diff --git a/ro-base.json b/ro-base.json index 517c1a57..462797fe 100644 --- a/ro-base.json +++ b/ro-base.json @@ -4842,11 +4842,26 @@ }, "type" : "PROPERTY", "lbl" : "correlated with condition" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002576", + "meta" : { + "definition" : { + "val" : "inverse of has skeleton", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "skeleton of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002213", "meta" : { "definition" : { - "val" : "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2.", + "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.", "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], @@ -4866,21 +4881,6 @@ }, "type" : "PROPERTY", "lbl" : "positively regulates" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002576", - "meta" : { - "definition" : { - "val" : "inverse of has skeleton", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - } ] - }, - "type" : "PROPERTY", - "lbl" : "skeleton of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0003303", "meta" : { @@ -5041,7 +5041,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002578", "meta" : { "definition" : { - "val" : "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.", + "val" : "p directly regulates q iff p is immediately causally upstream of q and p regulates q.", "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -5427,7 +5427,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002211", "meta" : { "definition" : { - "val" : "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2.", + "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.", "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -5440,12 +5440,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "David Hill" @@ -5546,7 +5540,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002212", "meta" : { "definition" : { - "val" : "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2.", + "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.", "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -5752,6 +5746,10 @@ }, { "id" : "http://purl.obolibrary.org/obo/RO_0002327", "meta" : { + "definition" : { + "val" : "c enables p iff c is capable of p and c acts to execute p.", + "xrefs" : [ ] + }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", @@ -7130,20 +7128,14 @@ }, "type" : "PROPERTY", "lbl" : "start, days post coitum" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002426", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - } ] - }, - "type" : "PROPERTY", - "lbl" : "differs in attribute" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002305", "meta" : { - "comments" : [ "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" ], + "definition" : { + "val" : "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002411" @@ -7154,6 +7146,16 @@ }, "type" : "PROPERTY", "lbl" : "causally upstream of, negative effect" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002426", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "differs in attribute" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002427", "meta" : { @@ -7362,6 +7364,10 @@ }, { "id" : "http://purl.obolibrary.org/obo/RO_0002304", "meta" : { + "definition" : { + "val" : "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.", + "xrefs" : [ ] + }, "comments" : [ "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" ], "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { @@ -7561,11 +7567,25 @@ }, "type" : "PROPERTY", "lbl" : "has end time value" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0019000", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8688-6599" + } ] + }, + "type" : "PROPERTY", + "lbl" : "regulates characteristic" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002418", "meta" : { "definition" : { - "val" : "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.", + "val" : "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.", "xrefs" : [ ] }, "synonyms" : [ { @@ -7586,20 +7606,6 @@ }, "type" : "PROPERTY", "lbl" : "causally upstream of or within" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0019000", - "meta" : { - "definition" : { - "val" : "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0002-8688-6599" - } ] - }, - "type" : "PROPERTY", - "lbl" : "regulates characteristic" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002539", "meta" : { @@ -7618,16 +7624,13 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002411", "meta" : { "definition" : { - "val" : "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain", + "val" : "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.", "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" } ] }, "type" : "PROPERTY", @@ -7647,42 +7650,39 @@ "type" : "CLASS", "lbl" : "sequentially ordered entity" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002533", + "id" : "http://purl.obolibrary.org/obo/RO_0002412", "meta" : { "definition" : { - "val" : "Any individual unit of a collection of like units arranged in a linear order", + "val" : "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.", "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair." } ] }, - "type" : "CLASS", - "lbl" : "sequence atomic unit" + "type" : "PROPERTY", + "lbl" : "immediately causally upstream of" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002412", + "id" : "http://purl.obolibrary.org/obo/RO_0002533", "meta" : { "definition" : { - "val" : "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q.", + "val" : "Any individual unit of a collection of like units arranged in a linear order", "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002411" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair." } ] }, - "type" : "PROPERTY", - "lbl" : "immediately causally upstream of" + "type" : "CLASS", + "lbl" : "sequence atomic unit" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002534", "meta" : { @@ -7704,13 +7704,10 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002413", "meta" : { "definition" : { - "val" : "p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c", + "val" : "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c.", "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { @@ -7839,21 +7836,18 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002410", "meta" : { "definition" : { - "val" : "This relation groups causal relations between material entities and causal relations between processes", - "xrefs" : [ ] + "val" : "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.", + "xrefs" : [ "https://en.wikipedia.org/wiki/Causality" ] }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." } ] }, "type" : "PROPERTY", @@ -7926,32 +7920,6 @@ }, "type" : "PROPERTY", "lbl" : "immediately causally downstream of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002406", - "meta" : { - "definition" : { - "val" : "p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "directly activates (process to process)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "directly positively regulates" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - } ] - }, - "type" : "PROPERTY", - "lbl" : "directly activates" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002527", "meta" : { @@ -7972,11 +7940,23 @@ }, "type" : "PROPERTY", "lbl" : "does not overlap sequence of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002406", + "meta" : { + "comments" : [ "This term was obsoleted because it has the same meaning as 'directly positively regulates'." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/RO_0002629" + } ], + "deprecated" : true + }, + "type" : "PROPERTY", + "lbl" : "obsolete directly activates" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002407", "meta" : { "definition" : { - "val" : "p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one.", + "val" : "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.", "xrefs" : [ ] }, "basicPropertyValues" : [ { @@ -7987,11 +7967,11 @@ "val" : "http://purl.obolibrary.org/obo/RO_0002213" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "indirectly positively regulates" + "val" : "indirectly activates" } ] }, "type" : "PROPERTY", - "lbl" : "indirectly activates" + "lbl" : "indirectly positively regulates" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002528", "meta" : { @@ -8177,22 +8157,15 @@ }, { "id" : "http://purl.obolibrary.org/obo/RO_0002408", "meta" : { + "comments" : [ "This term was obsoleted because it has the same meaning as 'directly negatively regulates'." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "directly inhibits (process to process)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "directly negatively regulates" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - } ] + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/RO_0002630" + } ], + "deprecated" : true }, "type" : "PROPERTY", - "lbl" : "directly inhibits" + "lbl" : "obsolete directly inhibits" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002529", "meta" : { @@ -8213,6 +8186,10 @@ }, { "id" : "http://purl.obolibrary.org/obo/RO_0002409", "meta" : { + "definition" : { + "val" : "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.", + "xrefs" : [ ] + }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" @@ -8221,14 +8198,11 @@ "val" : "http://purl.obolibrary.org/obo/RO_0002212" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "indirectly negatively regulates" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + "val" : "indirectly inhibits" } ] }, "type" : "PROPERTY", - "lbl" : "indirectly inhibits" + "lbl" : "indirectly negatively regulates" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002640", "meta" : { @@ -8618,7 +8592,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002630", "meta" : { "definition" : { - "val" : "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2.", + "val" : "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.", "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], @@ -8758,7 +8732,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002501", "meta" : { "definition" : { - "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.", + "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.", "xrefs" : [ ] }, "basicPropertyValues" : [ { @@ -8848,7 +8822,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002629", "meta" : { "definition" : { - "val" : "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2.", + "val" : "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.", "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], @@ -11569,6 +11543,24 @@ }, "type" : "PROPERTY", "lbl" : "is small molecule regulator of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012009", + "meta" : { + "definition" : { + "val" : "p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant.", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2022-09-26T06:01:01Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "pg" + } ] + }, + "type" : "PROPERTY", + "lbl" : "constitutively upstream of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0012007", "meta" : { @@ -11808,6 +11800,58 @@ }, "type" : "PROPERTY", "lbl" : "in hemiplasy relationship with" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012012", + "meta" : { + "definition" : { + "val" : "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "pg" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2022-09-26T06:08:01Z" + } ] + }, + "type" : "PROPERTY", + "lbl" : "indirectly regulates" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012010", + "meta" : { + "definition" : { + "val" : "p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q.", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2022-09-26T06:06:20Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "pg" + } ] + }, + "type" : "PROPERTY", + "lbl" : "removes input for" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012011", + "meta" : { + "definition" : { + "val" : "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2022-09-26T06:07:17Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "pg" + } ] + }, + "type" : "PROPERTY", + "lbl" : "indirectly causally upstream of" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000050", "meta" : { @@ -13667,14 +13711,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002505", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000057" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002555", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002574" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002578", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002211" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002555", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002574" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002375", "pred" : "subPropertyOf", @@ -13716,13 +13760,17 @@ "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002323" }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0011013", + "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0011004" + "obj" : "http://purl.obolibrary.org/obo/RO_0002211" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002083", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002081" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0011013", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0011004" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004007", "pred" : "subPropertyOf", @@ -13751,14 +13799,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002009", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002292" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002103", - "pred" : "inverseOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002120" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002110", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002113" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002103", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002120" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002567", "pred" : "subPropertyOf", @@ -13860,17 +13908,17 @@ "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002418" }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0004005", + "sub" : "http://purl.obolibrary.org/obo/RO_0002411", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0004000" + "obj" : "http://purl.obolibrary.org/obo/RO_0002418" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002016", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002017" }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002411", + "sub" : "http://purl.obolibrary.org/obo/RO_0004005", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002418" + "obj" : "http://purl.obolibrary.org/obo/RO_0004000" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0010001", "pred" : "inverseOf", @@ -14207,14 +14255,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002291", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002206" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002223", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002222" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002225", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002202" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002223", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002222" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002492", "pred" : "subPropertyOf", @@ -14359,14 +14407,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002339", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002344" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000015", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000003" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002418" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000015", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000003" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002209", "pred" : "subPropertyOf", @@ -14451,10 +14499,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002426", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002424" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002414", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002411" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000024", "pred" : "subPropertyOf", @@ -14519,38 +14563,34 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002333", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002328" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002406", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002629" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002315", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0040036" }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002455", + "sub" : "http://purl.obolibrary.org/obo/RO_0002466", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002442" + "obj" : "http://purl.obolibrary.org/obo/RO_0002465" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002252", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002375" }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002466", + "sub" : "http://purl.obolibrary.org/obo/RO_0002455", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002465" + "obj" : "http://purl.obolibrary.org/obo/RO_0002442" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002263", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002264" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002310", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000007", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002310", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0011014", "pred" : "subPropertyOf", @@ -14619,6 +14659,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002212", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002211" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012011", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002411" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004019", "pred" : "subPropertyOf", @@ -14663,6 +14707,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0004035", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0004033" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002407", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0012012" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002100", "pred" : "subPropertyOf", @@ -14704,17 +14752,17 @@ "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002428" }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002113", + "sub" : "http://purl.obolibrary.org/obo/RO_0002379", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002130" + "obj" : "http://purl.obolibrary.org/obo/RO_0002131" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002114", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002120" }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002379", + "sub" : "http://purl.obolibrary.org/obo/RO_0002113", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002131" + "obj" : "http://purl.obolibrary.org/obo/RO_0002130" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002329", "pred" : "subPropertyOf", @@ -14851,14 +14899,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002533", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/RO_0002532" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002022", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002334" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002260", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000087" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002022", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002334" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000012", "pred" : "subPropertyOf", @@ -15147,6 +15195,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0004003", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0004013" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012004", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002596" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002588", "pred" : "subPropertyOf", @@ -15311,6 +15363,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000062", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000007" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002085", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002092" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002084", "pred" : "inverseOf", @@ -15319,10 +15375,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002087", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002090" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002085", - "pred" : "inverseOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002092" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0011004", "pred" : "subPropertyOf", @@ -15355,14 +15407,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002233", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000057" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0001020", - "pred" : "inverseOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0001022" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002006", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002130" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0001020", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0001022" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002622", "pred" : "inverseOf", @@ -15391,14 +15443,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002000", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002002" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002216", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002500" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002495", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002494" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002216", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002500" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000044", "pred" : "subPropertyOf", @@ -15443,14 +15495,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002216", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002328" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002622", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002618" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002024", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002022" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002622", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002618" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002387", "pred" : "subPropertyOf", @@ -15503,6 +15555,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002299", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0040036" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002409", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0012012" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000069", "pred" : "subPropertyOf", @@ -15511,14 +15567,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0004023", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0040035" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0000080", - "pred" : "inverseOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000086" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0008501", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008502" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0000080", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0000086" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0013008", "pred" : "inverseOf", @@ -15575,14 +15631,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002203", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002286" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002588", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002297" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004034", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002263" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002588", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002297" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002219", "pred" : "inverseOf", @@ -15603,10 +15659,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002380", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002375" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0012004", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000056" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002485", "pred" : "subPropertyOf", @@ -15843,6 +15895,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002376", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002375" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002414", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0004047" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002608", "pred" : "subPropertyOf", @@ -15951,14 +16007,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002150", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002323" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002408", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002630" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002481", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002564" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012010", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002305" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002428", "pred" : "subPropertyOf", @@ -16011,6 +16067,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002459", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002574" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012009", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002304" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002177", "pred" : "subPropertyOf", @@ -16043,6 +16103,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002296", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0040036" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012006", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002597" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002341", "pred" : "subPropertyOf", @@ -16131,14 +16195,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0013003", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0013001" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002026", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002323" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002286", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002384" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002026", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002323" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000050", "pred" : "inverseOf", @@ -16207,14 +16271,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002237", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002444" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002014", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002013" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000063", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002222" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002014", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002013" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002377", "pred" : "subPropertyOf", @@ -16367,6 +16431,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002470", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012005", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002598" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002212", "pred" : "inverseOf", @@ -16555,14 +16623,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002641", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002635" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002326", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002329" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002091", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002222" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002326", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002329" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002512", "pred" : "inverseOf", @@ -16703,6 +16771,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0004000", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002410" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012012", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0012011" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002569", "pred" : "subPropertyOf", @@ -16727,14 +16799,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002229", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002222" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002020", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002313" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0013002", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002110" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002020", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002313" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002086", "pred" : "subPropertyOf", @@ -16796,7 +16868,7 @@ "pred" : "http://xmlns.com/foaf/0.1/homepage", "val" : " https://github.com/oborel/obo-relations/" } ], - "version" : "http://purl.obolibrary.org/obo/ro/releases/2022-09-07/ro-base.owl" + "version" : "http://purl.obolibrary.org/obo/ro/releases/2022-10-26/ro-base.owl" }, "equivalentNodesSets" : [ ], "logicalDefinitionAxioms" : [ ], @@ -16891,33 +16963,33 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000050", "allValuesFromEdges" : [ { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000003", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000003" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000019", + "sub" : "http://purl.obolibrary.org/obo/BFO_0000031", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000019" + "obj" : "http://purl.obolibrary.org/obo/BFO_0000031" }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000020", + "sub" : "http://purl.obolibrary.org/obo/BFO_0000003", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" + "obj" : "http://purl.obolibrary.org/obo/BFO_0000003" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000004", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000017", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000017" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000002", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000017", + "sub" : "http://purl.obolibrary.org/obo/BFO_0000019", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000017" + "obj" : "http://purl.obolibrary.org/obo/BFO_0000019" }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000031", + "sub" : "http://purl.obolibrary.org/obo/BFO_0000020", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000031" + "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" } ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -17396,13 +17468,13 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002214", "allValuesFromEdges" : [ { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000002", - "pred" : "http://purl.obolibrary.org/obo/RO_0002214", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" - }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000015", "pred" : "http://purl.obolibrary.org/obo/RO_0002214", "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000002", + "pred" : "http://purl.obolibrary.org/obo/RO_0002214", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" } ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002215", @@ -17482,9 +17554,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002255", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002203", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002409", "http://purl.obolibrary.org/obo/RO_0002408" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002295", "http://purl.obolibrary.org/obo/RO_0002162" ] @@ -17512,6 +17581,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002130", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002130", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002630" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0001018", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0001025", "http://purl.obolibrary.org/obo/BFO_0000050" ] @@ -17551,9 +17623,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002432", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/BFO_0000066" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002408", "http://purl.obolibrary.org/obo/RO_0002408" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002213", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002230", "http://purl.obolibrary.org/obo/RO_0002213" ] @@ -17581,6 +17650,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002162" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002409", "http://purl.obolibrary.org/obo/RO_0002630" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0010002", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0000059", "http://purl.obolibrary.org/obo/RO_0000053" ] @@ -17590,6 +17662,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002226", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002207", "http://purl.obolibrary.org/obo/RO_0001025" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002409" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002121", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002121", "http://purl.obolibrary.org/obo/BFO_0000050" ] @@ -17659,6 +17734,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002131", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002629", "http://purl.obolibrary.org/obo/RO_0002407" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002233", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002224", "http://purl.obolibrary.org/obo/RO_0002233" ] @@ -17689,18 +17767,18 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002526", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002524", "http://purl.obolibrary.org/obo/RO_0002525" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002407", "http://purl.obolibrary.org/obo/RO_0002406" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002214", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002408", "http://purl.obolibrary.org/obo/RO_0002409" ] + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002629", "http://purl.obolibrary.org/obo/RO_0002629" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002497", "http://purl.obolibrary.org/obo/BFO_0000063" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002407", "http://purl.obolibrary.org/obo/RO_0002629" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002450", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002629", "http://purl.obolibrary.org/obo/RO_0002333" ] @@ -17743,18 +17821,12 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002216", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002215", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002406", "http://purl.obolibrary.org/obo/RO_0002406" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004024", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0004025", "http://purl.obolibrary.org/obo/RO_0002215" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002566", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002411", "http://purl.obolibrary.org/obo/RO_0002333" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002406", "http://purl.obolibrary.org/obo/RO_0002407" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004025", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0004025", "http://purl.obolibrary.org/obo/BFO_0000050" ] diff --git a/ro-base.obo b/ro-base.obo index 96d3c1ce..5bd05499 100644 --- a/ro-base.obo +++ b/ro-base.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: ro/releases/2022-09-07/ro-base.owl +data-version: ro/releases/2022-10-26/ro-base.owl subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" @@ -20,7 +20,7 @@ property_value: http://purl.org/dc/elements/1.1/description "The OBO Relations O property_value: http://purl.org/dc/elements/1.1/title "OBO Relations Ontology" xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(DataProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (never in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (mutually spatially disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (taxonomic class assertion)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (ambiguous for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dubious for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (annotation property cardinality)\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: (logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on a property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an object property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an annotation property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dispositional interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has no connections with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (curator guidance link)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (always present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (measurement property has unit)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has start time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has end time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (month of gestation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has developmental stage marker)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is asymmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is symmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is direct form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indirect form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom where second argument is reflexive)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion involving identity)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (in approximate one to one relationship with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is approximately equivalent to)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is opposite of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indistinguishable from)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (evidential logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom has evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom contradicted by evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is representative IRI for equivalence set)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (nominally disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is directional form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is positive form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is negative form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is homeomorphic for)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (located in)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectComplementOf()))\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (synapsed by)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (gene product of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has member)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (differs in attribute of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (transcribed from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (ribosomal translation of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (ribosomally translates to)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has skeleton)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has role in modeling)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has inflammation site)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance removed)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (immersed in)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has primary substance added)\n\nIrreflexiveObjectProperty()\n\n\n############################\n# Data Properties\n############################\n\n# Data Property: (has increased age-specific mortality rate)\n\nDataPropertyRange( DatatypeRestriction(xsd:short xsd:minInclusive \"0\"^^xsd:short xsd:maxInclusive \"100\"^^xsd:short))\n\n\n\n############################\n# Classes\n############################\n\n# Class: (continuant)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (occurrent)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (material entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (immaterial entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: ()\n\nSubClassOf( ObjectHasSelf())\n\n# Class: ()\n\nSubClassOf( ObjectHasSelf())\n\n# Class: ()\n\nSubClassOf( ObjectHasSelf())\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z\"^^xsd:string) Annotation(rdfs:label \"infer input from direct reg\"^^xsd:string) Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),\ne.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'\") Annotation(rdfs:label \"enabling an MF enables its parts\") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'\"^^xsd:string) Annotation(rdfs:label \"involved in BP\"^^xsd:string) Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(DataProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (never in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (mutually spatially disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (taxonomic class assertion)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (ambiguous for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dubious for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (annotation property cardinality)\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: (logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on a property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an object property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an annotation property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dispositional interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has no connections with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (curator guidance link)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (always present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (measurement property has unit)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has start time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has end time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (month of gestation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has developmental stage marker)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is asymmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is symmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is direct form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indirect form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom where second argument is reflexive)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion involving identity)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (in approximate one to one relationship with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is approximately equivalent to)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is opposite of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indistinguishable from)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (evidential logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom has evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom contradicted by evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is representative IRI for equivalence set)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (nominally disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is directional form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is positive form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is negative form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is homeomorphic for)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (located in)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectComplementOf()))\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (synapsed by)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (gene product of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has member)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (differs in attribute of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (transcribed from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (ribosomal translation of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (ribosomally translates to)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has skeleton)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has role in modeling)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has inflammation site)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance removed)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (immersed in)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has primary substance added)\n\nIrreflexiveObjectProperty()\n\n\n############################\n# Data Properties\n############################\n\n# Data Property: (has increased age-specific mortality rate)\n\nDataPropertyRange( DatatypeRestriction(xsd:short xsd:minInclusive \"0\"^^xsd:short xsd:maxInclusive \"100\"^^xsd:short))\n\n\n\n############################\n# Classes\n############################\n\n# Class: (continuant)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (occurrent)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (material entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (immaterial entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: ()\n\nSubClassOf( ObjectHasSelf())\n\n# Class: ()\n\nSubClassOf( ObjectHasSelf())\n\n# Class: ()\n\nSubClassOf( ObjectHasSelf())\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z\"^^xsd:string) Annotation(rdfs:label \"infer input from direct reg\"^^xsd:string) Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),\ne.