From bb304b161e56d6770767369fb97dcc9f8a041c24 Mon Sep 17 00:00:00 2001 From: Colleen Xu Date: Thu, 17 Aug 2023 11:45:01 -0700 Subject: [PATCH 1/4] templateGroups: remove directional templates from treats --- data/templateGroups.json | 2 -- 1 file changed, 2 deletions(-) diff --git a/data/templateGroups.json b/data/templateGroups.json index 12562ba7..ecbd2a0c 100644 --- a/data/templateGroups.json +++ b/data/templateGroups.json @@ -10,8 +10,6 @@ ], "templates": [ "Chem-treats-DoP.json", - "Chem-decreaseGeneWithFunctionGainIn-Disease.json", - "Chem-increaseGeneWithFunctionLossIn-Disease.json", "Chem-treats-PhenoOfDisease.json", "Chem-regulates,affects-Gene-biomarker,associated_condition-DoP.json" ] From d0b01366038e8e3cb57a888d0acee6a7a3a11c67 Mon Sep 17 00:00:00 2001 From: Colleen Xu Date: Thu, 17 Aug 2023 11:53:33 -0700 Subject: [PATCH 2/4] templates: for used templates, replace interacts_with use physically_interacts_with instead --- data/templateGroups.json | 8 ++++---- ... Chem-physically_interacts-GeneThatDownregs-Gene.json} | 2 +- ...=> Chem-physically_interacts-GeneThatUpregs-Gene.json} | 2 +- ...with-Gene.json => Chem-physically_interacts-Gene.json} | 2 +- 4 files changed, 7 insertions(+), 7 deletions(-) rename data/templates/Chem-decreases-Gene/{Chem-interacts_with-GeneThatDownregs-Gene.json => Chem-physically_interacts-GeneThatDownregs-Gene.json} (94%) rename data/templates/Chem-increases-Gene/{Chem-interacts_with-GeneThatUpregs-Gene.json => Chem-physically_interacts-GeneThatUpregs-Gene.json} (94%) rename data/templates/{Chem-interacts_with-Gene.json => Chem-physically_interacts-Gene.json} (88%) diff --git a/data/templateGroups.json b/data/templateGroups.json index ecbd2a0c..3df3fd2e 100644 --- a/data/templateGroups.json +++ b/data/templateGroups.json @@ -29,8 +29,8 @@ "Chem-increasesGene.json", "Chem-IncreaseAnotherGeneThatUpregs-Gene.json", "Chem-DecreaseAnotherGeneThatDownregs-Gene.json", - "Chem-interacts_with-GeneThatUpregs-Gene.json", - "Chem-interacts_with-Gene.json" + "Chem-physically_interacts-GeneThatUpregs-Gene.json", + "Chem-physically_interacts-Gene.json" ] }, { @@ -48,8 +48,8 @@ "Chem-decreasesGene.json", "Chem-IncreaseAnotherGeneThatDownregs-Gene.json", "Chem-DecreaseAnotherGeneThatUpregs-Gene.json", - "Chem-interacts_with-GeneThatDownregs-Gene.json", - "Chem-interacts_with-Gene.json" + "Chem-physically_interacts-GeneThatDownregs-Gene.json", + "Chem-physically_interacts-Gene.json" ] } ] diff --git a/data/templates/Chem-decreases-Gene/Chem-interacts_with-GeneThatDownregs-Gene.json b/data/templates/Chem-decreases-Gene/Chem-physically_interacts-GeneThatDownregs-Gene.json similarity index 94% rename from data/templates/Chem-decreases-Gene/Chem-interacts_with-GeneThatDownregs-Gene.json rename to data/templates/Chem-decreases-Gene/Chem-physically_interacts-GeneThatDownregs-Gene.json index af52b986..f71b512d 100644 --- a/data/templates/Chem-decreases-Gene/Chem-interacts_with-GeneThatDownregs-Gene.json +++ b/data/templates/Chem-decreases-Gene/Chem-physically_interacts-GeneThatDownregs-Gene.json @@ -17,7 +17,7 @@ "eA": { "subject": "creativeQuerySubject", "object": "nA", - "predicates": ["biolink:interacts_with"] + "predicates": ["biolink:physically_interacts_with"] }, "eB": { "subject": "nA", diff --git a/data/templates/Chem-increases-Gene/Chem-interacts_with-GeneThatUpregs-Gene.json b/data/templates/Chem-increases-Gene/Chem-physically_interacts-GeneThatUpregs-Gene.json similarity index 94% rename from data/templates/Chem-increases-Gene/Chem-interacts_with-GeneThatUpregs-Gene.json