From c3a3a19631e3056d24a4bd104df714387653ae02 Mon Sep 17 00:00:00 2001 From: Clare72 Date: Mon, 9 Jan 2023 14:58:46 +0000 Subject: [PATCH] release files 2023-01-09 --- imports/caro_import.owl | 4 +- imports/fbbt_import.owl | 233 +++++++++++++++++++++++--- imports/obi_import.owl | 6 +- imports/ro_import.owl | 233 +++++++++++++++++++++++--- src/ontology/imports/caro_import.owl | 4 +- src/ontology/imports/fbbt_import.owl | 233 +++++++++++++++++++++++--- src/ontology/imports/obi_import.owl | 6 +- src/ontology/imports/ro_import.owl | 233 +++++++++++++++++++++++--- vfbext-base.json | 6 +- vfbext-base.obo | 6 +- vfbext-base.owl | 6 +- vfbext-full.json | 239 ++++++++++++++++++++++----- vfbext-full.obo | 87 +++++++--- vfbext-full.owl | 233 +++++++++++++++++++++++--- vfbext-non-classified.json | 239 ++++++++++++++++++++++----- vfbext-non-classified.obo | 97 ++++++++--- vfbext-non-classified.owl | 233 +++++++++++++++++++++++--- vfbext-simple.json | 6 +- vfbext-simple.obo | 6 +- vfbext-simple.owl | 6 +- vfbext.json | 239 ++++++++++++++++++++++----- vfbext.obo | 95 ++++++++--- vfbext.owl | 231 +++++++++++++++++++++++--- 23 files changed, 2324 insertions(+), 357 deletions(-) diff --git a/imports/caro_import.owl b/imports/caro_import.owl index 993b538..fe9d623 100644 --- a/imports/caro_import.owl +++ b/imports/caro_import.owl @@ -12,14 +12,14 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:oboInOwl1="ttp://www.geneontology.org/formats/oboInOwl#"> - + None Common Anatomy Reference Ontology Based on CARO 1.0, with modifications and additions by David Osumi-Sutherland, Chris Mungall, Ramona Walls and Melissa Haendal. 2022-02-18 - 2022-10-24 + 2023-01-09 diff --git a/imports/fbbt_import.owl b/imports/fbbt_import.owl index d942b22..0ed6fa3 100644 --- a/imports/fbbt_import.owl +++ b/imports/fbbt_import.owl @@ -18,9 +18,9 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - - 2022-10-24 + + + 2023-01-09 @@ -137,6 +137,12 @@ + + + + + + @@ -1052,9 +1058,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - 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 @@ -1082,7 +1086,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - 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) @@ -1111,7 +1115,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - 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) @@ -1279,6 +1283,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + 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 @@ -1294,9 +1299,11 @@ A continuant cannot have an occurrent as part: use 'participates in'. + 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 @@ -1361,6 +1368,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. 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 @@ -1540,18 +1548,75 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + + + + + + + + + + + + + + + + + + + p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. + Chris Mungall + indirectly activates + + indirectly positively regulates + + + + + + + + + + + + + + + + + + + + + + + p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. + Chris Mungall + indirectly inhibits + + indirectly negatively regulates + + + + - - 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. @@ -1564,6 +1629,12 @@ 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 + @@ -1573,8 +1644,7 @@ 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 @@ -1588,8 +1658,7 @@ 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 @@ -1603,7 +1672,7 @@ 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) @@ -1855,7 +1924,7 @@ 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. @@ -1955,7 +2024,7 @@ 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) @@ -2063,7 +2132,7 @@ 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) @@ -2080,7 +2149,7 @@ 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) @@ -2220,6 +2289,31 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + 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 + + + + @@ -2840,6 +2934,12 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + @@ -2849,6 +2949,9 @@ For example, A and B may be gene products and binding of B by A positively regul + + + @@ -3846,6 +3949,50 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -4022,6 +4169,50 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/imports/obi_import.owl b/imports/obi_import.owl index 87b7de4..d91e1ee 100644 --- a/imports/obi_import.owl +++ b/imports/obi_import.owl @@ -11,7 +11,7 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"> - + en Ontology for Biomedical Investigations Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester @@ -78,8 +78,8 @@ http://creativecommons.org/licenses/by/4.0/ Ontology for Biomedical Investigations Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. - 2022-07-11 - 2022-10-24 + 2022-12-14 + 2023-01-09 diff --git a/imports/ro_import.owl b/imports/ro_import.owl index 08ee84d..e9d2c2e 100644 --- a/imports/ro_import.owl +++ b/imports/ro_import.owl @@ -16,9 +16,9 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - - 2022-10-24 + + + 2023-01-09 @@ -135,6 +135,12 @@ + + + + + + @@ -961,9 +967,7 @@ Examples include: the relationship between two channels collected simultaneously - - 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 @@ -986,7 +990,7 @@ Examples include: the relationship between two channels collected simultaneously - 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) @@ -1010,7 +1014,7 @@ Examples include: the relationship between two channels collected simultaneously - 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) @@ -1158,6 +1162,7 @@ Examples include: the relationship between two channels collected simultaneously + 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 @@ -1173,9 +1178,11 @@ Examples include: the relationship between two channels collected simultaneously + 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 @@ -1240,6 +1247,7 @@ Examples include: the relationship between two channels collected simultaneously 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 @@ -1448,18 +1456,75 @@ Examples include: the relationship between two channels collected simultaneously + + + + + + + + + + + + + + + + + + + + + + + p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. + Chris Mungall + indirectly activates + + indirectly positively regulates + + + + + + + + + + + + + + + + + + + + + + + p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. + Chris Mungall + indirectly inhibits + + indirectly negatively regulates + + + + - - 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. @@ -1472,6 +1537,12 @@ 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 + @@ -1481,8 +1552,7 @@ 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 @@ -1496,8 +1566,7 @@ 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 @@ -1511,7 +1580,7 @@ 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) @@ -1763,7 +1832,7 @@ 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. @@ -1863,7 +1932,7 @@ 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) @@ -1971,7 +2040,7 @@ 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) @@ -1988,7 +2057,7 @@ 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) @@ -2128,6 +2197,31 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + 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 + + + + @@ -2610,6 +2704,12 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + @@ -2619,6 +2719,9 @@ For example, A and B may be gene products and binding of B by A positively regul + + + @@ -3616,6 +3719,50 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -3792,6 +3939,50 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/imports/caro_import.owl b/src/ontology/imports/caro_import.owl index 993b538..fe9d623 100644 --- a/src/ontology/imports/caro_import.owl +++ b/src/ontology/imports/caro_import.owl @@ -12,14 +12,14 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:oboInOwl1="ttp://www.geneontology.org/formats/oboInOwl#"> - + None Common Anatomy Reference Ontology Based on CARO 1.0, with modifications and additions by David Osumi-Sutherland, Chris Mungall, Ramona Walls and Melissa Haendal. 