The Population and Community Ontology (PCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators.
http://orcid.org/0000-0002-4366-3088
Ramona Walls
David Osumi-Sutherland
Jie Zheng
Pier Luigi Buttigieg
http://creativecommons.org/publicdomain/zero/1.0/
editor preferred term
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
editor preferred term
example
A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
example of usage
in branch
An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.
GROUP:OBI
OBI_0000277
in branch
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
OBI_0000281
has curation status
definition
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
2012-04-05:
Barry Smith
The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.
Can you fix to something like:
A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.
Alan Ruttenberg
Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria.
On the specifics of the proposed definition:
We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition.
Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable.
We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition
definition
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
editor note
term editor
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
term editor
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
alternative term
definition source
formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
PERSON:Daniel Schober
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition source
has obsolescence reason
Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.
PERSON:Alan Ruttenberg
PERSON:Melanie Courtot
has obsolescence reason
curator note
An administrative note of use for a curator but of no use for a user
PERSON:Alan Ruttenberg
curator note
is denotator type
relates an class defined in an ontology, to the type of it's denotator
In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')
Alan Ruttenberg
is denotator type
imported from
For external terms/classes, the ontology from which the term was imported
PERSON:Alan Ruttenberg
PERSON:Melanie Courtot
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
imported from
expand expression to
ObjectProperty: RO_0002104
Label: has plasma membrane part
Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones
Chris Mungall
expand expression to
expand assertion to
ObjectProperty: RO???
Label: spatially disjoint from
Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
Chris Mungall
expand assertion to
first order logic expression
An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property.
PERSON:Alan Ruttenberg
first order logic expression
antisymmetric property
part_of antisymmetric property xsd:true
use boolean value xsd:true to indicate that the property is an antisymmetric property
Alan Ruttenberg
antisymmetric property
OBO foundry unique label
An alternative name for a class or property which is unique across the OBO Foundry.
The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .
PERSON:Alan Ruttenberg
PERSON:Bjoern Peters
PERSON:Chris Mungall
PERSON:Melanie Courtot
GROUP:OBO Foundry <http://obofoundry.org/>
OBO foundry unique label
Ontology: <http://purl.obolibrary.org/obo/ro/idrange/>
Annotations:
'has ID prefix': "http://purl.obolibrary.org/obo/RO_"
'has ID digit count' : 7,
rdfs:label "RO id policy"
'has ID policy for': "RO"
Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits)
Person:Alan Ruttenberg
has ID digit count
Datatype: idrange:1
Annotations: 'has ID range allocated to': "Chris Mungall"
EquivalentTo: xsd:integer[> 2151 , <= 2300]
Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms
Person:Alan Ruttenberg
has ID range allocated to
Ontology: <http://purl.obolibrary.org/obo/ro/idrange/>
Annotations:
'has ID prefix': "http://purl.obolibrary.org/obo/RO_"
'has ID digit count' : 7,
rdfs:label "RO id policy"
'has ID policy for': "RO"
Relating an ontology used to record id policy to the ontology namespace whose policy it manages
Person:Alan Ruttenberg
has ID policy for
Ontology: <http://purl.obolibrary.org/obo/ro/idrange/>
Annotations:
'has ID prefix': "http://purl.obolibrary.org/obo/RO_"
'has ID digit count' : 7,
rdfs:label "RO id policy"
'has ID policy for': "RO"
Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created.
Person:Alan Ruttenberg
has ID prefix
elucidation
person:Alan Ruttenberg
Person:Barry Smith
Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms
elucidation
has associated axiom(nl)
Person:Alan Ruttenberg
Person:Alan Ruttenberg
An axiom associated with a term expressed using natural language
has associated axiom(nl)
has associated axiom(fol)
Person:Alan Ruttenberg
Person:Alan Ruttenberg
An axiom expressed in first order logic using CLIF syntax
has associated axiom(fol)
is allocated id range
Add as annotation triples in the granting ontology
Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999"
PERSON:Alan Ruttenberg
is allocated id range
has axiom id
Person:Alan Ruttenberg
Person:Alan Ruttenberg
A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI
has axiom label
term replaced by
Add as annotation triples in the granting ontology
Use on obsolete terms, relating the term to another term that can be used as a substitute
Person:Alan Ruttenberg
Person:Alan Ruttenberg
term replaced by
An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.
temporal interpretation
https://github.com/oborel/obo-relations/wiki/ROAndTime
tooth SubClassOf 'never in taxon' value 'Aves'
x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL.
Chris Mungall
?X DisjointWith RO_0002162 some ?Y
never in taxon
A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B.
non-overlapping with
shares no parts with
Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y)
mutually spatially disjoint with
https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern
An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon.
taxonomic class assertion
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.
https://orcid.org/0000-0002-6601-2165
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
https://orcid.org/0000-0002-6601-2165
present in taxon
defined by inverse
An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL.
logical macro assertion
https://github.com/oborel/obo-relations/wiki/ShortcutRelations
An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N.
annotation property cardinality
A logical macro assertion whose domain is an IRI for a class
The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL
logical macro assertion on a class
A logical macro assertion whose domain is an IRI for a property
logical macro assertion on a property
logical macro assertion on an object property
logical macro assertion on an annotation property
An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one.
dispositional interpretation
'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton'
A is has_no_connections_with B if there are no parts of A or B that have a connection with the other.
shares no connection with
Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y))
has no connections with
inherited annotation property
Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of)
curator guidance link
brain always_present_in_taxon 'Vertebrata'
forelimb always_present_in_taxon Euarchontoglires
S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S
This is a very strong relation. Often we will not have enough evidence to know for sure that there are no species within a lineage that lack the structure - loss is common in evolution. However, there are some statements we can make with confidence - no vertebrate lineage could persist without a brain or a heart. All primates are limbed.
never lost in
always present in taxon
This properties were created originally for the annotation of developmental or life cycle stages, such as for example Carnegie Stage 20 in humans.
temporal logical macro assertion on a class
measurement property has unit
has start time value
has end time value
Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property.
start, days post fertilization
Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property.
end, days post fertilization
Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1.
start, years post birth
Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2
end, years post birth
Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1.
start, months post birth
Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2
end, months post birth
Defines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. Thus if month_of_gestation=3, then the stage is 2 month in.
month of gestation
A relationship between a stage class and an anatomical structure or developmental process class, in which the stage is characterized by the appearance of the structure or the occurrence of the biological process
has developmental stage marker
Count of number of days intervening between the start of the stage and the time of coitum.
For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum)
start, days post coitum
Count of number of days intervening between the end of the stage and the time of coitum.
end, days post coitum
start, weeks post birth
end, weeks post birth
If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x subject-partner-in p, y object-partner-in p
is asymmetric relational form of process class
https://github.com/oborel/obo-relations/wiki/InteractionRelations
If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p
is symmetric relational form of process class
https://github.com/oborel/obo-relations/wiki/InteractionRelations
R is the relational form of a process if and only if either (1) R is the symmetric relational form of a process or (2) R is the asymmetric relational form of a process
is relational form of process class
https://github.com/oborel/obo-relations/wiki/InteractionRelations
relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y
The general property hierarchy is:
"directly P" SubPropertyOf "P"
Transitive(P)
Where we have an annotation assertion
"directly P" "is direct form of" "P"
If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q'
Chris Mungall
is direct form of
relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y
Chris Mungall
is indirect form of
logical macro assertion on an axiom
If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL
is a defining property chain axiom
If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.
is a defining property chain axiom where second argument is reflexive
An annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis.
is relational form of a class
A shortcut relationship that holds between two entities based on their identity criteria
logical macro assertion involving identity
A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds.
in approximate one to one relationship with
x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y
The precise meaning of this property is dependent upon some contexts. It is intended to group multiple possible formalisms. Possibilities include a probabilistic interpretation, for example, Pr(x=y) > 0.95. Other possibilities include reified statements of belief, for example, "Database D states that x=y"
is approximately equivalent to
'anterior end of organism' is-opposite-of 'posterior end of organism'
'increase in temperature' is-opposite-of 'decrease in temperature'
x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x).
is opposite of
x is indistinguishable from y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x).
is indistinguishable from
evidential logical macro assertion on an axiom
A relationship between a sentence and an instance of a piece of evidence in which the evidence supports the axiom
This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual.
axiom has evidence
A relationship between a sentence and an instance of a piece of evidence in which the evidence contradicts the axiom
This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual.
axiom contradicted by evidence
In the context of a particular project, the IRI with CURIE NCBIGene:64327 (which in this example denotes a class) is considered to be representative. This means that if we have equivalent classes with IRIs OMIM:605522, ENSEMBL:ENSG00000105983, HGNC:13243 forming an equivalence set, the NCBIGene is considered the representative member IRI. Depending on the policies of the project, the classes may be merged, or the NCBIGene IRI may be chosen as the default in a user interface context.
this property relates an IRI to the xsd boolean value "True" if the IRI is intended to be the representative IRI for a collection of classes that are mutually equivalent.
If it is necessary to make the context explicit, an axiom annotation can be added to the annotation assertion
is representative IRI for equivalence set
OWLAPI Reasoner documentation for representativeElement, which follows a similar idea, but selects an arbitrary member
eco subset
subset_property
has_broad_synonym
database_cross_reference
has_exact_synonym
has_obo_format_version
has_related_synonym
in_subset
shorthand
is defined by
is defined by
This is an experimental annotation
is part of
my brain is part of my body (continuant parthood, two material entities)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)
a core relation that holds between a part and its whole
Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)
A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
part_of
part of
http://www.obofoundry.org/ro/#OBO_REL:part_of
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
a core relation that holds between a whole and its part
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)
A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
has_part
has part
realized in
this disease is realized in this disease course
this fragility is realized in this shattering
this investigator role is realized in this investigation
is realized by
realized_in
[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
realized in
realizes
this disease course realizes this disease
this investigation realizes this investigator role
this shattering realizes this fragility
to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
realizes
accidentally included in BFO 1.2 proposal
- should have been BFO_0000062
obsolete preceded by
preceded by
x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
is preceded by
preceded_by
http://www.obofoundry.org/ro/#OBO_REL:preceded_by
preceded by
precedes
x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
precedes
occurs in
b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
occurs_in
unfolds in
unfolds_in
Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
occurs in
site of
[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
contains process
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.
Damion Dooley
has consumer
inheres in
this fragility inheres in this vase
this red color inheres in this apple
a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
A dependent inheres in its bearer at all times for which the dependent exists.
inheres_in
inheres in
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
bearer_of
is bearer of
bearer of
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
participates in
has participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
has_participant
http://www.obofoundry.org/ro/#OBO_REL:has_participant
has participant
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.
is concretized as
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.
concretizes
this catalysis function is a function of this enzyme
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
function_of
is function of
function of
this red color is a quality of this apple
a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
A quality inheres in its bearer at all times for which the quality exists.
is quality of
quality_of
quality of
this investigator role is a role of this person
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
is role of
role_of
role of
this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
has_function
has function
this apple has quality this red color
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
has_quality
has quality
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
has_role
has role
a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
has disposition
inverse of has disposition
disposition of
A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons.
David Osumi-Sutherland
(forall (?x ?y)
(iff
(neural_circuit_path ?x ?y)
(and
("neuron ; CL_0000540" ?x)
("neuron ; CL_0000540" ?y)
(or
(synapsed_by ?x ?y)
(synapsed_to ?x ?y)))))
(forall (...s ?x ?y ?z)
(iff
(neural_circuit_path ...s ?x ?y ?z)
(and
(neural_circuit_path ...s ?x ?y)
("neuron ; CL_0000540" ?z)
(or
(synapsed_by ?y ?z)
(synapsed_to ?y ?z)))))
(forall (?x ?y)
(iff
(in_neural_circuit_with ?x ?y)
(exists (...s)
(neural_circuit_path ?x ...s ?y))))
in neural circuit with
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.
David Osumi-Sutherland
(forall (?x ?y)
(iff
(upstream_neural_circuit_path ?x ?y)
(and
("neuron ; CL_0000540" ?x)
("neuron ; CL_0000540" ?y)
(synapsed_to ?x ?y))))
(forall (...s ?x ?y ?z)
(iff
(upstream_neural_circuit_path ...s ?x ?y ?z )
(and
(upstream_neural_circuit_path ...s ?x ?y)
("neuron ; CL_0000540" ?z)
(synapsed_to ?y ?z))))
(forall (?x ?y)
(iff
(upstream_in_neural_circuit_with ?x ?y)
(exists (...s)
(upstream_neural_circuit_path ?x ...s ?y))))
upstream in neural circuit with
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.
David Osumi-Sutherland
(forall (?x ?y)
(iff
(downstream_neural_circuit_path ?x ?y)
(and
("neuron ; CL_0000540" ?x)
("neuron ; CL_0000540" ?y)
(synapsed_by ?x ?y))))
(forall (...s ?x ?y ?z)
(iff
(downstream_neural_circuit_path ...s ?x ?y ?z )
(and
(downstream_neural_circuit_path ...s ?x ?y)
("neuron ; CL_0000540" ?z)
(synapsed_by ?y ?z))))
(forall (?x ?y)
(iff
(downstream_in_neural_circuit_with ?x ?y)
(exists (...s)
(downstream_neural_circuit_path ?x ...s ?y))))
downstream in neural circuit with
this cell derives from this parent cell (cell division)
this nucleus derives from this parent nucleus (nuclear division)
a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
derives_from
This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations.
derives from
this parent cell derives into this cell (cell division)
this parent nucleus derives into this nucleus (nuclear division)
a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.
derives_into
derives into
is location of
my head is the location of my brain
this cage is the location of this rat
a relation between two independent continuants, the location and the target, in which the target is entirely within the location
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
location_of
location of
contained in
Containment is location not involving parthood, and arises only where some immaterial continuant is involved.
Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):
Intended meaning:
domain: material entity
range: spatial region or site (immaterial continuant)
contained_in
contained in
contains
contains
penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)
A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.
is allergic trigger for
A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.
is autoimmune trigger for
penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)
A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.
has allergic trigger
A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.
has autoimmune trigger
located in
my brain is located in my head
this rat is located in this cage
a relation between two independent continuants, the target and the location, in which the target is entirely within the location
Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
located_in
http://www.obofoundry.org/ro/#OBO_REL:located_in
located in
the surface of my skin is a 2D boundary of my body
a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity
A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
2D_boundary_of
boundary of
is 2D boundary of
is boundary of
2D boundary of
David Osumi-Sutherland
aligned with
my body has 2D boundary the surface of my skin
a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity
A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
David Osumi-Sutherland
has boundary
has_2D_boundary
has 2D boundary
A relation that holds between two neurons that are electrically coupled via gap junctions.
David Osumi-Sutherland
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).
David Osumi-Sutherland
tracheates
David Osumi-Sutherland
http://www.ncbi.nlm.nih.gov/pubmed/22402613
innervated_by
David Osumi-Sutherland
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
David Osumi-Sutherland
A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane.
bounding layer of
A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other.
Note from NCEAS meeting: consider changing primary label
David Osumi-Sutherland
Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence.
coincident with
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.
David Osumi-Sutherland
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).
David Osumi-Sutherland
regulates in other organism
A relationship that holds between a process that regulates a transport process and the entity transported by that process.
David Osumi-Sutherland
regulates transport of
A part of relation that applies only between occurents.
occurent part of
A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.
dos
2017-05-24T09:30:46Z
has regulatory component activity
A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.
dos
2017-05-24T09:31:01Z
By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.
has negative regulatory component activity
A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.
dos
2017-05-24T09:31:17Z
By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.
has positive regulatory component activity
dos
2017-05-24T09:36:08Z
A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity.
has necessary component activity
dos
2017-05-24T09:44:33Z
A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.
has component activity
w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
dos
2017-05-24T09:49:21Z
has component process
A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function.
dos
2017-07-19T17:30:36Z
has ligand
A relationship 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.
GOC:dos
David Osumi-Sutherland
<=
Primitive instance level timing relation between events
before or simultaneous with
David Osumi-Sutherland
t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)
simultaneous with
David Osumi-Sutherland
t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)
before
David Osumi-Sutherland
Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
during which ends
David Osumi-Sutherland
di
Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
encompasses
David Osumi-Sutherland
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
ends after
David Osumi-Sutherland
starts_at_end_of
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately preceded by
David Osumi-Sutherland
Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
during which starts
David Osumi-Sutherland
starts before
David Osumi-Sutherland
ends_at_start_of
meets
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
immediately precedes
David Osumi-Sutherland
io
X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))
starts during
David Osumi-Sutherland
d
during
X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))
happens during
David Osumi-Sutherland
o
overlaps
X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y).
ends during
Relation between a neuron and an anatomical structure that its soma is part of.
David Osumi-Sutherland
<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.
David Osumi-Sutherland
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.
Chris Mungall
David Osumi-Sutherland
David Osumi-Sutherland
<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.
Chris Mungall
David Osumi-Sutherland
<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.
Alexander Diehl
Chris Mungall
Lindsay Cowell
<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.
David Osumi-Sutherland
Marta Costa
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.
David Osumi-Sutherland
Marta Costa
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.
David Osumi-Sutherland
Marta Costa
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.
David Osumi-Sutherland
Marta Costa
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.
David Osumi-Sutherland
Marta Costa
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.
Chris Mungall
David Osumi-Sutherland
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.
David Osumi-Sutherland
Marta Costa
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.
Chris Mungall
David Osumi-Sutherland
<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.
Chris Mungall
David Osumi-Sutherland
<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.
David Osumi-Sutherland
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.
David Osumi-Sutherland
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.
David Osumi-Sutherland
<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.
David Osumi-Sutherland
connected to
The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)
continuous with
FMA:85972
x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x
We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom
proper overlaps
(forall (?x ?y)
(iff
(proper_overlaps ?x ?y)
(and
(overlaps ?x ?y)
(not (part_of ?x ?y))
(not (part_of ?y ?x)))))
partially overlaps
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
Chris Mungall
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.
Chris Mungall
Jennifer Deegan
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.
Chris Mungall
Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy
BFO_0000051 exactly 0 (BFO_0000050 some ?Y)
spatially disjoint from
https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern
a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b
connected to
https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern
https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern
The M8 connects Glasgow and Edinburgh
a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system.
connects
https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern
https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern
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
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).
Chris Mungall
has phenotype
inverse of has phenotype
Chris Mungall
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
Chris Mungall
David Osumi-Sutherland
Melissa Haendel
Terry Meehan
This is the transitive form of the develops from relation
develops from
inverse of develops from
Chris Mungall
David Osumi-Sutherland
Terry Meehan
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.
Chris Mungall
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
Chris Mungall
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
Chris Mungall
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 participates in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of y comes from x, and the start of x is coincident with or after the end of y
Chris Mungall
David Osumi-Sutherland
has developmental precursor
FBbt
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
process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2.
We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit
Chris Mungall
David Hill
Tanya Berardini
GO
Regulation precludes parthood; the regulatory process may not be within the regulated process.
regulates (processual)
false
regulates
Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
Chris Mungall
negatively regulates (process to process)
negatively regulates
Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
Chris Mungall
positively regulates (process to process)
positively regulates
'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair'))
heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation')
x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation.
Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from)
This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants.
Chris Mungall
has prototype
mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
osteoclast SubClassOf 'capable of' some 'bone resorption'
A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
Chris Mungall
has function realized in
For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
RO_0000053 some (RO_0000054 only ?Y)
capable of
c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
Chris Mungall
has function in
RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))
capable of part of
true
x actively participates in y if and only if x participates in y and x realizes some active role
Chris Mungall
agent in
actively participates in
'heart development' has active participant some Shh protein
x has participant y if and only if x realizes some active role that inheres in y
This may be obsoleted and replaced by the original 'has agent' relation
Chris Mungall
has agent
has active participant
x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x
Chris Mungall
surrounded by
A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
The epidermis layer of a vertebrate is adjacent to the dermis.
