Discussion: investigate ingestion of GraphQL resources #629
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For ref only: this has has also been mentioned in this issue comment. Dunno how related it would be, LINCS has a Google BigQuery endpoint (which is discussed in that linked comment) |
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Some potentially useful links: |
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Couldn't GrpahQL by supported using the current framework? A graphQL query could be written and put as a POST parameter in the smartapi yaml, and then variables could be specified based on the queryInputs (like the python example on https://platform-docs.opentargets.org/data-access/graphql-api) Although, does the yaml structure currently support sending a JSON format? |
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NEW open target yaml using GraphQL |
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@rjawesome if this works, that would be pretty awesome. Have you tried adding your annotation to BTE via the local overrides and then executing a TRAPI query to retrieve a record from Open Targets? Would love to see the proof of concept! |
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Yes, this has been tested (requires biothings/api-respone-transform.js#51) Example Input: {
"message": {
"query_graph": {
"nodes": {
"n0": {
"ids":["ENSEMBL:ENSG00000169083"]
},
"n1": {
}
},
"edges": {
"e0": {
"subject": "n0",
"object": "n1"
}
}
}
}
}Example Output: JSON{
"description": "Query processed successfully, retrieved 19 results.",
"schema_version": "1.4.0",
"biolink_version": "3.1.1",
"workflow": [
{
"id": "lookup"
}
],
"message": {
"query_graph": {
"nodes": {
"n0": {
"ids": [
"ENSEMBL:ENSG00000169083"
],
"categories": [
"biolink:BiologicalEntity"
]
},
"n1": {}
},
"edges": {
"e0": {
"subject": "n0",
"object": "n1"
}
}
},
"knowledge_graph": {
"nodes": {
"CHEMBL.COMPOUND:806": {
"categories": [
"biolink:SmallMolecule"
],
"attributes": [
{
"attribute_type_id": "biolink:xref",
"value": [
"CHEMBL.COMPOUND:806"
]
},
{
"attribute_type_id": "biolink:synonym",
"value": [
"CHEMBL.COMPOUND:806"
]
}
]
},
"NCBIGene:367": {
"categories": [
"biolink:BiologicalEntity"
],
"name": "AR",
"attributes": [
{
"attribute_type_id": "biolink:xref",
"value": [
"NCBIGene:367",
"ENSEMBL:ENSG00000169083",
"HGNC:644",
"OMIM:313700",
"UMLS:C1367578",
"UniProtKB:A0A087WUX9",
"ENSEMBL:ENSP00000479013",
"ENSEMBL:ENSP00000479013.1",
"UniProtKB:F1D8N5",
"UniProtKB:G4VV16",
"UniProtKB:P10275",
"PR:P10275",
"UMLS:C1447749",
"UMLS:C4283898",
"UMLS:C4283899",
"UniProtKB:Q9NUA2"
]
},
{
"attribute_type_id": "biolink:synonym",
"value": [
"AR",
"AR gene",
"A0A087WUX9_HUMAN Androgen receptor (trembl)",
"F1D8N5_HUMAN Androgen nuclear receptor variant 2 (trembl)",
"G4VV16_HUMAN Androgen receptor isoform 8 (trembl)",
"ANDR_HUMAN Androgen receptor (sprot)",
"androgen receptor (human)",
"AR protein, human",
"Androgen Receptor Splice Variant 5,6,7es, Human",
"Androgen Receptor Splice Variant 3, Human",
"Q9NUA2_HUMAN Androgen receptor (Fragment) (trembl)"
]
}
]
},
"CHEMBL.COMPOUND:1082407": {
"categories": [
"biolink:SmallMolecule"
],
"attributes": [
{
"attribute_type_id": "biolink:xref",
"value": [
"CHEMBL.COMPOUND:1082407"
]
},
{
"attribute_type_id": "biolink:synonym",
"value": [
"CHEMBL.COMPOUND:1082407"
]
}
]
},
"CHEMBL.COMPOUND:409": {
"categories": [
"biolink:SmallMolecule"
],
"attributes": [
{
"attribute_type_id": "biolink:xref",
"value": [
"CHEMBL.COMPOUND:409"
]
},
{