2022-02-18 - 2022-10-24 + 2023-01-09 diff --git a/src/ontology/imports/fbbt_import.owl b/src/ontology/imports/fbbt_import.owl index d942b22..0ed6fa3 100644 --- a/src/ontology/imports/fbbt_import.owl +++ b/src/ontology/imports/fbbt_import.owl @@ -18,9 +18,9 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - - 2022-10-24 + + + 2023-01-09 @@ -137,6 +137,12 @@ + + + + + + @@ -1052,9 +1058,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - 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 @@ -1082,7 +1086,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - 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) @@ -1111,7 +1115,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - 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) @@ -1279,6 +1283,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + 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 @@ -1294,9 +1299,11 @@ A continuant cannot have an occurrent as part: use 'participates in'. + 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 @@ -1361,6 +1368,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. 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 @@ -1540,18 +1548,75 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + + + + + + + + + + + + + + + + + + + p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. + Chris Mungall + indirectly activates + + indirectly positively regulates + + + + + + + + + + + + + + + + + + + + + + + p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. + Chris Mungall + indirectly inhibits + + indirectly negatively regulates + + + + - - 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. @@ -1564,6 +1629,12 @@ 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 + @@ -1573,8 +1644,7 @@ 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 @@ -1588,8 +1658,7 @@ 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 @@ -1603,7 +1672,7 @@ 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) @@ -1855,7 +1924,7 @@ 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. @@ -1955,7 +2024,7 @@ 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) @@ -2063,7 +2132,7 @@ 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) @@ -2080,7 +2149,7 @@ 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) @@ -2220,6 +2289,31 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + 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 + + + + @@ -2840,6 +2934,12 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + @@ -2849,6 +2949,9 @@ For example, A and B may be gene products and binding of B by A positively regul + + + @@ -3846,6 +3949,50 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -4022,6 +4169,50 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/imports/obi_import.owl b/src/ontology/imports/obi_import.owl index 87b7de4..d91e1ee 100644 --- a/src/ontology/imports/obi_import.owl +++ b/src/ontology/imports/obi_import.owl @@ -11,7 +11,7 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"> - + en Ontology for Biomedical Investigations Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester @@ -78,8 +78,8 @@ http://creativecommons.org/licenses/by/4.0/ Ontology for Biomedical Investigations Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. - 2022-07-11 - 2022-10-24 + 2022-12-14 + 2023-01-09 diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl index 08ee84d..e9d2c2e 100644 --- a/src/ontology/imports/ro_import.owl +++ b/src/ontology/imports/ro_import.owl @@ -16,9 +16,9 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - - 2022-10-24 + + + 2023-01-09 @@ -135,6 +135,12 @@ + + + + + + @@ -961,9 +967,7 @@ Examples include: the relationship between two channels collected simultaneously - - 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 @@ -986,7 +990,7 @@ Examples include: the relationship between two channels collected simultaneously - 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) @@ -1010,7 +1014,7 @@ Examples include: the relationship between two channels collected simultaneously - 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) @@ -1158,6 +1162,7 @@ Examples include: the relationship between two channels collected simultaneously + 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 @@ -1173,9 +1178,11 @@ Examples include: the relationship between two channels collected simultaneously + 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 @@ -1240,6 +1247,7 @@ Examples include: the relationship between two channels collected simultaneously 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 @@ -1448,18 +1456,75 @@ Examples include: the relationship between two channels collected simultaneously + + + + + + + + + + + + + + + + + + + + + + + p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. + Chris Mungall + indirectly activates + + indirectly positively regulates + + + + + + + + + + + + + + + + + + + + + + + p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. + Chris Mungall + indirectly inhibits + + indirectly negatively regulates + + + + - - 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. @@ -1472,6 +1537,12 @@ 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 + @@ -1481,8 +1552,7 @@ 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 @@ -1496,8 +1566,7 @@ 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 @@ -1511,7 +1580,7 @@ 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) @@ -1763,7 +1832,7 @@ 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. @@ -1863,7 +1932,7 @@ 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) @@ -1971,7 +2040,7 @@ 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) @@ -1988,7 +2057,7 @@ 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) @@ -2128,6 +2197,31 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + 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 + + + + @@ -2610,6 +2704,12 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + @@ -2619,6 +2719,9 @@ For example, A and B may be gene products and binding of B by A positively regul + + + @@ -3616,6 +3719,50 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -3792,6 +3939,50 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/vfbext-base.json b/vfbext-base.json index ad34ffc..6b2bf3f 100644 --- a/vfbext-base.json +++ b/vfbext-base.json @@ -97,7 +97,7 @@ }, { "pred": "http://www.geneontology.org/formats/oboInOwl#date", - "val": "24:10:2022 12:05" + "val": "09:01:2023 14:46" }, { "pred": "http://www.w3.org/2000/01/rdf-schema#comment", @@ -105,10 +105,10 @@ }, { "pred": "http://www.w3.org/2002/07/owl#versionInfo", - "val": "2022-10-24" + "val": "2023-01-09" } ], - "version": "http://purl.obolibrary.org/obo/vfbext/releases/2022-10-24/vfbext-base.json" + "version": "http://purl.obolibrary.org/obo/vfbext/releases/2023-01-09/vfbext-base.json" }, "nodes": [ { diff --git a/vfbext-base.obo b/vfbext-base.obo index 53852f1..d602ec0 100644 --- a/vfbext-base.obo +++ b/vfbext-base.obo @@ -1,6 +1,6 @@ format-version: 1.2 -data-version: vfbext/releases/2022-10-24/vfbext-base.owl -date: 24:10:2022 12:05 +data-version: vfbext/releases/2023-01-09/vfbext-base.owl +date: 09:01:2023 14:46 subsetdef: clone "" subsetdef: neuron "" subsetdef: ns_part "" @@ -12,7 +12,7 @@ property_value: http://purl.org/dc/elements/1.1/description "An ontology of misc property_value: http://purl.org/dc/elements/1.1/title "VFB Extension Ontology" xsd:string property_value: http://purl.org/dc/elements/1.1/type IAO:8000001 property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/by/4.0/ xsd:string -property_value: owl:versionInfo "2022-10-24" xsd:string +property_value: owl:versionInfo "2023-01-09" xsd:string [Term] id: VFB:10000005 diff --git a/vfbext-base.owl b/vfbext-base.owl index 5039eed..7c42fa9 100644 --- a/vfbext-base.owl +++ b/vfbext-base.owl @@ -13,14 +13,14 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + An ontology of miscellaneous terms for data annotation in VFB. VFB Extension Ontology https://creativecommons.org/licenses/by/4.0/</terms:license> - 24:10:2022 12:05 + 09:01:2023 14:46 VFB extension ontology - 2022-10-24 + 2023-01-09 diff --git a/vfbext-full.json b/vfbext-full.json index e3fe649..5d78490 100644 --- a/vfbext-full.json +++ b/vfbext-full.json @@ -710,11 +710,26 @@ "pred": "subPropertyOf", "sub": "http://purl.obolibrary.org/obo/RO_0002578" }, + { + "obj": "http://purl.obolibrary.org/obo/RO_0002211", + "pred": "subPropertyOf", + "sub": "http://purl.obolibrary.org/obo/RO_0012012" + }, + { + "obj": "http://purl.obolibrary.org/obo/RO_0002212", + "pred": "subPropertyOf", + "sub": "http://purl.obolibrary.org/obo/RO_0002409" + }, { "obj": "http://purl.obolibrary.org/obo/RO_0002212", "pred": "subPropertyOf", "sub": "http://purl.obolibrary.org/obo/RO_0002630" }, + { + "obj": "http://purl.obolibrary.org/obo/RO_0002213", + "pred": "subPropertyOf", + "sub": "http://purl.obolibrary.org/obo/RO_0002407" + }, { "obj": "http://purl.obolibrary.org/obo/RO_0002213", "pred": "subPropertyOf", @@ -975,6 +990,11 @@ "pred": "subPropertyOf", "sub": "http://purl.obolibrary.org/obo/RO_0002412" }, + { + "obj": "http://purl.obolibrary.org/obo/RO_0002411", + "pred": "subPropertyOf", + "sub": "http://purl.obolibrary.org/obo/RO_0012011" + }, { "obj": "http://purl.obolibrary.org/obo/RO_0002412", "pred": "inverseOf", @@ -1205,6 +1225,21 @@ "pred": "subPropertyOf", "sub": "http://purl.obolibrary.org/obo/RO_0002448" }, + { + "obj": "http://purl.obolibrary.org/obo/RO_0012011", + "pred": "subPropertyOf", + "sub": "http://purl.obolibrary.org/obo/RO_0012012" + }, + { + "obj": "http://purl.obolibrary.org/obo/RO_0012012", + "pred": "subPropertyOf", + "sub": "http://purl.obolibrary.org/obo/RO_0002407" + }, + { + "obj": "http://purl.obolibrary.org/obo/RO_0012012", + "pred": "subPropertyOf", + "sub": "http://purl.obolibrary.org/obo/RO_0002409" + }, { "obj": "http://purl.obolibrary.org/obo/RO_0019000", "pred": "subPropertyOf", @@ -1289,7 +1324,7 @@ }, { "pred": "http://www.geneontology.org/formats/oboInOwl#date", - "val": "24:10:2022 12:05" + "val": "09:01:2023 14:46" }, { "pred": "http://www.w3.org/2000/01/rdf-schema#comment", @@ -1297,10 +1332,10 @@ }, { "pred": "http://www.w3.org/2002/07/owl#versionInfo", - "val": "2022-10-24" + "val": "2023-01-09" } ], - "version": "http://purl.obolibrary.org/obo/vfbext/releases/2022-10-24/vfbext-full.json" + "version": "http://purl.obolibrary.org/obo/vfbext/releases/2023-01-09/vfbext-full.json" }, "nodes": [ { @@ -3048,14 +3083,6 @@ "lbl": "regulates", "meta": { "basicPropertyValues": [ - { - "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": "Chris Mungall" @@ -3098,7 +3125,7 @@ } ], "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." }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", @@ -3144,7 +3171,7 @@ } ], "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." }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", @@ -3190,7 +3217,7 @@ } ], "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." }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", @@ -3465,6 +3492,9 @@ "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" ], + "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." + }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" @@ -3486,8 +3516,12 @@ "val": "cjm" } ], - "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." + }, + "subsets": [ + "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", + "http://purl.obolibrary.org/obo/valid_for_gocam" ] }, "type": "PROPERTY" @@ -3590,6 +3624,9 @@ "val": "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." } ], + "definition": { + "val": "c enables p iff c is capable of p and c acts to execute p." + }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ] @@ -3874,17 +3911,61 @@ "type": "PROPERTY" }, { - "id": "http://purl.obolibrary.org/obo/RO_0002410", - "lbl": "causally related to", + "id": "http://purl.obolibrary.org/obo/RO_0002407", + "lbl": "indirectly positively regulates", "meta": { "basicPropertyValues": [ { - "pred": "http://purl.obolibrary.org/obo/IAO_0000114", - "val": "http://purl.obolibrary.org/obo/IAO_0000428" + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Chris Mungall" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "indirectly activates" }, + { + "pred": "http://purl.obolibrary.org/obo/RO_0002579", + "val": "http://purl.obolibrary.org/obo/RO_0002213" + } + ], + "definition": { + "val": "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/RO_0002409", + "lbl": "indirectly negatively regulates", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Chris Mungall" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "indirectly inhibits" + }, + { + "pred": "http://purl.obolibrary.org/obo/RO_0002579", + "val": "http://purl.obolibrary.org/obo/RO_0002212" + } + ], + "definition": { + "val": "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/RO_0002410", + "lbl": "causally related to", + "meta": { + "basicPropertyValues": [ { "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." + "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_0000117", @@ -3896,7 +3977,10 @@ } ], "definition": { - "val": "This relation groups causal relations between material entities and causal relations between processes" + "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" + ] } }, "type": "PROPERTY" @@ -3906,17 +3990,13 @@ "lbl": "causally upstream of", "meta": { "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000114", - "val": "http://purl.obolibrary.org/obo/IAO_0000428" - }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "Chris Mungall" } ], "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." }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", @@ -3930,10 +4010,6 @@ "lbl": "immediately causally upstream of", "meta": { "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000114", - "val": "http://purl.obolibrary.org/obo/IAO_0000428" - }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "Chris Mungall" @@ -3944,7 +4020,7 @@ } ], "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." } }, "type": "PROPERTY" @@ -3968,7 +4044,7 @@ } ], "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." }, "synonyms": [ { @@ -4331,7 +4407,7 @@ } ], "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." } }, "type": "PROPERTY" @@ -4484,7 +4560,7 @@ } ], "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." }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", @@ -4649,7 +4725,7 @@ } ], "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." }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", @@ -4678,7 +4754,7 @@ } ], "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." }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", @@ -4880,6 +4956,46 @@ }, "type": "PROPERTY" }, + { + "id": "http://purl.obolibrary.org/obo/RO_0012011", + "lbl": "indirectly causally upstream of", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "pg" + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2022-09-26T06:07:17Z" + } + ], + "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." + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/RO_0012012", + "lbl": "indirectly regulates", + "meta": { + "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" + } + ], + "definition": { + "val": "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." + } + }, + "type": "PROPERTY" + }, { "id": "http://purl.obolibrary.org/obo/RO_0017001", "lbl": "device utilizes material", @@ -5516,12 +5632,61 @@ ], "predicateId": "http://purl.obolibrary.org/obo/RO_0004032" }, + { + "chainPredicateIds": [ + "http://purl.obolibrary.org/obo/RO_0002407", + "http://purl.obolibrary.org/obo/RO_0002629" + ], + "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_0002407" + }, + { + "chainPredicateIds": [ + "http://purl.obolibrary.org/obo/RO_0002409", + "http://purl.obolibrary.org/obo/RO_0002409" + ], + "predicateId": "http://purl.obolibrary.org/obo/RO_0002407" + }, + { + "chainPredicateIds": [ + "http://purl.obolibrary.org/obo/RO_0002409", + "http://purl.obolibrary.org/obo/RO_0002630" + ], + "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_0002409" + }, { "chainPredicateIds": [ "http://purl.obolibrary.org/obo/RO_0002578", "http://purl.obolibrary.org/obo/RO_0002578" ], "predicateId": "http://purl.obolibrary.org/obo/RO_0002211" + }, + { + "chainPredicateIds": [ + "http://purl.obolibrary.org/obo/RO_0002629", + "http://purl.obolibrary.org/obo/RO_0002629" + ], + "predicateId": "http://purl.obolibrary.org/obo/RO_0002407" + }, + { + "chainPredicateIds": [ + "http://purl.obolibrary.org/obo/RO_0002630", + "http://purl.obolibrary.org/obo/RO_0002630" + ], + "predicateId": "http://purl.obolibrary.org/obo/RO_0002409" } ] } diff --git a/vfbext-full.obo b/vfbext-full.obo index 8eda3f2..2bcc24e 100644 --- a/vfbext-full.obo +++ b/vfbext-full.obo @@ -1,6 +1,6 @@ format-version: 1.2 -data-version: vfbext/releases/2022-10-24/vfbext-full.owl -date: 24:10:2022 12:05 +data-version: vfbext/releases/2023-01-09/vfbext-full.owl +date: 09:01:2023 14:46 subsetdef: clone "" subsetdef: cur "" subsetdef: EmbDevSlim "" @@ -27,7 +27,7 @@ ontology: vfbext/vfbext-full property_value: http://purl.org/dc/elements/1.1/description "An ontology of miscellaneous terms for data annotation in VFB." xsd:string property_value: http://purl.org/dc/elements/1.1/title "VFB Extension Ontology" xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/by/4.0/ xsd:string -property_value: owl:versionInfo "2022-10-24" xsd:string +property_value: owl:versionInfo "2023-01-09" xsd:string [Term] id: BFO:0000001 @@ -720,6 +720,7 @@ is_a: RO:0002500 ! causal agent in process [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 @@ -731,7 +732,9 @@ 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 @@ -762,6 +765,7 @@ property_value: RO:0001900 RO:0001901 [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: example_of_usage "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -900,22 +904,49 @@ is_a: RO:0002087 ! immediately preceded by is_a: RO:0002404 ! causally downstream of inverse_of: RO:0002412 ! immediately causally upstream of +[Typedef] +id: 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." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "indirectly activates" xsd:string +property_value: RO:0002579 RO:0002213 +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: positively_regulates ! positively regulates +is_a: RO:0012012 ! indirectly regulates +transitive_over: RO:0002629 ! directly positively regulates + +[Typedef] +id: 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." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "indirectly inhibits" xsd:string +property_value: RO:0002579 RO:0002212 +holds_over_chain: RO:0002630 RO:0002409 +holds_over_chain: RO:0002630 RO:0002630 +is_transitive: true +is_a: negatively_regulates ! negatively regulates +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: editor_note "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:0000114 IAO:0000428 +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: editor_note "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 @@ -924,8 +955,7 @@ 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 @@ -934,7 +964,7 @@ is_a: RO:0002411 ! causally upstream of [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: editor_note "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 @@ -1089,7 +1119,7 @@ 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 @@ -1152,7 +1182,7 @@ is_a: RO:0002506 ! causal relation between entities [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 @@ -1220,7 +1250,7 @@ is_a: RO:0002410 ! causally related to [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 @@ -1233,7 +1263,7 @@ 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 @@ -1324,6 +1354,23 @@ domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002566 ! causally influences +[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: regulates ! regulates +is_a: RO:0012011 ! indirectly causally upstream of +created_by: pg +creation_date: 2022-09-26T06:08:01Z + [Typedef] id: RO:0017001 name: device utilizes material @@ -1529,7 +1576,7 @@ name: depicts id: negatively_regulates name: negatively regulates namespace: external -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 @@ -1601,7 +1648,7 @@ inverse_of: has_part ! has part id: positively_regulates name: positively regulates namespace: external -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 @@ -1620,13 +1667,11 @@ inverse_of: RO:0002336 ! positively regulated by id: regulates name: regulates namespace: external -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: editor_note "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:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 "David Hill" xsd:string property_value: IAO:0000117 "Tanya Berardini" xsd:string diff --git a/vfbext-full.owl b/vfbext-full.owl index 33e27c8..c0b92d7 100644 --- a/vfbext-full.owl +++ b/vfbext-full.owl @@ -21,13 +21,13 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:oboInOwl2="ttp://www.geneontology.org/formats/oboInOwl#"> - + An ontology of miscellaneous terms for data annotation in VFB. VFB Extension Ontology https://creativecommons.org/licenses/by/4.0/</terms:license> - 24:10:2022 12:05 + 09:01:2023 14:46 VFB extension ontology - 2022-10-24 + 2023-01-09 @@ -197,6 +197,12 @@ + + + + + + @@ -1349,9 +1355,7 @@ Examples include: the relationship between two channels collected simultaneously - - 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 @@ -1379,7 +1383,7 @@ Examples include: the relationship between two channels collected simultaneously - 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) @@ -1408,7 +1412,7 @@ Examples include: the relationship between two channels collected simultaneously - 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) @@ -1576,6 +1580,7 @@ Examples include: the relationship between two channels collected simultaneously + 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 @@ -1591,9 +1596,11 @@ Examples include: the relationship between two channels collected simultaneously + 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 @@ -1658,6 +1665,7 @@ Examples include: the relationship between two channels collected simultaneously 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 @@ -1866,18 +1874,75 @@ Examples include: the relationship between two channels collected simultaneously + + + + + + + + + + + + + + + + + + + + + + + p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. + Chris Mungall + indirectly activates + + indirectly positively regulates + + + + + + + + + + + + + + + + + + + + + + + p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. + Chris Mungall + indirectly inhibits + + indirectly negatively regulates + + + + - - 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. @@ -1890,6 +1955,12 @@ 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 + @@ -1899,8 +1970,7 @@ 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 @@ -1914,8 +1984,7 @@ 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 @@ -1929,7 +1998,7 @@ 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) @@ -2181,7 +2250,7 @@ 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. @@ -2281,7 +2350,7 @@ 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) @@ -2389,7 +2458,7 @@ 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) @@ -2406,7 +2475,7 @@ 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) @@ -2546,6 +2615,31 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + 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 + + + + @@ -3526,6 +3620,12 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + @@ -3535,6 +3635,9 @@ For example, A and B may be gene products and binding of B by A positively regul + + + @@ -4532,6 +4635,50 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -4708,6 +4855,50 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/vfbext-non-classified.json b/vfbext-non-classified.json index a3f1d2b..1194cd7 100644 --- a/vfbext-non-classified.json +++ b/vfbext-non-classified.json @@ -700,11 +700,26 @@ "pred": "subPropertyOf", "sub": "http://purl.obolibrary.org/obo/RO_0002578" }, + { + "obj": "http://purl.obolibrary.org/obo/RO_0002211", + "pred": "subPropertyOf", + "sub": "http://purl.obolibrary.org/obo/RO_0012012" + }, + { + "obj": "http://purl.obolibrary.org/obo/RO_0002212", + "pred": "subPropertyOf", + "sub": "http://purl.obolibrary.org/obo/RO_0002409" + }, { "obj": "http://purl.obolibrary.org/obo/RO_0002212", "pred": "subPropertyOf", "sub": "http://purl.obolibrary.org/obo/RO_0002630" }, + { + "obj": "http://purl.obolibrary.org/obo/RO_0002213", + "pred": "subPropertyOf", + "sub": "http://purl.obolibrary.org/obo/RO_0002407" + }, { "obj": "http://purl.obolibrary.org/obo/RO_0002213", "pred": "subPropertyOf", @@ -965,6 +980,11 @@ "pred": "subPropertyOf", "sub": "http://purl.obolibrary.org/obo/RO_0002412" }, + { + "obj": "http://purl.obolibrary.org/obo/RO_0002411", + "pred": "subPropertyOf", + "sub": "http://purl.obolibrary.org/obo/RO_0012011" + }, { "obj": "http://purl.obolibrary.org/obo/RO_0002412", "pred": "inverseOf", @@ -1195,6 +1215,21 @@ "pred": "subPropertyOf", "sub": "http://purl.obolibrary.org/obo/RO_0002448" }, + { + "obj": "http://purl.obolibrary.org/obo/RO_0012011", + "pred": "subPropertyOf", + "sub": "http://purl.obolibrary.org/obo/RO_0012012" + }, + { + "obj": "http://purl.obolibrary.org/obo/RO_0012012", + "pred": "subPropertyOf", + "sub": "http://purl.obolibrary.org/obo/RO_0002407" + }, + { + "obj": "http://purl.obolibrary.org/obo/RO_0012012", + "pred": "subPropertyOf", + "sub": "http://purl.obolibrary.org/obo/RO_0002409" + }, { "obj": "http://purl.obolibrary.org/obo/RO_0019000", "pred": "subPropertyOf", @@ -1279,7 +1314,7 @@ }, { "pred": "http://www.geneontology.org/formats/oboInOwl#date", - "val": "24:10:2022 12:05" + "val": "09:01:2023 14:46" }, { "pred": "http://www.w3.org/2000/01/rdf-schema#comment", @@ -1287,10 +1322,10 @@ }, { "pred": "http://www.w3.org/2002/07/owl#versionInfo", - "val": "2022-10-24" + "val": "2023-01-09" } ], - "version": "http://purl.obolibrary.org/obo/vfbext/releases/2022-10-24/vfbext-non-classified.json" + "version": "http://purl.obolibrary.org/obo/vfbext/releases/2023-01-09/vfbext-non-classified.json" }, "nodes": [ { @@ -3038,14 +3073,6 @@ "lbl": "regulates", "meta": { "basicPropertyValues": [ - { - "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": "Chris Mungall" @@ -3088,7 +3115,7 @@ } ], "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." }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", @@ -3134,7 +3161,7 @@ } ], "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." }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", @@ -3180,7 +3207,7 @@ } ], "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." }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", @@ -3455,6 +3482,9 @@ "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" ], + "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." + }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" @@ -3476,8 +3506,12 @@ "val": "cjm" } ], - "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." + }, + "subsets": [ + "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", + "http://purl.obolibrary.org/obo/valid_for_gocam" ] }, "type": "PROPERTY" @@ -3580,6 +3614,9 @@ "val": "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." } ], + "definition": { + "val": "c enables p iff c is capable of p and c acts to execute p." + }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ] @@ -3864,17 +3901,61 @@ "type": "PROPERTY" }, { - "id": "http://purl.obolibrary.org/obo/RO_0002410", - "lbl": "causally related to", + "id": "http://purl.obolibrary.org/obo/RO_0002407", + "lbl": "indirectly positively regulates", "meta": { "basicPropertyValues": [ { - "pred": "http://purl.obolibrary.org/obo/IAO_0000114", - "val": "http://purl.obolibrary.org/obo/IAO_0000428" + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Chris Mungall" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "indirectly activates" }, + { + "pred": "http://purl.obolibrary.org/obo/RO_0002579", + "val": "http://purl.obolibrary.org/obo/RO_0002213" + } + ], + "definition": { + "val": "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/RO_0002409", + "lbl": "indirectly negatively regulates", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Chris Mungall" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "indirectly inhibits" + }, + { + "pred": "http://purl.obolibrary.org/obo/RO_0002579", + "val": "http://purl.obolibrary.org/obo/RO_0002212" + } + ], + "definition": { + "val": "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/RO_0002410", + "lbl": "causally related to", + "meta": { + "basicPropertyValues": [ { "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." + "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_0000117", @@ -3886,7 +3967,10 @@ } ], "definition": { - "val": "This relation groups causal relations between material entities and causal relations between processes" + "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" + ] } }, "type": "PROPERTY" @@ -3896,17 +3980,13 @@ "lbl": "causally upstream of", "meta": { "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000114", - "val": "http://purl.obolibrary.org/obo/IAO_0000428" - }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "Chris Mungall" } ], "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." }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", @@ -3920,10 +4000,6 @@ "lbl": "immediately causally upstream of", "meta": { "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000114", - "val": "http://purl.obolibrary.org/obo/IAO_0000428" - }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "Chris Mungall" @@ -3934,7 +4010,7 @@ } ], "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." } }, "type": "PROPERTY" @@ -3958,7 +4034,7 @@ } ], "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." }, "synonyms": [ { @@ -4321,7 +4397,7 @@ } ], "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." } }, "type": "PROPERTY" @@ -4474,7 +4550,7 @@ } ], "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." }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", @@ -4639,7 +4715,7 @@ } ], "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." }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", @@ -4668,7 +4744,7 @@ } ], "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." }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", @@ -4870,6 +4946,46 @@ }, "type": "PROPERTY" }, + { + "id": "http://purl.obolibrary.org/obo/RO_0012011", + "lbl": "indirectly causally upstream of", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "pg" + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2022-09-26T06:07:17Z" + } + ], + "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." + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/RO_0012012", + "lbl": "indirectly regulates", + "meta": { + "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" + } + ], + "definition": { + "val": "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." + } + }, + "type": "PROPERTY" + }, { "id": "http://purl.obolibrary.org/obo/RO_0017001", "lbl": "device utilizes material", @@ -5506,12 +5622,61 @@ ], "predicateId": "http://purl.obolibrary.org/obo/RO_0004032" }, + { + "chainPredicateIds": [ + "http://purl.obolibrary.org/obo/RO_0002407", + "http://purl.obolibrary.org/obo/RO_0002629" + ], + "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_0002407" + }, + { + "chainPredicateIds": [ + "http://purl.obolibrary.org/obo/RO_0002409", + "http://purl.obolibrary.org/obo/RO_0002409" + ], + "predicateId": "http://purl.obolibrary.org/obo/RO_0002407" + }, + { + "chainPredicateIds": [ + "http://purl.obolibrary.org/obo/RO_0002409", + "http://purl.obolibrary.org/obo/RO_0002630" + ], + "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_0002409" + }, { "chainPredicateIds": [ "http://purl.obolibrary.org/obo/RO_0002578", "http://purl.obolibrary.org/obo/RO_0002578" ], "predicateId": "http://purl.obolibrary.org/obo/RO_0002211" + }, + { + "chainPredicateIds": [ + "http://purl.obolibrary.org/obo/RO_0002629", + "http://purl.obolibrary.org/obo/RO_0002629" + ], + "predicateId": "http://purl.obolibrary.org/obo/RO_0002407" + }, + { + "chainPredicateIds": [ + "http://purl.obolibrary.org/obo/RO_0002630", + "http://purl.obolibrary.org/obo/RO_0002630" + ], + "predicateId": "http://purl.obolibrary.org/obo/RO_0002409" } ] } diff --git a/vfbext-non-classified.obo b/vfbext-non-classified.obo index 912b43a..ee15cfe 100644 --- a/vfbext-non-classified.obo +++ b/vfbext-non-classified.obo @@ -1,6 +1,6 @@ format-version: 1.2 -data-version: vfbext/releases/2022-10-24/vfbext-non-classified.owl -date: 24:10:2022 12:05 +data-version: vfbext/releases/2023-01-09/vfbext-non-classified.owl +date: 09:01:2023 14:46 subsetdef: clone "" subsetdef: cur "" subsetdef: EmbDevSlim "" @@ -27,7 +27,7 @@ ontology: vfbext/vfbext-non-classified property_value: http://purl.org/dc/elements/1.1/description "An ontology of miscellaneous terms for data annotation in VFB." xsd:string property_value: http://purl.org/dc/elements/1.1/title "VFB Extension Ontology" xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/by/4.0/ xsd:string -property_value: owl:versionInfo "2022-10-24" xsd:string +property_value: owl:versionInfo "2023-01-09" xsd:string [Term] id: BFO:0000001 @@ -478,7 +478,7 @@ property_value: example_of_usage "this enzyme has function this catalysis functi property_value: IAO:0000118 "has_function" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000034 ! function -is_a: has_characteristic ! has characteristic +is_a: has_characteristic ! has_characteristic [Typedef] id: RO:0000086 @@ -488,7 +488,7 @@ property_value: editor_note "A bearer can have many qualities, and its qualities property_value: example_of_usage "this apple has quality this red color" xsd:string property_value: IAO:0000118 "has_quality" xsd:string range: BFO:0000019 ! quality -is_a: has_characteristic ! has characteristic +is_a: has_characteristic ! has_characteristic [Typedef] id: RO:0000087 @@ -499,7 +499,7 @@ property_value: example_of_usage "this person has role this investigator role (m property_value: IAO:0000118 "has_role" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000023 ! role -is_a: has_characteristic ! has characteristic +is_a: has_characteristic ! has_characteristic [Typedef] id: RO:0000091 @@ -507,7 +507,7 @@ name: has disposition def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] domain: BFO:0000004 ! independent continuant range: BFO:0000016 ! disposition -is_a: has_characteristic ! has characteristic +is_a: has_characteristic ! has_characteristic inverse_of: RO:0000092 ! disposition of [Typedef] @@ -718,6 +718,7 @@ is_a: RO:0002500 ! causal agent in process [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 @@ -729,7 +730,9 @@ 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 @@ -760,6 +763,7 @@ property_value: RO:0001900 RO:0001901 [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: example_of_usage "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -898,22 +902,49 @@ is_a: RO:0002087 ! immediately preceded by is_a: RO:0002404 ! causally downstream of inverse_of: RO:0002412 ! immediately causally upstream of +[Typedef] +id: 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." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "indirectly activates" xsd:string +property_value: RO:0002579 RO:0002213 +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: positively_regulates ! positively regulates +is_a: RO:0012012 ! indirectly regulates +transitive_over: RO:0002629 ! directly positively regulates + +[Typedef] +id: 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." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "indirectly inhibits" xsd:string +property_value: RO:0002579 RO:0002212 +holds_over_chain: RO:0002630 RO:0002409 +holds_over_chain: RO:0002630 RO:0002630 +is_transitive: true +is_a: negatively_regulates ! negatively regulates +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: editor_note "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:0000114 IAO:0000428 +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: editor_note "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 @@ -922,8 +953,7 @@ 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 @@ -932,7 +962,7 @@ is_a: RO:0002411 ! causally upstream of [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: editor_note "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 @@ -1087,7 +1117,7 @@ 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 @@ -1150,7 +1180,7 @@ is_a: RO:0002506 ! causal relation between entities [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 @@ -1218,7 +1248,7 @@ is_a: RO:0002410 ! causally related to [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 @@ -1231,7 +1261,7 @@ 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 @@ -1322,6 +1352,23 @@ domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002566 ! causally influences +[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: regulates ! regulates +is_a: RO:0012011 ! indirectly causally upstream of +created_by: pg +creation_date: 2022-09-26T06:08:01Z + [Typedef] id: RO:0017001 name: device utilizes material @@ -1441,7 +1488,7 @@ property_value: IAO:0000118 "inheres_in" xsd:string property_value: RO:0001900 RO:0001901 is_functional: true is_a: RO:0002314 ! characteristic of part of -inverse_of: has_characteristic ! has characteristic +inverse_of: has_characteristic ! has_characteristic [Typedef] id: editor_note @@ -1527,7 +1574,7 @@ name: depicts id: negatively_regulates name: negatively regulates namespace: external -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 @@ -1599,7 +1646,7 @@ inverse_of: has_part ! has part id: positively_regulates name: positively regulates namespace: external -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 @@ -1618,13 +1665,11 @@ inverse_of: RO:0002336 ! positively regulated by id: regulates name: regulates namespace: external -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: editor_note "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:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 "David Hill" xsd:string property_value: IAO:0000117 "Tanya Berardini" xsd:string diff --git a/vfbext-non-classified.owl b/vfbext-non-classified.owl index 160929d..7777626 100644 --- a/vfbext-non-classified.owl +++ b/vfbext-non-classified.owl @@ -21,13 +21,13 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:oboInOwl2="ttp://www.geneontology.org/formats/oboInOwl#"> - + An ontology of miscellaneous terms for data annotation in VFB. VFB Extension Ontology https://creativecommons.org/licenses/by/4.0/</terms:license> - 24:10:2022 12:05 + 09:01:2023 14:46 VFB extension ontology - 2022-10-24 + 2023-01-09 @@ -197,6 +197,12 @@ + + + + + + @@ -1349,9 +1355,7 @@ Examples include: the relationship between two channels collected simultaneously - - 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 @@ -1379,7 +1383,7 @@ Examples include: the relationship between two channels collected simultaneously - 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) @@ -1408,7 +1412,7 @@ Examples include: the relationship between two channels collected simultaneously - 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) @@ -1576,6 +1580,7 @@ Examples include: the relationship between two channels collected simultaneously + 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 @@ -1591,9 +1596,11 @@ Examples include: the relationship between two channels collected simultaneously + 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 @@ -1658,6 +1665,7 @@ Examples include: the relationship between two channels collected simultaneously 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 @@ -1866,18 +1874,75 @@ Examples include: the relationship between two channels collected simultaneously + + + + + + + + + + + + + + + + + + + + + + + p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. + Chris Mungall + indirectly activates + + indirectly positively regulates + + + + + + + + + + + + + + + + + + + + + + + p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. + Chris Mungall + indirectly inhibits + + indirectly negatively regulates + + + + - - 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. @@ -1890,6 +1955,12 @@ 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 + @@ -1899,8 +1970,7 @@ 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 @@ -1914,8 +1984,7 @@ 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 @@ -1929,7 +1998,7 @@ 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) @@ -2181,7 +2250,7 @@ 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. @@ -2281,7 +2350,7 @@ 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) @@ -2389,7 +2458,7 @@ 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) @@ -2406,7 +2475,7 @@ 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) @@ -2546,6 +2615,31 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + 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 + + + + @@ -3519,6 +3613,12 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + @@ -3528,6 +3628,9 @@ For example, A and B may be gene products and binding of B by A positively regul + + + @@ -4525,6 +4628,50 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -4701,6 +4848,50 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/vfbext-simple.json b/vfbext-simple.json index 24709bd..6689f1c 100644 --- a/vfbext-simple.json +++ b/vfbext-simple.json @@ -58,7 +58,7 @@ }, { "pred": "http://www.geneontology.org/formats/oboInOwl#date", - "val": "24:10:2022 12:05" + "val": "09:01:2023 14:46" }, { "pred": "http://www.w3.org/2000/01/rdf-schema#comment", @@ -66,10 +66,10 @@ }, { "pred": "http://www.w3.org/2002/07/owl#versionInfo", - "val": "2022-10-24" + "val": "2023-01-09" } ], - "version": "http://purl.obolibrary.org/obo/vfbext/releases/2022-10-24/vfbext-simple.json" + "version": "http://purl.obolibrary.org/obo/vfbext/releases/2023-01-09/vfbext-simple.json" }, "nodes": [ { diff --git a/vfbext-simple.obo b/vfbext-simple.obo index d0b5fe0..5b1afdf 100644 --- a/vfbext-simple.obo +++ b/vfbext-simple.obo @@ -1,6 +1,6 @@ format-version: 1.2 -data-version: vfbext/releases/2022-10-24/vfbext-simple.owl -date: 24:10:2022 12:05 +data-version: vfbext/releases/2023-01-09/vfbext-simple.owl +date: 09:01:2023 14:46 subsetdef: clone "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" @@ -15,7 +15,7 @@ ontology: vfbext/vfbext-simple property_value: http://purl.org/dc/elements/1.1/description "An ontology of miscellaneous terms for data annotation in VFB." xsd:string property_value: http://purl.org/dc/elements/1.1/title "VFB Extension Ontology" xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/by/4.0/ xsd:string -property_value: owl:versionInfo "2022-10-24" xsd:string +property_value: owl:versionInfo "2023-01-09" xsd:string [Term] id: VFB:10000005 diff --git a/vfbext-simple.owl b/vfbext-simple.owl index 7c930a9..bc73af8 100644 --- a/vfbext-simple.owl +++ b/vfbext-simple.owl @@ -13,13 +13,13 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + An ontology of miscellaneous terms for data annotation in VFB. VFB Extension Ontology https://creativecommons.org/licenses/by/4.0/</terms:license> - 24:10:2022 12:05 + 09:01:2023 14:46 VFB extension ontology - 2022-10-24 + 2023-01-09 