diff --git a/data/templateGroups.json b/data/templateGroups.json index 1a36e909..12562ba7 100644 --- a/data/templateGroups.json +++ b/data/templateGroups.json @@ -9,9 +9,11 @@ "DiseaseOrPhenotypicFeature" ], "templates": [ - "Chem-DoP.json", - "m4-Chem-Gene-DoP.json", - "m1-Chem-Pheno-DoP.json" + "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" ] }, { @@ -26,11 +28,11 @@ }, "object": ["Gene", "Protein"], "templates": [ - "direct-increase.json", - "increase-another-gene-that-upregs.json", - "decrease-another-gene-that-downregs.json", - "interacts-with-another-gene-that-upregs.json", - "Chem-interacts-with-Gene.json" + "Chem-increasesGene.json", + "Chem-IncreaseAnotherGeneThatUpregs-Gene.json", + "Chem-DecreaseAnotherGeneThatDownregs-Gene.json", + "Chem-interacts_with-GeneThatUpregs-Gene.json", + "Chem-interacts_with-Gene.json" ] }, { @@ -45,11 +47,11 @@ }, "object": ["Gene", "Protein"], "templates": [ - "direct-decrease.json", - "increase-another-gene-that-downregs.json", - "decrease-another-gene-that-upregs.json", - "interacts-with-another-gene-that-downregs.json", - "Chem-interacts-with-Gene.json" + "Chem-decreasesGene.json", + "Chem-IncreaseAnotherGeneThatDownregs-Gene.json", + "Chem-DecreaseAnotherGeneThatUpregs-Gene.json", + "Chem-interacts_with-GeneThatDownregs-Gene.json", + "Chem-interacts_with-Gene.json" ] } ] diff --git a/data/templates/Chem-decreases-Gene/decrease-another-gene-that-upregs.json b/data/templates/Chem-decreases-Gene/Chem-DecreaseAnotherGeneThatUpregs-Gene.json similarity index 77% rename from data/templates/Chem-decreases-Gene/decrease-another-gene-that-upregs.json rename to data/templates/Chem-decreases-Gene/Chem-DecreaseAnotherGeneThatUpregs-Gene.json index 95fcfeb5..7ff51ce3 100644 --- a/data/templates/Chem-decreases-Gene/decrease-another-gene-that-upregs.json +++ b/data/templates/Chem-decreases-Gene/Chem-DecreaseAnotherGeneThatUpregs-Gene.json @@ -27,19 +27,7 @@ }, { "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "activity" - } - ] - }, - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" - }, - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "abundance" + "qualifier_value": "activity_or_abundance" } ] } diff --git a/data/templates/Chem-decreases-Gene/increase-another-gene-that-downregs.json b/data/templates/Chem-decreases-Gene/Chem-IncreaseAnotherGeneThatDownregs-Gene.json similarity index 77% rename from data/templates/Chem-decreases-Gene/increase-another-gene-that-downregs.json rename to data/templates/Chem-decreases-Gene/Chem-IncreaseAnotherGeneThatDownregs-Gene.json index 05941133..5e1c5b09 100644 --- a/data/templates/Chem-decreases-Gene/increase-another-gene-that-downregs.json +++ b/data/templates/Chem-decreases-Gene/Chem-IncreaseAnotherGeneThatDownregs-Gene.json @@ -27,19 +27,7 @@ }, { "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "activity" - } - ] - }, - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" - }, - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "abundance" + "qualifier_value": "activity_or_abundance" } ] } diff --git a/data/templates/Chem-decreases-Gene/direct-decrease.json b/data/templates/Chem-decreases-Gene/Chem-decreasesGene.json similarity index 51% rename from data/templates/Chem-decreases-Gene/direct-decrease.json rename to data/templates/Chem-decreases-Gene/Chem-decreasesGene.json index ed1dc878..64a376b7 100644 --- a/data/templates/Chem-decreases-Gene/direct-decrease.json +++ b/data/templates/Chem-decreases-Gene/Chem-decreasesGene.json @@ -26,30 +26,6 @@ "qualifier_value": "activity_or_abundance" } ] - }, - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" - }, - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "activity" - } - ] - }, - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" - }, - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "abundance" - } - ] } ] } diff --git a/data/templates/Chem-decreases-Gene/interacts-with-another-gene-that-downregs.json b/data/templates/Chem-decreases-Gene/Chem-interacts_with-GeneThatDownregs-Gene.json similarity index 100% rename from data/templates/Chem-decreases-Gene/interacts-with-another-gene-that-downregs.json rename to data/templates/Chem-decreases-Gene/Chem-interacts_with-GeneThatDownregs-Gene.