From 1478f32955143f5f94b33e8b3779233a4d02fabe Mon Sep 17 00:00:00 2001 From: Colleen Xu Date: Wed, 16 Aug 2023 10:30:26 -0700 Subject: [PATCH] templates: add templates, not used for now requires more dev review to decide whether to add to templateGroups --- .../Chem-negatively_correlated-Gene.json | 21 +++++++++++ .../Chem-positively_correlated-Gene.json | 21 +++++++++++ ...ne-biomarker,associated_condition-DoP.json | 33 +++++++++++++++++ .../Chem-treats-DoP-causes,part-DoP.json | 33 +++++++++++++++++ .../Chem-treats-DoP-similar,part-DoP.json | 33 +++++++++++++++++ .../ChemDecreasesLikelihood-Disease.json | 35 +++++++++++++++++++ .../NonChem-treats-DoP.json | 22 ++++++++++++ ...Procedure-decreasesLikelihood-Disease.json | 35 +++++++++++++++++++ .../Treatment-related_to-DoP.json | 21 +++++++++++ 9 files changed, 254 insertions(+) create mode 100644 data/templates/Chem-decreases-Gene/Chem-negatively_correlated-Gene.json create mode 100644 data/templates/Chem-increases-Gene/Chem-positively_correlated-Gene.json create mode 100644 data/templates/Drug-treats-Disease/Chem-interacts,correlated,associated-Gene-biomarker,associated_condition-DoP.json create mode 100644 data/templates/Drug-treats-Disease/Chem-treats-DoP-causes,part-DoP.json create mode 100644 data/templates/Drug-treats-Disease/Chem-treats-DoP-similar,part-DoP.json create mode 100644 data/templates/Drug-treats-Disease/ChemDecreasesLikelihood-Disease.json create mode 100644 data/templates/NonChem-treats-Disease/NonChem-treats-DoP.json create mode 100644 data/templates/NonChem-treats-Disease/Procedure-decreasesLikelihood-Disease.json create mode 100644 data/templates/NonChem-treats-Disease/Treatment-related_to-DoP.json diff --git a/data/templates/Chem-decreases-Gene/Chem-negatively_correlated-Gene.json b/data/templates/Chem-decreases-Gene/Chem-negatively_correlated-Gene.json new file mode 100644 index 00000000..fee02cac --- /dev/null +++ b/data/templates/Chem-decreases-Gene/Chem-negatively_correlated-Gene.json @@ -0,0 +1,21 @@ +{ + "message": { + "query_graph": { + "nodes": { + "creativeQuerySubject": { + "categories":["biolink:ChemicalEntity"] + }, + "creativeQueryObject": { + "categories":["biolink:Gene", "biolink:Protein"] + } + }, + "edges": { + "eA": { + "subject": "creativeQuerySubject", + "object": "creativeQueryObject", + "predicates": ["biolink:negatively_correlated_with"] + } + } + } + } +} \ No newline at end of file diff --git a/data/templates/Chem-increases-Gene/Chem-positively_correlated-Gene.json b/data/templates/Chem-increases-Gene/Chem-positively_correlated-Gene.json new file mode 100644 index 00000000..4cd0895e --- /dev/null +++ b/data/templates/Chem-increases-Gene/Chem-positively_correlated-Gene.json @@ -0,0 +1,21 @@ +{ + "message": { + "query_graph": { + "nodes": { + "creativeQuerySubject": { + "categories":["biolink:ChemicalEntity"] + }, + "creativeQueryObject": { + "categories":["biolink:Gene", "biolink:Protein"] + } + }, + "edges": { + "eA": { + "subject": "creativeQuerySubject", + "object": "creativeQueryObject", + "predicates": ["biolink:positively_correlated_with"] + } + } + } + } +} \ No newline at end of file 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 new file mode 100644 index 00000000..6f0b05ce --- /dev/null +++ b/data/templates/Drug-treats-Disease/Chem-interacts,correlated,associated-Gene-biomarker,associated_condition-DoP.json @@ -0,0 +1,33 @@ +{ + "message": { + "query_graph": { + "nodes": { + "creativeQuerySubject": { + "categories":["biolink:ChemicalEntity"] + }, + "nA": { + "categories":["biolink:Gene"], + "is_set": true + }, + "creativeQueryObject": { + "categories":["biolink:DiseaseOrPhenotypicFeature"] + } + }, + "edges": { + "eA": { + "subject": "creativeQuerySubject", + "object": "nA", + "predicates": ["biolink:interacts_with", "biolink:correlated_with", "biolink:associated_with"] + }, + "eB": { + "subject": "nA", + "object": "creativeQueryObject", + "predicates": [ + "biolink:gene_associated_with_condition", + "biolink:biomarker_for" + ] + } + } + } + } +} \ No newline at end of file diff --git a/data/templates/Drug-treats-Disease/Chem-treats-DoP-causes,part-DoP.json b/data/templates/Drug-treats-Disease/Chem-treats-DoP-causes,part-DoP.json new file mode 100644 index 00000000..8daf2d70 --- /dev/null +++ b/data/templates/Drug-treats-Disease/Chem-treats-DoP-causes,part-DoP.json @@ -0,0 +1,33 @@ +{ + "message": { + "query_graph": { + "nodes": { + "creativeQuerySubject": { + "categories":["biolink:ChemicalEntity"] + }, + "nA": { + "categories":["biolink:DiseaseOrPhenotypicFeature"], + "is_set": true + }, + "creativeQueryObject": { + "categories":["biolink:DiseaseOrPhenotypicFeature"] + } + }, + "edges": { + "eA": { + "subject": "creativeQuerySubject", + "object": "nA", + "predicates": ["biolink:treats"] + }, + "eB": { + "subject": "nA", + "object": "creativeQueryObject", + "predicates": [ + "biolink:part_of", + "biolink:causes" + ] + } + } + } + } +} \ No newline at end of file diff --git a/data/templates/Drug-treats-Disease/Chem-treats-DoP-similar,part-DoP.json b/data/templates/Drug-treats-Disease/Chem-treats-DoP-similar,part-DoP.json new file mode 100644 index 00000000..fee3f292 --- /dev/null +++ b/data/templates/Drug-treats-Disease/Chem-treats-DoP-similar,part-DoP.json @@ -0,0 +1,33 @@ +{ + "message": { + "query_graph": { + "nodes": { + "creativeQuerySubject": { + "categories":["biolink:ChemicalEntity"] + }, + "nA": { + "categories":["biolink:DiseaseOrPhenotypicFeature"], + "is_set": true + }, + "creativeQueryObject": { + "categories":["biolink:DiseaseOrPhenotypicFeature"] + } + }, + "edges": { + "eA": { + "subject": "creativeQuerySubject", + "object": "nA", + "predicates": ["biolink:treats"] + }, + "eB": { + "subject": "creativeQueryObject", + "object": "nA", + "predicates": [ + "biolink:similar_to", + "biolink:has_part" + ] + } + } + } + } +} \ No newline at end of file diff --git a/data/templates/Drug-treats-Disease/ChemDecreasesLikelihood-Disease.json b/data/templates/Drug-treats-Disease/ChemDecreasesLikelihood-Disease.json new file mode 100644 index 00000000..3ad63f54 --- /dev/null +++ b/data/templates/Drug-treats-Disease/ChemDecreasesLikelihood-Disease.json @@ -0,0 +1,35 @@ +{ + "message": { + "query_graph": { + "nodes": { + "creativeQuerySubject": { + "categories": + ["ChemicalEntity"] + }, + "creativeQueryObject": { + "categories":["biolink:DiseaseOrPhenotypicFeature"] + } + }, + "edges": { + "eA": { + "subject": "creativeQuerySubject", + "object": "creativeQueryObject", + "qualifier_constraints": [ + { + "qualifier_set": [ + { + "qualifier_type_id": "biolink:object_direction_qualifier", + "qualifier_value": "decreased" + }, + { + "qualifier_type_id": "biolink:object_aspect_qualifier", + "qualifier_value": "likelihood" + } + ] + } + ] + } + } + } + } +} \ No newline at end of file diff --git a/data/templates/NonChem-treats-Disease/NonChem-treats-DoP.json b/data/templates/NonChem-treats-Disease/NonChem-treats-DoP.json new file mode 100644 index 00000000..2814c53e --- /dev/null +++ b/data/templates/NonChem-treats-Disease/NonChem-treats-DoP.json @@ -0,0 +1,22 @@ +{ + "message": { + "query_graph": { + "nodes": { + "creativeQuerySubject": { + "categories": + ["biolink:Procedure", "biolink:Treatment", "biolink:ClinicalIntervention"] + }, + "creativeQueryObject": { + "categories":["biolink:DiseaseOrPhenotypicFeature"] + } + }, + "edges": { + "eA": { + "subject": "creativeQuerySubject", + "object": "creativeQueryObject", + "predicates": ["biolink:treats"] + } + } + } + } +} \ No newline at end of file diff --git a/data/templates/NonChem-treats-Disease/Procedure-decreasesLikelihood-Disease.json b/data/templates/NonChem-treats-Disease/Procedure-decreasesLikelihood-Disease.json new file mode 100644 index 00000000..69caf9d0 --- /dev/null +++ b/data/templates/NonChem-treats-Disease/Procedure-decreasesLikelihood-Disease.json @@ -0,0 +1,35 @@ +{ + "message": { + "query_graph": { + "nodes": { + "creativeQuerySubject": { + "categories": + ["Procedure"] + }, + "creativeQueryObject": { + "categories":["biolink:DiseaseOrPhenotypicFeature"] + } + }, + "edges": { + "eA": { + "subject": "creativeQuerySubject", + "object": "creativeQueryObject", + "qualifier_constraints": [ + { + "qualifier_set": [ + { + "qualifier_type_id": "biolink:object_direction_qualifier", + "qualifier_value": "decreased" + }, + { + "qualifier_type_id": "biolink:object_aspect_qualifier", + "qualifier_value": "likelihood" + } + ] + } + ] + } + } + } + } +} \ No newline at end of file diff --git a/data/templates/NonChem-treats-Disease/Treatment-related_to-DoP.json b/data/templates/NonChem-treats-Disease/Treatment-related_to-DoP.json new file mode 100644 index 00000000..00851d43 --- /dev/null +++ b/data/templates/NonChem-treats-Disease/Treatment-related_to-DoP.json @@ -0,0 +1,21 @@ +{ + "message": { + "query_graph": { + "nodes": { + "creativeQuerySubject": { + "categories":["biolink:Treatment"] + }, + "creativeQueryObject": { + "categories":["biolink:DiseaseOrPhenotypicFeature"] + } + }, + "edges": { + "eA": { + "subject": "creativeQuerySubject", + "object": "creativeQueryObject", + "predicates": ["biolink:related_to"] + } + } + } + } +} \ No newline at end of file