diff --git a/vfbext.json b/vfbext.json index e1c7198..4de1ecf 100644 --- a/vfbext.json +++ b/vfbext.json @@ -710,11 +710,26 @@ "pred": "subPropertyOf", "sub": "http://purl.obolibrary.org/obo/RO_0002578" }, + { + "obj": "http://purl.obolibrary.org/obo/RO_0002211", + "pred": "subPropertyOf", + "sub": "http://purl.obolibrary.org/obo/RO_0012012" + }, + { + "obj": "http://purl.obolibrary.org/obo/RO_0002212", + "pred": "subPropertyOf", + "sub": "http://purl.obolibrary.org/obo/RO_0002409" + }, { "obj": "http://purl.obolibrary.org/obo/RO_0002212", "pred": "subPropertyOf", "sub": "http://purl.obolibrary.org/obo/RO_0002630" }, + { + "obj": "http://purl.obolibrary.org/obo/RO_0002213", + "pred": "subPropertyOf", + "sub": "http://purl.obolibrary.org/obo/RO_0002407" + }, { "obj": "http://purl.obolibrary.org/obo/RO_0002213", "pred": "subPropertyOf", @@ -975,6 +990,11 @@ "pred": "subPropertyOf", "sub": "http://purl.obolibrary.org/obo/RO_0002412" }, + { + "obj": "http://purl.obolibrary.org/obo/RO_0002411", + "pred": "subPropertyOf", + "sub": "http://purl.obolibrary.org/obo/RO_0012011" + }, { "obj": "http://purl.obolibrary.org/obo/RO_0002412", "pred": "inverseOf", @@ -1205,6 +1225,21 @@ "pred": "subPropertyOf", "sub": "http://purl.obolibrary.org/obo/RO_0002448" }, + { + "obj": "http://purl.obolibrary.org/obo/RO_0012011", + "pred": "subPropertyOf", + "sub": "http://purl.obolibrary.org/obo/RO_0012012" + }, + { + "obj": "http://purl.obolibrary.org/obo/RO_0012012", + "pred": "subPropertyOf", + "sub": "http://purl.obolibrary.org/obo/RO_0002407" + }, + { + "obj": "http://purl.obolibrary.org/obo/RO_0012012", + "pred": "subPropertyOf", + "sub": "http://purl.obolibrary.org/obo/RO_0002409" + }, { "obj": "http://purl.obolibrary.org/obo/RO_0019000", "pred": "subPropertyOf", @@ -1289,7 +1324,7 @@ }, { "pred": "http://www.geneontology.org/formats/oboInOwl#date", - "val": "24:10:2022 12:05" + "val": "09:01:2023 14:46" }, { "pred": "http://www.w3.org/2000/01/rdf-schema#comment", @@ -1297,10 +1332,10 @@ }, { "pred": "http://www.w3.org/2002/07/owl#versionInfo", - "val": "2022-10-24" + "val": "2023-01-09" } ], - "version": "http://purl.obolibrary.org/obo/vfbext/releases/2022-10-24/vfbext.json" + "version": "http://purl.obolibrary.org/obo/vfbext/releases/2023-01-09/vfbext.json" }, "nodes": [ { @@ -3048,14 +3083,6 @@ "lbl": "regulates", "meta": { "basicPropertyValues": [ - { - "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": "Chris Mungall" @@ -3098,7 +3125,7 @@ } ], "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." }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", @@ -3144,7 +3171,7 @@ } ], "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." }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", @@ -3190,7 +3217,7 @@ } ], "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." }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", @@ -3465,6 +3492,9 @@ "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" ], + "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." + }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" @@ -3486,8 +3516,12 @@ "val": "cjm" } ], - "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." + }, + "subsets": [ + "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", + "http://purl.obolibrary.org/obo/valid_for_gocam" ] }, "type": "PROPERTY" @@ -3590,6 +3624,9 @@ "val": "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." } ], + "definition": { + "val": "c enables p iff c is capable of p and c acts to execute p." + }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ] @@ -3874,17 +3911,61 @@ "type": "PROPERTY" }, { - "id": "http://purl.obolibrary.org/obo/RO_0002410", - "lbl": "causally related to", + "id": "http://purl.obolibrary.org/obo/RO_0002407", + "lbl": "indirectly positively regulates", "meta": { "basicPropertyValues": [ { - "pred": "http://purl.obolibrary.org/obo/IAO_0000114", - "val": "http://purl.obolibrary.org/obo/IAO_0000428" + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Chris Mungall" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "indirectly activates" }, + { + "pred": "http://purl.obolibrary.org/obo/RO_0002579", + "val": "http://purl.obolibrary.org/obo/RO_0002213" + } + ], + "definition": { + "val": "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/RO_0002409", + "lbl": "indirectly negatively regulates", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Chris Mungall" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "indirectly inhibits" + }, + { + "pred": "http://purl.obolibrary.org/obo/RO_0002579", + "val": "http://purl.obolibrary.org/obo/RO_0002212" + } + ], + "definition": { + "val": "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/RO_0002410", + "lbl": "causally related to", + "meta": { + "basicPropertyValues": [ { "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." + "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_0000117", @@ -3896,7 +3977,10 @@ } ], "definition": { - "val": "This relation groups causal relations between material entities and causal relations between processes" + "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" + ] } }, "type": "PROPERTY" @@ -3906,17 +3990,13 @@ "lbl": "causally upstream of", "meta": { "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000114", - "val": "http://purl.obolibrary.org/obo/IAO_0000428" - }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "Chris Mungall" } ], "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." }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", @@ -3930,10 +4010,6 @@ "lbl": "immediately causally upstream of", "meta": { "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000114", - "val": "http://purl.obolibrary.org/obo/IAO_0000428" - }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "Chris Mungall" @@ -3944,7 +4020,7 @@ } ], "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." } }, "type": "PROPERTY" @@ -3968,7 +4044,7 @@ } ], "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." }, "synonyms": [ { @@ -4331,7 +4407,7 @@ } ], "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." } }, "type": "PROPERTY" @@ -4484,7 +4560,7 @@ } ], "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." }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", @@ -4649,7 +4725,7 @@ } ], "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." }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", @@ -4678,7 +4754,7 @@ } ], "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." }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", @@ -4880,6 +4956,46 @@ }, "type": "PROPERTY" }, + { + "id": "http://purl.obolibrary.org/obo/RO_0012011", + "lbl": "indirectly causally upstream of", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "pg" + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2022-09-26T06:07:17Z" + } + ], + "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." + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/RO_0012012", + "lbl": "indirectly regulates", + "meta": { + "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" + } + ], + "definition": { + "val": "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." + } + }, + "type": "PROPERTY" + }, { "id": "http://purl.obolibrary.org/obo/RO_0017001", "lbl": "device utilizes material", @@ -5516,12 +5632,61 @@ ], "predicateId": "http://purl.obolibrary.org/obo/RO_0004032" }, + { + "chainPredicateIds": [ + "http://purl.obolibrary.org/obo/RO_0002407", + "http://purl.obolibrary.org/obo/RO_0002629" + ], + "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_0002407" + }, + { + "chainPredicateIds": [ + "http://purl.obolibrary.org/obo/RO_0002409", + "http://purl.obolibrary.org/obo/RO_0002409" + ], + "predicateId": "http://purl.obolibrary.org/obo/RO_0002407" + }, + { + "chainPredicateIds": [ + "http://purl.obolibrary.org/obo/RO_0002409", + "http://purl.obolibrary.org/obo/RO_0002630" + ], + "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_0002409" + }, { "chainPredicateIds": [ "http://purl.obolibrary.org/obo/RO_0002578", "http://purl.obolibrary.org/obo/RO_0002578" ], "predicateId": "http://purl.obolibrary.org/obo/RO_0002211" + }, + { + "chainPredicateIds": [ + "http://purl.obolibrary.org/obo/RO_0002629", + "http://purl.obolibrary.org/obo/RO_0002629" + ], + "predicateId": "http://purl.obolibrary.org/obo/RO_0002407" + }, + { + "chainPredicateIds": [ + "http://purl.obolibrary.org/obo/RO_0002630", + "http://purl.obolibrary.org/obo/RO_0002630" + ], + "predicateId": "http://purl.obolibrary.org/obo/RO_0002409" } ] } diff --git a/vfbext.obo b/vfbext.obo index c60ae7f..f6abc53 100644 --- a/vfbext.obo +++ b/vfbext.obo @@ -1,5 +1,5 @@ format-version: 1.2 -date: 24:10:2022 12:05 +date: 09:01:2023 14:46 subsetdef: clone "" subsetdef: cur "" subsetdef: EmbDevSlim "" @@ -26,7 +26,7 @@ ontology: http://virtualflybrain.org/data/VFB/OWL/vfbext.owl property_value: http://purl.org/dc/elements/1.1/description "An ontology of miscellaneous terms for data annotation in VFB." xsd:string property_value: http://purl.org/dc/elements/1.1/title "VFB Extension Ontology" xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/by/4.0/ xsd:string -property_value: owl:versionInfo "2022-10-24" xsd:string +property_value: owl:versionInfo "2023-01-09" xsd:string [Term] id: BFO:0000001 @@ -479,7 +479,7 @@ property_value: example_of_usage "this enzyme has function this catalysis functi property_value: IAO:0000118 "has_function" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000034 ! function -is_a: has_characteristic ! has_characteristic +is_a: has_characteristic ! has characteristic [Typedef] id: RO:0000086 @@ -489,7 +489,7 @@ property_value: editor_note "A bearer can have many qualities, and its qualities property_value: example_of_usage "this apple has quality this red color" xsd:string property_value: IAO:0000118 "has_quality" xsd:string range: BFO:0000019 ! quality -is_a: has_characteristic ! has_characteristic +is_a: has_characteristic ! has characteristic [Typedef] id: RO:0000087 @@ -500,7 +500,7 @@ property_value: example_of_usage "this person has role this investigator role (m property_value: IAO:0000118 "has_role" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000023 ! role -is_a: has_characteristic ! has_characteristic +is_a: has_characteristic ! has characteristic [Typedef] id: RO:0000091 @@ -508,7 +508,7 @@ name: has disposition def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] domain: BFO:0000004 ! independent continuant range: BFO:0000016 ! disposition -is_a: has_characteristic ! has_characteristic +is_a: has_characteristic ! has characteristic inverse_of: RO:0000092 ! disposition of [Typedef] @@ -719,6 +719,7 @@ is_a: RO:0002500 ! causal agent in process [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 @@ -730,7 +731,9 @@ 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 @@ -761,6 +764,7 @@ property_value: RO:0001900 RO:0001901 [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: example_of_usage "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -899,22 +903,49 @@ is_a: RO:0002087 ! immediately preceded by is_a: RO:0002404 ! causally downstream of inverse_of: RO:0002412 ! immediately causally upstream of +[Typedef] +id: 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." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "indirectly activates" xsd:string +property_value: RO:0002579 RO:0002213 +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: positively_regulates ! positively regulates +is_a: RO:0012012 ! indirectly regulates +transitive_over: RO:0002629 ! directly positively regulates + +[Typedef] +id: 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." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "indirectly inhibits" xsd:string +property_value: RO:0002579 RO:0002212 +holds_over_chain: RO:0002630 RO:0002409 +holds_over_chain: RO:0002630 RO:0002630 +is_transitive: true +is_a: negatively_regulates ! negatively regulates +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: editor_note "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:0000114 IAO:0000428 +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: editor_note "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 @@ -923,8 +954,7 @@ 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 @@ -933,7 +963,7 @@ is_a: RO:0002411 ! causally upstream of [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: editor_note "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 @@ -1088,7 +1118,7 @@ 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 @@ -1151,7 +1181,7 @@ is_a: RO:0002506 ! causal relation between entities [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 @@ -1219,7 +1249,7 @@ is_a: RO:0002410 ! causally related to [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 @@ -1232,7 +1262,7 @@ 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 @@ -1323,6 +1353,23 @@ domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002566 ! causally influences +[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: regulates ! regulates +is_a: RO:0012011 ! indirectly causally upstream of +created_by: pg +creation_date: 2022-09-26T06:08:01Z + [Typedef] id: RO:0017001 name: device utilizes material @@ -1442,7 +1489,7 @@ property_value: IAO:0000118 "inheres_in" xsd:string property_value: RO:0001900 RO:0001901 is_functional: true is_a: RO:0002314 ! characteristic of part of -inverse_of: has_characteristic ! has_characteristic +inverse_of: has_characteristic ! has characteristic [Typedef] id: editor_note @@ -1528,7 +1575,7 @@ name: depicts id: negatively_regulates name: negatively regulates namespace: external -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 @@ -1600,7 +1647,7 @@ inverse_of: has_part ! has part id: positively_regulates name: positively regulates namespace: external -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 @@ -1619,13 +1666,11 @@ inverse_of: RO:0002336 ! positively regulated by id: regulates name: regulates namespace: external -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: editor_note "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:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 "David Hill" xsd:string property_value: IAO:0000117 "Tanya Berardini" xsd:string diff --git a/vfbext.owl b/vfbext.owl index 56d9032..b67fb27 100644 --- a/vfbext.owl +++ b/vfbext.owl @@ -24,9 +24,9 @@ An ontology of miscellaneous terms for data annotation in VFB. VFB Extension Ontology https://creativecommons.org/licenses/by/4.0/</terms:license> - 24:10:2022 12:05 + 09:01:2023 14:46 VFB extension ontology - 2022-10-24 + 2023-01-09 @@ -196,6 +196,12 @@ + + + + + + @@ -1348,9 +1354,7 @@ Examples include: the relationship between two channels collected simultaneously - - 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 @@ -1378,7 +1382,7 @@ Examples include: the relationship between two channels collected simultaneously - 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) @@ -1407,7 +1411,7 @@ Examples include: the relationship between two channels collected simultaneously - 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) @@ -1575,6 +1579,7 @@ Examples include: the relationship between two channels collected simultaneously + 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 @@ -1590,9 +1595,11 @@ Examples include: the relationship between two channels collected simultaneously + 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 @@ -1657,6 +1664,7 @@ Examples include: the relationship between two channels collected simultaneously 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 @@ -1865,18 +1873,75 @@ Examples include: the relationship between two channels collected simultaneously + + + + + + + + + + + + + + + + + + + + + + + p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. + Chris Mungall + indirectly activates + + indirectly positively regulates + + + + + + + + + + + + + + + + + + + + + + + p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. + Chris Mungall + indirectly inhibits + + indirectly negatively regulates + + + + - - 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. @@ -1889,6 +1954,12 @@ 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 + @@ -1898,8 +1969,7 @@ 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 @@ -1913,8 +1983,7 @@ 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 @@ -1928,7 +1997,7 @@ 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) @@ -2180,7 +2249,7 @@ 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. @@ -2280,7 +2349,7 @@ 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) @@ -2388,7 +2457,7 @@ 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) @@ -2405,7 +2474,7 @@ 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) @@ -2545,6 +2614,31 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + 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 + + + + @@ -3525,6 +3619,12 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + @@ -3534,6 +3634,9 @@ For example, A and B may be gene products and binding of B by A positively regul + + + @@ -4531,6 +4634,50 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -4707,6 +4854,50 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +