From dd27a9d7b8ea281464cbd1aba7864f3389bafa77 Mon Sep 17 00:00:00 2001 From: Colleen Xu Date: Tue, 2 Apr 2024 23:35:15 -0700 Subject: [PATCH 1/3] feat: add pathfinder templates for chem-gene --- data/templateGroups.json | 3 +- .../Pathfinder/pf-chem-gene-gene-gene.json | 45 +++++++++++++++++++ .../Pathfinder/pf-chem-gene-gene.json | 39 ++++++++++++++++ 3 files changed, 86 insertions(+), 1 deletion(-) create mode 100644 data/templates/Pathfinder/pf-chem-gene-gene-gene.json create mode 100644 data/templates/Pathfinder/pf-chem-gene-gene.json diff --git a/data/templateGroups.json b/data/templateGroups.json index afb5409c..ffdf1810 100644 --- a/data/templateGroups.json +++ b/data/templateGroups.json @@ -76,7 +76,8 @@ "predicate": ["related_to"], "object": ["Gene", "Protein"], "templates": [ - + "pf-chem-gene-gene.json", + "pf-chem-gene-gene-gene.json" ] }, { diff --git a/data/templates/Pathfinder/pf-chem-gene-gene-gene.json b/data/templates/Pathfinder/pf-chem-gene-gene-gene.json new file mode 100644 index 00000000..5103208c --- /dev/null +++ b/data/templates/Pathfinder/pf-chem-gene-gene-gene.json @@ -0,0 +1,45 @@ +{ + "message": { + "query_graph": { + "nodes": { + "creativeQuerySubject": { + "categories":["biolink:ChemicalEntity"] + }, + "nA": { + "categories":["biolink:Gene", "biolink:Protein"] + }, + "nB": { + "categories":["biolink:Gene", "biolink:Protein"] + }, + "creativeQueryObject": { + "categories":["biolink:Gene", "biolink:Protein"] + } + }, + "edges": { + "eA": { + "subject": "creativeQuerySubject", + "object": "nA", + "predicates": [ + "biolink:regulates", + "biolink:affects", + "biolink:interacts_with" + ] + }, + "eB": { + "subject": "nA", + "object": "nB", + "predicates": [ + "biolink:regulates" + ] + }, + "eC": { + "subject": "nB", + "object": "creativeQueryObject", + "predicates": [ + "biolink:regulates" + ] + } + } + } + } +} \ No newline at end of file diff --git a/data/templates/Pathfinder/pf-chem-gene-gene.json b/data/templates/Pathfinder/pf-chem-gene-gene.json new file mode 100644 index 00000000..9fe30f19 --- /dev/null +++ b/data/templates/Pathfinder/pf-chem-gene-gene.json @@ -0,0 +1,39 @@ +{ + "message": { + "query_graph": { + "nodes": { + "creativeQuerySubject": { + "categories":["biolink:ChemicalEntity"] + }, + "nA": { + "categories":["biolink:Gene", "biolink:Protein"] + }, + "creativeQueryObject": { + "categories":["biolink:Gene", "biolink:Protein"] + } + }, + "edges": { + "eA": { + "subject": "creativeQuerySubject", + "object": "nA", + "predicates": [ + "biolink:regulates", + "biolink:affects", + "biolink:interacts_with" + ] + }, + "eB": { + "subject": "nA", + "object": "creativeQueryObject", + "predicates": [ + "biolink:regulates", + "biolink:regulated_by", + "biolink:affects", + "biolink:affected_by", + "biolink:interacts_with" + ] + } + } + } + } +} \ No newline at end of file From c9c9e8c2cf687ace574cc574ef8a4ee0f9df742d Mon Sep 17 00:00:00 2001 From: Colleen Xu Date: Tue, 2 Apr 2024 23:59:42 -0700 Subject: [PATCH 2/3] chore: remove extra predicate from pathfinder template --- data/templates/Pathfinder/pf-drug-gene-disease.json | 1 - 1 file changed, 1 deletion(-) diff --git a/data/templates/Pathfinder/pf-drug-gene-disease.json b/data/templates/Pathfinder/pf-drug-gene-disease.json index e5032697..a56433c2 100644 --- a/data/templates/Pathfinder/pf-drug-gene-disease.json +++ b/data/templates/Pathfinder/pf-drug-gene-disease.json @@ -30,7 +30,6 @@ "biolink:gene_associated_with_condition", "biolink:biomarker_for", "biolink:affects", - "biolink:causes", "biolink:contributes_to" ] } From 6f84108f1d7d11bad6f727f5875276fe806c8235 Mon Sep 17 00:00:00 2001 From: Colleen Xu Date: Wed, 3 Apr 2024 00:07:54 -0700 Subject: [PATCH 3/3] feat: add pathfinder templates for disease-disease --- data/templateGroups.json | 3 ++- .../Pathfinder/pf-disease-gene-disease.json | 27 +++++++++++++++++++ .../Pathfinder/pf-disease-seqvar-disease.json | 27 +++++++++++++++++++ 3 files changed, 56 insertions(+), 1 deletion(-) create mode 100644 data/templates/Pathfinder/pf-disease-gene-disease.json create mode 100644 data/templates/Pathfinder/pf-disease-seqvar-disease.json diff --git a/data/templateGroups.json b/data/templateGroups.json index ffdf1810..9afceb01 100644 --- a/data/templateGroups.json +++ b/data/templateGroups.json @@ -91,7 +91,8 @@ "DiseaseOrPhenotypicFeature" ], "templates": [ - + "pf-disease-seqvar-disease.json", + "pf-disease-gene-disease.json" ] }, { diff --git a/data/templates/Pathfinder/pf-disease-gene-disease.json b/data/templates/Pathfinder/pf-disease-gene-disease.json new file mode 100644 index 00000000..76c44b94 --- /dev/null +++ b/data/templates/Pathfinder/pf-disease-gene-disease.json @@ -0,0 +1,27 @@ +{ + "message": { + "query_graph": { + "nodes": { + "creativeQuerySubject": { + "categories":["biolink:DiseaseOrPhenotypicFeature"] + }, + "nA": { + "categories":["biolink:Gene", "biolink:Protein"] + }, + "creativeQueryObject": { + "categories":["biolink:DiseaseOrPhenotypicFeature"] + } + }, + "edges": { + "eA": { + "subject": "creativeQuerySubject", + "object": "nA" + }, + "eB": { + "subject": "nA", + "object": "creativeQueryObject" + } + } + } + } +} \ No newline at end of file diff --git a/data/templates/Pathfinder/pf-disease-seqvar-disease.json b/data/templates/Pathfinder/pf-disease-seqvar-disease.json new file mode 100644 index 00000000..08ebada4 --- /dev/null +++ b/data/templates/Pathfinder/pf-disease-seqvar-disease.json @@ -0,0 +1,27 @@ +{ + "message": { + "query_graph": { + "nodes": { + "creativeQuerySubject": { + "categories":["biolink:DiseaseOrPhenotypicFeature"] + }, + "nA": { + "categories":["biolink:SequenceVariant"] + }, + "creativeQueryObject": { + "categories":["biolink:DiseaseOrPhenotypicFeature"] + } + }, + "edges": { + "eA": { + "subject": "creativeQuerySubject", + "object": "nA" + }, + "eB": { + "subject": "nA", + "object": "creativeQueryObject" + } + } + } + } +} \ No newline at end of file