rename to data/templates/Chem-increases-Gene/Chem-physically_interacts-GeneThatUpregs-Gene.json index 669c8e88..a4282b18 100644 --- a/data/templates/Chem-increases-Gene/Chem-interacts_with-GeneThatUpregs-Gene.json +++ b/data/templates/Chem-increases-Gene/Chem-physically_interacts-GeneThatUpregs-Gene.json @@ -17,7 +17,7 @@ "eA": { "subject": "creativeQuerySubject", "object": "nA", - "predicates": ["biolink:interacts_with"] + "predicates": ["biolink:physically_interacts_with"] }, "eB": { "subject": "nA", diff --git a/data/templates/Chem-interacts_with-Gene.json b/data/templates/Chem-physically_interacts-Gene.json similarity index 88% rename from data/templates/Chem-interacts_with-Gene.json rename to data/templates/Chem-physically_interacts-Gene.json index d7b83857..263f9001 100644 --- a/data/templates/Chem-interacts_with-Gene.json +++ b/data/templates/Chem-physically_interacts-Gene.json @@ -13,7 +13,7 @@ "eA": { "subject": "creativeQuerySubject", "object": "creativeQueryObject", - "predicates": ["biolink:interacts_with"] + "predicates": ["biolink:physically_interacts"] } } } From cc9e078ede92078a80e4a733aef731f082d745ec Mon Sep 17 00:00:00 2001 From: Colleen Xu Date: Thu, 17 Aug 2023 11:55:38 -0700 Subject: [PATCH 3/4] templates: for unused, replace interacts_with use physically_interacts_with instead --- ...ated,associated-Gene-biomarker,associated_condition-DoP.json | 2 +- data/templates/less-promising/m6-Disease-Gene-Gene-Chem.json | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/data/templates/Drug-treats-Disease/Chem-interacts,correlated,associated-Gene-biomarker,associated_condition-DoP.json b/data/templates/Drug-treats-Disease/Chem-interacts,correlated,associated-Gene-biomarker,associated_condition-DoP.json index 6f0b05ce..404773ba 100644 --- a/data/templates/Drug-treats-Disease/Chem-interacts,correlated,associated-Gene-biomarker,associated_condition-DoP.json +++ b/data/templates/Drug-treats-Disease/Chem-interacts,correlated,associated-Gene-biomarker,associated_condition-DoP.json @@ -17,7 +17,7 @@ "eA": { "subject": "creativeQuerySubject", "object": "nA", - "predicates": ["biolink:interacts_with", "biolink:correlated_with", "biolink:associated_with"] + "predicates": ["biolink:physically_interacts_with", "biolink:correlated_with", "biolink:associated_with"] }, "eB": { "subject": "nA", diff --git a/data/templates/less-promising/m6-Disease-Gene-Gene-Chem.json b/data/templates/less-promising/m6-Disease-Gene-Gene-Chem.json index fccf5ca4..c1da2ca5 100644 --- a/data/templates/less-promising/m6-Disease-Gene-Gene-Chem.json +++ b/data/templates/less-promising/m6-Disease-Gene-Gene-Chem.json @@ -26,7 +26,7 @@ "eB": { "subject": "nA", "object": "nB", - "predicates": ["biolink:interacts_with"] + "predicates": ["biolink:physically_interacts_with"] }, "eC": { "subject": "nB", From f1b589100d23026c6ef4b170a348b27bc8430cdb Mon Sep 17 00:00:00 2001 From: Colleen Xu Date: Thu, 17 Aug 2023 12:31:02 -0700 Subject: [PATCH 4/4] templates: fix typo --- data/templates/Chem-physically_interacts-Gene.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/data/templates/Chem-physically_interacts-Gene.json b/data/templates/Chem-physically_interacts-Gene.json index 263f9001..ea54293b 100644 --- a/data/templates/Chem-physically_interacts-Gene.json +++ b/data/templates/Chem-physically_interacts-Gene.json @@ -13,7 +13,7 @@ "eA": { "subject": "creativeQuerySubject", "object": "creativeQueryObject", - "predicates": ["biolink:physically_interacts"] + "predicates": ["biolink:physically_interacts_with"] } } }