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'\") Annotation(rdfs:label \"enabling an MF enables its parts\") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'\"^^xsd:string) Annotation(rdfs:label \"involved in BP\"^^xsd:string) Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) [Term] id: BFO:0000002 @@ -1617,12 +1617,10 @@ is_a: RO:0002203 ! develops into [Typedef] id: RO:0002211 name: regulates -def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." [] +def: "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 "David Hill" xsd:string property_value: IAO:0000117 "Tanya Berardini" xsd:string @@ -1643,7 +1641,7 @@ transitive_over: RO:0002025 ! has effector activity [Typedef] id: RO:0002212 name: negatively regulates -def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +def: "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1659,7 +1657,7 @@ inverse_of: RO:0002335 ! negatively regulated by [Typedef] id: RO:0002213 name: positively regulates -def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +def: "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -2307,6 +2305,7 @@ is_a: RO:0002321 ! ecologically related to [Typedef] id: RO:0002304 name: causally upstream of, positive effect +def: "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." [] 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 subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -2318,7 +2317,9 @@ is_a: RO:0004047 ! causally upstream of or within, positive effect [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 +def: "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: http://purl.org/dc/terms/creator "cjm" xsd:string property_value: RO:0004050 RO:0002411 is_a: RO:0002411 ! causally upstream of @@ -2451,6 +2452,7 @@ is_a: RO:0002329 ! part of structure that is capable of [Typedef] id: RO:0002327 name: enables +def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2995,67 +2997,61 @@ inverse_of: RO:0002412 ! immediately causally upstream of [Typedef] id: RO:0002406 -name: directly activates -def: "p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q" [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "directly positively regulates" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly activates (process to process)" xsd:string -is_a: RO:0002629 ! directly positively regulates +name: obsolete directly activates +comment: This term was obsoleted because it has the same meaning as 'directly positively regulates'. +is_obsolete: true +replaced_by: RO:0002629 [Typedef] id: RO:0002407 -name: indirectly activates -def: "p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one." [] +name: indirectly positively regulates +def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "indirectly positively regulates" xsd:string +property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 -holds_over_chain: RO:0002406 RO:0002406 -holds_over_chain: RO:0002406 RO:0002407 holds_over_chain: RO:0002409 RO:0002409 +holds_over_chain: RO:0002629 RO:0002407 +holds_over_chain: RO:0002629 RO:0002629 is_transitive: true is_a: RO:0002213 ! positively regulates -transitive_over: RO:0002406 ! directly activates +is_a: RO:0012012 ! indirectly regulates +transitive_over: RO:0002629 ! directly positively regulates [Typedef] id: RO:0002408 -name: directly inhibits -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "directly negatively regulates" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly inhibits (process to process)" xsd:string -is_a: RO:0002630 ! directly negatively regulates +name: obsolete directly inhibits +comment: This term was obsoleted because it has the same meaning as 'directly negatively regulates'. +is_obsolete: true +replaced_by: RO:0002630 [Typedef] id: RO:0002409 -name: indirectly inhibits -property_value: IAO:0000114 IAO:0000428 +name: indirectly negatively regulates +def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "indirectly negatively regulates" xsd:string +property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 -holds_over_chain: RO:0002408 RO:0002408 -holds_over_chain: RO:0002408 RO:0002409 +holds_over_chain: RO:0002630 RO:0002409 +holds_over_chain: RO:0002630 RO:0002630 is_transitive: true is_a: RO:0002212 ! negatively regulates -transitive_over: RO:0002408 ! directly inhibits +is_a: RO:0012012 ! indirectly regulates +transitive_over: RO:0002630 ! directly negatively regulates [Typedef] id: RO:0002410 name: causally related to -def: "This relation groups causal relations between material entities and causal relations between processes" [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string +def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] +property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string [Typedef] id: RO:0002411 name: causally upstream of -def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" [] +def: "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string is_transitive: true is_a: BFO:0000063 ! precedes @@ -3064,8 +3060,7 @@ is_a: RO:0002418 ! causally upstream of or within [Typedef] id: RO:0002412 name: immediately causally upstream of -def: "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q." [] -property_value: IAO:0000114 IAO:0000428 +def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: RO:0002575 RO:0002411 is_a: RO:0002090 ! immediately precedes @@ -3074,8 +3069,7 @@ is_a: RO:0002411 ! causally upstream of [Typedef] id: RO:0002413 name: directly provides input for -def: "p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c" [] -property_value: IAO:0000114 IAO:0000428 +def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -3095,12 +3089,12 @@ property_value: IAO:0000589 "transitively provides input for (process to process domain: BFO:0000015 ! process range: BFO:0000015 ! process is_transitive: true -is_a: RO:0002411 ! causally upstream of +is_a: RO:0004047 ! causally upstream of or within, positive effect [Typedef] id: RO:0002418 name: causally upstream of or within -def: "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." [] +def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] synonym: "affects" RELATED [] property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -3776,7 +3770,7 @@ inverse_of: RO:0002608 ! process has causal agent [Typedef] id: RO:0002501 name: causal relation between processes -def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." [] +def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string @@ -4325,7 +4319,7 @@ is_a: BFO:0000050 ! part of [Typedef] id: RO:0002578 name: directly regulates -def: "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." [] +def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -4571,7 +4565,7 @@ is_a: RO:0002574 ! participates in a biotic-biotic interaction with [Typedef] id: RO:0002629 name: directly positively regulates -def: "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." [] +def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -4584,7 +4578,7 @@ is_a: RO:0002578 ! directly regulates [Typedef] id: RO:0002630 name: directly negatively regulates -def: "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." [] +def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -5512,7 +5506,7 @@ creation_date: 2020-06-08T17:21:33Z id: RO:0012004 name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] -is_a: RO:0000056 ! participates in +is_a: RO:0002596 ! capable of regulating created_by: pg creation_date: 2020-06-24T13:15:17Z @@ -5520,6 +5514,7 @@ creation_date: 2020-06-24T13:15:17Z id: RO:0012005 name: is small molecule activator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" [] +is_a: RO:0002598 ! capable of positively regulating is_a: RO:0012004 ! is small molecule regulator of created_by: pg creation_date: 2020-06-24T13:15:26Z @@ -5528,6 +5523,7 @@ creation_date: 2020-06-24T13:15:26Z id: RO:0012006 name: is small molecule inhibitor of def: "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process" [] +is_a: RO:0002597 ! capable of negatively regulating is_a: RO:0012004 ! is small molecule regulator of created_by: pg creation_date: 2020-06-24T13:15:35Z @@ -5550,6 +5546,43 @@ is_a: RO:0002592 ! results in organization of created_by: pg creation_date: 2021-02-26T07:28:29Z +[Typedef] +id: RO:0012009 +name: constitutively upstream of +def: "p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +is_a: RO:0002304 ! causally upstream of, positive effect +created_by: pg +creation_date: 2022-09-26T06:01:01Z + +[Typedef] +id: RO:0012010 +name: removes input for +def: "p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +is_a: RO:0002305 ! causally upstream of, negative effect +created_by: pg +creation_date: 2022-09-26T06:06:20Z + +[Typedef] +id: RO:0012011 +name: indirectly causally upstream of +def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] +is_a: RO:0002411 ! causally upstream of +created_by: pg +creation_date: 2022-09-26T06:07:17Z + +[Typedef] +id: RO:0012012 +name: indirectly regulates +def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." [] +is_a: RO:0002211 ! regulates +is_a: RO:0012011 ! indirectly causally upstream of +created_by: pg +creation_date: 2022-09-26T06:08:01Z + [Typedef] id: RO:0013001 name: has synaptic IO in region diff --git a/ro-base.owl b/ro-base.owl index 21494b43..fa099fa8 100644 --- a/ro-base.owl +++ b/ro-base.owl @@ -18,7 +18,7 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. OBO Relations Ontology @@ -3569,9 +3569,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. - We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit + p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. Chris Mungall David Hill Tanya Berardini @@ -3598,7 +3596,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. Chris Mungall negatively regulates (process to process) @@ -3626,7 +3624,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. Chris Mungall positively regulates (process to process) @@ -4581,6 +4579,7 @@ where + p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. cjm @@ -4596,9 +4595,11 @@ where + p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. 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 @@ -4815,6 +4816,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a particular instances of akt-2 enables some instance of protein kinase activity + c enables p iff c is capable of p and c acts to execute p. Chris Mungall catalyzes executes @@ -5636,14 +5638,10 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - - - p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q - Chris Mungall - directly positively regulates - - directly activates (process to process) - directly activates + + This term was obsoleted because it has the same meaning as 'directly positively regulates'. + obsolete directly activates + true @@ -5652,28 +5650,29 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ + - - + + - - + + + - - - + + - p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one. + p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. Chris Mungall - indirectly positively regulates + indirectly activates - indirectly activates + indirectly positively regulates @@ -5681,12 +5680,10 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - - Chris Mungall - directly negatively regulates - - directly inhibits (process to process) - directly inhibits + + This term was obsoleted because it has the same meaning as 'directly negatively regulates'. + obsolete directly inhibits + true @@ -5695,24 +5692,25 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ + - - + + - + - - + + - + p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. Chris Mungall - indirectly negatively regulates + indirectly inhibits - indirectly inhibits + indirectly negatively regulates @@ -5720,15 +5718,14 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - - This relation groups causal relations between material entities and causal relations between processes + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? - * Is the influence positive or negative + * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. @@ -5741,6 +5738,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to + + + + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. + https://en.wikipedia.org/wiki/Causality + @@ -5750,8 +5753,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain + p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. Chris Mungall @@ -5765,8 +5767,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. + p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. Chris Mungall immediately causally upstream of @@ -5783,8 +5784,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c + p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit Chris Mungall @@ -5797,7 +5797,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -5817,7 +5817,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. + p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) @@ -6960,7 +6960,7 @@ the a supports either the existence of b, or the truth value of b. - p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. + p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. @@ -7802,7 +7802,7 @@ the a supports either the existence of b, or the truth value of b. - Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + p directly regulates q iff p is immediately causally upstream of q and p regulates q. Chris Mungall directly regulates (processual) @@ -8202,7 +8202,7 @@ the a supports either the existence of b, or the truth value of b. - Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. + p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates (process to process) @@ -8219,7 +8219,7 @@ the a supports either the existence of b, or the truth value of b. - Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. + p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates (process to process) @@ -9684,7 +9684,7 @@ For example, protein A (transcription factor) indirectly increases by expression - + a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process pg 2020-06-24T13:15:17Z @@ -9696,6 +9696,7 @@ For example, protein A (transcription factor) indirectly increases by expression + a relation between a continuant and a process, in which the continuant is a small molecule that activates the process pg @@ -9708,6 +9709,7 @@ For example, protein A (transcription factor) indirectly increases by expression + a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process pg @@ -9743,6 +9745,59 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. + pg + 2022-09-26T06:01:01Z + + + constitutively upstream of + + + + + + + + + p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. + pg + 2022-09-26T06:06:20Z + + + removes input for + + + + + + + + + p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. + pg + 2022-09-26T06:07:17Z + indirectly causally upstream of + + + + + + + + + + p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. + pg + 2022-09-26T06:08:01Z + indirectly regulates + + + + @@ -12542,6 +12597,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -12551,6 +12612,9 @@ For example, protein A (transcription factor) indirectly increases by expression + + + @@ -13549,6 +13613,50 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -13725,6 +13833,50 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/ro.json b/ro.json index 5e5d05bb..a472bed5 100644 --- a/ro.json +++ b/ro.json @@ -2573,7 +2573,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002213", "meta" : { "definition" : { - "val" : "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2.", + "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.", "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], @@ -2874,7 +2874,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002211", "meta" : { "definition" : { - "val" : "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2.", + "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.", "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -2887,12 +2887,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "David Hill" @@ -2970,7 +2964,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002212", "meta" : { "definition" : { - "val" : "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2.", + "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.", "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -3950,7 +3944,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002418", "meta" : { "definition" : { - "val" : "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.", + "val" : "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.", "xrefs" : [ ] }, "synonyms" : [ { @@ -3975,16 +3969,13 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002411", "meta" : { "definition" : { - "val" : "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain", + "val" : "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.", "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" } ] }, "type" : "PROPERTY", @@ -3993,13 +3984,10 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002412", "meta" : { "definition" : { - "val" : "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q.", + "val" : "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.", "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002575", "val" : "http://purl.obolibrary.org/obo/RO_0002411" }, { @@ -4013,13 +4001,10 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002413", "meta" : { "definition" : { - "val" : "p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c", + "val" : "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c.", "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { @@ -4072,21 +4057,18 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002410", "meta" : { "definition" : { - "val" : "This relation groups causal relations between material entities and causal relations between processes", - "xrefs" : [ ] + "val" : "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.", + "xrefs" : [ "https://en.wikipedia.org/wiki/Causality" ] }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." } ] }, "type" : "PROPERTY", @@ -4124,34 +4106,20 @@ }, { "id" : "http://purl.obolibrary.org/obo/RO_0002406", "meta" : { - "definition" : { - "val" : "p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q", - "xrefs" : [ ] - }, + "comments" : [ "This term was obsoleted because it has the same meaning as 'directly positively regulates'." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "directly activates (process to process)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "directly positively regulates" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - } ] + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/RO_0002629" + } ], + "deprecated" : true }, "type" : "PROPERTY", - "lbl" : "directly activates" + "lbl" : "obsolete directly activates" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002407", "meta" : { "definition" : { - "val" : "p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one.", + "val" : "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.", "xrefs" : [ ] }, "basicPropertyValues" : [ { @@ -4162,11 +4130,11 @@ "val" : "http://purl.obolibrary.org/obo/RO_0002213" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "indirectly positively regulates" + "val" : "indirectly activates" } ] }, "type" : "PROPERTY", - "lbl" : "indirectly activates" + "lbl" : "indirectly positively regulates" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002400", "meta" : { @@ -4250,25 +4218,22 @@ }, { "id" : "http://purl.obolibrary.org/obo/RO_0002408", "meta" : { + "comments" : [ "This term was obsoleted because it has the same meaning as 'directly negatively regulates'." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "directly inhibits (process to process)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "directly negatively regulates" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - } ] + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/RO_0002630" + } ], + "deprecated" : true }, "type" : "PROPERTY", - "lbl" : "directly inhibits" + "lbl" : "obsolete directly inhibits" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002409", "meta" : { + "definition" : { + "val" : "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.", + "xrefs" : [ ] + }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" @@ -4277,14 +4242,11 @@ "val" : "http://purl.obolibrary.org/obo/RO_0002212" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "indirectly negatively regulates" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + "val" : "indirectly inhibits" } ] }, "type" : "PROPERTY", - "lbl" : "indirectly inhibits" + "lbl" : "indirectly negatively regulates" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002640", "meta" : { @@ -4411,7 +4373,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002630", "meta" : { "definition" : { - "val" : "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2.", + "val" : "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.", "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], @@ -4478,7 +4440,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002629", "meta" : { "definition" : { - "val" : "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2.", + "val" : "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.", "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], @@ -6688,6 +6650,24 @@ }, "type" : "PROPERTY", "lbl" : "is small molecule regulator of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012009", + "meta" : { + "definition" : { + "val" : "p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant.", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2022-09-26T06:01:01Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "pg" + } ] + }, + "type" : "PROPERTY", + "lbl" : "constitutively upstream of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0012007", "meta" : { @@ -6927,6 +6907,58 @@ }, "type" : "PROPERTY", "lbl" : "in hemiplasy relationship with" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012012", + "meta" : { + "definition" : { + "val" : "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "pg" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2022-09-26T06:08:01Z" + } ] + }, + "type" : "PROPERTY", + "lbl" : "indirectly regulates" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012010", + "meta" : { + "definition" : { + "val" : "p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q.", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2022-09-26T06:06:20Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "pg" + } ] + }, + "type" : "PROPERTY", + "lbl" : "removes input for" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012011", + "meta" : { + "definition" : { + "val" : "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2022-09-26T06:07:17Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "pg" + } ] + }, + "type" : "PROPERTY", + "lbl" : "indirectly causally upstream of" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym", "type" : "PROPERTY", @@ -10476,7 +10508,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002578", "meta" : { "definition" : { - "val" : "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.", + "val" : "p directly regulates q iff p is immediately causally upstream of q and p regulates q.", "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -10834,6 +10866,10 @@ }, { "id" : "http://purl.obolibrary.org/obo/RO_0002327", "meta" : { + "definition" : { + "val" : "c enables p iff c is capable of p and c acts to execute p.", + "xrefs" : [ ] + }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", @@ -11562,7 +11598,11 @@ }, { "id" : "http://purl.obolibrary.org/obo/RO_0002305", "meta" : { - "comments" : [ "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" ], + "definition" : { + "val" : "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002411" @@ -11701,6 +11741,10 @@ }, { "id" : "http://purl.obolibrary.org/obo/RO_0002304", "meta" : { + "definition" : { + "val" : "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.", + "xrefs" : [ ] + }, "comments" : [ "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" ], "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { @@ -12560,7 +12604,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002501", "meta" : { "definition" : { - "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.", + "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.", "xrefs" : [ ] }, "basicPropertyValues" : [ { @@ -14206,14 +14250,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002614", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002616" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0015001", - "pred" : "subPropertyOf", - "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0016301", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0016772" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0015001", + "pred" : "subPropertyOf", + "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0008504", "pred" : "subPropertyOf", @@ -14231,13 +14275,17 @@ "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002323" }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0011013", + "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0011004" + "obj" : "http://purl.obolibrary.org/obo/RO_0002211" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002083", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002081" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0011013", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0011004" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004007", "pred" : "subPropertyOf", @@ -14266,14 +14314,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002009", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002292" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002103", - "pred" : "inverseOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002120" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002110", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002113" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002103", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002120" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002567", "pred" : "subPropertyOf", @@ -14338,14 +14386,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002572", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002571" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002520", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002524" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002521", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002514" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002520", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002524" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002571", "pred" : "subPropertyOf", @@ -14378,14 +14426,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0004047", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002418" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0004005", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0004000" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002411", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002418" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0004005", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0004000" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002016", "pred" : "subPropertyOf", @@ -14582,14 +14630,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0004020", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0004019" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0016004", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002244" }, { "sub" : "http://purl.obolibrary.org/obo/CARO_0000003", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CARO_0000006" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0016004", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002244" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002507", "pred" : "inverseOf", @@ -14746,26 +14794,26 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002287", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002286" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0004004", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0004000" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002440", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002574" }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002291", + "sub" : "http://purl.obolibrary.org/obo/RO_0004004", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002206" + "obj" : "http://purl.obolibrary.org/obo/RO_0004000" }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002225", + "sub" : "http://purl.obolibrary.org/obo/RO_0002291", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002202" + "obj" : "http://purl.obolibrary.org/obo/RO_0002206" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002223", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002222" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002225", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002202" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002492", "pred" : "subPropertyOf", @@ -14930,14 +14978,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002339", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002344" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002012", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002418" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000015", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000003" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002012", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002418" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002209", "pred" : "subPropertyOf", @@ -15042,10 +15090,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002426", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002424" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002414", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002411" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000024", "pred" : "subPropertyOf", @@ -15070,10 +15114,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002509", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002131" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0008502", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002440" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001199", "pred" : "is_a", @@ -15082,6 +15122,10 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0030425", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0043005" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0008502", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002440" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002478", "pred" : "subPropertyOf", @@ -15110,50 +15154,46 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002599", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002597" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002130", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002131" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0044456", "pred" : "is_a", "obj" : "http://www.w3.org/2002/07/owl#Thing" }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002333", + "sub" : "http://purl.obolibrary.org/obo/RO_0002130", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002328" + "obj" : "http://purl.obolibrary.org/obo/RO_0002131" }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002406", + "sub" : "http://purl.obolibrary.org/obo/RO_0002333", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002629" + "obj" : "http://purl.obolibrary.org/obo/RO_0002328" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002315", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0040036" }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002252", + "sub" : "http://purl.obolibrary.org/obo/RO_0002455", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002375" + "obj" : "http://purl.obolibrary.org/obo/RO_0002442" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002466", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002465" }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002455", + "sub" : "http://purl.obolibrary.org/obo/RO_0002252", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002442" + "obj" : "http://purl.obolibrary.org/obo/RO_0002375" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002263", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002264" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000007", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000001" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002310", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000007", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000001" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0011014", "pred" : "subPropertyOf", @@ -15226,6 +15266,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002212", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002211" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012011", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002411" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004019", "pred" : "subPropertyOf", @@ -15270,6 +15314,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0004035", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0004033" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002407", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0012012" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002100", "pred" : "subPropertyOf", @@ -15314,6 +15362,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002430", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002428" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002379", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002131" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002113", "pred" : "subPropertyOf", @@ -15322,10 +15374,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002114", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002120" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002379", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002131" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002329", "pred" : "subPropertyOf", @@ -15354,14 +15402,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002203", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002388" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000037", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000007" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000034", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000037" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000037", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000007" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002203", "pred" : "subPropertyOf", @@ -15466,14 +15514,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002533", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/RO_0002532" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002260", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000087" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002022", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002334" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002260", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0000087" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000012", "pred" : "subPropertyOf", @@ -15770,14 +15818,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002229", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000050" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0004002", - "pred" : "inverseOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0004012" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0042734", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0044456" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0004002", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0004012" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002384", "pred" : "subPropertyOf", @@ -15798,6 +15846,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0004003", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0004013" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012004", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002596" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002588", "pred" : "subPropertyOf", @@ -15886,14 +15938,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002526", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002514" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002160", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002162" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002009", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002162" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002261", "pred" : "subPropertyOf", @@ -15926,6 +15978,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002088", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002091" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0004024", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0004023" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002007", "pred" : "subPropertyOf", @@ -15934,10 +15990,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0004012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0004010" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0004024", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0004023" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002525", "pred" : "subPropertyOf", @@ -16002,26 +16054,26 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002004", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0001018" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002476", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002258" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002458", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002476", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002258" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002233", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000057" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002006", - "pred" : "inverseOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002130" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0001020", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0001022" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002006", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002130" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002622", "pred" : "inverseOf", @@ -16170,6 +16222,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002299", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0040036" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002409", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0012012" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000069", "pred" : "subPropertyOf", @@ -16282,10 +16338,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002380", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002375" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0012004", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000056" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002485", "pred" : "subPropertyOf", @@ -16410,14 +16462,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002444", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002454" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002461", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000056" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002246", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002206" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002461", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0000056" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002232", "pred" : "subPropertyOf", @@ -16498,14 +16550,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000045", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000007" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002618", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002574" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002585", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0040036" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002618", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002574" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002623", "pred" : "subPropertyOf", @@ -16530,6 +16582,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002376", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002375" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002414", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0004047" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002608", "pred" : "subPropertyOf", @@ -16642,14 +16698,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002150", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002323" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002408", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002630" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002481", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002564" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012010", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002305" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002428", "pred" : "subPropertyOf", @@ -16706,6 +16762,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002459", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002574" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012009", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002304" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002177", "pred" : "subPropertyOf", @@ -16742,6 +16802,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002296", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0040036" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012006", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002597" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002341", "pred" : "subPropertyOf", @@ -16754,14 +16818,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0004014", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003303" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002349", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002295" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000054", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000062" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002349", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002295" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002445", "pred" : "subPropertyOf", @@ -16874,14 +16938,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002355", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0040036" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002256", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002258" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004015", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0004010" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002256", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002258" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002254", "pred" : "inverseOf", @@ -17082,6 +17146,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002470", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012005", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002598" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002212", "pred" : "inverseOf", @@ -17442,6 +17510,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0004000", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002410" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012012", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0012011" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002569", "pred" : "subPropertyOf", @@ -17551,12 +17623,12 @@ "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 146 Logical Axioms: 45]" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2022-09-07" + "val" : "2022-10-26" }, { "pred" : "http://xmlns.com/foaf/0.1/homepage", "val" : " https://github.com/oborel/obo-relations/" } ], - "version" : "http://purl.obolibrary.org/obo/ro/releases/2022-09-07/ro.owl" + "version" : "http://purl.obolibrary.org/obo/ro/releases/2022-10-26/ro.owl" }, "equivalentNodesSets" : [ ], "logicalDefinitionAxioms" : [ ], @@ -17647,13 +17719,13 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002207", "allValuesFromEdges" : [ { - "sub" : "http://purl.obolibrary.org/obo/CL_0000000", - "pred" : "http://purl.obolibrary.org/obo/RO_0002207", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" - }, { "sub" : "http://purl.obolibrary.org/obo/CARO_0010000", "pred" : "http://purl.obolibrary.org/obo/RO_0002207", "obj" : "http://purl.obolibrary.org/obo/CARO_0010000" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000000", + "pred" : "http://purl.obolibrary.org/obo/RO_0002207", + "obj" : "http://purl.obolibrary.org/obo/CL_0000000" } ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002449", @@ -17662,17 +17734,21 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000050", "allValuesFromEdges" : [ { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000020", + "sub" : "http://purl.obolibrary.org/obo/BFO_0000003", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" + "obj" : "http://purl.obolibrary.org/obo/BFO_0000003" }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000031", + "sub" : "http://purl.obolibrary.org/obo/BFO_0000020", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000031" + "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000002", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000031", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000031" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000004", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -17681,10 +17757,6 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000017", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/BFO_0000017" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000003", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000003" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000019", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -18167,13 +18239,13 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002214", "allValuesFromEdges" : [ { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000002", - "pred" : "http://purl.obolibrary.org/obo/RO_0002214", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" - }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000015", "pred" : "http://purl.obolibrary.org/obo/RO_0002214", "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000002", + "pred" : "http://purl.obolibrary.org/obo/RO_0002214", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" } ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002215", @@ -18253,9 +18325,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002255", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002203", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002409", "http://purl.obolibrary.org/obo/RO_0002408" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002295", "http://purl.obolibrary.org/obo/RO_0002162" ] @@ -18283,6 +18352,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002130", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002130", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002630" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0001018", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0001025", "http://purl.obolibrary.org/obo/BFO_0000050" ] @@ -18322,9 +18394,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002432", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/BFO_0000066" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002408", "http://purl.obolibrary.org/obo/RO_0002408" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002213", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002230", "http://purl.obolibrary.org/obo/RO_0002213" ] @@ -18352,6 +18421,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002162" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002409", "http://purl.obolibrary.org/obo/RO_0002630" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0010002", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0000059", "http://purl.obolibrary.org/obo/RO_0000053" ] @@ -18361,6 +18433,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002226", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002207", "http://purl.obolibrary.org/obo/RO_0001025" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002409" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002121", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002121", "http://purl.obolibrary.org/obo/BFO_0000050" ] @@ -18430,6 +18505,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002131", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002629", "http://purl.obolibrary.org/obo/RO_0002407" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002233", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002224", "http://purl.obolibrary.org/obo/RO_0002233" ] @@ -18460,18 +18538,18 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002526", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002524", "http://purl.obolibrary.org/obo/RO_0002525" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002407", "http://purl.obolibrary.org/obo/RO_0002406" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002214", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002408", "http://purl.obolibrary.org/obo/RO_0002409" ] + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002629", "http://purl.obolibrary.org/obo/RO_0002629" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002497", "http://purl.obolibrary.org/obo/BFO_0000063" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002407", "http://purl.obolibrary.org/obo/RO_0002629" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002450", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002629", "http://purl.obolibrary.org/obo/RO_0002333" ] @@ -18514,18 +18592,12 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002216", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002215", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002406", "http://purl.obolibrary.org/obo/RO_0002406" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004024", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0004025", "http://purl.obolibrary.org/obo/RO_0002215" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002566", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002411", "http://purl.obolibrary.org/obo/RO_0002333" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002406", "http://purl.obolibrary.org/obo/RO_0002407" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004025", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0004025", "http://purl.obolibrary.org/obo/BFO_0000050" ] diff --git a/ro.obo b/ro.obo index 2a084f4c..777f92f3 100644 --- a/ro.obo +++ b/ro.