From df4453cb7eb912f7da95b9e03bab8a1c9ea722a0 Mon Sep 17 00:00:00 2001 From: Krishna Udaiwal Date: Mon, 1 Nov 2021 20:50:43 -0400 Subject: [PATCH] Remove owl:nothing per issue #129 --- src/ontology/imports/pato_import.owl | 112 ------------------------ src/ontology/imports/po_import.owl | 122 ++------------------------- src/ontology/imports/ro_import.owl | 114 +------------------------ src/ontology/imports/to_import.owl | 122 ++------------------------- 4 files changed, 11 insertions(+), 459 deletions(-) diff --git a/src/ontology/imports/pato_import.owl b/src/ontology/imports/pato_import.owl index 1d9a69c..cb48235 100644 --- a/src/ontology/imports/pato_import.owl +++ b/src/ontology/imports/pato_import.owl @@ -3785,118 +3785,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/src/ontology/imports/po_import.owl b/src/ontology/imports/po_import.owl index 36503d6..f1caf1a 100644 --- a/src/ontology/imports/po_import.owl +++ b/src/ontology/imports/po_import.owl @@ -428,7 +428,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. Process(P2) is directly negatively regulated by process(P1) 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 P2 directly negatively regulated by P1. - GOC:dos + GOC:dos @@ -445,7 +445,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. Process(P2) is directly postively regulated by process(P1) 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 P2 is directly postively regulated by P1. - GOC:dos + GOC:dos @@ -462,7 +462,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos + GOC:dos @@ -1201,7 +1201,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. GOC:cjm - GOC:dos + GOC:dos @@ -6334,118 +6334,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -6538,5 +6426,5 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl index 4a72a27..c81cee0 100644 --- a/src/ontology/imports/ro_import.owl +++ b/src/ontology/imports/ro_import.owl @@ -2506,118 +2506,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -2710,5 +2598,5 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + diff --git a/src/ontology/imports/to_import.owl b/src/ontology/imports/to_import.owl index 723e96e..9284fbb 100644 --- a/src/ontology/imports/to_import.owl +++ b/src/ontology/imports/to_import.owl @@ -632,7 +632,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. Process(P2) is directly negatively regulated by process(P1) 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 P2 directly negatively regulated by P1. - GOC:dos + GOC:dos @@ -649,7 +649,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. Process(P2) is directly postively regulated by process(P1) 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 P2 is directly postively regulated by P1. - GOC:dos + GOC:dos @@ -667,7 +667,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos + GOC:dos @@ -1531,7 +1531,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. GOC:cjm - GOC:dos + GOC:dos @@ -19208,118 +19208,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -19412,5 +19300,5 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - +