biothings semmeddb: adjust fields, response-mapping for post-processing

for https://github.com/biothings/biothings_explorer/issues/833\#issuecomment-2301307891
NCATS-Tangerine · Aug 21, 2024 · 5f7ac52 · 5f7ac52
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diff --git a/semmeddb/AutoGen_SEMMEDDB.ipynb b/semmeddb/AutoGen_SEMMEDDB.ipynb
@@ -9139,7 +9139,7 @@
        "   'inputs': [{'id': 'UMLS', 'semantic': 'GrossAnatomicalStructure'}],\n",
        "   'requestBody': {'body': {'q': '{{ queryInputs }}',\n",
        "     'scopes': 'subject.umls'}},\n",
-       "   'parameters': {'fields': 'object.umls,predication.pmid,predication.sentence,subject.name,object.name',\n",
+       "   'parameters': {'fields': 'object.umls,predication,pmid_count,subject.name,object.name',\n",
        "    'size': 1000,\n",
        "    'filter': 'predicate:LOCATION_OF AND object.semantic_type_abbreviation:neop AND _exists_:object.umls AND pmid_count:>3'},\n",
        "   'outputs': [{'id': 'UMLS', 'semantic': 'Disease'}],\n",
@@ -9184,7 +9184,7 @@
        "   'inputs': [{'id': 'NCBIGene', 'semantic': 'Gene'}],\n",
        "   'requestBody': {'body': {'q': '{{ queryInputs }}',\n",
        "     'scopes': 'subject.ncbigene'}},\n",
-       "   'parameters': {'fields': 'object.umls,predication.pmid,predication.sentence,subject.name,object.name',\n",
+       "   'parameters': {'fields': 'object.umls,predication,pmid_count,subject.name,object.name',\n",
        "    'size': 1000,\n",
        "    'filter': 'predicate:ASSOCIATED_WITH AND object.semantic_type_abbreviation:neop AND _exists_:object.umls AND pmid_count:>3'},\n",
        "   'outputs': [{'id': 'UMLS', 'semantic': 'Disease'}],\n",
@@ -9229,7 +9229,7 @@
        "   'inputs': [{'id': 'UMLS', 'semantic': 'Polypeptide'}],\n",
        "   'requestBody': {'body': {'q': '{{ queryInputs }}',\n",
        "     'scopes': 'subject.umls'}},\n",
-       "   'parameters': {'fields': 'object.ncbigene,predication.pmid,predication.sentence,subject.name,object.name',\n",
+       "   'parameters': {'fields': 'object.ncbigene,predication,pmid_count,subject.name,object.name',\n",
        "    'size': 1000,\n",
        "    'filter': 'predicate:STIMULATES AND object.semantic_type_abbreviation:gngm AND _exists_:object.ncbigene AND pmid_count:>3'},\n",
        "   'outputs': [{'id': 'NCBIGene', 'semantic': 'Gene'}],\n",
@@ -9277,7 +9277,7 @@
        "   'inputs': [{'id': 'NCBIGene', 'semantic': 'Gene'}],\n",
        "   'requestBody': {'body': {'q': '{{ queryInputs }}',\n",
        "     'scopes': 'subject.ncbigene'}},\n",
-       "   'parameters': {'fields': 'object.ncbigene,predication.pmid,predication.sentence,subject.name,object.name',\n",
+       "   'parameters': {'fields': 'object.ncbigene,predication,pmid_count,subject.name,object.name',\n",
        "    'size': 1000,\n",
        "    'filter': 'predicate:STIMULATES AND object.semantic_type_abbreviation:gngm AND _exists_:object.ncbigene AND pmid_count:>3'},\n",
        "   'outputs': [{'id': 'NCBIGene', 'semantic': 'Gene'}],\n",
@@ -10023,7 +10023,7 @@
        "   'inputs': [{'id': 'UMLS', 'semantic': 'Disease'}],\n",
        "   'requestBody': {'body': {'q': '{{ queryInputs }}',\n",
        "     'scopes': 'object.umls'}},\n",
-       "   'parameters': {'fields': 'subject.umls,predication.pmid,predication.sentence,subject.name,object.name',\n",
+       "   'parameters': {'fields': 'subject.umls,predication,pmid_count,subject.name,object.name',\n",
        "    'size': 1000,\n",