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: releases/2022-09-07 +data-version: releases/2022-10-26 subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" @@ -26,8 +26,8 @@ property_value: http://purl.org/dc/elements/1.1/description "The OBO Relations O property_value: http://purl.org/dc/elements/1.1/title "OBO Relations Ontology" xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI -property_value: owl:versionInfo "2022-09-07" xsd:string -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(DataProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: (first order logic expression)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (never in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (mutually spatially disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (taxonomic class assertion)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (ambiguous for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dubious for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (annotation property cardinality)\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: (logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on a property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an object property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an annotation property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dispositional interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has no connections with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (curator guidance link)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (always present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (measurement property has unit)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has start time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has end time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (month of gestation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has developmental stage marker)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is asymmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is symmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is direct form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indirect form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom where second argument is reflexive)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion involving identity)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (in approximate one to one relationship with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is approximately equivalent to)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is opposite of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indistinguishable from)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (evidential logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom has evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom contradicted by evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is representative IRI for equivalence set)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (nominally disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is directional form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is positive form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is negative form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is homeomorphic for)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (located in)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectComplementOf()))\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (synapsed by)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (gene product of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has member)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (differs in attribute of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (transcribed from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (ribosomal translation of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (ribosomally translates to)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has skeleton)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has role in modeling)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has inflammation site)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance removed)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (immersed in)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has primary substance added)\n\nIrreflexiveObjectProperty()\n\n\n############################\n# Data Properties\n############################\n\n# Data Property: (has increased age-specific mortality rate)\n\nDataPropertyRange( DatatypeRestriction(xsd:short xsd:minInclusive \"0\"^^xsd:short xsd:maxInclusive \"100\"^^xsd:short))\n\n\n\n############################\n# Classes\n############################\n\n# Class: (continuant)\n\nSubClassOf( owl:Thing)\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (occurrent)\n\nSubClassOf( owl:Thing)\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (material entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (immaterial entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: ()\n\nSubClassOf( owl:Thing)\n\n# Class: (ubiquitin-protein ligase activity)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: ()\n\nSubClassOf( owl:Thing)\n\n# Class: (nucleus)\n\nSubClassOf( owl:Thing)\n\n# Class: (kinase activity)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: ()\n\nSubClassOf( owl:Thing)\nSubClassOf( ObjectHasSelf())\n\n# Class: (cell projection)\n\nSubClassOf( owl:Thing)\n\n# Class: (synapse part)\n\nSubClassOf( owl:Thing)\n\n# Class: (sequentially ordered entity)\n\nSubClassOf( owl:Thing)\n\n# Class: owl:Nothing (owl:Nothing)\n\nSubClassOf(owl:Nothing owl:Nothing)\n\n# Class: ()\n\nSubClassOf( owl:Thing)\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z\"^^xsd:string) Annotation(rdfs:label \"infer input from direct reg\"^^xsd:string) Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),\ne.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'\") Annotation(rdfs:label \"enabling an MF enables its parts\") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'\"^^xsd:string) Annotation(rdfs:label \"involved in BP\"^^xsd:string) Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) +property_value: owl:versionInfo "2022-10-26" xsd:string +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(DataProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: (first order logic expression)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (never in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (mutually spatially disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (taxonomic class assertion)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (ambiguous for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dubious for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (annotation property cardinality)\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: (logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on a property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an object property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an annotation property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dispositional interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has no connections with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (curator guidance link)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (always present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (measurement property has unit)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has start time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has end time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (month of gestation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has developmental stage marker)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is asymmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is symmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is direct form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indirect form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom where second argument is reflexive)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion involving identity)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (in approximate one to one relationship with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is approximately equivalent to)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is opposite of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indistinguishable from)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (evidential logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom has evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom contradicted by evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is representative IRI for equivalence set)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (nominally disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is directional form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is positive form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is negative form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is homeomorphic for)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (located in)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectComplementOf()))\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (synapsed by)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (gene product of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has member)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (differs in attribute of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (transcribed from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (ribosomal translation of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (ribosomally translates to)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has skeleton)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has role in modeling)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has inflammation site)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance removed)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (immersed in)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has primary substance added)\n\nIrreflexiveObjectProperty()\n\n\n############################\n# Data Properties\n############################\n\n# Data Property: (has increased age-specific mortality rate)\n\nDataPropertyRange( DatatypeRestriction(xsd:short xsd:minInclusive \"0\"^^xsd:short xsd:maxInclusive \"100\"^^xsd:short))\n\n\n\n############################\n# Classes\n############################\n\n# Class: (continuant)\n\nSubClassOf( owl:Thing)\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (occurrent)\n\nSubClassOf( owl:Thing)\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (material entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (immaterial entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: ()\n\nSubClassOf( owl:Thing)\n\n# Class: (ubiquitin-protein ligase activity)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: ()\n\nSubClassOf( owl:Thing)\n\n# Class: (nucleus)\n\nSubClassOf( owl:Thing)\n\n# Class: (kinase activity)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: ()\n\nSubClassOf( owl:Thing)\nSubClassOf( ObjectHasSelf())\n\n# Class: (cell projection)\n\nSubClassOf( owl:Thing)\n\n# Class: (synapse part)\n\nSubClassOf( owl:Thing)\n\n# Class: (sequentially ordered entity)\n\nSubClassOf( owl:Thing)\n\n# Class: owl:Nothing (owl:Nothing)\n\nSubClassOf(owl:Nothing owl:Nothing)\n\n# Class: ()\n\nSubClassOf( owl:Thing)\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z\"^^xsd:string) Annotation(rdfs:label \"infer input from direct reg\"^^xsd:string) Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),\ne.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'\") Annotation(rdfs:label \"enabling an MF enables its parts\") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'\"^^xsd:string) Annotation(rdfs:label \"involved in BP\"^^xsd:string) Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) [Term] id: BFO:0000002 @@ -1873,12 +1873,10 @@ is_a: RO:0002203 ! develops into [Typedef] id: RO:0002211 name: regulates -def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." [] +def: "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 "David Hill" xsd:string property_value: IAO:0000117 "Tanya Berardini" xsd:string @@ -1899,7 +1897,7 @@ transitive_over: RO:0002025 ! has effector activity [Typedef] id: RO:0002212 name: negatively regulates -def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +def: "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1915,7 +1913,7 @@ inverse_of: RO:0002335 ! negatively regulated by [Typedef] id: RO:0002213 name: positively regulates -def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +def: "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -2563,6 +2561,7 @@ is_a: RO:0002321 ! ecologically related to [Typedef] id: RO:0002304 name: causally upstream of, positive effect +def: "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." [] 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 subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -2574,7 +2573,9 @@ is_a: RO:0004047 ! causally upstream of or within, positive effect [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 +def: "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: http://purl.org/dc/terms/creator "cjm" xsd:string property_value: RO:0004050 RO:0002411 is_a: RO:0002411 ! causally upstream of @@ -2707,6 +2708,7 @@ is_a: RO:0002329 ! part of structure that is capable of [Typedef] id: RO:0002327 name: enables +def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -3251,67 +3253,61 @@ inverse_of: RO:0002412 ! immediately causally upstream of [Typedef] id: RO:0002406 -name: directly activates -def: "p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q" [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "directly positively regulates" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly activates (process to process)" xsd:string -is_a: RO:0002629 ! directly positively regulates +name: obsolete directly activates +comment: This term was obsoleted because it has the same meaning as 'directly positively regulates'. +is_obsolete: true +replaced_by: RO:0002629 [Typedef] id: RO:0002407 -name: indirectly activates -def: "p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one." [] +name: indirectly positively regulates +def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "indirectly positively regulates" xsd:string +property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 -holds_over_chain: RO:0002406 RO:0002406 -holds_over_chain: RO:0002406 RO:0002407 holds_over_chain: RO:0002409 RO:0002409 +holds_over_chain: RO:0002629 RO:0002407 +holds_over_chain: RO:0002629 RO:0002629 is_transitive: true is_a: RO:0002213 ! positively regulates -transitive_over: RO:0002406 ! directly activates +is_a: RO:0012012 ! indirectly regulates +transitive_over: RO:0002629 ! directly positively regulates [Typedef] id: RO:0002408 -name: directly inhibits -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "directly negatively regulates" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly inhibits (process to process)" xsd:string -is_a: RO:0002630 ! directly negatively regulates +name: obsolete directly inhibits +comment: This term was obsoleted because it has the same meaning as 'directly negatively regulates'. +is_obsolete: true +replaced_by: RO:0002630 [Typedef] id: RO:0002409 -name: indirectly inhibits -property_value: IAO:0000114 IAO:0000428 +name: indirectly negatively regulates +def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "indirectly negatively regulates" xsd:string +property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 -holds_over_chain: RO:0002408 RO:0002408 -holds_over_chain: RO:0002408 RO:0002409 +holds_over_chain: RO:0002630 RO:0002409 +holds_over_chain: RO:0002630 RO:0002630 is_transitive: true is_a: RO:0002212 ! negatively regulates -transitive_over: RO:0002408 ! directly inhibits +is_a: RO:0012012 ! indirectly regulates +transitive_over: RO:0002630 ! directly negatively regulates [Typedef] id: RO:0002410 name: causally related to -def: "This relation groups causal relations between material entities and causal relations between processes" [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string +def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] +property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string [Typedef] id: RO:0002411 name: causally upstream of -def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" [] +def: "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string is_transitive: true is_a: BFO:0000063 ! precedes @@ -3320,8 +3316,7 @@ is_a: RO:0002418 ! causally upstream of or within [Typedef] id: RO:0002412 name: immediately causally upstream of -def: "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q." [] -property_value: IAO:0000114 IAO:0000428 +def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: RO:0002575 RO:0002411 is_a: RO:0002090 ! immediately precedes @@ -3330,8 +3325,7 @@ is_a: RO:0002411 ! causally upstream of [Typedef] id: RO:0002413 name: directly provides input for -def: "p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c" [] -property_value: IAO:0000114 IAO:0000428 +def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -3351,12 +3345,12 @@ property_value: IAO:0000589 "transitively provides input for (process to process domain: BFO:0000015 ! process range: BFO:0000015 ! process is_transitive: true -is_a: RO:0002411 ! causally upstream of +is_a: RO:0004047 ! causally upstream of or within, positive effect [Typedef] id: RO:0002418 name: causally upstream of or within -def: "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." [] +def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] synonym: "affects" RELATED [] property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -4032,7 +4026,7 @@ inverse_of: RO:0002608 ! process has causal agent [Typedef] id: RO:0002501 name: causal relation between processes -def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." [] +def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string @@ -4581,7 +4575,7 @@ is_a: BFO:0000050 ! part of [Typedef] id: RO:0002578 name: directly regulates -def: "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." [] +def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -4827,7 +4821,7 @@ is_a: RO:0002574 ! participates in a biotic-biotic interaction with [Typedef] id: RO:0002629 name: directly positively regulates -def: "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." [] +def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -4840,7 +4834,7 @@ is_a: RO:0002578 ! directly regulates [Typedef] id: RO:0002630 name: directly negatively regulates -def: "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." [] +def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -5768,7 +5762,7 @@ creation_date: 2020-06-08T17:21:33Z id: RO:0012004 name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] -is_a: RO:0000056 ! participates in +is_a: RO:0002596 ! capable of regulating created_by: pg creation_date: 2020-06-24T13:15:17Z @@ -5776,6 +5770,7 @@ creation_date: 2020-06-24T13:15:17Z id: RO:0012005 name: is small molecule activator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" [] +is_a: RO:0002598 ! capable of positively regulating is_a: RO:0012004 ! is small molecule regulator of created_by: pg creation_date: 2020-06-24T13:15:26Z @@ -5784,6 +5779,7 @@ creation_date: 2020-06-24T13:15:26Z id: RO:0012006 name: is small molecule inhibitor of def: "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process" [] +is_a: RO:0002597 ! capable of negatively regulating is_a: RO:0012004 ! is small molecule regulator of created_by: pg creation_date: 2020-06-24T13:15:35Z @@ -5806,6 +5802,43 @@ is_a: RO:0002592 ! results in organization of created_by: pg creation_date: 2021-02-26T07:28:29Z +[Typedef] +id: RO:0012009 +name: constitutively upstream of +def: "p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +is_a: RO:0002304 ! causally upstream of, positive effect +created_by: pg +creation_date: 2022-09-26T06:01:01Z + +[Typedef] +id: RO:0012010 +name: removes input for +def: "p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +is_a: RO:0002305 ! causally upstream of, negative effect +created_by: pg +creation_date: 2022-09-26T06:06:20Z + +[Typedef] +id: RO:0012011 +name: indirectly causally upstream of +def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] +is_a: RO:0002411 ! causally upstream of +created_by: pg +creation_date: 2022-09-26T06:07:17Z + +[Typedef] +id: RO:0012012 +name: indirectly regulates +def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." [] +is_a: RO:0002211 ! regulates +is_a: RO:0012011 ! indirectly causally upstream of +created_by: pg +creation_date: 2022-09-26T06:08:01Z + [Typedef] id: RO:0013001 name: has synaptic IO in region diff --git a/ro.owl b/ro.owl index a3db7bcc..b4f6a7e1 100644 --- a/ro.owl +++ b/ro.owl @@ -18,7 +18,7 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + @@ -35,7 +35,7 @@ The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. OBO Relations Ontology - 2022-09-07 + 2022-10-26 https://github.com/oborel/obo-relations/ @@ -2841,9 +2841,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. - We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit + p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. Chris Mungall David Hill Tanya Berardini @@ -2870,7 +2868,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. Chris Mungall negatively regulates (process to process) @@ -2898,7 +2896,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. Chris Mungall positively regulates (process to process) @@ -3811,6 +3809,7 @@ where + p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. cjm @@ -3826,9 +3825,11 @@ where + p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. 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 @@ -4045,6 +4046,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a particular instances of akt-2 enables some instance of protein kinase activity + c enables p iff c is capable of p and c acts to execute p. Chris Mungall catalyzes executes @@ -4837,14 +4839,10 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - - - p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q - Chris Mungall - directly positively regulates - - directly activates (process to process) - directly activates + + This term was obsoleted because it has the same meaning as 'directly positively regulates'. + obsolete directly activates + true @@ -4853,28 +4851,29 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ + - - + + - - + + + - - - + + - p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one. + p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. Chris Mungall - indirectly positively regulates + indirectly activates - indirectly activates + indirectly positively regulates @@ -4882,12 +4881,10 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - - Chris Mungall - directly negatively regulates - - directly inhibits (process to process) - directly inhibits + + This term was obsoleted because it has the same meaning as 'directly negatively regulates'. + obsolete directly inhibits + true @@ -4896,24 +4893,25 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ + - - + + - + - - + + - + p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. Chris Mungall - indirectly negatively regulates + indirectly inhibits - indirectly inhibits + indirectly negatively regulates @@ -4921,15 +4919,14 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - - This relation groups causal relations between material entities and causal relations between processes + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? - * Is the influence positive or negative + * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. @@ -4942,6 +4939,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to + + + + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. + https://en.wikipedia.org/wiki/Causality + @@ -4951,8 +4954,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain + p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. Chris Mungall @@ -4966,8 +4968,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. + p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. Chris Mungall immediately causally upstream of @@ -4984,8 +4985,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c + p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit Chris Mungall @@ -4998,7 +4998,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -5018,7 +5018,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. + p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) @@ -6161,7 +6161,7 @@ the a supports either the existence of b, or the truth value of b. - p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. + p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. @@ -7003,7 +7003,7 @@ the a supports either the existence of b, or the truth value of b. - Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + p directly regulates q iff p is immediately causally upstream of q and p regulates q. Chris Mungall directly regulates (processual) @@ -7403,7 +7403,7 @@ the a supports either the existence of b, or the truth value of b. - Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. + p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates (process to process) @@ -7420,7 +7420,7 @@ the a supports either the existence of b, or the truth value of b. - Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. + p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates (process to process) @@ -8866,7 +8866,7 @@ For example, protein A (transcription factor) indirectly increases by expression - + a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process pg 2020-06-24T13:15:17Z @@ -8878,6 +8878,7 @@ For example, protein A (transcription factor) indirectly increases by expression + a relation between a continuant and a process, in which the continuant is a small molecule that activates the process pg @@ -8890,6 +8891,7 @@ For example, protein A (transcription factor) indirectly increases by expression + a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process pg @@ -8925,6 +8927,59 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. + pg + 2022-09-26T06:01:01Z + + + constitutively upstream of + + + + + + + + + p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. + pg + 2022-09-26T06:06:20Z + + + removes input for + + + + + + + + + p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. + pg + 2022-09-26T06:07:17Z + indirectly causally upstream of + + + + + + + + + + p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. + pg + 2022-09-26T06:08:01Z + indirectly regulates + + + + @@ -10354,6 +10409,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -10363,6 +10424,9 @@ For example, protein A (transcription factor) indirectly increases by expression + + + @@ -11189,6 +11253,50 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -11365,6 +11473,50 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/subsets/ro-causal.obo b/src/ontology/subsets/ro-causal.obo index dbeb953c..e70023eb 100644 --- a/src/ontology/subsets/ro-causal.obo +++ b/src/ontology/subsets/ro-causal.obo @@ -372,7 +372,7 @@ is_a: causally_related_to ! causally related to [Typedef] id: causal_relation_between_processes name: causal relation between processes -def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." [] +def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] xref: RO:0002501 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -440,21 +440,19 @@ is_a: causal_relation_between_entities ! causal relation between entities [Typedef] id: causally_related_to name: causally related to -def: "This relation groups causal relations between material entities and causal relations between processes" [] +def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] xref: RO:0002410 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string +property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string [Typedef] id: causally_upstream_of name: causally upstream of -def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" [] +def: "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002411 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within @@ -463,7 +461,9 @@ 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 +def: "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 property_value: http://purl.org/dc/terms/creator "cjm" xsd:string property_value: RO:0004050 RO:0002411 @@ -473,6 +473,7 @@ is_a: causally_upstream_of_or_within,_negative_effect ! causally upstream of or [Typedef] id: causally_upstream_of,_positive_effect name: causally upstream of, positive effect +def: "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." [] 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 subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -485,7 +486,7 @@ is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or [Typedef] id: causally_upstream_of_or_within name: causally upstream of or within -def: "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." [] +def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] synonym: "affects" RELATED [] xref: RO:0002418 property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string @@ -709,6 +710,17 @@ property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-art domain: BFO:0000004 is_a: mereotopologically_related_to ! mereotopologically related to +[Typedef] +id: constitutively_upstream_of +name: constitutively upstream of +def: "p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0012009 +is_a: causally_upstream_of,_positive_effect ! causally upstream of, positive effect +created_by: pg +creation_date: 2022-09-26T06:01:01Z + [Typedef] id: continuous_with name: continuous with @@ -993,18 +1005,6 @@ is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_develop_into ! has potential to develop into is_a: has_potential_to_directly_develop_into ! has potential to directly develop into -[Typedef] -id: directly_activates -name: directly activates -def: "p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q" [] -xref: RO:0002406 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "directly positively regulates" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly activates (process to process)" xsd:string -is_a: directly_positively_regulates ! directly positively regulates - [Typedef] id: directly_develops_from name: directly develops from @@ -1030,16 +1030,6 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "developmental precursor of" xsd:string is_a: develops_into ! develops into -[Typedef] -id: directly_inhibits -name: directly inhibits -xref: RO:0002408 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "directly negatively regulates" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly inhibits (process to process)" xsd:string -is_a: directly_negatively_regulates ! directly negatively regulates - [Typedef] id: directly_negatively_regulated_by name: directly negatively regulated by @@ -1053,7 +1043,7 @@ creation_date: 2017-09-17T13:52:38Z [Typedef] id: directly_negatively_regulates name: directly negatively regulates -def: "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." [] +def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1100,7 +1090,7 @@ creation_date: 2017-09-17T13:52:47Z [Typedef] id: directly_positively_regulates name: directly positively regulates -def: "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." [] +def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1137,9 +1127,8 @@ is_a: directly_regulates_quantity_of ! directly regulates quantity of [Typedef] id: directly_provides_input_for name: directly provides input for -def: "p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c" [] +def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] xref: RO:0002413 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -1160,7 +1149,7 @@ creation_date: 2017-09-17T13:52:24Z [Typedef] id: directly_regulates name: directly regulates -def: "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." [] +def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1416,6 +1405,7 @@ is_a: has_participant [Typedef] id: enables name: enables +def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002327 property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string @@ -2540,9 +2530,8 @@ inverse_of: immediately_causally_upstream_of ! immediately causally upstream of [Typedef] id: immediately_causally_upstream_of name: immediately causally upstream of -def: "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q." [] +def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] xref: RO:0002412 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of @@ -2616,25 +2605,24 @@ range: BFO:0000040 is_a: directly_positively_regulates_activity_of ! directly positively regulates activity of [Typedef] -id: indirectly_activates -name: indirectly activates -def: "p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one." [] -xref: RO:0002407 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "indirectly positively regulates" xsd:string -property_value: RO:0002579 RO:0002213 -is_transitive: true -is_a: positively_regulates ! positively regulates +id: indirectly_causally_upstream_of +name: indirectly causally upstream of +def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] +xref: RO:0012011 +is_a: causally_upstream_of ! causally upstream of +created_by: pg +creation_date: 2022-09-26T06:07:17Z [Typedef] -id: indirectly_inhibits -name: indirectly inhibits +id: indirectly_negatively_regulates +name: indirectly negatively regulates +def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] xref: RO:0002409 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "indirectly negatively regulates" xsd:string +property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 is_transitive: true +is_a: indirectly_regulates ! indirectly regulates is_a: negatively_regulates ! negatively regulates [Typedef] @@ -2654,6 +2642,18 @@ xref: RO:0011023 property_value: IAO:0000117 "Vasundra Touré" xsd:string is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of +[Typedef] +id: indirectly_positively_regulates +name: indirectly positively regulates +def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] +xref: RO:0002407 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "indirectly activates" xsd:string +property_value: RO:0002579 RO:0002213 +is_transitive: true +is_a: indirectly_regulates ! indirectly regulates +is_a: positively_regulates ! positively regulates + [Typedef] id: indirectly_positively_regulates_activity_of name: indirectly positively regulates activity of @@ -2673,6 +2673,16 @@ xref: RO:0011024 property_value: IAO:0000117 "Vasundra Touré" xsd:string is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of +[Typedef] +id: indirectly_regulates +name: indirectly regulates +def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." [] +xref: RO:0012012 +is_a: indirectly_causally_upstream_of ! indirectly causally upstream of +is_a: regulates ! regulates +created_by: pg +creation_date: 2022-09-26T06:08:01Z + [Typedef] id: indirectly_regulates_activity_of name: indirectly regulates activity of @@ -3012,6 +3022,7 @@ id: is_small_molecule_activator_of name: is small molecule activator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" [] xref: RO:0012005 +is_a: capable_of_positively_regulating ! capable of positively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of created_by: pg creation_date: 2020-06-24T13:15:26Z @@ -3021,6 +3032,7 @@ id: is_small_molecule_inhibitor_of name: is small molecule inhibitor of def: "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process" [] xref: RO:0012006 +is_a: capable_of_negatively_regulating ! capable of negatively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of created_by: pg creation_date: 2020-06-24T13:15:35Z @@ -3030,7 +3042,7 @@ id: is_small_molecule_regulator_of name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] xref: RO:0012004 -is_a: participates_in +is_a: capable_of_regulating ! capable of regulating created_by: pg creation_date: 2020-06-24T13:15:17Z @@ -3246,7 +3258,7 @@ is_a: regulated_by ! regulated by [Typedef] id: negatively_regulates name: negatively regulates -def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +def: "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -3513,7 +3525,7 @@ is_a: regulated_by ! regulated by [Typedef] id: positively_regulates name: positively regulates -def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +def: "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -3707,13 +3719,11 @@ is_a: causally_downstream_of_or_within ! causally downstream of or within [Typedef] id: regulates name: regulates -def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." [] +def: "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 "David Hill" xsd:string property_value: IAO:0000117 "Tanya Berardini" xsd:string @@ -3800,6 +3810,17 @@ property_value: IAO:0000232 "Do not use this relation directly. It is a grouping domain: BFO:0000015 range: BFO:0000002 +[Typedef] +id: removes_input_for +name: removes input for +def: "p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0012010 +is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect +created_by: pg +creation_date: 2022-09-26T06:06:20Z + [Typedef] id: represses_expression_of name: represses expression of @@ -4495,7 +4516,7 @@ property_value: IAO:0000589 "transitively provides input for (process to process domain: BFO:0000015 range: BFO:0000015 is_transitive: true -is_a: causally_upstream_of ! causally upstream of +is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or within, positive effect [Typedef] id: transmitted_by diff --git a/src/ontology/subsets/ro-causal.owl b/src/ontology/subsets/ro-causal.owl index 9f5aab9d..4632afce 100644 --- a/src/ontology/subsets/ro-causal.owl +++ b/src/ontology/subsets/ro-causal.owl @@ -1644,9 +1644,7 @@ N1 SubclassOf ( - - process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. - We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit + p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. Chris Mungall David Hill Tanya Berardini @@ -1671,7 +1669,7 @@ N1 SubclassOf ( - Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. Chris Mungall negatively regulates (process to process) @@ -1693,7 +1691,7 @@ N1 SubclassOf ( - Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. Chris Mungall positively regulates (process to process) @@ -2523,6 +2521,7 @@ where + p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. cjm RO:0002304 @@ -2540,11 +2539,13 @@ where + p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. 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 @@ -2717,6 +2718,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a particular instances of akt-2 enables some instance of protein kinase activity + c enables p iff c is capable of p and c acts to execute p. Chris Mungall catalyzes executes @@ -3483,50 +3485,19 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - - p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q - Chris Mungall - directly positively regulates - - directly activates (process to process) - RO:0002406 - directly_activates - directly activates - - - - + - p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one. + p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. Chris Mungall - indirectly positively regulates + indirectly activates RO:0002407 - indirectly_activates - indirectly activates - - - - - - - - - Chris Mungall - directly negatively regulates - - directly inhibits (process to process) - RO:0002408 - directly_inhibits - directly inhibits + indirectly_positively_regulates + indirectly positively regulates @@ -3535,14 +3506,15 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + - + p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. Chris Mungall - indirectly negatively regulates + indirectly inhibits RO:0002409 - indirectly_inhibits - indirectly inhibits + indirectly_negatively_regulates + indirectly negatively regulates @@ -3550,15 +3522,14 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - This relation groups causal relations between material entities and causal relations between processes + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? - * Is the influence positive or negative + * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. @@ -3573,6 +3544,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different causally_related_to causally related to + + + + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. + https://en.wikipedia.org/wiki/Causality + @@ -3582,8 +3559,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain + p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. Chris Mungall RO:0002411 @@ -3599,8 +3575,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. + p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. Chris Mungall RO:0002412 @@ -3615,8 +3590,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c + p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit Chris Mungall @@ -3631,7 +3605,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -3653,7 +3627,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. + p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) @@ -4485,7 +4459,7 @@ For example, A and B may be gene products and binding of B by A positively regul - p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. + p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. @@ -5202,7 +5176,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + p directly regulates q iff p is immediately causally upstream of q and p regulates q. Chris Mungall directly regulates (processual) @@ -5555,7 +5529,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. + p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates (process to process) @@ -5574,7 +5548,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. + p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates (process to process) @@ -6959,7 +6933,7 @@ For example, protein A (transcription factor) indirectly increases by expression - + a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process pg 2020-06-24T13:15:17Z @@ -6973,6 +6947,7 @@ For example, protein A (transcription factor) indirectly increases by expression + a relation between a continuant and a process, in which the continuant is a small molecule that activates the process pg @@ -6987,6 +6962,7 @@ For example, protein A (transcription factor) indirectly increases by expression + a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process pg @@ -7028,6 +7004,67 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. + pg + 2022-09-26T06:01:01Z + RO:0012009 + + + constitutively_upstream_of + constitutively upstream of + + + + + + + + + p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. + pg + 2022-09-26T06:06:20Z + RO:0012010 + + + removes_input_for + removes input for + + + + + + + + + p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. + pg + 2022-09-26T06:07:17Z + RO:0012011 + indirectly_causally_upstream_of + indirectly causally upstream of + + + + + + + + + + p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. + pg + 2022-09-26T06:08:01Z + RO:0012012 + indirectly_regulates + indirectly regulates + + + + diff --git a/src/ontology/subsets/ro-chado.obo b/src/ontology/subsets/ro-chado.obo index 2f7ad1fc..749cd64f 100644 --- a/src/ontology/subsets/ro-chado.obo +++ b/src/ontology/subsets/ro-chado.obo @@ -26,7 +26,7 @@ property_value: http://purl.org/dc/elements/1.1/description "The OBO Relations O property_value: http://purl.org/dc/elements/1.1/title "OBO Relations Ontology" xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI -property_value: owl:versionInfo "2022-09-07" xsd:string +property_value: owl:versionInfo "2022-10-26" xsd:string [Typedef] id: BFO:0000050 @@ -848,7 +848,7 @@ is_a: RO:0002203 ! develops into [Typedef] id: RO:0002211 name: regulates -def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." [] +def: "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." [] holds_over_chain: RO:0002230 RO:0002211 holds_over_chain: RO:0002578 RO:0002578 is_transitive: true @@ -859,7 +859,7 @@ transitive_over: RO:0002025 ! has effector activity [Typedef] id: RO:0002212 name: negatively_regulates -def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +def: "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." [] holds_over_chain: RO:0002230 RO:0002212 is_a: RO:0002211 ! regulates is_a: RO:0002305 ! causally upstream of, negative effect @@ -868,7 +868,7 @@ inverse_of: RO:0002335 ! negatively regulated by [Typedef] id: RO:0002213 name: positively_regulates -def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +def: "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." [] holds_over_chain: RO:0002212 RO:0002212 holds_over_chain: RO:0002230 RO:0002213 is_transitive: true @@ -1282,12 +1282,14 @@ is_a: RO:0002321 ! ecologically related to [Typedef] id: RO:0002304 name: causally_upstream_of,_positive_effect +def: "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." [] is_a: RO:0002411 ! causally upstream of is_a: RO:0004047 ! causally upstream of or within, positive effect [Typedef] id: RO:0002305 name: causally_upstream_of,_negative_effect +def: "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." [] is_a: RO:0002411 ! causally upstream of is_a: RO:0004046 ! causally upstream of or within, negative effect @@ -1364,6 +1366,7 @@ is_a: RO:0002329 ! part of structure that is capable of [Typedef] id: RO:0002327 name: enables +def: "c enables p iff c is capable of p and c acts to execute p." [] is_a: RO:0002215 ! capable of inverse_of: RO:0002333 ! enabled by transitive_over: BFO:0000051 ! has part @@ -1712,44 +1715,48 @@ inverse_of: RO:0002412 ! immediately causally upstream of [Typedef] id: RO:0002406 -name: directly_activates -def: "p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q" [] -is_a: RO:0002629 ! directly positively regulates +name: obsolete_directly_activates +is_obsolete: true +replaced_by: RO:0002629 [Typedef] id: RO:0002407 -name: indirectly_activates -def: "p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one." [] -holds_over_chain: RO:0002406 RO:0002406 -holds_over_chain: RO:0002406 RO:0002407 +name: indirectly_positively_regulates +def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] holds_over_chain: RO:0002409 RO:0002409 +holds_over_chain: RO:0002629 RO:0002407 +holds_over_chain: RO:0002629 RO:0002629 is_transitive: true is_a: RO:0002213 ! positively regulates -transitive_over: RO:0002406 ! directly activates +is_a: RO:0012012 ! indirectly regulates +transitive_over: RO:0002629 ! directly positively regulates [Typedef] id: RO:0002408 -name: directly_inhibits -is_a: RO:0002630 ! directly negatively regulates +name: obsolete_directly_inhibits +is_obsolete: true +replaced_by: RO:0002630 [Typedef] id: RO:0002409 -name: indirectly_inhibits -holds_over_chain: RO:0002408 RO:0002408 -holds_over_chain: RO:0002408 RO:0002409 +name: indirectly_negatively_regulates +def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] +holds_over_chain: RO:0002630 RO:0002409 +holds_over_chain: RO:0002630 RO:0002630 is_transitive: true is_a: RO:0002212 ! negatively regulates -transitive_over: RO:0002408 ! directly inhibits +is_a: RO:0012012 ! indirectly regulates +transitive_over: RO:0002630 ! directly negatively regulates [Typedef] id: RO:0002410 name: causally_related_to -def: "This relation groups causal relations between material entities and causal relations between processes" [] +def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] [Typedef] id: RO:0002411 name: causally_upstream_of -def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" [] +def: "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." [] is_transitive: true is_a: BFO:0000063 ! precedes is_a: RO:0002418 ! causally upstream of or within @@ -1757,14 +1764,14 @@ is_a: RO:0002418 ! causally upstream of or within [Typedef] id: RO:0002412 name: immediately_causally_upstream_of -def: "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q." [] +def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] is_a: RO:0002090 ! immediately precedes is_a: RO:0002411 ! causally upstream of [Typedef] id: RO:0002413 name: directly_provides_input_for -def: "p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c" [] +def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] holds_over_chain: RO:0002402 RO:0002400 is_a: RO:0002412 ! immediately causally upstream of is_a: RO:0002414 ! transitively provides input for @@ -1774,12 +1781,12 @@ id: RO:0002414 name: transitively_provides_input_for def: "transitive form of directly_provides_input_for" [] is_transitive: true -is_a: RO:0002411 ! causally upstream of +is_a: RO:0004047 ! causally upstream of or within, positive effect [Typedef] id: RO:0002418 name: causally_upstream_of_or_within -def: "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." [] +def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] synonym: "affects" RELATED [] is_transitive: true is_a: RO:0002501 ! causal relation between processes @@ -2238,7 +2245,7 @@ inverse_of: RO:0002608 ! process has causal agent [Typedef] id: RO:0002501 name: causal_relation_between_processes -def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." [] +def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] is_a: RO:0002410 ! causally related to [Typedef] @@ -2586,7 +2593,7 @@ is_a: BFO:0000050 ! part of [Typedef] id: RO:0002578 name: directly_regulates -def: "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." [] +def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] is_a: RO:0002211 ! regulates is_a: RO:0002412 ! immediately causally upstream of @@ -2790,14 +2797,14 @@ is_a: RO:0002574 ! participates in a biotic-biotic interaction with [Typedef] id: RO:0002629 name: directly_positively_regulates -def: "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." [] +def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] is_a: RO:0002213 ! positively regulates is_a: RO:0002578 ! directly regulates [Typedef] id: RO:0002630 name: directly_negatively_regulates -def: "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." [] +def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] is_a: RO:0002212 ! negatively regulates is_a: RO:0002578 ! directly regulates @@ -3441,18 +3448,20 @@ is_a: RO:0000057 ! has participant id: RO:0012004 name: is_small_molecule_regulator_of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] -is_a: RO:0000056 ! participates in +is_a: RO:0002596 ! capable of regulating [Typedef] id: RO:0012005 name: is_small_molecule_activator_of def: "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" [] +is_a: RO:0002598 ! capable of positively regulating is_a: RO:0012004 ! is small molecule regulator of [Typedef] id: RO:0012006 name: is_small_molecule_inhibitor_of def: "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process" [] +is_a: RO:0002597 ! capable of negatively regulating is_a: RO:0012004 ! is small molecule regulator of [Typedef] @@ -3466,6 +3475,31 @@ id: RO:0012008 name: results_in_fusion_of is_a: RO:0002592 ! results in organization of +[Typedef] +id: RO:0012009 +name: constitutively_upstream_of +def: "p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant." [] +is_a: RO:0002304 ! causally upstream of, positive effect + +[Typedef] +id: RO:0012010 +name: removes_input_for +def: "p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q." [] +is_a: RO:0002305 ! causally upstream of, negative effect + +[Typedef] +id: RO:0012011 +name: indirectly_causally_upstream_of +def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] +is_a: RO:0002411 ! causally upstream of + +[Typedef] +id: RO:0012012 +name: indirectly_regulates +def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." [] +is_a: RO:0002211 ! regulates +is_a: RO:0012011 ! indirectly causally upstream of + [Typedef] id: RO:0013001 name: has_synaptic_IO_in_region diff --git a/src/ontology/subsets/ro-developmental.obo b/src/ontology/subsets/ro-developmental.obo index 9607eee9..2cb5c2fc 100644 --- a/src/ontology/subsets/ro-developmental.obo +++ b/src/ontology/subsets/ro-developmental.obo @@ -372,7 +372,7 @@ is_a: causally_related_to ! causally related to [Typedef] id: causal_relation_between_processes name: causal relation between processes -def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." [] +def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] xref: RO:0002501 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -440,21 +440,19 @@ is_a: causal_relation_between_entities ! causal relation between entities [Typedef] id: causally_related_to name: causally related to -def: "This relation groups causal relations between material entities and causal relations between processes" [] +def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] xref: RO:0002410 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string +property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string [Typedef] id: causally_upstream_of name: causally upstream of -def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" [] +def: "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002411 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within @@ -463,7 +461,9 @@ 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 +def: "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 property_value: http://purl.org/dc/terms/creator "cjm" xsd:string property_value: RO:0004050 RO:0002411 @@ -473,6 +473,7 @@ is_a: causally_upstream_of_or_within,_negative_effect ! causally upstream of or [Typedef] id: causally_upstream_of,_positive_effect name: causally upstream of, positive effect +def: "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." [] 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 subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -485,7 +486,7 @@ is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or [Typedef] id: causally_upstream_of_or_within name: causally upstream of or within -def: "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." [] +def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] synonym: "affects" RELATED [] xref: RO:0002418 property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string @@ -709,6 +710,17 @@ property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-art domain: BFO:0000004 is_a: mereotopologically_related_to ! mereotopologically related to +[Typedef] +id: constitutively_upstream_of +name: constitutively upstream of +def: "p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0012009 +is_a: causally_upstream_of,_positive_effect ! causally upstream of, positive effect +created_by: pg +creation_date: 2022-09-26T06:01:01Z + [Typedef] id: continuous_with name: continuous with @@ -993,18 +1005,6 @@ is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_develop_into ! has potential to develop into is_a: has_potential_to_directly_develop_into ! has potential to directly develop into -[Typedef] -id: directly_activates -name: directly activates -def: "p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q" [] -xref: RO:0002406 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "directly positively regulates" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly activates (process to process)" xsd:string -is_a: directly_positively_regulates ! directly positively regulates - [Typedef] id: directly_develops_from name: directly develops from @@ -1030,16 +1030,6 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "developmental precursor of" xsd:string is_a: develops_into ! develops into -[Typedef] -id: directly_inhibits -name: directly inhibits -xref: RO:0002408 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "directly negatively regulates" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly inhibits (process to process)" xsd:string -is_a: directly_negatively_regulates ! directly negatively regulates - [Typedef] id: directly_negatively_regulated_by name: directly negatively regulated by @@ -1053,7 +1043,7 @@ creation_date: 2017-09-17T13:52:38Z [Typedef] id: directly_negatively_regulates name: directly negatively regulates -def: "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." [] +def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1100,7 +1090,7 @@ creation_date: 2017-09-17T13:52:47Z [Typedef] id: directly_positively_regulates name: directly positively regulates -def: "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." [] +def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1137,9 +1127,8 @@ is_a: directly_regulates_quantity_of ! directly regulates quantity of [Typedef] id: directly_provides_input_for name: directly provides input for -def: "p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c" [] +def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] xref: RO:0002413 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -1160,7 +1149,7 @@ creation_date: 2017-09-17T13:52:24Z [Typedef] id: directly_regulates name: directly regulates -def: "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." [] +def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1416,6 +1405,7 @@ is_a: has_participant [Typedef] id: enables name: enables +def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002327 property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string @@ -2540,9 +2530,8 @@ inverse_of: immediately_causally_upstream_of ! immediately causally upstream of [Typedef] id: immediately_causally_upstream_of name: immediately causally upstream of -def: "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q." [] +def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] xref: RO:0002412 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of @@ -2616,25 +2605,24 @@ range: BFO:0000040 is_a: directly_positively_regulates_activity_of ! directly positively regulates activity of [Typedef] -id: indirectly_activates -name: indirectly activates -def: "p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one." [] -xref: RO:0002407 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "indirectly positively regulates" xsd:string -property_value: RO:0002579 RO:0002213 -is_transitive: true -is_a: positively_regulates ! positively regulates +id: indirectly_causally_upstream_of +name: indirectly causally upstream of +def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] +xref: RO:0012011 +is_a: causally_upstream_of ! causally upstream of +created_by: pg +creation_date: 2022-09-26T06:07:17Z [Typedef] -id: indirectly_inhibits -name: indirectly inhibits +id: indirectly_negatively_regulates +name: indirectly negatively regulates +def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] xref: RO:0002409 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "indirectly negatively regulates" xsd:string +property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 is_transitive: true +is_a: indirectly_regulates ! indirectly regulates is_a: negatively_regulates ! negatively regulates [Typedef] @@ -2654,6 +2642,18 @@ xref: RO:0011023 property_value: IAO:0000117 "Vasundra Touré" xsd:string is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of +[Typedef] +id: indirectly_positively_regulates +name: indirectly positively regulates +def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] +xref: RO:0002407 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "indirectly activates" xsd:string +property_value: RO:0002579 RO:0002213 +is_transitive: true +is_a: indirectly_regulates ! indirectly regulates +is_a: positively_regulates ! positively regulates + [Typedef] id: indirectly_positively_regulates_activity_of name: indirectly positively regulates activity of @@ -2673,6 +2673,16 @@ xref: RO:0011024 property_value: IAO:0000117 "Vasundra Touré" xsd:string is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of +[Typedef] +id: indirectly_regulates +name: indirectly regulates +def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." [] +xref: RO:0012012 +is_a: indirectly_causally_upstream_of ! indirectly causally upstream of +is_a: regulates ! regulates +created_by: pg +creation_date: 2022-09-26T06:08:01Z + [Typedef] id: indirectly_regulates_activity_of name: indirectly regulates activity of @@ -3012,6 +3022,7 @@ id: is_small_molecule_activator_of name: is small molecule activator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" [] xref: RO:0012005 +is_a: capable_of_positively_regulating ! capable of positively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of created_by: pg creation_date: 2020-06-24T13:15:26Z @@ -3021,6 +3032,7 @@ id: is_small_molecule_inhibitor_of name: is small molecule inhibitor of def: "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process" [] xref: RO:0012006 +is_a: capable_of_negatively_regulating ! capable of negatively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of created_by: pg creation_date: 2020-06-24T13:15:35Z @@ -3030,7 +3042,7 @@ id: is_small_molecule_regulator_of name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] xref: RO:0012004 -is_a: participates_in +is_a: capable_of_regulating ! capable of regulating created_by: pg creation_date: 2020-06-24T13:15:17Z @@ -3246,7 +3258,7 @@ is_a: regulated_by ! regulated by [Typedef] id: negatively_regulates name: negatively regulates -def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +def: "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -3513,7 +3525,7 @@ is_a: regulated_by ! regulated by [Typedef] id: positively_regulates name: positively regulates -def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +def: "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -3707,13 +3719,11 @@ is_a: causally_downstream_of_or_within ! causally downstream of or within [Typedef] id: regulates name: regulates -def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." [] +def: "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 "David Hill" xsd:string property_value: IAO:0000117 "Tanya Berardini" xsd:string @@ -3800,6 +3810,17 @@ property_value: IAO:0000232 "Do not use this relation directly. It is a grouping domain: BFO:0000015 range: BFO:0000002 +[Typedef] +id: removes_input_for +name: removes input for +def: "p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0012010 +is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect +created_by: pg +creation_date: 2022-09-26T06:06:20Z + [Typedef] id: represses_expression_of name: represses expression of @@ -4495,7 +4516,7 @@ property_value: IAO:0000589 "transitively provides input for (process to process domain: BFO:0000015 range: BFO:0000015 is_transitive: true -is_a: causally_upstream_of ! causally upstream of +is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or within, positive effect [Typedef] id: transmitted_by diff --git a/src/ontology/subsets/ro-developmental.owl b/src/ontology/subsets/ro-developmental.owl index 798d2816..b438c670 100644 --- a/src/ontology/subsets/ro-developmental.owl +++ b/src/ontology/subsets/ro-developmental.owl @@ -1644,9 +1644,7 @@ N1 SubclassOf ( - - process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. - We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit + p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. Chris Mungall David Hill Tanya Berardini @@ -1671,7 +1669,7 @@ N1 SubclassOf ( - Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. Chris Mungall negatively regulates (process to process) @@ -1693,7 +1691,7 @@ N1 SubclassOf ( - Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. Chris Mungall positively regulates (process to process) @@ -2523,6 +2521,7 @@ where + p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. cjm RO:0002304 @@ -2540,11 +2539,13 @@ where + p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. 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 @@ -2717,6 +2718,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a particular instances of akt-2 enables some instance of protein kinase activity + c enables p iff c is capable of p and c acts to execute p. Chris Mungall catalyzes executes @@ -3483,50 +3485,19 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - - p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q - Chris Mungall - directly positively regulates - - directly activates (process to process) - RO:0002406 - directly_activates - directly activates - - - - + - p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one. + p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. Chris Mungall - indirectly positively regulates + indirectly activates RO:0002407 - indirectly_activates - indirectly activates - - - - - - - - - Chris Mungall - directly negatively regulates - - directly inhibits (process to process) - RO:0002408 - directly_inhibits - directly inhibits + indirectly_positively_regulates + indirectly positively regulates @@ -3535,14 +3506,15 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + - + p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. Chris Mungall - indirectly negatively regulates + indirectly inhibits RO:0002409 - indirectly_inhibits - indirectly inhibits + indirectly_negatively_regulates + indirectly negatively regulates @@ -3550,15 +3522,14 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - This relation groups causal relations between material entities and causal relations between processes + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? - * Is the influence positive or negative + * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. @@ -3573,6 +3544,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different causally_related_to causally related to + + + + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. + https://en.wikipedia.org/wiki/Causality + @@ -3582,8 +3559,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain + p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. Chris Mungall RO:0002411 @@ -3599,8 +3575,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. + p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. Chris Mungall RO:0002412 @@ -3615,8 +3590,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c + p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit Chris Mungall @@ -3631,7 +3605,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -3653,7 +3627,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. + p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) @@ -4485,7 +4459,7 @@ For example, A and B may be gene products and binding of B by A positively regul - p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. + p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. @@ -5202,7 +5176,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + p directly regulates q iff p is immediately causally upstream of q and p regulates q. Chris Mungall directly regulates (processual) @@ -5555,7 +5529,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. + p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates (process to process) @@ -5574,7 +5548,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. + p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates (process to process) @@ -6959,7 +6933,7 @@ For example, protein A (transcription factor) indirectly increases by expression - + a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process pg 2020-06-24T13:15:17Z @@ -6973,6 +6947,7 @@ For example, protein A (transcription factor) indirectly increases by expression + a relation between a continuant and a process, in which the continuant is a small molecule that activates the process pg @@ -6987,6 +6962,7 @@ For example, protein A (transcription factor) indirectly increases by expression + a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process pg @@ -7028,6 +7004,67 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. + pg + 2022-09-26T06:01:01Z + RO:0012009 + + + constitutively_upstream_of + constitutively upstream of + + + + + + + + + p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. + pg + 2022-09-26T06:06:20Z + RO:0012010 + + + removes_input_for + removes input for + + + + + + + + + p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. + pg + 2022-09-26T06:07:17Z + RO:0012011 + indirectly_causally_upstream_of + indirectly causally upstream of + + + + + + + + + + p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. + pg + 2022-09-26T06:08:01Z + RO:0012012 + indirectly_regulates + indirectly regulates + + + + diff --git a/src/ontology/subsets/ro-eco.obo b/src/ontology/subsets/ro-eco.obo index c6c8f58a..3ac96494 100644 --- a/src/ontology/subsets/ro-eco.obo +++ b/src/ontology/subsets/ro-eco.obo @@ -7,7 +7,7 @@ subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" subsetdef: ro-eco "" subsetdef: RO:0002259 "" ontology: ro/subsets/ro-eco -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(DataProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (never in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (mutually spatially disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (taxonomic class assertion)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (ambiguous for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dubious for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (annotation property cardinality)\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: (logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on a property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an object property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an annotation property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dispositional interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has no connections with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (curator guidance link)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (always present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (measurement property has unit)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has start time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has end time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (month of gestation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has developmental stage marker)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is asymmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is symmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is direct form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indirect form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom where second argument is reflexive)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion involving identity)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (in approximate one to one relationship with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is approximately equivalent to)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is opposite of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indistinguishable from)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (evidential logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom has evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom contradicted by evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is representative IRI for equivalence set)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (nominally disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is directional form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is positive form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is negative form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is homeomorphic for)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (has skeleton)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has role in modeling)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance removed)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (immersed in)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has primary substance added)\n\nIrreflexiveObjectProperty()\n\n\n############################\n# Data Properties\n############################\n\n# Data Property: (has increased age-specific mortality rate)\n\nDataPropertyRange( DatatypeRestriction(xsd:short xsd:minInclusive \"0\"^^xsd:short xsd:maxInclusive \"100\"^^xsd:short))\n\n\n\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Annotation(rdfs:comment \"If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(DataProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (never in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (mutually spatially disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (taxonomic class assertion)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (ambiguous for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dubious for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (annotation property cardinality)\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: (logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on a property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an object property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an annotation property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dispositional interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has no connections with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (curator guidance link)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (always present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (measurement property has unit)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has start time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has end time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (month of gestation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has developmental stage marker)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is asymmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is symmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is direct form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indirect form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom where second argument is reflexive)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion involving identity)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (in approximate one to one relationship with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is approximately equivalent to)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is opposite of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indistinguishable from)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (evidential logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom has evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom contradicted by evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is representative IRI for equivalence set)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (nominally disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is directional form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is positive form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is negative form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is homeomorphic for)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (has skeleton)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has role in modeling)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance removed)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (immersed in)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has primary substance added)\n\nIrreflexiveObjectProperty()\n\n\n############################\n# Data Properties\n############################\n\n# Data Property: (has increased age-specific mortality rate)\n\nDataPropertyRange( DatatypeRestriction(xsd:short xsd:minInclusive \"0\"^^xsd:short xsd:maxInclusive \"100\"^^xsd:short))\n\n\n\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Annotation(rdfs:comment \"If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) [Typedef] id: BFO:0000050 @@ -972,12 +972,10 @@ is_a: RO:0002203 ! develops into [Typedef] id: RO:0002211 name: regulates -def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." [] +def: "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 "David Hill" xsd:string property_value: IAO:0000117 "Tanya Berardini" xsd:string @@ -996,7 +994,7 @@ transitive_over: RO:0002025 ! has effector activity [Typedef] id: RO:0002212 name: negatively regulates -def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +def: "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1012,7 +1010,7 @@ inverse_of: RO:0002335 ! negatively regulated by [Typedef] id: RO:0002213 name: positively regulates -def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +def: "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1586,6 +1584,7 @@ is_a: RO:0002321 ! ecologically related to [Typedef] id: RO:0002304 name: causally upstream of, positive effect +def: "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." [] 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 subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1597,7 +1596,9 @@ is_a: RO:0004047 ! causally upstream of or within, positive effect [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 +def: "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: http://purl.org/dc/terms/creator "cjm" xsd:string property_value: RO:0004050 RO:0002411 is_a: RO:0002411 ! causally upstream of @@ -1725,6 +1726,7 @@ is_a: RO:0002329 ! part of structure that is capable of [Typedef] id: RO:0002327 name: enables +def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2227,67 +2229,61 @@ inverse_of: RO:0002412 ! immediately causally upstream of [Typedef] id: RO:0002406 -name: directly activates -def: "p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q" [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "directly positively regulates" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly activates (process to process)" xsd:string -is_a: RO:0002629 ! directly positively regulates +name: obsolete directly activates +comment: This term was obsoleted because it has the same meaning as 'directly positively regulates'. +is_obsolete: true +replaced_by: RO:0002629 [Typedef] id: RO:0002407 -name: indirectly activates -def: "p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one." [] +name: indirectly positively regulates +def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "indirectly positively regulates" xsd:string +property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 -holds_over_chain: RO:0002406 RO:0002406 -holds_over_chain: RO:0002406 RO:0002407 holds_over_chain: RO:0002409 RO:0002409 +holds_over_chain: RO:0002629 RO:0002407 +holds_over_chain: RO:0002629 RO:0002629 is_transitive: true is_a: RO:0002213 ! positively regulates -transitive_over: RO:0002406 ! directly activates +is_a: RO:0012012 ! indirectly regulates +transitive_over: RO:0002629 ! directly positively regulates [Typedef] id: RO:0002408 -name: directly inhibits -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "directly negatively regulates" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly inhibits (process to process)" xsd:string -is_a: RO:0002630 ! directly negatively regulates +name: obsolete directly inhibits +comment: This term was obsoleted because it has the same meaning as 'directly negatively regulates'. +is_obsolete: true +replaced_by: RO:0002630 [Typedef] id: RO:0002409 -name: indirectly inhibits -property_value: IAO:0000114 IAO:0000428 +name: indirectly negatively regulates +def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "indirectly negatively regulates" xsd:string +property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 -holds_over_chain: RO:0002408 RO:0002408 -holds_over_chain: RO:0002408 RO:0002409 +holds_over_chain: RO:0002630 RO:0002409 +holds_over_chain: RO:0002630 RO:0002630 is_transitive: true is_a: RO:0002212 ! negatively regulates -transitive_over: RO:0002408 ! directly inhibits +is_a: RO:0012012 ! indirectly regulates +transitive_over: RO:0002630 ! directly negatively regulates [Typedef] id: RO:0002410 name: causally related to -def: "This relation groups causal relations between material entities and causal relations between processes" [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string +def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] +property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string [Typedef] id: RO:0002411 name: causally upstream of -def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" [] +def: "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string is_transitive: true is_a: BFO:0000063 @@ -2296,8 +2292,7 @@ is_a: RO:0002418 ! causally upstream of or within [Typedef] id: RO:0002412 name: immediately causally upstream of -def: "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q." [] -property_value: IAO:0000114 IAO:0000428 +def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: RO:0002575 RO:0002411 is_a: RO:0002090 @@ -2306,8 +2301,7 @@ is_a: RO:0002411 ! causally upstream of [Typedef] id: RO:0002413 name: directly provides input for -def: "p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c" [] -property_value: IAO:0000114 IAO:0000428 +def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -2325,12 +2319,12 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'directly provides input for' (which may later be relabeled simply to 'provides input for')" xsd:string property_value: IAO:0000589 "transitively provides input for (process to process)" xsd:string is_transitive: true -is_a: RO:0002411 ! causally upstream of +is_a: RO:0004047 ! causally upstream of or within, positive effect [Typedef] id: RO:0002418 name: causally upstream of or within -def: "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." [] +def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] synonym: "affects" RELATED [] property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2985,7 +2979,7 @@ inverse_of: RO:0002608 ! process has causal agent [Typedef] id: RO:0002501 name: causal relation between processes -def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." [] +def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string @@ -3507,7 +3501,7 @@ is_a: BFO:0000050 [Typedef] id: RO:0002578 name: directly regulates -def: "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." [] +def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -3751,7 +3745,7 @@ is_a: RO:0002574 ! participates in a biotic-biotic interaction with [Typedef] id: RO:0002629 name: directly positively regulates -def: "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." [] +def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -3764,7 +3758,7 @@ is_a: RO:0002578 ! directly regulates [Typedef] id: RO:0002630 name: directly negatively regulates -def: "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." [] +def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -4610,6 +4604,7 @@ creation_date: 2020-06-08T17:21:33Z id: RO:0012004 name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] +is_a: RO:0002596 ! capable of regulating created_by: pg creation_date: 2020-06-24T13:15:17Z @@ -4617,6 +4612,7 @@ creation_date: 2020-06-24T13:15:17Z id: RO:0012005 name: is small molecule activator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" [] +is_a: RO:0002598 ! capable of positively regulating is_a: RO:0012004 ! is small molecule regulator of created_by: pg creation_date: 2020-06-24T13:15:26Z @@ -4625,6 +4621,7 @@ creation_date: 2020-06-24T13:15:26Z id: RO:0012006 name: is small molecule inhibitor of def: "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process" [] +is_a: RO:0002597 ! capable of negatively regulating is_a: RO:0012004 ! is small molecule regulator of created_by: pg creation_date: 2020-06-24T13:15:35Z @@ -4647,6 +4644,43 @@ is_a: RO:0002592 ! results in organization of created_by: pg creation_date: 2021-02-26T07:28:29Z +[Typedef] +id: RO:0012009 +name: constitutively upstream of +def: "p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +is_a: RO:0002304 ! causally upstream of, positive effect +created_by: pg +creation_date: 2022-09-26T06:01:01Z + +[Typedef] +id: RO:0012010 +name: removes input for +def: "p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +is_a: RO:0002305 ! causally upstream of, negative effect +created_by: pg +creation_date: 2022-09-26T06:06:20Z + +[Typedef] +id: RO:0012011 +name: indirectly causally upstream of +def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] +is_a: RO:0002411 ! causally upstream of +created_by: pg +creation_date: 2022-09-26T06:07:17Z + +[Typedef] +id: RO:0012012 +name: indirectly regulates +def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." [] +is_a: RO:0002211 ! regulates +is_a: RO:0012011 ! indirectly causally upstream of +created_by: pg +creation_date: 2022-09-26T06:08:01Z + [Typedef] id: RO:0013001 name: has synaptic IO in region diff --git a/src/ontology/subsets/ro-eco.owl b/src/ontology/subsets/ro-eco.owl index 2656244c..02fcc1d3 100644 --- a/src/ontology/subsets/ro-eco.owl +++ b/src/ontology/subsets/ro-eco.owl @@ -2698,9 +2698,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. - We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit + p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. Chris Mungall David Hill Tanya Berardini @@ -2727,7 +2725,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. Chris Mungall negatively regulates (process to process) @@ -2755,7 +2753,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. Chris Mungall positively regulates (process to process) @@ -3616,6 +3614,7 @@ where + p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. cjm @@ -3631,9 +3630,11 @@ where + p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. 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 @@ -3833,6 +3834,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a particular instances of akt-2 enables some instance of protein kinase activity + c enables p iff c is capable of p and c acts to execute p. Chris Mungall catalyzes executes @@ -4585,14 +4587,10 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - - - p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q - Chris Mungall - directly positively regulates - - directly activates (process to process) - directly activates + + This term was obsoleted because it has the same meaning as 'directly positively regulates'. + obsolete directly activates + true @@ -4601,28 +4599,29 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ + - - + + - - + + + - - - + + - p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one. + p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. Chris Mungall - indirectly positively regulates + indirectly activates - indirectly activates + indirectly positively regulates @@ -4630,12 +4629,10 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - - Chris Mungall - directly negatively regulates - - directly inhibits (process to process) - directly inhibits + + This term was obsoleted because it has the same meaning as 'directly negatively regulates'. + obsolete directly inhibits + true @@ -4644,24 +4641,25 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ + - - + + - + - - + + - + p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. Chris Mungall - indirectly negatively regulates + indirectly inhibits - indirectly inhibits + indirectly negatively regulates @@ -4669,15 +4667,14 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - - This relation groups causal relations between material entities and causal relations between processes + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? - * Is the influence positive or negative + * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. @@ -4690,6 +4687,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to + + + + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. + https://en.wikipedia.org/wiki/Causality + @@ -4699,8 +4702,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain + p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. Chris Mungall @@ -4714,8 +4716,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. + p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. Chris Mungall immediately causally upstream of @@ -4732,8 +4733,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c + p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit Chris Mungall @@ -4746,7 +4746,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + transitive form of directly_provides_input_for @@ -4764,7 +4764,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. + p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) @@ -5876,7 +5876,7 @@ the a supports either the existence of b, or the truth value of b. - p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. + p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. @@ -6639,7 +6639,7 @@ the a supports either the existence of b, or the truth value of b. - Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + p directly regulates q iff p is immediately causally upstream of q and p regulates q. Chris Mungall directly regulates (processual) @@ -7037,7 +7037,7 @@ the a supports either the existence of b, or the truth value of b. - Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. + p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates (process to process) @@ -7054,7 +7054,7 @@ the a supports either the existence of b, or the truth value of b. - Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. + p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates (process to process) @@ -8379,6 +8379,7 @@ For example, protein A (transcription factor) indirectly increases by expression + a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process pg 2020-06-24T13:15:17Z @@ -8390,6 +8391,7 @@ For example, protein A (transcription factor) indirectly increases by expression + a relation between a continuant and a process, in which the continuant is a small molecule that activates the process pg @@ -8402,6 +8404,7 @@ For example, protein A (transcription factor) indirectly increases by expression + a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process pg @@ -8437,6 +8440,59 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. + pg + 2022-09-26T06:01:01Z + + + constitutively upstream of + + + + + + + + + p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. + pg + 2022-09-26T06:06:20Z + + + removes input for + + + + + + + + + p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. + pg + 2022-09-26T06:07:17Z + indirectly causally upstream of + + + + + + + + + + p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. + pg + 2022-09-26T06:08:01Z + indirectly regulates + + + + @@ -9093,6 +9149,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -9111,6 +9173,9 @@ For example, protein A (transcription factor) indirectly increases by expression + + + If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. inferring direct reg edge from input to regulatory subfunction @@ -9511,6 +9576,50 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -9687,6 +9796,50 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/subsets/ro-interaction.obo b/src/ontology/subsets/ro-interaction.obo index 0f0e9a4c..6bb60283 100644 --- a/src/ontology/subsets/ro-interaction.obo +++ b/src/ontology/subsets/ro-interaction.obo @@ -372,7 +372,7 @@ is_a: causally_related_to ! causally related to [Typedef] id: causal_relation_between_processes name: causal relation between processes -def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." [] +def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] xref: RO:0002501 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -440,21 +440,19 @@ is_a: causal_relation_between_entities ! causal relation between entities [Typedef] id: causally_related_to name: causally related to -def: "This relation groups causal relations between material entities and causal relations between processes" [] +def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] xref: RO:0002410 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string +property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string [Typedef] id: causally_upstream_of name: causally upstream of -def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" [] +def: "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002411 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within @@ -463,7 +461,9 @@ 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 +def: "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 property_value: http://purl.org/dc/terms/creator "cjm" xsd:string property_value: RO:0004050 RO:0002411 @@ -473,6 +473,7 @@ is_a: causally_upstream_of_or_within,_negative_effect ! causally upstream of or [Typedef] id: causally_upstream_of,_positive_effect name: causally upstream of, positive effect +def: "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." [] 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 subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -485,7 +486,7 @@ is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or [Typedef] id: causally_upstream_of_or_within name: causally upstream of or within -def: "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." [] +def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] synonym: "affects" RELATED [] xref: RO:0002418 property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string @@ -709,6 +710,17 @@ property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-art domain: BFO:0000004 is_a: mereotopologically_related_to ! mereotopologically related to +[Typedef] +id: constitutively_upstream_of +name: constitutively upstream of +def: "p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0012009 +is_a: causally_upstream_of,_positive_effect ! causally upstream of, positive effect +created_by: pg +creation_date: 2022-09-26T06:01:01Z + [Typedef] id: continuous_with name: continuous with @@ -993,18 +1005,6 @@ is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_develop_into ! has potential to develop into is_a: has_potential_to_directly_develop_into ! has potential to directly develop into -[Typedef] -id: directly_activates -name: directly activates -def: "p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q" [] -xref: RO:0002406 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "directly positively regulates" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly activates (process to process)" xsd:string -is_a: directly_positively_regulates ! directly positively regulates - [Typedef] id: directly_develops_from name: directly develops from @@ -1030,16 +1030,6 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "developmental precursor of" xsd:string is_a: develops_into ! develops into -[Typedef] -id: directly_inhibits -name: directly inhibits -xref: RO:0002408 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "directly negatively regulates" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly inhibits (process to process)" xsd:string -is_a: directly_negatively_regulates ! directly negatively regulates - [Typedef] id: directly_negatively_regulated_by name: directly negatively regulated by @@ -1053,7 +1043,7 @@ creation_date: 2017-09-17T13:52:38Z [Typedef] id: directly_negatively_regulates name: directly negatively regulates -def: "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." [] +def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1100,7 +1090,7 @@ creation_date: 2017-09-17T13:52:47Z [Typedef] id: directly_positively_regulates name: directly positively regulates -def: "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." [] +def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1137,9 +1127,8 @@ is_a: directly_regulates_quantity_of ! directly regulates quantity of [Typedef] id: directly_provides_input_for name: directly provides input for -def: "p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c" [] +def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] xref: RO:0002413 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -1160,7 +1149,7 @@ creation_date: 2017-09-17T13:52:24Z [Typedef] id: directly_regulates name: directly regulates -def: "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." [] +def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1416,6 +1405,7 @@ is_a: has_participant [Typedef] id: enables name: enables +def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002327 property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string @@ -2540,9 +2530,8 @@ inverse_of: immediately_causally_upstream_of ! immediately causally upstream of [Typedef] id: immediately_causally_upstream_of name: immediately causally upstream of -def: "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q." [] +def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] xref: RO:0002412 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of @@ -2616,25 +2605,24 @@ range: BFO:0000040 is_a: directly_positively_regulates_activity_of ! directly positively regulates activity of [Typedef] -id: indirectly_activates -name: indirectly activates -def: "p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one." [] -xref: RO:0002407 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "indirectly positively regulates" xsd:string -property_value: RO:0002579 RO:0002213 -is_transitive: true -is_a: positively_regulates ! positively regulates +id: indirectly_causally_upstream_of +name: indirectly causally upstream of +def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] +xref: RO:0012011 +is_a: causally_upstream_of ! causally upstream of +created_by: pg +creation_date: 2022-09-26T06:07:17Z [Typedef] -id: indirectly_inhibits -name: indirectly inhibits +id: indirectly_negatively_regulates +name: indirectly negatively regulates +def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] xref: RO:0002409 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "indirectly negatively regulates" xsd:string +property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 is_transitive: true +is_a: indirectly_regulates ! indirectly regulates is_a: negatively_regulates ! negatively regulates [Typedef] @@ -2654,6 +2642,18 @@ xref: RO:0011023 property_value: IAO:0000117 "Vasundra Touré" xsd:string is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of +[Typedef] +id: indirectly_positively_regulates +name: indirectly positively regulates +def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] +xref: RO:0002407 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "indirectly activates" xsd:string +property_value: RO:0002579 RO:0002213 +is_transitive: true +is_a: indirectly_regulates ! indirectly regulates +is_a: positively_regulates ! positively regulates + [Typedef] id: indirectly_positively_regulates_activity_of name: indirectly positively regulates activity of @@ -2673,6 +2673,16 @@ xref: RO:0011024 property_value: IAO:0000117 "Vasundra Touré" xsd:string is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of +[Typedef] +id: indirectly_regulates +name: indirectly regulates +def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." [] +xref: RO:0012012 +is_a: indirectly_causally_upstream_of ! indirectly causally upstream of +is_a: regulates ! regulates +created_by: pg +creation_date: 2022-09-26T06:08:01Z + [Typedef] id: indirectly_regulates_activity_of name: indirectly regulates activity of @@ -3012,6 +3022,7 @@ id: is_small_molecule_activator_of name: is small molecule activator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" [] xref: RO:0012005 +is_a: capable_of_positively_regulating ! capable of positively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of created_by: pg creation_date: 2020-06-24T13:15:26Z @@ -3021,6 +3032,7 @@ id: is_small_molecule_inhibitor_of name: is small molecule inhibitor of def: "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process" [] xref: RO:0012006 +is_a: capable_of_negatively_regulating ! capable of negatively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of created_by: pg creation_date: 2020-06-24T13:15:35Z @@ -3030,7 +3042,7 @@ id: is_small_molecule_regulator_of name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] xref: RO:0012004 -is_a: participates_in +is_a: capable_of_regulating ! capable of regulating created_by: pg creation_date: 2020-06-24T13:15:17Z @@ -3246,7 +3258,7 @@ is_a: regulated_by ! regulated by [Typedef] id: negatively_regulates name: negatively regulates -def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +def: "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -3513,7 +3525,7 @@ is_a: regulated_by ! regulated by [Typedef] id: positively_regulates name: positively regulates -def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +def: "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -3707,13 +3719,11 @@ is_a: causally_downstream_of_or_within ! causally downstream of or within [Typedef] id: regulates name: regulates -def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." [] +def: "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 "David Hill" xsd:string property_value: IAO:0000117 "Tanya Berardini" xsd:string @@ -3800,6 +3810,17 @@ property_value: IAO:0000232 "Do not use this relation directly. It is a grouping domain: BFO:0000015 range: BFO:0000002 +[Typedef] +id: removes_input_for +name: removes input for +def: "p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0012010 +is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect +created_by: pg +creation_date: 2022-09-26T06:06:20Z + [Typedef] id: represses_expression_of name: represses expression of @@ -4495,7 +4516,7 @@ property_value: IAO:0000589 "transitively provides input for (process to process domain: BFO:0000015 range: BFO:0000015 is_transitive: true -is_a: causally_upstream_of ! causally upstream of +is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or within, positive effect [Typedef] id: transmitted_by diff --git a/src/ontology/subsets/ro-interaction.owl b/src/ontology/subsets/ro-interaction.owl index 8988ceb4..95d81d07 100644 --- a/src/ontology/subsets/ro-interaction.owl +++ b/src/ontology/subsets/ro-interaction.owl @@ -1644,9 +1644,7 @@ N1 SubclassOf ( - - process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. - We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit + p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. Chris Mungall David Hill Tanya Berardini @@ -1671,7 +1669,7 @@ N1 SubclassOf ( - Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. Chris Mungall negatively regulates (process to process) @@ -1693,7 +1691,7 @@ N1 SubclassOf ( - Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. Chris Mungall positively regulates (process to process) @@ -2523,6 +2521,7 @@ where + p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. cjm RO:0002304 @@ -2540,11 +2539,13 @@ where + p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. 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 @@ -2717,6 +2718,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a particular instances of akt-2 enables some instance of protein kinase activity + c enables p iff c is capable of p and c acts to execute p. Chris Mungall catalyzes executes @@ -3483,50 +3485,19 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - - p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q - Chris Mungall - directly positively regulates - - directly activates (process to process) - RO:0002406 - directly_activates - directly activates - - - - + - p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one. + p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. Chris Mungall - indirectly positively regulates + indirectly activates RO:0002407 - indirectly_activates - indirectly activates - - - - - - - - - Chris Mungall - directly negatively regulates - - directly inhibits (process to process) - RO:0002408 - directly_inhibits - directly inhibits + indirectly_positively_regulates + indirectly positively regulates @@ -3535,14 +3506,15 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + - + p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. Chris Mungall - indirectly negatively regulates + indirectly inhibits RO:0002409 - indirectly_inhibits - indirectly inhibits + indirectly_negatively_regulates + indirectly negatively regulates @@ -3550,15 +3522,14 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - This relation groups causal relations between material entities and causal relations between processes + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? - * Is the influence positive or negative + * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. @@ -3573,6 +3544,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different causally_related_to causally related to + + + + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. + https://en.wikipedia.org/wiki/Causality + @@ -3582,8 +3559,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain + p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. Chris Mungall RO:0002411 @@ -3599,8 +3575,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. + p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. Chris Mungall RO:0002412 @@ -3615,8 +3590,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c + p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit Chris Mungall @@ -3631,7 +3605,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -3653,7 +3627,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. + p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) @@ -4485,7 +4459,7 @@ For example, A and B may be gene products and binding of B by A positively regul - p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. + p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. @@ -5202,7 +5176,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + p directly regulates q iff p is immediately causally upstream of q and p regulates q. Chris Mungall directly regulates (processual) @@ -5555,7 +5529,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. + p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates (process to process) @@ -5574,7 +5548,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. + p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates (process to process) @@ -6959,7 +6933,7 @@ For example, protein A (transcription factor) indirectly increases by expression - + a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process pg 2020-06-24T13:15:17Z @@ -6973,6 +6947,7 @@ For example, protein A (transcription factor) indirectly increases by expression + a relation between a continuant and a process, in which the continuant is a small molecule that activates the process pg @@ -6987,6 +6962,7 @@ For example, protein A (transcription factor) indirectly increases by expression + a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process pg @@ -7028,6 +7004,67 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. + pg + 2022-09-26T06:01:01Z + RO:0012009 + + + constitutively_upstream_of + constitutively upstream of + + + + + + + + + p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. + pg + 2022-09-26T06:06:20Z + RO:0012010 + + + removes_input_for + removes input for + + + + + + + + + p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. + pg + 2022-09-26T06:07:17Z + RO:0012011 + indirectly_causally_upstream_of + indirectly causally upstream of + + + + + + + + + + p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. + pg + 2022-09-26T06:08:01Z + RO:0012012 + indirectly_regulates + indirectly regulates + + + + diff --git a/src/ontology/subsets/ro-mereotopology.obo b/src/ontology/subsets/ro-mereotopology.obo index e02dede5..d2b65cd6 100644 --- a/src/ontology/subsets/ro-mereotopology.obo +++ b/src/ontology/subsets/ro-mereotopology.obo @@ -372,7 +372,7 @@ is_a: causally_related_to ! causally related to [Typedef] id: causal_relation_between_processes name: causal relation between processes -def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." [] +def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] xref: RO:0002501 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -440,21 +440,19 @@ is_a: causal_relation_between_entities ! causal relation between entities [Typedef] id: causally_related_to name: causally related to -def: "This relation groups causal relations between material entities and causal relations between processes" [] +def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] xref: RO:0002410 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string +property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string [Typedef] id: causally_upstream_of name: causally upstream of -def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" [] +def: "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002411 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within @@ -463,7 +461,9 @@ 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 +def: "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 property_value: http://purl.org/dc/terms/creator "cjm" xsd:string property_value: RO:0004050 RO:0002411 @@ -473,6 +473,7 @@ is_a: causally_upstream_of_or_within,_negative_effect ! causally upstream of or [Typedef] id: causally_upstream_of,_positive_effect name: causally upstream of, positive effect +def: "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." [] 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 subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -485,7 +486,7 @@ is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or [Typedef] id: causally_upstream_of_or_within name: causally upstream of or within -def: "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." [] +def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] synonym: "affects" RELATED [] xref: RO:0002418 property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string @@ -709,6 +710,17 @@ property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-art domain: BFO:0000004 is_a: mereotopologically_related_to ! mereotopologically related to +[Typedef] +id: constitutively_upstream_of +name: constitutively upstream of +def: "p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0012009 +is_a: causally_upstream_of,_positive_effect ! causally upstream of, positive effect +created_by: pg +creation_date: 2022-09-26T06:01:01Z + [Typedef] id: continuous_with name: continuous with @@ -993,18 +1005,6 @@ is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_develop_into ! has potential to develop into is_a: has_potential_to_directly_develop_into ! has potential to directly develop into -[Typedef] -id: directly_activates -name: directly activates -def: "p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q" [] -xref: RO:0002406 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "directly positively regulates" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly activates (process to process)" xsd:string -is_a: directly_positively_regulates ! directly positively regulates - [Typedef] id: directly_develops_from name: directly develops from @@ -1030,16 +1030,6 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "developmental precursor of" xsd:string is_a: develops_into ! develops into -[Typedef] -id: directly_inhibits -name: directly inhibits -xref: RO:0002408 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "directly negatively regulates" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly inhibits (process to process)" xsd:string -is_a: directly_negatively_regulates ! directly negatively regulates - [Typedef] id: directly_negatively_regulated_by name: directly negatively regulated by @@ -1053,7 +1043,7 @@ creation_date: 2017-09-17T13:52:38Z [Typedef] id: directly_negatively_regulates name: directly negatively regulates -def: "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." [] +def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1100,7 +1090,7 @@ creation_date: 2017-09-17T13:52:47Z [Typedef] id: directly_positively_regulates name: directly positively regulates -def: "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." [] +def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1137,9 +1127,8 @@ is_a: directly_regulates_quantity_of ! directly regulates quantity of [Typedef] id: directly_provides_input_for name: directly provides input for -def: "p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c" [] +def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] xref: RO:0002413 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -1160,7 +1149,7 @@ creation_date: 2017-09-17T13:52:24Z [Typedef] id: directly_regulates name: directly regulates -def: "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." [] +def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1416,6 +1405,7 @@ is_a: has_participant [Typedef] id: enables name: enables +def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002327 property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string @@ -2540,9 +2530,8 @@ inverse_of: immediately_causally_upstream_of ! immediately causally upstream of [Typedef] id: immediately_causally_upstream_of name: immediately causally upstream of -def: "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q." [] +def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] xref: RO:0002412 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of @@ -2616,25 +2605,24 @@ range: BFO:0000040 is_a: directly_positively_regulates_activity_of ! directly positively regulates activity of [Typedef] -id: indirectly_activates -name: indirectly activates -def: "p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one." [] -xref: RO:0002407 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "indirectly positively regulates" xsd:string -property_value: RO:0002579 RO:0002213 -is_transitive: true -is_a: positively_regulates ! positively regulates +id: indirectly_causally_upstream_of +name: indirectly causally upstream of +def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] +xref: RO:0012011 +is_a: causally_upstream_of ! causally upstream of +created_by: pg +creation_date: 2022-09-26T06:07:17Z [Typedef] -id: indirectly_inhibits -name: indirectly inhibits +id: indirectly_negatively_regulates +name: indirectly negatively regulates +def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] xref: RO:0002409 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "indirectly negatively regulates" xsd:string +property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 is_transitive: true +is_a: indirectly_regulates ! indirectly regulates is_a: negatively_regulates ! negatively regulates [Typedef] @@ -2654,6 +2642,18 @@ xref: RO:0011023 property_value: IAO:0000117 "Vasundra Touré" xsd:string is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of +[Typedef] +id: indirectly_positively_regulates +name: indirectly positively regulates +def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] +xref: RO:0002407 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "indirectly activates" xsd:string +property_value: RO:0002579 RO:0002213 +is_transitive: true +is_a: indirectly_regulates ! indirectly regulates +is_a: positively_regulates ! positively regulates + [Typedef] id: indirectly_positively_regulates_activity_of name: indirectly positively regulates activity of @@ -2673,6 +2673,16 @@ xref: RO:0011024 property_value: IAO:0000117 "Vasundra Touré" xsd:string is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of +[Typedef] +id: indirectly_regulates +name: indirectly regulates +def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." [] +xref: RO:0012012 +is_a: indirectly_causally_upstream_of ! indirectly causally upstream of +is_a: regulates ! regulates +created_by: pg +creation_date: 2022-09-26T06:08:01Z + [Typedef] id: indirectly_regulates_activity_of name: indirectly regulates activity of @@ -3012,6 +3022,7 @@ id: is_small_molecule_activator_of name: is small molecule activator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" [] xref: RO:0012005 +is_a: capable_of_positively_regulating ! capable of positively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of created_by: pg creation_date: 2020-06-24T13:15:26Z @@ -3021,6 +3032,7 @@ id: is_small_molecule_inhibitor_of name: is small molecule inhibitor of def: "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process" [] xref: RO:0012006 +is_a: capable_of_negatively_regulating ! capable of negatively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of created_by: pg creation_date: 2020-06-24T13:15:35Z @@ -3030,7 +3042,7 @@ id: is_small_molecule_regulator_of name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] xref: RO:0012004 -is_a: participates_in +is_a: capable_of_regulating ! capable of regulating created_by: pg creation_date: 2020-06-24T13:15:17Z @@ -3246,7 +3258,7 @@ is_a: regulated_by ! regulated by [Typedef] id: negatively_regulates name: negatively regulates -def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +def: "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -3513,7 +3525,7 @@ is_a: regulated_by ! regulated by [Typedef] id: positively_regulates name: positively regulates -def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +def: "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -3707,13 +3719,11 @@ is_a: causally_downstream_of_or_within ! causally downstream of or within [Typedef] id: regulates name: regulates -def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." [] +def: "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 "David Hill" xsd:string property_value: IAO:0000117 "Tanya Berardini" xsd:string @@ -3800,6 +3810,17 @@ property_value: IAO:0000232 "Do not use this relation directly. It is a grouping domain: BFO:0000015 range: BFO:0000002 +[Typedef] +id: removes_input_for +name: removes input for +def: "p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0012010 +is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect +created_by: pg +creation_date: 2022-09-26T06:06:20Z + [Typedef] id: represses_expression_of name: represses expression of @@ -4495,7 +4516,7 @@ property_value: IAO:0000589 "transitively provides input for (process to process domain: BFO:0000015 range: BFO:0000015 is_transitive: true -is_a: causally_upstream_of ! causally upstream of +is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or within, positive effect [Typedef] id: transmitted_by diff --git a/src/ontology/subsets/ro-mereotopology.owl b/src/ontology/subsets/ro-mereotopology.owl index 54ce1ebb..51a49e7d 100644 --- a/src/ontology/subsets/ro-mereotopology.owl +++ b/src/ontology/subsets/ro-mereotopology.owl @@ -1644,9 +1644,7 @@ N1 SubclassOf ( - - process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. - We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit + p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. Chris Mungall David Hill Tanya Berardini @@ -1671,7 +1669,7 @@ N1 SubclassOf ( - Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. Chris Mungall negatively regulates (process to process) @@ -1693,7 +1691,7 @@ N1 SubclassOf ( - Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. Chris Mungall positively regulates (process to process) @@ -2523,6 +2521,7 @@ where + p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. cjm RO:0002304 @@ -2540,11 +2539,13 @@ where + p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. 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 @@ -2717,6 +2718,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a particular instances of akt-2 enables some instance of protein kinase activity + c enables p iff c is capable of p and c acts to execute p. Chris Mungall catalyzes executes @@ -3483,50 +3485,19 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - - p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q - Chris Mungall - directly positively regulates - - directly activates (process to process) - RO:0002406 - directly_activates - directly activates - - - - + - p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one. + p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. Chris Mungall - indirectly positively regulates + indirectly activates RO:0002407 - indirectly_activates - indirectly activates - - - - - - - - - Chris Mungall - directly negatively regulates - - directly inhibits (process to process) - RO:0002408 - directly_inhibits - directly inhibits + indirectly_positively_regulates + indirectly positively regulates @@ -3535,14 +3506,15 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + - + p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. Chris Mungall - indirectly negatively regulates + indirectly inhibits RO:0002409 - indirectly_inhibits - indirectly inhibits + indirectly_negatively_regulates + indirectly negatively regulates @@ -3550,15 +3522,14 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - This relation groups causal relations between material entities and causal relations between processes + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? - * Is the influence positive or negative + * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. @@ -3573,6 +3544,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different causally_related_to causally related to + + + + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. + https://en.wikipedia.org/wiki/Causality + @@ -3582,8 +3559,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain + p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. Chris Mungall RO:0002411 @@ -3599,8 +3575,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. + p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. Chris Mungall RO:0002412 @@ -3615,8 +3590,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c + p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit Chris Mungall @@ -3631,7 +3605,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -3653,7 +3627,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. + p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) @@ -4485,7 +4459,7 @@ For example, A and B may be gene products and binding of B by A positively regul - p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. + p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. @@ -5202,7 +5176,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + p directly regulates q iff p is immediately causally upstream of q and p regulates q. Chris Mungall directly regulates (processual) @@ -5555,7 +5529,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. + p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates (process to process) @@ -5574,7 +5548,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. + p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates (process to process) @@ -6959,7 +6933,7 @@ For example, protein A (transcription factor) indirectly increases by expression - + a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process pg 2020-06-24T13:15:17Z @@ -6973,6 +6947,7 @@ For example, protein A (transcription factor) indirectly increases by expression + a relation between a continuant and a process, in which the continuant is a small molecule that activates the process pg @@ -6987,6 +6962,7 @@ For example, protein A (transcription factor) indirectly increases by expression + a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process pg @@ -7028,6 +7004,67 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. + pg + 2022-09-26T06:01:01Z + RO:0012009 + + + constitutively_upstream_of + constitutively upstream of + + + + + + + + + p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. + pg + 2022-09-26T06:06:20Z + RO:0012010 + + + removes_input_for + removes input for + + + + + + + + + p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. + pg + 2022-09-26T06:07:17Z + RO:0012011 + indirectly_causally_upstream_of + indirectly causally upstream of + + + + + + + + + + p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. + pg + 2022-09-26T06:08:01Z + RO:0012012 + indirectly_regulates + indirectly regulates + + + + diff --git a/src/ontology/subsets/ro-sequence.obo b/src/ontology/subsets/ro-sequence.obo index 2d81dc8d..62bf49b1 100644 --- a/src/ontology/subsets/ro-sequence.obo +++ b/src/ontology/subsets/ro-sequence.obo @@ -372,7 +372,7 @@ is_a: causally_related_to ! causally related to [Typedef] id: causal_relation_between_processes name: causal relation between processes -def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." [] +def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] xref: RO:0002501 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -440,21 +440,19 @@ is_a: causal_relation_between_entities ! causal relation between entities [Typedef] id: causally_related_to name: causally related to -def: "This relation groups causal relations between material entities and causal relations between processes" [] +def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] xref: RO:0002410 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string +property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string [Typedef] id: causally_upstream_of name: causally upstream of -def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" [] +def: "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002411 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within @@ -463,7 +461,9 @@ 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 +def: "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 property_value: http://purl.org/dc/terms/creator "cjm" xsd:string property_value: RO:0004050 RO:0002411 @@ -473,6 +473,7 @@ is_a: causally_upstream_of_or_within,_negative_effect ! causally upstream of or [Typedef] id: causally_upstream_of,_positive_effect name: causally upstream of, positive effect +def: "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." [] 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 subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -485,7 +486,7 @@ is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or [Typedef] id: causally_upstream_of_or_within name: causally upstream of or within -def: "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." [] +def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] synonym: "affects" RELATED [] xref: RO:0002418 property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string @@ -709,6 +710,17 @@ property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-art domain: BFO:0000004 is_a: mereotopologically_related_to ! mereotopologically related to +[Typedef] +id: constitutively_upstream_of +name: constitutively upstream of +def: "p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0012009 +is_a: causally_upstream_of,_positive_effect ! causally upstream of, positive effect +created_by: pg +creation_date: 2022-09-26T06:01:01Z + [Typedef] id: continuous_with name: continuous with @@ -993,18 +1005,6 @@ is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_develop_into ! has potential to develop into is_a: has_potential_to_directly_develop_into ! has potential to directly develop into -[Typedef] -id: directly_activates -name: directly activates -def: "p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q" [] -xref: RO:0002406 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "directly positively regulates" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly activates (process to process)" xsd:string -is_a: directly_positively_regulates ! directly positively regulates - [Typedef] id: directly_develops_from name: directly develops from @@ -1030,16 +1030,6 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "developmental precursor of" xsd:string is_a: develops_into ! develops into -[Typedef] -id: directly_inhibits -name: directly inhibits -xref: RO:0002408 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "directly negatively regulates" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly inhibits (process to process)" xsd:string -is_a: directly_negatively_regulates ! directly negatively regulates - [Typedef] id: directly_negatively_regulated_by name: directly negatively regulated by @@ -1053,7 +1043,7 @@ creation_date: 2017-09-17T13:52:38Z [Typedef] id: directly_negatively_regulates name: directly negatively regulates -def: "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." [] +def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1100,7 +1090,7 @@ creation_date: 2017-09-17T13:52:47Z [Typedef] id: directly_positively_regulates name: directly positively regulates -def: "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." [] +def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1137,9 +1127,8 @@ is_a: directly_regulates_quantity_of ! directly regulates quantity of [Typedef] id: directly_provides_input_for name: directly provides input for -def: "p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c" [] +def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] xref: RO:0002413 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -1160,7 +1149,7 @@ creation_date: 2017-09-17T13:52:24Z [Typedef] id: directly_regulates name: directly regulates -def: "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." [] +def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1416,6 +1405,7 @@ is_a: has_participant [Typedef] id: enables name: enables +def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002327 property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string @@ -2540,9 +2530,8 @@ inverse_of: immediately_causally_upstream_of ! immediately causally upstream of [Typedef] id: immediately_causally_upstream_of name: immediately causally upstream of -def: "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q." [] +def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] xref: RO:0002412 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of @@ -2616,25 +2605,24 @@ range: BFO:0000040 is_a: directly_positively_regulates_activity_of ! directly positively regulates activity of [Typedef] -id: indirectly_activates -name: indirectly activates -def: "p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one." [] -xref: RO:0002407 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "indirectly positively regulates" xsd:string -property_value: RO:0002579 RO:0002213 -is_transitive: true -is_a: positively_regulates ! positively regulates +id: indirectly_causally_upstream_of +name: indirectly causally upstream of +def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] +xref: RO:0012011 +is_a: causally_upstream_of ! causally upstream of +created_by: pg +creation_date: 2022-09-26T06:07:17Z [Typedef] -id: indirectly_inhibits -name: indirectly inhibits +id: indirectly_negatively_regulates +name: indirectly negatively regulates +def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] xref: RO:0002409 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "indirectly negatively regulates" xsd:string +property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 is_transitive: true +is_a: indirectly_regulates ! indirectly regulates is_a: negatively_regulates ! negatively regulates [Typedef] @@ -2654,6 +2642,18 @@ xref: RO:0011023 property_value: IAO:0000117 "Vasundra Touré" xsd:string is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of +[Typedef] +id: indirectly_positively_regulates +name: indirectly positively regulates +def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] +xref: RO:0002407 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "indirectly activates" xsd:string +property_value: RO:0002579 RO:0002213 +is_transitive: true +is_a: indirectly_regulates ! indirectly regulates +is_a: positively_regulates ! positively regulates + [Typedef] id: indirectly_positively_regulates_activity_of name: indirectly positively regulates activity of @@ -2673,6 +2673,16 @@ xref: RO:0011024 property_value: IAO:0000117 "Vasundra Touré" xsd:string is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of +[Typedef] +id: indirectly_regulates +name: indirectly regulates +def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." [] +xref: RO:0012012 +is_a: indirectly_causally_upstream_of ! indirectly causally upstream of +is_a: regulates ! regulates +created_by: pg +creation_date: 2022-09-26T06:08:01Z + [Typedef] id: indirectly_regulates_activity_of name: indirectly regulates activity of @@ -3012,6 +3022,7 @@ id: is_small_molecule_activator_of name: is small molecule activator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" [] xref: RO:0012005 +is_a: capable_of_positively_regulating ! capable of positively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of created_by: pg creation_date: 2020-06-24T13:15:26Z @@ -3021,6 +3032,7 @@ id: is_small_molecule_inhibitor_of name: is small molecule inhibitor of def: "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process" [] xref: RO:0012006 +is_a: capable_of_negatively_regulating ! capable of negatively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of created_by: pg creation_date: 2020-06-24T13:15:35Z @@ -3030,7 +3042,7 @@ id: is_small_molecule_regulator_of name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] xref: RO:0012004 -is_a: participates_in +is_a: capable_of_regulating ! capable of regulating created_by: pg creation_date: 2020-06-24T13:15:17Z @@ -3246,7 +3258,7 @@ is_a: regulated_by ! regulated by [Typedef] id: negatively_regulates name: negatively regulates -def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +def: "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -3513,7 +3525,7 @@ is_a: regulated_by ! regulated by [Typedef] id: positively_regulates name: positively regulates -def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +def: "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -3707,13 +3719,11 @@ is_a: causally_downstream_of_or_within ! causally downstream of or within [Typedef] id: regulates name: regulates -def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." [] +def: "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 "David Hill" xsd:string property_value: IAO:0000117 "Tanya Berardini" xsd:string @@ -3800,6 +3810,17 @@ property_value: IAO:0000232 "Do not use this relation directly. It is a grouping domain: BFO:0000015 range: BFO:0000002 +[Typedef] +id: removes_input_for +name: removes input for +def: "p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0012010 +is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect +created_by: pg +creation_date: 2022-09-26T06:06:20Z + [Typedef] id: represses_expression_of name: represses expression of @@ -4495,7 +4516,7 @@ property_value: IAO:0000589 "transitively provides input for (process to process domain: BFO:0000015 range: BFO:0000015 is_transitive: true -is_a: causally_upstream_of ! causally upstream of +is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or within, positive effect [Typedef] id: transmitted_by diff --git a/src/ontology/subsets/ro-sequence.owl b/src/ontology/subsets/ro-sequence.owl index 0352d260..536119a0 100644 --- a/src/ontology/subsets/ro-sequence.owl +++ b/src/ontology/subsets/ro-sequence.owl @@ -1644,9 +1644,7 @@ N1 SubclassOf ( - - process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. - We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit + p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. Chris Mungall David Hill Tanya Berardini @@ -1671,7 +1669,7 @@ N1 SubclassOf ( - Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. Chris Mungall negatively regulates (process to process) @@ -1693,7 +1691,7 @@ N1 SubclassOf ( - Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. Chris Mungall positively regulates (process to process) @@ -2523,6 +2521,7 @@ where + p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. cjm RO:0002304 @@ -2540,11 +2539,13 @@ where + p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. 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 @@ -2717,6 +2718,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a particular instances of akt-2 enables some instance of protein kinase activity + c enables p iff c is capable of p and c acts to execute p. Chris Mungall catalyzes executes @@ -3483,50 +3485,19 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - - p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q - Chris Mungall - directly positively regulates - - directly activates (process to process) - RO:0002406 - directly_activates - directly activates - - - - + - p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one. + p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. Chris Mungall - indirectly positively regulates + indirectly activates RO:0002407 - indirectly_activates - indirectly activates - - - - - - - - - Chris Mungall - directly negatively regulates - - directly inhibits (process to process) - RO:0002408 - directly_inhibits - directly inhibits + indirectly_positively_regulates + indirectly positively regulates @@ -3535,14 +3506,15 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + - + p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. Chris Mungall - indirectly negatively regulates + indirectly inhibits RO:0002409 - indirectly_inhibits - indirectly inhibits + indirectly_negatively_regulates + indirectly negatively regulates @@ -3550,15 +3522,14 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - This relation groups causal relations between material entities and causal relations between processes + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? - * Is the influence positive or negative + * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. @@ -3573,6 +3544,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different causally_related_to causally related to + + + + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. + https://en.wikipedia.org/wiki/Causality + @@ -3582,8 +3559,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain + p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. Chris Mungall RO:0002411 @@ -3599,8 +3575,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. + p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. Chris Mungall RO:0002412 @@ -3615,8 +3590,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c + p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit Chris Mungall @@ -3631,7 +3605,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -3653,7 +3627,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. + p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) @@ -4485,7 +4459,7 @@ For example, A and B may be gene products and binding of B by A positively regul - p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. + p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. @@ -5202,7 +5176,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + p directly regulates q iff p is immediately causally upstream of q and p regulates q. Chris Mungall directly regulates (processual) @@ -5555,7 +5529,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. + p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates (process to process) @@ -5574,7 +5548,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. + p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates (process to process) @@ -6959,7 +6933,7 @@ For example, protein A (transcription factor) indirectly increases by expression - + a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process pg 2020-06-24T13:15:17Z @@ -6973,6 +6947,7 @@ For example, protein A (transcription factor) indirectly increases by expression + a relation between a continuant and a process, in which the continuant is a small molecule that activates the process pg @@ -6987,6 +6962,7 @@ For example, protein A (transcription factor) indirectly increases by expression + a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process pg @@ -7028,6 +7004,67 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. + pg + 2022-09-26T06:01:01Z + RO:0012009 + + + constitutively_upstream_of + constitutively upstream of + + + + + + + + + p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. + pg + 2022-09-26T06:06:20Z + RO:0012010 + + + removes_input_for + removes input for + + + + + + + + + p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. + pg + 2022-09-26T06:07:17Z + RO:0012011 + indirectly_causally_upstream_of + indirectly causally upstream of + + + + + + + + + + p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. + pg + 2022-09-26T06:08:01Z + RO:0012012 + indirectly_regulates + indirectly regulates + + + + diff --git a/src/ontology/subsets/ro-time-interval.obo b/src/ontology/subsets/ro-time-interval.obo index 8d5779d7..b7cf34dc 100644 --- a/src/ontology/subsets/ro-time-interval.obo +++ b/src/ontology/subsets/ro-time-interval.obo @@ -372,7 +372,7 @@ is_a: causally_related_to ! causally related to [Typedef] id: causal_relation_between_processes name: causal relation between processes -def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." [] +def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] xref: RO:0002501 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -440,21 +440,19 @@ is_a: causal_relation_between_entities ! causal relation between entities [Typedef] id: causally_related_to name: causally related to -def: "This relation groups causal relations between material entities and causal relations between processes" [] +def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] xref: RO:0002410 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string +property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string [Typedef] id: causally_upstream_of name: causally upstream of -def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" [] +def: "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002411 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within @@ -463,7 +461,9 @@ 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 +def: "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 property_value: http://purl.org/dc/terms/creator "cjm" xsd:string property_value: RO:0004050 RO:0002411 @@ -473,6 +473,7 @@ is_a: causally_upstream_of_or_within,_negative_effect ! causally upstream of or [Typedef] id: causally_upstream_of,_positive_effect name: causally upstream of, positive effect +def: "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." [] 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 subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -485,7 +486,7 @@ is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or [Typedef] id: causally_upstream_of_or_within name: causally upstream of or within -def: "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." [] +def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] synonym: "affects" RELATED [] xref: RO:0002418 property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string @@ -709,6 +710,17 @@ property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-art domain: BFO:0000004 is_a: mereotopologically_related_to ! mereotopologically related to +[Typedef] +id: constitutively_upstream_of +name: constitutively upstream of +def: "p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0012009 +is_a: causally_upstream_of,_positive_effect ! causally upstream of, positive effect +created_by: pg +creation_date: 2022-09-26T06:01:01Z + [Typedef] id: continuous_with name: continuous with @@ -993,18 +1005,6 @@ is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_develop_into ! has potential to develop into is_a: has_potential_to_directly_develop_into ! has potential to directly develop into -[Typedef] -id: directly_activates -name: directly activates -def: "p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q" [] -xref: RO:0002406 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "directly positively regulates" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly activates (process to process)" xsd:string -is_a: directly_positively_regulates ! directly positively regulates - [Typedef] id: directly_develops_from name: directly develops from @@ -1030,16 +1030,6 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "developmental precursor of" xsd:string is_a: develops_into ! develops into -[Typedef] -id: directly_inhibits -name: directly inhibits -xref: RO:0002408 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "directly negatively regulates" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly inhibits (process to process)" xsd:string -is_a: directly_negatively_regulates ! directly negatively regulates - [Typedef] id: directly_negatively_regulated_by name: directly negatively regulated by @@ -1053,7 +1043,7 @@ creation_date: 2017-09-17T13:52:38Z [Typedef] id: directly_negatively_regulates name: directly negatively regulates -def: "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." [] +def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1100,7 +1090,7 @@ creation_date: 2017-09-17T13:52:47Z [Typedef] id: directly_positively_regulates name: directly positively regulates -def: "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." [] +def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1137,9 +1127,8 @@ is_a: directly_regulates_quantity_of ! directly regulates quantity of [Typedef] id: directly_provides_input_for name: directly provides input for -def: "p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c" [] +def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] xref: RO:0002413 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -1160,7 +1149,7 @@ creation_date: 2017-09-17T13:52:24Z [Typedef] id: directly_regulates name: directly regulates -def: "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." [] +def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1416,6 +1405,7 @@ is_a: has_participant [Typedef] id: enables name: enables +def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002327 property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string @@ -2540,9 +2530,8 @@ inverse_of: immediately_causally_upstream_of ! immediately causally upstream of [Typedef] id: immediately_causally_upstream_of name: immediately causally upstream of -def: "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q." [] +def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] xref: RO:0002412 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of @@ -2616,25 +2605,24 @@ range: BFO:0000040 is_a: directly_positively_regulates_activity_of ! directly positively regulates activity of [Typedef] -id: indirectly_activates -name: indirectly activates -def: "p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one." [] -xref: RO:0002407 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "indirectly positively regulates" xsd:string -property_value: RO:0002579 RO:0002213 -is_transitive: true -is_a: positively_regulates ! positively regulates +id: indirectly_causally_upstream_of +name: indirectly causally upstream of +def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] +xref: RO:0012011 +is_a: causally_upstream_of ! causally upstream of +created_by: pg +creation_date: 2022-09-26T06:07:17Z [Typedef] -id: indirectly_inhibits -name: indirectly inhibits +id: indirectly_negatively_regulates +name: indirectly negatively regulates +def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] xref: RO:0002409 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "indirectly negatively regulates" xsd:string +property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 is_transitive: true +is_a: indirectly_regulates ! indirectly regulates is_a: negatively_regulates ! negatively regulates [Typedef] @@ -2654,6 +2642,18 @@ xref: RO:0011023 property_value: IAO:0000117 "Vasundra Touré" xsd:string is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of +[Typedef] +id: indirectly_positively_regulates +name: indirectly positively regulates +def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] +xref: RO:0002407 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "indirectly activates" xsd:string +property_value: RO:0002579 RO:0002213 +is_transitive: true +is_a: indirectly_regulates ! indirectly regulates +is_a: positively_regulates ! positively regulates + [Typedef] id: indirectly_positively_regulates_activity_of name: indirectly positively regulates activity of @@ -2673,6 +2673,16 @@ xref: RO:0011024 property_value: IAO:0000117 "Vasundra Touré" xsd:string is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of +[Typedef] +id: indirectly_regulates +name: indirectly regulates +def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." [] +xref: RO:0012012 +is_a: indirectly_causally_upstream_of ! indirectly causally upstream of +is_a: regulates ! regulates +created_by: pg +creation_date: 2022-09-26T06:08:01Z + [Typedef] id: indirectly_regulates_activity_of name: indirectly regulates activity of @@ -3012,6 +3022,7 @@ id: is_small_molecule_activator_of name: is small molecule activator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" [] xref: RO:0012005 +is_a: capable_of_positively_regulating ! capable of positively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of created_by: pg creation_date: 2020-06-24T13:15:26Z @@ -3021,6 +3032,7 @@ id: is_small_molecule_inhibitor_of name: is small molecule inhibitor of def: "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process" [] xref: RO:0012006 +is_a: capable_of_negatively_regulating ! capable of negatively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of created_by: pg creation_date: 2020-06-24T13:15:35Z @@ -3030,7 +3042,7 @@ id: is_small_molecule_regulator_of name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] xref: RO:0012004 -is_a: participates_in +is_a: capable_of_regulating ! capable of regulating created_by: pg creation_date: 2020-06-24T13:15:17Z @@ -3246,7 +3258,7 @@ is_a: regulated_by ! regulated by [Typedef] id: negatively_regulates name: negatively regulates -def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +def: "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -3513,7 +3525,7 @@ is_a: regulated_by ! regulated by [Typedef] id: positively_regulates name: positively regulates -def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +def: "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -3707,13 +3719,11 @@ is_a: causally_downstream_of_or_within ! causally downstream of or within [Typedef] id: regulates name: regulates -def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." [] +def: "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 "David Hill" xsd:string property_value: IAO:0000117 "Tanya Berardini" xsd:string @@ -3800,6 +3810,17 @@ property_value: IAO:0000232 "Do not use this relation directly. It is a grouping domain: BFO:0000015 range: BFO:0000002 +[Typedef] +id: removes_input_for +name: removes input for +def: "p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0012010 +is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect +created_by: pg +creation_date: 2022-09-26T06:06:20Z + [Typedef] id: represses_expression_of name: represses expression of @@ -4495,7 +4516,7 @@ property_value: IAO:0000589 "transitively provides input for (process to process domain: BFO:0000015 range: BFO:0000015 is_transitive: true -is_a: causally_upstream_of ! causally upstream of +is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or within, positive effect [Typedef] id: transmitted_by diff --git a/src/ontology/subsets/ro-time-interval.owl b/src/ontology/subsets/ro-time-interval.owl index 7a328db2..5924e64b 100644 --- a/src/ontology/subsets/ro-time-interval.owl +++ b/src/ontology/subsets/ro-time-interval.owl @@ -1644,9 +1644,7 @@ N1 SubclassOf ( - - process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. - We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit + p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. Chris Mungall David Hill Tanya Berardini @@ -1671,7 +1669,7 @@ N1 SubclassOf ( - Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. Chris Mungall negatively regulates (process to process) @@ -1693,7 +1691,7 @@ N1 SubclassOf ( - Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. Chris Mungall positively regulates (process to process) @@ -2523,6 +2521,7 @@ where + p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. cjm RO:0002304 @@ -2540,11 +2539,13 @@ where + p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. 