The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies.
OBO Relations Ontology
2024-04-24
https://github.com/oborel/obo-relations/
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 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
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
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
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>
term editor
alternative label
A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like.
OBO Operations committee
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).
alternative label
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
curator note
An administrative note of use for a curator but of no use for a user
PERSON:Alan Ruttenberg
curator note
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
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
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
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
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
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
'part disjoint with' 'defined by construct' """
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX : <http://example.org/
CONSTRUCT {
[
a owl:Restriction ;
owl:onProperty :part_of ;
owl:someValuesFrom ?a ;
owl:disjointWith [
a owl:Restriction ;
owl:onProperty :part_of ;
owl:someValuesFrom ?b
]
]
}
WHERE {
?a :part_disjoint_with ?b .
}
Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation.
defined by construct
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
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.
Class: ?X DisjointWith: RO_0002162 some ?Y
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162>
PREFIX never_in_taxon: <http://purl.obolibrary.org/obo/RO_0002161>
CONSTRUCT {
in_taxon: a owl:ObjectProperty .
?x owl:disjointWith [
a owl:Restriction ;
owl:onProperty in_taxon: ;
owl:someValuesFrom ?taxon
] .
?x rdfs:subClassOf [
a owl:Restriction ;
owl:onProperty in_taxon: ;
owl:someValuesFrom [
a owl:Class ;
owl:complementOf ?taxon
]
] .
}
WHERE {
?x never_in_taxon: ?taxon .
}
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)
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX part_of: <http://purl.obolibrary.org/obo/BFO_0000050>
PREFIX mutually_spatially_disjoint_with: <http://purl.obolibrary.org/obo/RO_0002171>
CONSTRUCT {
part_of: a owl:ObjectProperty .
[
a owl:Restriction ;
owl:onProperty part_of: ;
owl:someValuesFrom ?x ;
owl:disjointWith [
a owl:Restriction ;
owl:onProperty part_of: ;
owl:someValuesFrom ?y
]
]
}
WHERE {
?x mutually_spatially_disjoint_with: ?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
S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg]
ambiguous for taxon
S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T.
This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost
dubious for taxon
S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162>
PREFIX present_in_taxon: <http://purl.obolibrary.org/obo/RO_0002175>
CONSTRUCT {
in_taxon: a owl:ObjectProperty .
?witness rdfs:label ?label .
?witness rdfs:subClassOf ?x .
?witness rdfs:subClassOf [
a owl:Restriction ;
owl:onProperty in_taxon: ;
owl:someValuesFrom ?taxon
] .
}
WHERE {
?x present_in_taxon: ?taxon .
BIND(IRI(CONCAT(
"http://purl.obolibrary.org/obo/RO_0002175#",
MD5(STR(?x)),
"-",
MD5(STR(?taxon))
)) as ?witness)
BIND(CONCAT(STR(?x), " in taxon ", STR(?taxon)) AS ?label)
}
The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology.
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
http://purl.obolibrary.org/obo/ro/docs/shortcut-relations/
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
http://purl.obolibrary.org/obo/ro/docs/interaction-relations/
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
http://purl.obolibrary.org/obo/ro/docs/interaction-relations/
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
http://purl.obolibrary.org/obo/ro/docs/interaction-relations/
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'
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
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
true if the two properties are disjoint, according to OWL semantics. This should only be used if using a logical axiom introduces a non-simple property violation.
nominally disjoint with
Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be "+", "-" or "0"
2018-03-13T23:59:29Z
is directional form of
2018-03-14T00:03:16Z
is positive form of
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.
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
2020-09-22T11:05:29Z
valid_for_go_annotation_extension
2020-09-22T11:05:18Z
valid_for_go_gp2term
2020-09-22T11:04:12Z
valid_for_go_ontology
2020-09-22T11:05:45Z
valid_for_gocam
eco subset
subset_property
An alternative label for a class or property which has a more general meaning than the preferred name/primary label.
https://github.com/information-artifact-ontology/ontology-metadata/issues/18
has broad synonym
has_broad_synonym
https://github.com/information-artifact-ontology/ontology-metadata/issues/18
database_cross_reference
An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.
https://github.com/information-artifact-ontology/ontology-metadata/issues/20
has exact synonym
has_exact_synonym
https://github.com/information-artifact-ontology/ontology-metadata/issues/20
An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.
https://github.com/information-artifact-ontology/ontology-metadata/issues/19
has narrow synonym
has_narrow_synonym
https://github.com/information-artifact-ontology/ontology-metadata/issues/19
has_obo_format_version
An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct.
https://github.com/information-artifact-ontology/ontology-metadata/issues/21
has related synonym
has_related_synonym
https://github.com/information-artifact-ontology/ontology-metadata/issues/21
in_subset
is defined by
is defined by
This is an experimental annotation
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/
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
https://wiki.geneontology.org/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/
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
[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
https://wiki.geneontology.org/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
A relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist through the separation or transformation of a part of the old entity, and the new entity inherits a significant portion of the matter belonging to that part of the old entity.
derives from part of
inheres in
this fragility is a characteristic of this vase
this red color is a characteristic of this apple
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.
inheres_in
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.
characteristic of
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
Inverse of characteristic_of
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
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
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.
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 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.
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
OBSOLETE A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons.
Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other).
obsolete in neural circuit with
true
OBSOLETE A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next, in which the direction is from the last to the first.
Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other).
obsolete upstream in neural circuit with
true
OBSOLETE A relation that holds between a neuron that is synapsed_by another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_by the next, in which the direction is from the last to the first.
Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other).
obsolete downstream in neural circuit with
true
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/
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):
contained_in
obsolete contained in
true
contains
obsolete contains
true
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/
located_in
http://www.obofoundry.org/ro/#OBO_REL:located_in
located in
https://wiki.geneontology.org/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
surface of
2D boundary of
May be obsoleted, see https://github.com/oborel/obo-relations/issues/260
aligned with
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.
has boundary
has_2D_boundary
has 2D boundary
A relation that holds between two neurons that are electrically coupled via gap junctions.
electrically_synapsed_to
The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to).
tracheates
http://www.ncbi.nlm.nih.gov/pubmed/22402613
innervated_by
has synaptic terminal of
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
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
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
A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g.
x 'cell expresses' y iff:
cell(x)
AND gene(y)
AND exists some 'transcription, DNA templated (GO_0006351)'(t)
AND t occurs_in x
AND t has_input y
cell expresses
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).
regulates in other organism
regulates in another organism
A relationship that holds between a process that regulates a transport process and the entity transported by that process.
regulates transport of
A part of relation that applies only between occurrents.
occurrent 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.
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.
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.
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
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
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.
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.
2017-07-19T17:30:36Z
has ligand
Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another.
2017-07-20T17:11:08Z
transports
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.
2017-07-20T17:19:37Z
occurs across
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.
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.
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.
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.
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.
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.
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.
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
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.
David Osumi-Sutherland
<=
Primitive instance level timing relation between events
before or simultaneous with
x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), 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 and '=' indicates the same instance in time.
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
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
https://wiki.geneontology.org/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
Relation between a neuron and a material anatomical entity that its soma is part of.
<http://purl.obolibrary.org/obo/BFO_0000051> some (
<http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)
has soma location
relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.
fasciculates with
(forall (?x ?y)
(iff
(fasciculates_with ?x ?y)
(exists (?nps ?npbs)
(and
("neuron ; CL_0000540" ?x)
("neuron projection bundle ; CARO_0001001" ?y)
("neuron projection segment ; CARO_0001502" ?nps)
("neuron projection bundle segment ; CARO_0001500' " ?npbs)
(part_of ?npbs ?y)
(part_of ?nps ?x)
(part_of ?nps ?npbs)
(forall (?npbss)
(if
(and
("neuron projection bundle subsegment ; CARO_0001501" ?npbss)
(part_of ?npbss ?npbs)
)
(overlaps ?nps ?npbss)
))))))
fasciculates with
Relation between a neuron and some structure its axon forms (chemical) synapses in.
<http://purl.obolibrary.org/obo/BFO_0000051> some (
<http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some (
<http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some (
<http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)))
axon synapses in
Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it.
<http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))
synapsed by
Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]
Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part.
<http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y)
has plasma membrane part
A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton.
BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))
Expands to: has_part some ('type Ib terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))
synapsed_via_type_Ib_bouton_to
A relation between a motor neuron and a muscle that it synapses to via a type Is bouton.
BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))
Expands to: has_part some ('type Is terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))
synapsed_via_type_Is_bouton_to
A relation between a motor neuron and a muscle that it synapses to via a type II bouton.
BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))
Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))
synapsed_via_type_II_bouton_to
Relation between a muscle and a motor neuron that synapses to it via a type II bouton.
BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))
Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type II terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))
synapsed_by_via_type_II_bouton
Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton.
BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))
Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Ib terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))
synapsed_by_via_type_Ib_bouton
Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input.
synapsed in
http://purl.obolibrary.org/obo/BFO_0000051 some (
http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some (
http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))
has postsynaptic terminal in
has neurotransmitter
releases neurotransmitter
Relation between a muscle and a motor neuron that synapses to it via a type Is bouton.
BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))
Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Is terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))
synapsed_by_via_type_Is_bouton
Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input.
synapses in
<http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)
has presynaptic terminal in
A relation between a motor neuron and a muscle that it synapses to via a type III bouton.
BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0097467 that BFO_0000051 some ( that BFO_0000050 some ?Y))))
Expands to: has_part some ('type III terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))
synapsed_via_type_III_bouton_to
Relation between a muscle and a motor neuron that synapses to it via a type III bouton.
BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0097467 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))
Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type III terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))
synapsed_by_via_type_III_bouton
Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.
<http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))
N1 synapsed_to some N2
Expands to:
N1 SubclassOf (
has_part some (
‘pre-synaptic membrane ; GO:0042734’ that part_of some (
‘synapse ; GO:0045202’ that has_part some (
‘post-synaptic membrane ; GO:0045211’ that part_of some N2))))
synapsed to
Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input.
<http://purl.obolibrary.org/obo/BFO_0000051> some (
<http://purl.obolibrary.org/obo/GO_0030425> and <http://purl.obolibrary.org/obo/BFO_0000051> some (
http://purl.obolibrary.org/obo/GO_0042734 and <http://purl.obolibrary.org/obo/BFO_0000050> some (
<http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)))
dendrite synapsed in
A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input.
has synapse in
<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)
has synaptic terminal in
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
The relation between a neuron projection bundle and a neuron projection that is fasciculated with it.
has fasciculating component
(forall (?x ?y)
(iff
(has_fasciculating_neuron_projection ?x ?y)
(exists (?nps ?npbs)
(and
("neuron projection bundle ; CARO_0001001" ?x)
("neuron projection ; GO0043005" ?y)
("neuron projection segment ; CARO_0001502" ?nps)
("neuron projection bundle segment ; CARO_0001500" ?npbs)
(part_of ?nps ?y)
(part_of ?npbs ?x)
(part_of ?nps ?npbs)
(forall (?npbss)
(if
(and
("neuron projection bundle subsegment ; CARO_0001501" ?npbss)
(part_of ?npbss ?npbs)
)
(overlaps ?nps ?npbss)
))))))
has fasciculating neuron projection
Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.
T innervates some R
Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.
<http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))
innervates
X continuous_with Y if and only if X and Y share a fiat boundary.
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
d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a.
ancestral_stucture_of
evolutionarily_descended_from
derived by descent from
inverse of derived by descent from
has derived by descendant
two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a.
Consider obsoleting and merging with child relation, 'in homology relationship with'
VBO calls this homologous_to
shares ancestor with
serially homologous to
lactation SubClassOf 'only in taxon' some 'Mammalia'
x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z.
The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.
'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria
only in taxon
x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.
Connects a biological entity to its taxon of origin.
in taxon
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.
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
a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b.
attached to part of (anatomical structure to anatomical structure)
attached to part of
true
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
Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure.
Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure
drains
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
A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype).
has phenotype
inverse of has phenotype
phenotype of
x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y
This is the transitive form of the develops from relation
develops from
inverse of develops from
develops into
definition "x has gene product of y if and only if y 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 x"
We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g.
gene product 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
has gene product
'neural crest cell' SubClassOf expresses some 'Wnt1 gene'
x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process
expressed in
Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y.
FBbt
has developmental precursor
TODO - add child relations from DOS
directly develops from
A parasite that kills or sterilizes its host
parasitoid of
inverse of parasitoid of
has parasitoid
inverse of directly develops from
developmental precursor of
directly develops into
p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.
GO
Regulation precludes parthood; the regulatory process may not be within the regulated process.
regulates (processual)
false
regulates
p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.
negatively regulates (process to process)
negatively regulates
p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.
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.
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.
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)".
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.
has function in
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
agent in
Obsoleted as the inverse property was obsoleted.
obsolete actively participates in
true
OBSOLETE x has participant y if and only if x realizes some active role that inheres in y
has agent
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
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
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
surrounds
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
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
x develops from part of y if and only if there exists some z such that x develops from z and z is part of y
develops from part of
x develops_in y if x is located in y whilst x is developing
EHDAA2
Jonathan Bard, EHDAA2
develops in
A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host.
obligate parasite of
A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host.
facultative parasite of
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
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
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.
consumes
has input
https://wiki.geneontology.org/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 in the same state at the beginning of p.
produces
has output
https://wiki.geneontology.org/Has_output
A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)
stem parasite of
A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)
root parasite of
A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well.
hemiparasite of
X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys.
This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).
If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'.
has component participant
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
g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background.
over-expressed in
g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background.
under-expressed in
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
In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1.
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
Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]
x has developmental contribution from y iff x has some part z such that z develops from y
has developmental contribution from
inverse of has developmental contribution from
developmentally contributes to
t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T
induced by
Developmental Biology, Gilbert, 8th edition, figure 6.5(F)
GO:0001759
We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]
developmentally induced by
Inverse of developmentally induced by
developmentally induces
Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p
false
In general you should not use this relation to make assertions - use one of the more specific relations below this one
This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from
developmentally preceded by
c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)
has biological role
c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)
has application role
c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)
has chemical role
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
https://wiki.geneontology.org/Acts_upstream_of_or_within
x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else
This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage
replaces
developmentally replaces
Inverse of developmentally preceded by
developmentally succeeded by
'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue
part of developmental precursor of
x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x
Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part.
ubiquitously expressed in
y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process.
expresses
inverse of ubiquiotously expressed in
ubiquitously expresses
p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss).
This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint.
results in developmental progression of
every flower development (GO:0009908) results in development of some flower (PO:0009046)
p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state.
http://www.geneontology.org/GO.doc.development.shtml
results in development of
an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists.
every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062)
GOC:mtg_berkeley_2013
results in formation of anatomical entity
an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape.
tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)
The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state.
GOC:mtg_berkeley_2013
results in morphogenesis of
an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process
bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)
The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity.
GOC:mtg_berkeley_2013
results in maturation of
foramen ovale closure SubClassOf results in disappearance of foramen ovale
May be merged into parent relation
results in disappearance of
every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)
May be merged into parent relation
results in developmental regression of
Inverse of 'is substance that treats'
is treated by substance
Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat'
where
'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview
x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs.
adapted for living in
A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y.
has habitat
p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.
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
p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.
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.
2017-06-05T17:35:04Z
has exposure stimulus
evolutionary variant of
Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c.
regulates localization of
transports or maintains localization of
q characteristic of 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 characteristic of part of
inheres in part of
characteristic of part of
true
an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast.
The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity
GOC:mtg_berkeley_2013
results in acquisition of features of
A relationship that holds via some environmental process
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution.
evolutionarily related to
A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)
Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions
ecologically related to
An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial.
adapted for
confers advantage in
A mereological relationship or a topological relationship
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
A relationship that holds between entities participating in some developmental process (GO:0032502)
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development
developmentally 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].
In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]
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.
In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology.
contributes to
https://wiki.geneontology.org/Contributes_to
a particular instances of akt-2 enables some instance of protein kinase activity
c enables p iff c is capable of p and c acts to execute p.
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.
enables
https://wiki.geneontology.org/Enables
A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
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.
false
part of structure that is capable of
true
holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism
genomically related to
c involved_in p if and only if c enables some process p', and p' is part of p
actively involved in
enables part of
involved in
https://wiki.geneontology.org/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
regulates levels of (process to entity)
regulates levels of
inverse of enables
enabled by
https://wiki.geneontology.org/Enabled_by
inverse of regulates
regulated by (processual)
regulated by
inverse of negatively regulates
negatively regulated by
inverse of positively regulates
positively regulated by
A relationship that holds via some process of localization
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.
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.
has target end location
Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s.
imports
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
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.
results in transport across
'pollen tube growth' results_in growth_of some 'pollen tube'
results in growth of
'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)
results in transport to from or in
Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s.
exports
an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron.
p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type.
results in commitment to
p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment.
results in determination of
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
input of
inverse of has output
output of
formed as result of
A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity.
results in structural organization of
The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment.
results in specification of
p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c.
results in developmental induction of
http://neurolex.org/wiki/Property:DendriteLocation
has dendrite location
a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a
attached to (anatomical structure to anatomical structure)
attached to
m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to.
Wikipedia:Insertion_(anatomy)
has muscle origin
We need to import uberon muscle to create a stricter domain constraint
m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone.
Wikipedia:Insertion_(anatomy)
has muscle insertion
We need to import uberon muscle into RO to use as a stricter domain constraint
false
x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat
has fused element
A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B.
derived from ancestral fusion of
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.
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.
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
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.
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
This relation is added for formal completeness. It is unlikely to be used in many practical scenarios
spatially coextensive with
In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S
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
branching part of
FMA:85994
In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'.
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.
main stem of
x proper_distributary_of y iff x distributary_of y and x does not flow back into y
proper distributary of
x proper_tributary_of y iff x tributary_of y and x does not originate from y
proper tributary of
x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction).
has developmental potential involving
x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
has potential to developmentally contribute to
x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y
has potential to developmentally induce
x has the potential to develop into y iff x develops into y or if x is capable of developing into y
has potential to develop into
x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y
has potential to directly develop into
'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.
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
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.
directly produces
obsolete has direct output
true
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
causally downstream of
immediately causally downstream of
This term was obsoleted because it has the same meaning as 'directly positively regulates'.
obsolete directly activates
true
p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.
indirectly activates
indirectly positively regulates
https://wiki.geneontology.org/Indirectly_positively_regulates
This term was obsoleted because it has the same meaning as 'directly negatively regulates'.
obsolete directly inhibits
true
p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.
indirectly inhibits
indirectly negatively regulates
https://wiki.geneontology.org/Indirectly_negatively_regulates
relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
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.
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
relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
https://en.wikipedia.org/wiki/Causality
p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.
causally upstream of
p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.
immediately causally upstream of
p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c.
directly provides input for
directly provides input for (process to process)
provides input for
https://wiki.geneontology.org/Provides_input_for
transitive form of directly_provides_input_for
This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'.
transitively provides input for (process to process)
transitively provides input for
p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.
