https://github.com/oborel/obo-relations/ OBO Relations Ontology The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. 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. OBO foundry unique label 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. never in taxon 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. ?X DisjointWith RO_0002162 some ?Y Chris Mungall tooth SubClassOf 'never in taxon' value 'Aves' mutually spatially disjoint with https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern 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. Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y) non-overlapping with shares no parts with taxonomic class assertion 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. ambiguous for taxon 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] dubious 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 present in taxon https://orcid.org/0000-0002-6601-2165 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 logical macro assertion https://github.com/oborel/obo-relations/wiki/ShortcutRelations An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL. annotation property cardinality 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. logical macro assertion on a class 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 property A logical macro assertion whose domain is an IRI for a property logical macro assertion on an object property logical macro assertion on an annotation property dispositional interpretation 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. has no connections with 'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton' 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)) A is has_no_connections_with B if there are no parts of A or B that have a connection with the other. inherited annotation property curator guidance link 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) always present in taxon 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 brain always_present_in_taxon 'Vertebrata' forelimb always_present_in_taxon Euarchontoglires temporal logical macro assertion on a class This properties were created originally for the annotation of developmental or life cycle stages, such as for example Carnegie Stage 20 in humans. measurement property has unit has start time value has end time value start, days post fertilization 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. end, 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. start, years post birth 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. end, 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 start, months 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. end, 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 month of gestation 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. has developmental stage marker 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 start, days post 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) Count of number of days intervening between the start of the stage and the time of coitum. end, days post coitum Count of number of days intervening between the end of the stage and the time of coitum. start, weeks post birth end, weeks post birth 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 subject-partner-in p, y object-partner-in p is symmetric 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 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 direct form of Chris Mungall relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y The general property hierarchy is: "directly P" SubPropertyOf "P" Transitive(P) Where we have an annotation assertion "directly P" "is direct form of" "P" If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q' is indirect 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 logical macro assertion on an axiom is a defining property chain 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 where second argument is reflexive 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 relational form of a class 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. logical macro assertion involving identity A shortcut relationship that holds between two entities based on their identity criteria in approximate one to one relationship with 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. is approximately equivalent to 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" x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y is opposite of '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 indistinguishable from 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). evidential logical macro assertion on an axiom axiom has evidence 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. A relationship between a sentence and an instance of a piece of evidence in which the evidence supports the axiom axiom contradicted by evidence 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. A relationship between a sentence and an instance of a piece of evidence in which the evidence contradicts the axiom is representative IRI for equivalence set OWLAPI Reasoner documentation for representativeElement, which follows a similar idea, but selects an arbitrary member 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. If it is necessary to make the context explicit, an axiom annotation can be added to the annotation assertion 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. eco subset subset_property in_subset in neural circuit with (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)))) A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons. David Osumi-Sutherland upstream in neural circuit with (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)))) 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 downstream in neural circuit with (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)))) 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 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 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 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. penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520) is autoimmune 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. aligned with David Osumi-Sutherland David Osumi-Sutherland electrically_synapsed_to A relation that holds between two neurons that are electrically coupled via gap junctions. David Osumi-Sutherland tracheates 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 innervated_by http://www.ncbi.nlm.nih.gov/pubmed/22402613 David Osumi-Sutherland has synaptic terminal of David Osumi-Sutherland bounding layer of 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. 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 coincident with 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. 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. David Osumi-Sutherland Note from NCEAS meeting: consider changing primary label cell expresses 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 regulates in other organism David Osumi-Sutherland x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). regulates transport of David Osumi-Sutherland A relationship that holds between a process that regulates a transport process and the entity transported by that process. GOC:dos A relationship that holds between a process that regulates a transport process and the entity transported by that process. occurent part of A part of relation that applies only between occurents. A part of relation that applies only between occurents. GOC:dos David Osumi-Sutherland encompasses 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. di David Osumi-Sutherland David Osumi-Sutherland has soma location <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) David Osumi-Sutherland Relation between a neuron and an anatomical structure that its soma is part of. 