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 @@ -2717,6 +2718,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a particular instances of akt-2 enables some instance of protein kinase activity + c enables p iff c is capable of p and c acts to execute p. Chris Mungall catalyzes executes @@ -3483,50 +3485,19 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - - p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q - Chris Mungall - directly positively regulates - - directly activates (process to process) - RO:0002406 - directly_activates - directly activates - - - - + - p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one. + p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. Chris Mungall - indirectly positively regulates + indirectly activates RO:0002407 - indirectly_activates - indirectly activates - - - - - - - - - Chris Mungall - directly negatively regulates - - directly inhibits (process to process) - RO:0002408 - directly_inhibits - directly inhibits + indirectly_positively_regulates + indirectly positively regulates @@ -3535,14 +3506,15 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + - + p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. Chris Mungall - indirectly negatively regulates + indirectly inhibits RO:0002409 - indirectly_inhibits - indirectly inhibits + indirectly_negatively_regulates + indirectly negatively regulates @@ -3550,15 +3522,14 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - This relation groups causal relations between material entities and causal relations between processes + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? - * Is the influence positive or negative + * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. @@ -3573,6 +3544,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different causally_related_to causally related to + + + + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. + https://en.wikipedia.org/wiki/Causality + @@ -3582,8 +3559,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain + p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. Chris Mungall RO:0002411 @@ -3599,8 +3575,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. + p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. Chris Mungall RO:0002412 @@ -3615,8 +3590,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c + p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit Chris Mungall @@ -3631,7 +3605,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -3653,7 +3627,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. + p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) @@ -4485,7 +4459,7 @@ For example, A and B may be gene products and binding of B by A positively regul - p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. + p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. @@ -5202,7 +5176,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + p directly regulates q iff p is immediately causally upstream of q and p regulates q. Chris Mungall directly regulates (processual) @@ -5555,7 +5529,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. + p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates (process to process) @@ -5574,7 +5548,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. + p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates (process to process) @@ -6959,7 +6933,7 @@ For example, protein A (transcription factor) indirectly increases by expression - + a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process pg 2020-06-24T13:15:17Z @@ -6973,6 +6947,7 @@ For example, protein A (transcription factor) indirectly increases by expression + a relation between a continuant and a process, in which the continuant is a small molecule that activates the process pg @@ -6987,6 +6962,7 @@ For example, protein A (transcription factor) indirectly increases by expression + a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process pg @@ -7028,6 +7004,67 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. + pg + 2022-09-26T06:01:01Z + RO:0012009 + + + constitutively_upstream_of + constitutively upstream of + + + + + + + + + p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. + pg + 2022-09-26T06:06:20Z + RO:0012010 + + + removes_input_for + removes input for + + + + + + + + + p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. + pg + 2022-09-26T06:07:17Z + RO:0012011 + indirectly_causally_upstream_of + indirectly causally upstream of + + + + + + + + + + p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. + pg + 2022-09-26T06:08:01Z + RO:0012012 + indirectly_regulates + indirectly regulates + + + + diff --git a/subsets/ro-causal.obo b/subsets/ro-causal.obo index dbeb953c..e70023eb 100644 --- a/subsets/ro-causal.obo +++ b/subsets/ro-causal.obo @@ -372,7 +372,7 @@ is_a: causally_related_to ! causally related to [Typedef] id: causal_relation_between_processes name: causal relation between processes -def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." [] +def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] xref: RO:0002501 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -440,21 +440,19 @@ is_a: causal_relation_between_entities ! causal relation between entities [Typedef] id: causally_related_to name: causally related to -def: "This relation groups causal relations between material entities and causal relations between processes" [] +def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] xref: RO:0002410 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string +property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string [Typedef] id: causally_upstream_of name: causally upstream of -def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" [] +def: "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002411 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within @@ -463,7 +461,9 @@ 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 +def: "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 property_value: http://purl.org/dc/terms/creator "cjm" xsd:string property_value: RO:0004050 RO:0002411 @@ -473,6 +473,7 @@ is_a: causally_upstream_of_or_within,_negative_effect ! causally upstream of or [Typedef] id: causally_upstream_of,_positive_effect name: causally upstream of, positive effect +def: "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." [] 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 subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -485,7 +486,7 @@ is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or [Typedef] id: causally_upstream_of_or_within name: causally upstream of or within -def: "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." [] +def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] synonym: "affects" RELATED [] xref: RO:0002418 property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string @@ -709,6 +710,17 @@ property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-art domain: BFO:0000004 is_a: mereotopologically_related_to ! mereotopologically related to +[Typedef] +id: constitutively_upstream_of +name: constitutively upstream of +def: "p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0012009 +is_a: causally_upstream_of,_positive_effect ! causally upstream of, positive effect +created_by: pg +creation_date: 2022-09-26T06:01:01Z + [Typedef] id: continuous_with name: continuous with @@ -993,18 +1005,6 @@ is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_develop_into ! has potential to develop into is_a: has_potential_to_directly_develop_into ! has potential to directly develop into -[Typedef] -id: directly_activates -name: directly activates -def: "p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q" [] -xref: RO:0002406 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "directly positively regulates" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly activates (process to process)" xsd:string -is_a: directly_positively_regulates ! directly positively regulates - [Typedef] id: directly_develops_from name: directly develops from @@ -1030,16 +1030,6 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "developmental precursor of" xsd:string is_a: develops_into ! develops into -[Typedef] -id: directly_inhibits -name: directly inhibits -xref: RO:0002408 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "directly negatively regulates" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly inhibits (process to process)" xsd:string -is_a: directly_negatively_regulates ! directly negatively regulates - [Typedef] id: directly_negatively_regulated_by name: directly negatively regulated by @@ -1053,7 +1043,7 @@ creation_date: 2017-09-17T13:52:38Z [Typedef] id: directly_negatively_regulates name: directly negatively regulates -def: "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." [] +def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1100,7 +1090,7 @@ creation_date: 2017-09-17T13:52:47Z [Typedef] id: directly_positively_regulates name: directly positively regulates -def: "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." [] +def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1137,9 +1127,8 @@ is_a: directly_regulates_quantity_of ! directly regulates quantity of [Typedef] id: directly_provides_input_for name: directly provides input for -def: "p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c" [] +def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] xref: RO:0002413 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -1160,7 +1149,7 @@ creation_date: 2017-09-17T13:52:24Z [Typedef] id: directly_regulates name: directly regulates -def: "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." [] +def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1416,6 +1405,7 @@ is_a: has_participant [Typedef] id: enables name: enables +def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002327 property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string @@ -2540,9 +2530,8 @@ inverse_of: immediately_causally_upstream_of ! immediately causally upstream of [Typedef] id: immediately_causally_upstream_of name: immediately causally upstream of -def: "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q." [] +def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] xref: RO:0002412 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of @@ -2616,25 +2605,24 @@ range: BFO:0000040 is_a: directly_positively_regulates_activity_of ! directly positively regulates activity of [Typedef] -id: indirectly_activates -name: indirectly activates -def: "p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one." [] -xref: RO:0002407 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "indirectly positively regulates" xsd:string -property_value: RO:0002579 RO:0002213 -is_transitive: true -is_a: positively_regulates ! positively regulates +id: indirectly_causally_upstream_of +name: indirectly causally upstream of +def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] +xref: RO:0012011 +is_a: causally_upstream_of ! causally upstream of +created_by: pg +creation_date: 2022-09-26T06:07:17Z [Typedef] -id: indirectly_inhibits -name: indirectly inhibits +id: indirectly_negatively_regulates +name: indirectly negatively regulates +def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] xref: RO:0002409 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "indirectly negatively regulates" xsd:string +property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 is_transitive: true +is_a: indirectly_regulates ! indirectly regulates is_a: negatively_regulates ! negatively regulates [Typedef] @@ -2654,6 +2642,18 @@ xref: RO:0011023 property_value: IAO:0000117 "Vasundra Touré" xsd:string is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of +[Typedef] +id: indirectly_positively_regulates +name: indirectly positively regulates +def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] +xref: RO:0002407 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "indirectly activates" xsd:string +property_value: RO:0002579 RO:0002213 +is_transitive: true +is_a: indirectly_regulates ! indirectly regulates +is_a: positively_regulates ! positively regulates + [Typedef] id: indirectly_positively_regulates_activity_of name: indirectly positively regulates activity of @@ -2673,6 +2673,16 @@ xref: RO:0011024 property_value: IAO:0000117 "Vasundra Touré" xsd:string is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of +[Typedef] +id: indirectly_regulates +name: indirectly regulates +def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." [] +xref: RO:0012012 +is_a: indirectly_causally_upstream_of ! indirectly causally upstream of +is_a: regulates ! regulates +created_by: pg +creation_date: 2022-09-26T06:08:01Z + [Typedef] id: indirectly_regulates_activity_of name: indirectly regulates activity of @@ -3012,6 +3022,7 @@ id: is_small_molecule_activator_of name: is small molecule activator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" [] xref: RO:0012005 +is_a: capable_of_positively_regulating ! capable of positively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of created_by: pg creation_date: 2020-06-24T13:15:26Z @@ -3021,6 +3032,7 @@ id: is_small_molecule_inhibitor_of name: is small molecule inhibitor of def: "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process" [] xref: RO:0012006 +is_a: capable_of_negatively_regulating ! capable of negatively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of created_by: pg creation_date: 2020-06-24T13:15:35Z @@ -3030,7 +3042,7 @@ id: is_small_molecule_regulator_of name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] xref: RO:0012004 -is_a: participates_in +is_a: capable_of_regulating ! capable of regulating created_by: pg creation_date: 2020-06-24T13:15:17Z @@ -3246,7 +3258,7 @@ is_a: regulated_by ! regulated by [Typedef] id: negatively_regulates name: negatively regulates -def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +def: "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -3513,7 +3525,7 @@ is_a: regulated_by ! regulated by [Typedef] id: positively_regulates name: positively regulates -def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +def: "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -3707,13 +3719,11 @@ is_a: causally_downstream_of_or_within ! causally downstream of or within [Typedef] id: regulates name: regulates -def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." [] +def: "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 "David Hill" xsd:string property_value: IAO:0000117 "Tanya Berardini" xsd:string @@ -3800,6 +3810,17 @@ property_value: IAO:0000232 "Do not use this relation directly. It is a grouping domain: BFO:0000015 range: BFO:0000002 +[Typedef] +id: removes_input_for +name: removes input for +def: "p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0012010 +is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect +created_by: pg +creation_date: 2022-09-26T06:06:20Z + [Typedef] id: represses_expression_of name: represses expression of @@ -4495,7 +4516,7 @@ property_value: IAO:0000589 "transitively provides input for (process to process domain: BFO:0000015 range: BFO:0000015 is_transitive: true -is_a: causally_upstream_of ! causally upstream of +is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or within, positive effect [Typedef] id: transmitted_by diff --git a/subsets/ro-causal.owl b/subsets/ro-causal.owl index 9f5aab9d..4632afce 100644 --- a/subsets/ro-causal.owl +++ b/subsets/ro-causal.owl @@ -1644,9 +1644,7 @@ N1 SubclassOf ( - - process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. - We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit + p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. Chris Mungall David Hill Tanya Berardini @@ -1671,7 +1669,7 @@ N1 SubclassOf ( - Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. Chris Mungall negatively regulates (process to process) @@ -1693,7 +1691,7 @@ N1 SubclassOf ( - Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. Chris Mungall positively regulates (process to process) @@ -2523,6 +2521,7 @@ where + p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. cjm RO:0002304 @@ -2540,11 +2539,13 @@ where + p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. 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 @@ -2717,6 +2718,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a particular instances of akt-2 enables some instance of protein kinase activity + c enables p iff c is capable of p and c acts to execute p. Chris Mungall catalyzes executes @@ -3483,50 +3485,19 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - - p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q - Chris Mungall - directly positively regulates - - directly activates (process to process) - RO:0002406 - directly_activates - directly activates - - - - + - p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one. + p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. Chris Mungall - indirectly positively regulates + indirectly activates RO:0002407 - indirectly_activates - indirectly activates - - - - - - - - - Chris Mungall - directly negatively regulates - - directly inhibits (process to process) - RO:0002408 - directly_inhibits - directly inhibits + indirectly_positively_regulates + indirectly positively regulates @@ -3535,14 +3506,15 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + - + p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. Chris Mungall - indirectly negatively regulates + indirectly inhibits RO:0002409 - indirectly_inhibits - indirectly inhibits + indirectly_negatively_regulates + indirectly negatively regulates @@ -3550,15 +3522,14 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - This relation groups causal relations between material entities and causal relations between processes + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? - * Is the influence positive or negative + * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. @@ -3573,6 +3544,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different causally_related_to causally related to + + + + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. + https://en.wikipedia.org/wiki/Causality + @@ -3582,8 +3559,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain + p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. Chris Mungall RO:0002411 @@ -3599,8 +3575,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. + p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. Chris Mungall RO:0002412 @@ -3615,8 +3590,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c + p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit Chris Mungall @@ -3631,7 +3605,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -3653,7 +3627,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. + p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) @@ -4485,7 +4459,7 @@ For example, A and B may be gene products and binding of B by A positively regul - p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. + p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. @@ -5202,7 +5176,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + p directly regulates q iff p is immediately causally upstream of q and p regulates q. Chris Mungall directly regulates (processual) @@ -5555,7 +5529,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. + p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates (process to process) @@ -5574,7 +5548,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. + p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates (process to process) @@ -6959,7 +6933,7 @@ For example, protein A (transcription factor) indirectly increases by expression - + a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process pg 2020-06-24T13:15:17Z @@ -6973,6 +6947,7 @@ For example, protein A (transcription factor) indirectly increases by expression + a relation between a continuant and a process, in which the continuant is a small molecule that activates the process pg @@ -6987,6 +6962,7 @@ For example, protein A (transcription factor) indirectly increases by expression + a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process pg @@ -7028,6 +7004,67 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. + pg + 2022-09-26T06:01:01Z + RO:0012009 + + + constitutively_upstream_of + constitutively upstream of + + + + + + + + + p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. + pg + 2022-09-26T06:06:20Z + RO:0012010 + + + removes_input_for + removes input for + + + + + + + + + p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. + pg + 2022-09-26T06:07:17Z + RO:0012011 + indirectly_causally_upstream_of + indirectly causally upstream of + + + + + + + + + + p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. + pg + 2022-09-26T06:08:01Z + RO:0012012 + indirectly_regulates + indirectly regulates + + + + diff --git a/subsets/ro-chado.obo b/subsets/ro-chado.obo index 2f7ad1fc..749cd64f 100644 --- a/subsets/ro-chado.obo +++ b/subsets/ro-chado.obo @@ -26,7 +26,7 @@ property_value: http://purl.org/dc/elements/1.1/description "The OBO Relations O property_value: http://purl.org/dc/elements/1.1/title "OBO Relations Ontology" xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI -property_value: owl:versionInfo "2022-09-07" xsd:string +property_value: owl:versionInfo "2022-10-26" xsd:string [Typedef] id: BFO:0000050 @@ -848,7 +848,7 @@ is_a: RO:0002203 ! develops into [Typedef] id: RO:0002211 name: regulates -def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." [] +def: "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." [] holds_over_chain: RO:0002230 RO:0002211 holds_over_chain: RO:0002578 RO:0002578 is_transitive: true @@ -859,7 +859,7 @@ transitive_over: RO:0002025 ! has effector activity [Typedef] id: RO:0002212 name: negatively_regulates -def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +def: "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." [] holds_over_chain: RO:0002230 RO:0002212 is_a: RO:0002211 ! regulates is_a: RO:0002305 ! causally upstream of, negative effect @@ -868,7 +868,7 @@ inverse_of: RO:0002335 ! negatively regulated by [Typedef] id: RO:0002213 name: positively_regulates -def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +def: "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." [] holds_over_chain: RO:0002212 RO:0002212 holds_over_chain: RO:0002230 RO:0002213 is_transitive: true @@ -1282,12 +1282,14 @@ is_a: RO:0002321 ! ecologically related to [Typedef] id: RO:0002304 name: causally_upstream_of,_positive_effect +def: "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." [] is_a: RO:0002411 ! causally upstream of is_a: RO:0004047 ! causally upstream of or within, positive effect [Typedef] id: RO:0002305 name: causally_upstream_of,_negative_effect +def: "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." [] is_a: RO:0002411 ! causally upstream of is_a: RO:0004046 ! causally upstream of or within, negative effect @@ -1364,6 +1366,7 @@ is_a: RO:0002329 ! part of structure that is capable of [Typedef] id: RO:0002327 name: enables +def: "c enables p iff c is capable of p and c acts to execute p." [] is_a: RO:0002215 ! capable of inverse_of: RO:0002333 ! enabled by transitive_over: BFO:0000051 ! has part @@ -1712,44 +1715,48 @@ inverse_of: RO:0002412 ! immediately causally upstream of [Typedef] id: RO:0002406 -name: directly_activates -def: "p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q" [] -is_a: RO:0002629 ! directly positively regulates +name: obsolete_directly_activates +is_obsolete: true +replaced_by: RO:0002629 [Typedef] id: RO:0002407 -name: indirectly_activates -def: "p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one." [] -holds_over_chain: RO:0002406 RO:0002406 -holds_over_chain: RO:0002406 RO:0002407 +name: indirectly_positively_regulates +def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] holds_over_chain: RO:0002409 RO:0002409 +holds_over_chain: RO:0002629 RO:0002407 +holds_over_chain: RO:0002629 RO:0002629 is_transitive: true is_a: RO:0002213 ! positively regulates -transitive_over: RO:0002406 ! directly activates +is_a: RO:0012012 ! indirectly regulates +transitive_over: RO:0002629 ! directly positively regulates [Typedef] id: RO:0002408 -name: directly_inhibits -is_a: RO:0002630 ! directly negatively regulates +name: obsolete_directly_inhibits +is_obsolete: true +replaced_by: RO:0002630 [Typedef] id: RO:0002409 -name: indirectly_inhibits -holds_over_chain: RO:0002408 RO:0002408 -holds_over_chain: RO:0002408 RO:0002409 +name: indirectly_negatively_regulates +def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] +holds_over_chain: RO:0002630 RO:0002409 +holds_over_chain: RO:0002630 RO:0002630 is_transitive: true is_a: RO:0002212 ! negatively regulates -transitive_over: RO:0002408 ! directly inhibits +is_a: RO:0012012 ! indirectly regulates +transitive_over: RO:0002630 ! directly negatively regulates [Typedef] id: RO:0002410 name: causally_related_to -def: "This relation groups causal relations between material entities and causal relations between processes" [] +def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] [Typedef] id: RO:0002411 name: causally_upstream_of -def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" [] +def: "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." [] is_transitive: true is_a: BFO:0000063 ! precedes is_a: RO:0002418 ! causally upstream of or within @@ -1757,14 +1764,14 @@ is_a: RO:0002418 ! causally upstream of or within [Typedef] id: RO:0002412 name: immediately_causally_upstream_of -def: "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q." [] +def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] is_a: RO:0002090 ! immediately precedes is_a: RO:0002411 ! causally upstream of [Typedef] id: RO:0002413 name: directly_provides_input_for -def: "p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c" [] +def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] holds_over_chain: RO:0002402 RO:0002400 is_a: RO:0002412 ! immediately causally upstream of is_a: RO:0002414 ! transitively provides input for @@ -1774,12 +1781,12 @@ id: RO:0002414 name: transitively_provides_input_for def: "transitive form of directly_provides_input_for" [] is_transitive: true -is_a: RO:0002411 ! causally upstream of +is_a: RO:0004047 ! causally upstream of or within, positive effect [Typedef] id: RO:0002418 name: causally_upstream_of_or_within -def: "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." [] +def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] synonym: "affects" RELATED [] is_transitive: true is_a: RO:0002501 ! causal relation between processes @@ -2238,7 +2245,7 @@ inverse_of: RO:0002608 ! process has causal agent [Typedef] id: RO:0002501 name: causal_relation_between_processes -def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." [] +def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] is_a: RO:0002410 ! causally related to [Typedef] @@ -2586,7 +2593,7 @@ is_a: BFO:0000050 ! part of [Typedef] id: RO:0002578 name: directly_regulates -def: "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." [] +def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] is_a: RO:0002211 ! regulates is_a: RO:0002412 ! immediately causally upstream of @@ -2790,14 +2797,14 @@ is_a: RO:0002574 ! participates in a biotic-biotic interaction with [Typedef] id: RO:0002629 name: directly_positively_regulates -def: "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." [] +def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] is_a: RO:0002213 ! positively regulates is_a: RO:0002578 ! directly regulates [Typedef] id: RO:0002630 name: directly_negatively_regulates -def: "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." [] +def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] is_a: RO:0002212 ! negatively regulates is_a: RO:0002578 ! directly regulates @@ -3441,18 +3448,20 @@ is_a: RO:0000057 ! has participant id: RO:0012004 name: is_small_molecule_regulator_of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] -is_a: RO:0000056 ! participates in +is_a: RO:0002596 ! capable of regulating [Typedef] id: RO:0012005 name: is_small_molecule_activator_of def: "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" [] +is_a: RO:0002598 ! capable of positively regulating is_a: RO:0012004 ! is small molecule regulator of [Typedef] id: RO:0012006 name: is_small_molecule_inhibitor_of def: "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process" [] +is_a: RO:0002597 ! capable of negatively regulating is_a: RO:0012004 ! is small molecule regulator of [Typedef] @@ -3466,6 +3475,31 @@ id: RO:0012008 name: results_in_fusion_of is_a: RO:0002592 ! results in organization of +[Typedef] +id: RO:0012009 +name: constitutively_upstream_of +def: "p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant." [] +is_a: RO:0002304 ! causally upstream of, positive effect + +[Typedef] +id: RO:0012010 +name: removes_input_for +def: "p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q." [] +is_a: RO:0002305 ! causally upstream of, negative effect + +[Typedef] +id: RO:0012011 +name: indirectly_causally_upstream_of +def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] +is_a: RO:0002411 ! causally upstream of + +[Typedef] +id: RO:0012012 +name: indirectly_regulates +def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." [] +is_a: RO:0002211 ! regulates +is_a: RO:0012011 ! indirectly causally upstream of + [Typedef] id: RO:0013001 name: has_synaptic_IO_in_region diff --git a/subsets/ro-chado.obo.tmp b/subsets/ro-chado.obo.tmp index 3fb2f872..f27a97a1 100644 --- a/subsets/ro-chado.obo.tmp +++ b/subsets/ro-chado.obo.tmp @@ -15,6 +15,7 @@ remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 0 Logical Axioms: 0] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 45 Logical Axioms: 10] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 29 Logical Axioms: 9] +remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 3 Logical Axioms: 0] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 104 Logical Axioms: 26] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 20 Logical Axioms: 6] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 731 Logical Axioms: 148] @@ -24,8 +25,8 @@ property_value: http://purl.org/dc/elements/1.1/description "The OBO Relations O property_value: http://purl.org/dc/elements/1.1/title "OBO Relations Ontology" xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI -property_value: owl:versionInfo "2022-05-23" xsd:string -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(DataProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (has member)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (has skeleton)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has role in modeling)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance removed)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (immersed in)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has primary substance added)\n\nIrreflexiveObjectProperty()\n\n\n############################\n# Data Properties\n############################\n\n# Data Property: ()\n\nDataPropertyRange( DatatypeRestriction(xsd:short xsd:minInclusive \"0\"^^xsd:short xsd:maxInclusive \"100\"^^xsd:short))\n\n\n\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Annotation(rdfs:comment \"If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\n) +property_value: owl:versionInfo "2022-10-26" xsd:string +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(DataProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (has member)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (has skeleton)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has role in modeling)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance removed)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (immersed in)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has primary substance added)\n\nIrreflexiveObjectProperty()\n\n\n############################\n# Data Properties\n############################\n\n# Data Property: ()\n\nDataPropertyRange( DatatypeRestriction(xsd:short xsd:minInclusive \"0\"^^xsd:short xsd:maxInclusive \"100\"^^xsd:short))\n\n\n\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Annotation(rdfs:comment \"If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\n) [Typedef] id: BFO:0000050 @@ -660,6 +661,7 @@ transitive_over: BFO:0000050 ! part of id: RO:0002150 name: continuous with def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] +is_symmetric: true is_a: RO:0002323 ! mereotopologically related to [Typedef] @@ -846,7 +848,7 @@ is_a: RO:0002203 ! develops into [Typedef] id: RO:0002211 name: regulates -def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." [] +def: "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." [] holds_over_chain: RO:0002230 RO:0002211 holds_over_chain: RO:0002578 RO:0002578 is_transitive: true @@ -857,7 +859,7 @@ transitive_over: RO:0002025 ! has effector activity [Typedef] id: RO:0002212 name: negatively regulates -def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +def: "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." [] holds_over_chain: RO:0002230 RO:0002212 is_a: RO:0002211 ! regulates is_a: RO:0002305 ! causally upstream of, negative effect @@ -866,7 +868,7 @@ inverse_of: RO:0002335 ! negatively regulated by [Typedef] id: RO:0002213 name: positively regulates -def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +def: "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." [] holds_over_chain: RO:0002212 RO:0002212 holds_over_chain: RO:0002230 RO:0002213 is_transitive: true @@ -1280,12 +1282,14 @@ is_a: RO:0002321 ! ecologically related to [Typedef] id: RO:0002304 name: causally upstream of, positive effect +def: "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." [] is_a: RO:0002411 ! causally upstream of is_a: RO:0004047 ! causally upstream of or within, positive effect [Typedef] id: RO:0002305 name: causally upstream of, negative effect +def: "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." [] is_a: RO:0002411 ! causally upstream of is_a: RO:0004046 ! causally upstream of or within, negative effect @@ -1362,6 +1366,7 @@ is_a: RO:0002329 ! part of structure that is capable of [Typedef] id: RO:0002327 name: enables +def: "c enables p iff c is capable of p and c acts to execute p." [] is_a: RO:0002215 ! capable of inverse_of: RO:0002333 ! enabled by transitive_over: BFO:0000051 ! has part @@ -1710,44 +1715,48 @@ inverse_of: RO:0002412 ! immediately causally upstream of [Typedef] id: RO:0002406 -name: directly activates -def: "p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q" [] -is_a: RO:0002629 ! directly positively regulates +name: obsolete directly activates +is_obsolete: true +replaced_by: RO:0002629 [Typedef] id: RO:0002407 -name: indirectly activates -def: "p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one." [] -holds_over_chain: RO:0002406 RO:0002406 -holds_over_chain: RO:0002406 RO:0002407 +name: indirectly positively regulates +def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] holds_over_chain: RO:0002409 RO:0002409 +holds_over_chain: RO:0002629 RO:0002407 +holds_over_chain: RO:0002629 RO:0002629 is_transitive: true is_a: RO:0002213 ! positively regulates -transitive_over: RO:0002406 ! directly activates +is_a: RO:0012012 ! indirectly regulates +transitive_over: RO:0002629 ! directly positively regulates [Typedef] id: RO:0002408 -name: directly inhibits -is_a: RO:0002630 ! directly negatively regulates +name: obsolete directly inhibits +is_obsolete: true +replaced_by: RO:0002630 [Typedef] id: RO:0002409 -name: indirectly inhibits -holds_over_chain: RO:0002408 RO:0002408 -holds_over_chain: RO:0002408 RO:0002409 +name: indirectly negatively regulates +def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] +holds_over_chain: RO:0002630 RO:0002409 +holds_over_chain: RO:0002630 RO:0002630 is_transitive: true is_a: RO:0002212 ! negatively regulates -transitive_over: RO:0002408 ! directly inhibits +is_a: RO:0012012 ! indirectly regulates +transitive_over: RO:0002630 ! directly negatively regulates [Typedef] id: RO:0002410 name: causally related to -def: "This relation groups causal relations between material entities and causal relations between processes" [] +def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] [Typedef] id: RO:0002411 name: causally upstream of -def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" [] +def: "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." [] is_transitive: true is_a: BFO:0000063 ! precedes is_a: RO:0002418 ! causally upstream of or within @@ -1755,14 +1764,14 @@ is_a: RO:0002418 ! causally upstream of or within [Typedef] id: RO:0002412 name: immediately causally upstream of -def: "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q." [] +def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] is_a: RO:0002090 ! immediately precedes is_a: RO:0002411 ! causally upstream of [Typedef] id: RO:0002413 name: directly provides input for -def: "p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c" [] +def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] holds_over_chain: RO:0002402 RO:0002400 is_a: RO:0002412 ! immediately causally upstream of is_a: RO:0002414 ! transitively provides input for @@ -1772,12 +1781,12 @@ id: RO:0002414 name: transitively provides input for def: "transitive form of directly_provides_input_for" [] is_transitive: true -is_a: RO:0002411 ! causally upstream of +is_a: RO:0004047 ! causally upstream of or within, positive effect [Typedef] id: RO:0002418 name: causally upstream of or within -def: "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." [] +def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] synonym: "affects" RELATED [] is_transitive: true is_a: RO:0002501 ! causal relation between processes @@ -2236,7 +2245,7 @@ inverse_of: RO:0002608 ! process has causal agent [Typedef] id: RO:0002501 name: causal relation between processes -def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." [] +def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] is_a: RO:0002410 ! causally related to [Typedef] @@ -2543,6 +2552,7 @@ is_a: RO:0002567 ! biomechanically related to id: RO:0002569 name: has branching part def: "inverse of branching part of" [] +is_transitive: true is_a: BFO:0000051 ! has part is_a: RO:0002375 ! in branching relationship with @@ -2583,7 +2593,7 @@ is_a: BFO:0000050 ! part of [Typedef] id: RO:0002578 name: directly regulates -def: "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." [] +def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] is_a: RO:0002211 ! regulates is_a: RO:0002412 ! immediately causally upstream of @@ -2787,14 +2797,14 @@ is_a: RO:0002574 ! participates in a biotic-biotic interaction with [Typedef] id: RO:0002629 name: directly positively regulates -def: "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." [] +def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] is_a: RO:0002213 ! positively regulates is_a: RO:0002578 ! directly regulates [Typedef] id: RO:0002630 name: directly negatively regulates -def: "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." [] +def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] is_a: RO:0002212 ! negatively regulates is_a: RO:0002578 ! directly regulates @@ -3438,18 +3448,20 @@ is_a: RO:0000057 ! has participant id: RO:0012004 name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] -is_a: RO:0000056 ! participates in +is_a: RO:0002596 ! capable of regulating [Typedef] id: RO:0012005 name: is small molecule activator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" [] +is_a: RO:0002598 ! capable of positively regulating is_a: RO:0012004 ! is small molecule regulator of [Typedef] id: RO:0012006 name: is small molecule inhibitor of def: "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process" [] +is_a: RO:0002597 ! capable of negatively regulating is_a: RO:0012004 ! is small molecule regulator of [Typedef] @@ -3463,6 +3475,31 @@ id: RO:0012008 name: results in fusion of is_a: RO:0002592 ! results in organization of +[Typedef] +id: RO:0012009 +name: constitutively upstream of +def: "p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant." [] +is_a: RO:0002304 ! causally upstream of, positive effect + +[Typedef] +id: RO:0012010 +name: removes input for +def: "p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q." [] +is_a: RO:0002305 ! causally upstream of, negative effect + +[Typedef] +id: RO:0012011 +name: indirectly causally upstream of +def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] +is_a: RO:0002411 ! causally upstream of + +[Typedef] +id: RO:0012012 +name: indirectly regulates +def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." [] +is_a: RO:0002211 ! regulates +is_a: RO:0012011 ! indirectly causally upstream of + [Typedef] id: RO:0013001 name: has synaptic IO in region diff --git a/subsets/ro-developmental.obo b/subsets/ro-developmental.obo index 9607eee9..2cb5c2fc 100644 --- a/subsets/ro-developmental.obo +++ b/subsets/ro-developmental.obo @@ -372,7 +372,7 @@ is_a: causally_related_to ! causally related to [Typedef] id: causal_relation_between_processes name: causal relation between processes -def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." [] +def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] xref: RO:0002501 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -440,21 +440,19 @@ is_a: causal_relation_between_entities ! causal relation between entities [Typedef] id: causally_related_to name: causally related to -def: "This relation groups causal relations between material entities and causal relations between processes" [] +def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] xref: RO:0002410 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string +property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string [Typedef] id: causally_upstream_of name: causally upstream of -def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" [] +def: "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002411 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within @@ -463,7 +461,9 @@ 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 +def: "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 property_value: http://purl.org/dc/terms/creator "cjm" xsd:string property_value: RO:0004050 RO:0002411 @@ -473,6 +473,7 @@ is_a: causally_upstream_of_or_within,_negative_effect ! causally upstream of or [Typedef] id: causally_upstream_of,_positive_effect name: causally upstream of, positive effect +def: "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." [] 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 subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -485,7 +486,7 @@ is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or [Typedef] id: causally_upstream_of_or_within name: causally upstream of or within -def: "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." [] +def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] synonym: "affects" RELATED [] xref: RO:0002418 property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string @@ -709,6 +710,17 @@ property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-art domain: BFO:0000004 is_a: mereotopologically_related_to ! mereotopologically related to +[Typedef] +id: constitutively_upstream_of +name: constitutively upstream of +def: "p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0012009 +is_a: causally_upstream_of,_positive_effect ! causally upstream of, positive effect +created_by: pg +creation_date: 2022-09-26T06:01:01Z + [Typedef] id: continuous_with name: continuous with @@ -993,18 +1005,6 @@ is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_develop_into ! has potential to develop into is_a: has_potential_to_directly_develop_into ! has potential to directly develop into -[Typedef] -id: directly_activates -name: directly activates -def: "p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q" [] -xref: RO:0002406 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "directly positively regulates" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly activates (process to process)" xsd:string -is_a: directly_positively_regulates ! directly positively regulates - [Typedef] id: directly_develops_from name: directly develops from @@ -1030,16 +1030,6 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "developmental precursor of" xsd:string is_a: develops_into ! develops into -[Typedef] -id: directly_inhibits -name: directly inhibits -xref: RO:0002408 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "directly negatively regulates" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly inhibits (process to process)" xsd:string -is_a: directly_negatively_regulates ! directly negatively regulates - [Typedef] id: directly_negatively_regulated_by name: directly negatively regulated by @@ -1053,7 +1043,7 @@ creation_date: 2017-09-17T13:52:38Z [Typedef] id: directly_negatively_regulates name: directly negatively regulates -def: "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." [] +def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1100,7 +1090,7 @@ creation_date: 2017-09-17T13:52:47Z [Typedef] id: directly_positively_regulates name: directly positively regulates -def: "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." [] +def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1137,9 +1127,8 @@ is_a: directly_regulates_quantity_of ! directly regulates quantity of [Typedef] id: directly_provides_input_for name: directly provides input for -def: "p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c" [] +def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] xref: RO:0002413 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -1160,7 +1149,7 @@ creation_date: 2017-09-17T13:52:24Z [Typedef] id: directly_regulates name: directly regulates -def: "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." [] +def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1416,6 +1405,7 @@ is_a: has_participant [Typedef] id: enables name: enables +def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002327 property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string @@ -2540,9 +2530,8 @@ inverse_of: immediately_causally_upstream_of ! immediately causally upstream of [Typedef] id: immediately_causally_upstream_of name: immediately causally upstream of -def: "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q." [] +def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] xref: RO:0002412 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of @@ -2616,25 +2605,24 @@ range: BFO:0000040 is_a: directly_positively_regulates_activity_of ! directly positively regulates activity of [Typedef] -id: indirectly_activates -name: indirectly activates -def: "p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one." [] -xref: RO:0002407 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "indirectly positively regulates" xsd:string -property_value: RO:0002579 RO:0002213 -is_transitive: true -is_a: positively_regulates ! positively regulates +id: indirectly_causally_upstream_of +name: indirectly causally upstream of +def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] +xref: RO:0012011 +is_a: causally_upstream_of ! causally upstream of +created_by: pg +creation_date: 2022-09-26T06:07:17Z [Typedef] -id: indirectly_inhibits -name: indirectly inhibits +id: indirectly_negatively_regulates +name: indirectly negatively regulates +def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] xref: RO:0002409 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "indirectly negatively regulates" xsd:string +property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 is_transitive: true +is_a: indirectly_regulates ! indirectly regulates is_a: negatively_regulates ! negatively regulates [Typedef] @@ -2654,6 +2642,18 @@ xref: RO:0011023 property_value: IAO:0000117 "Vasundra Touré" xsd:string is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of +[Typedef] +id: indirectly_positively_regulates +name: indirectly positively regulates +def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] +xref: RO:0002407 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "indirectly activates" xsd:string +property_value: RO:0002579 RO:0002213 +is_transitive: true +is_a: indirectly_regulates ! indirectly regulates +is_a: positively_regulates ! positively regulates + [Typedef] id: indirectly_positively_regulates_activity_of name: indirectly positively regulates activity of @@ -2673,6 +2673,16 @@ xref: RO:0011024 property_value: IAO:0000117 "Vasundra Touré" xsd:string is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of +[Typedef] +id: indirectly_regulates +name: indirectly regulates +def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." [] +xref: RO:0012012 +is_a: indirectly_causally_upstream_of ! indirectly causally upstream of +is_a: regulates ! regulates +created_by: pg +creation_date: 2022-09-26T06:08:01Z + [Typedef] id: indirectly_regulates_activity_of name: indirectly regulates activity of @@ -3012,6 +3022,7 @@ id: is_small_molecule_activator_of name: is small molecule activator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" [] xref: RO:0012005 +is_a: capable_of_positively_regulating ! capable of positively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of created_by: pg creation_date: 2020-06-24T13:15:26Z @@ -3021,6 +3032,7 @@ id: is_small_molecule_inhibitor_of name: is small molecule inhibitor of def: "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process" [] xref: RO:0012006 +is_a: capable_of_negatively_regulating ! capable of negatively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of created_by: pg creation_date: 2020-06-24T13:15:35Z @@ -3030,7 +3042,7 @@ id: is_small_molecule_regulator_of name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] xref: RO:0012004 -is_a: participates_in +is_a: capable_of_regulating ! capable of regulating created_by: pg creation_date: 2020-06-24T13:15:17Z @@ -3246,7 +3258,7 @@ is_a: regulated_by ! regulated by [Typedef] id: negatively_regulates name: negatively regulates -def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +def: "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -3513,7 +3525,7 @@ is_a: regulated_by ! regulated by [Typedef] id: positively_regulates name: positively regulates -def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +def: "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -3707,13 +3719,11 @@ is_a: causally_downstream_of_or_within ! causally downstream of or within [Typedef] id: regulates name: regulates -def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." [] +def: "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 "David Hill" xsd:string property_value: IAO:0000117 "Tanya Berardini" xsd:string @@ -3800,6 +3810,17 @@ property_value: IAO:0000232 "Do not use this relation directly. It is a grouping domain: BFO:0000015 range: BFO:0000002 +[Typedef] +id: removes_input_for +name: removes input for +def: "p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0012010 +is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect +created_by: pg +creation_date: 2022-09-26T06:06:20Z + [Typedef] id: represses_expression_of name: represses expression of @@ -4495,7 +4516,7 @@ property_value: IAO:0000589 "transitively provides input for (process to process domain: BFO:0000015 range: BFO:0000015 is_transitive: true -is_a: causally_upstream_of ! causally upstream of +is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or within, positive effect [Typedef] id: transmitted_by diff --git a/subsets/ro-developmental.owl b/subsets/ro-developmental.owl index 798d2816..b438c670 100644 --- a/subsets/ro-developmental.owl +++ b/subsets/ro-developmental.owl @@ -1644,9 +1644,7 @@ N1 SubclassOf ( - - process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. - We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit + p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. Chris Mungall David Hill Tanya Berardini @@ -1671,7 +1669,7 @@ N1 SubclassOf ( - Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. Chris Mungall negatively regulates (process to process) @@ -1693,7 +1691,7 @@ N1 SubclassOf ( - Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. Chris Mungall positively regulates (process to process) @@ -2523,6 +2521,7 @@ where + p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. cjm RO:0002304 @@ -2540,11 +2539,13 @@ where + p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. 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 @@ -2717,6 +2718,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a particular instances of akt-2 enables some instance of protein kinase activity + c enables p iff c is capable of p and c acts to execute p. Chris Mungall catalyzes executes @@ -3483,50 +3485,19 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - - p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q - Chris Mungall - directly positively regulates - - directly activates (process to process) - RO:0002406 - directly_activates - directly activates - - - - + - p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one. + p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. Chris Mungall - indirectly positively regulates + indirectly activates RO:0002407 - indirectly_activates - indirectly activates - - - - - - - - - Chris Mungall - directly negatively regulates - - directly inhibits (process to process) - RO:0002408 - directly_inhibits - directly inhibits + indirectly_positively_regulates + indirectly positively regulates @@ -3535,14 +3506,15 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + - + p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. Chris Mungall - indirectly negatively regulates + indirectly inhibits RO:0002409 - indirectly_inhibits - indirectly inhibits + indirectly_negatively_regulates + indirectly negatively regulates @@ -3550,15 +3522,14 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - This relation groups causal relations between material entities and causal relations between processes + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? - * Is the influence positive or negative + * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. @@ -3573,6 +3544,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different causally_related_to causally related to + + + + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. + https://en.wikipedia.org/wiki/Causality + @@ -3582,8 +3559,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain + p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. Chris Mungall RO:0002411 @@ -3599,8 +3575,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. + p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. Chris Mungall RO:0002412 @@ -3615,8 +3590,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c + p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit Chris Mungall @@ -3631,7 +3605,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -3653,7 +3627,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. + p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) @@ -4485,7 +4459,7 @@ For example, A and B may be gene products and binding of B by A positively regul - p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. + p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. @@ -5202,7 +5176,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + p directly regulates q iff p is immediately causally upstream of q and p regulates q. Chris Mungall directly regulates (processual) @@ -5555,7 +5529,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. + p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates (process to process) @@ -5574,7 +5548,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. + p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates (process to process) @@ -6959,7 +6933,7 @@ For example, protein A (transcription factor) indirectly increases by expression - + a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process pg 2020-06-24T13:15:17Z @@ -6973,6 +6947,7 @@ For example, protein A (transcription factor) indirectly increases by expression + a relation between a continuant and a process, in which the continuant is a small molecule that activates the process pg @@ -6987,6 +6962,7 @@ For example, protein A (transcription factor) indirectly increases by expression + a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process pg @@ -7028,6 +7004,67 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. + pg + 2022-09-26T06:01:01Z + RO:0012009 + + + constitutively_upstream_of + constitutively upstream of + + + + + + + + + p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. + pg + 2022-09-26T06:06:20Z + RO:0012010 + + + removes_input_for + removes input for + + + + + + + + + p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. + pg + 2022-09-26T06:07:17Z + RO:0012011 + indirectly_causally_upstream_of + indirectly causally upstream of + + + + + + + + + + p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. + pg + 2022-09-26T06:08:01Z + RO:0012012 + indirectly_regulates + indirectly regulates + + + + diff --git a/subsets/ro-eco.obo b/subsets/ro-eco.obo index c6c8f58a..3ac96494 100644 --- a/subsets/ro-eco.obo +++ b/subsets/ro-eco.obo @@ -7,7 +7,7 @@ subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" subsetdef: ro-eco "" subsetdef: RO:0002259 "" ontology: ro/subsets/ro-eco -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(DataProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (never in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (mutually spatially disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (taxonomic class assertion)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (ambiguous for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dubious for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (annotation property cardinality)\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: (logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on a property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an object property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an annotation property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dispositional interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has no connections with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (curator guidance link)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (always present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (measurement property has unit)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has start time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has end time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (month of gestation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has developmental stage marker)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is asymmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is symmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is direct form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indirect form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom where second argument is reflexive)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion involving identity)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (in approximate one to one relationship with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is approximately equivalent to)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is opposite of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indistinguishable from)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (evidential logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom has evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom contradicted by evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is representative IRI for equivalence set)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (nominally disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is directional form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is positive form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is negative form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is homeomorphic for)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (has skeleton)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has role in modeling)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance removed)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (immersed in)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has primary substance added)\n\nIrreflexiveObjectProperty()\n\n\n############################\n# Data Properties\n############################\n\n# Data Property: (has increased age-specific mortality rate)\n\nDataPropertyRange( DatatypeRestriction(xsd:short xsd:minInclusive \"0\"^^xsd:short xsd:maxInclusive \"100\"^^xsd:short))\n\n\n\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Annotation(rdfs:comment \"If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(DataProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (never in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (mutually spatially disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (taxonomic class assertion)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (ambiguous for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dubious for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (annotation property cardinality)\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: (logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on a property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an object property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an annotation property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dispositional interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has no connections with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (curator guidance link)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (always present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (measurement property has unit)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has start time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has end time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (month of gestation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has developmental stage marker)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is asymmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is symmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is direct form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indirect form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom where second argument is reflexive)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion involving identity)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (in approximate one to one relationship with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is approximately equivalent to)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is opposite of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indistinguishable from)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (evidential logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom has evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom contradicted by evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is representative IRI for equivalence set)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (nominally disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is directional form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is positive form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is negative form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is homeomorphic for)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (has skeleton)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has role in modeling)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance removed)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (immersed in)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has primary substance added)\n\nIrreflexiveObjectProperty()\n\n\n############################\n# Data Properties\n############################\n\n# Data Property: (has increased age-specific mortality rate)\n\nDataPropertyRange( DatatypeRestriction(xsd:short xsd:minInclusive \"0\"^^xsd:short xsd:maxInclusive \"100\"^^xsd:short))\n\n\n\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Annotation(rdfs:comment \"If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) [Typedef] id: BFO:0000050 @@ -972,12 +972,10 @@ is_a: RO:0002203 ! develops into [Typedef] id: RO:0002211 name: regulates -def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." [] +def: "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 "David Hill" xsd:string property_value: IAO:0000117 "Tanya Berardini" xsd:string @@ -996,7 +994,7 @@ transitive_over: RO:0002025 ! has effector activity [Typedef] id: RO:0002212 name: negatively regulates -def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +def: "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1012,7 +1010,7 @@ inverse_of: RO:0002335 ! negatively regulated by [Typedef] id: RO:0002213 name: positively regulates -def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +def: "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1586,6 +1584,7 @@ is_a: RO:0002321 ! ecologically related to [Typedef] id: RO:0002304 name: causally upstream of, positive effect +def: "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." [] 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 subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1597,7 +1596,9 @@ is_a: RO:0004047 ! causally upstream of or within, positive effect [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 +def: "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: http://purl.org/dc/terms/creator "cjm" xsd:string property_value: RO:0004050 RO:0002411 is_a: RO:0002411 ! causally upstream of @@ -1725,6 +1726,7 @@ is_a: RO:0002329 ! part of structure that is capable of [Typedef] id: RO:0002327 name: enables +def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2227,67 +2229,61 @@ inverse_of: RO:0002412 ! immediately causally upstream of [Typedef] id: RO:0002406 -name: directly activates -def: "p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q" [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "directly positively regulates" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly activates (process to process)" xsd:string -is_a: RO:0002629 ! directly positively regulates +name: obsolete directly activates +comment: This term was obsoleted because it has the same meaning as 'directly positively regulates'. +is_obsolete: true +replaced_by: RO:0002629 [Typedef] id: RO:0002407 -name: indirectly activates -def: "p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one." [] +name: indirectly positively regulates +def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "indirectly positively regulates" xsd:string +property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 -holds_over_chain: RO:0002406 RO:0002406 -holds_over_chain: RO:0002406 RO:0002407 holds_over_chain: RO:0002409 RO:0002409 +holds_over_chain: RO:0002629 RO:0002407 +holds_over_chain: RO:0002629 RO:0002629 is_transitive: true is_a: RO:0002213 ! positively regulates -transitive_over: RO:0002406 ! directly activates +is_a: RO:0012012 ! indirectly regulates +transitive_over: RO:0002629 ! directly positively regulates [Typedef] id: RO:0002408 -name: directly inhibits -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "directly negatively regulates" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly inhibits (process to process)" xsd:string -is_a: RO:0002630 ! directly negatively regulates +name: obsolete directly inhibits +comment: This term was obsoleted because it has the same meaning as 'directly negatively regulates'. +is_obsolete: true +replaced_by: RO:0002630 [Typedef] id: RO:0002409 -name: indirectly inhibits -property_value: IAO:0000114 IAO:0000428 +name: indirectly negatively regulates +def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "indirectly negatively regulates" xsd:string +property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 -holds_over_chain: RO:0002408 RO:0002408 -holds_over_chain: RO:0002408 RO:0002409 +holds_over_chain: RO:0002630 RO:0002409 +holds_over_chain: RO:0002630 RO:0002630 is_transitive: true is_a: RO:0002212 ! negatively regulates -transitive_over: RO:0002408 ! directly inhibits +is_a: RO:0012012 ! indirectly regulates +transitive_over: RO:0002630 ! directly negatively regulates [Typedef] id: RO:0002410 name: causally related to -def: "This relation groups causal relations between material entities and causal relations between processes" [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string +def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] +property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string [Typedef] id: RO:0002411 name: causally upstream of -def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" [] +def: "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string is_transitive: true is_a: BFO:0000063 @@ -2296,8 +2292,7 @@ is_a: RO:0002418 ! causally upstream of or within [Typedef] id: RO:0002412 name: immediately causally upstream of -def: "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q." [] -property_value: IAO:0000114 IAO:0000428 +def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: RO:0002575 RO:0002411 is_a: RO:0002090 @@ -2306,8 +2301,7 @@ is_a: RO:0002411 ! causally upstream of [Typedef] id: RO:0002413 name: directly provides input for -def: "p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c" [] -property_value: IAO:0000114 IAO:0000428 +def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -2325,12 +2319,12 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'directly provides input for' (which may later be relabeled simply to 'provides input for')" xsd:string property_value: IAO:0000589 "transitively provides input for (process to process)" xsd:string is_transitive: true -is_a: RO:0002411 ! causally upstream of +is_a: RO:0004047 ! causally upstream of or within, positive effect [Typedef] id: RO:0002418 name: causally upstream of or within -def: "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." [] +def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] synonym: "affects" RELATED [] property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2985,7 +2979,7 @@ inverse_of: RO:0002608 ! process has causal agent [Typedef] id: RO:0002501 name: causal relation between processes -def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." [] +def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string @@ -3507,7 +3501,7 @@ is_a: BFO:0000050 [Typedef] id: RO:0002578 name: directly regulates -def: "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." [] +def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -3751,7 +3745,7 @@ is_a: RO:0002574 ! participates in a biotic-biotic interaction with [Typedef] id: RO:0002629 name: directly positively regulates -def: "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." [] +def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -3764,7 +3758,7 @@ is_a: RO:0002578 ! directly regulates [Typedef] id: RO:0002630 name: directly negatively regulates -def: "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." [] +def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -4610,6 +4604,7 @@ creation_date: 2020-06-08T17:21:33Z id: RO:0012004 name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] +is_a: RO:0002596 ! capable of regulating created_by: pg creation_date: 2020-06-24T13:15:17Z @@ -4617,6 +4612,7 @@ creation_date: 2020-06-24T13:15:17Z id: RO:0012005 name: is small molecule activator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" [] +is_a: RO:0002598 ! capable of positively regulating is_a: RO:0012004 ! is small molecule regulator of created_by: pg creation_date: 2020-06-24T13:15:26Z @@ -4625,6 +4621,7 @@ creation_date: 2020-06-24T13:15:26Z id: RO:0012006 name: is small molecule inhibitor of def: "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process" [] +is_a: RO:0002597 ! capable of negatively regulating is_a: RO:0012004 ! is small molecule regulator of created_by: pg creation_date: 2020-06-24T13:15:35Z @@ -4647,6 +4644,43 @@ is_a: RO:0002592 ! results in organization of created_by: pg creation_date: 2021-02-26T07:28:29Z +[Typedef] +id: RO:0012009 +name: constitutively upstream of +def: "p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +is_a: RO:0002304 ! causally upstream of, positive effect +created_by: pg +creation_date: 2022-09-26T06:01:01Z + +[Typedef] +id: RO:0012010 +name: removes input for +def: "p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +is_a: RO:0002305 ! causally upstream of, negative effect +created_by: pg +creation_date: 2022-09-26T06:06:20Z + +[Typedef] +id: RO:0012011 +name: indirectly causally upstream of +def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] +is_a: RO:0002411 ! causally upstream of +created_by: pg +creation_date: 2022-09-26T06:07:17Z + +[Typedef] +id: RO:0012012 +name: indirectly regulates +def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." [] +is_a: RO:0002211 ! regulates +is_a: RO:0012011 ! indirectly causally upstream of +created_by: pg +creation_date: 2022-09-26T06:08:01Z + [Typedef] id: RO:0013001 name: has synaptic IO in region diff --git a/subsets/ro-eco.owl b/subsets/ro-eco.owl index 2656244c..02fcc1d3 100644 --- a/subsets/ro-eco.owl +++ b/subsets/ro-eco.owl @@ -2698,9 +2698,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. - We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit + p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. Chris Mungall David Hill Tanya Berardini @@ -2727,7 +2725,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. Chris Mungall negatively regulates (process to process) @@ -2755,7 +2753,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. Chris Mungall positively regulates (process to process) @@ -3616,6 +3614,7 @@ where + p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. cjm @@ -3631,9 +3630,11 @@ where + p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. 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 @@ -3833,6 +3834,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a particular instances of akt-2 enables some instance of protein kinase activity + c enables p iff c is capable of p and c acts to execute p. Chris Mungall catalyzes executes @@ -4585,14 +4587,10 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - - - p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q - Chris Mungall - directly positively regulates - - directly activates (process to process) - directly activates + + This term was obsoleted because it has the same meaning as 'directly positively regulates'. + obsolete directly activates + true @@ -4601,28 +4599,29 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ + - - + + - - + + + - - - + + - p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one. + p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. Chris Mungall - indirectly positively regulates + indirectly activates - indirectly activates + indirectly positively regulates @@ -4630,12 +4629,10 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - - Chris Mungall - directly negatively regulates - - directly inhibits (process to process) - directly inhibits + + This term was obsoleted because it has the same meaning as 'directly negatively regulates'. + obsolete directly inhibits + true @@ -4644,24 +4641,25 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ + - - + + - + - - + + - + p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. Chris Mungall - indirectly negatively regulates + indirectly inhibits - indirectly inhibits + indirectly negatively regulates @@ -4669,15 +4667,14 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - - This relation groups causal relations between material entities and causal relations between processes + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? - * Is the influence positive or negative + * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. @@ -4690,6 +4687,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to + + + + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. + https://en.wikipedia.org/wiki/Causality + @@ -4699,8 +4702,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain + p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. Chris Mungall @@ -4714,8 +4716,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. + p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. Chris Mungall immediately causally upstream of @@ -4732,8 +4733,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c + p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit Chris Mungall @@ -4746,7 +4746,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + transitive form of directly_provides_input_for @@ -4764,7 +4764,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. + p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) @@ -5876,7 +5876,7 @@ the a supports either the existence of b, or the truth value of b. - p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. + p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. @@ -6639,7 +6639,7 @@ the a supports either the existence of b, or the truth value of b. - Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + p directly regulates q iff p is immediately causally upstream of q and p regulates q. Chris Mungall directly regulates (processual) @@ -7037,7 +7037,7 @@ the a supports either the existence of b, or the truth value of b. - Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. + p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates (process to process) @@ -7054,7 +7054,7 @@ the a supports either the existence of b, or the truth value of b. - Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. + p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates (process to process) @@ -8379,6 +8379,7 @@ For example, protein A (transcription factor) indirectly increases by expression + a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process pg 2020-06-24T13:15:17Z @@ -8390,6 +8391,7 @@ For example, protein A (transcription factor) indirectly increases by expression + a relation between a continuant and a process, in which the continuant is a small molecule that activates the process pg @@ -8402,6 +8404,7 @@ For example, protein A (transcription factor) indirectly increases by expression + a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process pg @@ -8437,6 +8440,59 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. + pg + 2022-09-26T06:01:01Z + + + constitutively upstream of + + + + + + + + + p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. + pg + 2022-09-26T06:06:20Z + + + removes input for + + + + + + + + + p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. + pg + 2022-09-26T06:07:17Z + indirectly causally upstream of + + + + + + + + + + p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. + pg + 2022-09-26T06:08:01Z + indirectly regulates + + + + @@ -9093,6 +9149,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -9111,6 +9173,9 @@ For example, protein A (transcription factor) indirectly increases by expression + + + If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. inferring direct reg edge from input to regulatory subfunction @@ -9511,6 +9576,50 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -9687,6 +9796,50 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/subsets/ro-interaction.obo b/subsets/ro-interaction.obo index 0f0e9a4c..6bb60283 100644 --- a/subsets/ro-interaction.obo +++ b/subsets/ro-interaction.obo @@ -372,7 +372,7 @@ is_a: causally_related_to ! causally related to [Typedef] id: causal_relation_between_processes name: causal relation between processes -def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." [] +def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] xref: RO:0002501 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -440,21 +440,19 @@ is_a: causal_relation_between_entities ! causal relation between entities [Typedef] id: causally_related_to name: causally related to -def: "This relation groups causal relations between material entities and causal relations between processes" [] +def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] xref: RO:0002410 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string +property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string [Typedef] id: causally_upstream_of name: causally upstream of -def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" [] +def: "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002411 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within @@ -463,7 +461,9 @@ 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 +def: "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 property_value: http://purl.org/dc/terms/creator "cjm" xsd:string property_value: RO:0004050 RO:0002411 @@ -473,6 +473,7 @@ is_a: causally_upstream_of_or_within,_negative_effect ! causally upstream of or [Typedef] id: causally_upstream_of,_positive_effect name: causally upstream of, positive effect +def: "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." [] 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 subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -485,7 +486,7 @@ is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or [Typedef] id: causally_upstream_of_or_within name: causally upstream of or within -def: "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." [] +def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] synonym: "affects" RELATED [] xref: RO:0002418 property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string @@ -709,6 +710,17 @@ property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-art domain: BFO:0000004 is_a: mereotopologically_related_to ! mereotopologically related to +[Typedef] +id: constitutively_upstream_of +name: constitutively upstream of +def: "p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0012009 +is_a: causally_upstream_of,_positive_effect ! causally upstream of, positive effect +created_by: pg +creation_date: 2022-09-26T06:01:01Z + [Typedef] id: continuous_with name: continuous with @@ -993,18 +1005,6 @@ is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_develop_into ! has potential to develop into is_a: has_potential_to_directly_develop_into ! has potential to directly develop into -[Typedef] -id: directly_activates -name: directly activates -def: "p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q" [] -xref: RO:0002406 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "directly positively regulates" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly activates (process to process)" xsd:string -is_a: directly_positively_regulates ! directly positively regulates - [Typedef] id: directly_develops_from name: directly develops from @@ -1030,16 +1030,6 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "developmental precursor of" xsd:string is_a: develops_into ! develops into -[Typedef] -id: directly_inhibits -name: directly inhibits -xref: RO:0002408 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "directly negatively regulates" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly inhibits (process to process)" xsd:string -is_a: directly_negatively_regulates ! directly negatively regulates - [Typedef] id: directly_negatively_regulated_by name: directly negatively regulated by @@ -1053,7 +1043,7 @@ creation_date: 2017-09-17T13:52:38Z [Typedef] id: directly_negatively_regulates name: directly negatively regulates -def: "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." [] +def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1100,7 +1090,7 @@ creation_date: 2017-09-17T13:52:47Z [Typedef] id: directly_positively_regulates name: directly positively regulates -def: "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." [] +def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1137,9 +1127,8 @@ is_a: directly_regulates_quantity_of ! directly regulates quantity of [Typedef] id: directly_provides_input_for name: directly provides input for -def: "p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c" [] +def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] xref: RO:0002413 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -1160,7 +1149,7 @@ creation_date: 2017-09-17T13:52:24Z [Typedef] id: directly_regulates name: directly regulates -def: "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." [] +def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1416,6 +1405,7 @@ is_a: has_participant [Typedef] id: enables name: enables +def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002327 property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string @@ -2540,9 +2530,8 @@ inverse_of: immediately_causally_upstream_of ! immediately causally upstream of [Typedef] id: immediately_causally_upstream_of name: immediately causally upstream of -def: "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q." [] +def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] xref: RO:0002412 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of @@ -2616,25 +2605,24 @@ range: BFO:0000040 is_a: directly_positively_regulates_activity_of ! directly positively regulates activity of [Typedef] -id: indirectly_activates -name: indirectly activates -def: "p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one." [] -xref: RO:0002407 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "indirectly positively regulates" xsd:string -property_value: RO:0002579 RO:0002213 -is_transitive: true -is_a: positively_regulates ! positively regulates +id: indirectly_causally_upstream_of +name: indirectly causally upstream of +def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] +xref: RO:0012011 +is_a: causally_upstream_of ! causally upstream of +created_by: pg +creation_date: 2022-09-26T06:07:17Z [Typedef] -id: indirectly_inhibits -name: indirectly inhibits +id: indirectly_negatively_regulates +name: indirectly negatively regulates +def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] xref: RO:0002409 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "indirectly negatively regulates" xsd:string +property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 is_transitive: true +is_a: indirectly_regulates ! indirectly regulates is_a: negatively_regulates ! negatively regulates [Typedef] @@ -2654,6 +2642,18 @@ xref: RO:0011023 property_value: IAO:0000117 "Vasundra Touré" xsd:string is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of +[Typedef] +id: indirectly_positively_regulates +name: indirectly positively regulates +def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] +xref: RO:0002407 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "indirectly activates" xsd:string +property_value: RO:0002579 RO:0002213 +is_transitive: true +is_a: indirectly_regulates ! indirectly regulates +is_a: positively_regulates ! positively regulates + [Typedef] id: indirectly_positively_regulates_activity_of name: indirectly positively regulates activity of @@ -2673,6 +2673,16 @@ xref: RO:0011024 property_value: IAO:0000117 "Vasundra Touré" xsd:string is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of +[Typedef] +id: indirectly_regulates +name: indirectly regulates +def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." [] +xref: RO:0012012 +is_a: indirectly_causally_upstream_of ! indirectly causally upstream of +is_a: regulates ! regulates +created_by: pg +creation_date: 2022-09-26T06:08:01Z + [Typedef] id: indirectly_regulates_activity_of name: indirectly regulates activity of @@ -3012,6 +3022,7 @@ id: is_small_molecule_activator_of name: is small molecule activator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" [] xref: RO:0012005 +is_a: capable_of_positively_regulating ! capable of positively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of created_by: pg creation_date: 2020-06-24T13:15:26Z @@ -3021,6 +3032,7 @@ id: is_small_molecule_inhibitor_of name: is small molecule inhibitor of def: "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process" [] xref: RO:0012006 +is_a: capable_of_negatively_regulating ! capable of negatively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of created_by: pg creation_date: 2020-06-24T13:15:35Z @@ -3030,7 +3042,7 @@ id: is_small_molecule_regulator_of name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] xref: RO:0012004 -is_a: participates_in +is_a: capable_of_regulating ! capable of regulating created_by: pg creation_date: 2020-06-24T13:15:17Z @@ -3246,7 +3258,7 @@ is_a: regulated_by ! regulated by [Typedef] id: negatively_regulates name: negatively regulates -def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +def: "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -3513,7 +3525,7 @@ is_a: regulated_by ! regulated by [Typedef] id: positively_regulates name: positively regulates -def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +def: "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -3707,13 +3719,11 @@ is_a: causally_downstream_of_or_within ! causally downstream of or within [Typedef] id: regulates name: regulates -def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." [] +def: "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 "David Hill" xsd:string property_value: IAO:0000117 "Tanya Berardini" xsd:string @@ -3800,6 +3810,17 @@ property_value: IAO:0000232 "Do not use this relation directly. It is a grouping domain: BFO:0000015 range: BFO:0000002 +[Typedef] +id: removes_input_for +name: removes input for +def: "p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0012010 +is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect +created_by: pg +creation_date: 2022-09-26T06:06:20Z + [Typedef] id: represses_expression_of name: represses expression of @@ -4495,7 +4516,7 @@ property_value: IAO:0000589 "transitively provides input for (process to process domain: BFO:0000015 range: BFO:0000015 is_transitive: true -is_a: causally_upstream_of ! causally upstream of +is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or within, positive effect [Typedef] id: transmitted_by diff --git a/subsets/ro-interaction.owl b/subsets/ro-interaction.owl index 8988ceb4..95d81d07 100644 --- a/subsets/ro-interaction.owl +++ b/subsets/ro-interaction.owl @@ -1644,9 +1644,7 @@ N1 SubclassOf ( - - process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. - We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit + p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. Chris Mungall David Hill Tanya Berardini @@ -1671,7 +1669,7 @@ N1 SubclassOf ( - Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. Chris Mungall negatively regulates (process to process) @@ -1693,7 +1691,7 @@ N1 SubclassOf ( - Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. Chris Mungall positively regulates (process to process) @@ -2523,6 +2521,7 @@ where + p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. cjm RO:0002304 @@ -2540,11 +2539,13 @@ where + p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. 