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/decrease-another-gene-that-downregs.json b/data/templates/Chem-increases-Gene/Chem-DecreaseAnotherGeneThatDownregs-Gene.json similarity index 77% rename from data/templates/Chem-increases-Gene/decrease-another-gene-that-downregs.json rename to data/templates/Chem-increases-Gene/Chem-DecreaseAnotherGeneThatDownregs-Gene.json index a5bc6f38..9099b453 100644 --- a/data/templates/Chem-increases-Gene/decrease-another-gene-that-downregs.json +++ b/data/templates/Chem-increases-Gene/Chem-DecreaseAnotherGeneThatDownregs-Gene.json @@ -27,19 +27,7 @@ }, { "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "activity" - } - ] - }, - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" - }, - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "abundance" + "qualifier_value": "activity_or_abundance" } ] } diff --git a/data/templates/Chem-increases-Gene/increase-another-gene-that-upregs.json b/data/templates/Chem-increases-Gene/Chem-IncreaseAnotherGeneThatUpregs-Gene.json similarity index 77% rename from data/templates/Chem-increases-Gene/increase-another-gene-that-upregs.json rename to data/templates/Chem-increases-Gene/Chem-IncreaseAnotherGeneThatUpregs-Gene.json index 8944f54a..515cdfb0 100644 --- a/data/templates/Chem-increases-Gene/increase-another-gene-that-upregs.json +++ b/data/templates/Chem-increases-Gene/Chem-IncreaseAnotherGeneThatUpregs-Gene.json @@ -27,19 +27,7 @@ }, { "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "activity" - } - ] - }, - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" - }, - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "abundance" + "qualifier_value": "activity_or_abundance" } ] } diff --git a/data/templates/Chem-increases-Gene/direct-increase.json b/data/templates/Chem-increases-Gene/Chem-increasesGene.json similarity index 51% rename from data/templates/Chem-increases-Gene/direct-increase.json rename to data/templates/Chem-increases-Gene/Chem-increasesGene.json index f3a3b790..b8e8dcef 100644 --- a/data/templates/Chem-increases-Gene/direct-increase.json +++ b/data/templates/Chem-increases-Gene/Chem-increasesGene.json @@ -26,30 +26,6 @@ "qualifier_value": "activity_or_abundance" } ] - }, - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" - }, - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "activity" - } - ] - }, - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" - }, - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "abundance" - } - ] } ] } diff --git a/data/templates/Chem-increases-Gene/interacts-with-another-gene-that-upregs.json b/data/templates/Chem-increases-Gene/Chem-interacts_with-GeneThatUpregs-Gene.json similarity index 100% rename from data/templates/Chem-increases-Gene/interacts-with-another-gene-that-upregs.json rename to data/templates/Chem-increases-Gene/Chem-interacts_with-GeneThatUpregs-Gene.json 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/Chem-interacts-with-Gene.json b/data/templates/Chem-interacts_with-Gene.json similarity index 100% rename from data/templates/Chem-interacts-with-Gene.json rename to data/templates/Chem-interacts_with-Gene.json diff --git a/data/templates/Drug-treats-Disease/Chem-decreaseGeneWithFunctionGainIn-Disease.json b/data/templates/Drug-treats-Disease/Chem-decreaseGeneWithFunctionGainIn-Disease.json new file mode 100644 index 00000000..c0d8fc0e --- /dev/null +++ b/data/templates/Drug-treats-Disease/Chem-decreaseGeneWithFunctionGainIn-Disease.json @@ -0,0 +1,52 @@ +{ + "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", + "qualifier_constraints": [ + { + "qualifier_set": [ + { + "qualifier_type_id": "biolink:object_direction_qualifier", + "qualifier_value": "decreased" + }, + { + "qualifier_type_id": "biolink:object_aspect_qualifier", + "qualifier_value": "activity_or_abundance" + } + ] + } + ] + }, + "eB": { + "subject": "nA", + "object": "creativeQueryObject", + "qualifier_constraints": [ + { + "qualifier_set": [ + { + "qualifier_type_id": "biolink:subject_form_or_variant_qualifier", + "qualifier_value": "gain_of_function_variant_form" + } + ] + } + ] + } + } + } + } +} \ No newline at end of file diff --git a/data/templates/Drug-treats-Disease/Chem-increaseGeneWithFunctionLossIn-Disease.json b/data/templates/Drug-treats-Disease/Chem-increaseGeneWithFunctionLossIn-Disease.json new file mode 100644 index 00000000..9ce2d114 --- /dev/null +++ b/data/templates/Drug-treats-Disease/Chem-increaseGeneWithFunctionLossIn-Disease.json @@ -0,0 +1,52 @@ +{ + "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", + "qualifier_constraints": [ + { + "qualifier_set": [ + { + "qualifier_type_id": "biolink:object_direction_qualifier", + "qualifier_value": "increased" + }, + { + "qualifier_type_id": "biolink:object_aspect_qualifier", + "qualifier_value": "activity_or_abundance" + } + ] + } + ] + }, + "eB": { + "subject": "nA", + "object": "creativeQueryObject", + "qualifier_constraints": [ + { + "qualifier_set": [ + { + "qualifier_type_id": "biolink:subject_form_or_variant_qualifier", + "qualifier_value": "loss_of_function_variant_form" + } + ] + } + ] + } + } + } + } +} \ 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/m4-Chem-Gene-DoP.json b/data/templates/Drug-treats-Disease/Chem-regulates,affects-Gene-biomarker,associated_condition-DoP.json similarity index 83% rename from data/templates/Drug-treats-Disease/m4-Chem-Gene-DoP.json rename to data/templates/Drug-treats-Disease/Chem-regulates,affects-Gene-biomarker,associated_condition-DoP.json index 2a9d9a10..cfe084e1 100644 --- a/data/templates/Drug-treats-Disease/m4-Chem-Gene-DoP.json +++ b/data/templates/Drug-treats-Disease/Chem-regulates,affects-Gene-biomarker,associated_condition-DoP.json @@ -22,7 +22,10 @@ "eB": { "subject": "nA", "object": "creativeQueryObject", - "predicates": ["biolink:causes"] + "predicates": [ + "biolink:gene_associated_with_condition", + "biolink:biomarker_for" + ] } } } diff --git a/data/templates/Drug-treats-Disease/Chem-regulates,affects-Gene-cause,contribute,affects-DoP.json b/data/templates/Drug-treats-Disease/Chem-regulates,affects-Gene-cause,contribute,affects-DoP.json new file mode 100644 index 00000000..b7e39755 --- /dev/null +++ b/data/templates/Drug-treats-Disease/Chem-regulates,affects-Gene-cause,contribute,affects-DoP.json @@ -0,0 +1,34 @@ +{ + "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:regulates", "biolink:affects"] + }, + "eB": { + "subject": "nA", + "object": "creativeQueryObject", + "predicates": [ + "biolink:affects", + "biolink:causes", + "biolink:contributes_to" + ] + } + } + } + } +} \ 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/Chem-DoP.json b/data/templates/Drug-treats-Disease/Chem-treats-DoP.json similarity index 100% rename from data/templates/Drug-treats-Disease/Chem-DoP.json rename to data/templates/Drug-treats-Disease/Chem-treats-DoP.json diff --git a/data/templates/Drug-treats-Disease/m1-Chem-Pheno-DoP.json b/data/templates/Drug-treats-Disease/Chem-treats-PhenoOfDisease.json similarity index 100% rename from data/templates/Drug-treats-Disease/m1-Chem-Pheno-DoP.json rename to data/templates/Drug-treats-Disease/Chem-treats-PhenoOfDisease.json 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