diff --git a/ro.obo b/ro.obo index ed95ca04..22e3de7e 100644 --- a/ro.obo +++ b/ro.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: releases/2016-09-02 +data-version: releases/2016-10-24 subsetdef: ro-eco "" subsetdef: RO:0002259 "" remark: Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0] @@ -1735,6 +1735,7 @@ property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relati property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string holds_over_chain: RO:0002230 RO:0002212 is_a: RO:0002211 ! regulates +is_a: RO:0002305 ! causally upstream of, negative effect inverse_of: RO:0002335 ! negatively regulated by [Typedef] @@ -1747,6 +1748,7 @@ property_value: IAO:0000589 "positively regulates (process to process)" xsd:stri holds_over_chain: RO:0002212 RO:0002212 holds_over_chain: RO:0002230 RO:0002213 is_a: RO:0002211 ! regulates +is_a: RO:0002304 ! causally upstream of, positive effect inverse_of: RO:0002336 ! positively regulated by [Typedef] @@ -2171,7 +2173,7 @@ id: RO:0002263 name: acts upstream of def: "c involved in regulation of p if c enables 'p' and p' causally upstream of p" [] holds_over_chain: RO:0002327 RO:0002411 -is_a: RO:0002500 ! causal agent in +is_a: RO:0002264 ! acts upstream of or within [Typedef] id: RO:0002264 @@ -2243,6 +2245,15 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "May be merged into parent relation" xsd:string is_a: RO:0002552 ! results in ending of +[Typedef] +id: RO:0002302 +name: is treated by substance +def: "Inverse of 'is substance that treats'" [] +subset: RO:0002259 +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: RO:0002410 ! causally related to +inverse_of: RO:0002606 ! is substance that treats + [Typedef] id: RO:0002303 name: has habitat @@ -2257,6 +2268,20 @@ domain: CARO:0000006 ! material anatomical entity range: ENVO:01000254 ! environmental system is_a: RO:0002321 ! ecologically related to +[Typedef] +id: RO:0002304 +name: causally upstream of, positive effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: RO:0002411 ! causally upstream of + +[Typedef] +id: RO:0002305 +name: causally upstream of, negative effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: RO:0002411 ! causally upstream of + [Typedef] id: RO:0002312 name: evolutionary variant of @@ -3012,6 +3037,7 @@ def: "c involved in regulation of p if c is involved in some 'p' and p' regulate property_value: IAO:0000117 "Chris Mungall" xsd:string holds_over_chain: RO:0002327 RO:0002211 holds_over_chain: RO:0002331 RO:0002211 +is_a: RO:0002263 ! acts upstream of is_a: RO:0002431 ! involved in or involved in regulation of [Typedef] @@ -3036,6 +3062,7 @@ name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "involved in or reguates" xsd:string +is_a: RO:0002264 ! acts upstream of or within is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in diff --git a/ro.owl b/ro.owl index e82e447c..a79bf5dc 100644 --- a/ro.owl +++ b/ro.owl @@ -13,7 +13,7 @@ xmlns:cito="http://purl.org/spar/cito/" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#"> - + @@ -2336,6 +2336,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + @@ -2355,6 +2356,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + @@ -2971,7 +2973,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + @@ -3189,6 +3191,19 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + + + + Inverse of 'is substance that treats' + cjm + + is treated by substance + + + + @@ -3209,6 +3224,28 @@ where + + + + + cjm + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y + causally upstream of, positive effect + + + + + + + + + cjm + holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y + causally upstream of, negative effect + + + + @@ -4398,6 +4435,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -4453,6 +4491,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p @@ -7515,5 +7554,5 @@ Environments include natural environments or exposures, experimentally applied c - + diff --git a/src/ontology/ro.obo b/src/ontology/ro.obo index ed95ca04..22e3de7e 100644 --- a/src/ontology/ro.obo +++ b/src/ontology/ro.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: releases/2016-09-02 +data-version: releases/2016-10-24 subsetdef: ro-eco "" subsetdef: RO:0002259 "" remark: Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0] @@ -1735,6 +1735,7 @@ property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relati property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string holds_over_chain: RO:0002230 RO:0002212 is_a: RO:0002211 ! regulates +is_a: RO:0002305 ! causally upstream of, negative effect inverse_of: RO:0002335 ! negatively regulated by [Typedef] @@ -1747,6 +1748,7 @@ property_value: IAO:0000589 "positively regulates (process to process)" xsd:stri holds_over_chain: RO:0002212 RO:0002212 holds_over_chain: RO:0002230 RO:0002213 is_a: RO:0002211 ! regulates +is_a: RO:0002304 ! causally upstream of, positive effect inverse_of: RO:0002336 ! positively regulated by [Typedef] @@ -2171,7 +2173,7 @@ id: RO:0002263 name: acts upstream of def: "c involved in regulation of p if c enables 'p' and p' causally upstream of p" [] holds_over_chain: RO:0002327 RO:0002411 -is_a: RO:0002500 ! causal agent in +is_a: RO:0002264 ! acts upstream of or within [Typedef] id: RO:0002264 @@ -2243,6 +2245,15 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "May be merged into parent relation" xsd:string is_a: RO:0002552 ! results in ending of +[Typedef] +id: RO:0002302 +name: is treated by substance +def: "Inverse of 'is substance that treats'" [] +subset: RO:0002259 +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: RO:0002410 ! causally related to +inverse_of: RO:0002606 ! is substance that treats + [Typedef] id: RO:0002303 name: has habitat @@ -2257,6 +2268,20 @@ domain: CARO:0000006 ! material anatomical entity range: ENVO:01000254 ! environmental system is_a: RO:0002321 ! ecologically related to +[Typedef] +id: RO:0002304 +name: causally upstream of, positive effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: RO:0002411 ! causally upstream of + +[Typedef] +id: RO:0002305 +name: causally upstream of, negative effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: RO:0002411 ! causally upstream of + [Typedef] id: RO:0002312 name: evolutionary variant of @@ -3012,6 +3037,7 @@ def: "c involved in regulation of p if c is involved in some 'p' and p' regulate property_value: IAO:0000117 "Chris Mungall" xsd:string holds_over_chain: RO:0002327 RO:0002211 holds_over_chain: RO:0002331 RO:0002211 +is_a: RO:0002263 ! acts upstream of is_a: RO:0002431 ! involved in or involved in regulation of [Typedef] @@ -3036,6 +3062,7 @@ name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "involved in or reguates" xsd:string +is_a: RO:0002264 ! acts upstream of or within is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in diff --git a/src/ontology/ro.owl b/src/ontology/ro.owl index e82e447c..a79bf5dc 100644 --- a/src/ontology/ro.owl +++ b/src/ontology/ro.owl @@ -13,7 +13,7 @@ xmlns:cito="http://purl.org/spar/cito/" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#"> - + @@ -2336,6 +2336,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + @@ -2355,6 +2356,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + @@ -2971,7 +2973,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + @@ -3189,6 +3191,19 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + + + + Inverse of 'is substance that treats' + cjm + + is treated by substance + + + + @@ -3209,6 +3224,28 @@ where + + + + + cjm + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y + causally upstream of, positive effect + + + + + + + + + cjm + holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y + causally upstream of, negative effect + + + + @@ -4398,6 +4435,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -4453,6 +4491,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p @@ -7515,5 +7554,5 @@ Environments include natural environments or exposures, experimentally applied c - + diff --git a/src/ontology/subsets/ro-causal.obo b/src/ontology/subsets/ro-causal.obo index 346fa484..2ceaf227 100644 --- a/src/ontology/subsets/ro-causal.obo +++ b/src/ontology/subsets/ro-causal.obo @@ -41,7 +41,7 @@ id: acts_upstream_of name: acts upstream of def: "c involved in regulation of p if c enables 'p' and p' causally upstream of p" [] xref: RO:0002263 -is_a: causal_agent_in ! causal agent in +is_a: acts_upstream_of_or_within ! acts upstream of or within [Typedef] id: acts_upstream_of_or_within @@ -380,6 +380,22 @@ is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within is_a: precedes +[Typedef] +id: causally_upstream_of,_negative_effect +name: causally upstream of, negative effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y +xref: RO:0002305 +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: causally_upstream_of ! causally upstream of + +[Typedef] +id: causally_upstream_of,_positive_effect +name: causally upstream of, positive effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y +xref: RO:0002304 +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: causally_upstream_of ! causally upstream of + [Typedef] id: causally_upstream_of_or_within name: causally upstream of or within @@ -1824,6 +1840,7 @@ def: "c involved in or regulates p if and only if either (i) c is involved in p xref: RO:0002431 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "involved in or reguates" xsd:string +is_a: acts_upstream_of_or_within ! acts upstream of or within is_a: causal_agent_in ! causal agent in is_a: functionally_related_to ! functionally related to @@ -1840,6 +1857,7 @@ name: involved in regulation of def: "c involved in regulation of p if c is involved in some 'p' and p' regulates some p" [] xref: RO:0002428 property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: acts_upstream_of ! acts upstream of is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of [Typedef] @@ -2010,6 +2028,16 @@ property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relati property_value: seeAlso https://code.google.com/p/obo-relations/issues/detail?id=46 is_a: capable_of_inhibiting_or_preventing_pathological_process ! capable of inhibiting or preventing pathological process +[Typedef] +id: is_treated_by_substance +name: is treated by substance +def: "Inverse of 'is substance that treats'" [] +subset: RO:0002259 +xref: RO:0002302 +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: causally_related_to ! causally related to +inverse_of: is_substance_that_treats ! is substance that treats + [Typedef] id: is_upstream_of_sequence_of name: is upstream of sequence of @@ -2164,6 +2192,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string +is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect is_a: regulates ! regulates inverse_of: negatively_regulated_by ! negatively regulated by @@ -2390,6 +2419,7 @@ xref: RO:0002213 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string +is_a: causally_upstream_of,_positive_effect ! causally upstream of, positive effect is_a: regulates ! regulates inverse_of: positively_regulated_by ! positively regulated by diff --git a/src/ontology/subsets/ro-causal.owl b/src/ontology/subsets/ro-causal.owl index 7e6fb44b..1c9b4160 100644 --- a/src/ontology/subsets/ro-causal.owl +++ b/src/ontology/subsets/ro-causal.owl @@ -1098,6 +1098,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y @@ -1115,6 +1116,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y Chris Mungall @@ -1660,7 +1662,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - + c involved in regulation of p if c enables 'p' and p' causally upstream of p RO:0002263 acts_upstream_of @@ -1845,6 +1847,21 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + + + Inverse of 'is substance that treats' + cjm + RO:0002302 + + is_treated_by_substance + is treated by substance + + + + @@ -1867,6 +1884,32 @@ where + + + + + cjm + RO:0002304 + causally_upstream_of,_positive_effect + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y + causally upstream of, positive effect + + + + + + + + + cjm + RO:0002305 + causally_upstream_of,_negative_effect + holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y + causally upstream of, negative effect + + + + @@ -2949,6 +2992,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + c involved in regulation of p if c is involved in some 'p' and p' regulates some p Chris Mungall @@ -2986,6 +3030,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p @@ -5191,5 +5236,5 @@ Environments include natural environments or exposures, experimentally applied c - + diff --git a/src/ontology/subsets/ro-chado.obo b/src/ontology/subsets/ro-chado.obo index 9bcfbd15..39f1209c 100644 --- a/src/ontology/subsets/ro-chado.obo +++ b/src/ontology/subsets/ro-chado.obo @@ -754,6 +754,7 @@ name: negatively_regulates def: "x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y" [] holds_over_chain: RO:0002230 RO:0002212 is_a: RO:0002211 ! regulates +is_a: RO:0002305 ! causally upstream of, negative effect inverse_of: RO:0002335 ! negatively regulated by [Typedef] @@ -763,6 +764,7 @@ def: "x positively regulates y if and only if the progression of x increases the holds_over_chain: RO:0002212 RO:0002212 holds_over_chain: RO:0002230 RO:0002213 is_a: RO:0002211 ! regulates +is_a: RO:0002304 ! causally upstream of, positive effect inverse_of: RO:0002336 ! positively regulated by [Typedef] @@ -1054,7 +1056,7 @@ id: RO:0002263 name: acts_upstream_of def: "c involved in regulation of p if c enables 'p' and p' causally upstream of p" [] holds_over_chain: RO:0002327 RO:0002411 -is_a: RO:0002500 ! causal agent in +is_a: RO:0002264 ! acts upstream of or within [Typedef] id: RO:0002264 @@ -1105,12 +1107,29 @@ id: RO:0002301 name: results_in_developmental_regression_of is_a: RO:0002552 ! results in ending of +[Typedef] +id: RO:0002302 +name: is_treated_by_substance +def: "Inverse of 'is substance that treats'" [] +is_a: RO:0002410 ! causally related to +inverse_of: RO:0002606 ! is substance that treats + [Typedef] id: RO:0002303 name: has_habitat def: "x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs." [] is_a: RO:0002321 ! ecologically related to +[Typedef] +id: RO:0002304 +name: causally_upstream_of,_positive_effect +is_a: RO:0002411 ! causally upstream of + +[Typedef] +id: RO:0002305 +name: causally_upstream_of,_negative_effect +is_a: RO:0002411 ! causally upstream of + [Typedef] id: RO:0002312 name: evolutionary_variant_of @@ -1614,6 +1633,7 @@ name: involved_in_regulation_of def: "c involved in regulation of p if c is involved in some 'p' and p' regulates some p" [] holds_over_chain: RO:0002327 RO:0002211 holds_over_chain: RO:0002331 RO:0002211 +is_a: RO:0002263 ! acts upstream of is_a: RO:0002431 ! involved in or involved in regulation of [Typedef] @@ -1634,6 +1654,7 @@ is_a: RO:0002428 ! involved in regulation of id: RO:0002431 name: involved_in_or_involved_in_regulation_of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] +is_a: RO:0002264 ! acts upstream of or within is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in diff --git a/src/ontology/subsets/ro-developmental.obo b/src/ontology/subsets/ro-developmental.obo index e7727a51..c58f4a4f 100644 --- a/src/ontology/subsets/ro-developmental.obo +++ b/src/ontology/subsets/ro-developmental.obo @@ -41,7 +41,7 @@ id: acts_upstream_of name: acts upstream of def: "c involved in regulation of p if c enables 'p' and p' causally upstream of p" [] xref: RO:0002263 -is_a: causal_agent_in ! causal agent in +is_a: acts_upstream_of_or_within ! acts upstream of or within [Typedef] id: acts_upstream_of_or_within @@ -380,6 +380,22 @@ is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within is_a: precedes +[Typedef] +id: causally_upstream_of,_negative_effect +name: causally upstream of, negative effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y +xref: RO:0002305 +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: causally_upstream_of ! causally upstream of + +[Typedef] +id: causally_upstream_of,_positive_effect +name: causally upstream of, positive effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y +xref: RO:0002304 +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: causally_upstream_of ! causally upstream of + [Typedef] id: causally_upstream_of_or_within name: causally upstream of or within @@ -1824,6 +1840,7 @@ def: "c involved in or regulates p if and only if either (i) c is involved in p xref: RO:0002431 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "involved in or reguates" xsd:string +is_a: acts_upstream_of_or_within ! acts upstream of or within is_a: causal_agent_in ! causal agent in is_a: functionally_related_to ! functionally related to @@ -1840,6 +1857,7 @@ name: involved in regulation of def: "c involved in regulation of p if c is involved in some 'p' and p' regulates some p" [] xref: RO:0002428 property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: acts_upstream_of ! acts upstream of is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of [Typedef] @@ -2010,6 +2028,16 @@ property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relati property_value: seeAlso https://code.google.com/p/obo-relations/issues/detail?id=46 is_a: capable_of_inhibiting_or_preventing_pathological_process ! capable of inhibiting or preventing pathological process +[Typedef] +id: is_treated_by_substance +name: is treated by substance +def: "Inverse of 'is substance that treats'" [] +subset: RO:0002259 +xref: RO:0002302 +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: causally_related_to ! causally related to +inverse_of: is_substance_that_treats ! is substance that treats + [Typedef] id: is_upstream_of_sequence_of name: is upstream of sequence of @@ -2164,6 +2192,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string +is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect is_a: regulates ! regulates inverse_of: negatively_regulated_by ! negatively regulated by @@ -2390,6 +2419,7 @@ xref: RO:0002213 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string +is_a: causally_upstream_of,_positive_effect ! causally upstream of, positive effect is_a: regulates ! regulates inverse_of: positively_regulated_by ! positively regulated by diff --git a/src/ontology/subsets/ro-developmental.owl b/src/ontology/subsets/ro-developmental.owl index 7d3bd409..27502e4f 100644 --- a/src/ontology/subsets/ro-developmental.owl +++ b/src/ontology/subsets/ro-developmental.owl @@ -1098,6 +1098,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y @@ -1115,6 +1116,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y Chris Mungall @@ -1660,7 +1662,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - + c involved in regulation of p if c enables 'p' and p' causally upstream of p RO:0002263 acts_upstream_of @@ -1845,6 +1847,21 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + + + Inverse of 'is substance that treats' + cjm + RO:0002302 + + is_treated_by_substance + is treated by substance + + + + @@ -1867,6 +1884,32 @@ where + + + + + cjm + RO:0002304 + causally_upstream_of,_positive_effect + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y + causally upstream of, positive effect + + + + + + + + + cjm + RO:0002305 + causally_upstream_of,_negative_effect + holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y + causally upstream of, negative effect + + + + @@ -2949,6 +2992,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + c involved in regulation of p if c is involved in some 'p' and p' regulates some p Chris Mungall @@ -2986,6 +3030,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p @@ -5191,5 +5236,5 @@ Environments include natural environments or exposures, experimentally applied c - + diff --git a/src/ontology/subsets/ro-eco.obo b/src/ontology/subsets/ro-eco.obo index 4f7c14a9..46591c15 100644 --- a/src/ontology/subsets/ro-eco.obo +++ b/src/ontology/subsets/ro-eco.obo @@ -814,6 +814,7 @@ property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relati property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string holds_over_chain: RO:0002230 RO:0002212 is_a: RO:0002211 ! regulates +is_a: RO:0002305 ! causally upstream of, negative effect inverse_of: RO:0002335 ! negatively regulated by [Typedef] @@ -826,6 +827,7 @@ property_value: IAO:0000589 "positively regulates (process to process)" xsd:stri holds_over_chain: RO:0002212 RO:0002212 holds_over_chain: RO:0002230 RO:0002213 is_a: RO:0002211 ! regulates +is_a: RO:0002304 ! causally upstream of, positive effect inverse_of: RO:0002336 ! positively regulated by [Typedef] @@ -1185,7 +1187,7 @@ id: RO:0002263 name: acts upstream of def: "c involved in regulation of p if c enables 'p' and p' causally upstream of p" [] holds_over_chain: RO:0002327 RO:0002411 -is_a: RO:0002500 ! causal agent in +is_a: RO:0002264 ! acts upstream of or within [Typedef] id: RO:0002264 @@ -1257,6 +1259,15 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "May be merged into parent relation" xsd:string is_a: RO:0002552 ! results in ending of +[Typedef] +id: RO:0002302 +name: is treated by substance +def: "Inverse of 'is substance that treats'" [] +subset: RO:0002259 +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: RO:0002410 ! causally related to +inverse_of: RO:0002606 ! is substance that treats + [Typedef] id: RO:0002303 name: has habitat @@ -1269,6 +1280,20 @@ property_value: IAO:0000117 "Pier Buttigieg" xsd:string property_value: IAO:0000118 "adapted for living in" xsd:string is_a: RO:0002321 ! ecologically related to +[Typedef] +id: RO:0002304 +name: causally upstream of, positive effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: RO:0002411 ! causally upstream of + +[Typedef] +id: RO:0002305 +name: causally upstream of, negative effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: RO:0002411 ! causally upstream of + [Typedef] id: RO:0002312 name: evolutionary variant of @@ -1978,6 +2003,7 @@ def: "c involved in regulation of p if c is involved in some 'p' and p' regulate property_value: IAO:0000117 "Chris Mungall" xsd:string holds_over_chain: RO:0002327 RO:0002211 holds_over_chain: RO:0002331 RO:0002211 +is_a: RO:0002263 ! acts upstream of is_a: RO:0002431 ! involved in or involved in regulation of [Typedef] @@ -2002,6 +2028,7 @@ name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "involved in or reguates" xsd:string +is_a: RO:0002264 ! acts upstream of or within is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in diff --git a/src/ontology/subsets/ro-eco.owl b/src/ontology/subsets/ro-eco.owl index 9d9682de..815ad3da 100644 --- a/src/ontology/subsets/ro-eco.owl +++ b/src/ontology/subsets/ro-eco.owl @@ -2163,6 +2163,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + @@ -2182,6 +2183,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + @@ -2758,7 +2760,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + @@ -2971,6 +2973,19 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + + + + Inverse of 'is substance that treats' + cjm + + is treated by substance + + + + @@ -2989,6 +3004,28 @@ where + + + + + cjm + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y + causally upstream of, positive effect + + + + + + + + + cjm + holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y + causally upstream of, negative effect + + + + @@ -4109,6 +4146,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -4164,6 +4202,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p @@ -6616,5 +6655,5 @@ Environments include natural environments or exposures, experimentally applied c - + diff --git a/src/ontology/subsets/ro-hom.owl b/src/ontology/subsets/ro-hom.owl index 2bb5e145..7a10d6fa 100644 --- a/src/ontology/subsets/ro-hom.owl +++ b/src/ontology/subsets/ro-hom.owl @@ -55,5 +55,5 @@ - + diff --git a/src/ontology/subsets/ro-interaction.obo b/src/ontology/subsets/ro-interaction.obo index a26d0676..0636c4a7 100644 --- a/src/ontology/subsets/ro-interaction.obo +++ b/src/ontology/subsets/ro-interaction.obo @@ -41,7 +41,7 @@ id: acts_upstream_of name: acts upstream of def: "c involved in regulation of p if c enables 'p' and p' causally upstream of p" [] xref: RO:0002263 -is_a: causal_agent_in ! causal agent in +is_a: acts_upstream_of_or_within ! acts upstream of or within [Typedef] id: acts_upstream_of_or_within @@ -380,6 +380,22 @@ is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within is_a: precedes +[Typedef] +id: causally_upstream_of,_negative_effect +name: causally upstream of, negative effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y +xref: RO:0002305 +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: causally_upstream_of ! causally upstream of + +[Typedef] +id: causally_upstream_of,_positive_effect +name: causally upstream of, positive effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y +xref: RO:0002304 +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: causally_upstream_of ! causally upstream of + [Typedef] id: causally_upstream_of_or_within name: causally upstream of or within @@ -1824,6 +1840,7 @@ def: "c involved in or regulates p if and only if either (i) c is involved in p xref: RO:0002431 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "involved in or reguates" xsd:string +is_a: acts_upstream_of_or_within ! acts upstream of or within is_a: causal_agent_in ! causal agent in is_a: functionally_related_to ! functionally related to @@ -1840,6 +1857,7 @@ name: involved in regulation of def: "c involved in regulation of p if c is involved in some 'p' and p' regulates some p" [] xref: RO:0002428 property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: acts_upstream_of ! acts upstream of is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of [Typedef] @@ -2010,6 +2028,16 @@ property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relati property_value: seeAlso https://code.google.com/p/obo-relations/issues/detail?id=46 is_a: capable_of_inhibiting_or_preventing_pathological_process ! capable of inhibiting or preventing pathological process +[Typedef] +id: is_treated_by_substance +name: is treated by substance +def: "Inverse of 'is substance that treats'" [] +subset: RO:0002259 +xref: RO:0002302 +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: causally_related_to ! causally related to +inverse_of: is_substance_that_treats ! is substance that treats + [Typedef] id: is_upstream_of_sequence_of name: is upstream of sequence of @@ -2164,6 +2192,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string +is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect is_a: regulates ! regulates inverse_of: negatively_regulated_by ! negatively regulated by @@ -2390,6 +2419,7 @@ xref: RO:0002213 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string +is_a: causally_upstream_of,_positive_effect ! causally upstream of, positive effect is_a: regulates ! regulates inverse_of: positively_regulated_by ! positively regulated by diff --git a/src/ontology/subsets/ro-interaction.owl b/src/ontology/subsets/ro-interaction.owl index 65c08cba..02be0d3b 100644 --- a/src/ontology/subsets/ro-interaction.owl +++ b/src/ontology/subsets/ro-interaction.owl @@ -1098,6 +1098,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y @@ -1115,6 +1116,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y Chris Mungall @@ -1660,7 +1662,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - + c involved in regulation of p if c enables 'p' and p' causally upstream of p RO:0002263 acts_upstream_of @@ -1845,6 +1847,21 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + + + Inverse of 'is substance that treats' + cjm + RO:0002302 + + is_treated_by_substance + is treated by substance + + + + @@ -1867,6 +1884,32 @@ where + + + + + cjm + RO:0002304 + causally_upstream_of,_positive_effect + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y + causally upstream of, positive effect + + + + + + + + + cjm + RO:0002305 + causally_upstream_of,_negative_effect + holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y + causally upstream of, negative effect + + + + @@ -2949,6 +2992,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + c involved in regulation of p if c is involved in some 'p' and p' regulates some p Chris Mungall @@ -2986,6 +3030,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p @@ -5191,5 +5236,5 @@ Environments include natural environments or exposures, experimentally applied c - + diff --git