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 David Osumi-Sutherland relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. axon synapses in <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y))) Chris Mungall David Osumi-Sutherland David Osumi-Sutherland Relation between a neuron and some structure its axon forms (chemical) synapses in. synapsed by <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?))) Chris Mungall David Osumi-Sutherland Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. has plasma membrane part Lindsay Cowell Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) Alexander Diehl Chris Mungall Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] synapsed_via_type_Ib_bouton_to 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)))) A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton. Marta Costa David Osumi-Sutherland BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) synapsed_via_type_Is_bouton_to Marta Costa David Osumi-Sutherland 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)))) BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) A relation between a motor neuron and a muscle that it synapses to via a type Is bouton. synapsed_via_type_II_bouton_to A relation between a motor neuron and a muscle that it synapses to via a type II bouton. BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) Marta Costa David Osumi-Sutherland synapsed_by_via_type_II_bouton Marta Costa David Osumi-Sutherland 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))))) Relation between a muscle and a motor neuron that synapses to it via a type II bouton. synapsed_by_via_type_Ib_bouton Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton. 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))))) 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))) Marta Costa David Osumi-Sutherland has postsynaptic terminal in Chris Mungall David Osumi-Sutherland 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)) Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. synapsed in releases neurotransmitter has neurotransmitter synapsed_by_via_type_Is_bouton BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) David Osumi-Sutherland Marta Costa Relation between a muscle and a motor neuron that synapses to it via a type Is bouton. 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))))) has presynaptic terminal 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?) Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. synapses in synapsed_via_type_III_bouton_to 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_by_via_type_III_bouton 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))))) 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))) synapsed to Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. Chris Mungall 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)))) <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?))) David Osumi-Sutherland dendrite synapsed in <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))) Chris Mungall David Osumi-Sutherland Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input. has synaptic terminal 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?) overlaps http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) x overlaps y if and only if there exists some z such that x has part z and z part of y true has fasciculating neuron projection (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) )))))) David Osumi-Sutherland The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. has fasciculating component innervates <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?))) David Osumi-Sutherland 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. continuous with X continuous_with Y if and only if X and Y share a fiat boundary. connected to The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) FMA:85972 David Osumi-Sutherland RO:cjm The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) partially overlaps (forall (?x ?y) (iff (proper_overlaps ?x ?y) (and (overlaps ?x ?y) (not (part_of ?x ?y)) (not (part_of ?y ?x))))) proper overlaps 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 derived by descent from ancestral_stucture_of 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. evolutionarily_descended_from has derived by descendant shares ancestor with VBO calls this homologous_to 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' serially homologous to only in taxon 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 in taxon Connects a biological entity to its taxon of origin. Chris Mungall Jennifer Deegan 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. spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern 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) A is spatially_disjoint_from B if and only if they have no parts in common Chris Mungall 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. connected to https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern 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 a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). connects https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern 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. a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). The M8 connects Glasgow and Edinburgh attached to part of 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. true supplies 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 Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy. drains 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 has component 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. 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. has phenotype 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 phenotype of Chris Mungall develops from Melissa Haendel x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y This is the transitive form of the develops from relation Chris Mungall David Osumi-Sutherland Terry Meehan develops into Chris Mungall David Osumi-Sutherland Terry Meehan gene product of Chris Mungall 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. has gene product 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 every HOTAIR lncRNA is the gene product of some HOXC gene expressed in 'neural crest cell' SubClassOf expresses some 'Wnt1 gene' Chris Mungall 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 directly develops from TODO - add child relations from DOS FBbt 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 has developmental precursor David Osumi-Sutherland parasitoid of A parasite that kills or sterilizes its host A parasite that kills or sterilizes its host has parasitoid directly develops into developmental precursor of regulates false x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y David Hill Tanya Berardini Regulation precludes parthood; the regulatory process may not be within the regulated process. Chris Mungall