From 1a8b903223197fb74159398798252b10dfa0967a Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Sat, 29 Jul 2017 12:31:26 -0700 Subject: [PATCH] Fixing IDs and syntax of DPs, #13692 --- .../validated_patterns/activator_activity.tsv | 16 ++++++++-------- .../validated_patterns/envenomation.yaml | 4 ++-- .../validated_patterns/import_into_cell.yaml | 4 ++-- .../validated_patterns/inhibitor_activity.yaml | 8 ++++---- .../validated_patterns/regulator_activity.yaml | 8 ++++---- 5 files changed, 20 insertions(+), 20 deletions(-) diff --git a/src/design_patterns/validated_patterns/activator_activity.tsv b/src/design_patterns/validated_patterns/activator_activity.tsv index d213e9bbd6..aea76fa423 100644 --- a/src/design_patterns/validated_patterns/activator_activity.tsv +++ b/src/design_patterns/validated_patterns/activator_activity.tsv @@ -1,8 +1,8 @@ -iri iri label regulated activity regulated activity label -GO:0008047 enzyme activator activity GO:0003824 catalytic activity -GO:0019209 kinase activator activity GO:0016301 kinase activity -GO:0019211 phosphatase activator activity GO:0016791 phosphatase activity -GO:0030295 protein kinase activator activity GO:0004672 protein kinase activity -GO:0072542 protein phosphatase activator activity GO:0004721 phosphoprotein phosphatase activity -GO:0030296 protein tyrosine kinase activator activity GO:0004713 protein tyrosine kinase activity -GO:0030297 transmembrane receptor protein tyrosine kinase activator activity GO:0004714 transmembrane receptor protein tyrosine kinase activity +?defined_class ?defined_class_label ?regulated_activity ?regulated_activity_label + "enzyme activator activity" "catalytic activity" + "kinase activator activity" "kinase activity" + "phosphatase activator activity" "phosphatase activity" + "protein kinase activator activity" "protein kinase activity" + "protein phosphatase activator activity" "phosphoprotein phosphatase activity" + "protein tyrosine kinase activator activity" "protein tyrosine kinase activity" + "transmembrane receptor protein tyrosine kinase activator activity" "transmembrane receptor protein tyrosine kinase activity" diff --git a/src/design_patterns/validated_patterns/envenomation.yaml b/src/design_patterns/validated_patterns/envenomation.yaml index de60ffa92c..1c7c2d32e1 100644 --- a/src/design_patterns/validated_patterns/envenomation.yaml +++ b/src/design_patterns/validated_patterns/envenomation.yaml @@ -21,6 +21,6 @@ def: - mod # Need a way to specify regex transformation that subs 'in the bitten organism' for 'in other organism' equivalentTo: - text: "'envenomation resulting in modification of morphology or physiology of other organism' and 'has part' some '%s'" + text: "'envenomation resulting in modification of morphology or physiology of other organism' and 'has part' some %s" vars: - - mod \ No newline at end of file + - mod diff --git a/src/design_patterns/validated_patterns/import_into_cell.yaml b/src/design_patterns/validated_patterns/import_into_cell.yaml index 3ae194034a..d99ee873a7 100644 --- a/src/design_patterns/validated_patterns/import_into_cell.yaml +++ b/src/design_patterns/validated_patterns/import_into_cell.yaml @@ -1,9 +1,9 @@ pattern_name: import_into_cell -classes: +classes: transport: GO:0006810 extracellular region: GO:0005576 intracellular part: GO:0044424 - chemical entity: CHEBI_24431 # encompasses protein + chemical entity: CHEBI:24431 # encompasses protein macromolecular complex: GO:0043234 # encompasses protein complex relations: diff --git a/src/design_patterns/validated_patterns/inhibitor_activity.yaml b/src/design_patterns/validated_patterns/inhibitor_activity.yaml index 222471fd61..5bd5e8705b 100644 --- a/src/design_patterns/validated_patterns/inhibitor_activity.yaml +++ b/src/design_patterns/validated_patterns/inhibitor_activity.yaml @@ -1,12 +1,12 @@ pattern_name: inhibitor_activity classes: - molecular_function: GO_0003674 - catalytic activity: GO_0003824 + molecular function: GO:0003674 + catalytic activity: GO:0003824 relations: - directly negatively regulates: RO_0002630 + directly negatively regulates: RO:0002630 vars: @@ -34,6 +34,6 @@ def: equivalentTo: - text: "'molecular_function that 'directly negatively regulates' some %s" + text: "'molecular function' that 'directly negatively regulates' some %s" vars: - regulated_activity diff --git a/src/design_patterns/validated_patterns/regulator_activity.yaml b/src/design_patterns/validated_patterns/regulator_activity.yaml index a96d02cdab..3e7c3cefe5 100644 --- a/src/design_patterns/validated_patterns/regulator_activity.yaml +++ b/src/design_patterns/validated_patterns/regulator_activity.yaml @@ -1,12 +1,12 @@ pattern_name: regulator_activity classes: - molecular_function: GO_0003674 - catalytic activity: GO_0003824 + molecular_function: GO:0003674 + catalytic activity: GO:0003824 relations: - directly regulates: RO_0002578 + directly regulates: RO:0002578 vars: regulated_activity: "'catalytic activity'" @@ -33,6 +33,6 @@ def: equivalentTo: - text: "'molecular_function that 'directly regulates' some %s" + text: "'molecular_function' that 'directly regulates' some %s" vars: - regulated_activity