diff --git a/ro.obo b/ro.obo index 7a3a7950..c3e0b525 100644 --- a/ro.obo +++ b/ro.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: releases/2016-02-24 +data-version: releases/2016-05-13 subsetdef: ro-eco "" remark: Includes Ontology(OntologyID(OntologyIRI())) [Axioms: 61 Logical Axioms: 0] remark: Includes Ontology(OntologyID(OntologyIRI())) [Axioms: 53 Logical Axioms: 12] @@ -816,6 +816,21 @@ subset: ro-eco property_value: IAO:0000111 "contains" xsd:string property_value: RO:0001900 RO:0001901 +[Typedef] +id: RO:0001020 +name: is allergic trigger for +def: "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." [] +property_value: IAO:0000112 "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" xsd:string +domain: BFO:0000040 ! material entity +is_a: RO:0003302 ! causes or contributes to condition + +[Typedef] +id: RO:0001021 +name: is autoimmune trigger for +def: "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." [] +domain: BFO:0000040 ! material entity +is_a: RO:0003302 ! causes or contributes to condition + [Typedef] id: RO:0001025 name: located in @@ -944,6 +959,15 @@ subset: ro-eco property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string holds_over_chain: RO:0002211 RO:0002313 +[Typedef] +id: RO:0002012 +name: occurent part of +def: "A part of relation that applies only between occurents." [GOC:dos] +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent +is_a: BFO:0000050 ! part of +is_a: RO:0002418 ! causally upstream of or within + [Typedef] id: RO:0002081 name: before or simultaneous with @@ -1658,7 +1682,7 @@ property_value: IAO:0000117 "David Hill" xsd:string property_value: IAO:0000117 "Tanya Berardini" xsd:string property_value: IAO:0000119 "GO" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Regulation does not preclude parthood; the regulatory process may be upstream, or may be within the regulated process." xsd:string +property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string property_value: IAO:0000589 "regulates (processual)" xsd:string property_value: IAO:0000600 "false" xsd:boolean domain: BFO:0000015 ! process @@ -1666,9 +1690,8 @@ range: BFO:0000015 ! process holds_over_chain: RO:0002230 RO:0002211 holds_over_chain: RO:0002578 RO:0002578 is_transitive: true -is_a: RO:0002418 ! causally upstream of or within +is_a: RO:0002411 ! causally upstream of inverse_of: RO:0002334 ! regulated by -transitive_over: BFO:0000050 ! part of [Typedef] id: RO:0002212 @@ -1771,7 +1794,11 @@ inverse_of: RO:0002221 ! surrounds [Typedef] id: RO:0002220 name: adjacent to -def: "x adjacent to y if and only if x and y share a boundary" [] +def: "x adjacent to y if and only if x and y share a boundary." [] +property_value: IAO:0000112 "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." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string +property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string +property_value: IAO:0000112 "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." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1950,6 +1977,39 @@ name: hemiparasite of def: "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." [https://en.wikipedia.org/wiki/Parasitic_plant] is_a: RO:0002444 ! parasite of +[Typedef] +id: RO:0002240 +name: has exposure receptor +def: "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" [] +property_value: IAO:0000119 ExO:0000001 xsd:string +is_a: RO:0002244 ! related via exposure to + +[Typedef] +id: RO:0002241 +name: has exposure stressor +def: "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." [] +property_value: IAO:0000119 ExO:0000000 xsd:string +is_a: RO:0002244 ! related via exposure to + +[Typedef] +id: RO:0002242 +name: has exposure route +def: "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" [] +property_value: IAO:0000119 ExO:0000055 xsd:string +is_a: RO:0002244 ! related via exposure to + +[Typedef] +id: RO:0002243 +name: has exposure transport path +def: "A broad relationship between an exposure event or process and a the material an agent takes from the source to the target." [] +is_a: RO:0002244 ! related via exposure to + +[Typedef] +id: RO:0002244 +name: related via exposure to +domain: BFO:0000015 ! process +is_a: RO:0002410 ! causally related to + [Typedef] id: RO:0002254 name: has developmental contribution from @@ -2935,13 +2995,17 @@ is_a: RO:0002574 ! participates in a biotic-biotic interaction with [Typedef] id: RO:0002439 name: preys on -def: "An interaction relationship involving a predation process, where the subject consumes all or part of the target" [] +def: "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" [] subset: ro-eco +property_value: IAO:0000112 "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" xsd:string property_value: IAO:0000112 "Baleen whale preys on krill" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "Jorrit Poelen" xsd:string +property_value: IAO:0000117 "Katja Shulz" xsd:string property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string property_value: seeAlso http://eol.org/schema/terms/preysUpon xsd:string +property_value: seeAlso http://www.inaturalist.org/observations/2942824 xsd:string is_a: RO:0002438 ! trophically interacts with inverse_of: RO:0002458 ! preyed upon by diff --git a/ro.owl b/ro.owl index 038b9d3b..ef744391 100644 --- a/ro.owl +++ b/ro.owl @@ -24,7 +24,7 @@ - + @@ -715,11 +715,11 @@ Where we have an annotation assertion - + - + @@ -900,6 +900,29 @@ range: spatial region or site (immaterial continuant) + + + + 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. + + + + + + @@ -1017,7 +1040,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Note from NCEAS meeting: consider changing primary label - + @@ -1027,8 +1050,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - - + + @@ -1038,7 +1061,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - + @@ -1087,14 +1110,33 @@ AND t has_input y - 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 + + + + + + @@ -1403,6 +1445,10 @@ AND t has_input y + + + + @@ -1414,10 +1460,6 @@ AND t has_input y - - - - @@ -1613,7 +1655,7 @@ N1 SubclassOf ( - + @@ -1621,7 +1663,7 @@ N1 SubclassOf ( - + @@ -1725,8 +1767,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - 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) 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) @@ -1847,43 +1889,43 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + - + - + - + - + - + - + - + - + - + @@ -1919,12 +1961,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). - - - - - - @@ -1937,6 +1973,12 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + + + + + @@ -2167,22 +2209,22 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + - - + + - + @@ -2234,21 +2276,17 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.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 - Regulation does not preclude parthood; the regulatory process may be upstream, or may be within the regulated process. - + - - - - @@ -2290,14 +2328,14 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - + + + + @@ -2419,15 +2457,25 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. adjacent to - x adjacent to y if and only if x and y share a boundary + 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. + + + + @@ -2687,6 +2735,59 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + + 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 + + + + + + @@ -3024,11 +3125,11 @@ where - + - + @@ -3646,18 +3747,18 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - drains to - - - - GAZ Deschutes River tributary_of Columbia River + + drains to + + + + @@ -3966,8 +4067,8 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - - + + @@ -3978,8 +4079,8 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - - + + @@ -4009,16 +4110,16 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - + - + - + @@ -4126,6 +4227,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different 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 @@ -4376,12 +4478,16 @@ Each of these 3 primitives can be composed to yield a cross-product of different preys on - Baleen whale preys on krill + Katja Shulz is subject of predation interaction with - http://eol.org/schema/terms/preysUpon Chris Mungall - An interaction relationship involving a predation process, where the subject consumes all or part of the target + 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 @@ -5093,11 +5199,11 @@ the a supports either the existence of b, or the truth value of b. - + - + @@ -5158,21 +5264,17 @@ the a supports either the existence of b, or the truth value of b.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). + - + - - - - - @@ -5181,8 +5283,12 @@ the a supports either the existence of b, or the truth value of b. - + + + + + @@ -5197,11 +5303,8 @@ the a supports either the existence of b, or the truth value of b.Chris Mungall - - - - - + + @@ -5212,16 +5315,19 @@ the a supports either the existence of b, or the truth value of b. + - - + - - + + + + + @@ -5854,8 +5960,8 @@ the a supports either the existence of b, or the truth value of b. - GOC:mtg_berkeley_2013 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 @@ -7185,8 +7291,8 @@ Environments include natural environments or exposures, experimentally applied c is defined by - is defined by This is an experimental annotation + is defined by diff --git a/subsets/ro-causal.obo b/subsets/ro-causal.obo index 5132d855..7455e376 100644 --- a/subsets/ro-causal.obo +++ b/subsets/ro-causal.obo @@ -31,8 +31,12 @@ inverse_of: has_active_participant ! has active participant [Typedef] id: adjacent_to name: adjacent to -def: "x adjacent to y if and only if x and y share a boundary" [] +def: "x adjacent to y if and only if x and y share a boundary." [] xref: RO:0002220 +property_value: IAO:0000112 "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." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string +property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string +property_value: IAO:0000112 "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." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1149,6 +1153,37 @@ name: has endoparasite xref: RO:0002635 is_a: parasitized_by ! parasitized by +[Typedef] +id: has_exposure_receptor +name: has exposure receptor +def: "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" [] +xref: RO:0002240 +property_value: IAO:0000119 ExO:0000001 xsd:string +is_a: related_via_exposure_to ! related via exposure to + +[Typedef] +id: has_exposure_route +name: has exposure route +def: "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" [] +xref: RO:0002242 +property_value: IAO:0000119 ExO:0000055 xsd:string +is_a: related_via_exposure_to ! related via exposure to + +[Typedef] +id: has_exposure_stressor +name: has exposure stressor +def: "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." [] +xref: RO:0002241 +property_value: IAO:0000119 ExO:0000000 xsd:string +is_a: related_via_exposure_to ! related via exposure to + +[Typedef] +id: has_exposure_transport_path +name: has exposure transport path +def: "A broad relationship between an exposure event or process and a the material an agent takes from the source to the target." [] +xref: RO:0002243 +is_a: related_via_exposure_to ! related via exposure to + [Typedef] id: has_fasciculating_neuron_projection name: has fasciculating neuron projection @@ -1713,6 +1748,23 @@ xref: RO:0002428 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: involved_in_or_regulates ! involved in or regulates +[Typedef] +id: is_allergic_trigger_for +name: is allergic trigger for +def: "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." [] +xref: RO:0001020 +property_value: IAO:0000112 "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" xsd:string +domain: BFO:0000040 +is_a: causes_or_contributes_to_condition ! causes or contributes to condition + +[Typedef] +id: is_autoimmune_trigger_for +name: is autoimmune trigger for +def: "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." [] +xref: RO:0001021 +domain: BFO:0000040 +is_a: causes_or_contributes_to_condition ! causes or contributes to condition + [Typedef] id: is_bound_by_sequence_of name: is bound by sequence of @@ -2030,6 +2082,16 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: has_output ! has output is_obsolete: true +[Typedef] +id: occurent_part_of +name: occurent part of +def: "A part of relation that applies only between occurents." [GOC:dos] +xref: RO:0002012 +domain: BFO:0000003 +range: BFO:0000003 +is_a: causally_upstream_of_or_within ! causally upstream of or within +is_a: part_of + [Typedef] id: output_of name: output of @@ -2251,14 +2313,18 @@ is_a: trophically_interacts_with ! trophically interacts with [Typedef] id: preys_on name: preys on -def: "An interaction relationship involving a predation process, where the subject consumes all or part of the target" [] +def: "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" [] subset: ro-eco xref: RO:0002439 +property_value: IAO:0000112 "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" xsd:string property_value: IAO:0000112 "Baleen whale preys on krill" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "Jorrit Poelen" xsd:string +property_value: IAO:0000117 "Katja Shulz" xsd:string property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string property_value: seeAlso http://eol.org/schema/terms/preysUpon xsd:string +property_value: seeAlso http://www.inaturalist.org/observations/2942824 xsd:string is_a: trophically_interacts_with ! trophically interacts with inverse_of: preyed_upon_by ! preyed upon by @@ -2323,13 +2389,13 @@ property_value: IAO:0000117 "David Hill" xsd:string property_value: IAO:0000117 "Tanya Berardini" xsd:string property_value: IAO:0000119 "GO" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Regulation does not preclude parthood; the regulatory process may be upstream, or may be within the regulated process." xsd:string +property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string property_value: IAO:0000589 "regulates (processual)" xsd:string property_value: IAO:0000600 "false" xsd:boolean domain: BFO:0000015 range: BFO:0000015 is_transitive: true -is_a: causally_upstream_of_or_within ! causally upstream of or within +is_a: causally_upstream_of ! causally upstream of inverse_of: regulated_by ! regulated by [Typedef] @@ -2360,6 +2426,13 @@ def: "A relationship that holds between two entities, where the relationship hol xref: RO:0002609 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +[Typedef] +id: related_via_exposure_to +name: related via exposure to +xref: RO:0002244 +domain: BFO:0000015 +is_a: causally_related_to ! causally related to + [Typedef] id: related_via_localization_to name: related via localization to diff --git a/subsets/ro-causal.owl b/subsets/ro-causal.owl index eecb0029..c6eeff6f 100644 --- a/subsets/ro-causal.owl +++ b/subsets/ro-causal.owl @@ -268,6 +268,33 @@ + + + + is allergic trigger for + RO:0001020 + 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 + RO:0001021 + 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. + + + + + + @@ -390,6 +417,27 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + occurent part of + RO:0002012 + occurent_part_of + A part of relation that applies only between occurents. + + + + + + + A part of relation that applies only between occurents. + GOC:dos + + + + + + @@ -945,22 +993,22 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - + - - + + - + @@ -1020,16 +1068,16 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 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 - Regulation does not preclude parthood; the regulatory process may be upstream, or may be within the regulated process. - + @@ -1165,15 +1213,25 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 adjacent to RO:0002220 adjacent_to - x adjacent to y if and only if x and y share a boundary + 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. + + + + @@ -1407,6 +1465,69 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + has exposure receptor + RO:0002240 + 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 + RO:0002241 + 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 + RO:0002242 + 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 + RO:0002243 + 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 + RO:0002244 + related_via_exposure_to + + + + + + @@ -2300,14 +2421,14 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - GAZ - Deschutes River tributary_of Columbia River + FMA + inferior epigastric vein tributary_of external iliac vein - FMA - inferior epigastric vein tributary_of external iliac vein + GAZ + Deschutes River tributary_of Columbia River @@ -2331,8 +2452,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - GAZ Deschutes River distributary_of Little Lava Lake + GAZ @@ -2754,6 +2875,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different 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 @@ -2952,12 +3074,16 @@ Each of these 3 primitives can be composed to yield a cross-product of different preys on RO:0002439 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 - An interaction relationship involving a predation process, where the subject consumes all or part of the target + Jorrit Poelen @@ -4064,8 +4190,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - 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 + Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c @@ -4405,8 +4531,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - treats Usage of the term 'treats' applies when we believe there to be a an inhibitory relationship + treats diff --git a/subsets/ro-developmental.obo b/subsets/ro-developmental.obo index e84e3498..0292c98e 100644 --- a/subsets/ro-developmental.obo +++ b/subsets/ro-developmental.obo @@ -31,8 +31,12 @@ inverse_of: has_active_participant ! has active participant [Typedef] id: adjacent_to name: adjacent to -def: "x adjacent to y if and only if x and y share a boundary" [] +def: "x adjacent to y if and only if x and y share a boundary." [] xref: RO:0002220 +property_value: IAO:0000112 "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." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string +property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string +property_value: IAO:0000112 "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." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1149,6 +1153,37 @@ name: has endoparasite xref: RO:0002635 is_a: parasitized_by ! parasitized by +[Typedef] +id: has_exposure_receptor +name: has exposure receptor +def: "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" [] +xref: RO:0002240 +property_value: IAO:0000119 ExO:0000001 xsd:string +is_a: related_via_exposure_to ! related via exposure to + +[Typedef] +id: has_exposure_route +name: has exposure route +def: "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" [] +xref: RO:0002242 +property_value: IAO:0000119 ExO:0000055 xsd:string +is_a: related_via_exposure_to ! related via exposure to + +[Typedef] +id: has_exposure_stressor +name: has exposure stressor +def: "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." [] +xref: RO:0002241 +property_value: IAO:0000119 ExO:0000000 xsd:string +is_a: related_via_exposure_to ! related via exposure to + +[Typedef] +id: has_exposure_transport_path +name: has exposure transport path +def: "A broad relationship between an exposure event or process and a the material an agent takes from the source to the target." [] +xref: RO:0002243 +is_a: related_via_exposure_to ! related via exposure to + [Typedef] id: has_fasciculating_neuron_projection name: has fasciculating neuron projection @@ -1713,6 +1748,23 @@ xref: RO:0002428 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: involved_in_or_regulates ! involved in or regulates +[Typedef] +id: is_allergic_trigger_for +name: is allergic trigger for +def: "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." [] +xref: RO:0001020 +property_value: IAO:0000112 "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" xsd:string +domain: BFO:0000040 +is_a: causes_or_contributes_to_condition ! causes or contributes to condition + +[Typedef] +id: is_autoimmune_trigger_for +name: is autoimmune trigger for +def: "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." [] +xref: RO:0001021 +domain: BFO:0000040 +is_a: causes_or_contributes_to_condition ! causes or contributes to condition + [Typedef] id: is_bound_by_sequence_of name: is bound by sequence of @@ -2030,6 +2082,16 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: has_output ! has output is_obsolete: true +[Typedef] +id: occurent_part_of +name: occurent part of +def: "A part of relation that applies only between occurents." [GOC:dos] +xref: RO:0002012 +domain: BFO:0000003 +range: BFO:0000003 +is_a: causally_upstream_of_or_within ! causally upstream of or within +is_a: part_of + [Typedef] id: output_of name: output of @@ -2251,14 +2313,18 @@ is_a: trophically_interacts_with ! trophically interacts with [Typedef] id: preys_on name: preys on -def: "An interaction relationship involving a predation process, where the subject consumes all or part of the target" [] +def: "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" [] subset: ro-eco xref: RO:0002439 +property_value: IAO:0000112 "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" xsd:string property_value: IAO:0000112 "Baleen whale preys on krill" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "Jorrit Poelen" xsd:string +property_value: IAO:0000117 "Katja Shulz" xsd:string property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string property_value: seeAlso http://eol.org/schema/terms/preysUpon xsd:string +property_value: seeAlso http://www.inaturalist.org/observations/2942824 xsd:string is_a: trophically_interacts_with ! trophically interacts with inverse_of: preyed_upon_by ! preyed upon by @@ -2323,13 +2389,13 @@ property_value: IAO:0000117 "David Hill" xsd:string property_value: IAO:0000117 "Tanya Berardini" xsd:string property_value: IAO:0000119 "GO" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Regulation does not preclude parthood; the regulatory process may be upstream, or may be within the regulated process." xsd:string +property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string property_value: IAO:0000589 "regulates (processual)" xsd:string property_value: IAO:0000600 "false" xsd:boolean domain: BFO:0000015 range: BFO:0000015 is_transitive: true -is_a: causally_upstream_of_or_within ! causally upstream of or within +is_a: causally_upstream_of ! causally upstream of inverse_of: regulated_by ! regulated by [Typedef] @@ -2360,6 +2426,13 @@ def: "A relationship that holds between two entities, where the relationship hol xref: RO:0002609 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +[Typedef] +id: related_via_exposure_to +name: related via exposure to +xref: RO:0002244 +domain: BFO:0000015 +is_a: causally_related_to ! causally related to + [Typedef] id: related_via_localization_to name: related via localization to diff --git a/subsets/ro-developmental.owl b/subsets/ro-developmental.owl index bc4dda3e..9f1cc323 100644 --- a/subsets/ro-developmental.owl +++ b/subsets/ro-developmental.owl @@ -268,6 +268,33 @@ + + + + is allergic trigger for + RO:0001020 + 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 + RO:0001021 + 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. + + + + + + @@ -390,6 +417,27 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + occurent part of + RO:0002012 + occurent_part_of + A part of relation that applies only between occurents. + + + + + + + A part of relation that applies only between occurents. + GOC:dos + + + + + + @@ -945,22 +993,22 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - + - - + + - + @@ -1020,16 +1068,16 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 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 - Regulation does not preclude parthood; the regulatory process may be upstream, or may be within the regulated process. - + @@ -1165,15 +1213,25 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 adjacent to RO:0002220 adjacent_to - x adjacent to y if and only if x and y share a boundary + 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. + + + + @@ -1407,6 +1465,69 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + has exposure receptor + RO:0002240 + 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 + RO:0002241 + 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 + RO:0002242 + 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 + RO:0002243 + 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 + RO:0002244 + related_via_exposure_to + + + + + + @@ -2300,14 +2421,14 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - GAZ - Deschutes River tributary_of Columbia River + FMA + inferior epigastric vein tributary_of external iliac vein - FMA - inferior epigastric vein tributary_of external iliac vein + GAZ + Deschutes River tributary_of Columbia River @@ -2331,8 +2452,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - GAZ Deschutes River distributary_of Little Lava Lake + GAZ @@ -2754,6 +2875,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different 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 @@ -2952,12 +3074,16 @@ Each of these 3 primitives can be composed to yield a cross-product of different preys on RO:0002439 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 - An interaction relationship involving a predation process, where the subject consumes all or part of the target + Jorrit Poelen @@ -4064,8 +4190,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - 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 + Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c @@ -4405,8 +4531,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - treats Usage of the term 'treats' applies when we believe there to be a an inhibitory relationship + treats diff --git a/subsets/ro-eco.obo b/subsets/ro-eco.obo index 7d059ddf..bf81cb7b 100644 --- a/subsets/ro-eco.obo +++ b/subsets/ro-eco.obo @@ -76,6 +76,19 @@ subset: ro-eco property_value: IAO:0000111 "contains" xsd:string property_value: RO:0001900 RO:0001901 +[Typedef] +id: RO:0001020 +name: is allergic trigger for +def: "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." [] +property_value: IAO:0000112 "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" xsd:string +is_a: RO:0003302 ! causes or contributes to condition + +[Typedef] +id: RO:0001021 +name: is autoimmune trigger for +def: "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." [] +is_a: RO:0003302 ! causes or contributes to condition + [Typedef] id: RO:0002001 name: aligned with @@ -160,6 +173,13 @@ subset: ro-eco property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string holds_over_chain: RO:0002211 RO:0002313 +[Typedef] +id: RO:0002012 +name: occurent part of +def: "A part of relation that applies only between occurents." [GOC:dos] +is_a: BFO:0000050 +is_a: RO:0002418 ! causally upstream of or within + [Typedef] id: RO:0002085 name: encompasses @@ -741,15 +761,14 @@ property_value: IAO:0000117 "David Hill" xsd:string property_value: IAO:0000117 "Tanya Berardini" xsd:string property_value: IAO:0000119 "GO" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Regulation does not preclude parthood; the regulatory process may be upstream, or may be within the regulated process." xsd:string +property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string property_value: IAO:0000589 "regulates (processual)" xsd:string property_value: IAO:0000600 "false" xsd:boolean holds_over_chain: RO:0002230 RO:0002211 holds_over_chain: RO:0002578 RO:0002578 is_transitive: true -is_a: RO:0002418 ! causally upstream of or within +is_a: RO:0002411 ! causally upstream of inverse_of: RO:0002334 ! regulated by -transitive_over: BFO:0000050 [Typedef] id: RO:0002212 @@ -848,7 +867,11 @@ inverse_of: RO:0002221 ! surrounds [Typedef] id: RO:0002220 name: adjacent to -def: "x adjacent to y if and only if x and y share a boundary" [] +def: "x adjacent to y if and only if x and y share a boundary." [] +property_value: IAO:0000112 "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." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string +property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string +property_value: IAO:0000112 "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." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -966,6 +989,38 @@ name: hemiparasite of def: "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." [https://en.wikipedia.org/wiki/Parasitic_plant] is_a: RO:0002444 ! parasite of +[Typedef] +id: RO:0002240 +name: has exposure receptor +def: "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" [] +property_value: IAO:0000119 ExO:0000001 xsd:string +is_a: RO:0002244 ! related via exposure to + +[Typedef] +id: RO:0002241 +name: has exposure stressor +def: "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." [] +property_value: IAO:0000119 ExO:0000000 xsd:string +is_a: RO:0002244 ! related via exposure to + +[Typedef] +id: RO:0002242 +name: has exposure route +def: "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" [] +property_value: IAO:0000119 ExO:0000055 xsd:string +is_a: RO:0002244 ! related via exposure to + +[Typedef] +id: RO:0002243 +name: has exposure transport path +def: "A broad relationship between an exposure event or process and a the material an agent takes from the source to the target." [] +is_a: RO:0002244 ! related via exposure to + +[Typedef] +id: RO:0002244 +name: related via exposure to +is_a: RO:0002410 ! causally related to + [Typedef] id: RO:0002254 name: has developmental contribution from @@ -1893,13 +1948,17 @@ is_a: RO:0002574 ! participates in a biotic-biotic interaction with [Typedef] id: RO:0002439 name: preys on -def: "An interaction relationship involving a predation process, where the subject consumes all or part of the target" [] +def: "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" [] subset: ro-eco +property_value: IAO:0000112 "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" xsd:string property_value: IAO:0000112 "Baleen whale preys on krill" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "Jorrit Poelen" xsd:string +property_value: IAO:0000117 "Katja Shulz" xsd:string property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string property_value: seeAlso http://eol.org/schema/terms/preysUpon xsd:string +property_value: seeAlso http://www.inaturalist.org/observations/2942824 xsd:string is_a: RO:0002438 ! trophically interacts with inverse_of: RO:0002458 ! preyed upon by diff --git a/subsets/ro-eco.owl b/subsets/ro-eco.owl index b5e3cc24..5f9331e7 100644 --- a/subsets/ro-eco.owl +++ b/subsets/ro-eco.owl @@ -958,6 +958,27 @@ range: spatial region or site (immaterial continuant) + + + + 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. + + + + + @@ -1100,14 +1121,31 @@ AND t has_input y - GOC:dos A relationship that holds between a process that regulates a transport process and the entity transported by that process. + GOC:dos + + + + occurent part of + A part of relation that applies only between occurents. + + + + + A part of relation that applies only between occurents. + GOC:dos + + + + + + @@ -1622,8 +1660,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - 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) + RO:cjm @@ -1743,7 +1781,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + @@ -1751,15 +1789,15 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + - + - + @@ -1767,7 +1805,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + @@ -1775,7 +1813,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + @@ -2077,26 +2115,22 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.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 - Regulation does not preclude parthood; the regulatory process may be upstream, or may be within the regulated process. - + - - - - - - + + @@ -2256,13 +2290,23 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. adjacent to - x adjacent to y if and only if x and y share a boundary + 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. + 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 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. + + + + @@ -2501,6 +2545,58 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + + 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 + + + + + @@ -2957,8 +3053,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - http://www.arabidopsis.org/ enables + http://www.arabidopsis.org/ @@ -3395,14 +3491,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - GAZ - Deschutes River tributary_of Columbia River - - - - - inferior epigastric vein tributary_of external iliac vein FMA + inferior epigastric vein tributary_of external iliac vein @@ -3412,6 +3502,12 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + + Deschutes River tributary_of Columbia River + GAZ + + + @@ -3430,8 +3526,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - GAZ Deschutes River distributary_of Little Lava Lake + GAZ @@ -3707,20 +3803,20 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - - + + - + - - + + - + @@ -3750,7 +3846,7 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - + @@ -3758,7 +3854,7 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - + @@ -3865,6 +3961,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different 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 @@ -3923,11 +4020,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different Chris Mungall - + - + @@ -3941,11 +4038,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different Chris Mungall - + - + @@ -3959,11 +4056,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different Chris Mungall - + - + @@ -4089,12 +4186,16 @@ Each of these 3 primitives can be composed to yield a cross-product of different preys on - Baleen whale preys on krill + Katja Shulz is subject of predation interaction with - http://eol.org/schema/terms/preysUpon Chris Mungall - An interaction relationship involving a predation process, where the subject consumes all or part of the target + 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 @@ -4722,11 +4823,11 @@ the a supports either the existence of b, or the truth value of b. - + - + @@ -4785,11 +4886,11 @@ the a supports either the existence of b, or the truth value of b. - + - + @@ -4849,31 +4950,31 @@ the a supports either the existence of b, or the truth value of b.