regulates (processual) GO 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 negatively regulates Chris Mungall x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y negatively regulates (process to process) positively regulates Chris Mungall x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y positively regulates (process to process) has prototype 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. heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation') 'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair')) Chris Mungall 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) capable of 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)". mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' Chris Mungall has function realized in 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. RO_0000053 some (RO_0000054 only ?Y) capable of part of RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) has function in 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 true actively participates in Chris Mungall agent in x actively participates in y if and only if x participates in y and x realizes some active role has active participant 'heart development' has active participant some Shh protein has agent Chris Mungall This may be obsoleted and replaced by the original 'has agent' relation x has participant y if and only if x realizes some active role that inheres in y surrounded by 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 adjacent to x adjacent to y if and only if x and y share a boundary. 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. This relation acts as a join point with BSPO Chris Mungall 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. A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. surrounds Chris Mungall https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 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. Chris Mungall Chris Mungall develops from part of 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 in Chris Mungall EHDAA2 Jonathan Bard, EHDAA2 x develops_in y if x is located in y whilst x is developing obligate parasite of A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host. A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host. facultative parasite of A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host. A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host. Chris Mungall Chris Mungall has start location starts with process that occurs in Chris Mungall 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 has end location Chris Mungall ends with process that occurs in 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 has input 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 output Chris Mungall 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. produces stem parasite of A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047) A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047) root parasite of A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005) A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005) hemiparasite 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. 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. has exposure receptor A broad relationship between an exposure event or process and any entity (e.g., a human, human population, or a human organ) that interacts with an exposure stressor during the exposure event ExO:0000001 has exposure stressor ExO:0000000 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. has exposure route 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 transport path A broad relationship between an exposure event or process and a the material an agent takes from the source to the target. related via exposure to has developmental contribution from Chris Mungall 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 developmentally contributes to Chris Mungall developmentally induced by GO:0001759 We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm] David Osumi-Sutherland 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 induced by Melissa Haendel Chris Mungall Developmental Biology, Gilbert, 8th edition, figure 6.5(F) developmentally induces Chris Mungall Inverse of developmentally induced by developmentally preceded by false 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 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 replaces replaces 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 developmentally succeeded by Inverse of developmentally preceded by Chris Mungall part of developmental precursor of 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue Chris Mungall ubiquitously expressed in x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x Chris Mungall 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. expresses Chris Mungall Inverse of 'expressed in' ubiquitously expresses inverse of ubiquiotously expressed in Chris Mungall results in developmental progression of results_in_developmental_progression_of Chris Mungall 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. results in development of http://www.geneontology.org/GO.doc.development.shtml results_in_development_of 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 every flower development (GO:0009908) results in development of some flower (PO:0009046) results in formation of results_in_formation_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. GOC:mtg_berkeley_2013 Chris Mungall every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) results in morphogenesis of results_in_morphogenesis_of GOC:mtg_berkeley_2013 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. 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. Chris Mungall tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) results in maturation of results_in_maturation_of Chris Mungall 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. 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 GOC:mtg_berkeley_2013 bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) results in disappearance of results_in_disappearance_of May be merged into parent relation Chris Mungall foramen ovale closure SubClassOf results in disappearance of foramen ovale results in developmental regression of every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890) Chris Mungall May be merged into parent relation has habitat 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 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 A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y. evolutionary variant of Chris Mungall transports or maintains localization of regulates location of transports Chris Mungall 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 inheres in part 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. Chris Mungall Because part_of is transitive, inheres in is a sub-relation of inheres in part of true results in acquisition of features of results_in_acquisition_of_features_of The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity GOC:mtg_berkeley_2013 Chris Mungall 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. evolutionarily related to A relationship that holds via some environmental process Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. Chris Mungall ecologically related to Chris Mungall A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions confers advantage in An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial. adapted for Chris Mungall mereotopologically related to 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 developmentally 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 colocalizes with 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]. Gene Ontology Consortium 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] contributes to 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. 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. Chris Mungall 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. In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to 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 enables This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. a particular instances of akt-2 enables some instance of protein kinase activity has 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. is executing Chris Mungall executes catalyzes is catalyzing http://www.arabidopsis.org/ enables functionally related to Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function part of structure that is capable of false this relation holds between c and p when c is part of some c', and c' is capable of p. Chris Mungall true genomically related to 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 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 involved in actively involved in c involved_in p if and only if c enables some process p', and p' is part of p enables part of Chris Mungall regulates levels of Chris Mungall p regulates levels of c if p regulates some amount (PATO:0000070) of c regulates levels of (process to entity) every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid enabled by inverse of enables Chris Mungall regulated by inverse of regulates Chris Mungall regulated by (processual) negatively regulated by Chris Mungall positively regulated by Chris Mungall related via localization to Chris Mungall A relationship that holds via some process of localization 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 some initial location l to some destination. Chris Mungall has target end location Chris Mungall 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. imports 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 results in transport along Chris Mungall Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l results in transport across Chris Mungall Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. results in growth of Chris Mungall 'pollen tube growth' results_in growth_of some 'pollen tube' results in transport to from or in 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) Chris Mungall exports Chris Mungall results in commitment to http://www.geneontology.org/GO.doc.development.shtml#fate Chris Mungall an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron. p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type. results in determination of http://www.geneontology.org/GO.doc.development.shtml#fate Chris Mungall 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. input of Chris Mungall output of Chris Mungall formed as result of Chris Mungall results in structural organization 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 specification of http://www.geneontology.org/GO.doc.development.shtml#fate Chris Mungall The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. results in developmental induction 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 has dendrite location http://neurolex.org/wiki/Property:DendriteLocation Chris Mungall attached to 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 has muscle origin Chris Mungall Wikipedia:Insertion_(anatomy) 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. has muscle insertion Chris Mungall Wikipedia:Insertion_(anatomy) 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. has fused element false 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. Chris Mungall 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 in branching relationship with https://github.com/obophenotype/uberon/issues/170 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) Chris Mungall tributary of This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries) http://en.wikipedia.org/wiki/Tributary tributary channel of Chris Mungall http://www.medindia.net/glossary/venous_tributary.htm drains to drains into 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. http://en.wikipedia.org/wiki/Tributary FMA inferior epigastric vein tributary_of external iliac vein GAZ Deschutes River tributary_of Columbia River drains to distributary of 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 http://en.wikipedia.org/wiki/Distributary Deschutes River distributary_of Little Lava Lake branch of Chris Mungall distributary channel of GAZ Deschutes River distributary_of Little Lava Lake anabranch of x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y. anastomoses with Chris Mungall spatially coextensive with x spatially_coextensive_with y if and inly if x and y have the same location This relation is added for formal completeness. It is unlikely to be used in many practical scenarios A lump of clay and a statue Chris Mungall branching part of 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 FMA:85994 main stem of 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 proper distributary of Chris Mungall x proper_distributary_of y iff x distributary_of y and x does not flow back into y proper tributary of Chris Mungall x proper_tributary_of y iff x tributary_of y and x does not originate from y has developmental potential involving Chris Mungall x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). has potential to developmentally contribute to Chris Mungall x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y has potential to developmentally induce Chris Mungall x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y has potential to develop into Chris Mungall x has the potential to develop into y iff x develops into y or if x is capable of developing into y has potential to directly develop into Chris Mungall x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y has direct input 'protein catabolic process' SubClassOf has_direct_input some protein p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. directly consumes This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate' Chris Mungall obsolete has indirect input true Likely to be obsoleted. See: https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit Chris Mungall obsolete has direct output true 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. translation SubClassOf has_direct_output some protein Chris Mungall directly produces obsolete has indirect output true Chris Mungall Likely to be obsoleted. See: https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit causally downstream of inverse of upstream of Chris Mungall immediately causally downstream of Chris Mungall directly activates directly positively regulates 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 directly activates (process to process) Chris Mungall indirectly activates indirectly positively regulates Chris Mungall 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 directly inhibits directly negatively regulates directly inhibits (process to process) Chris Mungall indirectly inhibits indirectly negatively regulates Chris Mungall causally related to This relation groups causal relations between material entities and causal relations between processes 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. 