a/src/ontology/subsets/ro-mereotopology.obo b/src/ontology/subsets/ro-mereotopology.obo index b9acd974..12a5025c 100644 --- a/src/ontology/subsets/ro-mereotopology.obo +++ b/src/ontology/subsets/ro-mereotopology.obo @@ -41,7 +41,7 @@ id: acts_upstream_of name: acts upstream of def: "c involved in regulation of p if c enables 'p' and p' causally upstream of p" [] xref: RO:0002263 -is_a: causal_agent_in ! causal agent in +is_a: acts_upstream_of_or_within ! acts upstream of or within [Typedef] id: acts_upstream_of_or_within @@ -380,6 +380,22 @@ is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within is_a: precedes +[Typedef] +id: causally_upstream_of,_negative_effect +name: causally upstream of, negative effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y +xref: RO:0002305 +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: causally_upstream_of ! causally upstream of + +[Typedef] +id: causally_upstream_of,_positive_effect +name: causally upstream of, positive effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y +xref: RO:0002304 +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: causally_upstream_of ! causally upstream of + [Typedef] id: causally_upstream_of_or_within name: causally upstream of or within @@ -1824,6 +1840,7 @@ def: "c involved in or regulates p if and only if either (i) c is involved in p xref: RO:0002431 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "involved in or reguates" xsd:string +is_a: acts_upstream_of_or_within ! acts upstream of or within is_a: causal_agent_in ! causal agent in is_a: functionally_related_to ! functionally related to @@ -1840,6 +1857,7 @@ name: involved in regulation of def: "c involved in regulation of p if c is involved in some 'p' and p' regulates some p" [] xref: RO:0002428 property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: acts_upstream_of ! acts upstream of is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of [Typedef] @@ -2010,6 +2028,16 @@ property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relati property_value: seeAlso https://code.google.com/p/obo-relations/issues/detail?id=46 is_a: capable_of_inhibiting_or_preventing_pathological_process ! capable of inhibiting or preventing pathological process +[Typedef] +id: is_treated_by_substance +name: is treated by substance +def: "Inverse of 'is substance that treats'" [] +subset: RO:0002259 +xref: RO:0002302 +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: causally_related_to ! causally related to +inverse_of: is_substance_that_treats ! is substance that treats + [Typedef] id: is_upstream_of_sequence_of name: is upstream of sequence of @@ -2164,6 +2192,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string +is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect is_a: regulates ! regulates inverse_of: negatively_regulated_by ! negatively regulated by @@ -2390,6 +2419,7 @@ xref: RO:0002213 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string +is_a: causally_upstream_of,_positive_effect ! causally upstream of, positive effect is_a: regulates ! regulates inverse_of: positively_regulated_by ! positively regulated by diff --git a/src/ontology/subsets/ro-mereotopology.owl b/src/ontology/subsets/ro-mereotopology.owl index c71812f4..9ac8fdca 100644 --- a/src/ontology/subsets/ro-mereotopology.owl +++ b/src/ontology/subsets/ro-mereotopology.owl @@ -1098,6 +1098,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y @@ -1115,6 +1116,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y Chris Mungall @@ -1660,7 +1662,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - + c involved in regulation of p if c enables 'p' and p' causally upstream of p RO:0002263 acts_upstream_of @@ -1845,6 +1847,21 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + + + Inverse of 'is substance that treats' + cjm + RO:0002302 + + is_treated_by_substance + is treated by substance + + + + @@ -1867,6 +1884,32 @@ where + + + + + cjm + RO:0002304 + causally_upstream_of,_positive_effect + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y + causally upstream of, positive effect + + + + + + + + + cjm + RO:0002305 + causally_upstream_of,_negative_effect + holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y + causally upstream of, negative effect + + + + @@ -2949,6 +2992,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + c involved in regulation of p if c is involved in some 'p' and p' regulates some p Chris Mungall @@ -2986,6 +3030,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p @@ -5191,5 +5236,5 @@ Environments include natural environments or exposures, experimentally applied c - + diff --git a/src/ontology/subsets/ro-sequence.obo b/src/ontology/subsets/ro-sequence.obo index 94dd2b4a..6c5b0edd 100644 --- a/src/ontology/subsets/ro-sequence.obo +++ b/src/ontology/subsets/ro-sequence.obo @@ -41,7 +41,7 @@ id: acts_upstream_of name: acts upstream of def: "c involved in regulation of p if c enables 'p' and p' causally upstream of p" [] xref: RO:0002263 -is_a: causal_agent_in ! causal agent in +is_a: acts_upstream_of_or_within ! acts upstream of or within [Typedef] id: acts_upstream_of_or_within @@ -380,6 +380,22 @@ is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within is_a: precedes +[Typedef] +id: causally_upstream_of,_negative_effect +name: causally upstream of, negative effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y +xref: RO:0002305 +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: causally_upstream_of ! causally upstream of + +[Typedef] +id: causally_upstream_of,_positive_effect +name: causally upstream of, positive effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y +xref: RO:0002304 +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: causally_upstream_of ! causally upstream of + [Typedef] id: causally_upstream_of_or_within name: causally upstream of or within @@ -1824,6 +1840,7 @@ def: "c involved in or regulates p if and only if either (i) c is involved in p xref: RO:0002431 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "involved in or reguates" xsd:string +is_a: acts_upstream_of_or_within ! acts upstream of or within is_a: causal_agent_in ! causal agent in is_a: functionally_related_to ! functionally related to @@ -1840,6 +1857,7 @@ name: involved in regulation of def: "c involved in regulation of p if c is involved in some 'p' and p' regulates some p" [] xref: RO:0002428 property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: acts_upstream_of ! acts upstream of is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of [Typedef] @@ -2010,6 +2028,16 @@ property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relati property_value: seeAlso https://code.google.com/p/obo-relations/issues/detail?id=46 is_a: capable_of_inhibiting_or_preventing_pathological_process ! capable of inhibiting or preventing pathological process +[Typedef] +id: is_treated_by_substance +name: is treated by substance +def: "Inverse of 'is substance that treats'" [] +subset: RO:0002259 +xref: RO:0002302 +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: causally_related_to ! causally related to +inverse_of: is_substance_that_treats ! is substance that treats + [Typedef] id: is_upstream_of_sequence_of name: is upstream of sequence of @@ -2164,6 +2192,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string +is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect is_a: regulates ! regulates inverse_of: negatively_regulated_by ! negatively regulated by @@ -2390,6 +2419,7 @@ xref: RO:0002213 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string +is_a: causally_upstream_of,_positive_effect ! causally upstream of, positive effect is_a: regulates ! regulates inverse_of: positively_regulated_by ! positively regulated by diff --git a/src/ontology/subsets/ro-sequence.owl b/src/ontology/subsets/ro-sequence.owl index a495feca..7ba39349 100644 --- a/src/ontology/subsets/ro-sequence.owl +++ b/src/ontology/subsets/ro-sequence.owl @@ -1098,6 +1098,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y @@ -1115,6 +1116,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y Chris Mungall @@ -1660,7 +1662,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - + c involved in regulation of p if c enables 'p' and p' causally upstream of p RO:0002263 acts_upstream_of @@ -1845,6 +1847,21 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + + + Inverse of 'is substance that treats' + cjm + RO:0002302 + + is_treated_by_substance + is treated by substance + + + + @@ -1867,6 +1884,32 @@ where + + + + + cjm + RO:0002304 + causally_upstream_of,_positive_effect + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y + causally upstream of, positive effect + + + + + + + + + cjm + RO:0002305 + causally_upstream_of,_negative_effect + holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y + causally upstream of, negative effect + + + + @@ -2949,6 +2992,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + c involved in regulation of p if c is involved in some 'p' and p' regulates some p Chris Mungall @@ -2986,6 +3030,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p @@ -5191,5 +5236,5 @@ Environments include natural environments or exposures, experimentally applied c - + diff --git a/src/ontology/subsets/ro-time-interval.obo b/src/ontology/subsets/ro-time-interval.obo index 5d5e4a92..1ef0ef03 100644 --- a/src/ontology/subsets/ro-time-interval.obo +++ b/src/ontology/subsets/ro-time-interval.obo @@ -41,7 +41,7 @@ id: acts_upstream_of name: acts upstream of def: "c involved in regulation of p if c enables 'p' and p' causally upstream of p" [] xref: RO:0002263 -is_a: causal_agent_in ! causal agent in +is_a: acts_upstream_of_or_within ! acts upstream of or within [Typedef] id: acts_upstream_of_or_within @@ -380,6 +380,22 @@ is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within is_a: precedes +[Typedef] +id: causally_upstream_of,_negative_effect +name: causally upstream of, negative effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y +xref: RO:0002305 +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: causally_upstream_of ! causally upstream of + +[Typedef] +id: causally_upstream_of,_positive_effect +name: causally upstream of, positive effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y +xref: RO:0002304 +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: causally_upstream_of ! causally upstream of + [Typedef] id: causally_upstream_of_or_within name: causally upstream of or within @@ -1824,6 +1840,7 @@ def: "c involved in or regulates p if and only if either (i) c is involved in p xref: RO:0002431 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "involved in or reguates" xsd:string +is_a: acts_upstream_of_or_within ! acts upstream of or within is_a: causal_agent_in ! causal agent in is_a: functionally_related_to ! functionally related to @@ -1840,6 +1857,7 @@ name: involved in regulation of def: "c involved in regulation of p if c is involved in some 'p' and p' regulates some p" [] xref: RO:0002428 property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: acts_upstream_of ! acts upstream of is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of [Typedef] @@ -2010,6 +2028,16 @@ property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relati property_value: seeAlso https://code.google.com/p/obo-relations/issues/detail?id=46 is_a: capable_of_inhibiting_or_preventing_pathological_process ! capable of inhibiting or preventing pathological process +[Typedef] +id: is_treated_by_substance +name: is treated by substance +def: "Inverse of 'is substance that treats'" [] +subset: RO:0002259 +xref: RO:0002302 +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: causally_related_to ! causally related to +inverse_of: is_substance_that_treats ! is substance that treats + [Typedef] id: is_upstream_of_sequence_of name: is upstream of sequence of @@ -2164,6 +2192,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string +is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect is_a: regulates ! regulates inverse_of: negatively_regulated_by ! negatively regulated by @@ -2390,6 +2419,7 @@ xref: RO:0002213 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string +is_a: causally_upstream_of,_positive_effect ! causally upstream of, positive effect is_a: regulates ! regulates inverse_of: positively_regulated_by ! positively regulated by diff --git a/src/ontology/subsets/ro-time-interval.owl b/src/ontology/subsets/ro-time-interval.owl index 1fc68add..f2b11d22 100644 --- a/src/ontology/subsets/ro-time-interval.owl +++ b/src/ontology/subsets/ro-time-interval.owl @@ -1098,6 +1098,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y @@ -1115,6 +1116,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y Chris Mungall @@ -1660,7 +1662,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - + c involved in regulation of p if c enables 'p' and p' causally upstream of p RO:0002263 acts_upstream_of @@ -1845,6 +1847,21 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + + + Inverse of 'is substance that treats' + cjm + RO:0002302 + + is_treated_by_substance + is treated by substance + + + + @@ -1867,6 +1884,32 @@ where + + + + + cjm + RO:0002304 + causally_upstream_of,_positive_effect + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y + causally upstream of, positive effect + + + + + + + + + cjm + RO:0002305 + causally_upstream_of,_negative_effect + holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y + causally upstream of, negative effect + + + + @@ -2949,6 +2992,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + c involved in regulation of p if c is involved in some 'p' and p' regulates some p Chris Mungall @@ -2986,6 +3030,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p @@ -5191,5 +5236,5 @@ Environments include natural environments or exposures, experimentally applied c - + diff --git a/subsets/ro-causal.obo b/subsets/ro-causal.obo index 346fa484..2ceaf227 100644 --- a/subsets/ro-causal.obo +++ b/subsets/ro-causal.obo @@ -41,7 +41,7 @@ id: acts_upstream_of name: acts upstream of def: "c involved in regulation of p if c enables 'p' and p' causally upstream of p" [] xref: RO:0002263 -is_a: causal_agent_in ! causal agent in +is_a: acts_upstream_of_or_within ! acts upstream of or within [Typedef] id: acts_upstream_of_or_within @@ -380,6 +380,22 @@ is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within is_a: precedes +[Typedef] +id: causally_upstream_of,_negative_effect +name: causally upstream of, negative effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y +xref: RO:0002305 +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: causally_upstream_of ! causally upstream of + +[Typedef] +id: causally_upstream_of,_positive_effect +name: causally upstream of, positive effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y +xref: RO:0002304 +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: causally_upstream_of ! causally upstream of + [Typedef] id: causally_upstream_of_or_within name: causally upstream of or within @@ -1824,6 +1840,7 @@ def: "c involved in or regulates p if and only if either (i) c is involved in p xref: RO:0002431 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "involved in or reguates" xsd:string +is_a: acts_upstream_of_or_within ! acts upstream of or within is_a: causal_agent_in ! causal agent in is_a: functionally_related_to ! functionally related to @@ -1840,6 +1857,7 @@ name: involved in regulation of def: "c involved in regulation of p if c is involved in some 'p' and p' regulates some p" [] xref: RO:0002428 property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: acts_upstream_of ! acts upstream of is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of [Typedef] @@ -2010,6 +2028,16 @@ property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relati property_value: seeAlso https://code.google.com/p/obo-relations/issues/detail?id=46 is_a: capable_of_inhibiting_or_preventing_pathological_process ! capable of inhibiting or preventing pathological process +[Typedef] +id: is_treated_by_substance +name: is treated by substance +def: "Inverse of 'is substance that treats'" [] +subset: RO:0002259 +xref: RO:0002302 +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: causally_related_to ! causally related to +inverse_of: is_substance_that_treats ! is substance that treats + [Typedef] id: is_upstream_of_sequence_of name: is upstream of sequence of @@ -2164,6 +2192,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string +is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect is_a: regulates ! regulates inverse_of: negatively_regulated_by ! negatively regulated by @@ -2390,6 +2419,7 @@ xref: RO:0002213 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string +is_a: causally_upstream_of,_positive_effect ! causally upstream of, positive effect is_a: regulates ! regulates inverse_of: positively_regulated_by ! positively regulated by diff --git a/subsets/ro-causal.owl b/subsets/ro-causal.owl index 7e6fb44b..1c9b4160 100644 --- a/subsets/ro-causal.owl +++ b/subsets/ro-causal.owl @@ -1098,6 +1098,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y @@ -1115,6 +1116,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y Chris Mungall @@ -1660,7 +1662,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - + c involved in regulation of p if c enables 'p' and p' causally upstream of p RO:0002263 acts_upstream_of @@ -1845,6 +1847,21 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + + + Inverse of 'is substance that treats' + cjm + RO:0002302 + + is_treated_by_substance + is treated by substance + + + + @@ -1867,6 +1884,32 @@ where + + + + + cjm + RO:0002304 + causally_upstream_of,_positive_effect + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y + causally upstream of, positive effect + + + + + + + + + cjm + RO:0002305 + causally_upstream_of,_negative_effect + holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y + causally upstream of, negative effect + + + + @@ -2949,6 +2992,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + c involved in regulation of p if c is involved in some 'p' and p' regulates some p Chris Mungall @@ -2986,6 +3030,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p @@ -5191,5 +5236,5 @@ Environments include natural environments or exposures, experimentally applied c - + diff --git a/subsets/ro-chado.obo b/subsets/ro-chado.obo index 9bcfbd15..39f1209c 100644 --- a/subsets/ro-chado.obo +++ b/subsets/ro-chado.obo @@ -754,6 +754,7 @@ name: negatively_regulates def: "x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y" [] holds_over_chain: RO:0002230 RO:0002212 is_a: RO:0002211 ! regulates +is_a: RO:0002305 ! causally upstream of, negative effect inverse_of: RO:0002335 ! negatively regulated by [Typedef] @@ -763,6 +764,7 @@ def: "x positively regulates y if and only if the progression of x increases the holds_over_chain: RO:0002212 