        "    'filter': 'predicate:LOCATION_OF AND subject.semantic_type_abbreviation:bpoc AND _exists_:subject.umls AND pmid_count:>3'},\n",
        "   'outputs': [{'id': 'UMLS', 'semantic': 'GrossAnatomicalStructure'}],\n",
@@ -10068,7 +10068,7 @@
        "   'inputs': [{'id': 'UMLS', 'semantic': 'Disease'}],\n",
        "   'requestBody': {'body': {'q': '{{ queryInputs }}',\n",
        "     'scopes': 'object.umls'}},\n",
-       "   'parameters': {'fields': 'subject.ncbigene,predication.pmid,predication.sentence,subject.name,object.name',\n",
+       "   'parameters': {'fields': 'subject.ncbigene,predication,pmid_count,subject.name,object.name',\n",
        "    'size': 1000,\n",
        "    'filter': 'predicate:ASSOCIATED_WITH AND subject.semantic_type_abbreviation:gngm AND _exists_:subject.ncbigene AND pmid_count:>3'},\n",
        "   'outputs': [{'id': 'NCBIGene', 'semantic': 'Gene'}],\n",
@@ -10113,7 +10113,7 @@
        "   'inputs': [{'id': 'NCBIGene', 'semantic': 'Gene'}],\n",
        "   'requestBody': {'body': {'q': '{{ queryInputs }}',\n",
        "     'scopes': 'object.ncbigene'}},\n",
-       "   'parameters': {'fields': 'subject.umls,predication.pmid,predication.sentence,subject.name,object.name',\n",
+       "   'parameters': {'fields': 'subject.umls,predication,pmid_count,subject.name,object.name',\n",
        "    'size': 1000,\n",
        "    'filter': 'predicate:STIMULATES AND subject.semantic_type_abbreviation:aapp AND _exists_:subject.umls AND pmid_count:>3'},\n",
        "   'outputs': [{'id': 'UMLS', 'semantic': 'Polypeptide'}],\n",
@@ -10161,7 +10161,7 @@
        "   'inputs': [{'id': 'NCBIGene', 'semantic': 'Gene'}],\n",
        "   'requestBody': {'body': {'q': '{{ queryInputs }}',\n",
        "     'scopes': 'object.ncbigene'}},\n",
-       "   'parameters': {'fields': 'subject.ncbigene,predication.pmid,predication.sentence,subject.name,object.name',\n",
+       "   'parameters': {'fields': 'subject.ncbigene,predication,pmid_count,subject.name,object.name',\n",
        "    'size': 1000,\n",
        "    'filter': 'predicate:STIMULATES AND subject.semantic_type_abbreviation:gngm AND _exists_:subject.ncbigene AND pmid_count:>3'},\n",
        "   'outputs': [{'id': 'NCBIGene', 'semantic': 'Gene'}],\n",
@@ -10334,7 +10334,7 @@
       "  'inputs': [{'id': 'NCBIGene', 'semantic': 'Gene'}],\n",
       "  'requestBody': {'body': {'q': '{{ queryInputs }}',\n",
       "                           'scopes': 'object.ncbigene'}},\n",
-      "  'parameters': {'fields': 'subject.umls,predication.pmid,predication.sentence,subject.name,object.name',\n",
+      "  'parameters': {'fields': 'subject.umls,predication,pmid_count,subject.name,object.name',\n",
       "                 'size': 1000,\n",
       "                 'filter': 'predicate:INHIBITS AND '\n",
       "                           'subject.semantic_type_abbreviation:orch AND '\n",
@@ -10380,7 +10380,7 @@
       "  'useTemplating': True,\n",
       "  'inputs': [{'id': 'UMLS', 'semantic': 'ChemicalEntity'}],\n",
       "  'requestBody': {'body': {'q': '{{ queryInputs }}', 'scopes': 'subject.umls'}},\n",
-      "  'parameters': {'fields': 'object.umls,predication.pmid,predication.sentence,subject.name,object.name',\n",
+      "  'parameters': {'fields': 'object.umls,predication,pmid_count,subject.name,object.name',\n",
       "                 'size': 1000,\n",
       "                 'filter': 'predicate:CAUSES AND '\n",
       "                           'object.semantic_type_abbreviation:neop AND '\n",