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. causally upstream of Chris Mungall p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain immediately 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 directly provides input for Chris Mungall directly provides input for (process to process) 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 transitively provides input for Chris Mungall transitive form of directly_provides_input_for This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'directly provides input for' (which may later be relabeled simply to 'provides input for') transitively provides input for (process to process) causally upstream of or within influences (processual) Chris Mungall 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 affects differs in false https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions This is an exploratory relation Chris Mungall differs in attribute of Chris Mungall differs in attribute Chris Mungall causally downstream of or within Chris Mungall involved in regulation of c involved in regulation of p if c is involved in some 'p' and p' regulates some p Chris Mungall involved in positive regulation of Chris Mungall involved in negative regulation of Chris Mungall involved in or regulates 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 involved in or involved in regulation of Chris Mungall enables activity in A protein that enables activity in a cytosol. Chris Mungall c executes activity in d if and only if c enables p and p occurs_in d executes activity in true contributes to morphology of 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 interacts with Considering relabeling as 'pairwise interacts with' http://purl.obolibrary.org/obo/MI_0914 https://github.com/oborel/obo-relations/wiki/InteractionRelations Chris Mungall in pairwise interaction 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. A relationship that holds between two entities in which the processes executed by the two entities are causally connected. 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. genetically interacts with http://purl.obolibrary.org/obo/MI_0208 An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis) Chris Mungall molecularly interacts with http://purl.obolibrary.org/obo/MI_0915 An interaction relationship in which the two partners are molecular entities and are executing molecular processes that are directly causally connected. molecularly binds with binds Chris Mungall biotically interacts with http://eol.org/schema/terms/interactsWith interacts with on organism level 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 trophically interacts with An interaction relationship in which the partners are related via a feeding relationship. Chris Mungall preys on Katja Shulz is subject of predation interaction with Chris Mungall 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 A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824] preys upon http://www.inaturalist.org/observations/2942824 Baleen whale preys on krill http://eol.org/schema/terms/preysUpon Jorrit Poelen symbiotically interacts with http://www.ncbi.nlm.nih.gov/pubmed/19278549 A biotic interaction in which the two organisms live together in more or less intimate association. We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism 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 commensually interacts with http://www.ncbi.nlm.nih.gov/pubmed/19278549 Chris Mungall 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). mutualistically interacts with http://www.ncbi.nlm.nih.gov/pubmed/19278549 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 interacts with via parasite-host interaction http://www.ncbi.nlm.nih.gov/pubmed/19278549 This relation groups a pair of inverse relations, parasite of and parasitized by Chris Mungall 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). parasite of direct parasite of http://eol.org/schema/terms/parasitizes Chris Mungall Pediculus humanus capitis parasite of human parasitizes parasitized by Chris Mungall directly parasitized by has parasite http://eol.org/schema/terms/hasParasite parasitised by participates in a abiotic-biotic interaction with semibiotically interacts with Chris Mungall 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. phosphorylates An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. Chris Mungall Axiomatization to GO to be added later molecularly controls Chris Mungall Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b molecularly decreases activity of Holds between molecules a and b if and only if a executes a process that directly diminishes a process executed by b. inhibits Chris Mungall molecularly increases activity of activates Holds between molecules a and b if and only if a executes a process that directly activates a process executed by b. Chris Mungall transmitted by A relationship that holds between a disease and organism Add domain and range constraints Chris Mungall all dengue disease transmitted by some mosquito has symptom A relation that holds between a disease or an organism and a phenotype Chris Mungall host of The term host is usually used for the larger (macro) of the two members of a symbiosis (GO) Chris Mungall has host http://eol.org/schema/terms/hasHost Chris Mungall pollinates 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. http://eol.org/schema/terms/pollinates Chris Mungall Bees pollinate Flowers is subject of pollination interaction with pollinated by Chris Mungall http://eol.org/schema/terms/hasPollinator is target of pollination interaction with has polinator acquires nutrients from 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. preyed upon by http://eol.org/schema/terms/HasPredator is target of predation interaction with has predator Chris Mungall http://polytraits.lifewatchgreece.eu/terms/PRED is vector for a is a vector for b if a carries and transmits an infectious pathogen b into another living organism Chris Mungall Anopheles is a vector for Plasmodium has vector Chris Mungall partner in 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 Chris Mungall subject participant in Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed. Chris Mungall target participant in Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed. Chris Mungall helper property This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. Chris Mungall is symbiosis Chris Mungall is commensalism Chris Mungall is mutualism Chris Mungall is parasitism Chris Mungall provides nutrients for Chris Mungall eats is subject of eating interaction with Chris Mungall is eaten by is target of eating interaction with Chris Mungall eaten by is evidence for Chris Mungall 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. composed primarily of '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 child nucleus of 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. 