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.
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.
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
pg
2020-09-22T11:05:29Z
valid_for_go_annotation_extension
pg
2020-09-22T11:05:18Z
valid_for_go_gp2term
pg
2020-09-22T11:04:12Z
valid_for_go_ontology
pg
2020-09-22T11:05:45Z
valid_for_gocam
eco subset
subset_property
has_narrow_synonym
in_subset
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
contained in
Containment is location not involving parthood, and arises only where some immaterial continuant is involved.
Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):
Intended meaning:
domain: material entity
range: spatial region or site (immaterial continuant)
contained_in
contained in
contains
contains
penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)
A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.
is allergic trigger for
A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.
is autoimmune trigger for
penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)
A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.
has allergic trigger
A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.
has autoimmune trigger
surface of
May be obsoleted, see https://github.com/oborel/obo-relations/issues/260
aligned with
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
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.
dos
2017-05-24T09:30:46Z
has regulatory component activity
A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.
dos
2017-05-24T09:31:01Z
By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.
has negative regulatory component activity
A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.
dos
2017-05-24T09:31:17Z
By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.
has positive regulatory component activity
dos
2017-05-24T09:36:08Z
A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity.
has necessary component activity
dos
2017-05-24T09:44:33Z
A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.
has component activity
w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
dos
2017-05-24T09:49:21Z
has component process
A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function.
dos
2017-07-19T17:30:36Z
has ligand
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.
dos
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.
dos
2017-07-20T17:19:37Z
occurs across
dos
2017-09-17T13:52:24Z
Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
directly regulated by
Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
GOC:dos
Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
dos
2017-09-17T13:52:38Z
directly negatively regulated by
Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
GOC:dos
Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
dos
2017-09-17T13:52:47Z
directly positively regulated by
Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
GOC:dos
A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
dos
2017-09-22T14:14:36Z
This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.
has effector activity
A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
GOC:dos
A relationship that holds between two images, A and B, where:
A depicts X;
B depicts Y;
X and Y are both of type T'
C is a 2 layer image consiting of layers A and B;
A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.
Note: A and B may be 2D or 3D.
Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.
dos
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.
GOC:dos
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
Relation between a neuron and an anatomical structure 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
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
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
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
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
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
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
Inverse of 'expressed in'
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
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
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
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
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
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
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
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
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
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
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
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.
This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit
directly provides input for
directly provides input for (process to process)
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
true
c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
GOC:cjm
GOC:dos
p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm.
contributes to morphology of
A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
Considering relabeling as 'pairwise interacts with'
This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
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
parasitizes
direct parasite of
parasite of
http://eol.org/schema/terms/parasitizes
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
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
provides nutrients for
is subject of eating interaction with
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
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
pathogen of
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.
GOC:cjm
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
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
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
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:cjm
GOC:dph
GOC:kva
GOC:pt
PMID:27812932
p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.
2018-12-13T11:26:56Z
has primary input
p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.
GOC:cjm
GOC:dph
GOC:kva
GOC:pt
PMID:27812932
Do not use this relation directly. It is intended as a grouping for a more specific relations
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
2018-01-26T23:49:51Z
acts upstream of or within, negative effect
c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive
2018-01-26T23:53:14Z
acts upstream of, positive effect
c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative
2018-01-26T23:53:22Z
acts upstream of, negative effect
2018-03-13T23:55:05Z
causally upstream of or within, negative effect
2018-03-13T23:55:19Z
causally upstream of or within, positive effect
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
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 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
RO:cjm
Genetic information generically depend on molecules of DNA.
The novel *War and Peace* generically depends on this copy of the novel.
The pattern shared by chess boards generically depends on any chess board.
The score of a symphony g-depends on a copy of the score.
This pdf file generically depends on this server.
A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*.
[072-ISO]
g-depends on
generically depends on
Molecules of DNA are carriers of genetic information.
This copy of *War and Peace* is carrier of the novel written by Tolstoy.
This hard drive is carrier of these data items.
*b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*
[072-ISO]
is carrier of
The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.
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
pg
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
pg
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
pg
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
pg
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
pg
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
pg
2020-06-24T13:15:26Z
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
pg
2020-06-24T13:15:35Z
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.
pg
2020-08-27T08:13:59Z
results in adhesion of
pg
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.
pg
2022-09-26T06:01:01Z
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.
pg
2022-09-26T06:06:20Z
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.
pg
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.
pg
2022-09-26T06:08:01Z
indirectly regulates
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
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
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
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
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.
dos
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
true
inverse of has disposition
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.
TODO: Add homeomorphy axiom
is defined by
is defined by
This is an experimental annotation
If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.
inferring direct reg edge from input to regulatory subfunction
inferring direct neg reg edge from input to regulatory subfunction
inferring direct positive reg edge from input to regulatory subfunction
effector input is compound function input
Input of effector is input of its parent MF
if effector directly regulates X, its parent MF directly regulates X
if effector directly positively regulates X, its parent MF directly positively regulates X
if effector directly negatively regulates X, its parent MF directly negatively regulates X