RO:0002212 holds_over_chain: RO:0002230 RO:0002213 is_a: RO:0002211 ! regulates +is_a: RO:0002304 ! causally upstream of, positive effect inverse_of: RO:0002336 ! positively regulated by [Typedef] @@ -1054,7 +1056,7 @@ id: RO:0002263 name: acts_upstream_of def: "c involved in regulation of p if c enables 'p' and p' causally upstream of p" [] holds_over_chain: RO:0002327 RO:0002411 -is_a: RO:0002500 ! causal agent in +is_a: RO:0002264 ! acts upstream of or within [Typedef] id: RO:0002264 @@ -1105,12 +1107,29 @@ id: RO:0002301 name: results_in_developmental_regression_of is_a: RO:0002552 ! results in ending of +[Typedef] +id: RO:0002302 +name: is_treated_by_substance +def: "Inverse of 'is substance that treats'" [] +is_a: RO:0002410 ! causally related to +inverse_of: RO:0002606 ! is substance that treats + [Typedef] id: RO:0002303 name: has_habitat def: "x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs." [] is_a: RO:0002321 ! ecologically related to +[Typedef] +id: RO:0002304 +name: causally_upstream_of,_positive_effect +is_a: RO:0002411 ! causally upstream of + +[Typedef] +id: RO:0002305 +name: causally_upstream_of,_negative_effect +is_a: RO:0002411 ! causally upstream of + [Typedef] id: RO:0002312 name: evolutionary_variant_of @@ -1614,6 +1633,7 @@ name: involved_in_regulation_of def: "c involved in regulation of p if c is involved in some 'p' and p' regulates some p" [] holds_over_chain: RO:0002327 RO:0002211 holds_over_chain: RO:0002331 RO:0002211 +is_a: RO:0002263 ! acts upstream of is_a: RO:0002431 ! involved in or involved in regulation of [Typedef] @@ -1634,6 +1654,7 @@ is_a: RO:0002428 ! involved in regulation of id: RO:0002431 name: involved_in_or_involved_in_regulation_of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] +is_a: RO:0002264 ! acts upstream of or within is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in diff --git a/subsets/ro-developmental.obo b/subsets/ro-developmental.obo index e7727a51..c58f4a4f 100644 --- a/subsets/ro-developmental.obo +++ b/subsets/ro-developmental.obo @@ -41,7 +41,7 @@ id: acts_upstream_of name: acts upstream of def: "c involved in regulation of p if c enables 'p' and p' causally upstream of p" [] xref: RO:0002263 -is_a: causal_agent_in ! causal agent in +is_a: acts_upstream_of_or_within ! acts upstream of or within [Typedef] id: acts_upstream_of_or_within @@ -380,6 +380,22 @@ is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within is_a: precedes +[Typedef] +id: causally_upstream_of,_negative_effect +name: causally upstream of, negative effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y +xref: RO:0002305 +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: causally_upstream_of ! causally upstream of + +[Typedef] +id: causally_upstream_of,_positive_effect +name: causally upstream of, positive effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y +xref: RO:0002304 +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: causally_upstream_of ! causally upstream of + [Typedef] id: causally_upstream_of_or_within name: causally upstream of or within @@ -1824,6 +1840,7 @@ def: "c involved in or regulates p if and only if either (i) c is involved in p xref: RO:0002431 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "involved in or reguates" xsd:string +is_a: acts_upstream_of_or_within ! acts upstream of or within is_a: causal_agent_in ! causal agent in is_a: functionally_related_to ! functionally related to @@ -1840,6 +1857,7 @@ name: involved in regulation of def: "c involved in regulation of p if c is involved in some 'p' and p' regulates some p" [] xref: RO:0002428 property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: acts_upstream_of ! acts upstream of is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of [Typedef] @@ -2010,6 +2028,16 @@ property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relati property_value: seeAlso https://code.google.com/p/obo-relations/issues/detail?id=46 is_a: capable_of_inhibiting_or_preventing_pathological_process ! capable of inhibiting or preventing pathological process +[Typedef] +id: is_treated_by_substance +name: is treated by substance +def: "Inverse of 'is substance that treats'" [] +subset: RO:0002259 +xref: RO:0002302 +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: causally_related_to ! causally related to +inverse_of: is_substance_that_treats ! is substance that treats + [Typedef] id: is_upstream_of_sequence_of name: is upstream of sequence of @@ -2164,6 +2192,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string +is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect is_a: regulates ! regulates inverse_of: negatively_regulated_by ! negatively regulated by @@ -2390,6 +2419,7 @@ xref: RO:0002213 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string +is_a: causally_upstream_of,_positive_effect ! causally upstream of, positive effect is_a: regulates ! regulates inverse_of: positively_regulated_by ! positively regulated by diff --git a/subsets/ro-developmental.owl b/subsets/ro-developmental.owl index 7d3bd409..27502e4f 100644 --- a/subsets/ro-developmental.owl +++ b/subsets/ro-developmental.owl @@ -1098,6 +1098,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y @@ -1115,6 +1116,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y Chris Mungall @@ -1660,7 +1662,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - + c involved in regulation of p if c enables 'p' and p' causally upstream of p RO:0002263 acts_upstream_of @@ -1845,6 +1847,21 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + + + Inverse of 'is substance that treats' + cjm + RO:0002302 + + is_treated_by_substance + is treated by substance + + + + @@ -1867,6 +1884,32 @@ where + + + + + cjm + RO:0002304 + causally_upstream_of,_positive_effect + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y + causally upstream of, positive effect + + + + + + + + + cjm + RO:0002305 + causally_upstream_of,_negative_effect + holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y + causally upstream of, negative effect + + + + @@ -2949,6 +2992,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + c involved in regulation of p if c is involved in some 'p' and p' regulates some p Chris Mungall @@ -2986,6 +3030,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p @@ -5191,5 +5236,5 @@ Environments include natural environments or exposures, experimentally applied c - + diff --git a/subsets/ro-eco.obo b/subsets/ro-eco.obo index 4f7c14a9..46591c15 100644 --- a/subsets/ro-eco.obo +++ b/subsets/ro-eco.obo @@ -814,6 +814,7 @@ property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relati property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string holds_over_chain: RO:0002230 RO:0002212 is_a: RO:0002211 ! regulates +is_a: RO:0002305 ! causally upstream of, negative effect inverse_of: RO:0002335 ! negatively regulated by [Typedef] @@ -826,6 +827,7 @@ property_value: IAO:0000589 "positively regulates (process to process)" xsd:stri holds_over_chain: RO:0002212 RO:0002212 holds_over_chain: RO:0002230 RO:0002213 is_a: RO:0002211 ! regulates +is_a: RO:0002304 ! causally upstream of, positive effect inverse_of: RO:0002336 ! positively regulated by [Typedef] @@ -1185,7 +1187,7 @@ id: RO:0002263 name: acts upstream of def: "c involved in regulation of p if c enables 'p' and p' causally upstream of p" [] holds_over_chain: RO:0002327 RO:0002411 -is_a: RO:0002500 ! causal agent in +is_a: RO:0002264 ! acts upstream of or within [Typedef] id: RO:0002264 @@ -1257,6 +1259,15 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "May be merged into parent relation" xsd:string is_a: RO:0002552 ! results in ending of +[Typedef] +id: RO:0002302 +name: is treated by substance +def: "Inverse of 'is substance that treats'" [] +subset: RO:0002259 +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: RO:0002410 ! causally related to +inverse_of: RO:0002606 ! is substance that treats + [Typedef] id: RO:0002303 name: has habitat @@ -1269,6 +1280,20 @@ property_value: IAO:0000117 "Pier Buttigieg" xsd:string property_value: IAO:0000118 "adapted for living in" xsd:string is_a: RO:0002321 ! ecologically related to +[Typedef] +id: RO:0002304 +name: causally upstream of, positive effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: RO:0002411 ! causally upstream of + +[Typedef] +id: RO:0002305 +name: causally upstream of, negative effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: RO:0002411 ! causally upstream of + [Typedef] id: RO:0002312 name: evolutionary variant of @@ -1978,6 +2003,7 @@ def: "c involved in regulation of p if c is involved in some 'p' and p' regulate property_value: IAO:0000117 "Chris Mungall" xsd:string holds_over_chain: RO:0002327 RO:0002211 holds_over_chain: RO:0002331 RO:0002211 +is_a: RO:0002263 ! acts upstream of is_a: RO:0002431 ! involved in or involved in regulation of [Typedef] @@ -2002,6 +2028,7 @@ name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "involved in or reguates" xsd:string +is_a: RO:0002264 ! acts upstream of or within is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in diff --git a/subsets/ro-eco.owl b/subsets/ro-eco.owl index 9d9682de..815ad3da 100644 --- a/subsets/ro-eco.owl +++ b/subsets/ro-eco.owl @@ -2163,6 +2163,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + @@ -2182,6 +2183,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + @@ -2758,7 +2760,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + @@ -2971,6 +2973,19 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + + + + Inverse of 'is substance that treats' + cjm + + is treated by substance + + + + @@ -2989,6 +3004,28 @@ where + + + + + cjm + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y + causally upstream of, positive effect + + + + + + + + + cjm + holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y + causally upstream of, negative effect + + + + @@ -4109,6 +4146,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -4164,6 +4202,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p @@ -6616,5 +6655,5 @@ Environments include natural environments or exposures, experimentally applied c - + diff --git a/subsets/ro-hom.owl b/subsets/ro-hom.owl index 2bb5e145..7a10d6fa 100644 --- a/subsets/ro-hom.owl +++ b/subsets/ro-hom.owl @@ -55,5 +55,5 @@ - + diff --git a/subsets/ro-interaction.obo b/subsets/ro-interaction.obo index a26d0676..0636c4a7 100644 --- a/subsets/ro-interaction.obo +++ b/subsets/ro-interaction.obo @@ -41,7 +41,7 @@ id: acts_upstream_of name: acts upstream of def: "c involved in regulation of p if c enables 'p' and p' causally upstream of p" [] xref: RO:0002263 -is_a: causal_agent_in ! causal agent in +is_a: acts_upstream_of_or_within ! acts upstream of or within [Typedef] id: acts_upstream_of_or_within @@ -380,6 +380,22 @@ is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within is_a: precedes +[Typedef] +id: causally_upstream_of,_negative_effect +name: causally upstream of, negative effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y +xref: RO:0002305 +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: causally_upstream_of ! causally upstream of + +[Typedef] +id: causally_upstream_of,_positive_effect +name: causally upstream of, positive effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y +xref: RO:0002304 +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: causally_upstream_of ! causally upstream of + [Typedef] id: causally_upstream_of_or_within name: causally upstream of or within @@ -1824,6 +1840,7 @@ def: "c involved in or regulates p if and only if either (i) c is involved in p xref: RO:0002431 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "involved in or reguates" xsd:string +is_a: acts_upstream_of_or_within ! acts upstream of or within is_a: causal_agent_in ! causal agent in is_a: functionally_related_to ! functionally related to @@ -1840,6 +1857,7 @@ name: involved in regulation of def: "c involved in regulation of p if c is involved in some 'p' and p' regulates some p" [] xref: RO:0002428 property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: acts_upstream_of ! acts upstream of is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of [Typedef] @@ -2010,6 +2028,16 @@ property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relati property_value: seeAlso https://code.google.com/p/obo-relations/issues/detail?id=46 is_a: capable_of_inhibiting_or_preventing_pathological_process ! capable of inhibiting or preventing pathological process +[Typedef] +id: is_treated_by_substance +name: is treated by substance +def: "Inverse of 'is substance that treats'" [] +subset: RO:0002259 +xref: RO:0002302 +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: causally_related_to ! causally related to +inverse_of: is_substance_that_treats ! is substance that treats + [Typedef] id: is_upstream_of_sequence_of name: is upstream of sequence of @@ -2164,6 +2192,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string +is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect is_a: regulates ! regulates inverse_of: negatively_regulated_by ! negatively regulated by @@ -2390,6 +2419,7 @@ xref: RO:0002213 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string +is_a: causally_upstream_of,_positive_effect ! causally upstream of, positive effect is_a: regulates ! regulates inverse_of: positively_regulated_by ! positively regulated by diff --git a/subsets/ro-interaction.owl b/subsets/ro-interaction.owl index 65c08cba..02be0d3b 100644 --- a/subsets/ro-interaction.owl +++ b/subsets/ro-interaction.owl @@ -1098,6 +1098,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y @@ -1115,6 +1116,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y Chris Mungall @@ -1660,7 +1662,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - + c involved in regulation of p if c enables 'p' and p' causally upstream of p RO:0002263 acts_upstream_of @@ -1845,6 +1847,21 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + + + Inverse of 'is substance that treats' + cjm + RO:0002302 + + is_treated_by_substance + is treated by substance + + + + @@ -1867,6 +1884,32 @@ where + + + + + cjm + RO:0002304 + causally_upstream_of,_positive_effect + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y + causally upstream of, positive effect + + + + + + + + + cjm + RO:0002305 + causally_upstream_of,_negative_effect + holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y + causally upstream of, negative effect + + + + @@ -2949,6 +2992,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + c involved in regulation of p if c is involved in some 'p' and p' regulates some p Chris Mungall @@ -2986,6 +3030,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p @@ -5191,5 +5236,5 @@ Environments include natural environments or exposures, experimentally applied c - + diff --git a/subsets/ro-mereotopology.obo b/subsets/ro-mereotopology.obo index b9acd974..12a5025c 100644 --- a/subsets/ro-mereotopology.obo +++ b/subsets/ro-mereotopology.obo @@ -41,7 +41,7 @@ id: acts_upstream_of name: acts upstream of def: "c involved in regulation of p if c enables 'p' and p' causally upstream of p" [] xref: RO:0002263 -is_a: causal_agent_in ! causal agent in +is_a: acts_upstream_of_or_within ! acts upstream of or within [Typedef] id: acts_upstream_of_or_within @@ -380,6 +380,22 @@ is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within is_a: precedes +[Typedef] +id: causally_upstream_of,_negative_effect +name: causally upstream of, negative effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y +xref: RO:0002305 +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: causally_upstream_of ! causally upstream of + +[Typedef] +id: causally_upstream_of,_positive_effect +name: causally upstream of, positive effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y +xref: RO:0002304 +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: causally_upstream_of ! causally upstream of + [Typedef] id: causally_upstream_of_or_within name: causally upstream of or within @@ -1824,6 +1840,7 @@ def: "c involved in or regulates p if and only if either (i) c is involved in p xref: RO:0002431 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "involved in or reguates" xsd:string +is_a: acts_upstream_of_or_within ! acts upstream of or within is_a: causal_agent_in ! causal agent in is_a: functionally_related_to ! functionally related to @@ -1840,6 +1857,7 @@ name: involved in regulation of def: "c involved in regulation of p if c is involved in some 'p' and p' regulates some p" [] xref: RO:0002428 property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: acts_upstream_of ! acts upstream of is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of [Typedef] @@ -2010,6 +2028,16 @@ property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relati property_value: seeAlso https://code.google.com/p/obo-relations/issues/detail?id=46 is_a: capable_of_inhibiting_or_preventing_pathological_process ! capable of inhibiting or preventing pathological process +[Typedef] +id: is_treated_by_substance +name: is treated by substance +def: "Inverse of 'is substance that treats'" [] +subset: RO:0002259 +xref: RO:0002302 +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: causally_related_to ! causally related to +inverse_of: is_substance_that_treats ! is substance that treats + [Typedef] id: is_upstream_of_sequence_of name: is upstream of sequence of @@ -2164,6 +2192,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string +is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect is_a: regulates ! regulates inverse_of: negatively_regulated_by ! negatively regulated by @@ -2390,6 +2419,7 @@ xref: RO:0002213 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string +is_a: causally_upstream_of,_positive_effect ! causally upstream of, positive effect is_a: regulates ! regulates inverse_of: positively_regulated_by ! positively regulated by diff --git a/subsets/ro-mereotopology.owl b/subsets/ro-mereotopology.owl index c71812f4..9ac8fdca 100644 --- a/subsets/ro-mereotopology.owl +++ b/subsets/ro-mereotopology.owl @@ -1098,6 +1098,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y @@ -1115,6 +1116,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y Chris Mungall @@ -1660,7 +1662,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - + c involved in regulation of p if c enables 'p' and p' causally upstream of p RO:0002263 acts_upstream_of @@ -1845,6 +1847,21 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + + + Inverse of 'is substance that treats' + cjm + RO:0002302 + + is_treated_by_substance + is treated by substance + + + + @@ -1867,6 +1884,32 @@ where + + + + + cjm + RO:0002304 + causally_upstream_of,_positive_effect + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y + causally upstream of, positive effect + + + + + + + + + cjm + RO:0002305 + causally_upstream_of,_negative_effect + holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y + causally upstream of, negative effect + + + + @@ -2949,6 +2992,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + c involved in regulation of p if c is involved in some 'p' and p' regulates some p Chris Mungall @@ -2986,6 +3030,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p @@ -5191,5 +5236,5 @@ Environments include natural environments or exposures, experimentally applied c - + diff --git a/subsets/ro-sequence.obo b/subsets/ro-sequence.obo index 94dd2b4a..6c5b0edd 100644 --- a/subsets/ro-sequence.obo +++ b/subsets/ro-sequence.obo @@ -41,7 +41,7 @@ id: acts_upstream_of name: acts upstream of def: "c involved in regulation of p if c enables 'p' and p' causally upstream of p" [] xref: RO:0002263 -is_a: causal_agent_in ! causal agent in +is_a: acts_upstream_of_or_within ! acts upstream of or within [Typedef] id: acts_upstream_of_or_within @@ -380,6 +380,22 @@ is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within is_a: precedes +[Typedef] +id: causally_upstream_of,_negative_effect +name: causally upstream of, negative effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y +xref: RO:0002305 +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: causally_upstream_of ! causally upstream of + +[Typedef] +id: causally_upstream_of,_positive_effect +name: causally upstream of, positive effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y +xref: RO:0002304 +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: causally_upstream_of ! causally upstream of + [Typedef] id: causally_upstream_of_or_within name: causally upstream of or within @@ -1824,6 +1840,7 @@ def: "c involved in or regulates p if and only if either (i) c is involved in p xref: RO:0002431 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "involved in or reguates" xsd:string +is_a: acts_upstream_of_or_within ! acts upstream of or within is_a: causal_agent_in ! causal agent in is_a: functionally_related_to ! functionally related to @@ -1840,6 +1857,7 @@ name: involved in regulation of def: "c involved in regulation of p if c is involved in some 'p' and p' regulates some p" [] xref: RO:0002428 property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: acts_upstream_of ! acts upstream of is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of [Typedef] @@ -2010,6 +2028,16 @@ property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relati property_value: seeAlso https://code.google.com/p/obo-relations/issues/detail?id=46 is_a: capable_of_inhibiting_or_preventing_pathological_process ! capable of inhibiting or preventing pathological process +[Typedef] +id: is_treated_by_substance +name: is treated by substance +def: "Inverse of 'is substance that treats'" [] +subset: RO:0002259 +xref: RO:0002302 +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: causally_related_to ! causally related to +inverse_of: is_substance_that_treats ! is substance that treats + [Typedef] id: is_upstream_of_sequence_of name: is upstream of sequence of @@ -2164,6 +2192,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string +is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect is_a: regulates ! regulates inverse_of: negatively_regulated_by ! negatively regulated by @@ -2390,6 +2419,7 @@ xref: RO:0002213 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string +is_a: causally_upstream_of,_positive_effect ! causally upstream of, positive effect is_a: regulates ! regulates inverse_of: positively_regulated_by ! positively regulated by diff --git a/subsets/ro-sequence.owl b/subsets/ro-sequence.owl index a495feca..7ba39349 100644 --- a/subsets/ro-sequence.owl +++ b/subsets/ro-sequence.owl @@ -1098,6 +1098,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y @@ -1115,6 +1116,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y Chris Mungall @@ -1660,7 +1662,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - + c involved in regulation of p if c enables 'p' and p' causally upstream of p RO:0002263 acts_upstream_of @@ -1845,6 +1847,21 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + + + Inverse of 'is substance that treats' + cjm + RO:0002302 + + is_treated_by_substance + is treated by substance + + + + @@ -1867,6 +1884,32 @@ where + + + + + cjm + RO:0002304 + causally_upstream_of,_positive_effect + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y + causally upstream of, positive effect + + + + + + + + + cjm + RO:0002305 + causally_upstream_of,_negative_effect + holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y + causally upstream of, negative effect + + + + @@ -2949,6 +2992,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + c involved in regulation of p if c is involved in some 'p' and p' regulates some p Chris Mungall @@ -2986,6 +3030,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p @@ -5191,5 +5236,5 @@ Environments include natural environments or exposures, experimentally applied c - + diff --git a/subsets/ro-time-interval.obo b/subsets/ro-time-interval.obo index 5d5e4a92..1ef0ef03 100644 --- a/subsets/ro-time-interval.obo +++ b/subsets/ro-time-interval.obo @@ -41,7 +41,7 @@ id: acts_upstream_of name: acts upstream of def: "c involved in regulation of p if c enables 'p' and p' causally upstream of p" [] xref: RO:0002263 -is_a: causal_agent_in ! causal agent in +is_a: acts_upstream_of_or_within ! acts upstream of or within [Typedef] id: acts_upstream_of_or_within @@ -380,6 +380,22 @@ is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within is_a: precedes +[Typedef] +id: causally_upstream_of,_negative_effect +name: causally upstream of, negative effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y +xref: RO:0002305 +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: causally_upstream_of ! causally upstream of + +[Typedef] +id: causally_upstream_of,_positive_effect +name: causally upstream of, positive effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y +xref: RO:0002304 +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: causally_upstream_of ! causally upstream of + [Typedef] id: causally_upstream_of_or_within name: causally upstream of or within @@ -1824,6 +1840,7 @@ def: "c involved in or regulates p if and only if either (i) c is involved in p xref: RO:0002431 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "involved in or reguates" xsd:string +is_a: acts_upstream_of_or_within ! acts upstream of or within is_a: causal_agent_in ! causal agent in is_a: functionally_related_to ! functionally related to @@ -1840,6 +1857,7 @@ name: involved in regulation of def: "c involved in regulation of p if c is involved in some 'p' and p' regulates some p" [] xref: RO:0002428 property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: acts_upstream_of ! acts upstream of is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of [Typedef] @@ -2010,6 +2028,16 @@ property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relati property_value: seeAlso https://code.google.com/p/obo-relations/issues/detail?id=46 is_a: capable_of_inhibiting_or_preventing_pathological_process ! capable of inhibiting or preventing pathological process +[Typedef] +id: is_treated_by_substance +name: is treated by substance +def: "Inverse of 'is substance that treats'" [] +subset: RO:0002259 +xref: RO:0002302 +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +is_a: causally_related_to ! causally related to +inverse_of: is_substance_that_treats ! is substance that treats + [Typedef] id: is_upstream_of_sequence_of name: is upstream of sequence of @@ -2164,6 +2192,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string +is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect is_a: regulates ! regulates inverse_of: negatively_regulated_by ! negatively regulated by @@ -2390,6 +2419,7 @@ xref: RO:0002213 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string +is_a: causally_upstream_of,_positive_effect ! causally upstream of, positive effect is_a: regulates ! regulates inverse_of: positively_regulated_by ! positively regulated by diff --git a/subsets/ro-time-interval.owl b/subsets/ro-time-interval.owl index 1fc68add..f2b11d22 100644 --- a/subsets/ro-time-interval.owl +++ b/subsets/ro-time-interval.owl @@ -1098,6 +1098,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y @@ -1115,6 +1116,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y Chris Mungall @@ -1660,7 +1662,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - + c involved in regulation of p if c enables 'p' and p' causally upstream of p RO:0002263 acts_upstream_of @@ -1845,6 +1847,21 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + + + Inverse of 'is substance that treats' + cjm + RO:0002302 + + is_treated_by_substance + is treated by substance + + + + @@ -1867,6 +1884,32 @@ where + + + + + cjm + RO:0002304 + causally_upstream_of,_positive_effect + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y + causally upstream of, positive effect + + + + + + + + + cjm + RO:0002305 + causally_upstream_of,_negative_effect + holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y + causally upstream of, negative effect + + + + @@ -2949,6 +2992,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + c involved in regulation of p if c is involved in some 'p' and p' regulates some p Chris Mungall @@ -2986,6 +3030,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p @@ -5191,5 +5236,5 @@ Environments include natural environments or exposures, experimentally applied c - +