We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
influences (processual)
affects
causally upstream of or within
false
This is an exploratory relation
differs in
https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions
differs in attribute of
differs in attribute
inverse of causally upstream of or within
causally downstream of or within
c involved in regulation of p if c is involved in some p' and p' regulates some p
involved in regulation of
c involved in regulation of p if c is involved in some p' and p' positively regulates some p
involved in positive regulation of
c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
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
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.
executes activity in
enables activity in
is active in
https://wiki.geneontology.org/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.
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.
contributes to morphology of
A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
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.
Considering relabeling as 'pairwise interacts with'
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/ro/docs/interaction-relations/
http://purl.obolibrary.org/obo/MI_0914
An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)
genetically interacts with
http://purl.obolibrary.org/obo/MI_0208
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.
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.
interacts with on organism level
biotically interacts with
http://eol.org/schema/terms/interactsWith
An interaction relationship in which the partners are related via a feeding relationship.
trophically interacts with
A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]
Baleen whale preys on krill
An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members
is subject of predation interaction with
preys upon
preys on
http://eol.org/schema/terms/preysUpon
http://www.inaturalist.org/observations/2942824
A biotic interaction in which the two organisms live together in more or less intimate association.
http://www.ncbi.nlm.nih.gov/pubmed/19278549
We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism
symbiotically interacts with
An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO).
http://www.ncbi.nlm.nih.gov/pubmed/19278549
commensually interacts with
An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO).
http://www.ncbi.nlm.nih.gov/pubmed/19278549
mutualistically interacts with
An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO).
http://www.ncbi.nlm.nih.gov/pubmed/19278549
This relation groups a pair of inverse relations, parasite of and parasitized by
interacts with via parasite-host interaction
Pediculus humanus capitis parasite of human
A parasite-host relationship where an organism benefits at the expense of another.
parasitizes
direct parasite of
parasite of
http://eol.org/schema/terms/parasitizes
Inverse of parasite of
has parasite
parasitised by
directly parasitized by
parasitized by
http://eol.org/schema/terms/hasParasite
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.
semibiotically interacts with
participates in a abiotic-biotic interaction with
Axiomatization to GO to be added later
An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.
phosphorylates
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.
molecularly controls
directly regulates activity of
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.
directly inhibits
molecularly decreases activity of
directly negatively regulates activity of
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.
directly activates
molecularly increases activity of
directly positively regulates activity of
all dengue disease transmitted by some mosquito
A relationship that holds between a disease and organism
Add domain and range constraints
transmitted by
A relation that holds between a disease or an organism and a phenotype
has symptom
The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)
host of
X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y
has host
http://eol.org/schema/terms/hasHost
Bees pollinate Flowers
This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this.
is subject of pollination interaction with
pollinates
http://eol.org/schema/terms/pollinates
has polinator
is target of pollination interaction with
pollinated by
http://eol.org/schema/terms/hasPollinator
Inverse of provides nutrients for
Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion.
acquires nutrients from
inverse of preys on
has predator
is target of predation interaction with
preyed upon by
http://eol.org/schema/terms/HasPredator
http://polytraits.lifewatchgreece.eu/terms/PRED
Anopheles is a vector for Plasmodium
a is a vector for b if a carries and transmits an infectious pathogen b into another living organism
is vector for
has vector
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
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
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
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)
is symbiosis
is commensalism
is mutualism
is parasitism
A biotic interaction where a material entity provides nutrition for an organism.
provides nutrients for
A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening.
is subject of eating interaction with
eats
Inverse of eats
eaten by
is target of eating interaction with
is eaten by
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.
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.
composed primarily of
ABal nucleus child nucleus of ABa nucleus (in C elegans)
c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d
This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage.
child nucleus of
A child nucleus relationship in which the cells are part of a hermaphroditic organism
child nucleus of in hermaphrodite
A child nucleus relationship in which the cells are part of a male organism
child nucleus of in male
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.
has part that occurs in
true
An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y
Axiomatization to GO to be added later
ubiquitinates
is kinase activity
is ubiquitination
See notes for inverse relation
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.
sends output to
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage.
relation between physical entity and a process or stage
x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y).
existence starts during
x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y).
existence starts with
x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))
The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
existence overlaps
x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)
exists during
The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
existence starts and ends during
x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y).
The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
existence ends during
x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y).
The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
existence ends with
x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships
transformation of
x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t
immediate transformation of
x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y).
The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
existence starts during or after
x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends.
The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
existence ends during or before
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 where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.
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
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.
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
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
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
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
determined by (system to material entity)
determined by
inverse of determined by
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.
determined by part of
true
x is transcribed from y if and only if x is synthesized from template y
http://www.ncbi.nlm.nih.gov/pubmed/20226267
transcribed from
inverse of transcribed from
http://www.ncbi.nlm.nih.gov/pubmed/20226267
transcribed to
x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y
http://www.ncbi.nlm.nih.gov/pubmed/20226267
ribosomal translation of
inverse of ribosomal translation of
http://www.ncbi.nlm.nih.gov/pubmed/20226267
ribosomally translates to
A relation that holds between two entities that have the property of being sequences or having sequences.
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
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
started by
http://www.ncbi.nlm.nih.gov/pubmed/20226267
has start sequence
inverse of has start sequence
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
ended by
http://www.ncbi.nlm.nih.gov/pubmed/20226267
has end sequence
inverse of has end sequence
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
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
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
bounds sequence of
inverse of bounds sequence of
is bound by sequence of
x has subsequence y iff all of the sequence parts of y are sequence parts of x
contains
http://www.ncbi.nlm.nih.gov/pubmed/20226267
has subsequence
inverse of has subsequence
contained by
is subsequence of
x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y.
overlaps sequence of
x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y.
disconnected from
does not overlap sequence of
inverse of downstream of sequence of
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.
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
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
is immediately upstream of sequence of
Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'
A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision.
has supporting framework
The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell).
has skeleton
This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional.
p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded.
results in ending of
x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y
Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism
http://eol.org/schema/terms/hyperparasitoidOf
https://en.wikipedia.org/wiki/Hyperparasite
hyperparasitoid of
epiparasite of
hyperparasite of
inverse of hyperparasite of
has epiparasite
has hyperparasite
hyperparasitoidized by
hyperparasitized by
http://en.wikipedia.org/wiki/Allelopathy
allelopath of
http://eol.org/schema/terms/allelopathyYes
x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y
Inverse of has pathogen
pathogen of
A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member
has pathogen
inverse of is evidence for
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
causally influenced by (entity-centric)
causally influenced by
interaction relation helper property
http://purl.obolibrary.org/obo/ro/docs/interaction-relations/
molecular interaction relation helper property
Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c
results in movement of
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).
causally influences (entity-centric)
causally influences
A relation that holds between elements of a musculoskeletal system or its analogs.
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes.
biomechanically related to
m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position.
Wikipedia:Antagonist_(muscle)
has muscle antagonist
inverse of branching part of
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.
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.
lumen of
s is luminal space of x iff s is lumen_of x and s is an immaterial entity
luminal space of
A relation that holds between an attribute or a qualifier and another attribute.
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
participates in a biotic-biotic interaction with
inverse of has skeleton
skeleton of
p directly regulates q iff p is immediately causally upstream of q and p regulates q.
directly regulates (processual)
directly regulates
holds between x and y if and only if the time point at which x starts is equivalent to the time point at which y ends. Formally: iff α(x) = ω(y).
existence starts at end of
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
has part structure that is capable of
p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed.
results in closure 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
results in synthesis of
results in assembly 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
results in disassembly of
results in remodeling of
p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c
results in organization of
holds between x and y if and only if the time point at which x ends is equivalent to the time point at which y starts. Formally: iff ω(x) = α(y).
existence ends at start 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.
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
visits
https://github.com/oborel/obo-relations/issues/74
visited by
visits flowers of
has flowers visited by
lays eggs in
has eggs laid in by
https://github.com/jhpoelen/eol-globi-data/issues/143
kills
is killed by
p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.
directly positively regulates (process to process)
directly positively regulates
https://wiki.geneontology.org/Directly_positively_regulates
p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.
directly negatively regulates (process to process)
directly negatively regulates
https://wiki.geneontology.org/Directly_negatively_regulates
A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host
ectoparasite of
inverse of ectoparasite of
has ectoparasite
A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system
lives inside of
endoparasite of
has endoparasite
A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite
mesoparasite of
inverse of mesoparasite of
has mesoparasite
A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells.
intercellular endoparasite of
inverse of intercellular endoparasite of
has intercellular endoparasite
A sub-relation of endoparasite-of in which the parasite inhabits host cells.
intracellular endoparasite of
inverse of intracellular endoparasite of
has intracellular endoparasite
Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting.
co-roosts with
An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s.
A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host.
A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts.
reservoir host of
An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s.
inverse of reservoir host of
has reservoir host
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.
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.
produced by
Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA.
represses expression of
Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA.
increases expression of
A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity.
is used to study
The primary 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. But the relation is defined more broadly to support other use cases, such as linking genes in which alterations are made to create model systems to the condition the system is used to interrogate, or computational models to real-world phenomena they are defined to simulate.
has role in modeling
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
2017-11-05T02:38:20Z
condition has genetic basis in
2017-11-05T02:45:20Z
has material basis in gain of function germline mutation in
2017-11-05T02:45:37Z
has material basis in loss of function germline mutation in
2017-11-05T02:45:54Z
has material basis in germline mutation in
2017-11-05T02:46:07Z
has material basis in somatic mutation in
2017-11-05T02:46:26Z
has major susceptibility factor
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.
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.
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: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.
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:dph
GOC:kva
GOC:pt
PMID:27812932
Do not use this relation directly. It is intended as a grouping for a more specific relations
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].
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].
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].
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].
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].
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].
2017-11-05T02:58:43Z
is causal germline mutation partially giving rise to
2017-11-05T03:20:01Z
realizable has basis in
2017-11-05T03:20:29Z
is basis for realizable
2017-11-05T03:26:47Z
disease has basis in
A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function.
disease has basis in dysfunction of (disease to anatomical structure)
2017-11-05T03:29:32Z
disease has basis in dysfunction of
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)
2017-11-05T03:37:52Z
disease has basis in disruption of
A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature.
2017-11-05T03:46:07Z
disease has basis in feature
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject.
2017-11-05T03:50:54Z
causal relationship with disease as subject
A relationship between a disease and a process where the disease process disrupts the execution of the process.
disease causes disruption of (disease to process)
2017-11-05T03:51:09Z
disease causes disruption of
disease causes dysfunction of (disease to anatomical entity)
2017-11-05T03:58:20Z
disease causes dysfunction of
A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity.
TODO: complete range axiom once more of CARO has been mireoted in to this ontology
This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here.
2017-11-05T04:06:02Z
disease has location
A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity
2017-12-26T19:37:31Z
disease has inflammation site
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.
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.
2017-12-26T19:50:53Z
disease has feature
A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles.
2017-12-26T19:58:44Z
disease arises from alteration in structure
Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.
2018-01-25T23:20:13Z
enables subfunction
2018-01-26T23:49:30Z
acts upstream of or within, positive effect
https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect
2018-01-26T23:49:51Z
acts upstream of or within, negative effect
https://wiki.geneontology.org/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
2018-01-26T23:53:14Z
acts upstream of, positive effect
https://wiki.geneontology.org/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
2018-01-26T23:53:22Z
acts upstream of, negative effect
https://wiki.geneontology.org/Acts_upstream_of,_negative_effect
2018-03-13T23:55:05Z
causally upstream of or within, negative effect
https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect
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
A relation between two entities, in which one of the entities is any natural or human-influenced factor that directly or indirectly causes a change in the other entity.
has driver
A relation between an entity and a disease of a host, in which the entity is not part of the host itself, and the condition results in pathological processes.
has disease driver
An interaction relationship wherein a plant or algae is living on the outside surface of another plant.
https://en.wikipedia.org/wiki/Epiphyte
epiphyte of
inverse of epiphyte of
has epiphyte
A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material
https://en.wikipedia.org/wiki/Kleptoparasitism
kleptoparasite of
inverse of kleptoparasite of
kleptoparasitized by
An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism.
creates habitat for
An interaction relationship describing organisms that often occur together at the same time and space or in the same environment.
ecologically co-occurs with
An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation.
lays eggs on
inverse of lays eggs on
has eggs laid on by
Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis)
x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x.
2023-01-18T14:28:21Z
A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y.
has roost
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.
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.
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.
immersed in
sardine has consumer some homo sapiens
'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect.
has consumer
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.
has primary substance added
A mass measurement assay measures an material's mass characteristic. A radioactivity detection assay measures the amount of radiation (alpha, beta or gamma ray emmissions) coming from a material.
A relation between an assay and a characteristic, in which the assay generates a data item which is a measure of a characteristic.
2023-05-23T15:24:15Z
assay measures characteristic
Inverse of 'assay measures characteristic'
2023-05-23T15:29:50Z
characteristic measured by assay
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.
triggered by process
realized in response to
https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit
triggered by process
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.
regulates activity of
The entity A has an activity that regulates the quantity or abundance or concentration of the entity B.
regulates quantity of
The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B.
indirectly regulates activity of
The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.
For example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B.
decreases by repression quantity of
The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.
For example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B.
increases by expression quantity of
The entity A has an activity that directly positively regulates the quantity of B.
directly positively regulates quantity of
The entity A has an activity that directly negatively regulates the quantity of B.
directly negatively regulates quantity of
The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B.
indirectly activates
indirectly positively regulates activity of
AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844)
An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it.
destabilizes quantity of
AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488)
An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it.
stabilizes quantity of
The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B.
indirectly inhibits
indirectly negatively regulates activity of
The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B.
directly regulates quantity of
The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B.
indirectly regulates quantity of
The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B.
indirectly negatively regulates quantity of
The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B.
indirectly positively regulates quantity of
a relation between a process and a continuant, in which the process is regulated by the small molecule continuant
2020-04-22T20:27:26Z
has small molecule regulator
a relation between a process and a continuant, in which the process is activated by the small molecule continuant
2020-04-22T20:28:37Z
has small molecule activator
a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant
2020-04-22T20:28:54Z
has small molecule inhibitor
p acts on population of c iff c' is a collection, has members of type c, and p has participant c
2020-06-08T17:21:33Z
acts on population of
a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process
2020-06-24T13:15:17Z
is small molecule regulator of
a relation between a continuant and a process, in which the continuant is a small molecule that activates the process
2020-06-24T13:15:26Z
is small molecule activator of
https://wiki.geneontology.org/Is_small_molecule_activator_of
a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process
2020-06-24T13:15:35Z
is small molecule inhibitor of
https://wiki.geneontology.org/Is_small_molecule_inhibitor_of
The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities.
2020-08-27T08:13:59Z
results in adhesion of
2021-02-26T07:28:29Z
results in fusion of
p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant.
2022-09-26T06:01:01Z
constitutively upstream of
https://wiki.geneontology.org/Constitutively_upstream_of
p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q.
2022-09-26T06:06:20Z
removes input for
https://wiki.geneontology.org/Removes_input_for
p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.
2022-09-26T06:07:17Z
indirectly causally upstream of
p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.
2022-09-26T06:08:01Z
indirectly regulates
x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase 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).
2023-10-12T10:02:28Z
positively regulates in other organism
positively regulates in another organism
x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce 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).
2023-10-12T10:02:42Z
negatively regulates in other organism
negatively regulates in another organism
A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region.
2020-07-17T09:26:52Z
has synaptic input or output in
has synaptic IO in region
A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region.
2020-07-17T09:42:23Z
receives synaptic input in region
A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region.
2020-07-17T09:45:06Z
sends synaptic output to region
A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion).
2020-07-17T09:52:19Z
has synaptic IO throughout
A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion).
2020-07-17T09:55:36Z
receives synaptic input throughout
A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion).
2020-07-17T09:57:27Z
sends synaptic output throughout
Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite.
2020-07-20T12:10:09Z
has sensory dendrite location
has sensory terminal in
has sensory terminal location
has sensory dendrite in
A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it.
2021-05-26T08:40:18Z
receives synaptic input from neuron
A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to.
2021-05-26T08:41:07Z
Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron.
sends synaptic output to cell
A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent.
disease has infectious agent
transcriptomically defined cell type X equivalent to ‘cell’ and (has_exemplar_data value [transcriptomic profile data])
A relation between a material entity and some data in which the data is taken as exemplifying the material entity.
C has_exemplar_data y iff x is an instance of C and y is data about x that is taken as exemplifying of C.
This relation is not meant to capture the relation between occurrents and data.
has exemplar data
exemplar data of
A relation between a group and another group it is part of but does not fully constitute.
X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y.
This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics.
subcluster of
'Lamp5-like Egln3_1 primary motor cortex GABAergic interneuron (Mus musculus)' subClass_of: has_characterizing_marker_set some 'NS forest marker set of Lamp5-like Egln3_1 MOp (Mouse).'; NS forest marker set of Lamp5-like Egln3_1 SubClass_of: ('has part' some 'Mouse Fbn2') and ('has part' some 'Mouse Chrna7') and ('has part' some 'Mouse Fam19a1').
transcriptomically defined cell type X subClass_of: (has_characterizing_marker_set some S1); S1 has_part some gene 1, S1 has_part some gene 2, S1 has_part some gene 3.
A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type.
C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types.
This relation is not meant for cases where set of genes/proteins are only useful as markers in some specific context - e.g. in some specific location. In these cases it is recommended to make a more specific cell class restricted to the relevant context.
has marker gene combination
has marker signature set
has characterizing marker set
q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
different in magnitude relative to
q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
https://orcid.org/0000-0002-6601-2165
q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'.
increased in magnitude relative to
q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
https://orcid.org/0000-0002-6601-2165
q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'.
decreased in magnitude relative to
q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
https://orcid.org/0000-0002-6601-2165
q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
similar in magnitude relative to
q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
https://orcid.org/0000-0002-6601-2165
has relative magnitude
s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.
Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round.
has cross section
s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.
https://orcid.org/0000-0002-6601-2165
q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e.
There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality.
reciprocal of
q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e.
https://orcid.org/0000-0002-6601-2165
'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')
A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface.
has high plasma membrane amount
A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface.
PMID:19243617
'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')
A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface.
has low plasma membrane amount
A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface.
PMID:19243617
Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease.
2021-11-05T17:30:14Z
has phenotype or disease
https://github.com/oborel/obo-relations/issues/478
A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.
2021-11-05T17:30:44Z
has disease
https://github.com/oborel/obo-relations/issues/478
X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y.
ExO:0000083
2021-12-14T20:41:45Z
has exposure medium
A diagnostic testing device utilizes a specimen.
X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.
A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.
See github ticket https://github.com/oborel/obo-relations/issues/497
2021-11-08T12:00:00Z
utilizes
device utilizes material
A relation between entities in which one increases or decreases as the other does the same.
directly correlated with
positively correlated with
A relation between entities in which one increases as the other decreases.
inversely correlated with
negatively correlated with
anticoagulant-containing test tube contains measured amount 5 ml of blood specimen.
A relation between a container and measurement datum that specifies the actual amount of material in the container.
contains measured amount
anticoagulant-containing test tube has maximum capacity 10 ml.
A relation that relates a container to a measurement datum that specifies the maximum capacity of the container. Capacity can refer to either weight or volume.
has maximum capacity
biobank organization owns a specimen
hospital owns a laboratory facility
A primitive relation that holds between entities x and y in which y is at x's full disposal.
This primitive relation is the foundation of the owner's right to have the owned entity at his/her full disposal.
2023-03-29T16:57:03Z
owns
freezer is owned by a biobank organization
Inverse of the owns relation.
2023-03-29T17:06:06Z
is owned by
Helper relation for OWL definition of RO:0018002 myristoylates
is myristoyltransferase activity
A molecularly-interacts-with relationship between two entities, where the subject catalyzes a myristoylation activity that takes the object as input
myristoylates
inverse of myristoylates
myristoylated by
mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)
a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor
is agonist of
pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)
a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level
is inverse agonist of
tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)
a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level
is antagonist of
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a chemical.
chemical relationship
pyruvate anion (CHEBI:15361) is the conjugate base of the neutral pyruvic acid (CHEBI:32816)
A is a direct conjugate base of B if and only if A is chemical entity that is a Brønsted–Lowry Base (i.e., can receive a proton) and by receiving a particular proton transforms it into B.
is direct conjugate base of
neutral pyruvic acid (CHEBI:32816) is the conjugate acid of the pyruvate anion (CHEBI:15361)
A is a direct conjugate acid of B if and only if A is chemical entity that is a Brønsted–Lowry Acid (i.e., can give up a proton) and by removing a particular proton transforms it into B.
is direct conjugate acid of
(E)-cinnamoyl-CoA(4-) (CHEBI:57252) is a deprotonated form (E)-cinnamoyl-CoA (CHEBI:10956), which involves removing four protons.
A is a deprotonated form of B if and only if A is chemical entity that is a Brønsted–Lowry Base (i.e., can receive a proton) and by adding some nonzero number of protons transforms it into B.
This is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations.
obo:chebi#is_conjugate_base_of
is deprotonated form of
(E)-cinnamoyl-CoA (CHEBI:10956) is a protonated form of (E)-cinnamoyl-CoA(4-) (CHEBI:57252), which involves adding four protons.
A is a protonated form of B if and only if A is chemical entity that is a Brønsted–Lowry Acid (i.e., can give up a proton) and by removing some nonzero number of protons transforms it into B.
This is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations.
obo:chebi#is_conjugate_acid_of
is protonated form of
phenol (CHEBI:15882) and aniline (CHEBI:17296) are matched molecular pairs because they differ by one chemical transformation i.e., the replacement of aryl primary amine with aryl primary alcohol.
A and B are a matched small molecular pair (MMP) if their chemical structures define by a single, relatively small, well-defined structural modification.
While this is normally called "matched molecular pair" in the cheminformatics literaturel, it is labeled as "matched small molecular pair" so as to reduce confusion with peptides and other macromolecules, which are also referenced as "molecules" in some contexts.
This relationship is symmetric, meaning if A is a MMP with B iff B is a MMP with A.
This relationship is not transitive, meaning that A is a MMP with B and B is a MMP with C, then A is not necessarily an MMP with C.
2023-02-28T18:53:32Z
is MMP with
is matched molecular pair with
is matched small molecular pair with
A and B are a matched small molecular pair (MMP) if their chemical structures define by a single, relatively small, well-defined structural modification.
While this is normally called "matched molecular pair" in the cheminformatics literaturel, it is labeled as "matched small molecular pair" so as to reduce confusion with peptides and other macromolecules, which are also referenced as "molecules" in some contexts.
This relationship is symmetric, meaning if A is a MMP with B iff B is a MMP with A.
This relationship is not transitive, meaning that A is a MMP with B and B is a MMP with C, then A is not necessarily an MMP with C.
3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol.
Two chemicals are tautomers if they can be readily interconverted.
This commonly refers to prototropy in which a hydrogen's position is changed, such as between ketones and enols. This is also often observed in heterocyclic rings, e.g., ones containing nitrogens and/or have aryl functional groups containing heteroatoms.
2023-03-18T23:49:31Z
obo:chebi#is_tautomer_of
is desmotrope of
is tautomer of
3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol.
carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795)
Group A is a substituent group from Chemical B if A represents the functional part of A and includes information about where it is connected. A is not itself a chemical with a fully formed chemical graph, but is rather a partial graph with one or more connection points that can be used to attach to another chemical graph, typically as a functionalization.
2023-03-18T23:49:31Z
obo:chebi#is_substituent_group_from
is substitutent group from
carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795)
hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851)
Chemical A has functional parent Chemical B if there is chemical transformation through which chemical B can be produced from chemical A.
For example, the relationship between a salt and a freebased compound is a "has functional parent" relationship.
2023-03-18T23:49:31Z
obo:chebi#has_functional_parent
has functional parent
hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851)
dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped.
Chemicals A and B are enantiomers if they share the same molecular graph except the change of the configuration of substituents around exactly one chiral center.
A chemical with no chiral centers can not have an enantiomer. A chemical with multiple chiral centers can have multiple enantiomers, but its enantiomers are not themselves enantiomers (they are diastereomers).
2023-03-18T23:49:31Z
obo:chebi#is_enantiomer_of
is optical isomer of
is enantiomer of
dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped.
pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates.
Chemical A has parent hydride Chemical B if there exists a molecular graphical transformation where functional groups on A are replaced with hydrogens in order to yield B.
2023-03-18T23:49:31Z
obo:chebi#has_parent_hydride
has parent hydride
pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates.
A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.
regulates characteristic
A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C.
positively regulates characteristic
A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C.
negatively regulates characteristic
Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition.
confers susceptibility to condition
brachial artery vessel supplies blood to brachialis muscle
x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y.
2024-02-01T10:09:22Z
vessel supplies blood to
cystic vein vessel drains blood from gallbladder
x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y.
2024-02-01T10:09:41Z
vessel drains blood from
alveolar capillary directly supplies and drains some alveolus
x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y.
2024-02-01T10:09:59Z
directly supplies and drains
A relationship between a ratio or proportion and its dividend.
has dividend
has numerator
A relationship between a ratio or proportion and its divisor.
has divisor
has denominator
This relation groups relations between diseases and any other kind of entity.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease.
2018-09-26T00:00:32Z
disease relationship
p has anatomical participant c iff p has participant c, and c is an anatomical entity
2018-09-26T01:08:58Z
results in changes to anatomical or cellular structure
Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.
TODO: Add homeomorphy axiom
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.
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
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
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.
continuant
An entity that has temporal parts and that happens, unfolds or develops through time.
occurrent
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])
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
independent continuant
spatial region
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])
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
process
disposition
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.
realizable
realizable entity
quality
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])
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.
characteristic
specifically dependent continuant
https://github.com/OBOFoundry/COB/issues/65
https://github.com/oborel/obo-relations/pull/284
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.
role
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])
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.
generically dependent continuant
function
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
material entity
immaterial entity
A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
A material entity that has a plasma membrane and results from cellular division.
CALOHA:TS-2035
FBbt:00007002
FMA:68646
GO:0005623
KUPO:0000002
MESH:D002477
VHOG:0001533
WBbt:0004017
XAO:0003012
CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc.
The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).
We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism.
cell
cell
A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
CARO:mah
Any neuron having a sensory function; an afferent neuron conveying sensory impulses.
BTO:0001037
FBbt:00005124
FMA:84649
MESH:D011984
WBbt:0005759
sensory neuron
Any neuron having a sensory function; an afferent neuron conveying sensory impulses.
ISBN:0721662544
The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
BTO:0000938
CALOHA:TS-0683
FBbt:00005106
FMA:54527
VHOG:0001483
WBbt:0003679
nerve cell
These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma.
neuron
The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
MESH:D009474
http://en.wikipedia.org/wiki/Neuron
measurement datum
A process during which an organism comes into contact with another entity.
exposure of organism
A system which has the disposition to environ one or more material entities.
2013-09-23T16:04:08Z
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 system which has the disposition to environ one or more material entities.
DOI:10.1186/2041-1480-4-43
An environmental system which can sustain and allow the growth of an ecological population.
EcoLexicon:habitat
LTER:238
SWEETRealm:Habitat
https://en.wikipedia.org/wiki/Habitat
A habitat's specificity to an ecological population differentiates it from other environment classes.
habitat
An environmental system which can sustain and allow the growth of an ecological population.
EnvO:EnvO
A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.
molecular function
GO:0003674
Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
This is the same as GO molecular function
gene product or complex activity
molecular_function
A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.
GOC:pdt
true
Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y = Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
E2
E3
KEGG_REACTION:R03876
Reactome:R-HSA-1169394
Reactome:R-HSA-1169395
Reactome:R-HSA-1169397
Reactome:R-HSA-1169398
Reactome:R-HSA-1169402
Reactome:R-HSA-1169405
Reactome:R-HSA-1169406
Reactome:R-HSA-1234163
Reactome:R-HSA-1234172
Reactome:R-HSA-1253282
Reactome:R-HSA-1358789
Reactome:R-HSA-1358790
Reactome:R-HSA-1358792
Reactome:R-HSA-1363331
Reactome:R-HSA-168915
Reactome:R-HSA-173542
Reactome:R-HSA-173545
Reactome:R-HSA-174057
Reactome:R-HSA-174104
Reactome:R-HSA-174144
Reactome:R-HSA-174159
Reactome:R-HSA-174195
Reactome:R-HSA-174227
Reactome:R-HSA-179417
Reactome:R-HSA-180540
Reactome:R-HSA-180597
Reactome:R-HSA-182986
Reactome:R-HSA-182993
Reactome:R-HSA-183036
Reactome:R-HSA-183051
Reactome:R-HSA-183084
Reactome:R-HSA-183089
Reactome:R-HSA-1852623
Reactome:R-HSA-187575
Reactome:R-HSA-1912357
Reactome:R-HSA-1912386
Reactome:R-HSA-1918092
Reactome:R-HSA-1918095
Reactome:R-HSA-1977296
Reactome:R-HSA-1980074
Reactome:R-HSA-1980118
Reactome:R-HSA-201425
Reactome:R-HSA-202453
Reactome:R-HSA-202534
Reactome:R-HSA-205118
Reactome:R-HSA-209063
Reactome:R-HSA-211734
Reactome:R-HSA-2169050
Reactome:R-HSA-2172172
Reactome:R-HSA-2179276
Reactome:R-HSA-2186747
Reactome:R-HSA-2186785
Reactome:R-HSA-2187368
Reactome:R-HSA-2213017
Reactome:R-HSA-264444
Reactome:R-HSA-2682349
Reactome:R-HSA-2730904
Reactome:R-HSA-2737728
Reactome:R-HSA-2769007
Reactome:R-HSA-2900765
Reactome:R-HSA-3000335
Reactome:R-HSA-3134804
Reactome:R-HSA-3134946
Reactome:R-HSA-3249386
Reactome:R-HSA-3780995
Reactome:R-HSA-3781009
Reactome:R-HSA-3788724
Reactome:R-HSA-3797226
Reactome:R-HSA-400267
Reactome:R-HSA-4332236
Reactome:R-HSA-446877
Reactome:R-HSA-450358
Reactome:R-HSA-451418
Reactome:R-HSA-5205682
Reactome:R-HSA-5357757
Reactome:R-HSA-5362412
Reactome:R-HSA-5483238
Reactome:R-HSA-5607725
Reactome:R-HSA-5607728
Reactome:R-HSA-5607756
Reactome:R-HSA-5607757
Reactome:R-HSA-5610742
Reactome:R-HSA-5610745
Reactome:R-HSA-5610746
Reactome:R-HSA-5652009
Reactome:R-HSA-5655170
Reactome:R-HSA-5660753
Reactome:R-HSA-5667107
Reactome:R-HSA-5667111
Reactome:R-HSA-5668454
Reactome:R-HSA-5668534
Reactome:R-HSA-5675470
Reactome:R-HSA-5684250
Reactome:R-HSA-5691108
Reactome:R-HSA-5693108
Reactome:R-HSA-68712
Reactome:R-HSA-69598
Reactome:R-HSA-741386
Reactome:R-HSA-75824
Reactome:R-HSA-870449
Reactome:R-HSA-8948709
Reactome:R-HSA-8956106
Reactome:R-HSA-9013069
Reactome:R-HSA-9013974
Reactome:R-HSA-9014342
Reactome:R-HSA-918224
Reactome:R-HSA-936412
Reactome:R-HSA-936942
Reactome:R-HSA-936986
Reactome:R-HSA-9628444
Reactome:R-HSA-9645394
Reactome:R-HSA-9645414
Reactome:R-HSA-9688831
Reactome:R-HSA-9701000
Reactome:R-HSA-9750946
Reactome:R-HSA-975118
Reactome:R-HSA-975147
Reactome:R-HSA-9758604
Reactome:R-HSA-9793444
Reactome:R-HSA-9793485
Reactome:R-HSA-9793679
Reactome:R-HSA-9796346
Reactome:R-HSA-9796387
Reactome:R-HSA-9796626
Reactome:R-HSA-9815507
Reactome:R-HSA-9817362
Reactome:R-HSA-983140
Reactome:R-HSA-983153
Reactome:R-HSA-983156
ubiquitin conjugating enzyme activity
ubiquitin ligase activity
ubiquitin protein ligase activity
ubiquitin protein-ligase activity
ubiquitin-conjugating enzyme activity
GO:0004842
ubiquitin-protein transferase activity
Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y = Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
GOC:BioGRID
GOC:jh2
PMID:9635407
Reactome:R-HSA-1169394
ISGylation of IRF3
Reactome:R-HSA-1169395
ISGylation of viral protein NS1
Reactome:R-HSA-1169397
Activation of ISG15 by UBA7 E1 ligase
Reactome:R-HSA-1169398
ISGylation of host protein filamin B
Reactome:R-HSA-1169402
ISGylation of E2 conjugating enzymes
Reactome:R-HSA-1169405
ISGylation of protein phosphatase 1 beta (PP2CB)
Reactome:R-HSA-1169406
ISGylation of host proteins
Reactome:R-HSA-1234163
Cytosolic VBC complex ubiquitinylates hydroxyprolyl-HIF-alpha
Reactome:R-HSA-1234172
Nuclear VBC complex ubiquitinylates HIF-alpha
Reactome:R-HSA-1253282
ERBB4 ubiquitination by WWP1/ITCH
Reactome:R-HSA-1358789
Self-ubiquitination of RNF41
Reactome:R-HSA-1358790
RNF41 ubiquitinates ERBB3
Reactome:R-HSA-1358792
RNF41 ubiquitinates activated ERBB3
Reactome:R-HSA-1363331
Ubiquitination of p130 (RBL2) by SCF (Skp2)
Reactome:R-HSA-168915
K63-linked ubiquitination of RIP1 bound to the activated TLR complex
Reactome:R-HSA-173542
SMURF2 ubiquitinates SMAD2
Reactome:R-HSA-173545
Ubiquitin-dependent degradation of the SMAD complex terminates TGF-beta signaling
Reactome:R-HSA-174057
Multiubiquitination of APC/C-associated Cdh1
Reactome:R-HSA-174104
Ubiquitination of Cyclin A by APC/C:Cdc20 complex
Reactome:R-HSA-174144
Ubiquitination of Securin by phospho-APC/C:Cdc20 complex
Reactome:R-HSA-174159
Ubiquitination of Emi1 by SCF-beta-TrCP
Reactome:R-HSA-174195
Ubiquitination of cell cycle proteins targeted by the APC/C:Cdh1complex
Reactome:R-HSA-174227
Ubiquitination of Cyclin B by phospho-APC/C:Cdc20 complex
Reactome:R-HSA-179417
Multiubiquitination of Nek2A
Reactome:R-HSA-180540
Multi-ubiquitination of APOBEC3G
Reactome:R-HSA-180597
Ubiquitination of CD4 by Vpu:CD4:beta-TrCP:SKP1 complex
Reactome:R-HSA-182986
CBL-mediated ubiquitination of CIN85
Reactome:R-HSA-182993
Ubiquitination of stimulated EGFR (CBL)
Reactome:R-HSA-183036
Ubiquitination of stimulated EGFR (CBL:GRB2)
Reactome:R-HSA-183051
CBL ubiquitinates Sprouty
Reactome:R-HSA-183084
CBL escapes CDC42-mediated inhibition by down-regulating the adaptor molecule Beta-Pix
Reactome:R-HSA-183089
CBL binds and ubiquitinates phosphorylated Sprouty
Reactome:R-HSA-1852623
Ubiquitination of NICD1 by FBWX7
Reactome:R-HSA-187575
Ubiquitination of phospho-p27/p21
Reactome:R-HSA-1912357
ITCH ubiquitinates DTX
Reactome:R-HSA-1912386
Ubiquitination of NOTCH1 by ITCH in the absence of ligand
Reactome:R-HSA-1918092
CHIP (STUB1) mediates ubiquitination of ERBB2
Reactome:R-HSA-1918095
CUL5 mediates ubiquitination of ERBB2
Reactome:R-HSA-1977296
NEDD4 ubiquitinates ERBB4jmAcyt1s80 dimer
Reactome:R-HSA-1980074
Ubiquitination of DLL/JAG ligands upon binding to NOTCH1
Reactome:R-HSA-1980118
ARRB mediates NOTCH1 ubiquitination
Reactome:R-HSA-201425
Ubiquitin-dependent degradation of the Smad complex terminates BMP2 signalling
Reactome:R-HSA-202453
Auto-ubiquitination of TRAF6
Reactome:R-HSA-202534
Ubiquitination of NEMO by TRAF6
Reactome:R-HSA-205118
TRAF6 polyubiquitinates NRIF
Reactome:R-HSA-209063
Beta-TrCP ubiquitinates NFKB p50:p65:phospho IKBA complex
Reactome:R-HSA-211734
Ubiquitination of PAK-2p34
Reactome:R-HSA-2169050
SMURFs/NEDD4L ubiquitinate phosphorylated TGFBR1 and SMAD7
Reactome:R-HSA-2172172
Ubiquitination of DLL/JAG ligands upon binding to NOTCH2
Reactome:R-HSA-2179276
SMURF2 monoubiquitinates SMAD3
Reactome:R-HSA-2186747
Ubiquitination of SKI/SKIL by RNF111/SMURF2
Reactome:R-HSA-2186785
RNF111 ubiquitinates SMAD7
Reactome:R-HSA-2187368
STUB1 (CHIP) ubiquitinates SMAD3
Reactome:R-HSA-2213017
Auto-ubiquitination of TRAF3
Reactome:R-HSA-264444
Autoubiquitination of phospho-COP1(Ser-387 )
Reactome:R-HSA-2682349
RAF1:SGK:TSC22D3:WPP ubiquitinates SCNN channels
Reactome:R-HSA-2730904
Auto-ubiquitination of TRAF6
Reactome:R-HSA-2737728
Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 HD domain mutants
Reactome:R-HSA-2769007
Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 PEST domain mutants
Reactome:R-HSA-2900765
Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 HD+PEST domain mutants
Reactome:R-HSA-3000335
SCF-beta-TrCp1/2 ubiquitinates phosphorylated BORA
Reactome:R-HSA-3134804
STING ubiquitination by TRIM32 or TRIM56
Reactome:R-HSA-3134946
DDX41 ubiquitination by TRIM21
Reactome:R-HSA-3249386
DTX4 ubiquitinates p-S172-TBK1 within NLRP4:DTX4:dsDNA:ZBP1:TBK1
Reactome:R-HSA-3780995
NHLRC1 mediated ubiquitination of EPM2A (laforin) and PPP1RC3 (PTG) associated with glycogen-GYG2
Reactome:R-HSA-3781009
NHLRC1 mediated ubiquitination of EPM2A and PPP1RC3 associated with glycogen-GYG1
Reactome:R-HSA-3788724
Cdh1:APC/C ubiquitinates EHMT1 and EHMT2
Reactome:R-HSA-3797226
Defective NHLRC1 does not ubiquitinate EPM2A (laforin) and PPP1R3C (PTG) (type 2B disease)
Reactome:R-HSA-400267
BTRC:CUL1:SKP1 (SCF-beta-TrCP1) ubiquitinylates PER proteins
Reactome:R-HSA-4332236
CBL neddylates TGFBR2
Reactome:R-HSA-446877
TRAF6 is K63 poly-ubiquitinated
Reactome:R-HSA-450358
Activated TRAF6 synthesizes unanchored polyubiquitin chains upon TLR stimulation
Reactome:R-HSA-451418
Pellino ubiquitinates IRAK1
Reactome:R-HSA-5205682
Parkin promotes the ubiquitination of mitochondrial substrates
Reactome:R-HSA-5357757
BIRC(cIAP1/2) ubiquitinates RIPK1
Reactome:R-HSA-5362412
SYVN1 ubiquitinates Hh C-terminal fragments
Reactome:R-HSA-5483238
Hh processing variants are ubiquitinated
Reactome:R-HSA-5607725
SCF-beta-TRCP ubiquitinates p-7S-p100:RELB in active NIK:p-176,S180-IKKA dimer:p-7S-p100:SCF-beta-TRCP
Reactome:R-HSA-5607728
beta-TRCP ubiquitinates IkB-alpha in p-S32,33-IkB-alpha:NF-kB complex
Reactome:R-HSA-5607756
TRAF6 oligomer autoubiquitinates
Reactome:R-HSA-5607757
K63polyUb-TRAF6 ubiquitinates TAK1
Reactome:R-HSA-5610742
SCF(beta-TrCP) ubiquitinates p-GLI1
Reactome:R-HSA-5610745
SCF(beta-TrCP) ubiquitinates p-GLI2
Reactome:R-HSA-5610746
SCF(beta-TrCP) ubiquitinates p-GLI3
Reactome:R-HSA-5652009
RAD18:UBE2B or RBX1:CUL4:DDB1:DTL monoubiquitinates PCNA
Reactome:R-HSA-5655170
RCHY1 monoubiquitinates POLH
Reactome:R-HSA-5660753
SIAH1:UBE2L6:Ubiquitin ubiquitinates SNCA
Reactome:R-HSA-5667107
SIAH1, SIAH2 ubiquitinate SNCAIP
Reactome:R-HSA-5667111
PARK2 K63-Ubiquitinates SNCAIP
Reactome:R-HSA-5668454
K63polyUb-cIAP1,2 ubiquitinates TRAF3
Reactome:R-HSA-5668534
cIAP1,2 ubiquitinates NIK in cIAP1,2:TRAF2::TRAF3:NIK
Reactome:R-HSA-5675470
BIRC2/3 (cIAP1/2) is autoubiquitinated
Reactome:R-HSA-5684250
SCF betaTrCP ubiquitinates NFKB p105 within p-S927, S932-NFkB p105:TPL2:ABIN2
Reactome:R-HSA-5691108
SKP1:FBXL5:CUL1:NEDD8 ubiquitinylates IREB2
Reactome:R-HSA-5693108
TNFAIP3 (A20) ubiquitinates RIPK1 with K48-linked Ub chains
Reactome:R-HSA-68712
The geminin component of geminin:Cdt1 complexes is ubiquitinated, releasing Cdt1
Reactome:R-HSA-69598
Ubiquitination of phosphorylated Cdc25A
Reactome:R-HSA-741386
RIP2 induces K63-linked ubiquitination of NEMO
Reactome:R-HSA-75824
Ubiquitination of Cyclin D1
Reactome:R-HSA-870449
TRIM33 monoubiquitinates SMAD4
Reactome:R-HSA-8948709
DTX4 ubiquitinates p-S172-TBK1 within NLRP4:DTX4:STING:TBK1:IRF3
Reactome:R-HSA-8956106
VHL:EloB,C:NEDD8-CUL2:RBX1 complex ubiquitinylates HIF-alpha
Reactome:R-HSA-9013069
Ubiquitination of DLL/JAG ligands upon binding to NOTCH3
Reactome:R-HSA-9013974
Auto-ubiquitination of TRAF3 within activated TLR3 complex
Reactome:R-HSA-9014342
K63-linked ubiquitination of RIP1 bound to the activated TLR complex
Reactome:R-HSA-918224
DDX58 is K63 polyubiquitinated
Reactome:R-HSA-936412
RNF125 mediated ubiquitination of DDX58, IFIH1 and MAVS
Reactome:R-HSA-936942
Auto ubiquitination of oligo-TRAF6 bound to p-IRAK2
Reactome:R-HSA-936986
Activated TRAF6 synthesizes unanchored polyubiquitin chains
Reactome:R-HSA-9628444
Activated TRAF6 synthesizes unanchored polyubiquitin chains upon TLR3 stimulation
Reactome:R-HSA-9645394
Activated TRAF6 synthesizes unanchored polyubiquitin chains upon ALPK1:ADP-heptose stimulation
Reactome:R-HSA-9645414
Auto ubiquitination of TRAF6 bound to ALPK1:ADP-heptose:TIFA oligomer
Reactome:R-HSA-9688831
STUB1 ubiquitinates RIPK3 at K55, K363
Reactome:R-HSA-9701000
BRCA1:BARD1 heterodimer autoubiquitinates
Reactome:R-HSA-9750946
TRAF2,6 ubiquitinates NLRC5
Reactome:R-HSA-975118
TRAF6 ubiquitinqtes IRF7 within the activated TLR7/8 or 9 complex
Reactome:R-HSA-975147
Auto ubiquitination of oligo-TRAF6 bound to p-IRAK2 at endosome membrane
Reactome:R-HSA-9758604
Ubiquitination of IKBKG by TRAF6
Reactome:R-HSA-9793444
ITCH polyubiquitinates MLKL at K50
Reactome:R-HSA-9793485
PRKN polyubiquitinates RIPK3
Reactome:R-HSA-9793679
LUBAC ubiquitinates RIPK1 at K627
Reactome:R-HSA-9796346
MIB2 ubiquitinates RIPK1 at K377, K604, K634
Reactome:R-HSA-9796387
STUB1 ubiquitinates RIPK1 at K571, K604, K627
Reactome:R-HSA-9796626
MIB2 ubiquitinates CFLAR
Reactome:R-HSA-9815507
MIB2 ubiquitinates CYLD at K338, K530
Reactome:R-HSA-9817362
SPATA2:CYLD-bound LUBAC ubiquitinates RIPK1 at K627 within the TNFR1 signaling complex
Reactome:R-HSA-983140
Transfer of Ub from E2 to substrate and release of E2
Reactome:R-HSA-983153
E1 mediated ubiquitin activation
Reactome:R-HSA-983156
Polyubiquitination of substrate
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
NIF_Subcellular:sao1702920020
Wikipedia:Cell_nucleus
cell nucleus
horsetail nucleus
GO:0005634
cell nucleus
nucleus
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
GOC:go_curators
horsetail nucleus
GOC:al
GOC:mah
GOC:vw
PMID:15030757
A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. 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.
A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective.
jl
2012-09-19T15:05:24Z
Wikipedia:Biological_process
biological process
physiological process
single organism process
single-organism process
GO:0008150
A biological process is an evolved 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
biological_process
A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. 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
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
Reactome:R-HSA-6788855
Reactome:R-HSA-6788867
phosphokinase activity
GO:0016301
Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.
kinase activity
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
ISBN:0198506732
Reactome:R-HSA-6788855
FN3KRP phosphorylates PsiAm, RibAm
Reactome:R-HSA-6788867
FN3K phosphorylates ketosamines
true
Catalysis of the transfer of a myristoyl (CH3-[CH2]12-CO-) group to an acceptor molecule.
Reactome:R-HSA-141367
Reactome:R-HSA-162914
GO:0019107
myristoyltransferase activity
Catalysis of the transfer of a myristoyl (CH3-[CH2]12-CO-) group to an acceptor molecule.
GOC:ai
Reactome:R-HSA-141367
Myristoylation of tBID by NMT1
Reactome:R-HSA-162914
Myristoylation of Nef
information content entity
information content entity
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
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.
'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
planned process
processed material
Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
Is a material entity that is created or changed during material processing.
PERSON: Alan Ruttenberg
processed material
assay
Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation.
