datum
obsolete inpatient hospital encounter
true
'PCORnet gay identity information content entity'
obsolete PCORnet gay identity datum
true
'PCORnet lesbian identity information content entity'
obsolete PCORnet lesbian identity datum
true
'PCORnet multiple sexual orientations identity information content entity'
obsolete PCORnet multiple sexual orientations identity datum
true
'PCORnet queer identity information content entity'
obsolete PCORnet queer identity datum
true
'PCORnet questioning sexual orientation identity information content entity'
obsolete PCORnet questioning identity datum
true
'PCORnet something else sexual orientation identity information content entity'
obsolete PCORnet something else identity datum
true
'PCORnet straight identity information content entity'
obsolete PCORnet straight identity datum
true
'PCORnet gender identity information content entity'
A gender identity that is the output of a racial identification process that uses the PCORnet CDM race or terminology. PCORnet CDM claims to use the 2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, but the crucial difference is that PCORnet CDM requires persons to identify with only one category whereas the other does not have a multiple gender option, which changes the meaning of the values in the value set.
obsolete PCORnet gender identity datum
true
'PCORnet genderqueer/non-binary identity information content entity'
obsolete PCORnet genderqueer identity datum
true
'PCORnet man identity information content entity'
obsolete PCORnet man identity datum
true
'PCORnet multiple gender categories identity information content entity'
obsolete PCORnet multiple genders datum
true
'PCORnet something else gender identity information content entity'
obsolete PCORnet something else identity datum
true
'PCORnet transgender female/trans woman/male-to-female identity information content entity'
obsolete PCORnet transgenderfemale/transwoman/male-to-female identity datum
true
'PCORnet transgender male/trans man/female-to-male identity information content entity'
obsolete PCORnet transgendermale/transman/female-to-male identity datum
true
'PCORnet woman identity information content entity'
obsolete PCORnet woman identity datum
true
An identifier that denotes a diagnosis.
PCORnet diagnosis identifier
This class is superfluous, given the addition of PNO: code set.
DEPRECATED obsolete code set
true
A data item that is about a documentation activity that records either (i) that some healthcare encounter ends with a patient discharge; (ii) that some healthcare encounter is terminated by a patient without any patient discharge; or (iii) that some healthcare encounter continues while the patient remains in the same hospital and while the hospital is billing a healthcare payor for services after a specified period.
If the healthcare encounter ends with a patient discharge, then the status might also indicate the type of facility or organization, if any, to which the patient is discharged.
Mathias Brochhausen
Matthew Diller
S. Clint Dowland
William R. Hogan
PCORnet discharge status data item
A PCORnet discharge status data item that is about a discharge process in which a patient is discharged to a skilled nursing facility.
Matthew Diller
S. Clint Dowland
PCORnet skilled nursing facility discharge status data item
A PCORnet discharge status data item that is about a discharge process in which a patient is discharged to an adult foster home facility.
Matthew Diller
S. Clint Dowland
PCORnet adult foster home facility discharge status data item
A PCORnet discharge status data item that is about a discharge process in which a patient is discharged to an assisted living facility.
Matthew Diller
S. Clint Dowland
PCORnet assisted living facility discharge status data item
A PCORnet discharge status data item that is about a discharge process in which a patient is discharged to another hospital.
Amanda Hicks
Matthew Diller
S. Clint Dowland
PCORnet other acute inpatient hospital discharge status data item
A PCORnet discharge status data item that is about a discharge process in which a patient is discharged to a nursing home facility.
Matthew Diller
S. Clint Dowland
PCORnet nursing home facility discharge status data item
A PCORnet discharge status data item that is about a discharge process in which a patient is discharged to a rehabilitation facility.
Matthew Diller
S. Clint Dowland
PCORnet rehabilitation facility discharge status data item
A PCORnet discharge status data item that is about a discharge process in which a patient is discharged to a residential facility.
Matthew Diller
S. Clint Dowland
PCORnet residential facility discharge status data item
A PCORnet discharge status data item that is about a discharge process in which a patient is discharged under the care of a hospice organization.
Matthew Diller
S. Clint Dowland
PCORnet hospice discharge status data item
A PCORnet discharge status data item that is about a discharge process in which a patient is discharged upon deciding to end the encounter against the advice of a healthcare provider.
Matthew Diller
S. Clint Dowland
PCORnet against medical advice discharge status data item
A PCORnet discharge status data item that is about a healthcare encounter that continues while the patient remains in the same hospital, and while the hospital is billing a healthcare payor for services after a specified period (typically 90 days).
Matthew Diller
S. Clint Dowland
William R. Hogan
PCORnet still in hospital discharge status data item
A PCORnet discharge status data item that is about a discharge process in which a patient is discharged (i) to a housing unit, and (ii) under the care of a home healthcare organization.
Matthew Diller
S. Clint Dowland
William R. Hogan
PCORnet home health discharge status data item
A data item that is about a patient admission and the type of facility from which a patient was discharged prior to admission.
Matthew Diller
S. Clint Dowland
PCORnet admitting source data item
A PCORnet data item that is about a home healthcare organization and the household from which a patient was discharged prior to admission.
Matthew Diller
S. Clint Dowland
PCORnet home health admitting source data item
A PCORnet data item that is about a skilled nursing facility from which a patient was discharged prior to admission.
Matthew Diller
S. Clint Dowland
PCORnet skilled nursing facility admitting source data item
An ethnic identity information content entity that uses PCORnet CDM terminology for ethnicity, where this terminology corresponds to values for the "Hispanic" field of the Demographic Table.
S. Clint Dowland
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
PCORnet ethnic identity information content entity
A PCORnet ethnic identity information content entity that is about some person's identifying as Hispanic, which is intended to mean being of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race.
S. Clint Dowland
Amanda Hicks
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
PCORnet Hispanic identity information content entity
A PCORnet ethnic identity information content entity that is about some person's identifying as not Hispanic, where "Hispanic" is intended to mean being of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race.
S. Clint Dowland
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
PCORnet non-Hispanic identity information content entity
A gender identity information content entity that uses the PCORnet CDM terminology for gender, where this terminology corresponds to values for the "gender identity" field of the Demographic Table.
S. Clint Dowland
Amanda Hicks
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
The PCORnet CDM cites the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services as the source for its terminology, but the two differ in that the PCORnet CDM allows one to select only one value for gender and includes 'multiple gender' as an option, while the other lacks a 'multiple gender' option and allows multiple options to be selected. For that source used by PCORnet, see here: https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base
PCORnet gender identity information content entity
A PCORnet gender identity information content entity that is about some person's identifying as neither exclusively male nor exclusively female in gender.
S. Clint Dowland
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
PCORnet genderqueer/non-binary identity information content entity
A PCORnet gender identity information content entity that is about some person's identifying as a man.
S. Clint Dowland
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
PCORnet man identity information content entity
A PCORnet gender identity information content entity that is about some person's identifying as more than one gender.
S. Clint Dowland
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
PCORnet multiple gender categories identity information content entity
A PCORnet gender identity information content entity that is about some person's identifying as some gender that is not referred to or described by the other value options for the "gender identity" field of the PCORnet Demographic Table.
S. Clint Dowland
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
PCORnet something else gender identity information content entity
A PCORnet gender identity information content entity that is about some person's identifying as transgender female, a trans woman, or male-to-female.
S. Clint Dowland
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
PCORnet transgender female/trans woman/male-to-female identity information content entity
A PCORnet gender identity information content entity that is about some person's identifying as transgender male, a trans man, or female-to-male.
Mathias Brochhausen
Matthew Diller
S. Clint Dowland
William R. Hogan
Sarah Bost
PCORnet transgender male/trans man/female-to-male identity information content entity
A PCORnet gender identity information content entity that is about some person's identifying as a woman.
S. Clint Dowland
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
PCORnet woman identity information content entity
A racial identity information content entity that uses the PCORnet CDM terminology for race, where this terminology corresponds to the values for the "race" field of the Demographic Table.
S. Clint Dowland
Amanda Hicks
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
The PCORnet CDM's values for the race field are based on the OMB racial classification, but differ in that the PCORnet CDM allows one to select only one value for race and includes "multiple race" as an option, while OMB lacks a 'multiple race' option and allows multiple options to be selected.
PCORnet racial identity information content entity
A PCORnet racial identity information content entity that is about some person's identifying as American Indian or Alaska Native, which is intended to mean having origins in any of the original peoples of North and South America (including Central America), and maintains tribal affiliation or community attachment.
S. Clint Dowland
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
This definition corresponds to that used by OMB, which is PCORnet's source for the terminology used for the value options of the 'race' field. It is worth noting that the OMB definition from which this one is derived is problematic, in that it implies that one's race cannot be Native American or Alaskan Native unless one maintains tribal affiliations or community attachment.
PCORnet American Indian or Alaska Native identity information content entity
A PCORnet racial identity information content entity that is about some person's identifying as Asian, which is intended to mean having origins in any of the original peoples of the Far East, Southeast Asia, or the Indian subcontinent.
S. Clint Dowland
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
PCORnet Asian identity information content entity
A PCORnet racial identity information content entity that is about some person's identifying as black or African American, which is intended to mean having origins in any of the black racial groups of Africa.
S. Clint Dowland
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
PCORnet black or African American identity information content entity
A PCORnet racial identity information content entity that is about some person's identifying as more than one race.
S. Clint Dowland
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
PCORnet multiple race identity information content entity
A PCORnet racial identity information content entity that is about some person's identifying as Native Hawaiian or other Pacific Islander, which is intended to mean having origins in any of the original peoples of Hawaii, Guam, Samoa, or other Pacific Islands.
S. Clint Dowland
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
PCORnet Native Hawaiian or other Pacific Islander identity information content entity
A PCORnet racial identity information content entity that is about some person's identifying as white which is intended to mean having origins in any of the original peoples of Europe, the Middle East, or North Africa.
S. Clint Dowland
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
PCORnet white identity information content entity
A sexual orientation identity information content entity that uses the PCORnet terminology for sexual orientation, where this terminology corresponds to the permitted values for the "sexual orientation" field of the Demographic Table.
S. Clint Dowland
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
The labels and definitions used for the subclasses of 'PCORnet sexual orientation identity information content entity' are based on the terminology used for the value set options for the PCORnet Common Data Model's 'sexual orientation' field, which is a modifed version of the terms for, and categories of, sexual orientation that are found in the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services (https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base). Neither the PCORnet CDM nor the other source provide definitions of their terms for sexual orientations. Our definitions for the corresponding classes thus point to the terms, rather than explain what they mean, as it is unclear how PCORnet intends them to be understood. Furthermore, these terms may be understood differently by different patients who select them as self-descriptions, as some may understand them to be defined in terms of phenotypic sex, others in terms of gender, and others in terms of some combination of the two.
PCORnet sexual orientation identity information content entity
A PCORnet sexual orientation identity information content entity that is about some person's identifying as having a sexual orientation referred to by the PCORnet CDM with the term "asexual."
S. Clint Dowland
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
The labels and definitions used for the subclasses of 'PCORnet sexual orientation identity information content entity' are based on the terminology used for the value set options for the PCORnet Common Data Model's 'sexual orientation' field, which is a modifed version of the terms for, and categories of, sexual orientation that are found in the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services (https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base). Neither the PCORnet CDM nor the other source provide definitions of their terms for sexual orientations. Our definitions for the corresponding classes thus point to the terms, rather than explain what they mean, as it is unclear how PCORnet intends them to be understood. Furthermore, these terms may be understood differently by different patients who select them as self-descriptions, as some may understand them to be defined in terms of phenotypic sex, others in terms of gender, and others in terms of some combination of the two.
PCORnet asexual identity information content entity
A PCORnet sexual orientation identity information content entity that is about some person's identifying as having a sexual orientation referred to by the PCORnet CDM with the term "bisexual."
S. Clint Dowland
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
The labels and definitions used for the subclasses of 'PCORnet sexual orientation identity information content entity' are based on the terminology used for the value set options for the PCORnet Common Data Model's 'sexual orientation' field, which is a modifed version of the terms for, and categories of, sexual orientation that are found in the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services (https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base). Neither the PCORnet CDM nor the other source provide definitions of their terms for sexual orientations. Our definitions for the corresponding classes thus point to the terms, rather than explain what they mean, as it is unclear how PCORnet intends them to be understood. Furthermore, these terms may be understood differently by different patients who select them as self-descriptions, as some may understand them to be defined in terms of phenotypic sex, others in terms of gender, and others in terms of some combination of the two.
PCORnet bisexual identity information content entity
A PCORnet sexual orientation identity information content entity that is about some person's identifying as having a sexual orientation referred to by the PCORnet CDM with the term "gay."
S. Clint Dowland
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
The labels and definitions used for the subclasses of 'PCORnet sexual orientation identity information content entity' are based on the terminology used for the value set options for the PCORnet Common Data Model's 'sexual orientation' field, which is a modifed version of the terms for, and categories of, sexual orientation that are found in the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services (https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base). Neither the PCORnet CDM nor the other source provide definitions of their terms for sexual orientations. Our definitions for the corresponding classes thus point to the terms, rather than explain what they mean, as it is unclear how PCORnet intends them to be understood. Furthermore, these terms may be understood differently by different patients who select them as self-descriptions, as some may understand them to be defined in terms of phenotypic sex, others in terms of gender, and others in terms of some combination of the two.
PCORnet gay identity information content entity
Internationalized Resource Identifier
An identifier that is the specified output of a planned process that realizes the Internet standard RFC 3987 which is available from http://www.ietf.org/rfc/rfc3987.txt.
IRI
RFC 3987 has the title "Internationalized Resource Identifiers (IRIs)". It was published in 2005.
Internationalized Resource Identifier
A PCORnet data item that is about an emergency department from which a patient was discharged prior to admission.
Matthew Diller
S. Clint Dowland
PCORnet emergency department admitting source data item
A PCORnet data item that is about another department in the same hospital from which a patient was discharged prior to admission.
Matthew Diller
S. Clint Dowland
PCORnet intra-hospital admitting source data item
A PCORnet data item that is about a patient admission that is causally upstream of an outpatient encounter.
Matthew Diller
S. Clint Dowland
PCORnet ambulatory visit admitting source data item
An identifier that denotes a health care encounter and has part some symbol.
Matthew Diller
S. Clint Dowland
PCORnet health care encounter identifier
An identifier that denotes a health care facility and has part some symbol.
Matthew Diller
S. Clint Dowland
PCORnet facility identifier
A health care encounter that realizes some health care provider role that inheres in some Homo sapiens.
Matthew Diller
S. Clint Dowland
institutional professional consult
A health care encounter that occurs in some hospice facility, skilled nursing facility, rehabilitation facility, nursing home facility, residential home facility, overnight non-hospital dialysis facility, adult foster home facility, or assisted living facility.
Matthew Diller
S. Clint Dowland
non-acute institutional stay
A PCORnet discharge status data item that is about a termination of an inpatient encounter, initiated by the patient, that lacks a discharge process as a proper part.
Mathias Brochhausen
Matthew Diller
S. Clint Dowland
William R. Hogan
PCORnet absent without leave discharge status data item
A health care encounter that occurs in some hospital facility or emergency department and that realizes some healthcare provider role that inheres in some organization.
Matthew Diller
observation stay
An identifier that denotes a human being who is a bearer of a person healthcare provider role.
Matthew Diller
S. Clint Dowland
PCORnet provider identifier
A PCORnet sexual orientation identity information content entity that is about some person's identifying as having multiple sexual orientations.
S. Clint Dowland
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
The labels and definitions used for the subclasses of 'PCORnet sexual orientation identity information content entity' are based on the terminology used for the value set options for the PCORnet Common Data Model's 'sexual orientation' field, which is a modifed version of the terms for, and categories of, sexual orientation that are found in the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services (https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base). Neither the PCORnet CDM nor the other source provide definitions of their terms for sexual orientations. Our definitions for the corresponding classes thus point to the terms, rather than explain what they mean, as it is unclear how PCORnet intends them to be understood. Furthermore, these terms may be understood differently by different patients who select them as self-descriptions, as some may understand them to be defined in terms of phenotypic sex, others in terms of gender, and others in terms of some combination of the two.
PCORnet multiple sexual orientations identity information content entity
A PCORnet sexual orientation identity information content entity that is about some person's identifying as having a sexual orientation referred to by the PCORnet CDM with the term "queer."
S. Clint Dowland
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
The labels and definitions used for the subclasses of 'PCORnet sexual orientation identity information content entity' are based on the terminology used for the value set options for the PCORnet Common Data Model's 'sexual orientation' field, which is a modifed version of the terms for, and categories of, sexual orientation that are found in the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services (https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base). Neither the PCORnet CDM nor the other source provide definitions of their terms for sexual orientations. Our definitions for the corresponding classes thus point to the terms, rather than explain what they mean, as it is unclear how PCORnet intends them to be understood. Furthermore, these terms may be understood differently by different patients who select them as self-descriptions, as some may understand them to be defined in terms of phenotypic sex, others in terms of gender, and others in terms of some combination of the two.
PCORnet queer identity information content entity
A PCORnet sexual orientation identity information content entity that is about some person's identifying as having a sexual orientation referred to by the PCORnet CDM with the term "queer."
S. Clint Dowland
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
The labels and definitions used for the subclasses of 'PCORnet sexual orientation identity information content entity' are based on the terminology used for the value set options for the PCORnet Common Data Model's 'sexual orientation' field, which is a modifed version of the terms for, and categories of, sexual orientation that are found in the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services (https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base). Neither the PCORnet CDM nor the other source provide definitions of their terms for sexual orientations. Our definitions for the corresponding classes thus point to the terms, rather than explain what they mean, as it is unclear how PCORnet intends them to be understood. Furthermore, these terms may be understood differently by different patients who select them as self-descriptions, as some may understand them to be defined in terms of phenotypic sex, others in terms of gender, and others in terms of some combination of the two.
While this is not about one's identifying as having or not having some sexual orientation, we regard it as a 'sexual orientation identity information content entity,' which is defined as being about "whether one identifies as having some sexual orientation." For example, if one is uncertain whether one is bisexual or heterosexual, one might be in a state of questioning one's sexuality, and an information content entity about that would seem to qualify as being about whether one identifies as having some sexual orientations. Indeed, there would be two sexual orientations in that example, and the information content entity could be both about whether one identifies as bisexual and about whether one identifies as heterosexual.
PCORnet questioning sexual orientation identity information content entity
A PCORnet sexual orientation identity information content entity that is about some person's identifying as some sexual orientation that is not represented by the other value set options for the "sexual orientation" field of the PCORnet Demographic Table.
S. Clint Dowland
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
The labels and definitions used for the subclasses of 'PCORnet sexual orientation identity information content entity' are based on the terminology used for the value set options for the PCORnet Common Data Model's 'sexual orientation' field, which is a modifed version of the terms for, and categories of, sexual orientation that are found in the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services (https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base). Neither the PCORnet CDM nor the other source provide definitions of their terms for sexual orientations. Our definitions for the corresponding classes thus point to the terms, rather than explain what they mean, as it is unclear how PCORnet intends them to be understood. Furthermore, these terms may be understood differently by different patients who select them as self-descriptions, as some may understand them to be defined in terms of phenotypic sex, others in terms of gender, and others in terms of some combination of the two.
PCORnet something else sexual orientation identity information content entity
A PCORnet sexual orientation identity information content entity that is about some person's identifying as having a sexual orientation referred to by the PCORnet CDM with the term "straight."
S. Clint Dowland
Mathias Brochhausen
Matthew Diller
Sarah Bost
William R. Hogan
The labels and definitions used for the subclasses of 'PCORnet sexual orientation identity information content entity' are based on the terminology used for the value set options for the PCORnet Common Data Model's 'sexual orientation' field, which is a modifed version of the terms for, and categories of, sexual orientation that are found in the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services (https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base). Neither the PCORnet CDM nor the other source provide definitions of their terms for sexual orientations. Our definitions for the corresponding classes thus point to the terms, rather than explain what they mean, as it is unclear how PCORnet intends them to be understood. Furthermore, these terms may be understood differently by different patients who select them as self-descriptions, as some may understand them to be defined in terms of phenotypic sex, others in terms of gender, and others in terms of some combination of the two.
PCORnet straight identity information content entity
A PCORnet specimen source value name that is about a patient.
Matthew Diller
William R. Hogan
The LOINC codes that this value name applies to are 59768-2 (Procedure indications [Interpretation] Narrative), 32624-9 (Race), 56850-1 (Interpretation and review of laboratory results), and 56794-1 (Internal identifier).
This value name is not about an actual specimen.
patient PCORnet specimen source value name
A PCORnet specimen source value name that is about some identifier that denotes a physician.
Matthew Diller
William R. Hogan
The PROVIDER value name might denote something other than a physician identifier, like a telephone number, depending on the data source. We limit it to being about an identifier that denotes a physician because this is what our data sources apply the value name to.
This value name is not about an actual specimen.
provider PCORnet specimen source value name
A health care encounter that first occurs as an emergency department visit and then becomes an inpatient hospital stay
Amanda Hicks
PCORnet CDM 4.1
Permissible substitution for preferred state of separate ED and IP records. Only for use with data sources where the individual records for ED and IP cannot be distinguished.
emergency department admit to inpatient hospital stay
A planned process that realizes a patient role.
William R. Hogan
Matthew Diller
S. Clint Dowland
Sarah Bost
PCORnet medical procedure
An identifier that denotes a LOINC information content entity that itself is about some material entity that is the bearer of a specimen role.
Matthew Diller
PCORnet Common Data Model Specification v5.1
William R. Hogan
The use of 'value name' in the label is a product of PCORnet calling these identifiers "value names."
PCORnet specimen source value name
A PCORnet specimen source value name that is about some blood serum, blood plasma, or urine samples.
Matthew Diller
William R. Hogan
The use of 'value name' in the label is a product of PCORnet calling these identifiers "value names."
This class, while not ideal in that it doesn’t refer to an actual universal, is a consequence of LOINC system identifiers that consist of disjunctions (e.g., ‘Serum or plasma’).
serum, plasma, or urine PCORnet specimen source value name
A PCORnet specimen source value name that is about some blood serum or blood plasma samples.
Matthew Diller
William R. Hogan
The use of 'value name' in the label is a product of PCORnet calling these identifiers "value names."
This class, while not ideal in that it doesn’t refer to an actual universal, is a consequence of LOINC system identifiers that consist of disjunctions (e.g., ‘Serum or plasma’).
serum or plasma PCORnet specimen source value name
A PCORnet specimen source value name that is about some blood serum, blood plasma, or whole blood samples.
Matthew Diller
William R. Hogan
The use of 'value name' in the label is a product of PCORnet calling these identifiers "value names."
This class, while not ideal in that it doesn’t refer to an actual universal, is a consequence of LOINC system identifiers that consist of disjunctions (e.g., ‘Serum or plasma’).
serum, plasma, or blood PCORnet specimen source value name
A PCORnet specimen source value name that is about some blood plasma or tissue samples.
Matthew Diller
William R. Hogan
The use of 'value name' in the label is a product of PCORnet calling these identifiers "value names."
This class, while not ideal in that it doesn’t refer to an actual universal, is a consequence of LOINC system identifiers that consist of disjunctions (e.g., ‘Serum or plasma’).
blood or tissue PCORnet specimen source value name
A PCORnet specimen source value name that is about some specimen of blood plasma.
Matthew Diller
William R. Hogan
The use of 'value name' in the label is a product of PCORnet calling these identifiers "value names."
blood plasma PCORnet specimen source value name
A PCORnet specimen source value name that is about some specimen of cerebrospinal fluid.
Matthew Diller
William R. Hogan
The use of 'value name' in the label is a product of PCORnet calling these identifiers "value names."
cerebrospinal fluid PCORnet specimen source value name
A PCORnet specimen source value name that is about some vaginal specimen.
Matthew Diller
William R. Hogan
The use of 'value name' in the label is a product of PCORnet calling these identifiers "value names."
vagina PCORnet specimen source value name
A PCORnet specimen source value name that is about some cervical specimen.
Matthew Diller
William R. Hogan
The use of 'value name' in the label is a product of PCORnet calling these identifiers "value names."
cervix PCORnet specimen source value name
A PCORnet specimen source value name that is about some specimen of pericardial fluid.
Matthew Diller
William R. Hogan
The use of 'value name' in the label is a product of PCORnet calling these identifiers "value names."
pericardial fluid PCORnet specimen source value name
An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved.
http://purl.obolibrary.org/obo/pato.owl
quality
PATO:0000047
biological sex
morphology
A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
morphology
length
A 1-D extent quality which is equal to the distance between two points.
length
mass
A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
mass
An organismal quality inhering in a bearer or a population by virtue of the bearer's disposition to survive and develop normally or the number of surviving individuals in a given population.
http://purl.obolibrary.org/obo/pato.owl
quality
PATO:0000169
viability
A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes.
http://purl.obolibrary.org/obo/pato.owl
quality
PATO:0000383
female
A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes.
http://purl.obolibrary.org/obo/pato.owl
quality
PATO:0000384
male
physical quality
A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
physical quality
physical object quality
A quality which inheres in a continuant.
physical object quality
A viability quality inhering in a bearer by virtue of the bearer's condition before death.
http://purl.obolibrary.org/obo/pato.owl
quality
PATO:0001421
alive
A viability quality inhering in a bearer by virtue of the cessation of the bearer's life.
http://purl.obolibrary.org/obo/pato.owl
quality
PATO:0001422
dead
http://purl.obolibrary.org/obo/pato.owl
quality
PATO:0001894
phenotypic sex
A quality that inheres in an entire organism or part of an organism.
http://purl.obolibrary.org/obo/pato.owl
quality
PATO:0001995
organismal quality
A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption.
Needs axioms for family relationships.
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25173
Family membership through marriage or adoption apply primarily to human families. In most species, family membership is defined by common anscestry.
family
A material entity consisting of multiple components that are causally integrated.
May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43
Chris Mungall
http://www.jbiomedsem.com/content/4/1/43
system
Lower, narrow portion of the uterus where it joins with the top end of the vagina.
http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl
The narrow caudal end of the uterus that opens into the vagina. [TFD][VHOG]
The evolution of mammals is associated with radical changes in their reproductive biology, particularly the structure and function of the female reproductive organs. These changes include the evolution of the uterus, cervix, vagina, placenta and specialized cell types associated with each of those structures.[well established][VHOG]
cervical
2012-09-17
VHOG:0001359
cervix
BTO:0001421
BTO:0002249
CALOHA:TS-0134
EFO:0000979
EMAPA:29927
EV:0100114
FMA:17740
FMA:TA
GAID:376
MA:0000392
MAT:0000292
MESH:D002584
NCIT:C12311
OpenCyc:Mx4rvVipEJwpEbGdrcN5Y29ycA
UMLS:C0007874
VHOG:0001359
galen:CervixUteri
canalis cervicis uteri
caudal segment of uterus
cervical canal of uterus
cervix uteri
neck of uterus
uterine cervix
uberon
cervical canal
cervix of uterus
UBERON:0000002
VHOG
DOI:10.1098/rspb.2004.2848 Lynch VJ, Roth JJ, Takahashi K, Dunn CW, Nonaka DF, Stopper GF, Wagner GP, Adaptive evolution of HoxA-11 and HoxA-13 at the origin of the uterus in mammals. Proceedings of the Royal Society of London, Series B (2004)
ncithesaurus:Cervix
uterine cervix
The olfactory organ of vertebrates, consisting of nares, olfactory epithelia and the structures and skeletal framework of the nasal cavity.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
Organ that is the specialized structure of the face that contains olfactory neurons. The peripheral olfactory organ is paired[ZFA:0000047].
a protuberance in vertebrates that houses the nostrils, or nares, which admit and expel air for respiration in conjunction with the mouth. Behind the nose are the olfactory mucosa and the sinuses. Behind the nasal cavity, air next passes through the pharynx, shared with the digestive system, and then into the rest of the respiratory system. In humans, the nose is located centrally on the face; on most other mammals, it is on the upper tip of the snout[WP]. GO: The nose is the specialized structure of the face that serves as the organ of the sense of smell and as part of the respiratory system. Includes the nasi externus (external nose) and cavitas nasi (nasal cavity)[Wikipedia:Nose].
the organ that is specialized for smell and is part of the respiratory system
the structure of the nose varies across vertebrates. In tetrapods the nose is part of the respiratory system.[PMID:25312359]
BTO:0000840
CALOHA:TS-2037
EHDAA2:0001274
EHDAA:1502
EMAPA:16542
EV:0100037
EV:0100370
FMA:46472
GAID:77
MA:0000281
MAT:0000139
MESH:D009666
MIAA:0000139
NCIT:C12756
OpenCyc:Mx4rvViCbJwpEbGdrcN5Y29ycA
TAO:0000047
UBERON:cjm
UMLS:C0028429
ZFA:0000047
galen:Nose
nasal sac
nose
peripheral olfactory organ
uberon
nasus
olfactory apparatus
proboscis
UBERON:0000004
MP:0002233
ZFA:0000047
ncithesaurus:Nose
nose
Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis.
Note the distinction between the entire skin of the body, of which there is only 1 in an organism, and zones of skin, of which there can be many. Examples: skin of knee
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
(...) it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina (...).[well established][VHOG]
we assume that mouse, HOG and GAID all mean zone of skin when they say skin. We also choose skin as an exact synonym, as it is more intuitive
2012-09-17
VHOG:0000860
EHDAA2:0001844
EHDAA:6530
EMAPA:17525
EV:0100152
FMA:86166
GAID:933
MA:0000151
MAT:0000284
MESH:D012867
MIAA:0000284
OpenCyc:Mx4rvVjX3ZwpEbGdrcN5Y29ycA
VHOG:0000860
portion of skin
region of skin
skin
skin region
skin zone
uberon
UBERON:0000014
VHOG
DOI:10.1111/j.1469-7580.2008.01043.x Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009)
zone of skin
An organ that is capable of transducing sensory stimulus to the nervous system.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
AEO:0000094
BSA:0000121
BTO:0000202
CALOHA:TS-2043
EHDAA2:0001824
EHDAA:500
EMAPA:35955
FBbt:00005155
GAID:63
HAO:0000930
MA:0000017
MESH:D012679
NCIT:C33224
OBOL:accepted
OBOL:automatic
UMLS:C0935626
VHOG:0001407
WBbt:0006929
organ of sense organ system
organ of sensory organ system
organ of sensory system
sense organ system organ
sensory organ
sensory organ system organ
sensory system organ
sensillum
uberon
Sinnesorgan
sensor
UBERON:0000020
ncithesaurus:Organ_of_the_Special_Sense
sense organ
Anatomical projection that protrudes from the skin. Examples: hair, nail, feather, claw, hoof, horn, wattle, spur, beak, antler, bristle and some scales.
Mammary glands develop by similar mechanisms, and there is an argument for including them here (e.g. http://www.ncbi.nlm.nih.gov/pubmed/20484386), but these structures do not fit the current definition (lactiferous glands are part of the integumentary system in FMA). Note the FMA class is a subdivision of epidermis, which may be too restrictive for our purposes here.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
CALOHA:TS-0051
FMA:71012
skin appendage
epidermal appendage
uberon
epidermal growth
UBERON:0000021
cutaneous appendage
one of the epidermal growths that form the distinctive outer covering, or plumage, on birds. Feathers are formed in tiny follicles in the epidermis, or outer skin layer, that produce keratin proteins.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
Among the characteristics that distinguish the extant Aves from other living groups. Feathers have also been noticed in those Theropoda which have been termed feathered dinosaurs. Although feathers cover most parts of the body of birds, they arise only from certain well-defined tracts on the skin. They aid in flight, thermal insulation, waterproofing and coloration that helps in communication and protection
The beta-keratins in feathers, beaks and claws - and the claws, scales and shells of reptiles - are composed of protein strands hydrogen-bonded into beta-pleated sheets, which are then further twisted and crosslinked by disulfide bridges into structures even tougher than the alpha-keratins of mammalian hair, horns and hoof.
BTO:0000447
EFO:0000955
GAID:1214
MAT:0000156
MESH:D005241
OpenCyc:Mx4rvVjW-5wpEbGdrcN5Y29ycA
uberon
UBERON:0000022
feather
http://xkcd.com/1104/
multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO]
a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP]
in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA.
2012-08-14
TAO:0005425
FMA
FMA:9581
GAID:19
MESH:D012704
NCIT:C13169
TAO:0005425
UMLS:C0036760
ZFA:0005425
tunica serosa
wall of serous sac
uberon
serosa
UBERON:0000042
TAO
ncithesaurus:Serosa
serous membrane
the fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
urethral
In human males, the urethra travels through the penis, and carries semen as well as urine. In females, the urethra is shorter and emerges above the vaginal opening.
BTO:0001426
CALOHA:TS-1132
EFO:0000931
EMAPA:30901
EV:0100099
FMA:19667
GAID:390
MA:0000379
MAT:0000121
MESH:D014521
MGI:anna
MIAA:0000121
MP:0000537
NCIT:C12417
OpenCyc:Mx4rvVjkypwpEbGdrcN5Y29ycA
UMLS:C0041967
VHOG:0001264
XAO:0000153
galen:Urethra
uberon
UBERON:0000057
ncithesaurus:Urethra
urethra
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
AAO:0010825
AEO:0000003
BILA:0000003
CARO:0000003
EHDAA2:0003003
EMAPA:0
FBbt:00007001
FMA:305751
FMA:67135
GAID:781
HAO:0000003
MA:0003000
MESH:D000825
TAO:0000037
TGMA:0001823
VHOG:0001759
XAO:0003000
ZFA:0000037
biological structure
connected biological structure
uberon
UBERON:0000061
anatomical structure
Anatomical structure that performs a specific function or group of functions [WP].
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4
CARO:0020004
EFO:0000634
EMAPA:35949
ENVO:01000162
FMA:67498
MA:0003001
NCIT:C13018
OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA
OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA
UMLS:C0178784
WBbt:0003760
uberon
anatomical unit
body organ
element
UBERON:0000062
GO:0048513
ncithesaurus:Organ
organ
A multicellular structure that is a part of an organ.
currently defined in a very broad sense, may be replaced by more specific classes in the future
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
AAO:0011124
EFO:0000635
FMA:82472
NIFSTD:birnlex_16
cardinal organ part
uberon
regional part of organ
UBERON:0000064
organ part
End of the life of an organism.
http://purl.obolibrary.org/obo/uberon.owl
ncit:Death is an outcome
XAO:0000437
XtroDO:0000085
uberon
death
UBERON:0000071
death stage
The organs associated with producing offspring in the gender that produces spermatozoa.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG]
2012-09-17
VHOG:0000725
BTO:0000082
CALOHA:TS-1310
EFO:0000970
EHDAA2:0001054
EHDAA:8136
EMAPA:17968
EV:0100101
FBbt:00004927
FMA:45664
GAID:386
HAO:0000505
MA:0000396
MESH:D005837
MP:0001145
NCIT:C12722
OBOL:automatic
OpenCyc:Mx4rvViCepwpEbGdrcN5Y29ycA
TGMA:0000634
UMLS:C0017422
UMLS:C1963704
VHOG:0000725
WBbt:0008423
XAO:0000155
genitalia of male organism
male genital system
male genitalia
male genitals
male organism genitalia
male organism reproductive system
reproductive system of male organism
uberon
male genital organ
male genital tract
male reproductive tract
systema genitale masculinum
UBERON:0000079
VHOG
ISBN:978-0792383369 Lombardi J, Comparative vertebrate reproduction (1998) p.43
ncithesaurus:Male_Genitalia
ncithesaurus:Male_Reproductive_System
male reproductive system
An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism.
http://purl.obolibrary.org/obo/uberon.owl
FBdv:00000000
HsapDv:0000001
MmusDv:0000001
OGES:000011
ncithesaurus:Life
entire life cycle
entire lifespan
life
lifespan
uberon
UBERON:0000104
life cycle
A spatiotemporal region encompassing some part of the life cycle of an organism.
this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here
http://purl.obolibrary.org/obo/uberon.owl
the WBls class 'all stages' belongs here as it is the superclass of other WBls stages
we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage
BILS:0000105
EFO:0000399
FBdv:00007012
FMA:24120
HsapDv:0000000
MmusDv:0000000
OlatDv:0000010
PdumDv:0000090
WBls:0000002
XAO:1000000
ZFS:0000000
ZFS:0100000
ncithesaurus:Developmental_Stage
developmental stage
stage
uberon
UBERON:0000105
life cycle stage
The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks).
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]
Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]
oral
some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives
in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips
2012-06-20
2012-09-17
AAO:0010355
VHOG:0000812
FMA
AAO:0010355
BTO:0001090
BTO:0004698
CALOHA:TS-1315
EFO:0000825
EHDAA2:0001326
EHDAA:542
EMAPA:16262
FBbt:00003126
FMA:49184
FMA:TA
GAID:75
MA:0000341
MA:0002474
MAT:0000038
MESH:D009055
MIAA:0000038
OpenCyc:Mx4rvVidh5wpEbGdrcN5Y29ycA
TADS:0000040
TAO:0000547
TAO:0000590
TGMA:0000131
VHOG:0000280
VHOG:0000812
XAO:0003029
ZFA:0000547
ZFA:0000590
galen:Mouth
regio oralis
adult mouth
uberon
cavital oralis
cavitas oris
cavum oris
mouth cavity
oral region
oral vestibule
rima oris
stoma
stomatodaeum
trophic apparatus
vestibule of mouth
vestibulum oris
UBERON:0000165
AAO
VHOG
AAO:BJB
DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008)
mouth
A bodily fluid consisting of the expulsed contents of the stomach disgorged through the mouth or nose that happens as a result of a vomit reflex.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
ENVO:00000338
NCIT:C77666
OpenCyc:Mx4rvViQTJwpEbGdrcN5Y29ycA
UBERON:cjm
galen:Vomitus
vomitus
uberon
UBERON:0000172
vomit
Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion. It allows the fetus to move freely without the walls of the uterus being too tight against its body. Buoyancy is also provided. The composition of the fluid changes over the course of gestation. Initially, amniotic fluid is similar to maternal plasma, mainly water with electrolytes. As the fetus develops, proteins, carbohydrates, lipids, phospholipids originating from the lungs, fetal cells, and urea are deposited in the fluid.
http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl
BTO:0000068
CALOHA:TS-0034
EMAPA:36771
ENVO:02000021
EV:0100123
FMA:305905
GAID:1155
MA:0002893
MESH:D000653
MP:MP
NCIT:C13188
UMLS:C0002638
VHOG:0001267
uberon
acqua amnii
liquor amnii
UBERON:0000173
ncithesaurus:Amniotic_Fluid
amniotic fluid
A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
UBERON:0000324
UBERON:0007550
AEO:0000184
BTO:0000491
EHDAA2_RETIRED:0003184
ENVO:02000022
FMA:9674
GO:0007588
galen:Excretion
excreted substance
portion of excreted substance
waste substance
uberon
excretion
UBERON:0000174
excreta
Pus is a bodily fluid consisting of a whitish-yellow or yellow substance produced during inflammatory responses of the body that can be found in regions of pyogenic bacterial infections. Pus is produced from the dead and living cells which travel into the intercellular spaces around the affected cells.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
biospecimen in NCIT
NCIT
ENVO:02000038
OpenCyc:Mx4rvVjG6ZwpEbGdrcN5Y29ycA
galen:Pus
ncithesaurus:Pus
uberon
purulent exudate
UBERON:0000177
pus
A fluid that is composed of blood plasma and erythrocytes.
This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]
Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]
relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]
Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]
2012-06-20
2012-08-14
2012-09-17
AAO:0000046
TAO:0000007
VHOG:0000224
AAO:0000046
BTO:0000089
CALOHA:TS-0079
EFO:0000296
EHDAA2:0000176
EHDAA:418
EMAPA:16332
ENVO:02000027
EV:0100047
FMA:9670
GAID:965
MA:0000059
MESH:D001769
MIAA:0000315
NCIT:C12434
OpenCyc:Mx4rvVjI8JwpEbGdrcN5Y29ycA
TAO:0000007
UMLS:C0005767
VHOG:0000224
XAO:0000124
ZFA:0000007
galen:Blood
portion of blood
vertebrate blood
uberon
whole blood
UBERON:0000178
AAO
TAO
VHOG
AAO:LAP
DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006)
ZFIN:curator
ncithesaurus:Blood
blood
Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
cjm
2009-04-08T04:38:19Z
CARO:0000081
uberon
blood or blood analog
circulating fluid
UBERON:0000179
haemolymphatic fluid
The upper ventral region of the torso of an organism.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
The breasts of a female primate's body contain the mammary glands, which secrete milk used to feed infants. Both men and women develop breasts from the same embryological tissues. However, at puberty female sex hormones, mainly estrogens, promote breast development, which does not happen with men. As a result women's breasts become more prominent than men's.
