Merge branch 'pathfinder-templates' into pathfinder

biothings · Mar 28, 2024 · d12742e · d12742e
2 parents bd77b6d + f52c0f8
commit d12742e
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Showing 8 changed files with 209 additions and 15 deletions.
diff --git a/data/templateGroups.json b/data/templateGroups.json
@@ -51,5 +51,58 @@
       "Chem-physically_interacts-GeneThatDownregs-Gene.json",
       "Chem-physically_interacts-Gene.json"
     ]
+  },
+  {
+    "name": "Pathfinder: Drug-Disease",
+    "pathfinder": true,
+    "subject": ["Drug", "SmallMolecule", 
+                "ChemicalEntity", "ComplexMolecularMixture", "MolecularMixture"
+               ],
+    "predicate": ["related_to"],
+    "object": ["Disease", "PhenotypicFeature",
+               "DiseaseOrPhenotypicFeature"
+              ],
+    "templates": [
+      "pf-drug-gene-disease.json",
+      "pf-drug-gene-cell-disease.json",
+      "pf-drug-gene-physioAndpath-disease.json"
+    ]
+  },
+  {
+    "name": "Pathfinder: Chem-Gene",
+    "subject": ["Drug", "SmallMolecule", 
+                "ChemicalEntity", "ComplexMolecularMixture", "MolecularMixture"
+               ],
+    "predicate": ["related_to"],
+    "object": ["Gene", "Protein"],
+    "templates": [
+
+    ]
+  },
+  {
+    "name": "Pathfinder: Disease-Disease",
+    "pathfinder": true,
+    "subject": ["Disease", "PhenotypicFeature",
+               "DiseaseOrPhenotypicFeature"
+              ],
+    "predicate": ["related_to"],
+    "object": ["Disease", "PhenotypicFeature",
+               "DiseaseOrPhenotypicFeature"
+              ],
+    "templates": [
+
+    ]
+  },
+  {
+    "name": "Pathfinder: Gene-Disease",
+    "pathfinder": true,
+    "subject": ["Gene", "Protein"],
+    "predicate": ["related_to"],
+    "object": ["Disease", "PhenotypicFeature",
+               "DiseaseOrPhenotypicFeature"
+              ],
+    "templates": [
+
+    ]
   }
 ]
diff --git a/data/templates/Drug-treats-Disease/Chem-treats-DoP.json b/data/templates/Drug-treats-Disease/Chem-treats-DoP.json
@@ -13,7 +13,7 @@
                 "eA": {
                     "subject": "creativeQuerySubject",
                     "object": "creativeQueryObject",
-                    "predicates": ["biolink:treats"]
+                    "predicates": ["biolink:treats_or_applied_or_studied_to_treat"]
                 }
             }
         }

diff --git a/data/templates/Drug-treats-Disease/Chem-treats-PhenoOfDisease.json b/data/templates/Drug-treats-Disease/Chem-treats-PhenoOfDisease.json
@@ -17,7 +17,7 @@
                 "eA": {
                     "subject": "creativeQuerySubject",
                     "object": "nA",
-                    "predicates": ["biolink:treats"]
+                    "predicates": ["biolink:treats_or_applied_or_studied_to_treat"]
                 },
                 "eB": {
                     "subject": "creativeQueryObject",