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 ABal nucleus child nucleus of ABa nucleus (in C elegans) child nucleus of in hermaphrodite A child nucleus relationship in which the cells are part of a hermaphroditic organism Chris Mungall child nucleus of in male Chris Mungall A child nucleus relationship in which the cells are part of a male organism has part that occurs in Chris Mungall 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. true ubiquitinates Chris Mungall Axiomatization to GO to be added later An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y is kinase activity Chris Mungall is ubiquitination Chris Mungall receives input from Chris Mungall See notes for inverse relation sends output to 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 relation between structure and stage 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. existence starts during Chris Mungall x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). existence starts with Chris Mungall x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). existence overlaps x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. Chris Mungall existence starts and ends during Chris Mungall 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) 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 Chris Mungall x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends with x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. Chris Mungall transformation of 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 immediate 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 existence starts during or after 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. 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). existence ends during or before x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. Chris Mungall causal agent in A relationship between a material entity and a process where the material entity has some causal role that influences the process causal relation between processes 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 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. depends on Chris Mungall towards 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 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 has intermediate 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate Chris Mungall p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c has intermediate product causal relation between material entities 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 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 determined by A coral reef environment is determined by a particular coral reef Pier Buttigieg Chris Mungall 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 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. Chris Mungall determined by (system to material entity) determines determines (material entity to system) Chris Mungall determined by part of 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 true transcribed from http://www.ncbi.nlm.nih.gov/pubmed/20226267 x is transcribed from y if and only if x is synthesized from template y Chris Mungall transcribed to http://www.ncbi.nlm.nih.gov/pubmed/20226267 Chris Mungall ribosomal translation of http://www.ncbi.nlm.nih.gov/pubmed/20226267 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 ribosomally translates to http://www.ncbi.nlm.nih.gov/pubmed/20226267 Chris Mungall inverse of ribosomal translation of sequentially related to 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. Chris Mungall 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. A relation that holds between two entities that have the property of being sequences or having sequences. sequentially adjacent to http://www.ncbi.nlm.nih.gov/pubmed/20226267 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 Two exons on a processed transcript that were previously connected by an intron are adjacent Two consecutive DNA residues are sequentially adjacent Every UTR is adjacent to a CDS of the same transcript Chris Mungall has start sequence http://www.ncbi.nlm.nih.gov/pubmed/20226267 Chris Mungall Every CDS has as a start sequence the start codon for that transcript started by x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence is start sequence of http://www.ncbi.nlm.nih.gov/pubmed/20226267 starts inverse of has start sequence Chris Mungall has end sequence http://www.ncbi.nlm.nih.gov/pubmed/20226267 Chris Mungall ended by x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence 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) is end sequence of http://www.ncbi.nlm.nih.gov/pubmed/20226267 Chris Mungall inverse of has end sequence ends is consecutive sequence of http://www.ncbi.nlm.nih.gov/pubmed/20226267 Chris Mungall In the SO paper, this was defined as an instance-type relation 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. is sequentially aligned with Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence. Chris Mungall 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 bounds sequence of Chris Mungall 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 is bound by sequence of Chris Mungall inverse of bounds sequence of has subsequence http://www.ncbi.nlm.nih.gov/pubmed/20226267 x has subsequence y iff all of the sequence parts of x are sequence parts of y contains Chris Mungall is subsequence of Chris Mungall inverse of has subsequence contained by overlaps sequence 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 does not overlap sequence of Chris Mungall disconnected from 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. is upstream of sequence of Chris Mungall inverse of downstream of sequence of is downstream of sequence of Chris Mungall x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. is immediately downstream of sequence of 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 A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript Chris Mungall is immediately upstream of sequence of Chris Mungall inverse of immediately downstream of A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript has skeleton Chris Mungall has supporting framework 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. 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). results in ending of 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 hyperparasite of http://eol.org/schema/terms/hyperparasitoidOf Chris Mungall https://en.wikipedia.org/wiki/Hyperparasite epiparasite 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 hyperparasitoid of hyperparasitized by has epiparasite has hyperparasite hyperparasitoidized by Chris Mungall allelopath of Chris Mungall x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y http://en.wikipedia.org/wiki/Allelopathy http://eol.org/schema/terms/allelopathyYes pathogen of Chris Mungall has pathogen Chris Mungall has evidence 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. causally influenced by causally influenced by (material entity to material entity) Chris Mungall interaction relation helper property https://github.com/oborel/obo-relations/wiki/InteractionRelations Chris Mungall molecular interaction relation helper property Chris Mungall results in movement of 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 Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c GOC:mtg_berkeley_2013 causally influences 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) biomechanically related to 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. A relation that holds between elements of a musculoskeletal system or its analogs. has muscle antagonist Wikipedia:Antagonist_(muscle) Chris Mungall 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. has branching part Chris Mungall conduit for 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. UBERON:cjm