The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies.
The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used.
x adjacent to y if and only if x and y share a boundary.
This relation acts as a join point with BSPO
Chris Mungall
adjacent to
A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
inverse of surrounded by
Chris Mungall
surrounds
Chris Mungall
Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporally related to
inverse of starts with
Chris Mungall
Allen
starts
Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
Chris Mungall
started by
starts with
x develops from part of y if and only if there exists some z such that x develops from z and z is part of y
Chris Mungall
develops from part of
x develops_in y if x is located in y whilst x is developing
Chris Mungall
EHDAA2
Jonathan Bard, EHDAA2
develops in
A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host.
obligate parasite of
A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host.
facultative parasite of
inverse of ends with
Chris Mungall
ends
x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
Chris Mungall
finished by
ends with
x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y
Chris Mungall
starts with process that occurs in
has start location
x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y
Chris Mungall
ends with process that occurs in
has end location
p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p.
Chris Mungall
consumes
has input
p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p.
Chris Mungall
produces
has output
A 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
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'
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
Chris Mungall
has developmental contribution from
inverse of has developmental contribution from
Chris Mungall
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 anatomical structure type T to T', where T' develops_from T
Chris Mungall
David Osumi-Sutherland
Melissa Haendel
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
Chris Mungall
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
Chris Mungall
In general you should not use this relation to make assertions - use one of the more specific relations below this one
This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from
developmentally preceded by
c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)
has biological role
c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)
has application role
c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)
has chemical role
c involved in regulation of p if c enables 'p' and p' causally upstream of p
acts upstream of
c acts upstream of or within p if c is enables 'p' and p' causally upstream of or within p
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
Chris Mungall
replaces
developmentally replaces
Inverse of developmentally preceded by
Chris Mungall
developmentally succeeded by
'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue
Chris Mungall
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.
Chris Mungall
ubiquitously expressed in
Inverse of 'expressed in'
Chris Mungall
expresses
inverse of ubiquiotously expressed in
Chris Mungall
ubiquitously expresses
p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure 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.
Chris Mungall
results_in_developmental_progression_of
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.
Chris Mungall
http://www.geneontology.org/GO.doc.development.shtml
results_in_development_of
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)
Chris Mungall
GOC:mtg_berkeley_2013
results_in_formation_of
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.
Chris Mungall
GOC:mtg_berkeley_2013
results_in_morphogenesis_of
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.
Chris Mungall
GOC:mtg_berkeley_2013
results_in_maturation_of
results in maturation of
foramen ovale closure SubClassOf results in disappearance of foramen ovale
Chris Mungall
May be merged into parent relation
results_in_disappearance_of
results in disappearance of
every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)
Chris Mungall
May be merged into parent relation
results in developmental regression of
Inverse of 'is substance that treats'
cjm
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.
Pier Buttigieg
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
cjm
holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y
causally upstream of, positive effect
cjm
holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y
causally upstream of, negative effect
A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event.
Austin Meier
Chris Mungall
Marie Angelique Laporte
cjm
2017-06-05T17:35:04Z
has exposure stimulus
Chris Mungall
evolutionary variant of
Holds between p and c when p is a transportation or localization process and the outcome of this process is to regulate the location of c
Chris Mungall
regulates location of
transports
transports or maintains localization of
q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w.
Because part_of is transitive, inheres in is a sub-relation of inheres in part of
Chris Mungall
inheres in part of
true
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
Chris Mungall
GOC:mtg_berkeley_2013
results_in_acquisition_of_features_of
results in acquisition of features of
A relationship that holds via some environmental process
Chris Mungall
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)
Chris Mungall
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.
Chris Mungall
adapted for
confers advantage in
A mereological relationship or a topological relationship
Chris Mungall
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
mereotopologically related to
A relationship that holds between entities participating in some developmental process (GO:0032502)
Chris Mungall
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].
Chris Mungall
http://www.geneontology.org/GO.annotation.conventions.shtml#colocalizes_with
In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]
Gene Ontology Consortium
colocalizes with
ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity.
Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity.
eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex
We would like to say
if and only if
exists c', p'
c part_of c' and c' capable_of p
and
c capable_of p' and p' part_of p
then
c contributes_to p
However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction.
Chris Mungall
http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to
In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology.
contributes to
a particular instances of akt-2 enables some instance of protein kinase activity
Chris Mungall
catalyzes
executes
has
is catalyzing
is executing
This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time.
enables
Chris Mungall
This is a grouping relation that collects relations used for the purpose of connecting structure and function
functionally related to
this relation holds between c and p when c is part of some c', and c' is capable of p.
Chris Mungall
false
part of structure that is capable of
true
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.
Chris Mungall
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
Chris Mungall
actively involved in
enables part of
involved in
every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid
p regulates levels of c if p regulates some amount (PATO:0000070) of c
Chris Mungall
regulates levels of (process to entity)
regulates levels of
inverse of enables
Chris Mungall
enabled by
inverse of regulates
Chris Mungall
regulated by (processual)
regulated by
inverse of negatively regulates
Chris Mungall
negatively regulated by
inverse of positively regulates
Chris Mungall
positively regulated by
A relationship that holds via some process of localization
Chris Mungall
related via localization to
This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination.
Chris Mungall
has target start location
This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l.
Chris Mungall
has target end location
Holds between p and 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.
Chris Mungall
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
Chris Mungall
results in transport along
Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m.
Chris Mungall
results in transport across
'pollen tube growth' results_in growth_of some 'pollen tube'
Chris Mungall
results in growth of
'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)
Chris Mungall
results in transport to from or in
Chris Mungall
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.
Chris Mungall
http://www.geneontology.org/GO.doc.development.shtml#fate
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.
Chris Mungall
http://www.geneontology.org/GO.doc.development.shtml#fate
results in determination of
An organism that is a member of a population of organisms
is member of is a mereological relation between a item and a collection.
is member of
member part of
SIO
member of
has member is a mereological relation between a collection and an item.
SIO
has member
inverse of has input
Chris Mungall
input of
inverse of has output
Chris Mungall
output of
Chris Mungall
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.
Chris Mungall
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.
Chris Mungall
http://www.geneontology.org/GO.doc.development.shtml#fate
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.
Chris Mungall
results in developmental induction of
Chris Mungall
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
Chris Mungall
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.
Chris Mungall
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.
Chris Mungall
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
Chris Mungall
Chris Mungall
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.
has fused element
A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network.
Chris Mungall
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships
This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)
in branching relationship with
https://github.com/obophenotype/uberon/issues/170
Deschutes River tributary_of Columbia River
inferior epigastric vein tributary_of external iliac vein
x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein.
Chris Mungall
drains into
drains to
tributary channel of
http://en.wikipedia.org/wiki/Tributary
http://www.medindia.net/glossary/venous_tributary.htm
This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)
tributary of
http://en.wikipedia.org/wiki/Tributary
Deschutes River distributary_of Little Lava Lake
x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x
Chris Mungall
branch of
distributary channel of
http://en.wikipedia.org/wiki/Distributary
This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes
distributary of
x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y.
Chris Mungall
anastomoses with
anabranch of
A lump of clay and a statue
x spatially_coextensive_with y if and inly if x and y have the same location
Chris Mungall
This relation is added for formal completeness. It is unlikely to be used in many practical scenarios
spatially coextensive with
x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y
Chris Mungall
branching part of
FMA:85994
x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path.
Chris Mungall
main stem of
x proper_distributary_of y iff x distributary_of y and x does not flow back into y
Chris Mungall
proper distributary of
x proper_tributary_of y iff x tributary_of y and x does not originate from y
Chris Mungall
proper tributary of
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).
Chris Mungall
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
Chris Mungall
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
Chris Mungall
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
Chris Mungall
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
Chris Mungall
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.
Chris Mungall
directly consumes
This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'
has direct input
Chris Mungall
Likely to be obsoleted. See:
https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit
obsolete has indirect input
true
translation SubClassOf has_direct_output some protein
p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c.
Chris Mungall
directly produces
obsolete has direct output
true
Chris Mungall
Likely to be obsoleted. See:
https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit
obsolete has indirect output
true
inverse of upstream of
Chris Mungall
causally downstream of
Chris Mungall
immediately causally downstream of
p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q
Chris Mungall
directly positively regulates
directly activates (process to process)
directly activates
p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q
Chris Mungall
indirectly positively regulates
indirectly activates
Chris Mungall
directly negatively regulates
directly inhibits (process to process)
directly inhibits
Chris Mungall
indirectly negatively regulates
indirectly inhibits
This relation groups causal relations between material entities and causal relations between processes
This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.
To define causal relations in an activity-flow type network, we make use of 3 primitives:
* Temporal: how do the intervals of the two occurrents relate?
* Is the causal relation regulatory?
* Is the influence positive or negative
The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.
For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.
For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.
Each of these 3 primitives can be composed to yield a cross-product of different relation types.
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causally related to
p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain
Chris Mungall
causally upstream of
p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q.
Chris Mungall
immediately causally upstream of
p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c
This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit
Chris Mungall
directly provides input for (process to process)
directly provides input for
transitive form of directly_provides_input_for
Chris Mungall
This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'directly provides input for' (which may later be relabeled simply to 'provides input for')
transitively provides input for (process to process)
transitively provides input for
p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.
We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
Chris Mungall
influences (processual)
affects
causally upstream of or within
false
Chris Mungall
This is an exploratory relation
differs in
https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions
Chris Mungall
differs in attribute of
Chris Mungall
differs in attribute
inverse of causally upstream of or within
Chris Mungall
causally downstream of or within
c involved in regulation of p if c is involved in some 'p' and p' regulates some p
Chris Mungall
involved in regulation of
Chris Mungall
involved in positive regulation of
Chris Mungall
involved in negative regulation of
c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
Chris Mungall
involved in or reguates
involved in or involved in regulation of
A protein that enables activity in a cytosol.
c executes activity in d if and only if c enables p and p occurs_in d
Chris Mungall
executes activity in
enables activity in
true
p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm.