BTO:0000149
CALOHA:TS-2083
EV:0100124
FMA:9601
GAID:33
MESH:D001940
NCIT:C12971
OpenCyc:Mx4rvVjV7ZwpEbGdrcN5Y29ycA
UMLS:C0006141
galen:Breast
mammary part of chest
mammary region
uberon
mamma
UBERON:0000310
WP,unvetted
ncithesaurus:Breast
breast
A portion of organism substance that is produced by exocrine glands.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions
BTO
UBERON:0006540
secretion
AEO:0001005
BTO:0002977
BTO:0002979
EMAPA:36535
FMA:9675
MA:0002504
MESH:D012634
NCIT:C34062
UMLS:C1516992
galen:Secretion
bodily secretion
exocrine gland fluid/secretion
secreted substance
uberon
exocrine gland fluid
exocrine gland fluid or secretion
exocrine gland secretion
external secretion
UBERON:0000456
ncithesaurus:Exocrine_Gland_Fluid_or_Secretion
secretion of exocrine gland
Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
AAO:0010839
AEO:0000004
BILA:0000004
CALOHA:TS-2101
CARO:0000004
EHDAA2:0003004
EMAPA:35178
FBbt:00007019
FMA:9669
HAO:0000004
MA:0002450
NCIT:C13236
SPD:0000008
TAO:0001487
TGMA:0001824
VHOG:0001726
XAO:0004001
ZFA:0001487
galen:BodySubstance
body fluid or substance
body substance
organism substance
portion of body substance
portion of organism substance
uberon
UBERON:0000463
organism substance
Anatomical entity that has mass.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
AAO:0010264
AEO:0000006
BILA:0000006
CARO:0000006
EHDAA2:0003006
FBbt:00007016
FMA:67165
HAO:0000006
TAO:0001836
TGMA:0001826
VHOG:0001721
uberon
UBERON:0000465
material anatomical entity
A gonad of a male animal. A gonad produces and releases sperm.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
Male reproductive organ.[TAO]
(...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG]
testicular
The testes are descended in metatherian and eutherian mammals, first transabdominally, then inguinoscrotally
2012-08-14
2012-09-17
TAO:0000598
VHOG:0000252
UBERON:0002117
AAO:0000606
BILA:0000124
BSA:0000085
BTO:0001363
CALOHA:TS-1030
EFO:0000984
EHDAA2:0002007
EHDAA:8146
EMAPA:17972
EV:0100102
FBbt:00004928
FMA:7210
GAID:396
HAO:0001007
MA:0000411
MAT:0000132
MESH:D013737
MIAA:0000132
NCIT:C12412
OBOL:automatic
OpenCyc:Mx4rvVjM25wpEbGdrcN5Y29ycA
TAO:0000598
UMLS:C0039597
VHOG:0000252
WBbt:0006794
XAO:0000157
ZFA:0000598
galen:Testis
gonad of male genitalia
gonad of male reproductive system
male gonad
testicle
uberon
orchis
testes
testiculus
UBERON:0000473
TAO
VHOG
DOI:10.1093/icb/icm052 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across the Bilateria. Integrative and Comparative Biology (2007), DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T and Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)
ISBN-10:0123971756
ZFIN:curator
ncithesaurus:Testis
NCBITaxon:40674
testis
Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.
changed label and definition to reflect CARO2
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
AAO:0000607
AAO:0010054
AEO:0000043
BILA:0000043
CALOHA:TS-2090
CARO:0000043
EHDAA2:0003043
EMAPA:35868
FBbt:00007003
FMA:9637
HAO:0000043
MA:0003002
MESH:D014024
NCIT:C12801
TAO:0001477
TGMA:0001844
UMLS:C0040300
VHOG:0001757
WBbt:0005729
XAO:0003040
ZFA:0001477
galen:Tissue
portion of tissue
tissue portion
simple tissue
uberon
UBERON:0000479
ncithesaurus:Tissue
tissue
Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
AAO:0010048
AEO:0000055
BILA:0000055
CARO:0000055
EHDAA2:0003055
FBbt:00007010
HAO:0000055
TAO:0001488
TGMA:0001847
VHOG:0001762
XAO:0003037
ZFA:0001488
uberon
multi-tissue structures
UBERON:0000481
multi-tissue structure
An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO]
It appears that the stomach has an ancient origin. The stomach first appears in the fish lineage. The prevertebrate chordates do not have a true stomach, whereas the cartilaginous and bony fish do. Although most fish do have a true stomach, some fish species appear to have lost the stomach secondarily. The remaining vertebrate lineages do have a true stomach (at least in the adult animal), although there is great variation in the size and shape of the stomach.[well established][VHOG]
We restrict this to the vertebrate specific structure - see the grouping class 'food storage organ' for analogous structures in other species. Teleosts: Zebrafish is functionally stomach-less, but may retain ontogenic footprint. Although the precise shape and size of the stomach varies widely among different vertebrates, the relative positions of the oesophageal and duodenal openings remain relatively constant. As a result, the organ always curves somewhat to the left before curving back to meet the pyloric sphincter. However, lampreys, hagfishes, chimaeras, lungfishes, and some teleost fish have no stomach at all, with the oesophagus opening directly into the intestine. The gastric lining is usually divided into two regions, an anterior portion lined by fundic glands, and a posterior with pyloric glands. Cardiac glands are unique to mammals, and even then are absent in a number of species. The distributions of these glands vary between species, and do not always correspond with the same regions as in man. Furthermore, in many non-human mammals, a portion of the stomach anterior to the cardiac glands is lined with epithelium essentially identical to that of the oesophagus. Ruminants, in particular, have a complex stomach, the first three chambers of which are all lined with oesophageal mucosa
2012-06-20
2012-09-17
AAO:0000579
VHOG:0000408
AAO:0000579
ANISEED:1235297
BTO:0001307
CALOHA:TS-0980
EFO:0000837
EHDAA2:0001915
EHDAA:2993
EMAPA:17021
EV:0100070
FMA:7148
GAID:293
ISBN10:0073040584
MA:0000353
MAT:0000051
MESH:A03.492.766
MIAA:0000051
NCIT:C12391
OpenCyc:Mx4rvVjlqpwpEbGdrcN5Y29ycA
TAO:0002121
UMLS:C0038351
VHOG:0000408
XAO:0000128
galen:Stomach
stomach chamber
uberon
anterior intestine
gaster
mesenteron
ventriculus
UBERON:0000945
AAO
VHOG
AAO:EJS
DOI:10.1046/j.1525-142x.2000.00076.x Smith DM, Grasty RC, Theodosiou NA, Tabin CJ, Nascone-Yoder NM, Evolutionary relationships between the amphibian, avian, and mammalian stomachs. Evolution and development (2000)
WP:Stomach#In_other_animals
ncithesaurus:Stomach
stomach
The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP].
requires review for applicability to invertebrate structures, e.g. synganglion
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO]
Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO]
The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO)
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]
2012-06-20
2012-08-14
2012-09-17
AAO:0010478
TAO:0000008
VHOG:0000157
AAO:0010478
ABA:Brain
BAMS:Br
BAMS:Brain
BILA:0000135
BTO:0000142
CALOHA:TS-0095
DHBA:10155
EFO:0000302
EHDAA2:0000183
EHDAA:2641
EHDAA:6485
EMAPA:16894
EV:0100164
FBbt:00005095
FMA:50801
GAID:571
HBA:4005
MA:0000168
MAT:0000098
MBA:8
MBA:997
MESH:D001921
MIAA:0000098
NCIT:C12439
NeuroNames:21
OpenCyc:Mx4rvVjT65wpEbGdrcN5Y29ycA
PBA:3999
TAO:0000008
UMLS:C0006104
UMLS:C1269537
VHOG:0000157
XAO:0000010
ZFA:0000008
galen:Brain
http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=21
uberon
encephalon
suprasegmental levels of nervous system
suprasegmental structures
synganglion
the brain
UBERON:0000955
AAO
TAO
VHOG
AAO:BJB
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165
NIFSTD:birnlex_796
ZFIN:curator
ncithesaurus:Brain
brain
An organ that detects light.
This class encompasses a variety of light-detecting structures from different phyla with no implication of homology, from the compound insect eye to the vertebrate camera-type eye (distinct classes are provided for each)
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
ocular
optic
Note that whilst this is classified as an organ, it is in fact more of a unit composed of different structures: in Drosophila, it includes the interommatidial bristle as a part; we consider here the vertebrate eye to include the eyeball/eye proper as a part, with the eye having as parts (when present): eyelids, conjuctiva,
BILA:0000017
BTO:0000439
CALOHA:TS-0309
EFO:0000827
EV:0100336
FBbt:00005162
GAID:69
MAT:0000140
MESH:D005123
MIAA:0000140
OpenCyc:Mx4rvViTvpwpEbGdrcN5Y29ycA
uberon
light-detecting organ
visual apparatus
UBERON:0000970
eye
The invaginated serous membrane that surrounds the lungs (the visceral portion) and lines the walls of the pleural cavity (parietal portion).
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
The serous membrane that covers the lungs and lines the pleural cavity. [Kaufman_MH_and_Bard_JBL, The_anatomical_basis_of_mouse_development_(1999)_San_Diego:_Academic_Press, p.264][VHOG]
pleural
In MA, is_a cavity lining (which we equate to parietal). In FMA, is_a (viscous) serous membrane (which includes mesothelium plus connective tissue). Note the MA structure should probably be associated with the mesothelium of pleura in FMA. JB/EHDAA2 argues the term 'pleura' is best used for the mesothelial lining (thus excluding connective tissue). See https://github.com/obophenotype/uberon/issues/86
2012-09-17
VHOG:0000394
BTO:0001791
CALOHA:TS-2081
EFO:0001980
EMAPA:16775
EV:0100044
FMA:9583
GAID:360
ISBN:0-683-40008-8
MA:0000433
MESH:D010994
MP:0010820
NCIT:C12469
OpenCyc:Mx4rv3zwLZwpEbGdrcN5Y29ycA
UBERON:cjm
UMLS:C0032225
VHOG:0000394
wall of pleural sac
uberon
pleura
pleural tissue
UBERON:0000977
VHOG
BGEE:AN
ISBN10:0124020607
ISBN:978-0030223693
ncithesaurus:Pleural_Tissue
pleura
A intromittent organ in certain biologically male organisms. In placental mammals, this also serves as the organ of urination
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
penile
phallic
Most male birds (e.g., roosters and turkeys) have a cloaca (also present on the female), but not a penis. Among bird species with a penis are paleognathes (tinamous and ratites), Anatidae (ducks, geese and swans), and a very few other species (such as flamingoes). A bird penis is different in structure from mammal penises, being an erectile expansion of the cloacal wall and being erected by lymph, not blood. It is usually partially feathered and in some species features spines and brush-like filaments, and in flaccid state curls up inside the cloaca
BTO:0000405
CALOHA:TS-0758
EFO:0000987
EHDAA2:0001433
EHDAA:9380
EMAPA:18682
EMAPA_RETIRED:18996
EV:0100107
FMA:9707
GAID:389
ISBN:0-683-40008-8
MA:0000408
MAT:0000186
MESH:D010413
MIAA:0000186
MP:0005187
NCIT:C12409
OpenCyc:Mx4rvVjkCZwpEbGdrcN5Y29ycA
UMLS:C0030851
VHOG:0000727
galen:Penis
uberon
penes
phallus
UBERON:0000989
WP
ncithesaurus:Penis
penis
Reproductive organ that produces and releases eggs (ovary) or sperm (testis).
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO]
The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO]
Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG]
gonadal
FMA xref is a 'general anatomical term'
2012-06-20
2012-08-14
2012-09-17
AAO:0000213
TAO:0000413
VHOG:0000397
FMA
AAO:0000213
BILA:0000123
BSA:0000079
BTO:0000534
EMAPA:17383
FBbt:00004858
FMA:18250
GAID:368
HAO:0000379
ISBN:0140512888
MA:0002420
MESH:D006066
NCIT:C12725
OpenCyc:Mx4rwQvdiZwpEbGdrcN5Y29ycA
TAO:0000413
UMLS:C0018067
VHOG:0000397
WBbt:0005175
XAO:0003146
ZFA:0000413
ZFIN:curator
gonada
uberon
gonads
UBERON:0000991
AAO
TAO
VHOG
AAO:BJB
DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T, Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)
ZFIN:curator
ncithesaurus:Gonad
gonad
the gonad of a female organism which contains germ cells
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
Either of paired female reproductive organs involved in production of ova and female sex hormones.[AAO]
Female reproductive organ.[TAO]
(...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG]
ovarian
Ovaries of some kind are found in the female reproductive system of many animals that employ sexual reproduction, including invertebrates. However, they develop in a very different way in most invertebrates than they do in vertebrates, and are not truly homologous. Many of the features found in human ovaries are common to all vertebrates, including the presence of follicular cells, tunica albuginea, and so on. However, many species produce a far greater number of eggs during their lifetime than do humans, so that, in fish and amphibians, there may be hundreds, or even millions of fertile eggs present in the ovary at any given time. In these species, fresh eggs may be developing from the germinal epithelium throughout life. Corpora lutea are found only in mammals, and in some elasmobranch fish; in other species, the remnants of the follicle are quickly resorbed by the ovary. In birds, reptiles, and monotremes, the egg is relatively large, filling the follicle, and distorting the shape of the ovary at maturity. Amphibians and reptiles have no ovarian medulla; the central part of the ovary is a hollow, lymph-filled space. The ovary of teleosts is also often hollow, but in this case, the eggs are shed into the cavity, which opens into the oviduct. Although most normal female vertebrates have two ovaries, this is not the case in all species. In birds and platypuses, the right ovary never matures, so that only the left is functional. In some elasmobranchs, the reverse is true, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo
2012-06-20
2012-08-14
2012-09-17
AAO:0000371
TAO:0000403
VHOG:0000251
AAO:0000371
BILA:0000125
BSA:0000080
BTO:0000975
CALOHA:TS-0730
EFO:0000973
EHDAA2:0001360
EHDAA:8124
EMAPA:17962
EV:0100111
FBbt:00004865
FMA:7209
GAID:367
GO:0061039
ISBN:0-683-40008-8
MA:0000384
MESH:D010053
MIAA:0000125
MP:0001126
NCIT:C12404
OBOL:automatic
OpenCyc:Mx4rvVi9QJwpEbGdrcN5Y29ycA
TAO:0000403
UMLS:C0029939
VHOG:0000251
XAO:0000258
ZFA:0000403
animal ovary
female gonad
female organism genitalia gonad
female organism genitalia gonada
female organism reproductive system gonad
female organism reproductive system gonada
female reproductive system gonad
female reproductive system gonada
genitalia of female organism gonad
genitalia of female organism gonada
gonad of female organism genitalia
gonad of female organism reproductive system
gonad of female reproductive system
gonad of genitalia of female organism
gonad of reproductive system of female organism
gonada of female organism genitalia
gonada of female organism reproductive system
gonada of female reproductive system
gonada of genitalia of female organism
gonada of reproductive system of female organism
ovum-producing ovary
reproductive system of female organism gonad
reproductive system of female organism gonada
uberon
ovaries
ovarium
UBERON:0000992
AAO
TAO
VHOG
AAO:BJB
DOI:10.1093/icb/icm052 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across the Bilateria. Integrative and Comparative Biology (2007), DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T and Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)
WP
ZFIN:curator
ncithesaurus:Ovary
ovary
the female muscular organ of gestation in which the developing embryo or fetus is nourished until birth
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
The hollow muscular organ in female mammals in which the blastocyst normally becomes embedded and in which the developing embryo and fetus is nourished. Its cavity opens into the vagina below and into a uterine tube on either side. [TFD][VHOG]
An infundibulum, uterine tube, uterus, and vagina also differentiate along the oviducts of eutherian mammals.[well established][VHOG]
uterine
Most animals that lay eggs, such as birds and reptiles, have an oviduct instead of a uterus. In monotremes, mammals which lay eggs and include the platypus, either the term uterus or oviduct is used to describe the same organ, but the egg does not develop a placenta within the mother and thus does not receive further nourishment after formation and fertilization. Marsupials have two uteruses, each of which connect to a lateral vagina and which both use a third, middle 'vagina' which functions as the birth canal. Marsupial embryos form a choriovitelline 'placenta' (which can be thought of as something between a monotreme egg and a 'true' placenta), in which the egg's yolk sac supplies a large part of the embryo's nutrition but also attaches to the uterine wall and takes nutrients from the mother's bloodstream.
Two uteruses usually form initially in a female fetus, and in placental mammals they may partially or completely fuse into a single uterus depending on the species. In many species with two uteruses, only one is functional. Humans and other higher primates such as chimpanzees, along with horses, usually have a single completely fused uterus, although in some individuals the uteruses may not have completely fused [Wikipedia:Uterus]
2012-09-17
VHOG:0001137
BTO:0001424
CALOHA:TS-1102
EFO:0000975
EMAPA:29915
EV:0100113
FMA:17558
GAID:172
MA:0000389
MAT:0000127
MESH:D014599
MGI:csmith
MIAA:0000127
MP:0001120
NCIT:C12405
OpenCyc:Mx4rvViojJwpEbGdrcN5Y29ycA
UMLS:C0042149
VHOG:0001137
galen:Uterus
uberon
UBERON:0000995
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.678
ncithesaurus:Uterus
uterus
A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP].
http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl
Organ with organ cavity which connects the cervical canal of uterus to the vestibule of vagina.[FMA]
The genital canal in the female, leading from the opening of the vulva to the cervix of the uterus. [TFD][VHOG]
The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.[well established][VHOG]
vaginal
'The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.' Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective, Third Edition (2001) Orlando Fla.: Harcourt College Publishers, p.688
2012-09-17
2012-11-29
FMA:19949
VHOG:0001138
BTO:0000243
CALOHA:TS-1103
EFO:0000976
EMAPA:18986
EV:0100117
FMA:19949
GAID:381
MA:0000394
MAT:0000128
MESH:D014621
MIAA:0000128
NCIT:C12407
OpenCyc:Mx4rvVj1B5wpEbGdrcN5Y29ycA
UMLS:C0042232
VHOG:0001138
galen:Vagina
uberon
distal oviductal region
distal portion of oviduct
vaginae
UBERON:0000996
FMA
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.688
ncithesaurus:Vagina
vagina
A filament, mostly protein, that grows from follicles found in the dermis[WP].
TODO for now we treat vibrissa/whisker as a syonym, but these have different follicles. We could introduce subclasses (see also: Pangolin scales)
this class defines an individual hair
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
BTO:0001501
CALOHA:TS-0430
EFO:0000958
EMAPA:18769
EV:0100157
FMA:53667
GAID:71
MA:0000155
MAT:0000160
MESH:D006197
MIAA:0000160
NCIT:C32705
OpenCyc:Mx4rvVjOX5wpEbGdrcN5Y29ycA-Mp88EdaAAACgycbRww
UMLS:C0018494
VHOG:0001191
hair
uberon
coat hair
coat/ hair
fur
microchaeta
quill
setulae
vibrissa
whisker
UBERON:0001037
ncithesaurus:Hair
strand of hair
the terminal portion of the intestinal tube, terminating with the anus
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
The terminal portion of the large intestine between the ileo-pelvic colon and the anus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
rectal
In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html
2012-09-17
VHOG:0001751
AAO:0010401
BTO:0001158
CALOHA:TS-1180
EFO:0000848
EHDAA2:0001592
EHDAA:5836
EMAPA:17896
EV:0100081
FMA:14544
GAID:311
ISBN:0-683-40008-8
MA:0000336
MAT:0000050
MESH:A03.492.411.495.767
MIAA:0000050
MP:0000492
NCIT:C12390
OpenCyc:Mx4rvVjaU5wpEbGdrcN5Y29ycA
UMLS:C0034896
VHOG:0001751
XAO:0000238
galen:Rectum
terminal portion of intestine
uberon
intestinum rectum
rectal sac
terminal portion of large intestine
UBERON:0001052
VHOG
ncithesaurus:Rectum
rectum
Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
AAO:0010841
AEO:0000000
BILA:0000000
CARO:0000000
EHDAA2:0002229
FBbt:10000000
FBbt_root:00000000
FMA:62955
HAO:0000000
MA:0000001
NCIT:C12219
TAO:0100000
TGMA:0001822
UMLS:C1515976
WBbt:0000100
XAO:0000000
ZFA:0100000
uberon
UBERON:0001062
ncithesaurus:Anatomic_Structure_System_or_Substance
anatomical entity
Excretion that is the output of a kidney
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
kidney excreta from some taxa (e.g. in aves) may not be liquid
BTO:0001419
CALOHA:TS-1092
EFO:0001939
EMAPA:36554
ENVO:00002047
FMA:12274
GAID:1189
MA:0002545
MAT:0000058
MESH:D014556
MIAA:0000058
NCIT:C13283
OpenCyc:Mx4rvVjGppwpEbGdrcN5Y29ycA
UMLS:C0042036
galen:Urine
uberon
UBERON:0001088
ncithesaurus:Urine
urine
Secretion produced by a sweat gland.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
BTO:0001254
ENVO:02000025
FMA:12275
GAID:1172
MA:0002539
MESH:D013542
NCIT:C13280
OpenCyc:Mx4rvVjJtZwpEbGdrcN5Y29ycA
UMLS:C0038984
uberon
skin exudate
UBERON:0001089
ncithesaurus:Sweat
sweat
Last portion of the large intestine before it becomes the rectum.
TODO - abstract this such that it legitimately covers all vertebrates
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
The last portion of the digestive system, it extracts water and salt from solid wastes before they are eliminated from the body.[AAO]
The posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates. Wallace et al, 2005.[TAO]
Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]
colonic
In mammals, the colon consists of four sections: the ascending colon, the transverse colon, the descending colon, and the sigmoid colon[WP]
In zebrafish, the posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates[ZFIN]
it extracts water and salt from solid wastes before they are eliminated from the body[WP]
2012-06-20
2012-08-14
2012-09-17
AAO:0010400
TAO:0000706
VHOG:0000648
AAO:0010400
BTO:0000269
CALOHA:TS-0158
EFO:0000361
EMAPA:18939
EV:0100079
FMA:14543
GAID:309
MA:0000335
MAP:0000001
MAT:0000526
MESH:A03.492.411.495.356
NCIT:C12382
OpenCyc:Mx4rvgLEM5wpEbGdrcN5Y29ycA
TAO:0000706
UMLS:C0009368
VHOG:0000648
XAO:0000243
ZFA:0000706
ZFIN:curator
galen:Colon
large bowel
posterior intestine
uberon
hindgut
UBERON:0001155
AAO
TAO
VHOG
ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11
UBERON:0001155
ZFIN:curator
ncithesaurus:Colon
colon
An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[GO].
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
Organ which secretes a fluid containing enzymes that aid in the digestion of food.[AAO]
In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG]
pancreatic
As a secretory organ serving exocrine and endocrine functions, the pancreas is specific to the vertebrates[PMID:16417468] Hagfishes and lampreys are unique in the complete separation of their endocrine pancreas (islet or- gan) and their exocrine pancreas (50). The endocrine and exocrine pancreas are coassociated in crown gnathostomes (50). In Branchiostoma and Ciona, there is no diverticulum as there is in hagfishes, lampreys, and gnathostomes, only dispersed insulin-secreting cells in the walls of the gastrointestinal tract (51, 52)
The zebrafish does not have a discrete pancreas. Exocrine pancreatic tissue can be found scattered along the intestinal tract. The acinar structure of the exocrine pancreas is very similar to that of mammals and comprises cells with a very dark, basophilic cytoplasm
The mature pancreas of higher vertebrates and mammals comprises two major functional units: the exocrine pancreas, which is responsible for the production of digestive enzymes to be secreted into the gut lumen, and the endocrine pancreas, which has its role in the synthesis of several hormones with key regulatory functions in food uptake and metabolism. The exocrine portion constitutes the majority of the mass of the pancreas, and contains only two different cell types, the secretory acinar cells and the ductular cells. The endocrine portion, which comprises only 1-2% of the total mass, contains five different cell types, which are organized into mixed functional assemblies referred to as the islets of Langerhans
2012-06-20
2012-09-17
AAO:0010112
VHOG:0000050
AAO:0010112
BTO:0000988
CALOHA:TS-0736
EFO:0000855
EHDAA2:0001367
EHDAA:6893
EMAPA:17503
EV:0100092
FMA:7198
GAID:334
GO:0031016
MA:0000120
MAT:0000075
MESH:D010179
MIAA:0000075
NCIT:C12393
OpenCyc:Mx4rvVimZZwpEbGdrcN5Y29ycA
TAO:0000140
UMLS:C0030274
VHOG:0000050
XAO:0000136
ZFA:0000140
galen:Pancreas
uberon
UBERON:0001264
AAO
VHOG
AAO:BJB
DOI:10.1016/j.crvi.2007.03.006 Madsen OD, Pancreas phylogeny and ontogeny in relation to a 'pancreatic stem cell'. C.R. Biologies (2007)
ncithesaurus:Pancreas
pancreas
A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord.
many sources state the CP as sole producer of CSF, but this is disputed [DOI:10.1007/s11064-015-1581-6]
http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl
Portion of organism substance that is a clear fluid that occupies the subarachnoid space and the ventricular system around and inside the brain.[TAO]
In vertebrates, at early stages of Central Nervous System (CNS) development, the architecture of the brain primordium reveals the presence of the cavity of brain vesicles, which is filled by Embryonic Cerebro-Spinal Fluid (E-CSF). (...) Rat and chick E-CSF proteomes are similar, although rat is more complex in certain groups of proteins, e.g., apolipoproteins, which may be involved in the control of neural diversity, and has soluble enzymes present, just like adult human CSF, but unlike chick E-CSF, revealing phylogenetic brain differences between these groups of vertebrates.[uncertain][VHOG]
EHDAA2 models this as developing from CP, which is wrong
the FMA def states that this is subarachnoid spaces only. ZFA def states subarachnoid spaces and brain ventricles, but not SC (and has part_of to brain). Circulation: It circulates from the lateral ventricles to the foramen of Monro (Interventricular foramen), third ventricle, aqueduct of Sylvius (Cerebral aqueduct), fourth ventricle, foramen of Magendie (Median aperture) and foramina of Luschka (Lateral apertures), subarachnoid space over brain and spinal cord. It should be noted that the CSF moves in a pulsatile manner throughout the CSF system with nearly zero net flow. CSF is reabsorbed into venous sinus blood via arachnoid granulations.