Chris Mungall 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. lumen of Chris Mungall x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. GOC:cjm luminal space of s is luminal space of x iff s is lumen_of x and s is an immaterial entity Chris Mungall has modifier 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. Chris Mungall A relation that holds between an attribute or a qualifier and another attribute. participates in a biotic-biotic interaction with Chris Mungall skeleton of Chris Mungall directly regulates Chris Mungall directly regulates (processual) p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p existence starts at point 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. has part structure that is capable of Chris Mungall 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 gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' results in closure 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 breakdown 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 synthesis of results in assembly of results in catabolism 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 disassembly of results in remodeling of results in organization of p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c existence ends at point 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. causal relation between material entity and a process Chris Mungall 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. capable of regulating Holds between c and p if and only if c is capable of some activity a, and a regulates p. pyrethroid -> growth capable of negatively regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. capable of positively 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 inhibiting or preventing pathological process treats pazopanib -> pathological angiogenesis 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. 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 Usage of the term 'treats' applies when we believe there to be a an inhibitory relationship capable of upregulating or causing pathological process causes disease 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. benzene -> cancer [CHEBI] is substance that treats treats 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. is marker for May be ceded to OBI 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. has causal agent Inverse of 'causal agent in' related via dependence to 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. correlated with 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 is evidence with support from 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 An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support. has model Inverse of is-model-of 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 kills https://github.com/jhpoelen/eol-globi-data/issues/143 is killed by directly positively regulates p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p directly positively regulates (process to process) directly negatively regulates directly negatively regulates (process to process) p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p ectoparasite of A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host has ectoparasite endoparasite of lives inside of A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system has endoparasite mesoparasite of A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite has mesoparasite intercellular endoparasite of A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells. has intercellular endoparasite intracellular endoparasite of A sub-relation of endoparasite-of in which the parasite inhabits host cells. has intracellular endoparasite produces 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. 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 produced by a produced_by b iff some process that occurs_in b has_output a. Melissa Haendel represses expression of Logical axioms to be added after the relevant branch of GO is MIREOTed in Holds between protein a (a transcription factor) and DNA element b if and only if a diminishes the process of transcription of b. increases 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 is model of 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. Matthew Brush 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? 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. causes or contributes to 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'. A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some causal or contributing role that influences the condition. 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'. Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. Environments include natural environments or exposures, experimentally applied conditions, or clinical interventions. causes condition A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has a causal role for the condition. contributes to condition A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some contributing role in the manifestation of the condition. contributes to severity of condition contributes to expressivity of condition A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the severity with which a condition manifests in an individual. contributes to frequency of condition contributes to penetrance of condition A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the frequency of the condition in a population. is preventative for condition A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity prevents or reduces the severity of a condition. Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. Environments include natural environments or exposures, experimentally applied conditions, or clinical interventions. correlated with condition A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship. anatomical structure material anatomical entity immaterial anatomical entity connected anatomical system cell part cell part (CARO) multi-cell-part structure neuron projection bundle multicellular anatomical structure cell neuron biome environmental system molecular process true nucleus biological_process membrane true axon dendrite presynaptic membrane cell projection neuron projection true synapse part cell part synapse postsynaptic membrane true true true quality (PATO) shape branched branchiness sequentially ordered entity Any entity that is ordered in discrete units along a linear axis. Chris Mungall sequence atomic unit Chris Mungall Any individual unit of a collection of like units arranged in a linear order An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair. sequence bearer Chris Mungall Any entity that can be divided into parts such that each part is an atomical unit of a sequence Sequence bearers can be molecular entities, such as a portion of a DNA molecule, or they can be abstract entities, such as an entity representing all human sonic hedgehog regions of the genome with a particular DNA sequence. system May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43 Chris Mungall A material entity consisting of multiple components that are causally integrated. http://www.jbiomedsem.com/content/4/1/43 pending final vetting obsolescence reason specification ready for release curation status specification is defined by This is an experimental annotation is defined by term replaced by 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. requires discussion