Chris Mungall
contributes to morphology of
A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
Considering relabeling as 'pairwise interacts with'
This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
Chris Mungall
Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.
in pairwise interaction with
interacts with
http://purl.obolibrary.org/obo/MI_0914
https://github.com/oborel/obo-relations/wiki/InteractionRelations
An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)
Chris Mungall
genetically interacts with
http://purl.obolibrary.org/obo/MI_0208
An interaction relationship in which the two partners are molecular entities and are executing molecular processes that are directly causally connected.
Chris Mungall
binds
molecularly binds with
molecularly interacts with
http://purl.obolibrary.org/obo/MI_0915
An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts.
Chris Mungall
interacts with on organism level
biotically interacts with
http://eol.org/schema/terms/interactsWith
An interaction relationship in which the partners are related via a feeding relationship.
Chris Mungall
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
Chris Mungall
Jorrit Poelen
Katja Shulz
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.
Chris Mungall
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).
Chris Mungall
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).
Chris Mungall
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).
Chris Mungall
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
Chris Mungall
parasitizes
direct parasite of
parasite of
http://eol.org/schema/terms/parasitizes
Chris Mungall
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.
Chris Mungall
semibiotically interacts with
participates in a abiotic-biotic interaction with
Axiomatization to GO to be added later
Chris Mungall
An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.
phosphorylates
Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b
Chris Mungall
molecularly controls
Holds between molecules a and b if and only if a executes a process that directly diminishes a process executed by b.
Chris Mungall
inhibits
molecularly decreases activity of
Holds between molecules a and b if and only if a executes a process that directly activates a process executed by b.
Chris Mungall
activates
molecularly increases activity of
all dengue disease transmitted by some mosquito
A relationship that holds between a disease and organism
Add domain and range constraints
Chris Mungall
transmitted by
A relation that holds between a disease or an organism and a phenotype
Chris Mungall
has symptom
Chris Mungall
The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)
host of
Chris Mungall
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.
Chris Mungall
is subject of pollination interaction with
pollinates
http://eol.org/schema/terms/pollinates
Chris Mungall
has polinator
is target of pollination interaction with
pollinated by
http://eol.org/schema/terms/hasPollinator
Chris Mungall
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
Chris Mungall
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
Chris Mungall
a is a vector for b if a carries and transmits an infectious pathogen b into another living organism
is vector for
Chris Mungall
has vector
Chris Mungall
Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target
partner in
Chris Mungall
Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed.
subject participant in
Chris Mungall
Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed.
target participant in
Chris Mungall
This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.
helper property
Chris Mungall
is symbiosis
Chris Mungall
is commensalism
Chris Mungall
is mutualism
Chris Mungall
is parasitism
Chris Mungall
provides nutrients for
Chris Mungall
is subject of eating interaction with
eats
Chris Mungall
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.
Chris Mungall
is evidence for
'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'
x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y.
Chris Mungall
composed primarily of
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
Chris Mungall
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
Chris Mungall
child nucleus of in hermaphrodite
A child nucleus relationship in which the cells are part of a male organism
Chris Mungall
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.
Chris Mungall
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
Chris Mungall
ubiquitinates
Chris Mungall
is kinase activity
Chris Mungall
is ubiquitination
See notes for inverse relation
Chris Mungall
receives input from
This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in.
Chris Mungall
sends output to
Chris Mungall
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 structure and 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).
Chris Mungall
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).
Chris Mungall
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))
Chris Mungall
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 existence starts and ends during y if and only if the start of x is part of y and 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) & ω(x) <= ω(y) & ω(x) >= α(y)
Chris Mungall
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).
Chris Mungall
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).
Chris Mungall
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
Chris Mungall
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
Chris Mungall
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).
Chris Mungall
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.
Chris Mungall
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
p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causal relation between processes
Chris Mungall
depends on
q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2
This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C.
Chris Mungall
towards
'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate
p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c
Chris Mungall
has intermediate product
has intermediate
The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causal relation between material entities
A coral reef environment is determined by a particular coral reef
s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s.
The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future
Chris Mungall
determined by (system to material entity)
Chris Mungall
Pier Buttigieg
determined by
inverse of determined by
Chris Mungall
determines (material entity to system)
determines
s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w.
Chris Mungall
determined by part of
true
x is transcribed from y if and only if x is synthesized from template y
Chris Mungall
http://www.ncbi.nlm.nih.gov/pubmed/20226267
transcribed from
inverse of transcribed from
Chris Mungall
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
Chris Mungall
http://www.ncbi.nlm.nih.gov/pubmed/20226267
ribosomal translation of
inverse of ribosomal translation of
Chris Mungall
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.
Chris Mungall
http://www.ncbi.nlm.nih.gov/pubmed/20226267
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect.
The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene.
sequentially related to
Every UTR is adjacent to a CDS of the same transcript
Two consecutive DNA residues are sequentially adjacent
Two exons on a processed transcript that were previously connected by an intron are adjacent
x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y
Chris Mungall
http://www.ncbi.nlm.nih.gov/pubmed/20226267
sequentially adjacent to
Every CDS has as a start sequence the start codon for that transcript
x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence
Chris Mungall
started by
http://www.ncbi.nlm.nih.gov/pubmed/20226267
has start sequence
inverse of has start sequence
Chris Mungall
starts
http://www.ncbi.nlm.nih.gov/pubmed/20226267
is start sequence of
Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)
x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence
Chris Mungall
ended by
http://www.ncbi.nlm.nih.gov/pubmed/20226267
has end sequence
inverse of has end sequence
Chris Mungall
ends
http://www.ncbi.nlm.nih.gov/pubmed/20226267
is end sequence of
x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y.
In the SO paper, this was defined as an instance-type relation
Chris Mungall
http://www.ncbi.nlm.nih.gov/pubmed/20226267
is consecutive sequence of
Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence.
x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering
Chris Mungall
is sequentially aligned with
The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)
x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y
Chris Mungall
bounds sequence of
inverse of bounds sequence of
Chris Mungall
is bound by sequence of
x has subsequence y iff all of the sequence parts of x are sequence parts of y
Chris Mungall
contains
http://www.ncbi.nlm.nih.gov/pubmed/20226267
has subsequence
inverse of has subsequence
Chris Mungall
contained by
is subsequence of
x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y.
Chris Mungall
overlaps sequence of
x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y.
Chris Mungall
disconnected from
does not overlap sequence of
inverse of downstream of sequence of
Chris Mungall
is upstream of sequence of
x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y.
Chris Mungall
is downstream of sequence of
A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript
x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y
Chris Mungall
is immediately downstream of sequence of
A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript
inverse of immediately downstream of
Chris Mungall
is immediately upstream of sequence of
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.
Chris Mungall
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.
Chris Mungall
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
Chris Mungall
http://eol.org/schema/terms/hyperparasitoidOf
https://en.wikipedia.org/wiki/Hyperparasite
epiparasite of
hyperparasitoid of
hyperparasite of
inverse of hyperparasite of
Chris Mungall
has epiparasite
has hyperparasite
hyperparasitoidized by
hyperparasitized by
Chris Mungall
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
Chris Mungall
pathogen of
Chris Mungall
has pathogen
inverse of is evidence for
Chris Mungall
x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x.
has evidence
Chris Mungall
causally influenced by (material entity to material entity)
causally influenced by
Chris Mungall
interaction relation helper property
https://github.com/oborel/obo-relations/wiki/InteractionRelations
Chris Mungall
molecular interaction relation helper property
Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c
Chris Mungall
results in movement of
Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b
Chris Mungall
causally influences (material entity to material entity)
causally influences
A relation that holds between elements of a musculoskeletal system or its analogs.
Chris Mungall
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.
Chris Mungall
Wikipedia:Antagonist_(muscle)
has muscle antagonist
inverse of branching part of
Chris Mungall
has branching part
x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x.
Chris Mungall
UBERON:cjm
This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through.
conduit for
x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull.
Chris Mungall
GOC:cjm
lumen of
s is luminal space of x iff s is lumen_of x and s is an immaterial entity
Chris Mungall
luminal space of
A relation that holds between an attribute or a qualifier and another attribute.
Chris Mungall
This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are.
has modifier
Chris Mungall
participates in a biotic-biotic interaction with
inverse of has skeleton
Chris Mungall
skeleton of
Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
Chris Mungall
directly regulates (processual)
directly regulates
x existence starts at point y if and only if the time point at which x starts is equivalent to the time point at which y ends.
existence starts at point
gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p
Chris Mungall
has part structure that is capable of
p 'results in 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
x existence starts at point y if and only if the time point at which x starts is equivalent to the time point at which y ends.
existence ends at point
A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
Chris Mungall
causal relation between material entity and a process
pyrethroid -> growth
Holds between c and p if and only if c is capable of some activity a, and a regulates p.
capable of regulating
Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
capable of negatively regulating
renin -> arteriolar smooth muscle contraction
Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
capable of positively regulating
pazopanib -> pathological angiogenesis
Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p.
treats
The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber.
capable of inhibiting or preventing pathological process
treats
Usage of the term 'treats' applies when we believe there to be a an inhibitory relationship
benzene -> cancer [CHEBI]
Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p.
causes disease
capable of upregulating or causing pathological process
c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d.
treats
is substance that treats
c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d.
May be ceded to OBI
is marker for
Inverse of 'causal agent in'
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.
related via dependence to
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
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
Process(P1) directly regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2.
directly positively regulates (process to process)
directly positively regulates
Process(P1) directly regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2.
directly negatively regulates (process to process)
directly negatively regulates
A 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
a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.
Melissa Haendel
Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue.
produces
a produced_by b iff some process that occurs_in b has_output a.
Melissa Haendel
produced by
Holds between protein a (a transcription factor) and DNA element b if and only if a diminishes the process of transcription of b.
Logical axioms to be added after the relevant branch of GO is MIREOTed in
represses expression of
Holds between protein a (a transcription factor) and DNA element b if and only if a activates the process of transcription of b.
Logical axioms to be added after the relevant branch of GO is MIREOTed in
increases expression of
Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity.
To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader?
Matthew Brush
The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest.
is model of
The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'.
An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'.
A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition.
Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'.
Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to.
Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions.
causes or contributes to condition
A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition.
causes condition
A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition.
contributes to condition
A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual.
contributes to expressivity of condition
contributes to severity of condition
A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population.
contributes to penetrance of condition
contributes to frequency of condition
A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition.
is preventative for condition
Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to.
Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions.
ameliorates condition
A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship.
correlated with condition
A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition.
exacerbates condition
A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity.
condition ameliorated by
A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity.
condition exacerbated by
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.
co-occurs
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
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.
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.
Damion Dooley
has substance added
'egg white' 'has substance removed' some 'egg yolk'
"has substance removed" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time.
Damion Dooley
has substance removed
sardines 'immersed in' some 'oil and mustard'
"immersed in" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance.
Damion Dooley
immersed in
bread 'has primary substance added' some 'flour'
'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance.
Damion Dooley
has primary substance added
A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions.
Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph.
r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r.
Austin Meier
Chris Mungall
David Osumi-Sutherland
Marie Angelique Laporte
realized in response to
https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit
Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.
ECO:0000041
SO:similar_to
sameness
similar to
correspondence
resemblance
in similarity relationship with
Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.
BGEE:curator
correspondence
Similarity that results from common evolutionary origin.
homologous to
This broad definition encompasses all the working definitions proposed so far in the literature.
in homology relationship with
Similarity that results from common evolutionary origin.
Similarity that results from independent evolution.
homoplasous to
analogy
in homoplasy relationship with
Similarity that results from independent evolution.
Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes.
ECO:0000075
homocracous to
Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues.
in homocracy relationship with
Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes.
Homoplasy that involves different underlying mechanisms or structures.
analogy
Convergence usually implies a notion of adaptation.
in convergence relationship with
Homoplasy that involves different underlying mechanisms or structures.
Homoplasy that involves homologous underlying mechanisms or structures.
parallel evolution
Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage.
in parallelism relationship with
Homoplasy that involves homologous underlying mechanisms or structures.
Homology that is defined by similarity with regard to selected structural parameters.
ECO:0000071
MI:2163
structural homologous to
idealistic homology
in structural homology relationship with
Homology that is defined by similarity with regard to selected structural parameters.
ISBN:0123195837
Homology that is defined by common descent.
homology
ECO:0000080
RO_proposed_relation:homologous_to
SO:0000330
SO:0000853
SO:0000857
SO:homologous_to
TAO:homologous_to
cladistic homology
historical homologous to
phylogenetic homology
taxic homology
true homology
in historical homology relationship with
Homology that is defined by common descent.
ISBN:0123195837
Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype.
ECO:0000067
biological homologous to
transformational homology
Applicable only to morphology. A certain degree of ambiguity is accepted between biological homology and parallelism.
in biological homology relationship with
Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype.
Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage.
atavism
rudiment
reversion
in reversal relationship with
Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage.
Structural homology that is detected by similarity in content and organization between chromosomes.
MeSH:Synteny
SO:0000860
SO:0005858
syntenic homologous to
synteny
in syntenic homology relationship with
Structural homology that is detected by similarity in content and organization between chromosomes.
MeSH:Synteny
Historical homology that involves genes that diverged after a duplication event.
SO:0000854
SO:0000859
SO:paralogous_to
paralogous to
in paralogy relationship with
Historical homology that involves genes that diverged after a duplication event.
Paralogy that involves sets of syntenic blocks.
syntenic paralogous to
duplicon
paralogon
in syntenic paralogy relationship with
Paralogy that involves sets of syntenic blocks.
DOI:10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y
Syntenic homology that involves chromosomes of different species.
syntenic orthologous to
in syntenic orthology relationship with
Syntenic homology that involves chromosomes of different species.
Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous.
fractional homology
partial homologous to
segmental homology
mixed homology
modular homology
partial correspondence
percent homology
in partial homology relationship with
Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous.
ISBN:0123195837
ISBN:978-0471984931
Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence.
MeSH:Structural_Homology,_Protein
protein structural homologous to
in protein structural homology relationship with
Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence.
Structural homology that involves a pseudogenic feature and its functional ancestor.
pseudogene
SO:non_functional_homolog_of
non functional homologous to
in non functional homology relationship with
Structural homology that involves a pseudogenic feature and its functional ancestor.
SO:non_functional_homolog_of
Historical homology that involves genes that diverged after a speciation event.
ECO:00000060
SO:0000855
SO:0000858
SO:orthologous_to
orthologous to
The term is sometimes also used for anatomical structures.
in orthology relationship with
Historical homology that involves genes that diverged after a speciation event.
Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor.
xenologous to
The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis).
in xenology relationship with
Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor.
Historical homology that involves two members sharing no other homologs in the lineages considered.
1 to 1 homologous to
1:1 homology
one-to-one homology
in 1 to 1 homology relationship with
Historical homology that involves two members sharing no other homologs in the lineages considered.
BGEE:curator
Orthology that involves two genes that did not experience any duplication after the speciation event that created them.
1 to 1 orthologous to
1:1 orthology
one-to-one orthology
in 1 to 1 orthology relationship with
Orthology that involves two genes that did not experience any duplication after the speciation event that created them.
Paralogy that results from a whole genome duplication event.
ohnologous to
homoeology
in ohnology relationship with
Paralogy that results from a whole genome duplication event.
Paralogy that results from a lineage-specific duplication subsequent to a given speciation event.
in-paralogous to
inparalogy
symparalogy
in in-paralogy relationship with
Paralogy that results from a lineage-specific duplication subsequent to a given speciation event.
Paralogy that results from a duplication preceding a given speciation event.
alloparalogy
out-paralogous to
outparalogy
in out-paralogy relationship with
Paralogy that results from a duplication preceding a given speciation event.
1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A.
pro-orthologous to
in pro-orthology relationship with
1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A.
1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B.
semi-orthologous to
The converse of pro-orthologous.
in semi-orthology relationship with
1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B.
Iterative homology that involves structures arranged along the main body axis.
serial homologous to
homonomy
in serial homology relationship with
Iterative homology that involves structures arranged along the main body axis.
Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures.
heterochronous homologous to
heterochrony
in heterochronous homology relationship with
Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures.
ISBN:978-0674639416
Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles.
juvenification
pedomorphosis
in paedomorphorsis relationship with
Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles.
ISBN:978-0674639416
Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits.
in peramorphosis relationship with
Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits.
Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage.
in progenesis relationship with
Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage.
ISBN:978-0674639416
Paedomorphosis that is produced by a retardation of somatic development.
juvenilization
neotenous to
in neoteny relationship with
Paedomorphosis that is produced by a retardation of somatic development.
ISBN:978-0674639416
Convergence that results from co-evolution usually involving an evolutionary arms race.
mimicrous to
in mimicry relationship with
Convergence that results from co-evolution usually involving an evolutionary arms race.
Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other.
1 to many orthologous to
1:many orthology
one-to-many orthology
co-orthology
many to 1 orthology
in 1 to many orthology relationship with
Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other.
Historical homology that involves two members of a larger set of homologs.
many to many homologous to
many-to-many homology
many:many homology
in many to many homology relationship with
Historical homology that involves two members of a larger set of homologs.
Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species.
1 to many homologous to
one-to-many homology
1:many homology
in 1 to many homology relationship with
Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species.
BGEE:curator
Historical homology that is based on recent shared ancestry, characterizing a monophyletic group.
apomorphous to
synapomorphy
in apomorphy relationship with
Historical homology that is based on recent shared ancestry, characterizing a monophyletic group.
ISBN:978-0252068140
Historical homology that is based on distant shared ancestry.
plesiomorphous to
symplesiomorphy
This term is usually contrasted to apomorphy.
in plesiomorphy relationship with
Historical homology that is based on distant shared ancestry.
ISBN:978-0252068140
Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution.
deep genetic homology
deep homologous to
generative homology
homoiology
Used for structures in distantly related taxa.
in deep homology relationship with
Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution.
Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree.
hemiplasous to
in hemiplasy relationship with
Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree.
Historical homology that involves not recombining and subsequently differentiated sex chromosomes.
gametologous to
in gametology relationship with
Historical homology that involves not recombining and subsequently differentiated sex chromosomes.
Historical homology that involves the chromosomes able to pair (synapse) during meiosis.
MeSH:Chromosome_Pairing
chromosomal homologous to
in chromosomal homology relationship with
Historical homology that involves the chromosomes able to pair (synapse) during meiosis.
ISBN:0195307615
Orthology that involves two genes that experienced duplications more recent than the species split that created them.
many to many orthologous to
many-to-many orthology
many:many orthology
trans-orthology
co-orthology
trans-homology
in many to many orthology relationship with
Orthology that involves two genes that experienced duplications more recent than the species split that created them.
Paralogy that involves genes from the same species.
within-species paralogous to
in within-species paralogy relationship with
Paralogy that involves genes from the same species.
Paralogy that involves genes from different species.
between-species paralogous to
The genes have diverged before a speciation event.
in between-species paralogy relationship with
Paralogy that involves genes from different species.
Paedomorphosis that is produced by delayed growth of immature structures into the adult form.
post-displacement
in postdisplacement relationship with
Paedomorphosis that is produced by delayed growth of immature structures into the adult form.
Peramorphosis that is produced by a delay in the offset of development.
in hypermorphosis relationship with
Peramorphosis that is produced by a delay in the offset of development.
ISBN:978-0674639416
Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species.
synologous to
in synology relationship with
Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species.
Orthology that involves functional equivalent genes with retention of the ancestral function.
ECO:0000080
isoorthologous to
in isoorthology relationship with
Orthology that involves functional equivalent genes with retention of the ancestral function.
Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment.
tandem paralogous to
iterative paralogy
serial paralogy
in tandem paralogy relationship with
Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment.
ISBN:978-0878932665
Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character).
apomorphic tendency
cryptic homology
latent homologous to
underlying synapomorphy
homoiology
homoplastic tendency
re-awakening
Used for structures in closely related taxa.
in latent homology relationship with
Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character).