2012-08-14
2012-09-17
TAO:0002184
VHOG:0001278
EHDAA2
FMA
BIRNLEX:1798
BTO:0000237
CALOHA:TS-0130
EFO:0000329
EHDAA2:0004441
ENVO:02000029
EV:0100311
FMA:20935
GAID:1181
MA:0002503
MAT:0000499
MESH:A12.207.268
NCIT:C12692
TAO:0002184
UMLS:C0007806
VHOG:0001278
ZFA:0001626
CSF
cerebral spinal fluid
uberon
liquor cerebrospinalis
spinal fluid
UBERON:0001359
TAO
VHOG
BIRNLEX:1798
DOI:10.1021/pr050213t Parada C, Gato A, Bueno D, Mammalian embryonic cerebrospinal fluid proteome has greater apolipoprotein and enzyme pattern complexity than the avian proteome. Journal of Proteome Research (2005)
ZFIN:curator
ncithesaurus:Cerebrospinal_Fluid
cerebrospinal fluid
http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl
FMA:45733
organ neck
uberon
UBERON:0001560
neck of organ
Sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
The organ of hearing and of equilibrium. [TFD][VHOG]
Both vertebrate and invertebrate auditory organs are thought to have evolved from primitive mechanosensors, but the nature of the ancestral structure and the evolutionary trajectories followed in distinct animal lineages remain unknown. In particular, we do not know how many types of mechanosensor existed in the protostome-deuterostome ancestor from which insects and vertebrates evolved or whether the PDA had an auditory organ.[well established][VHOG]
auricular
2012-09-17
VHOG:0000330
AAO:0011014
BTO:0000368
CALOHA:TS-1165
EFO:0000826
EHDAA2:0000423
EHDAA:502
EMAPA:16193
EV:0100353
FMA:52780
GAID:62
GO:0042471
MA:0000236
MAT:0000138
MESH:D004423
MIAA:0000138
NCIT:C12394
OpenCyc:Mx4rvViXS5wpEbGdrcN5Y29ycA
OpenCyc:Mx4rvVjL05wpEbGdrcN5Y29ycA
UMLS:C0013443
UMLS:C0521421
VHOG:0000330
XAO:0000189
galen:Ear
uberon
auditory apparatus
auris
UBERON:0001690
VHOG
DOI:10.1002/dvdy.20207 Boekhoff-Falk G, Hearing in Drosophila: Development of Johnston's organ and emerging parallels to vertebrate ear development. Developmental Dynamics (2005)
NIFSTD:birnlex_1062
ncithesaurus:Ear
ear
A horn-like keratin structure covering the dorsal aspect of the terminal phalanges of fingers and toes[WP].
Use this class for both the nails of primates and the homologous claws of mammals such as mouse.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
A primate's nail consists of the unguis alone; the subunguis has disappeared
BTO:0001719
CALOHA:TS-2034
EFO:0000956
EMAPA:35580
EV:0100159
FMA:54326
GAID:1320
MA:0002703
MAT:0000158
MESH:D009262
MIAA:0000158
NCIT:C33156
OpenCyc:Mx4rvVjJv5wpEbGdrcN5Y29ycA
UMLS:C0027342
VHOG:0001361
XAO:0003103
galen:Nail
nail/claw
claw
uberon
talon
UBERON:0001705
ncithesaurus:Nail
The nails of humans and the claws are moth are highly similar. Both species have a proximal nail fold, cuticle, nail matrix, nail bed, nail plate, and hyponychium. Distinguishing features are the shape of the nail and the presence of an extended hyponychium in the mouse [PMC3579226]
nail
Aqueous substance secreted by the lacrimal gland.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
BTO:0001499
CALOHA:TS-1016
EMAPA:36537
ENVO:02000034
FMA:59756
GAID:1173
MA:0002508
MESH:D013666
NCIT:C33739
UMLS:C0039409
galen:Tear
galen:Tears
lacrimal fluid
lacrimal gland secretion
lacrimal secretion
tear
tears
uberon
tear fluid
UBERON:0001827
ncithesaurus:Tear
secretion of lacrimal gland
A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
salivary
We classify a wide variety of not necessarily homologous fluids here. In humans, the saliva is a turbid and slightly viscous fluid, generally of an alkaline reaction, and is secreted by the parotid, submaxillary, and sublingual glands. In the mouth the saliva is mixed with the secretion from the buccal glands. In man and many animals, saliva is an important digestive fluid on account of the presence of the peculiar enzyme, ptyalin
BTO:0001202
CALOHA:TS-0891
EMAPA:36536
ENVO:02000036
FMA:59862
GAID:1167
GO:0046541
MA:0002507
MAT:0000444
MESH:D012463
NCIT:C13275
OpenCyc:Mx4rvVjJ95wpEbGdrcN5Y29ycA
UMLS:C0036087
galen:Saliva
salivary gland secretion
uberon
sailva normalis
saliva atomaris
saliva molecularis
UBERON:0001836
GO
ncithesaurus:Saliva
saliva
An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation.
to axiomatize the different forms of mammary gland secretion an ontology of the phases of pregnancy/lactation is required. Using the existing GO def of lactation is circular.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
The detailed similarities of mammary glands in living monotremes, marsupials, and eutherians argue for a monophyletic origin of these glands, perhaps by the combination of parts of preexisting sebaceous and sweat glands.[well established][VHOG]
ncit:Milk refers specifically to cow milk
2012-09-17
VHOG:0001263
ncit
BTO:0000868
CALOHA:TS-0636
EMAPA:36540
ENVO:02000031
EV:0100126
FMA:62100
GAID:1230
MA:0002552
MAT:0000056
MESH:A13.622
MIAA:0000056
NCIT:C13401
OpenCyc:Mx4rvVjGZJwpEbGdrcN5Y29ycA
UMLS:C1511310
VHOG:0001263
galen:Milk
mammary gland milk
uberon
UBERON:0001913
VHOG
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.224
ncithesaurus:Breast_Fluid_or_Secretion
milk
Organism substance that is composed of sperm cells suspended in seminal fluid.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
seminal
Note that in this ontology, semen is defined as the sum of sperm and seminal fluid, where seminal fluid is defined in taxonomically generic way (see comments for UBERON:0006530).
BTO:0001230
CALOHA:TS-0917
EMAPA:31488
FMA:62966
GAID:1169
MA:0002522
MESH:D012661
NCIT:C13277
NCIT:C13713
OpenCyc:Mx4rvgC-zpwpEbGdrcN5Y29ycA
UMLS:C1518159
UMLS:C2756969
uberon
ejaculate
sperm
UBERON:0001968
ncithesaurus:Male_Genital_System_Fluid_or_Secretion
ncithesaurus:Semen
semen
The liquid component of blood, in which erythrocytes are suspended.
http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl
plasma
portion of plasma
BTO:0000131
CALOHA:TS-0800
EFO:0001905
EMAPA:35690
FMA:62970
GAID:1178
MA:0002501
MAT:0000052
MESH:D010949
MIAA:0000052
NCIT:C13356
OpenCyc:Mx4rEg4ZYrIbEduAAAAOpmP6tw
UMLS:C0032105
blood plasm
portion of blood plasma
uberon
UBERON:0001969
ncithesaurus:Plasma
blood plasma
vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium.
http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl
In many species, bile is stored in the gallbladder and upon eating is discharged into the duodenum.
aids the process of digestion of lipids in the small intestine
bile salts function to emulsify dietary fats and facilitate their intestinal absorption
elimination of cholesterol
major excretory route for potentially harmful exogenous lipophilic substances
many hormones and pheromones are excreted in bile, and contribute to growth and development of the intestine in some species and provide attractants for the weaning of non-human vertebrates
protects the organism from enteric infections by excreting immune globulin A (IgA), inflammatory cytokines, and stimulating the innate immune system in the intestine
BTO:0000121
CALOHA:TS-1172
ENVO:02000023
FMA:62971
GAID:1157
MA:0002513
MESH:D001646
NCIT:C13192
UMLS:C0005388
ZFA:0005857
galen:Bile
uberon
fel
gall
UBERON:0001970
ncithesaurus:Bile
bile
The portion of blood plasma that excludes clotting factors.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
BTO:0000133
BTO:0001239
CALOHA:TS-0923
EHDAA2:0004728
EMAPA:35770
FMA:63083
MA:0002502
NCIT:C13325
UMLS:C0229671
serum
uberon
UBERON:0001977
ncithesaurus:Serum
blood serum
Portion of semisolid bodily waste discharged through the anus[MW,modified]
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
Excretion in semisolid state processed by the intestine.[FMA]
fecal
excreta
BTO:0000440
CALOHA:TS-2345
ENVO:00002003
FMA:64183
GAID:1199
MA:0002509
MAT:0000053
MESH:D005243
MIAA:0000053
NCIT:C13234
OpenCyc:Mx4rvVjJMZwpEbGdrcN5Y29ycA
UMLS:C0015733
galen:Feces
faeces
fecal material
fecal matter
matières fécales@fr
merde@fr
partie de la merde@fr
piece of shit
porción de mierda@es
portion of excrement
portion of faeces
portion of fecal material
portion of fecal matter
portion of feces
portionem cacas
stool
teil der fäkalien@de
cow dung
cow pat
dung
fewmet
frass
guano
portion of dung
portion of guano
portion of scat
scat
spraint
uberon
droppings
excrement
ordure
spoor
UBERON:0001988
FMA:64183
ncithesaurus:Feces
feces
A two-lobed endocrine gland found in all vertebrates, located in front of and on either side of the trachea in humans, and producing various hormones, such as triiodothyronine and calcitonin[BTO].
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
Either of paired structures located in the throat which develop from the ventral wall of the pharynx and excretes hormones involved in the morphological and functional changes during metamorphosis as well as influencing other tissues.[AAO]
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (2) a groove in the pharyngeal floor known as the endostyle, or a thyroid gland derived from part of the endostyle (...).[well established][VHOG]
In fish, it is usually located below the gills and is not always divided into distinct lobes. However, in some teleosts, patches of thyroid tissue are found elsewhere in the body, associated with the kidneys, spleen, heart, or eyes
In larval lampreys, the thyroid originates as an exocrine gland, secreting its hormones into the gut, and associated with the larva's filter-feeding apparatus. In the adult lamprey, the gland separates from the gut, and becomes endocrine, but this path of development may reflect the evolutionary origin of the thyroid. For instance, the closest living relatives of vertebrates, the tunicates and Amphioxus, have a structure very similar to that of larval lampreys, and this also secretes iodine-containing compounds (albeit not thyroxine)
In tetrapods, the thyroid is always found somewhere in the neck region. In most tetrapod species, there are two paired thyroid glands - that is, the right and left lobes are not joined together. However, there is only ever a single thyroid gland in most mammals, and the shape found in humans is common to many other species
2012-06-20
2012-09-17
AAO:0010544
VHOG:0000418
AAO:0010544
BTO:0001379
CALOHA:TS-1047
EFO:0000861
EHDAA2:0002028
EHDAA:2148
EHDAA:2975
EMAPA:17068
EV:0100133
FMA:9603
GAID:465
MA:0000129
MAT:0000081
MESH:D013961
MIAA:0000081
NCIT:C12400
OpenCyc:Mx4rvVjLT5wpEbGdrcN5Y29ycA
UMLS:C0040132
VHOG:0000418
XAO:0000162
galen:ThyroidGland
thyroid
uberon
glandula thyroidea
NCBITaxon:32443
NCBITaxon:32523
NCBITaxon:7746
UBERON:0002046
AAO
VHOG
AAO:BJB
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28
Romer
ncithesaurus:Thyroid_Gland
thyroid gland
Respiration organ that develops as an oupocketing of the esophagus.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO]
Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ (reference 1); Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung (reference 2).[well established][VHOG]
pulmonary
respiration organ in all air-breathing animals, including most tetrapods, a few fish and a few snails. In mammals and the more complex life forms, the two lungs are located in the chest on either side of the heart. Their principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere. This exchange of gases is accomplished in the mosaic of specialized cells that form millions of tiny, exceptionally thin-walled air sacs called alveoli. // Avian lungs do not have alveoli as mammalian lungs do, they have Faveolar lungs. They contain millions of tiny passages known as para-bronchi, connected at both ends by the dorsobronchi
2012-06-20
2012-09-17
AAO:0010567
VHOG:0000310
AAO:0000275
AAO:0010567
BTO:0000763
CALOHA:TS-0568
EFO:0000934
EHDAA2:0001042
EHDAA:1554
EHDAA:2205
EMAPA:16728
EV:0100042
FMA:7195
GAID:345
MA:0000415
MAT:0000135
MESH:D008168
MIAA:0000135
NCIT:C12468
OpenCyc:Mx4rvVjKy5wpEbGdrcN5Y29ycA
UMLS:C0024109
VHOG:0000310
XAO:0000119
galen:Lung
pulmo
uberon
UBERON:0002048
AAO
VHOG
AAO:SBH
ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210, DOI:10.1371/journal.pone.0024019 Zheng W, Wang Z, Collins JE, Andrews RM, Stemple D, Gong Z, Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung. PLoS One (2011)
ncithesaurus:Lung
Snakes and limbless lizards typically possess only the right lung as a major respiratory organ; the left lung is greatly reduced, or even absent. Amphisbaenians, however, have the opposite arrangement, with a major left lung, and a reduced or absent right lung [WP]
lung
An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO]
general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs.
2012-06-20
AAO:0010386
FMA
AAO:0010386
BTO:0001491
EHDAA:512
EMAPA:16245
FMA:7085
MA:0000019
MESH:D014781
NCIT:C28287
RETIRED_EHDAA2:0002201
UMLS:C0042779
XAO:0003034
visceral organ
visceral organ system
uberon
Organsystem@de
splanchnic tissue
viscera
visceral tissue
UBERON:0002075
AAO
BTO:0001491
ncithesaurus:Viscera
viscus
the organ that functions to filter blood and to store red corpuscles and platelets
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
An organ involved in red blood cell filtration and immune response.[AAO]
With the advent of clonal selection, the accumulation and segregation of T and B cells in specialized organs for antigen presentation became necessary, and indeed the spleen is found in all jawed vertebrates, but not in agnathans or invertebrates.[well established][VHOG]
lienal
splenic
In humans, it is located in the left upper quadrant of the abdomen. It removes old red blood cells and holds a reserve in case of hemorrhagic shock, especially in animals like horses (not in humans), while recycling iron
Neither hagfish nor lampreys possess what might be considered a discrete and condensed spleen. Hagfish possess dispersed lymphoid tissue within the submucosa of the intestine (96) associated with the portal vein (97), whereas lymphoid tissue is associated with the typhlosole portion of the intestine in lampreys (96)
It synthesizes antibodies in its white pulp and removes, from blood and lymph node circulation, antibody-coated bacteria along with antibody-coated blood cells
2012-06-20
2012-09-17
AAO:0010395
VHOG:0000120
AAO:0010395
BTO:0001281
CALOHA:TS-0956
EFO:0000869
EMAPA:18767
EV:0100055
FMA:7196
GAID:1289
ISBN:0-683-40008-8
MA:0000141
MAT:0000085
MESH:A15.382.520.604.713
MIAA:0000085
MP:0000689
NCIT:C12432
OpenCyc:Mx4rvVjgw5wpEbGdrcN5Y29ycA
TAO:0000436
UMLS:C0037993
VHOG:0000120
XAO:0000328
ZFA:0000436
galen:Spleen
uberon
lien
UBERON:0002106
AAO
VHOG
AAO:BMZ
ISBN:978-0781765190 Paul WE, Fundamental Immunology (2008) p.94
ncithesaurus:Spleen
spleen
An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
Organ which secretes bile and participates in formation of certain blood proteins.[AAO]
relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO]
All vertebrates possess a liver (reference 1); Later in craniate evolution, an anterior gill arch was transformed into jaws, and many new types of feeding subsequently evolved.(...) A liver evolved that, among its many functions, stores considerable energy as glycogen or lipid (reference 2).[well established][VHOG]
hepatic
An organ sometimes referred to as a liver is found associated with the digestive tract of the primitive chordate Amphioxus. However, this is an enzyme secreting gland, not a metabolic organ, and it is unclear how truly homologous it is to the vertebrate liver. The zebrafish liver differs from the mammalian liver in that the hepatocytes are not clearly organized in cords or lobules and the typical portal triads are not apparent. In addition, the zebrafish liver does not have Kuppfer cells. Furthermore, a clear distinction can be made between the male and female liver in the adult zebrafish. The female hepatocytes are very basophilic (Figure 15c) as a result of the production of vitellogenin (Van der Ven et al. 2003).
The liver is found in all vertebrates, and is typically the largest visceral organ. Its form varies considerably in different species, and is largely determined by the shape and arrangement of the surrounding organs. Nonetheless, in most species it is divided into right and left lobes; exceptions to this general rule include snakes, where the shape of the body necessitates a simple cigar-like form. The internal structure of the liver is broadly similar in all vertebrates.
secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].
Only ZFA considers this part_of immune system - we weaken this to an overlaps relation, as in general it's only a subset of cells that have clear immune function.
2012-06-20
2012-09-17
AAO:0010111
VHOG:0000257
ZFA
AAO:0010111
BTO:0000759
CALOHA:TS-0564
EFO:0000887
EHDAA2:0000997
EHDAA:2197
EMAPA:16846
EV:0100089
FMA:7197
GAID:288
MA:0000358
MAT:0000097
MESH:D008099
MIAA:0000097
NCIT:C12392
OpenCyc:Mx4rvVimppwpEbGdrcN5Y29ycA
TAO:0000123
UMLS:C0023884
VHOG:0000257
XAO:0000133
ZFA:0000123
galen:Liver
uberon
iecur
jecur
UBERON:0002107
AAO
VHOG
AAO:BJB
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.526, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43
ncithesaurus:Liver
liver
A paired organ of the urinary tract which has the production of urine as its primary function.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
One of either of a pair of structures lying on either side of the dorsal aorta in which fluid balance is regulated and waste is excreted out in the form of urine.[AAO]
renal
2012-06-20
AAO:0000250
AAO:0000250
BTO:0000671
CALOHA:TS-0510
EFO:0000929
EMAPA:17373
EV:0100096
FMA:7203
GAID:423
MA:0000368
MAT:0000119
MESH:D007668
MIAA:0000119
NCIT:C12415
OpenCyc:Mx4rvVjlYpwpEbGdrcN5Y29ycA
UMLS:C0022646
XAO:0003267
galen:Kidney
reniculate kidney
uberon
UBERON:0002113
AAO
AAO:BJB
ncithesaurus:Kidney
kidney
An organ that houses olfactory neurons and is responsible for the sense of smell. Examples include the vertebrate nose and the Drosophila dorsal organ.
An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
fma general anatomical term. xao has no subtypes (but Johnstons organ develops from this). An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint
AAO:0010180
BTO:0001772
FBbt:00005158
FMA:77659
UBERON:cjm
VHOG:0000287
XAO:0000273
olfactory organ
olfactory sense organ
olfactory sensory organ
main olfactory organ
primary olfactory organ
uberon
olfactory neuroepithelium
organ olfactus
organum olfactorium
UBERON:0002268
olfactory organ
A serous membrane that lines the peritoneal cavity[VHOG,modified].
TODO - in ZFA is_a epithelium
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
An epithelium that lines the peritoneal cavity.[TAO]
Serous membrane that forms the lining of the abdominal cavity or the coelom. It covers most of the intra-abdominal organs, supports the abdominal organs, and serves as a conduit for their blood and lymph vessels and nerves. It is composed of a layer of mesothelium.[AAO]
peritoneal
todo: check MA/EMAPA.
2012-06-20
2012-08-14
AAO:0010814
TAO:0005120
MA
AAO:0010814
BTO:0001472
CALOHA:TS-2072
EV:0100087
FMA:9584
GAID:18
MA:0000449
MESH:A01.047.025.600
NCIT:C12770
OpenCyc:Mx4rvjJ72ZwpEbGdrcN5Y29ycA
TAO:0005120
UMLS:C0031153
VHOG:0001257
XAO:0000139
ZFA:0005120
galen:Peritoneum
uberon
peritonaeum
UBERON:0002358
AAO
TAO
AAO:JMG
ZFIN:curator
ncithesaurus:Peritoneum
peritoneum
The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid.
TODO - FMA treats the gland as part of the prostate - see also FMA:74119.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
prostatic
BTO:0001129
CALOHA:TS-0828
EFO:0000858
EMAPA:19287
EV:0100104
FMA:9600
GAID:392
GO:0030850
MA:0000404
MAT:0000078
MESH:D011467
MIAA:0000078
NCIT:C12410
OpenCyc:Mx4rv6trqZwpEbGdrcN5Y29ycA
UMLS:C0033572
VHOG:0001261
galen:ProstateGland
male prostate
prostate
uberon
prostata
UBERON:0002367
ncithesaurus:Prostate_Gland
prostate gland
Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified].
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
AEO:0000098
BTO:0001488
CALOHA:TS-1300
EHDAA2:0003098
EMAPA:35999
FMA:9602
GAID:335
MA:0002563
MESH:D004702
NCIT:C12704
OpenCyc:Mx4rvbkiRZwpEbGdrcN5Y29ycA
UMLS:C0014133
ductless gland
glandula endocrina
uberon
ductless gland
glandulae endocrinae
UBERON:0002368
ncithesaurus:Endocrine_Gland
endocrine gland
Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO].
http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl
Anatomical structure which is found on the surface of the kidney and secretes various hormones including epinephrine, norephinephrine, aldosterone, corticosterone, and cortisol.[AAO]
All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG]
The origin of the adrenal gland is still controversial. It is thought to share the same origin as the kidney and gonads, derived from coelomic epithelium of the urogenital ridge and/or the underlying mesenchyme (Keegan and Hammer, 2002; Morohashi, 1997). We follow Kardong and state homology at the level of the cortex and medulla rather than gland as a whole
suprarenal cortex manufactures corticosteroids; suprarenal medulla manufactures epinephrine and norepinephrine; suprarenal medulla receives preganglionic sympathetic innervation from the greater thoracic splanchnic n.
2012-06-20
2012-09-17
AAO:0010551
VHOG:0001141
AAO:0010551
BTO:0000047
CALOHA:TS-0016
EFO:0000238
EMAPA:18426
EV:0100135
FMA:9604
GAID:446
GO:0030325
MA:0000116
MAT:0000071
MESH:D000311
MIAA:0000071
NCIT:C12666
OpenCyc:Mx4rvXYiz5wpEbGdrcN5Y29ycA
UMLS:C0001625
VHOG:0001141
XAO:0000164
galen:AdrenalGland
glandula adrenalis
glandula suprarenalis
uberon
adrenal
adrenal capsule
adrenal medulla cell
atrabiliary capsule
epinephric gland
epinephros
glandula suprarenalis
interrenal gland
suprarenal capsule
suprarenal gland
UBERON:0002369
AAO
VHOG
AAO:BJB
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9
ncithesaurus:Adrenal_Gland
adrenal gland
the soft tissue that fills the cavities of bones
TODO - create superclass for bone marrow / head kidney. both are portions of tissue in the hematopoetic system. also consider adding as subclass of zone of bone organ for consistency with FMA. See also: Leydig and epigonal organs
consider placement of NCIT:C53466 medullary bone
http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl
The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG]
In adults, marrow in large bones produces new blood cells[Wikipedia:Bone_marrow]
2012-09-17
VHOG:0001218
AAO:0011007
BTO:0000141
BTO:0000829
CALOHA:TS-0087
EFO:0000868
EMAPA:32760
EV:0100046
FMA:9608
GAID:1287
MA:0000134
MAT:0000084
MESH:D001853
MGI:cwg
MIAA:0000084
MP:0002397
NCIT:C12431
OpenCyc:Mx4rvVm-FpwpEbGdrcN5Y29ycA
UMLS:C0005953
VHOG:0001218
XAO:0000123
galen:BoneMarrow
medulla ossea
medulla ossium
uberon
medulla of bone
medullary bone
UBERON:0002371
VHOG
DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood Cells and Blood Cell Development in the Animal Kingdom. Annual Review of Cell and Developmental Biology (2006)
ncithesaurus:Bone_Marrow
bone marrow
Transudate contained in the pericardial cavity.[FMA]
http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl
BTO:0001016
FMA:9887
MA:0002530
uberon
UBERON:0002409
pericardial fluid
an organ that functions as a secretory or excretory organ
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
glandular
UBERON:MIAA_0000021
AAO:0000212
AEO:0000096
BTO:0000522
EFO:0000797
EHDAA2:0003096
EHDAA:2161
EHDAA:4475
EHDAA:6522
EMAPA:18425
FBbt:00100317
FMA:7146
FMA:86294
HAO:0000375
MA:0003038
MAT:0000021
MGI:csmith
MIAA:0000021
MP:0002163
NCIT:C13319
OpenCyc:Mx4rwP3vyJwpEbGdrcN5Y29ycA
UMLS:C1285092
WikipediaCategory:Glands
galen:Gland
glandular organ
uberon
Druese
glandula
UBERON:0002530
ncithesaurus:Gland
gland
An organ involved in reproduction
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
GO uses genitalia for the singular organ
GO
EMAPA:17381
EMAPA:37731
MA:0001752
MESH:D005835
NCIT:C25177
OpenCyc:Mx4rwO39aJwpEbGdrcN5Y29ycA
TGMA:0000591
UBERON:xp
UMLS:C0017420
WBbt:0008422
genital organ
reproductive system organ
sex organ
uberon
genitalia
UBERON:0003133
MA:th
ncithesaurus:Genitalia
reproductive organ
Any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
MA:0001751
MP:0000653
OBOL:automatic
genitalia gland
gland of genitalia
gland of reproductive system
reproductive gland
reproductive system gland
sex gland
uberon
UBERON:0003937
reproductive gland
A proximal-distal subdivision of the digestive tract.
intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
FBbt:00100315
FMA:71131
uberon
alimentary system subdivision
intestinal tract
segment of intestinal tract
subdivision of alimentary system
UBERON:0004921
subdivision of digestive tract
An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
MA:0000522
abdomen organ
uberon
UBERON:0005172
abdomen element
An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
EMAPA:37062
MA:0000529
abdominal segment organ
uberon
UBERON:0005173
MA:th
abdominal segment element
An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
EMAPA:37270
MA:0000516
trunk organ
uberon
UBERON:0005177
MA:th
trunk region element
An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
EMAPA:37273
MA:0000557
thoracic cavity organ
uberon
UBERON:0005178
MA:th
thoracic cavity element
An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
EMAPA:37271
MA:0000563
uberon
upper body organ
UBERON:0005181
MA:th
thoracic segment organ
A sex gland that is part of a male reproductive system.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
BTO:0000080
EMAPA:19285
MA:0000399
OBOL:automatic
uberon
accessory sex gland
UBERON:0005399
male reproductive gland
Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers.
add subclasses based on resolution of CARO tracker item. Also check: adnexal gland. Note that MP implicitly includes hypodermis.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
the tissue or structures associated with or embedded in the skin such as hair and hair follicles, sweat glands, sebaceous glands and claws or nails[MP:0010678]
EMAPA:37883
GO:GO
body hair or bristle
uberon
adnexae cutis
skin adnexa
skin adnexal structure
skin appendage
UBERON:0006003
MA:th
MP:0010678
integumentary adnexa
Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
fluid
EMAPA:37441
FMA:280556
GAID:266
MESH:A12.207
MESH:D001826
galen:BodyFluid
body fluid
uberon
UBERON:0006314
MA:th
bodily fluid
A portion of organism substance that secreted_by a respiratory system.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
EMAPA:36550
MA:0002533
NCIT:C13722
OBOL:automatic
UMLS:C1514899
uberon
respiratory system fluid
respiratory system secretion
UBERON:0006538
ncithesaurus:Respiratory_System_Fluid_or_Secretion
respiratory system fluid/secretion
A substance that is secreted by a mammary gland. The substance may differ depending on phase, with colostrum produced during pregancy/early lactation, and milk produced afterwards.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
EMAPA:36538
MA:0002505
uberon
lactiferous gland fluid
lactiferous gland secretion
mammary gland fluid
mammary gland secreted fluid
mammary gland secretion
secretion of mammary gland
UBERON:0006539
mammary gland fluid/secretion
The pharynx is the part of the digestive system immediately posterior to the mouth[GO].
currently this is an extremely generic class, encompassing both protostomes and deuterostomes.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
branchial
pharyngeal
FBbt:00005380
GO:0060465
MAT:0000049
MIAA:0000049
uberon
anterior part of foregut
pharyngeal tube
UBERON:0006562
pharynx
This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells[GO]
keep this grouping class so long as it is required for GO
http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl
All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG]
2012-09-17
VHOG:0001141
GO:0030325
VHOG:0001141
adrenal gland - interrenal gland
adrenal gland/interrenal tissue
uberon
adrenal - interrenal gland
suprarenal gland - interrenal gland
UBERON:0006858
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9
adrenal/interrenal gland
Any gland that is part of the digestive system.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
AAO:0000130
BTO:0000345
UBERON:cjm
uberon
digestive gland
UBERON:0006925
digestive system gland
A dark greenish mass that accumulates in the bowel during fetal life and is discharged shortly after birth.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
BTO:0000838
ncithesaurus:Meconium
uberon
UBERON:0007109
meconium
Of or pertaining to the period of time immediately following birth, or to the newborn.
consider splitting infant/newborn
http://purl.obolibrary.org/obo/uberon.owl
BTO:0001762
EV:0300037
HsapDv:0000082
MmusDv:0000096
NIF_Organism:birnlex_695
OGES:000025
neonatal stage
fledgling stage
hatchling
hatchling stage
infant stage
nestling stage
pouch stage
puggle
puggle stage
uberon
newborn stage
UBERON:0007221
neonate stage
Matter ejected from the lungs, bronchi, and trachea, through the mouth.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
BTO:0001297
CALOHA:TS-0963
Dorlands_Medical_Dictionary:MerckSource
EMAPA:36553
FMA:312401
GAID:1171
MA:0002536
MESH:D013183
NCIT:C13278
UMLS:C0038056
uberon
expectoration
UBERON:0007311
ncithesaurus:Sputum
sputum
Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces
http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl
transudative
characteristically low in protein and cellular content (unless there has been secondary concentration)
FMA:12276
GAID:1195
MESH:D005122
ncithesaurus:Transudate
uberon
plasma ultrafiltrate
UBERON:0007779
transudate
Any fluid produced by a serous gland.
http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl
serous fluid
UBERON:cjm
serosal fluid
serous gland fluid
uberon
UBERON:0007794
secretion of serous gland
An external organ of a male organism that is specialized to deliver sperm during copulation. Intromittent organs are found most often in terrestrial species, as most aquatic species fertilize their eggs externally, although there are exceptions[WP].
this is a broad grouping class connecting a number of different analagous organs by their function. We place the insect aedeagus here rather than penis, although this is somewhat arbitrary given the broadness of the current definition
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
Surface structure that is an external structure of a male organism through which sperm is transferred to a female organism during mating.[TAO]
2012-08-14
TAO:0002036
AAO:0010255
FBbt:00004850
HAO:0000091
TAO:0002036
TGMA:0000585
aedeagus
penis
uberon
copulatory organ
UBERON:0008811
TAO
TAO:wd
intromittent organ
A nail, hoof or claw.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
MESH:D006724
uberon
hoof or claw
hoof, claw or nail
keratin plate
keratin sheath
unguis
UBERON:0009564
distal limb integumentary appendage
An anatomical structure that has more than one cell as a part.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
CARO:0010000
FBbt:00100313
multicellular structure
uberon
UBERON:0010000
multicellular anatomical structure
Any gland, other than the gonad, associated with the genital tract, such as the ampulla of the ductus deferens and the bulbourethral, prostate and vesicular glands of the male.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
BTO:0004798
uberon
male accessory gland
male accessory reproductive gland
UBERON:0010147
male accessory sex gland
The portion of the left ventricular outflow tract delineated by the sinotubular ridge superiorly and the bases of the valve leaflets inferiorly; it comprises the aortic sinuses, the aortic valve leaflets, the commissures, and the interleaflet triangles
http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl
The dilated first part of the aorta containing the aortic semilunar valves and the aortic sinuses.
BTO:0004695
FMA:3740
FMA:TA
MP:0011572
MP:0011575
aorta bulb
aortic bulb
aortic root
bulb of ascending aorta
bulbus aortae
root of aorta
supraaortic valve area
uberon
UBERON:0010172
bulb of aorta
blood that remains in the placenta and in the attached umbilical cord after childbirth[WP].
http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl
BTO:0004053
CALOHA:TS-1079
EFO:0001942
MESH:A12.207.152.200
MESH:D005312
uberon
cord blood
fetal blood
umbilical cord blood
UBERON:0012168
Cord blood is collected because it contains stem cells, which can be used to treat hematopoietic and genetic disorders.[WP]
umbilical cord blood
A section through the tube or network of tubes that connects the ovaries to the outside of the body.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
FMA class may only represent the uterine portion
FMA
FMA:18302
subdivision of oviduct
subdivision of uterine tube
uterine tube zone
zone of uterine tube
subdivision of fallopian tube
uberon
UBERON:0013515
subdivision of oviduct
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
uberon
UBERON:0013522
subdivision of tube
Anatomical projection that is part of the integumentl system.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
skin projection
uberon
UBERON:0013703
integumentary projection
A blood that is part of a artery.
http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl
FMA:83066
OBOL:automatic
arterial blood
blood in artery
portion of arterial blood
uberon
UBERON:0013755
arterial blood
A blood that is part of a vein.
http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl
FMA:83067
OBOL:automatic
blood in vein
portion of venous blood
venous blood
uberon
UBERON:0013756
venous blood
A viscus that is part of a abdomen.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
FMA:32413
FMA:67355
OBOL:automatic
abdominal viscera
abdominal viscera set
set of abdominal viscera
uberon
UBERON:0017672
abdominal viscera
Any substance in the body or expelled from the body that is in a gaseous state.
http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl
FMA:84580
gas in anatomical space
portion of gas in anatomical space
uberon
UBERON:0034873
bodily gas
A region or zone on the surface of an organism that encompasses skin and any adnexa, down through muscles and bounded by underlying skeletal support structures.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
uberon
UBERON:0034929
external soft tissue zone
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
FMA:55268
organ sector
organ zonal region
organ zone
uberon
organ region with floating fiat boundary
UBERON:0034944
zone of organ
Any portion of gas located in a part of the respiratory system.
http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl
respiratory gas
respiratory system gas
uberon
UBERON:0034947
gas in respiratory system
A temporal boundary connecting two life cycle stages that follow in immediate succession. A temporal boundary is an abstract, instantaneous entity.
uberon
UBERON:0035943
life cycle temporal boundary
A life cycle temporal boundary that marks the end of the life cycle of the organism.
end of life cycle
moment of death
time of death
uberon
death
end of life
UBERON:0035944
life-death temporal boundary
A life cycle temporal boundary that marks the start of the neonate stage of the organism.
moment of birth
time of birth
uberon
birth
UBERON:0035946
start of neonate stage
A bodily fluid consisting of the contents of the digestive tract expulsed through the anterior portion of the digestive tract.
http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
UBERON:cjm
uberon
regurgitate
UBERON:0036017
regurgitated substance
length unit
A unit which is a standard measure of the distance between two points.
length unit
mass unit
A unit which is a standard measure of the amount of matter/energy of a physical object.
mass unit
time unit
A unit which is a standard measure of the dimension in which events occur in sequence.
time unit
A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements.
Sarah Bost
obsolete obligee role
true
A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements.
Sarah Bost
obsolete obligor role
true
quality
pressure
Obsolete Class
example to be eventually removed
example to be eventually removed
failed exploratory term
The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
Person:Alan Ruttenberg
failed exploratory term
metadata complete
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
metadata complete
organizational term
Term created to ease viewing/sort terms for development purpose, and will not be included in a release
organizational term
ready for release
Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
ready for release
metadata incomplete
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
metadata incomplete
uncurated
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
uncurated
pending final vetting
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
pending final vetting
Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
obsolete_core
true
placeholder removed
placeholder removed
terms merged
An editor note should explain what were the merged terms and the reason for the merge.
terms merged
term imported
This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.
term imported
term split
This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.
term split
This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason.
We expect to be able to mine these new reasons and add instances as required.
obsolete_other
true
universal
Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
Alan Ruttenberg
A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
universal
defined class
A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
"definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
Alan Ruttenberg
defined class
named class expression
A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
Alan Ruttenberg
named class expression
to be replaced with external ontology term
Terms with this status should eventually replaced with a term from another ontology.
Alan Ruttenberg
group:OBI
to be replaced with external ontology term
requires discussion
A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
Alan Ruttenberg
group:OBI
requires discussion
An extension of the ICD-10 created by the U.S. National Center for Health Statistics so that the system could be used to capture more morbidity data. This extension included a section of procedure codes.
ICD-10-CM
NCI
International Classification of Diseases, Tenth Revision, Clinical Modification
Published by the College of American Pathologists, the Systematized Nomenclature of Medicine Clinical Terms is a combination of content of SNOMED Reference Terminology and READ codes.
SNOMED CT
NCI
Systematized Nomenclature of Medicine Clinical Terms
An extension of the ICD-9 created by the U.S. National Center for Health Statistics so that the system could be used to capture more morbidity data. This extension included a section of procedure codes.
ICD-9-CM
NCI
International Classification of Diseases, Ninth Revision, Clinical Modification
John Doe
John Doe's birth
23:59
John Doe's neonate stage
1D temporal interval occuped by John Doe's neonate stage
2000-02-02
rta1
eiqap1
Jane Doe
g
p4
f1
p5
John Doe's patient role
m1
ridqap1
Jane Doe's American Indian or Alaska Native identity datum
p6
rta2
Jane Doe's racial identification process
ETL process of Jane Doe’s racial identity datum
John Doe's Hispanic or Latino identity datum
John Doe’s ethnic identification process
John Doe’s PCORnet Hispanic identity datum
ETL process of John Doe’s ethnic identity datum
Jane Doe's not Hispanic or Latino identity datum
Jane Doe’s ethnic identification process
Jane Doe’s PCORnet not Hispanic identity datum
ETL process of John Doe’s ethnic identity datum
ETL process of Jane Doe’s ethnic identity datum
John Doe's patient role
1234
ICD-10-PCS
International Classification of Diseases, Tenth Revision, Procedure Coding System
CPT
Current Procedural Terminology
HCPCS
Healthcare Common Procedural Coding System
UB-04 FL 42 Revenue Codes
Uniform Billing 04 Form Locator 42 Revenue Codes
## Elucidation
This is used when the statement/axiom is assumed to hold true 'eternally'
## How to interpret (informal)
First the "atemporal" FOL is derived from the OWL using the standard
interpretation. This axiom is temporalized by embedding the axiom
within a for-all-times quantified sentence. The t argument is added to
all instantiation predicates and predicates that use this relation.
## Example
Class: nucleus
SubClassOf: part_of some cell
forall t :
forall n :
instance_of(n,Nucleus,t)
implies
exists c :
instance_of(c,Cell,t)
part_of(n,c,t)
## Notes
This interpretation is *not* the same as an at-all-times relation
axiom holds for all times
## Elucidation
This is used when the first-order logic form of the relation is
binary, and takes no temporal argument.
## Example:
Class: limb
SubClassOf: develops_from some lateral-plate-mesoderm
forall t, t2:
forall x :
instance_of(x,Limb,t)
implies
exists y :
instance_of(y,LPM,t2)
develops_from(x,y)
relation has no temporal argument
A reference to a place on the Earth, by its name or by its geographical location.
geographic location
A health care encounter that occurs in an emergency department facillity and realizes the health care provider role of an organization and the emergency department function of the facility.
PCORnet CDM 4.1
emergency department encounter
Includes ED encounters that become inpatient stays (in which case inpatient stays would be a separate encounter). Excludes urgent care facility visits. ED claims should be pulled before hospitalization claims to ensure that ED with subsequent admission won't be rolled up in the hospital event. Does not include observation stays, where known.
Amanda Hicks
Mathias Brochhausen
William R. Hogan
PCORnet lesbian identity information content entity
Matthew Diller
Sarah Bost
The labels and definitions used for the subclasses of 'PCORnet sexual orientation identity information content entity' are based on the terminology used for the value set options for the PCORnet Common Data Model's 'sexual orientation' field, which is a modifed version of the terms for, and categories of, sexual orientation that are found in the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services (https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base). Neither the PCORnet CDM nor the other source provide definitions of their terms for sexual orientations. Our definitions for the corresponding classes thus point to the terms, rather than explain what they mean, as it is unclear how PCORnet intends them to be understood. Furthermore, these terms may be understood differently by different patients who select them as self-descriptions, as some may understand them to be defined in terms of phenotypic sex, others in terms of gender, and others in terms of some combination of the two.
S. Clint Dowland
A PCORnet sexual orientation identity information content entity that is about some person's identifying as having a sexual orientation referred to by the PCORnet CDM with the term "lesbian."
this fragility is a characteristic of this vase
this fragility inheres in this vase
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
Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
inheres in
inheres in
characteristic of
A dependent inheres in its bearer at all times for which the dependent exists.
a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
this red color inheres in this apple
this red color is a characteristic of this apple
inheres_in
true
MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z
infer input from direct reg
GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),
e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'
enabling an MF enables its parts
true
GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'
involved in BP
This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps"
If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.
inferring direct reg edge from input to regulatory subfunction
inferring direct neg reg edge from input to regulatory subfunction
inferring direct positive reg edge from input to regulatory subfunction
effector input is compound function input
Input of effector is input of its parent MF
if effector directly regulates X, its parent MF directly regulates X
if effector directly positively regulates X, its parent MF directly positively regulates X
if effector directly negatively regulates X, its parent MF directly negatively regulates X
'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).