Merge branch 'pathfinder-templates' of https://github.com/biothings/b…

…te_trapi_query_graph_handler into pathfinder
biothings · Apr 4, 2024 · 3cd3b90 · 3cd3b90
2 parents b6aed6f + 6f84108
commit 3cd3b90
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Showing 6 changed files with 142 additions and 3 deletions.
diff --git 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"
     ]
   },
   {
@@ -90,7 +91,8 @@
                "DiseaseOrPhenotypicFeature"
               ],
     "templates": [
-
+      "pf-disease-seqvar-disease.json",
+      "pf-disease-gene-disease.json"
     ]
   },
   {

diff --git a/data/templates/Pathfinder/pf-chem-gene-gene-gene.json 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"
+                    ]
+                }
+            }
+        }
+    }
+}
diff --git a/data/templates/Pathfinder/pf-chem-gene-gene.json 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"
+                    ]
+                }
+            }
+        }
+    }
+}
diff --git a/data/templates/Pathfinder/pf-disease-gene-disease.json 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"
+                }
+            }
+        }
+    }
+}
diff --git a/data/templates/Pathfinder/pf-disease-seqvar-disease.json 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"
+                }
+            }
+        }
+    }
+}
diff --git 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"
                     ]
                 }