ISBN:0199141118
Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual.
generative homology
syngenous to
Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes.
in syngeny relationship with
Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual.
DOI:10.1002/1521-1878(200009)22:9<846::AID-BIES10>3.0.CO;2-R
Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss.
1:1 paralogy
apparent 1:1 orthology
apparent orthologous to
pseudoorthology
The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss.
in apparent orthology relationship with
Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss.
Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer.
pseudoparalogous to
These genes may come out as paralogs in a single-genome analysis.
in pseudoparalogy relationship with
Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer.
Historical homology that involves functional equivalent genes with retention of the ancestral function.
equivalogous to
This may include examples of orthology, paralogy and xenology.
in equivalogy relationship with
Historical homology that involves functional equivalent genes with retention of the ancestral function.
Historical homology that involves orthologous pairs of interacting molecules in different organisms.
interologous to
in interology relationship with
Historical homology that involves orthologous pairs of interacting molecules in different organisms.
Similarity that is characterized by interchangeability in function.
functional similarity
in functional equivalence relationship with
Similarity that is characterized by interchangeability in function.
Biological homology that involves parts of the same organism.
iterative homologous to
in iterative homology relationship with
Biological homology that involves parts of the same organism.
Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome.
duplicate xenology
multiple xenology
paraxenologous to
in paraxenology relationship with
Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome.
Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution.
plerologous to
This phenomenon is usually due to gene conversion process.
in plerology relationship with
Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution.
Structural homology that involves structures with the same or similar relative positions.
homotopous to
Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use.
in homotopy relationship with
Structural homology that involves structures with the same or similar relative positions.
ISBN:0123195837
Biological homology that involves an ectopic structure and the normally positioned structure.
heterotopy
in homeosis relationship with
Biological homology that involves an ectopic structure and the normally positioned structure.
Synology that results from allopolyploidy.
homoeologous to
On a long term, it is hard to distinguish allopolyploidy from whole genome duplication.
in homoeology relationship with
Synology that results from allopolyploidy.
Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure.
axis paramorphism
in paramorphism relationship with
Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure.
Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms.
regulogous to
in regulogy relationship with
Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms.
entity
An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
continuant
An entity that has temporal parts and that happens, unfolds or develops through time.
occurrent
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
independent continuant
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities.
obsolete dependent continuant
true
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
process
p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
disposition
A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
realizable entity
quality
A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
specifically dependent continuant
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
role
object aggregate
site
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
generically dependent continuant
function
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
material entity
immaterial entity
anatomical structure
material anatomical entity
immaterial anatomical entity
connected anatomical system
cell part (CARO)
cell part
multi-cell-part structure
neuron projection bundle
Material anatomical entity that is a member of an individual species or is a viral or viroid particle.
organism or virus
Melissa Haendel
9/18/11
organism or virus or viroid
multicellular anatomical structure
An individual member of a clade.
organism
mah
7.16.2011
A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms.
organism
cell
neuron
macroscopic spatial feature
geographic feature
An anthropogenic geographic feature is a geographic feature
resulting from the influence of human beings on nature.
man-made feature
manmade feature
anthropogenic geographic feature
An anthropogenic geographic feature is a geographic feature
resulting from the influence of human beings on nature.
ORCID:0000-0002-4366-3088
A feature that has been constructed by deliberate human effort.
constructed feature
construction
A feature that has been constructed by deliberate human effort.
MA:ma
biome
An environmental feature that is, or can be, contained and is predominantly composed of one or a few types of stuff.
mesoscopic physical object
An environmental feature that is, or can be, contained and is predominantly composed of one or a few types of stuff.
MA:ma
A material entity which determines an environmental system.
environmental feature
A material entity which determines an environmental system.
DOI:10.1186/2041-1480-4-43
NM:nm
ORCID:0000-0002-4366-3088
A material entity that has been processed by humans or their technology in any way, including intermediate products as well as final products.
manufactured good
manufactured product
A material entity that has been processed by humans or their technology in any way, including intermediate products as well as final products.
https://en.wikipedia.org/wiki/Manufactured_product
anthropogenic abiotic mesoscopic feature
A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system.
portion of environmental material
environmental material
A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system.
DOI:10.1186/2041-1480-4-43
MA:ma
ORCID:0000-0002-4366-3088
URL:http://ontology.buffalo.edu/smith/articles/niches.html
abiotic mesoscopic physical object
A system which has the disposition to environ one or more material entities.
environment
environmental system
A system which has the disposition to environ one or more material entities.
DOI:10.1186/2041-1480-4-43
An anthropogenic environment is an environmental system which is the product of human activity.
anthropogenic environment
Outer space is a hard vacuum containing a low density of particles, predominantly a plasma of hydrogen and helium as well as electromagnetic radiation, magnetic fields, neutrinos, dust and cosmic rays that exists between celestial bodies.
space
outer space
Outer space is a hard vacuum containing a low density of particles, predominantly a plasma of hydrogen and helium as well as electromagnetic radiation, magnetic fields, neutrinos, dust and cosmic rays that exists between celestial bodies.
https://en.wikipedia.org/wiki/Outer_space
A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning.
human dwelling
A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning.
https://en.wikipedia.org/wiki/Dwelling accessed 11/25/2015
An object which is naturally occuring, bound together by gravitational or electromagnetic forces, and surrounded by space.
celestial body
astronomical body
An object which is naturally occuring, bound together by gravitational or electromagnetic forces, and surrounded by space.
https://en.wikipedia.org/wiki/Astronomical_object
1
An object which is composed of one or more gravitationally bound structures that are associated with a position in space.
celestial object
astronomical object
An object which is composed of one or more gravitationally bound structures that are associated with a position in space.
https://en.wikipedia.org/wiki/Astronomical_object
A material part of an astronomical body.
astronomical body part
A biosphere is an environmental system which includes, as parts, all the living entities within the gravitational sphere of influence of an astronomical body, and the non-living and dead entities which they interact with.
biosphere
A biosphere is an environmental system which includes, as parts, all the living entities within the gravitational sphere of influence of an astronomical body, and the non-living and dead entities which they interact with.
http://www.biology-online.org/dictionary/Biosphere
https://en.wikipedia.org/wiki/Biosphere
An environmental system in which minimal to no anthropisation has occurred and non-human agents are the primary determinants of the system's dynamics and composition.
natural environment
An environmental system in which minimal to no anthropisation has occurred and non-human agents are the primary determinants of the system's dynamics and composition.
https://en.wikipedia.org/wiki/Anthropization
https://en.wikipedia.org/wiki/Natural_environment
A process during which a natural environmental system is altered by human action.
anthropization
anthropisation
A process during which a natural environmental system is altered by human action.
https://en.wikipedia.org/wiki/Anthropization
An environmental system which includes, as parts, all the entities which have been constructed or manufactured by humans or their technology within the gravitational sphere of influence of an astronomical body.
technosphere
An environmental system which includes, as parts, all the entities which have been constructed or manufactured by humans or their technology within the gravitational sphere of influence of an astronomical body.
http://dx.doi.org/10.1177/2053019616677743
http://www.yourdictionary.com/technosphere
https://www.sciencedaily.com/releases/2016/11/161130085021.htm
A planned process during which raw or recycled materials are transformed into products for use or sale using labour and machines, tools, chemical and biological processing, or formulation.
manufacturing process
A planned process during which raw or recycled materials are transformed into products for use or sale using labour and machines, tools, chemical and biological processing, or formulation.
https://en.wikipedia.org/wiki/Manufacturing
An process during which natural or manufactured materials and products are processed and arranged by humans or their technology into structures.
construction process
An environmental system which is determined by materials bearing roughly homogeneous qualities.
environmental system determined by a quality
An environmental system within which an environmental material strongly influences the system's composition and properties.
environmental system determined by a material
An environmental system which is determined by a living organism.
host-associated environment
environmental system determined by an organism
An environmental system determined by an animal.
animal environment
Metazoan-associated environment
animal-associated environment
An environmental system determined by part of a living or dead animal, or a whole small animal.
environment associated with an animal part or small animal
An environmental system determined by part of a living or dead plant, or a whole small plant.
environment associated with a plant part or small plant
An environmental system which includes both living and non-living components.
ecosystem
An environmental system which includes both living and non-living components.
https://en.wikipedia.org/wiki/Ecosystem
A process in which includes the components of an environmental system as participants.
environmental system process
An environmental process which is driven by the action of humans.
anthropogenic environmental process
molecular process
molecular_function
catalytic activity
true
ubiquitin-protein ligase activity
receptor activity
nucleus
The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity.
behavioral response to stimulus
behaviour
behavioural response to stimulus
single-organism behavior
behavior
The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity.
GOC:ems
GOC:jl
ISBN:0395448956
PMID:20160973
feeding behavior
Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
biological process
physiological process
single organism process
single-organism process
biological_process
Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
GOC:go_curators
GOC:isa_complete
membrane
true
kinase activity
transferase activity
transferase activity, transferring phosphorus-containing groups
ligase activity
ligase activity, forming carbon-nitrogen bonds
acid-amino acid ligase activity
small conjugating protein ligase activity
axon
dendrite
Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group.
social behaviour
cooperative behavior
social behavior
Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group.
GOC:jh2
PMID:12848939
Wikipedia:Social_behavior
presynaptic membrane
cell projection
neuron projection
true
symbiosis, encompassing mutualism through parasitism
Any process in which an organism has an effect on an organism of a different species.
interaction with another species
interspecies interaction
interspecies interaction with other organisms
interspecies interaction between organisms
Any process in which an organism has an effect on an organism of a different species.
GOC:cc
synapse part
cell part
synapse
postsynaptic membrane
response to stimulus
interaction with symbiont
Any process in which an organism has an effect on an organism of the same species.
intraspecies interaction with other organisms
intraspecies interaction between organisms
Any process in which an organism has an effect on an organism of the same species.
GOC:ai
A biological process which involves another organism of the same or different species.
interaction between organisms
physiological interaction between organisms
physiological interaction with other organism
multi-organism process
A biological process which involves another organism of the same or different species.