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). - - + + + + + - + + - - - - - - + + - + @@ -4888,8 +4989,8 @@ the a supports either the existence of b, or the truth value of b.Chris Mungall + - @@ -4900,19 +5001,19 @@ the a supports either the existence of b, or the truth value of b. - + + - - + - + @@ -6355,8 +6456,8 @@ Environments include natural environments or exposures, experimentally applied c is defined by - is defined by This is an experimental annotation + is defined by @@ -6389,13 +6490,13 @@ Environments include natural environments or exposures, experimentally applied c + + + requires discussion - - - diff --git a/subsets/ro-interaction.obo b/subsets/ro-interaction.obo index bc39f064..cd627ddf 100644 --- a/subsets/ro-interaction.obo +++ b/subsets/ro-interaction.obo @@ -31,8 +31,12 @@ inverse_of: has_active_participant ! has active participant [Typedef] id: adjacent_to name: adjacent to -def: "x adjacent to y if and only if x and y share a boundary" [] +def: "x adjacent to y if and only if x and y share a boundary." [] xref: RO:0002220 +property_value: IAO:0000112 "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." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string +property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string +property_value: IAO:0000112 "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." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1149,6 +1153,37 @@ name: has endoparasite xref: RO:0002635 is_a: parasitized_by ! parasitized by +[Typedef] +id: has_exposure_receptor +name: has exposure receptor +def: "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" [] +xref: RO:0002240 +property_value: IAO:0000119 ExO:0000001 xsd:string +is_a: related_via_exposure_to ! related via exposure to + +[Typedef] +id: has_exposure_route +name: has exposure route +def: "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" [] +xref: RO:0002242 +property_value: IAO:0000119 ExO:0000055 xsd:string +is_a: related_via_exposure_to ! related via exposure to + +[Typedef] +id: has_exposure_stressor +name: has exposure stressor +def: "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." [] +xref: RO:0002241 +property_value: IAO:0000119 ExO:0000000 xsd:string +is_a: related_via_exposure_to ! related via exposure to + +[Typedef] +id: has_exposure_transport_path +name: has exposure transport path +def: "A broad relationship between an exposure event or process and a the material an agent takes from the source to the target." [] +xref: RO:0002243 +is_a: related_via_exposure_to ! related via exposure to + [Typedef] id: has_fasciculating_neuron_projection name: has fasciculating neuron projection @@ -1713,6 +1748,23 @@ xref: RO:0002428 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: involved_in_or_regulates ! involved in or regulates +[Typedef] +id: is_allergic_trigger_for +name: is allergic trigger for +def: "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." [] +xref: RO:0001020 +property_value: IAO:0000112 "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" xsd:string +domain: BFO:0000040 +is_a: causes_or_contributes_to_condition ! causes or contributes to condition + +[Typedef] +id: is_autoimmune_trigger_for +name: is autoimmune trigger for +def: "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." [] +xref: RO:0001021 +domain: BFO:0000040 +is_a: causes_or_contributes_to_condition ! causes or contributes to condition + [Typedef] id: is_bound_by_sequence_of name: is bound by sequence of @@ -2030,6 +2082,16 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: has_output ! has output is_obsolete: true +[Typedef] +id: occurent_part_of +name: occurent part of +def: "A part of relation that applies only between occurents." [GOC:dos] +xref: RO:0002012 +domain: BFO:0000003 +range: BFO:0000003 +is_a: causally_upstream_of_or_within ! causally upstream of or within +is_a: part_of + [Typedef] id: output_of name: output of @@ -2251,14 +2313,18 @@ is_a: trophically_interacts_with ! trophically interacts with [Typedef] id: preys_on name: preys on -def: "An interaction relationship involving a predation process, where the subject consumes all or part of the target" [] +def: "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" [] subset: ro-eco xref: RO:0002439 +property_value: IAO:0000112 "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" xsd:string property_value: IAO:0000112 "Baleen whale preys on krill" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "Jorrit Poelen" xsd:string +property_value: IAO:0000117 "Katja Shulz" xsd:string property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string property_value: seeAlso http://eol.org/schema/terms/preysUpon xsd:string +property_value: seeAlso http://www.inaturalist.org/observations/2942824 xsd:string is_a: trophically_interacts_with ! trophically interacts with inverse_of: preyed_upon_by ! preyed upon by @@ -2323,13 +2389,13 @@ property_value: IAO:0000117 "David Hill" xsd:string property_value: IAO:0000117 "Tanya Berardini" xsd:string property_value: IAO:0000119 "GO" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Regulation does not preclude parthood; the regulatory process may be upstream, or may be within the regulated process." xsd:string +property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string property_value: IAO:0000589 "regulates (processual)" xsd:string property_value: IAO:0000600 "false" xsd:boolean domain: BFO:0000015 range: BFO:0000015 is_transitive: true -is_a: causally_upstream_of_or_within ! causally upstream of or within +is_a: causally_upstream_of ! causally upstream of inverse_of: regulated_by ! regulated by [Typedef] @@ -2360,6 +2426,13 @@ def: "A relationship that holds between two entities, where the relationship hol xref: RO:0002609 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +[Typedef] +id: related_via_exposure_to +name: related via exposure to +xref: RO:0002244 +domain: BFO:0000015 +is_a: causally_related_to ! causally related to + [Typedef] id: related_via_localization_to name: related via localization to diff --git a/subsets/ro-interaction.owl b/subsets/ro-interaction.owl index f58403cb..b5d7955c 100644 --- a/subsets/ro-interaction.owl +++ b/subsets/ro-interaction.owl @@ -268,6 +268,33 @@ + + + + is allergic trigger for + RO:0001020 + 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 + RO:0001021 + 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. + + + + + + @@ -390,6 +417,27 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + occurent part of + RO:0002012 + occurent_part_of + A part of relation that applies only between occurents. + + + + + + + A part of relation that applies only between occurents. + GOC:dos + + + + + + @@ -945,22 +993,22 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - + - - + + - + @@ -1020,16 +1068,16 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 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 - Regulation does not preclude parthood; the regulatory process may be upstream, or may be within the regulated process. - + @@ -1165,15 +1213,25 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 adjacent to RO:0002220 adjacent_to - x adjacent to y if and only if x and y share a boundary + 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. + + + + @@ -1407,6 +1465,69 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + has exposure receptor + RO:0002240 + 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 + RO:0002241 + 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 + RO:0002242 + 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 + RO:0002243 + 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 + RO:0002244 + related_via_exposure_to + + + + + + @@ -2300,14 +2421,14 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - GAZ - Deschutes River tributary_of Columbia River + FMA + inferior epigastric vein tributary_of external iliac vein - FMA - inferior epigastric vein tributary_of external iliac vein + GAZ + Deschutes River tributary_of Columbia River @@ -2331,8 +2452,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - GAZ Deschutes River distributary_of Little Lava Lake + GAZ @@ -2754,6 +2875,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different 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 @@ -2952,12 +3074,16 @@ Each of these 3 primitives can be composed to yield a cross-product of different preys on RO:0002439 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 - An interaction relationship involving a predation process, where the subject consumes all or part of the target + Jorrit Poelen @@ -4064,8 +4190,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - 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 + Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c @@ -4405,8 +4531,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - treats Usage of the term 'treats' applies when we believe there to be a an inhibitory relationship + treats diff --git a/subsets/ro-mereotopology.obo b/subsets/ro-mereotopology.obo index d7566e39..eaa8da2b 100644 --- a/subsets/ro-mereotopology.obo +++ b/subsets/ro-mereotopology.obo @@ -31,8 +31,12 @@ inverse_of: has_active_participant ! has active participant [Typedef] id: adjacent_to name: adjacent to -def: "x adjacent to y if and only if x and y share a boundary" [] +def: "x adjacent to y if and only if x and y share a boundary." [] xref: RO:0002220 +property_value: IAO:0000112 "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." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string +property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string +property_value: IAO:0000112 "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." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1149,6 +1153,37 @@ name: has endoparasite xref: RO:0002635 is_a: parasitized_by ! parasitized by +[Typedef] +id: has_exposure_receptor +name: has exposure receptor +def: "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" [] +xref: RO:0002240 +property_value: IAO:0000119 ExO:0000001 xsd:string +is_a: related_via_exposure_to ! related via exposure to + +[Typedef] +id: has_exposure_route +name: has exposure route +def: "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" [] +xref: RO:0002242 +property_value: IAO:0000119 ExO:0000055 xsd:string +is_a: related_via_exposure_to ! related via exposure to + +[Typedef] +id: has_exposure_stressor +name: has exposure stressor +def: "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." [] +xref: RO:0002241 +property_value: IAO:0000119 ExO:0000000 xsd:string +is_a: related_via_exposure_to ! related via exposure to + +[Typedef] +id: has_exposure_transport_path +name: has exposure transport path +def: "A broad relationship between an exposure event or process and a the material an agent takes from the source to the target." [] +xref: RO:0002243 +is_a: related_via_exposure_to ! related via exposure to + [Typedef] id: has_fasciculating_neuron_projection name: has fasciculating neuron projection @@ -1713,6 +1748,23 @@ xref: RO:0002428 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: involved_in_or_regulates ! involved in or regulates +[Typedef] +id: is_allergic_trigger_for +name: is allergic trigger for +def: "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." [] +xref: RO:0001020 +property_value: IAO:0000112 "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" xsd:string +domain: BFO:0000040 +is_a: causes_or_contributes_to_condition ! causes or contributes to condition + +[Typedef] +id: is_autoimmune_trigger_for +name: is autoimmune trigger for +def: "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." [] +xref: RO:0001021 +domain: BFO:0000040 +is_a: causes_or_contributes_to_condition ! causes or contributes to condition + [Typedef] id: is_bound_by_sequence_of name: is bound by sequence of @@ -2030,6 +2082,16 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: has_output ! has output is_obsolete: true +[Typedef] +id: occurent_part_of +name: occurent part of +def: "A part of relation that applies only between occurents." [GOC:dos] +xref: RO:0002012 +domain: BFO:0000003 +range: BFO:0000003 +is_a: causally_upstream_of_or_within ! causally upstream of or within +is_a: part_of + [Typedef] id: output_of name: output of @@ -2251,14 +2313,18 @@ is_a: trophically_interacts_with ! trophically interacts with [Typedef] id: preys_on name: preys on -def: "An interaction relationship involving a predation process, where the subject consumes all or part of the target" [] +def: "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" [] subset: ro-eco xref: RO:0002439 +property_value: IAO:0000112 "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" xsd:string property_value: IAO:0000112 "Baleen whale preys on krill" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "Jorrit Poelen" xsd:string +property_value: IAO:0000117 "Katja Shulz" xsd:string property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string property_value: seeAlso http://eol.org/schema/terms/preysUpon xsd:string +property_value: seeAlso http://www.inaturalist.org/observations/2942824 xsd:string is_a: trophically_interacts_with ! trophically interacts with inverse_of: preyed_upon_by ! preyed upon by @@ -2323,13 +2389,13 @@ property_value: IAO:0000117 "David Hill" xsd:string property_value: IAO:0000117 "Tanya Berardini" xsd:string property_value: IAO:0000119 "GO" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Regulation does not preclude parthood; the regulatory process may be upstream, or may be within the regulated process." xsd:string +property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string property_value: IAO:0000589 "regulates (processual)" xsd:string property_value: IAO:0000600 "false" xsd:boolean domain: BFO:0000015 range: BFO:0000015 is_transitive: true -is_a: causally_upstream_of_or_within ! causally upstream of or within +is_a: causally_upstream_of ! causally upstream of inverse_of: regulated_by ! regulated by [Typedef] @@ -2360,6 +2426,13 @@ def: "A relationship that holds between two entities, where the relationship hol xref: RO:0002609 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +[Typedef] +id: related_via_exposure_to +name: related via exposure to +xref: RO:0002244 +domain: BFO:0000015 +is_a: causally_related_to ! causally related to + [Typedef] id: related_via_localization_to name: related via localization to diff --git a/subsets/ro-mereotopology.owl b/subsets/ro-mereotopology.owl index 66ea4b82..4ceff754 100644 --- a/subsets/ro-mereotopology.owl +++ b/subsets/ro-mereotopology.owl @@ -268,6 +268,33 @@ + + + + is allergic trigger for + RO:0001020 + 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 + RO:0001021 + 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. + + + + + + @@ -390,6 +417,27 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + occurent part of + RO:0002012 + occurent_part_of + A part of relation that applies only between occurents. + + + + + + + A part of relation that applies only between occurents. + GOC:dos + + + + + + @@ -945,22 +993,22 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - + - - + + - + @@ -1020,16 +1068,16 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 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 - Regulation does not preclude parthood; the regulatory process may be upstream, or may be within the regulated process. - + @@ -1165,15 +1213,25 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 adjacent to RO:0002220 adjacent_to - x adjacent to y if and only if x and y share a boundary + 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. + + + + @@ -1407,6 +1465,69 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + has exposure receptor + RO:0002240 + 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 + RO:0002241 + 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 + RO:0002242 + 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 + RO:0002243 + 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 + RO:0002244 + related_via_exposure_to + + + + + + @@ -2300,14 +2421,14 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - GAZ - Deschutes River tributary_of Columbia River + FMA + inferior epigastric vein tributary_of external iliac vein - FMA - inferior epigastric vein tributary_of external iliac vein + GAZ + Deschutes River tributary_of Columbia River @@ -2331,8 +2452,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - GAZ Deschutes River distributary_of Little Lava Lake + GAZ @@ -2754,6 +2875,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different 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 @@ -2952,12 +3074,16 @@ Each of these 3 primitives can be composed to yield a cross-product of different preys on RO:0002439 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 - An interaction relationship involving a predation process, where the subject consumes all or part of the target + Jorrit Poelen @@ -4064,8 +4190,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - 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 + Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c @@ -4405,8 +4531,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - treats Usage of the term 'treats' applies when we believe there to be a an inhibitory relationship + treats diff --git a/subsets/ro-sequence.obo b/subsets/ro-sequence.obo index 89719b1a..e5b5fc96 100644 --- a/subsets/ro-sequence.obo +++ b/subsets/ro-sequence.obo @@ -31,8 +31,12 @@ inverse_of: has_active_participant ! has active participant [Typedef] id: adjacent_to name: adjacent to -def: "x adjacent to y if and only if x and y share a boundary" [] +def: "x adjacent to y if and only if x and y share a boundary." [] xref: RO:0002220 +property_value: IAO:0000112 "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." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string +property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string +property_value: IAO:0000112 "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." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1149,6 +1153,37 @@ name: has endoparasite xref: RO:0002635 is_a: parasitized_by ! parasitized by +[Typedef] +id: has_exposure_receptor +name: has exposure receptor +def: "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" [] +xref: RO:0002240 +property_value: IAO:0000119 ExO:0000001 xsd:string +is_a: related_via_exposure_to ! related via exposure to + +[Typedef] +id: has_exposure_route +name: has exposure route +def: "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" [] +xref: RO:0002242 +property_value: IAO:0000119 ExO:0000055 xsd:string +is_a: related_via_exposure_to ! related via exposure to + +[Typedef] +id: has_exposure_stressor +name: has exposure stressor +def: "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." [] +xref: RO:0002241 +property_value: IAO:0000119 ExO:0000000 xsd:string +is_a: related_via_exposure_to ! related via exposure to + +[Typedef] +id: has_exposure_transport_path +name: has exposure transport path +def: "A broad relationship between an exposure event or process and a the material an agent takes from the source to the target." [] +xref: RO:0002243 +is_a: related_via_exposure_to ! related via exposure to + [Typedef] id: has_fasciculating_neuron_projection name: has fasciculating neuron projection @@ -1713,6 +1748,23 @@ xref: RO:0002428 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: involved_in_or_regulates ! involved in or regulates +[Typedef] +id: is_allergic_trigger_for +name: is allergic trigger for +def: "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." [] +xref: RO:0001020 +property_value: IAO:0000112 "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" xsd:string +domain: BFO:0000040 +is_a: causes_or_contributes_to_condition ! causes or contributes to condition + +[Typedef] +id: is_autoimmune_trigger_for +name: is autoimmune trigger for +def: "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." [] +xref: RO:0001021 +domain: BFO:0000040 +is_a: causes_or_contributes_to_condition ! causes or contributes to condition + [Typedef] id: is_bound_by_sequence_of name: is bound by sequence of @@ -2030,6 +2082,16 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: has_output ! has output is_obsolete: true +[Typedef] +id: occurent_part_of +name: occurent part of +def: "A part of relation that applies only between occurents." [GOC:dos] +xref: RO:0002012 +domain: BFO:0000003 +range: BFO:0000003 +is_a: causally_upstream_of_or_within ! causally upstream of or within +is_a: part_of + [Typedef] id: output_of name: output of @@ -2251,14 +2313,18 @@ is_a: trophically_interacts_with ! trophically interacts with [Typedef] id: preys_on name: preys on -def: "An interaction relationship involving a predation process, where the subject consumes all or part of the target" [] +def: "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" [] subset: ro-eco xref: RO:0002439 +property_value: IAO:0000112 "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" xsd:string property_value: IAO:0000112 "Baleen whale preys on krill" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "Jorrit Poelen" xsd:string +property_value: IAO:0000117 "Katja Shulz" xsd:string property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string property_value: seeAlso http://eol.org/schema/terms/preysUpon xsd:string +property_value: seeAlso http://www.inaturalist.org/observations/2942824 xsd:string is_a: trophically_interacts_with ! trophically interacts with inverse_of: preyed_upon_by ! preyed upon by @@ -2323,13 +2389,13 @@ property_value: IAO:0000117 "David Hill" xsd:string property_value: IAO:0000117 "Tanya Berardini" xsd:string property_value: IAO:0000119 "GO" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Regulation does not preclude parthood; the regulatory process may be upstream, or may be within the regulated process." xsd:string +property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string property_value: IAO:0000589 "regulates (processual)" xsd:string property_value: IAO:0000600 "false" xsd:boolean domain: BFO:0000015 range: BFO:0000015 is_transitive: true -is_a: causally_upstream_of_or_within ! causally upstream of or within +is_a: causally_upstream_of ! causally upstream of inverse_of: regulated_by ! regulated by [Typedef] @@ -2360,6 +2426,13 @@ def: "A relationship that holds between two entities, where the relationship hol xref: RO:0002609 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +[Typedef] +id: related_via_exposure_to +name: related via exposure to +xref: RO:0002244 +domain: BFO:0000015 +is_a: causally_related_to ! causally related to + [Typedef] id: related_via_localization_to name: related via localization to diff --git a/subsets/ro-sequence.owl b/subsets/ro-sequence.owl index cf7929d4..be05136a 100644 --- a/subsets/ro-sequence.owl +++ b/subsets/ro-sequence.owl @@ -268,6 +268,33 @@ + + + + is allergic trigger for + RO:0001020 + 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 + RO:0001021 + 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. + + + + + + @@ -390,6 +417,27 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + occurent part of + RO:0002012 + occurent_part_of + A part of relation that applies only between occurents. + + + + + + + A part of relation that applies only between occurents. + GOC:dos + + + + + + @@ -945,22 +993,22 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - + - - + + - + @@ -1020,16 +1068,16 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 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 - Regulation does not preclude parthood; the regulatory process may be upstream, or may be within the regulated process. - + @@ -1165,15 +1213,25 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 adjacent to RO:0002220 adjacent_to - x adjacent to y if and only if x and y share a boundary + 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. + + + + @@ -1407,6 +1465,69 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + has exposure receptor + RO:0002240 + 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 + RO:0002241 + 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 + RO:0002242 + 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 + RO:0002243 + 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 + RO:0002244 + related_via_exposure_to + + + + + + @@ -2300,14 +2421,14 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - GAZ - Deschutes River tributary_of Columbia River + FMA + inferior epigastric vein tributary_of external iliac vein - FMA - inferior epigastric vein tributary_of external iliac vein + GAZ + Deschutes River tributary_of Columbia River @@ -2331,8 +2452,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - GAZ Deschutes River distributary_of Little Lava Lake + GAZ @@ -2754,6 +2875,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different 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 @@ -2952,12 +3074,16 @@ Each of these 3 primitives can be composed to yield a cross-product of different preys on RO:0002439 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 - An interaction relationship involving a predation process, where the subject consumes all or part of the target + Jorrit Poelen @@ -4064,8 +4190,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - 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 + Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c @@ -4405,8 +4531,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - treats Usage of the term 'treats' applies when we believe there to be a an inhibitory relationship + treats diff --git a/subsets/ro-time-interval.obo b/subsets/ro-time-interval.obo index 313f882d..009c2d38 100644 --- a/subsets/ro-time-interval.obo +++ b/subsets/ro-time-interval.obo @@ -31,8 +31,12 @@ inverse_of: has_active_participant ! has active participant [Typedef] id: adjacent_to name: adjacent to -def: "x adjacent to y if and only if x and y share a boundary" [] +def: "x adjacent to y if and only if x and y share a boundary." [] xref: RO:0002220 +property_value: IAO:0000112 "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." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string +property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string +property_value: IAO:0000112 "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." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1149,6 +1153,37 @@ name: has endoparasite xref: RO:0002635 is_a: parasitized_by ! parasitized by +[Typedef] +id: has_exposure_receptor +name: has exposure receptor +def: "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" [] +xref: RO:0002240 +property_value: IAO:0000119 ExO:0000001 xsd:string +is_a: related_via_exposure_to ! related via exposure to + +[Typedef] +id: has_exposure_route +name: has exposure route +def: "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" [] +xref: RO:0002242 +property_value: IAO:0000119 ExO:0000055 xsd:string +is_a: related_via_exposure_to ! related via exposure to + +[Typedef] +id: has_exposure_stressor +name: has exposure stressor +def: "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." [] +xref: RO:0002241 +property_value: IAO:0000119 ExO:0000000 xsd:string +is_a: related_via_exposure_to ! related via exposure to + +[Typedef] +id: has_exposure_transport_path +name: has exposure transport path +def: "A broad relationship between an exposure event or process and a the material an agent takes from the source to the target." [] +xref: RO:0002243 +is_a: related_via_exposure_to ! related via exposure to + [Typedef] id: has_fasciculating_neuron_projection name: has fasciculating neuron projection @@ -1713,6 +1748,23 @@ xref: RO:0002428 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: involved_in_or_regulates ! involved in or regulates +[Typedef] +id: is_allergic_trigger_for +name: is allergic trigger for +def: "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." [] +xref: RO:0001020 +property_value: IAO:0000112 "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" xsd:string +domain: BFO:0000040 +is_a: causes_or_contributes_to_condition ! causes or contributes to condition + +[Typedef] +id: is_autoimmune_trigger_for +name: is autoimmune trigger for +def: "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." [] +xref: RO:0001021 +domain: BFO:0000040 +is_a: causes_or_contributes_to_condition ! causes or contributes to condition + [Typedef] id: is_bound_by_sequence_of name: is bound by sequence of @@ -2030,6 +2082,16 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: has_output ! has output is_obsolete: true +[Typedef] +id: occurent_part_of +name: occurent part of +def: "A part of relation that applies only between occurents." [GOC:dos] +xref: RO:0002012 +domain: BFO:0000003 +range: BFO:0000003 +is_a: causally_upstream_of_or_within ! causally upstream of or within +is_a: part_of + [Typedef] id: output_of name: output of @@ -2251,14 +2313,18 @@ is_a: trophically_interacts_with ! trophically interacts with [Typedef] id: preys_on name: preys on -def: "An interaction relationship involving a predation process, where the subject consumes all or part of the target" [] +def: "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" [] subset: ro-eco xref: RO:0002439 +property_value: IAO:0000112 "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" xsd:string property_value: IAO:0000112 "Baleen whale preys on krill" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "Jorrit Poelen" xsd:string +property_value: IAO:0000117 "Katja Shulz" xsd:string property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string property_value: seeAlso http://eol.org/schema/terms/preysUpon xsd:string +property_value: seeAlso http://www.inaturalist.org/observations/2942824 xsd:string is_a: trophically_interacts_with ! trophically interacts with inverse_of: preyed_upon_by ! preyed upon by @@ -2323,13 +2389,13 @@ property_value: IAO:0000117 "David Hill" xsd:string property_value: IAO:0000117 "Tanya Berardini" xsd:string property_value: IAO:0000119 "GO" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Regulation does not preclude parthood; the regulatory process may be upstream, or may be within the regulated process." xsd:string +property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string property_value: IAO:0000589 "regulates (processual)" xsd:string property_value: IAO:0000600 "false" xsd:boolean domain: BFO:0000015 range: BFO:0000015 is_transitive: true -is_a: causally_upstream_of_or_within ! causally upstream of or within +is_a: causally_upstream_of ! causally upstream of inverse_of: regulated_by ! regulated by [Typedef] @@ -2360,6 +2426,13 @@ def: "A relationship that holds between two entities, where the relationship hol xref: RO:0002609 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +[Typedef] +id: related_via_exposure_to +name: related via exposure to +xref: RO:0002244 +domain: BFO:0000015 +is_a: causally_related_to ! causally related to + [Typedef] id: related_via_localization_to name: related via localization to diff --git a/subsets/ro-time-interval.owl b/subsets/ro-time-interval.owl index 00c66a6b..6a7eec89 100644 --- a/subsets/ro-time-interval.owl +++ b/subsets/ro-time-interval.owl @@ -268,6 +268,33 @@ + + + + is allergic trigger for + RO:0001020 + 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 + RO:0001021 + 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. + + + + + + @@ -390,6 +417,27 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + occurent part of + RO:0002012 + occurent_part_of + A part of relation that applies only between occurents. + + + + + + + A part of relation that applies only between occurents. + GOC:dos + + + + + + @@ -945,22 +993,22 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - + - - + + - + @@ -1020,16 +1068,16 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 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 - Regulation does not preclude parthood; the regulatory process may be upstream, or may be within the regulated process. - + @@ -1165,15 +1213,25 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 adjacent to RO:0002220 adjacent_to - x adjacent to y if and only if x and y share a boundary + 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. + + + + @@ -1407,6 +1465,69 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + has exposure receptor + RO:0002240 + 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 + RO:0002241 + 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 + RO:0002242 + 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 + RO:0002243 + 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 + RO:0002244 + related_via_exposure_to + + + + + + @@ -2300,14 +2421,14 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - GAZ - Deschutes River tributary_of Columbia River + FMA + inferior epigastric vein tributary_of external iliac vein - FMA - inferior epigastric vein tributary_of external iliac vein + GAZ + Deschutes River tributary_of Columbia River @@ -2331,8 +2452,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - GAZ Deschutes River distributary_of Little Lava Lake + GAZ @@ -2754,6 +2875,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different 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 @@ -2952,12 +3074,16 @@ Each of these 3 primitives can be composed to yield a cross-product of different preys on RO:0002439 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 - An interaction relationship involving a predation process, where the subject consumes all or part of the target + Jorrit Poelen @@ -4064,8 +4190,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - 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 + Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c @@ -4405,8 +4531,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - treats Usage of the term 'treats' applies when we believe there to be a an inhibitory relationship + treats