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 @@ -2717,6 +2718,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a particular instances of akt-2 enables some instance of protein kinase activity + c enables p iff c is capable of p and c acts to execute p. Chris Mungall catalyzes executes @@ -3483,50 +3485,19 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - - p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q - Chris Mungall - directly positively regulates - - directly activates (process to process) - RO:0002406 - directly_activates - directly activates - - - - + - p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one. + p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. Chris Mungall - indirectly positively regulates + indirectly activates RO:0002407 - indirectly_activates - indirectly activates - - - - - - - - - Chris Mungall - directly negatively regulates - - directly inhibits (process to process) - RO:0002408 - directly_inhibits - directly inhibits + indirectly_positively_regulates + indirectly positively regulates @@ -3535,14 +3506,15 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + - + p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. Chris Mungall - indirectly negatively regulates + indirectly inhibits RO:0002409 - indirectly_inhibits - indirectly inhibits + indirectly_negatively_regulates + indirectly negatively regulates @@ -3550,15 +3522,14 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - This relation groups causal relations between material entities and causal relations between processes + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? - * Is the influence positive or negative + * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. @@ -3573,6 +3544,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different causally_related_to causally related to + + + + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. + https://en.wikipedia.org/wiki/Causality + @@ -3582,8 +3559,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain + p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. Chris Mungall RO:0002411 @@ -3599,8 +3575,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. + p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. Chris Mungall RO:0002412 @@ -3615,8 +3590,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c + p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit Chris Mungall @@ -3631,7 +3605,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -3653,7 +3627,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. + p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) @@ -4485,7 +4459,7 @@ For example, A and B may be gene products and binding of B by A positively regul - p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. + p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. @@ -5202,7 +5176,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + p directly regulates q iff p is immediately causally upstream of q and p regulates q. Chris Mungall directly regulates (processual) @@ -5555,7 +5529,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. + p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates (process to process) @@ -5574,7 +5548,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. + p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates (process to process) @@ -6959,7 +6933,7 @@ For example, protein A (transcription factor) indirectly increases by expression - + a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process pg 2020-06-24T13:15:17Z @@ -6973,6 +6947,7 @@ For example, protein A (transcription factor) indirectly increases by expression + a relation between a continuant and a process, in which the continuant is a small molecule that activates the process pg @@ -6987,6 +6962,7 @@ For example, protein A (transcription factor) indirectly increases by expression + a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process pg @@ -7028,6 +7004,67 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. + pg + 2022-09-26T06:01:01Z + RO:0012009 + + + constitutively_upstream_of + constitutively upstream of + + + + + + + + + p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. + pg + 2022-09-26T06:06:20Z + RO:0012010 + + + removes_input_for + removes input for + + + + + + + + + p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. + pg + 2022-09-26T06:07:17Z + RO:0012011 + indirectly_causally_upstream_of + indirectly causally upstream of + + + + + + + + + + p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. + pg + 2022-09-26T06:08:01Z + RO:0012012 + indirectly_regulates + indirectly regulates + + + + diff --git a/subsets/ro-mereotopology.obo b/subsets/ro-mereotopology.obo index e02dede5..d2b65cd6 100644 --- a/subsets/ro-mereotopology.obo +++ b/subsets/ro-mereotopology.obo @@ -372,7 +372,7 @@ is_a: causally_related_to ! causally related to [Typedef] id: causal_relation_between_processes name: causal relation between processes -def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." [] +def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] xref: RO:0002501 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -440,21 +440,19 @@ is_a: causal_relation_between_entities ! causal relation between entities [Typedef] id: causally_related_to name: causally related to -def: "This relation groups causal relations between material entities and causal relations between processes" [] +def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] xref: RO:0002410 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string +property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string [Typedef] id: causally_upstream_of name: causally upstream of -def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" [] +def: "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002411 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within @@ -463,7 +461,9 @@ 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 +def: "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 property_value: http://purl.org/dc/terms/creator "cjm" xsd:string property_value: RO:0004050 RO:0002411 @@ -473,6 +473,7 @@ is_a: causally_upstream_of_or_within,_negative_effect ! causally upstream of or [Typedef] id: causally_upstream_of,_positive_effect name: causally upstream of, positive effect +def: "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." [] 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 subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -485,7 +486,7 @@ is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or [Typedef] id: causally_upstream_of_or_within name: causally upstream of or within -def: "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." [] +def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] synonym: "affects" RELATED [] xref: RO:0002418 property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string @@ -709,6 +710,17 @@ property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-art domain: BFO:0000004 is_a: mereotopologically_related_to ! mereotopologically related to +[Typedef] +id: constitutively_upstream_of +name: constitutively upstream of +def: "p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0012009 +is_a: causally_upstream_of,_positive_effect ! causally upstream of, positive effect +created_by: pg +creation_date: 2022-09-26T06:01:01Z + [Typedef] id: continuous_with name: continuous with @@ -993,18 +1005,6 @@ is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_develop_into ! has potential to develop into is_a: has_potential_to_directly_develop_into ! has potential to directly develop into -[Typedef] -id: directly_activates -name: directly activates -def: "p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q" [] -xref: RO:0002406 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "directly positively regulates" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly activates (process to process)" xsd:string -is_a: directly_positively_regulates ! directly positively regulates - [Typedef] id: directly_develops_from name: directly develops from @@ -1030,16 +1030,6 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "developmental precursor of" xsd:string is_a: develops_into ! develops into -[Typedef] -id: directly_inhibits -name: directly inhibits -xref: RO:0002408 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "directly negatively regulates" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly inhibits (process to process)" xsd:string -is_a: directly_negatively_regulates ! directly negatively regulates - [Typedef] id: directly_negatively_regulated_by name: directly negatively regulated by @@ -1053,7 +1043,7 @@ creation_date: 2017-09-17T13:52:38Z [Typedef] id: directly_negatively_regulates name: directly negatively regulates -def: "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." [] +def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1100,7 +1090,7 @@ creation_date: 2017-09-17T13:52:47Z [Typedef] id: directly_positively_regulates name: directly positively regulates -def: "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." [] +def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1137,9 +1127,8 @@ is_a: directly_regulates_quantity_of ! directly regulates quantity of [Typedef] id: directly_provides_input_for name: directly provides input for -def: "p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c" [] +def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] xref: RO:0002413 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -1160,7 +1149,7 @@ creation_date: 2017-09-17T13:52:24Z [Typedef] id: directly_regulates name: directly regulates -def: "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." [] +def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1416,6 +1405,7 @@ is_a: has_participant [Typedef] id: enables name: enables +def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002327 property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string @@ -2540,9 +2530,8 @@ inverse_of: immediately_causally_upstream_of ! immediately causally upstream of [Typedef] id: immediately_causally_upstream_of name: immediately causally upstream of -def: "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q." [] +def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] xref: RO:0002412 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of @@ -2616,25 +2605,24 @@ range: BFO:0000040 is_a: directly_positively_regulates_activity_of ! directly positively regulates activity of [Typedef] -id: indirectly_activates -name: indirectly activates -def: "p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one." [] -xref: RO:0002407 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "indirectly positively regulates" xsd:string -property_value: RO:0002579 RO:0002213 -is_transitive: true -is_a: positively_regulates ! positively regulates +id: indirectly_causally_upstream_of +name: indirectly causally upstream of +def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] +xref: RO:0012011 +is_a: causally_upstream_of ! causally upstream of +created_by: pg +creation_date: 2022-09-26T06:07:17Z [Typedef] -id: indirectly_inhibits -name: indirectly inhibits +id: indirectly_negatively_regulates +name: indirectly negatively regulates +def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] xref: RO:0002409 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "indirectly negatively regulates" xsd:string +property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 is_transitive: true +is_a: indirectly_regulates ! indirectly regulates is_a: negatively_regulates ! negatively regulates [Typedef] @@ -2654,6 +2642,18 @@ xref: RO:0011023 property_value: IAO:0000117 "Vasundra Touré" xsd:string is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of +[Typedef] +id: indirectly_positively_regulates +name: indirectly positively regulates +def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] +xref: RO:0002407 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "indirectly activates" xsd:string +property_value: RO:0002579 RO:0002213 +is_transitive: true +is_a: indirectly_regulates ! indirectly regulates +is_a: positively_regulates ! positively regulates + [Typedef] id: indirectly_positively_regulates_activity_of name: indirectly positively regulates activity of @@ -2673,6 +2673,16 @@ xref: RO:0011024 property_value: IAO:0000117 "Vasundra Touré" xsd:string is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of +[Typedef] +id: indirectly_regulates +name: indirectly regulates +def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." [] +xref: RO:0012012 +is_a: indirectly_causally_upstream_of ! indirectly causally upstream of +is_a: regulates ! regulates +created_by: pg +creation_date: 2022-09-26T06:08:01Z + [Typedef] id: indirectly_regulates_activity_of name: indirectly regulates activity of @@ -3012,6 +3022,7 @@ id: is_small_molecule_activator_of name: is small molecule activator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" [] xref: RO:0012005 +is_a: capable_of_positively_regulating ! capable of positively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of created_by: pg creation_date: 2020-06-24T13:15:26Z @@ -3021,6 +3032,7 @@ id: is_small_molecule_inhibitor_of name: is small molecule inhibitor of def: "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process" [] xref: RO:0012006 +is_a: capable_of_negatively_regulating ! capable of negatively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of created_by: pg creation_date: 2020-06-24T13:15:35Z @@ -3030,7 +3042,7 @@ id: is_small_molecule_regulator_of name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] xref: RO:0012004 -is_a: participates_in +is_a: capable_of_regulating ! capable of regulating created_by: pg creation_date: 2020-06-24T13:15:17Z @@ -3246,7 +3258,7 @@ is_a: regulated_by ! regulated by [Typedef] id: negatively_regulates name: negatively regulates -def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +def: "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -3513,7 +3525,7 @@ is_a: regulated_by ! regulated by [Typedef] id: positively_regulates name: positively regulates -def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +def: "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -3707,13 +3719,11 @@ is_a: causally_downstream_of_or_within ! causally downstream of or within [Typedef] id: regulates name: regulates -def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." [] +def: "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 "David Hill" xsd:string property_value: IAO:0000117 "Tanya Berardini" xsd:string @@ -3800,6 +3810,17 @@ property_value: IAO:0000232 "Do not use this relation directly. It is a grouping domain: BFO:0000015 range: BFO:0000002 +[Typedef] +id: removes_input_for +name: removes input for +def: "p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0012010 +is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect +created_by: pg +creation_date: 2022-09-26T06:06:20Z + [Typedef] id: represses_expression_of name: represses expression of @@ -4495,7 +4516,7 @@ property_value: IAO:0000589 "transitively provides input for (process to process domain: BFO:0000015 range: BFO:0000015 is_transitive: true -is_a: causally_upstream_of ! causally upstream of +is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or within, positive effect [Typedef] id: transmitted_by diff --git a/subsets/ro-mereotopology.owl b/subsets/ro-mereotopology.owl index 54ce1ebb..51a49e7d 100644 --- a/subsets/ro-mereotopology.owl +++ b/subsets/ro-mereotopology.owl @@ -1644,9 +1644,7 @@ N1 SubclassOf ( - - process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. - We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit + p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. Chris Mungall David Hill Tanya Berardini @@ -1671,7 +1669,7 @@ N1 SubclassOf ( - Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. Chris Mungall negatively regulates (process to process) @@ -1693,7 +1691,7 @@ N1 SubclassOf ( - Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. Chris Mungall positively regulates (process to process) @@ -2523,6 +2521,7 @@ where + p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. cjm RO:0002304 @@ -2540,11 +2539,13 @@ where + p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. 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 @@ -2717,6 +2718,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a particular instances of akt-2 enables some instance of protein kinase activity + c enables p iff c is capable of p and c acts to execute p. Chris Mungall catalyzes executes @@ -3483,50 +3485,19 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - - p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q - Chris Mungall - directly positively regulates - - directly activates (process to process) - RO:0002406 - directly_activates - directly activates - - - - + - p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one. + p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. Chris Mungall - indirectly positively regulates + indirectly activates RO:0002407 - indirectly_activates - indirectly activates - - - - - - - - - Chris Mungall - directly negatively regulates - - directly inhibits (process to process) - RO:0002408 - directly_inhibits - directly inhibits + indirectly_positively_regulates + indirectly positively regulates @@ -3535,14 +3506,15 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + - + p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. Chris Mungall - indirectly negatively regulates + indirectly inhibits RO:0002409 - indirectly_inhibits - indirectly inhibits + indirectly_negatively_regulates + indirectly negatively regulates @@ -3550,15 +3522,14 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - This relation groups causal relations between material entities and causal relations between processes + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? - * Is the influence positive or negative + * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. @@ -3573,6 +3544,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different causally_related_to causally related to + + + + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. + https://en.wikipedia.org/wiki/Causality + @@ -3582,8 +3559,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain + p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. Chris Mungall RO:0002411 @@ -3599,8 +3575,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. + p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. Chris Mungall RO:0002412 @@ -3615,8 +3590,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c + p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit Chris Mungall @@ -3631,7 +3605,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -3653,7 +3627,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. + p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) @@ -4485,7 +4459,7 @@ For example, A and B may be gene products and binding of B by A positively regul - p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. + p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. @@ -5202,7 +5176,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + p directly regulates q iff p is immediately causally upstream of q and p regulates q. Chris Mungall directly regulates (processual) @@ -5555,7 +5529,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. + p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates (process to process) @@ -5574,7 +5548,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. + p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates (process to process) @@ -6959,7 +6933,7 @@ For example, protein A (transcription factor) indirectly increases by expression - + a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process pg 2020-06-24T13:15:17Z @@ -6973,6 +6947,7 @@ For example, protein A (transcription factor) indirectly increases by expression + a relation between a continuant and a process, in which the continuant is a small molecule that activates the process pg @@ -6987,6 +6962,7 @@ For example, protein A (transcription factor) indirectly increases by expression + a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process pg @@ -7028,6 +7004,67 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. + pg + 2022-09-26T06:01:01Z + RO:0012009 + + + constitutively_upstream_of + constitutively upstream of + + + + + + + + + p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. + pg + 2022-09-26T06:06:20Z + RO:0012010 + + + removes_input_for + removes input for + + + + + + + + + p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. + pg + 2022-09-26T06:07:17Z + RO:0012011 + indirectly_causally_upstream_of + indirectly causally upstream of + + + + + + + + + + p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. + pg + 2022-09-26T06:08:01Z + RO:0012012 + indirectly_regulates + indirectly regulates + + + + diff --git a/subsets/ro-sequence.obo b/subsets/ro-sequence.obo index 2d81dc8d..62bf49b1 100644 --- a/subsets/ro-sequence.obo +++ b/subsets/ro-sequence.obo @@ -372,7 +372,7 @@ is_a: causally_related_to ! causally related to [Typedef] id: causal_relation_between_processes name: causal relation between processes -def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." [] +def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] xref: RO:0002501 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -440,21 +440,19 @@ is_a: causal_relation_between_entities ! causal relation between entities [Typedef] id: causally_related_to name: causally related to -def: "This relation groups causal relations between material entities and causal relations between processes" [] +def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] xref: RO:0002410 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string +property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string [Typedef] id: causally_upstream_of name: causally upstream of -def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" [] +def: "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002411 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within @@ -463,7 +461,9 @@ 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 +def: "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 property_value: http://purl.org/dc/terms/creator "cjm" xsd:string property_value: RO:0004050 RO:0002411 @@ -473,6 +473,7 @@ is_a: causally_upstream_of_or_within,_negative_effect ! causally upstream of or [Typedef] id: causally_upstream_of,_positive_effect name: causally upstream of, positive effect +def: "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." [] 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 subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -485,7 +486,7 @@ is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or [Typedef] id: causally_upstream_of_or_within name: causally upstream of or within -def: "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." [] +def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] synonym: "affects" RELATED [] xref: RO:0002418 property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string @@ -709,6 +710,17 @@ property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-art domain: BFO:0000004 is_a: mereotopologically_related_to ! mereotopologically related to +[Typedef] +id: constitutively_upstream_of +name: constitutively upstream of +def: "p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0012009 +is_a: causally_upstream_of,_positive_effect ! causally upstream of, positive effect +created_by: pg +creation_date: 2022-09-26T06:01:01Z + [Typedef] id: continuous_with name: continuous with @@ -993,18 +1005,6 @@ is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_develop_into ! has potential to develop into is_a: has_potential_to_directly_develop_into ! has potential to directly develop into -[Typedef] -id: directly_activates -name: directly activates -def: "p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q" [] -xref: RO:0002406 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "directly positively regulates" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly activates (process to process)" xsd:string -is_a: directly_positively_regulates ! directly positively regulates - [Typedef] id: directly_develops_from name: directly develops from @@ -1030,16 +1030,6 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "developmental precursor of" xsd:string is_a: develops_into ! develops into -[Typedef] -id: directly_inhibits -name: directly inhibits -xref: RO:0002408 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "directly negatively regulates" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly inhibits (process to process)" xsd:string -is_a: directly_negatively_regulates ! directly negatively regulates - [Typedef] id: directly_negatively_regulated_by name: directly negatively regulated by @@ -1053,7 +1043,7 @@ creation_date: 2017-09-17T13:52:38Z [Typedef] id: directly_negatively_regulates name: directly negatively regulates -def: "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." [] +def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1100,7 +1090,7 @@ creation_date: 2017-09-17T13:52:47Z [Typedef] id: directly_positively_regulates name: directly positively regulates -def: "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." [] +def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1137,9 +1127,8 @@ is_a: directly_regulates_quantity_of ! directly regulates quantity of [Typedef] id: directly_provides_input_for name: directly provides input for -def: "p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c" [] +def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] xref: RO:0002413 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -1160,7 +1149,7 @@ creation_date: 2017-09-17T13:52:24Z [Typedef] id: directly_regulates name: directly regulates -def: "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." [] +def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1416,6 +1405,7 @@ is_a: has_participant [Typedef] id: enables name: enables +def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002327 property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string @@ -2540,9 +2530,8 @@ inverse_of: immediately_causally_upstream_of ! immediately causally upstream of [Typedef] id: immediately_causally_upstream_of name: immediately causally upstream of -def: "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q." [] +def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] xref: RO:0002412 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of @@ -2616,25 +2605,24 @@ range: BFO:0000040 is_a: directly_positively_regulates_activity_of ! directly positively regulates activity of [Typedef] -id: indirectly_activates -name: indirectly activates -def: "p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one." [] -xref: RO:0002407 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "indirectly positively regulates" xsd:string -property_value: RO:0002579 RO:0002213 -is_transitive: true -is_a: positively_regulates ! positively regulates +id: indirectly_causally_upstream_of +name: indirectly causally upstream of +def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] +xref: RO:0012011 +is_a: causally_upstream_of ! causally upstream of +created_by: pg +creation_date: 2022-09-26T06:07:17Z [Typedef] -id: indirectly_inhibits -name: indirectly inhibits +id: indirectly_negatively_regulates +name: indirectly negatively regulates +def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] xref: RO:0002409 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "indirectly negatively regulates" xsd:string +property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 is_transitive: true +is_a: indirectly_regulates ! indirectly regulates is_a: negatively_regulates ! negatively regulates [Typedef] @@ -2654,6 +2642,18 @@ xref: RO:0011023 property_value: IAO:0000117 "Vasundra Touré" xsd:string is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of +[Typedef] +id: indirectly_positively_regulates +name: indirectly positively regulates +def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] +xref: RO:0002407 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "indirectly activates" xsd:string +property_value: RO:0002579 RO:0002213 +is_transitive: true +is_a: indirectly_regulates ! indirectly regulates +is_a: positively_regulates ! positively regulates + [Typedef] id: indirectly_positively_regulates_activity_of name: indirectly positively regulates activity of @@ -2673,6 +2673,16 @@ xref: RO:0011024 property_value: IAO:0000117 "Vasundra Touré" xsd:string is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of +[Typedef] +id: indirectly_regulates +name: indirectly regulates +def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." [] +xref: RO:0012012 +is_a: indirectly_causally_upstream_of ! indirectly causally upstream of +is_a: regulates ! regulates +created_by: pg +creation_date: 2022-09-26T06:08:01Z + [Typedef] id: indirectly_regulates_activity_of name: indirectly regulates activity of @@ -3012,6 +3022,7 @@ id: is_small_molecule_activator_of name: is small molecule activator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" [] xref: RO:0012005 +is_a: capable_of_positively_regulating ! capable of positively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of created_by: pg creation_date: 2020-06-24T13:15:26Z @@ -3021,6 +3032,7 @@ id: is_small_molecule_inhibitor_of name: is small molecule inhibitor of def: "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process" [] xref: RO:0012006 +is_a: capable_of_negatively_regulating ! capable of negatively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of created_by: pg creation_date: 2020-06-24T13:15:35Z @@ -3030,7 +3042,7 @@ id: is_small_molecule_regulator_of name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] xref: RO:0012004 -is_a: participates_in +is_a: capable_of_regulating ! capable of regulating created_by: pg creation_date: 2020-06-24T13:15:17Z @@ -3246,7 +3258,7 @@ is_a: regulated_by ! regulated by [Typedef] id: negatively_regulates name: negatively regulates -def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +def: "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -3513,7 +3525,7 @@ is_a: regulated_by ! regulated by [Typedef] id: positively_regulates name: positively regulates -def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +def: "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -3707,13 +3719,11 @@ is_a: causally_downstream_of_or_within ! causally downstream of or within [Typedef] id: regulates name: regulates -def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." [] +def: "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 "David Hill" xsd:string property_value: IAO:0000117 "Tanya Berardini" xsd:string @@ -3800,6 +3810,17 @@ property_value: IAO:0000232 "Do not use this relation directly. It is a grouping domain: BFO:0000015 range: BFO:0000002 +[Typedef] +id: removes_input_for +name: removes input for +def: "p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0012010 +is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect +created_by: pg +creation_date: 2022-09-26T06:06:20Z + [Typedef] id: represses_expression_of name: represses expression of @@ -4495,7 +4516,7 @@ property_value: IAO:0000589 "transitively provides input for (process to process domain: BFO:0000015 range: BFO:0000015 is_transitive: true -is_a: causally_upstream_of ! causally upstream of +is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or within, positive effect [Typedef] id: transmitted_by diff --git a/subsets/ro-sequence.owl b/subsets/ro-sequence.owl index 0352d260..536119a0 100644 --- a/subsets/ro-sequence.owl +++ b/subsets/ro-sequence.owl @@ -1644,9 +1644,7 @@ N1 SubclassOf ( - - process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. - We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit + p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. Chris Mungall David Hill Tanya Berardini @@ -1671,7 +1669,7 @@ N1 SubclassOf ( - Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. Chris Mungall negatively regulates (process to process) @@ -1693,7 +1691,7 @@ N1 SubclassOf ( - Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. Chris Mungall positively regulates (process to process) @@ -2523,6 +2521,7 @@ where + p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. cjm RO:0002304 @@ -2540,11 +2539,13 @@ where + p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. 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 @@ -2717,6 +2718,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a particular instances of akt-2 enables some instance of protein kinase activity + c enables p iff c is capable of p and c acts to execute p. Chris Mungall catalyzes executes @@ -3483,50 +3485,19 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - - p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q - Chris Mungall - directly positively regulates - - directly activates (process to process) - RO:0002406 - directly_activates - directly activates - - - - + - p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one. + p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. Chris Mungall - indirectly positively regulates + indirectly activates RO:0002407 - indirectly_activates - indirectly activates - - - - - - - - - Chris Mungall - directly negatively regulates - - directly inhibits (process to process) - RO:0002408 - directly_inhibits - directly inhibits + indirectly_positively_regulates + indirectly positively regulates @@ -3535,14 +3506,15 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + - + p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. Chris Mungall - indirectly negatively regulates + indirectly inhibits RO:0002409 - indirectly_inhibits - indirectly inhibits + indirectly_negatively_regulates + indirectly negatively regulates @@ -3550,15 +3522,14 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - This relation groups causal relations between material entities and causal relations between processes + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? - * Is the influence positive or negative + * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. @@ -3573,6 +3544,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different causally_related_to causally related to + + + + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. + https://en.wikipedia.org/wiki/Causality + @@ -3582,8 +3559,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain + p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. Chris Mungall RO:0002411 @@ -3599,8 +3575,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. + p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. Chris Mungall RO:0002412 @@ -3615,8 +3590,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c + p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit Chris Mungall @@ -3631,7 +3605,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -3653,7 +3627,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. + p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) @@ -4485,7 +4459,7 @@ For example, A and B may be gene products and binding of B by A positively regul - p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. + p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. @@ -5202,7 +5176,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + p directly regulates q iff p is immediately causally upstream of q and p regulates q. Chris Mungall directly regulates (processual) @@ -5555,7 +5529,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. + p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates (process to process) @@ -5574,7 +5548,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. + p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates (process to process) @@ -6959,7 +6933,7 @@ For example, protein A (transcription factor) indirectly increases by expression - + a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process pg 2020-06-24T13:15:17Z @@ -6973,6 +6947,7 @@ For example, protein A (transcription factor) indirectly increases by expression + a relation between a continuant and a process, in which the continuant is a small molecule that activates the process pg @@ -6987,6 +6962,7 @@ For example, protein A (transcription factor) indirectly increases by expression + a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process pg @@ -7028,6 +7004,67 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. + pg + 2022-09-26T06:01:01Z + RO:0012009 + + + constitutively_upstream_of + constitutively upstream of + + + + + + + + + p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. + pg + 2022-09-26T06:06:20Z + RO:0012010 + + + removes_input_for + removes input for + + + + + + + + + p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. + pg + 2022-09-26T06:07:17Z + RO:0012011 + indirectly_causally_upstream_of + indirectly causally upstream of + + + + + + + + + + p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. + pg + 2022-09-26T06:08:01Z + RO:0012012 + indirectly_regulates + indirectly regulates + + + + diff --git a/subsets/ro-time-interval.obo b/subsets/ro-time-interval.obo index 8d5779d7..b7cf34dc 100644 --- a/subsets/ro-time-interval.obo +++ b/subsets/ro-time-interval.obo @@ -372,7 +372,7 @@ is_a: causally_related_to ! causally related to [Typedef] id: causal_relation_between_processes name: causal relation between processes -def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." [] +def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] xref: RO:0002501 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -440,21 +440,19 @@ is_a: causal_relation_between_entities ! causal relation between entities [Typedef] id: causally_related_to name: causally related to -def: "This relation groups causal relations between material entities and causal relations between processes" [] +def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] xref: RO:0002410 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string +property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string [Typedef] id: causally_upstream_of name: causally upstream of -def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" [] +def: "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002411 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within @@ -463,7 +461,9 @@ 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 +def: "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 property_value: http://purl.org/dc/terms/creator "cjm" xsd:string property_value: RO:0004050 RO:0002411 @@ -473,6 +473,7 @@ is_a: causally_upstream_of_or_within,_negative_effect ! causally upstream of or [Typedef] id: causally_upstream_of,_positive_effect name: causally upstream of, positive effect +def: "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." [] 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 subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -485,7 +486,7 @@ is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or [Typedef] id: causally_upstream_of_or_within name: causally upstream of or within -def: "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." [] +def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] synonym: "affects" RELATED [] xref: RO:0002418 property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string @@ -709,6 +710,17 @@ property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-art domain: BFO:0000004 is_a: mereotopologically_related_to ! mereotopologically related to +[Typedef] +id: constitutively_upstream_of +name: constitutively upstream of +def: "p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0012009 +is_a: causally_upstream_of,_positive_effect ! causally upstream of, positive effect +created_by: pg +creation_date: 2022-09-26T06:01:01Z + [Typedef] id: continuous_with name: continuous with @@ -993,18 +1005,6 @@ is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_develop_into ! has potential to develop into is_a: has_potential_to_directly_develop_into ! has potential to directly develop into -[Typedef] -id: directly_activates -name: directly activates -def: "p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q" [] -xref: RO:0002406 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "directly positively regulates" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly activates (process to process)" xsd:string -is_a: directly_positively_regulates ! directly positively regulates - [Typedef] id: directly_develops_from name: directly develops from @@ -1030,16 +1030,6 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "developmental precursor of" xsd:string is_a: develops_into ! develops into -[Typedef] -id: directly_inhibits -name: directly inhibits -xref: RO:0002408 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "directly negatively regulates" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly inhibits (process to process)" xsd:string -is_a: directly_negatively_regulates ! directly negatively regulates - [Typedef] id: directly_negatively_regulated_by name: directly negatively regulated by @@ -1053,7 +1043,7 @@ creation_date: 2017-09-17T13:52:38Z [Typedef] id: directly_negatively_regulates name: directly negatively regulates -def: "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." [] +def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1100,7 +1090,7 @@ creation_date: 2017-09-17T13:52:47Z [Typedef] id: directly_positively_regulates name: directly positively regulates -def: "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." [] +def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1137,9 +1127,8 @@ is_a: directly_regulates_quantity_of ! directly regulates quantity of [Typedef] id: directly_provides_input_for name: directly provides input for -def: "p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c" [] +def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] xref: RO:0002413 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -1160,7 +1149,7 @@ creation_date: 2017-09-17T13:52:24Z [Typedef] id: directly_regulates name: directly regulates -def: "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." [] +def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -1416,6 +1405,7 @@ is_a: has_participant [Typedef] id: enables name: enables +def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002327 property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string @@ -2540,9 +2530,8 @@ inverse_of: immediately_causally_upstream_of ! immediately causally upstream of [Typedef] id: immediately_causally_upstream_of name: immediately causally upstream of -def: "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q." [] +def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] xref: RO:0002412 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of @@ -2616,25 +2605,24 @@ range: BFO:0000040 is_a: directly_positively_regulates_activity_of ! directly positively regulates activity of [Typedef] -id: indirectly_activates -name: indirectly activates -def: "p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one." [] -xref: RO:0002407 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "indirectly positively regulates" xsd:string -property_value: RO:0002579 RO:0002213 -is_transitive: true -is_a: positively_regulates ! positively regulates +id: indirectly_causally_upstream_of +name: indirectly causally upstream of +def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] +xref: RO:0012011 +is_a: causally_upstream_of ! causally upstream of +created_by: pg +creation_date: 2022-09-26T06:07:17Z [Typedef] -id: indirectly_inhibits -name: indirectly inhibits +id: indirectly_negatively_regulates +name: indirectly negatively regulates +def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] xref: RO:0002409 -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "indirectly negatively regulates" xsd:string +property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 is_transitive: true +is_a: indirectly_regulates ! indirectly regulates is_a: negatively_regulates ! negatively regulates [Typedef] @@ -2654,6 +2642,18 @@ xref: RO:0011023 property_value: IAO:0000117 "Vasundra Touré" xsd:string is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of +[Typedef] +id: indirectly_positively_regulates +name: indirectly positively regulates +def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] +xref: RO:0002407 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "indirectly activates" xsd:string +property_value: RO:0002579 RO:0002213 +is_transitive: true +is_a: indirectly_regulates ! indirectly regulates +is_a: positively_regulates ! positively regulates + [Typedef] id: indirectly_positively_regulates_activity_of name: indirectly positively regulates activity of @@ -2673,6 +2673,16 @@ xref: RO:0011024 property_value: IAO:0000117 "Vasundra Touré" xsd:string is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of +[Typedef] +id: indirectly_regulates +name: indirectly regulates +def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." [] +xref: RO:0012012 +is_a: indirectly_causally_upstream_of ! indirectly causally upstream of +is_a: regulates ! regulates +created_by: pg +creation_date: 2022-09-26T06:08:01Z + [Typedef] id: indirectly_regulates_activity_of name: indirectly regulates activity of @@ -3012,6 +3022,7 @@ id: is_small_molecule_activator_of name: is small molecule activator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" [] xref: RO:0012005 +is_a: capable_of_positively_regulating ! capable of positively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of created_by: pg creation_date: 2020-06-24T13:15:26Z @@ -3021,6 +3032,7 @@ id: is_small_molecule_inhibitor_of name: is small molecule inhibitor of def: "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process" [] xref: RO:0012006 +is_a: capable_of_negatively_regulating ! capable of negatively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of created_by: pg creation_date: 2020-06-24T13:15:35Z @@ -3030,7 +3042,7 @@ id: is_small_molecule_regulator_of name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] xref: RO:0012004 -is_a: participates_in +is_a: capable_of_regulating ! capable of regulating created_by: pg creation_date: 2020-06-24T13:15:17Z @@ -3246,7 +3258,7 @@ is_a: regulated_by ! regulated by [Typedef] id: negatively_regulates name: negatively regulates -def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +def: "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -3513,7 +3525,7 @@ is_a: regulated_by ! regulated by [Typedef] id: positively_regulates name: positively regulates -def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +def: "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -3707,13 +3719,11 @@ is_a: causally_downstream_of_or_within ! causally downstream of or within [Typedef] id: regulates name: regulates -def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." [] +def: "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 "David Hill" xsd:string property_value: IAO:0000117 "Tanya Berardini" xsd:string @@ -3800,6 +3810,17 @@ property_value: IAO:0000232 "Do not use this relation directly. It is a grouping domain: BFO:0000015 range: BFO:0000002 +[Typedef] +id: removes_input_for +name: removes input for +def: "p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0012010 +is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect +created_by: pg +creation_date: 2022-09-26T06:06:20Z + [Typedef] id: represses_expression_of name: represses expression of @@ -4495,7 +4516,7 @@ property_value: IAO:0000589 "transitively provides input for (process to process domain: BFO:0000015 range: BFO:0000015 is_transitive: true -is_a: causally_upstream_of ! causally upstream of +is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or within, positive effect [Typedef] id: transmitted_by diff --git a/subsets/ro-time-interval.owl b/subsets/ro-time-interval.owl index 7a328db2..5924e64b 100644 --- a/subsets/ro-time-interval.owl +++ b/subsets/ro-time-interval.owl @@ -1644,9 +1644,7 @@ N1 SubclassOf ( - - process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. - We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit + p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. Chris Mungall David Hill Tanya Berardini @@ -1671,7 +1669,7 @@ N1 SubclassOf ( - Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. Chris Mungall negatively regulates (process to process) @@ -1693,7 +1691,7 @@ N1 SubclassOf ( - Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. Chris Mungall positively regulates (process to process) @@ -2523,6 +2521,7 @@ where + p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. cjm RO:0002304 @@ -2540,11 +2539,13 @@ where + p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. 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 @@ -2717,6 +2718,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a particular instances of akt-2 enables some instance of protein kinase activity + c enables p iff c is capable of p and c acts to execute p. Chris Mungall catalyzes executes @@ -3483,50 +3485,19 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - - p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q - Chris Mungall - directly positively regulates - - directly activates (process to process) - RO:0002406 - directly_activates - directly activates - - - - + - p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one. + p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. Chris Mungall - indirectly positively regulates + indirectly activates RO:0002407 - indirectly_activates - indirectly activates - - - - - - - - - Chris Mungall - directly negatively regulates - - directly inhibits (process to process) - RO:0002408 - directly_inhibits - directly inhibits + indirectly_positively_regulates + indirectly positively regulates @@ -3535,14 +3506,15 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + - + p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. Chris Mungall - indirectly negatively regulates + indirectly inhibits RO:0002409 - indirectly_inhibits - indirectly inhibits + indirectly_negatively_regulates + indirectly negatively regulates @@ -3550,15 +3522,14 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - This relation groups causal relations between material entities and causal relations between processes + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? - * Is the influence positive or negative + * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. @@ -3573,6 +3544,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different causally_related_to causally related to + + + + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. + https://en.wikipedia.org/wiki/Causality + @@ -3582,8 +3559,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain + p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. Chris Mungall RO:0002411 @@ -3599,8 +3575,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. + p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. Chris Mungall RO:0002412 @@ -3615,8 +3590,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c + p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit Chris Mungall @@ -3631,7 +3605,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -3653,7 +3627,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. + p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) @@ -4485,7 +4459,7 @@ For example, A and B may be gene products and binding of B by A positively regul - p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. + p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. @@ -5202,7 +5176,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + p directly regulates q iff p is immediately causally upstream of q and p regulates q. Chris Mungall directly regulates (processual) @@ -5555,7 +5529,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. + p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates (process to process) @@ -5574,7 +5548,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. + p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates (process to process) @@ -6959,7 +6933,7 @@ For example, protein A (transcription factor) indirectly increases by expression - + a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process pg 2020-06-24T13:15:17Z @@ -6973,6 +6947,7 @@ For example, protein A (transcription factor) indirectly increases by expression + a relation between a continuant and a process, in which the continuant is a small molecule that activates the process pg @@ -6987,6 +6962,7 @@ For example, protein A (transcription factor) indirectly increases by expression + a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process pg @@ -7028,6 +7004,67 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. + pg + 2022-09-26T06:01:01Z + RO:0012009 + + + constitutively_upstream_of + constitutively upstream of + + + + + + + + + p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. + pg + 2022-09-26T06:06:20Z + RO:0012010 + + + removes_input_for + removes input for + + + + + + + + + p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. + pg + 2022-09-26T06:07:17Z + RO:0012011 + indirectly_causally_upstream_of + indirectly causally upstream of + + + + + + + + + + p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. + pg + 2022-09-26T06:08:01Z + RO:0012012 + indirectly_regulates + indirectly regulates + + + +