GOC:jl
Any process in which an organism has a behavioral effect on another organism of the same or different species.
behavioral interaction between organisms
behavioral interaction with other organism
behavioural interaction between organisms
behavioural interaction with other organism
behavioral signaling
behavioral signalling
multi-organism behavior
Any process in which an organism has a behavioral effect on another organism of the same or different species.
GOC:ai
behavioral signalling
GOC:mah
acquisition of nutrients from other organism during symbiotic interaction
acquisition of nutrients from symbiont
true
parasitism
true
mutualism
true
commensalism
data item
information content entity
curation status specification
The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
PERSON:Bill Bug
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
OBI_0000266
curation status specification
data about an ontology part is a data item about a part of an ontology, for example a term
Person:Alan Ruttenberg
data about an ontology part
obsolescence reason specification
The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
obsolescence reason specification
The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.
A denotator type indicates how a term should be interpreted from an ontological perspective.
Alan Ruttenberg
Barry Smith, Werner Ceusters
denotator type
all
root
all
all
Vira
Viridae
viruses
Viruses
Vira
Viridae
viruses
Teleostomi
bony vertebrates
Euteleostomi
bony vertebrates
Viroid
viroids
Viroids
Viroid
viroids
Charophyta/Embryophyta group
charophyte/embryophyte group
Streptophytina
Charophyta/Embryophyta group
charophyte/embryophyte group
biota
cellular organisms
biota
biota
Dipnotetrapodomorpha
Boreotheria
Boreoeutheria
Boreotheria
Acrogymnospermae
eubacteria
Monera
Procaryotae
Prokaryota
Prokaryotae
bacteria
not Bacteria Haeckel 1894
prokaryote
prokaryotes
Bacteria
eubacteria
Monera
Procaryotae
Prokaryota
Prokaryotae
bacteria
not Bacteria Haeckel 1894
prokaryote
prokaryotes
Homo/Pan/Gorilla group
Homininae
Homo/Pan/Gorilla group
Archaebacteria
Mendosicutes
Metabacteria
Monera
Procaryotae
Prokaryota
Prokaryotae
archaea
prokaryote
prokaryotes
Archaea
Archaebacteria
Mendosicutes
Metabacteria
Monera
Procaryotae
Prokaryota
Prokaryotae
archaea
prokaryote
prokaryotes
eucaryotes
eukaryotes
Eucarya
Eucaryotae
Eukarya
Eukaryotae
eukaryotes
Eukaryota
eucaryotes
eucaryotes
eukaryotes
eukaryotes
Eucarya
Eucarya
Eucaryotae
Eucaryotae
Eukarya
Eukarya
Eukaryotae
Eukaryotae
eukaryotes
eukaryotes
green algae
Chlorophycota
Chlorophyta sensu Bremer 1985
algae
green algae
Chlorophyta
green algae
Chlorophycota
Chlorophyta sensu Bremer 1985
algae
green algae
Euarchontoglires
Anthropoidea
Simiiformes
Anthropoidea
ape
apes
Hominoidea
ape
apes
higher plants
land plants
plants
land plants
Embryophyta
higher plants
land plants
plants
land plants
tetrapods
Tetrapoda
tetrapods
amniotes
Amniota
amniotes
Theria
Theria <Mammalia>
Theria
green plants
Chlorobionta
Chlorophyta/Embryophyta group
chlorophyte/embryophyte group
green plants
Viridiplantae
green plants
Chlorobionta
Chlorophyta/Embryophyta group
chlorophyte/embryophyte group
green plants
Fungi/Metazoa group
opisthokonts
Opisthokonta
Fungi/Metazoa group
opisthokonts
metazoans
multicellular animals
Animalia
animals
Metazoa
metazoans
multicellular animals
Animalia
animals
Bilateria
deuterostomes
Deuterostomia
deuterostomes
angiosperms
flowering plants
Angiospermae
flowering plants
Magnoliophyta
angiosperms
flowering plants
Angiospermae
flowering plants
Streptophyta
Haplorrhini
mammals
mammals
Mammalia
mammals
mammals
vascular plants
vascular plants
Tracheophyta
vascular plants
vascular plants
seed plants
seed plants
Spermatophyta
seed plants
seed plants
Eumetazoa
chordates
chordates
Chordata
chordates
chordates
Vertebrata
vertebrates
vertebrates
Vertebrata <Metazoa>
Vertebrata
vertebrates
vertebrates
Gnathostomata
jawed vertebrates
Gnathostomata <vertebrate>
Gnathostomata
jawed vertebrates
euphyllophytes
Euphyllophyta
euphyllophytes
Sarcopterygii
Craniata
Craniata <chordata>
Craniata
eutherian mammals
placental mammals
placentals
Placentalia
placentals
Eutheria
eutherian mammals
placental mammals
placentals
Placentalia
placentals
primate
Primata
primates
Primates
primate
Primata
primates
Catarrhini
great apes
Pongidae
Hominidae
great apes
Pongidae
humans
Homo
humans
human
man
humans
Homo sapiens
human
man
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
quality (PATO)
trait
quality
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
PATOC:GVG
A composite chromatic quality composed of hue, saturation and intensity parts.
colour
relative color
color
A composite chromatic quality composed of hue, saturation and intensity parts.
PATOC:GVG
A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
morphology
shape
qualitative
A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average.
deviation(from_normal)
A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude.
size
structure
A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time.
rate
A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time.
PATOC:melissa
A color hue with high wavelength of the long-wave end of the visible spectrum, evoked in the human observer by radiant energy with wavelengths of approximately 630 to 750 nanometers.
red
A color hue with high wavelength of the long-wave end of the visible spectrum, evoked in the human observer by radiant energy with wavelengths of approximately 630 to 750 nanometers.
Dictionary:http://dictionary.reference.com/
branched
A size quality which is relatively low.
hypoplasia
underdeveloped
reduced
small
tiny
decreased size
A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
relational physical quality
physical quality
A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
PATOC:GVG
linear
A quality which inheres in an process.
quality of a process
quality of occurrent
quality of process
relational quality of occurrent
process quality
A quality which inheres in an process.
PATOC:GVG
A quality which inheres in a continuant.
monadic quality of a continuant
multiply inhering quality of a physical entity
quality of a continuant
quality of a single physical entity
quality of an object
quality of continuant
monadic quality of an object
monadic quality of continuant
physical object quality
A quality which inheres in a continuant.
PATOC:GVG
A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation.
electromagnetic (EM) radiation quality
A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation.
Wikipedia:http://en.wikipedia.org/wiki/Electromagnetic_radiation
An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light.
optical quality
An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light.
PATOC:GVG
A biological sex quality inhering in a population of multiple sexes.
mixed sex
A biological sex quality inhering in a population of multiple sexes.
MGED:MGED
A quality inhering in a population by virtue of the proportion of its members that are ill at a given time.
morbidity
A quality inhering in a population by virtue of the proportion of its members that are ill at a given time.
PATOC:GVG
A quality that inheres in an bearer by virtue of how that bearer interacts with radiation.
radiation quality
A quality that inheres in an bearer by virtue of how that bearer interacts with radiation.
PATOC:GVG
A quality that inheres in an entire population or part of a population.
population quality
A quality that inheres in an entire population or part of a population.
PATOC:GVG
branchiness
physical quality of a process
laminar
A quality that has a value that is decreased compared to normal or average.
decreased quality
A quality of an object that has a value that is decreased compared to normal or average.
decreased object quality
2
Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family.
A material entity that consists of two or more organisms, viruses, or viroids.
A material entity that consists of two or more organisms, viruses, or viroids.
group of organism
organism collection
May be of the same or different species.
collection of organisms
collection of organisms
This a general term that can include every organism of a species living in an area or any subset of them. Subclasses can be more specific as needed.
A collection of organisms, all of the same species, that live in the same place.
ISBN:0878932739
It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population.
Classes for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across OBO Foundry ontologies and only one term used.
population of organisms
2
A community of at least two different species, living in a particular area. Must have at least two populations of different species as members.
Not sure if the equivalancy axiom specifies that both populations are located in the same site.
multispecies community
ISBN:0865423504
Ecological community is defined broadly here, but includes both ecological interactions (inherited from parent term community) and spatial co-existence. It may be used to describe every organisms living in an area, but is often used to refer only to organisms of a particular taxon or guild (e.g., the plant community, the insect community, the herbivore community). The word community, as it often used to describe a group of humans living together, is a type of single-species collection of organisms, not an ecological community.
ecological community
A quality that inheres in a biological population.
See Chris's comments on population qualities at: http://code.google.com/p/popcomm-ontology/issues/detail?id=4. These may not belong under BFO:quality. May be better to call them population characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2.
Includes qualities like population size, population growth rate, carrying capacity, immigration rate, emigration rate, fecundity, and death rate. A population quality may depend on the qualities of individual organisms in the population, but cannot be measured or described for a single organism. This term may be replaced by a PATO term.
quality of a population
A quality that inheres in a community.
These may not belong under BFO:quality. May be better to call them community characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2.
Includes qualities like diversity, species richness, stability, resilience, community structure, number of trophic levels. A community quality may depend on the qualities of individual organism in the community, but cannot be measured or described for a single individual.
quality of an ecological community
A process that has as primary participant a population.
Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms {e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction. The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but tPCOhese categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes.
population process
population birth rate
population death rate
Is a rate a quality? Population growth rate may be better classified as a process profile.
population growth rate
The maximum number of individuals that can be supported in a population that is growing according to logistic growth.
Carrying capacity is better defined as a quality of the environment in which a population lives. This term will be deprecated from PCO and moved to ecoCORE.
ISBN:0878932739
obsolete carrying capacity
true
The number of different species represented in an ecological community.
This is a quality of an ecological community (PCO_0000002). If your metric includes the abundances of species (evenness) as well as the number, you should use community species diversity (PCO_0000019).
adapted from http://en.wikipedia.org/wiki/Species_richness
community species richness
A process that leads to a change in the number of individuals (positive or negative) in a population.
population growth
A population process that leads to an increase in the numbers of individuals in a population following a logistic (S-shaped) curve. Generally occurs when the population has a carrying capacity in a particular habitat.
logistic population growth
A population growth process that leads to an exponential increase in the number of individuals in a population.
exponential population growth
predator role
prey role
symbiont role
A collection of organisms that has as parts every organism of given species and no organisms of any other species.