diff --git a/data/templates/Pathfinder/pf-drug-gene-cell-disease.json b/data/templates/Pathfinder/pf-drug-gene-cell-disease.json
@@ -0,0 +1,46 @@
+{
+    "message": {
+        "query_graph": {
+            "nodes": {
+                "creativeQuerySubject": {
+                    "categories":["biolink:ChemicalEntity"]
+                },
+                "nA": {
+                    "categories":["biolink:Gene"]
+                },
+                "nB": {
+                    "categories":["biolink:Cell"]
+                },
+                "creativeQueryObject": {
+                    "categories":["biolink:DiseaseOrPhenotypicFeature"]
+               }
+            },
+            "edges": {
+                "eA": {
+                    "subject": "creativeQuerySubject",
+                    "object": "nA",
+                    "predicates": [
+                        "biolink:regulates",
+                        "biolink:affects",
+                        "biolink:interacts_with",
+                        "biolink:associated_with"
+                    ]
+                },
+                "eB": {
+                    "subject": "nA",
+                    "object": "nB",
+                    "predicates": [
+                        "biolink:related_to_at_instance_level"
+                    ]
+                },
+                "eC": {
+                    "subject": "nB",
+                    "object": "creativeQueryObject",
+                    "predicates": [
+                        "biolink:related_to_at_instance_level"
+                    ]
+                }
+            }
+        }
+    }
+}
diff --git a/data/templates/Pathfinder/pf-drug-gene-disease.json b/data/templates/Pathfinder/pf-drug-gene-disease.json
@@ -0,0 +1,40 @@
+{
+    "message": {
+        "query_graph": {
+            "nodes": {
+                "creativeQuerySubject": {
+                    "categories":["biolink:ChemicalEntity"]
+                },
+                "nA": {
+                    "categories":["biolink:Gene"]
+                },
+                "creativeQueryObject": {
+                    "categories":["biolink:DiseaseOrPhenotypicFeature"]
+               }
+            },
+            "edges": {
+                "eA": {
+                    "subject": "creativeQuerySubject",
+                    "object": "nA",
+                    "predicates": [
+                        "biolink:regulates",
+                        "biolink:affects",
+                        "biolink:interacts_with",
+                        "biolink:associated_with"
+                    ]
+                },
+                "eB": {
+                    "subject": "nA",
+                    "object": "creativeQueryObject",
+                    "predicates": [
+                        "biolink:gene_associated_with_condition",
+                        "biolink:biomarker_for",
+                        "biolink:affects",
+                        "biolink:causes",
+                        "biolink:contributes_to"
+                    ]
+                }
+            }
+        }
+    }
+}
diff --git a/data/templates/Pathfinder/pf-drug-gene-physioAndpath-disease.json b/data/templates/Pathfinder/pf-drug-gene-physioAndpath-disease.json
@@ -0,0 +1,49 @@
+{
+    "message": {
+        "query_graph": {
+            "nodes": {
+                "creativeQuerySubject": {
+                    "categories":["biolink:ChemicalEntity"]
+                },
+                "nA": {
+                    "categories":["biolink:Gene"]
+                },
+                "nB": {
+                    "categories":["biolink:PhysiologicalProcess", "biolink:Pathway"]
+                },
+                "creativeQueryObject": {
+                    "categories":["biolink:DiseaseOrPhenotypicFeature"]
+               }
+            },
+            "edges": {
+                "eA": {
+                    "subject": "creativeQuerySubject",
+                    "object": "nA",
+                    "predicates": [
+                        "biolink:regulates",
+                        "biolink:affects",
+                        "biolink:interacts_with",
+                        "biolink:associated_with"
+                    ]
+                },
+                "eB": {
+                    "subject": "nA",
+                    "object": "nB",
+                    "predicates": [
+                        "biolink:affects",
+                        "biolink:contributes_to"
+                    ]
+                },
+                "eC": {
+                    "subject": "nB",
+                    "object": "creativeQueryObject",
+                    "predicates": [
+                        "biolink:affects",
+                        "biolink:affected_by",
+                        "biolink:occurs_in"
+                    ]
+                }
+            }
+        }
+    }
+}
diff --git a/src/edge_manager.ts b/src/edge_manager.ts
@@ -231,7 +231,7 @@ export default class QueryEdgeManager {
     return keep;
   }
 
-  collectRecords(): void {
+  collectRecords(): boolean {
     //go through edges and collect records organized by edge
     let recordsByQEdgeID: RecordsByQEdgeID = {};
     //all res merged
@@ -268,12 +268,10 @@ export default class QueryEdgeManager {
         new LogEntry(
           'WARNING',
           null,
-          `qEdges ${JSON.stringify(brokenEdges)} ` + `resulted in (0) records. No complete paths can be formed.`,
+          `qEdges ${brokenEdges} resulted in (0) records. No complete paths can be formed.`,
         ).getLog(),
       );
-      debug(
-        `(12) qEdges ${JSON.stringify(brokenEdges)} ` + `resulted in (0) records. No complete paths can be formed.`,
-      );
+      debug(`(12) qEdges ${brokenEdges} resulted in (0) records. No complete paths can be formed.`);
     }
     //Organized by edge: update query records
     this._organizedRecords = recordsByQEdgeID;
@@ -289,8 +287,12 @@ export default class QueryEdgeManager {
     //         console.log(err);
     //     }
     // });
-    debug(`(12) Collected (${this._records.length}) records!`);
-    this.logs.push(new LogEntry('DEBUG', null, `Edge manager collected (${this._records.length}) records!`).getLog());
+    if (!brokenChain) {
+      debug(`(12) Collected (${this._records.length}) records!`);
+      this.logs.push(new LogEntry('DEBUG', null, `Edge manager collected (${this._records.length}) records!`).getLog());
+    }
+
+    return !brokenChain;
   }
 
   updateEdgeRecords(currentQEdge: QEdge): void {
@@ -474,7 +476,13 @@ export default class QueryEdgeManager {
     }
     this._logSkippedQueries(unavailableAPIs);
     // collect and organize records
-    this.collectRecords();
+    if (!this.collectRecords()) {
+      debug(`(X) Terminating...No complete paths.`);
+      this.logs.push(
+        new LogEntry('WARNING', null, `No complete paths could be formed. Your query terminates.`).getLog(),
+      );
+      return;
+    }
     // dump records if set to do so
     if (process.env.DUMP_RECORDS) {
       await this.dumpRecords(this.getRecords());

diff --git a/src/inferred_mode/inferred_mode.ts b/src/inferred_mode/inferred_mode.ts
@@ -110,11 +110,9 @@ export default class InferredQueryHandler {
       return false;
     }
 
-    const tooManyIDs =
-      1 <
-      Object.values(this.queryGraph.nodes).reduce((sum, node) => {
-        return typeof node.ids !== 'undefined' ? sum + node.ids.length : sum;
-      }, 0);
+    const tooManyIDs = Object.values(this.queryGraph.nodes).some((node) => {
+      return typeof node.ids !== 'undefined' && node.ids.length > 1;
+    });
     if (tooManyIDs && !this.pathfinder) {
       const message = 'Inferred Mode queries with multiple IDs are not supported. Your query terminates.';
       this.logs.push(new LogEntry('WARNING', null, message).getLog());