PlanAndPlannedProcess Branch
measuring
scientific observation
OBI branch derived
assay
container
A device that can be used to restrict the location of material entities over time
03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?)
PERSON: Bjoern Peters
container
device
A voltmeter is a measurement device which is intended to perform some measure function.
An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform.
2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example:
(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part.
(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay.
(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel.
In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay.
PERSON: Helen Parkinson
instrument
OBI development call 2012-12-17.
device
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
A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
disease
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
PATO:0000001
quality
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
PATOC:GVG
A branchiness quality inhering in a bearer by virtue of the bearer's having branches.
ramified
ramiform
PATO:0000402
branched
A branchiness quality inhering in a bearer by virtue of the bearer's having branches.
WordNet:WordNet
A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel.
PATO:0001199
linear
A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel.
ISBN:0881923214
A quality inhering in a bearer by virtue of the bearer's magnitude in respect to a related entity.
proportion
proportionality
quotient
ratio
rate
PATO:0001470
Examples: height to weight; brain size to body size. These could all be children of proportionality. Proportions can be measured as ratios. Some measures may be dimensionless. Not all ratios measure proportionality, eg m/s measures velocity which is not a proportion in the sense defined above, it is a quality in its own right.
proportionality to
A quality inhering in a bearer by virtue of the bearer's magnitude in respect to a related entity.
PATOC:nw
A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer.
2009-10-06T04:37:14Z
PATO:0002124
laminar
A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer.
PATOC:GVG
An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human,
An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes.
OBSOLETE A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism.
This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions.
2017-06-05T17:55:39Z
obsolete exposure event or process
https://github.com/oborel/obo-relations/pull/173
true
Any entity that is ordered in discrete units along a linear axis.
sequentially ordered entity
Any individual unit of a collection of like units arranged in a linear order
An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair.
sequence atomic unit
Any entity that can be divided into parts such that each part is an atomical unit of a sequence
Sequence bearers can be molecular entities, such as a portion of a DNA molecule, or they can be abstract entities, such as an entity representing all human sonic hedgehog regions of the genome with a particular DNA sequence.
sequence bearer
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
http://www.jbiomedsem.com/content/4/1/43
system
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
AAO:0010825
AEO:0000003
BILA:0000003
CARO:0000003
EHDAA2:0003003
EMAPA:0
FMA:305751
FMA:67135
GAID:781
HAO:0000003
MA:0003000
MESH:D000825
SCTID:362889002
TAO:0000037
TGMA:0001823
VHOG:0001759
XAO:0003000
ZFA:0000037
http://dbpedia.org/ontology/AnatomicalStructure
biological structure
connected biological structure
UBERON:0000061
anatomical structure
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
CARO:0000003
connected biological structure
CARO:0000003
A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.
CARO:0001001
NLX:147821
funiculus
nerve fiber bundle
neural fiber bundle
UBERON:0000122
neuron projection bundle
A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.
CARO:0001001
FBC:DOS
FBbt:00005099
nerve fiber bundle
FBbt:00005099
Anatomical entity that has mass.
AAO:0010264
AEO:0000006
BILA:0000006
CARO:0000006
EHDAA2:0003006
FMA:67165
HAO:0000006
TAO:0001836
TGMA:0001826
VHOG:0001721
UBERON:0000465
material anatomical entity
Anatomical entity that has mass.
http://orcid.org/0000-0001-9114-8737
Anatomical entity that has no mass.
AAO:0010265
AEO:0000007
BILA:0000007
CARO:0000007
EHDAA2:0003007
FMA:67112
HAO:0000007
TAO:0001835
TGMA:0001827
VHOG:0001727
immaterial physical anatomical entity
UBERON:0000466
immaterial anatomical entity
Anatomical entity that has no mass.
http://orcid.org/0000-0001-9114-8737
immaterial physical anatomical entity
FMA:67112
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.
AAO:0010841
AEO:0000000
BFO:0000004
BILA:0000000
BIRNLEX:6
CARO:0000000
EHDAA2:0002229
FMA:62955
HAO:0000000
MA:0000001
NCIT:C12219
TAO:0100000
TGMA:0001822
UMLS:C1515976
WBbt:0000100
XAO:0000000
ZFA:0100000
UBERON:0001062
anatomical entity
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.
FMA:62955
http://orcid.org/0000-0001-9114-8737
UMLS:C1515976
ncithesaurus:Anatomic_Structure_System_or_Substance
A vessel through which blood circulates in the body.
consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus
vascular element
AAO:0011004
AEO:0000207
BTO:0001102
CALOHA:TS-0080
EFO:0000817
EHDAA2:0003252
EHDAA:240
EMAPA:32743
EMAPA:35993
FMA:50722
FMA:63183
GAID:169
MA:0000060
MAT:0000393
MESH:D001808
NCIT:C12679
NLXANAT:090901
SCTID:361097006
TAO:0002137
UMLS:C0005847
VHOG:0001250
Wikipedia:Blood_vessel
XAO:0001011
ZFA:0005314
region of vascular tree organ
vascular tree organ region
UBERON:0001981
blood vessel
A vessel through which blood circulates in the body.
BTO:0001102
Wikipedia:Blood_vessel
vascular element
EMAPA:35993
UMLS:C0005847
ncithesaurus:Blood_Vessel
region of vascular tree organ
FMA:50722
vascular tree organ region
FMA:50722
Any of the smallest blood vessels connecting arterioles with venules.
not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element
AAO:0010252
BTO:0002045
CALOHA:TS-2006
EFO:0001906
EMAPA:35198
EV:0100035
FMA:63194
MA:0000065
MESH:D002196
NCIT:C12685
NLXANAT:090902
TAO:0005250
UMLS:C0935624
VHOG:0001253
Wikipedia:Capillary
XAO:0000116
ZFA:0005250
blood capillary
capillary vessel
UBERON:0001982
capillary
https://github.com/obophenotype/uberon/issues/2186
Any of the smallest blood vessels connecting arterioles with venules.
ISBN:0073040584
Wikipedia:Capillary
https://github.com/obophenotype/uberon/issues/137
UMLS:C0935624
ncithesaurus:Capillary
An anatomical structure that has more than one cell as a part.
CARO:0010000
multicellular structure
UBERON:0010000
multicellular anatomical structure
An anatomical structure that has more than one cell as a part.
CARO:0010000
multicellular structure
FBbt:00100313
phenotype
example to be eventually removed
example to be eventually removed
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
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
## 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
Researcher ORCID=0000-0001-6677-8489
Aleix Puig-Barbé
Researcher ORCID=0000-0001-6677-8489
Aleix Puig-Barbé
Researcher
Austin Meier
Researcher
Austin Meier
researcher
Shawn Zheng Kai Tan
researcher
Shawn Zheng Kai Tan
researcher
Raymund Stefancsik
researcher
Raymund Stefancsik
researcher, metadata, diseases, University of Maryland
Lynn Schriml
researcher, metadata, diseases, University of Maryland
Lynn Schriml
researcher
William D Duncan
researcher
William D Duncan
data scientist
Anne Thessen
data scientist
Anne Thessen
researcher (ORCID 0000-0002-2999-0103)
Jie Zheng
researcher (ORCID 0000-0002-2999-0103)
Jie Zheng
researcher
Pier Luigi Buttigieg
researcher
Pier Luigi Buttigieg
researcher
Christian J Stoeckert
researcher
Christian J Stoeckert
bioinformatics researcher
Christopher J. Mungall
bioinformatics researcher
Christopher J. Mungall
researcher
David Osumi-Sutherland
researcher
David Osumi-Sutherland
researcher
Lauren E. Chan
researcher
Lauren E. Chan
researcher
Marie-Angélique Laporte
researcher
Marie-Angélique Laporte
researcher
James P. Balhoff
researcher
James P. Balhoff
researcher (ORCID 0000-0002-8844-9165)
Damion M Dooley
researcher (ORCID 0000-0002-8844-9165)
Damion M Dooley
researcher
Lindsay G Cowell
researcher
Lindsay G Cowell
Canadian biocurator
Pascale Gaudet
Canadian biocurator
Pascale Gaudet
researcher
Mathias Brochhausen
researcher
Mathias Brochhausen
Researcher ORCID=0000-0003-1909-9269
S. Clint Dowland
Researcher ORCID=0000-0003-1909-9269
S. Clint Dowland
researcher
Anna Maria Masci
researcher
Anna Maria Masci
Researcher ORCID=0000-0003-2620-0345
Asiyah Yu Lin
Researcher ORCID=0000-0003-2620-0345
Asiyah Yu Lin
software/data engineer
Jorrit Poelen
software/data engineer
Jorrit Poelen
American chemist
Charles Tapley Hoyt
American chemist
Charles Tapley Hoyt
data item
data item
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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(fol)
Person:Alan Ruttenberg
Person:Alan Ruttenberg
An axiom expressed in first order logic using CLIF syntax
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
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
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
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
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
The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not.
This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease.
out of scope
This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL.
OBO Operations call
logical characteristic of object property
CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation)
A synonym type for describing abbreviations or initalisms
abbreviation
A synonym type for describing ambiguous synonyms
ambiguous synonym
A synonym type for describing dubious synonyms
dubious synonym
EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym)
A synonym type for describing layperson or colloquial synonyms
layperson synonym
CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form)
A synonym type for describing pluralization synonyms
plural form
CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym)
A synonym type for describing UK spelling variants
UK spelling synonym
A synonym type for common misspellings
misspelling
A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway
misnomer
MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol.
A synonym type for names that have been used as primary labels in the past.
previous name
The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College
A synonym type for the legal entity name
legal name