At the moment there is no way to specify in an OWL axiom that the collection includes every individual of a species. This should be added, if possible.
This term is neutral with respect to which organisms are included in a species. Membership will depend on the species concept and the taxonomic assertions used to define the species. These criteria must be specified by the user.
species as a collection of organisms
1
2
A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species.
collection of organisms of the same species
single-species collection of organisms
The number of different species that are represented in a given community, weighted by their abundance. Community species diversity can be calculated in different ways, but consists of two components: species richness and species evenness.
If your metric does not include the abundances of different species, but rather just the numer of species, you should use community species richness (PCO_0000010). More specific subclasses or instances of this class may be created to describe specific ways of measuring diversity.
adapted from http://en.wikipedia.org/wiki/Species_diversity
The Shannon Index and Simpson Index are examples of ways in which species diversity is quantified.
community species diversity
A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption.
Needs axioms for family relationships.
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25173
Family membership through marriage or adoption apply primarily to human families. In most species, family membership is defined by common anscestry.
family
A population process that ultimately leads to the death of all individuals in a population.
population extinction
A process that ultimately leads to the death of all individuals in a population.
species extinction
If there are 40 foxes, and 1000 dogs, the community is not very even, but if there are 40 foxes and 42 dogs, the community is quite even.
A quality of a community that reflects how close in abundance all species in a community are.
adapted from http://en.wikipedia.org/wiki/Species_evenness
community species evenness
1
A material entity that consists of one or more people who live in the same dwelling and also share at meals or living accommodation, and may consist of a single family or some other grouping of people.
Person: Jie Zheng
WEB: http://en.wikipedia.org/wiki/Household
household
This is an example population added to demonstrate the modeling pattern for collections of organisms.
red population
true
An example class added to demonstrate the design pattern for collections of organism. Red organism should be automatically classified as a member of red population when the reasoner is synchronized using a DL query.
red organism
true
2
A collection of organisms of the same species that has as members only humans.
human community
human population
collection of humans
A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other.
Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete.
These relations can include shared values, occupying the same spatial regkion. A community be be a single species collection of organsisms (as in a human community, which is also a type of population) or a or multi-species collection of organisms (as in an ecological community).
community
A collection of organisms that consists of two or more organisms from at least two species.
Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say "('has member' only ('member of' min 2 'species as a collection of organisms'))".
multi-species collection of organisms
A household in which the majority of the income of its members is derived from agricultural activities.
This is a more narrow definition in which the majority of income of a house comes from agricultural activities, as opposed to the broad definition in which any income comes from agricultural activities. The narrow definition was chosen to be consistent with the SDGIO (UN Sustainable Development Goals) which requested this term.
agricultural household
A material entity that is one or more organisms, viruses or viroids.
organismal entity
A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other.
genealogical family
Matthew Brush, as part of http://datamodel.clinicalgenome.org/interpretation/
biological family
A type of social behavior in which a collection of humans intentionally gathers together on a temporary basis to engage socially.
Intented to replace http://purl.obolibrary.org/obo/GENEPIO_0001029
GenEpiO curators
human social gathering activity
A human social event in which humans living in the same area or neighborhood gather to carry out activiites relevent to the people living in the area.
Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001034
GenEpio curators
human community event
A human social gathering in which the intention is to have a good time. Often the intention is to celebrate something like a birthday, anniversary, or holiday, but there is not always a purpose.
Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001030
GenEpiO curators
party
Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001033
A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering.
GenEpio curators
potluck
A human social gathering at which two people are married. May include a legal or social ceremony.
Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001031
GenEpio curators
wedding
A human social gathering at which the key participant is an expectant parent and other guests bring presents for the soon to be born baby.
Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001032
GenEpiO curators
baby shower
2
pair of interacting organisms
1
pair of interacting organisms of the same species
A population which is participating in a migration process.
migratory population
A population process during which a population moves from one area to another.
https://en.wikipedia.org/wiki/Migration
The distance between the areas is not specified here, nor is the minimum distance required for such movements to be considered migrations.
population migration
A population migration during which a population of humans moves from one area to another with the intention of settling permanently in the new location.
https://en.wikipedia.org/wiki/Human_migration
The distance between the areas is not specified here, nor is the minimum distance required for such movements to be considered migrations. "Nomadic movements are normally not regarded as migrations as there is no intention to settle in the new place and because the movement is generally seasonal. Only a few nomadic people have retained this form of lifestyle in modern times. Also, the temporary movement of people for the purpose of travel, tourism, pilgrimages, or the commute is not regarded as migration, in the absence of an intention to live and settle in the visited places." - https://en.wikipedia.org/wiki/Human_migration
human population migration
A migratory population of humans, travelling with the intention of settling in a new area.
https://en.wikipedia.org/wiki/Human_migration
human migratory population
An ecological community which is composed of co-existing populations of microbial organisms that interact, directly or indirectly, such that they impact one another's ecological fitness.
A class for a collection of organisms considered "microbial" and an accompanying quality in PATO (e.g. "microscopic") would be useful to better axiomatise this class. See https://github.com/PopulationAndCommunityOntology/pco/issues/22
http://orcid.org/0000-0002-4366-3088
http://dx.doi.org/10.1038/ismej.2009.88
The definition of a microbial species is deeply debated, however, units of phylogenetic and functional diversity are recognised with respect to their varying roles in an ecosystem. In turn, there exist multiple operational definitions of microbial community, such as local, phenomenological, and indexical communities. This class seeks to capture microbial communities in a very broad sense, as collections of phylogenetically and functionally divergent microbial organisms co-existing, potentially interacting, and competing for niche space in the same ecosystem over a period of time in which their causal footprints overlap one another.
microbial community
A plant structure (PO:0005679) which is a whole organism.
genet (broad)
ramet (broad)
planta entera (Spanish, exact)
植物体全体 (Japanese, exact)
bush (narrow)
frutex (narrow)
frutices (narrow)
gametophyte (narrow)
herb (narrow)
liana (narrow)
prothalli (narrow)
prothallium (narrow)
prothallus (narrow)
seedling (narrow)
shrub (narrow)
sporophyte (narrow)
suffrutex (narrow)
suffrutices (narrow)
tree (narrow)
vine (narrow)
woody clump (narrow)
clonal colony (related)
colony (related)
whole plant
An anatomical structure that is or was part of a plant, or was derived from a part of a plant.
estructura vegetal (Spanish, exact)
植物 構造 (Japanese, exact)
plant structure
An anatomical entity that is or was part of a plant.
entidad anatómica vegetal (Spanish, exact)
植物 解剖学(形態)的実体 (Japanese, exact)
plant anatomical entity
An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human,
An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes.
A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism.
This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions.
Chris Mungall
cjm
2017-06-05T17:55:39Z
exposure event or process
https://github.com/oborel/obo-relations/pull/173
Any entity that is ordered in discrete units along a linear axis.
Chris Mungall
sequentially ordered entity
Any individual unit of a collection of like units arranged in a linear order
Chris Mungall
An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair.
sequence atomic unit
Any entity that can be divided into parts such that each part is an atomical unit of a sequence
Chris Mungall
Sequence bearers can be molecular entities, such as a portion of a DNA molecule, or they can be abstract entities, such as an entity representing all human sonic hedgehog regions of the genome with a particular DNA sequence.
sequence bearer
A material entity consisting of multiple components that are causally integrated.
May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43
Chris Mungall
http://www.jbiomedsem.com/content/4/1/43
system
Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
anatomical entity
A material entity that is one or more organisms, viruses or viroids.
wrong IRI form
http://purl.obolibrary.org/obo/PCO_0000031
obsolete organismal entity
true
Obsolete Class
example to be eventually removed
The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
Person:Alan Ruttenberg
failed exploratory term
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
metadata complete
term created to ease viewing/sort terms for development purpose, and will not be included in a release
organizational term
Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
ready for release
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
metadata incomplete
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
uncurated
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
pending final vetting
Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
core
placeholder removed
An editor note should explain what were the merged terms and the reason for the merge.
terms merged
This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.
term imported
This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.
term split
Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
Alan Ruttenberg
A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
universal
A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
"definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
Alan Ruttenberg
defined class
A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
Alan Ruttenberg
named class expression
Terms with this status should eventually replaced with a term from another ontology.
Alan Ruttenberg
group:OBI
to be replaced with external ontology term
A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
Alan Ruttenberg
group:OBI
requires discussion
## Elucidation
This is used when the statement/axiom is assumed to hold true 'eternally'
## How to interpret (informal)
First the "atemporal" FOL is derived from the OWL using the standard
interpretation. This axiom is temporalized by embedding the axiom
within a for-all-times quantified sentence. The t argument is added to
all instantiation predicates and predicates that use this relation.
## Example
Class: nucleus
SubClassOf: part_of some cell
forall t :
forall n :
instance_of(n,Nucleus,t)
implies
exists c :
instance_of(c,Cell,t)
part_of(n,c,t)
## Notes
This interpretation is *not* the same as an at-all-times relation
axiom holds for all times
## Elucidation
This is used when the first-order logic form of the relation is
binary, and takes no temporal argument.
## Example:
Class: limb
SubClassOf: develops_from some lateral-plate-mesoderm
forall t, t2:
forall x :
instance_of(x,Limb,t)
implies
exists y :
instance_of(y,LPM,t2)
develops_from(x,y)
relation has no temporal argument
true
MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z
infer input from direct reg
true
GP(X) part_of complex(Y) enables MF(Z) -> X contributes_to Z
contrib to MF
GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),
e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'
enabling an MF enables its parts
true
GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'
involved in BP
From ligand activity to has_ligand
This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps"
If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.
inferring direct reg edge from input to regulatory subfunction
inferring direct neg reg edge from input to regulatory subfunction
inferring direct positive reg edge from input to regulatory subfunction
From has_ligand to ligand activity
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