Merge pull request #190 from biothings/kl-at

Add knowledge_level/agent_type to edges
biothings · Apr 12, 2024 · 499b09c · 499b09c
2 parents 55811ee + ac88bfc
commit 499b09c
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Showing 4 changed files with 22 additions and 3 deletions.
diff --git a/src/graph/graph.ts b/src/graph/graph.ts
@@ -104,6 +104,12 @@ export default class BTEGraph {
           .map((item) => {
             this.edges[recordHash].addAdditionalAttributes(item, record.mappedResponse[item]);
           });
+        if (record.knowledge_level) {
+          this.edges[recordHash].addAdditionalAttributes('biolink:knowledge_level', record.knowledge_level);
+        }
+        if (record.agent_type) {
+          this.edges[recordHash].addAdditionalAttributes('biolink:agent_type', record.agent_type);
+        }
         this.edges[recordHash].addSource(record.provenanceChain);
         Object.entries(record.qualifiers).forEach(([qualifierType, qualifier]) => {
           this.edges[recordHash].addQualifier(qualifierType, qualifier);

diff --git a/src/graph/knowledge_graph.ts b/src/graph/knowledge_graph.ts
@@ -17,6 +17,8 @@ import { APIDefinition } from '@biothings-explorer/types';
 
 const debug = Debug('bte:biothings-explorer-trapi:KnowledgeGraph');
 
+const NON_ARRAY_ATTRIBUTES = ['biolink:knowledge_level', 'biolink:agent_type'];
+
 export default class KnowledgeGraph {
   nodes: {
     [nodePrimaryID: string]: TrapiKGNode;
@@ -114,11 +116,14 @@ export default class KnowledgeGraph {
     }
 
     Object.entries(kgEdge.attributes).forEach(([key, value]) => {
-      if (key == 'edge-attributes') return;
+      if (key === 'edge-attributes') return;
       // if (key == 'edge-attributes') return;
       attributes.push({
         attribute_type_id: key,
-        value: Array.from(value as Set<string>),
+        value: // technically works for numbers as well
+          NON_ARRAY_ATTRIBUTES.includes(key)
+            ? [...(value as Set<string>)].reduce((acc, val) => acc + val)
+            : Array.from(value as Set<string>),
         //value_type_id: 'bts:' + key,
       });
     });

diff --git a/src/index.ts b/src/index.ts
@@ -173,6 +173,8 @@ export default class TRAPIQueryHandler {
         const source = Object.entries(ontologyKnowledgeSourceMapping).find(([prefix]) => {
           return expanded.includes(prefix);
         })[1];
+        subclassEdge.addAdditionalAttributes('biolink:knowledge_level', 'knowledge_assertion')
+        subclassEdge.addAdditionalAttributes('biolink:agent_type', 'manual_agent')
         subclassEdge.addSource([
           { resource_id: source, resource_role: 'primary_knowledge_source' },
           {
@@ -221,6 +223,8 @@ export default class TRAPIQueryHandler {
           object: object,
         });
         boundEdge.addAdditionalAttributes('biolink:support_graphs', [supportGraphID]);
+        boundEdge.addAdditionalAttributes('biolink:knowledge_level', 'logical_entailment')
+        boundEdge.addAdditionalAttributes('biolink:agent_type', 'automated_agent')
         boundEdge.addSource([
           {
             resource_id: this.options.provenanceUsesServiceProvider

diff --git a/src/inferred_mode/inferred_mode.ts b/src/inferred_mode/inferred_mode.ts
@@ -332,7 +332,11 @@ export default class InferredQueryHandler {
                 resource_role: 'primary_knowledge_source',
               },
             ],
-            attributes: [{ attribute_type_id: 'biolink:support_graphs', value: [] }],
+            attributes: [
+              { attribute_type_id: 'biolink:support_graphs', value: [] },
+              { attribute_type_id: 'biolink:knowledge_level', value: "prediction" },
+              { attribute_type_id: 'biolink:agent_type', value: "computational_model" },
+            ],
           };
         }
         let auxGraphSuffix = 0;