"attribute_type_id": "biolink:synonym",
"value": [
"CHEMBL.COMPOUND:409"
]
}
]
},
"CHEMBL.COMPOUND:3183409": {
"categories": [
"biolink:SmallMolecule"
],
"attributes": [
{
"attribute_type_id": "biolink:xref",
"value": [
"CHEMBL.COMPOUND:3183409"
]
},
{
"attribute_type_id": "biolink:synonym",
"value": [
"CHEMBL.COMPOUND:3183409"
]
}
]
},
"CHEMBL.COMPOUND:254328": {
"categories": [
"biolink:SmallMolecule"
],
"attributes": [
{
"attribute_type_id": "biolink:xref",
"value": [
"CHEMBL.COMPOUND:254328"
]
},
{
"attribute_type_id": "biolink:synonym",
"value": [
"CHEMBL.COMPOUND:254328"
]
}
]
},
"CHEMBL.COMPOUND:1274": {
"categories": [
"biolink:SmallMolecule"
],
"attributes": [
{
"attribute_type_id": "biolink:xref",
"value": [
"CHEMBL.COMPOUND:1274"
]
},
{
"attribute_type_id": "biolink:synonym",
"value": [
"CHEMBL.COMPOUND:1274"
]
}
]
},
"CHEMBL.COMPOUND:4297185": {
"categories": [
"biolink:SmallMolecule"
],
"attributes": [
{
"attribute_type_id": "biolink:xref",
"value": [
"CHEMBL.COMPOUND:4297185"
]
},
{
"attribute_type_id": "biolink:synonym",
"value": [
"CHEMBL.COMPOUND:4297185"
]
}
]
},
"CHEMBL.COMPOUND:2107067": {
"categories": [
"biolink:SmallMolecule"
],
"attributes": [
{
"attribute_type_id": "biolink:xref",
"value": [
"CHEMBL.COMPOUND:2107067"
]
},
{
"attribute_type_id": "biolink:synonym",
"value": [
"CHEMBL.COMPOUND:2107067"
]
}
]
},
"CHEMBL.COMPOUND:386630": {
"categories": [
"biolink:SmallMolecule"
],
"attributes": [
{
"attribute_type_id": "biolink:xref",
"value": [
"CHEMBL.COMPOUND:386630"
]
},
{
"attribute_type_id": "biolink:synonym",
"value": [
"CHEMBL.COMPOUND:386630"
]
}
]
},
"CHEMBL.COMPOUND:1201101": {
"categories": [
"biolink:SmallMolecule"
],
"attributes": [
{
"attribute_type_id": "biolink:xref",
"value": [
"CHEMBL.COMPOUND:1201101"
]
},
{
"attribute_type_id": "biolink:synonym",
"value": [
"CHEMBL.COMPOUND:1201101"
]
}
]
},
"CHEMBL.COMPOUND:1445": {
"categories": [
"biolink:SmallMolecule"
],
"attributes": [
{
"attribute_type_id": "biolink:xref",
"value": [
"CHEMBL.COMPOUND:1445"
]
},
{
"attribute_type_id": "biolink:synonym",
"value": [
"CHEMBL.COMPOUND:1445"
]
}
]
},
"CHEMBL.COMPOUND:1395": {
"categories": [
"biolink:SmallMolecule"
],
"attributes": [
{
"attribute_type_id": "biolink:xref",
"value": [
"CHEMBL.COMPOUND:1395"
]
},
{
"attribute_type_id": "biolink:synonym",
"value": [
"CHEMBL.COMPOUND:1395"
]
}
]
},
"CHEMBL.COMPOUND:1200335": {
"categories": [
"biolink:SmallMolecule"
],
"attributes": [
{
"attribute_type_id": "biolink:xref",
"value": [
"CHEMBL.COMPOUND:1200335"
]
},
{
"attribute_type_id": "biolink:synonym",
"value": [
"CHEMBL.COMPOUND:1200335"
]
}
]
},
"CHEMBL.COMPOUND:1200436": {
"categories": [
"biolink:SmallMolecule"
],
"attributes": [
{
"attribute_type_id": "biolink:xref",
"value": [
"CHEMBL.COMPOUND:1200436"
]
},
{
"attribute_type_id": "biolink:synonym",
"value": [
"CHEMBL.COMPOUND:1200436"
]
}
]
},
"CHEMBL.COMPOUND:139835": {
"categories": [
"biolink:SmallMolecule"
],
"attributes": [
{
"attribute_type_id": "biolink:xref",
"value": [
"CHEMBL.COMPOUND:139835"
]
},
{
"attribute_type_id": "biolink:synonym",
"value": [
"CHEMBL.COMPOUND:139835"
]
}
]
},
"CHEMBL.COMPOUND:4594417": {
"categories": [
"biolink:SmallMolecule"
],
"attributes": [
{
"attribute_type_id": "biolink:xref",
"value": [
"CHEMBL.COMPOUND:4594417"
]
},
{
"attribute_type_id": "biolink:synonym",
"value": [
"CHEMBL.COMPOUND:4594417"
]
}
]
},
"CHEMBL.COMPOUND:3545333": {
"categories": [
"biolink:SmallMolecule"
],
"attributes": [
{
"attribute_type_id": "biolink:xref",
"value": [
"CHEMBL.COMPOUND:3545333"
]
},
{
"attribute_type_id": "biolink:synonym",
"value": [
"CHEMBL.COMPOUND:3545333"
]
}
]
},
"CHEMBL.COMPOUND:1479": {
"categories": [
"biolink:SmallMolecule"
],
"attributes": [
{
"attribute_type_id": "biolink:xref",
"value": [
"CHEMBL.COMPOUND:1479"
]
},
{
"attribute_type_id": "biolink:synonym",
"value": [
"CHEMBL.COMPOUND:1479"
]
}
]
},
"CHEMBL.COMPOUND:3590187": {
"categories": [
"biolink:SmallMolecule"
],
"attributes": [
{
"attribute_type_id": "biolink:xref",
"value": [
"CHEMBL.COMPOUND:3590187"
]
},
{
"attribute_type_id": "biolink:synonym",
"value": [
"CHEMBL.COMPOUND:3590187"
]
}
]
}
},
"edges": {
"4a259a7adcf6af171acdd155ca4b61f5": {
"predicate": "biolink:related_to",
"subject": "NCBIGene:367",
"object": "CHEMBL.COMPOUND:806",
"attributes": [
{
"attribute_type_id": "moleculeType",
"value": [
"Small molecule"
]
}
],
"sources": []
},
"99a55e0e5dde8e4392ad1015eca3e362": {
"predicate": "biolink:related_to",
"subject": "NCBIGene:367",
"object": "CHEMBL.COMPOUND:1082407",
"attributes": [
{
"attribute_type_id": "moleculeType",
"value": [
"Small molecule"
]
}
],
"sources": []
},
"94ebc51a78d8a8b69747275f54937775": {
"predicate": "biolink:related_to",
"subject": "NCBIGene:367",
"object": "CHEMBL.COMPOUND:409",
"attributes": [
{
"attribute_type_id": "moleculeType",
"value": [
"Small molecule"
]
}
],
"sources": []
},
"eb9e71e4de4c781bfd24414ec7f66c6a": {
"predicate": "biolink:related_to",
"subject": "NCBIGene:367",
"object": "CHEMBL.COMPOUND:3183409",
"attributes": [
{
"attribute_type_id": "moleculeType",
"value": [
"Small molecule"
]
}
],
"sources": []
},
"5c6b00df38f2a5b0ff1ab9a63f008d20": {
"predicate": "biolink:related_to",
"subject": "NCBIGene:367",
"object": "CHEMBL.COMPOUND:254328",
"attributes": [
{
"attribute_type_id": "moleculeType",
"value": [
"Small molecule"
]
}
],
"sources": []
},
"ac9449e3fde58d443d3ab417251b49d7": {
"predicate": "biolink:related_to",
"subject": "NCBIGene:367",
"object": "CHEMBL.COMPOUND:1274",
"attributes": [
{
"attribute_type_id": "moleculeType",
"value": [
"Small molecule"
]
}
],
"sources": []
},
"d33ab0ff3ec2b1d83b5254dfad027801": {
"predicate": "biolink:related_to",
"subject": "NCBIGene:367",
"object": "CHEMBL.COMPOUND:4297185",
"attributes": [
{
"attribute_type_id": "moleculeType",
"value": [
"Small molecule"
]
}
],
"sources": []
},
"09f70c7b2623b22b445d9550b9ef0f26": {
"predicate": "biolink:related_to",
"subject": "NCBIGene:367",
"object": "CHEMBL.COMPOUND:2107067",
"attributes": [
{
"attribute_type_id": "moleculeType",
"value": [
"Small molecule"
]
}
],
"sources": []
},
"0c49f94ed6ade3405f748d53e5afbfe8": {
"predicate": "biolink:related_to",
"subject": "NCBIGene:367",
"object": "CHEMBL.COMPOUND:386630",
"attributes": [
{
"attribute_type_id": "moleculeType",
"value": [
"Small molecule"
]
}
],
"sources": []
},
"30aeac2469d218b2352d7ab0169155a8": {
"predicate": "biolink:related_to",
"subject": "NCBIGene:367",
"object": "CHEMBL.COMPOUND:1201101",
"attributes": [
{
"attribute_type_id": "moleculeType",
"value": [
"Small molecule"
]
}
],
"sources": []
},
"5bbac1295b807766b57836d899f621b5": {
"predicate": "biolink:related_to",
"subject": "NCBIGene:367",
"object": "CHEMBL.COMPOUND:1445",
"attributes": [
{
"attribute_type_id": "moleculeType",
"value": [
"Small molecule"
]
}
],
"sources": []
},
"dba5a64d63473662cb8d61f390649c4e": {
"predicate": "biolink:related_to",
"subject": "NCBIGene:367",
"object": "CHEMBL.COMPOUND:1395",
"attributes": [
{
"attribute_type_id": "moleculeType",
"value": [
"Small molecule"
]
}
],
"sources": []
},
"ea3009bf1aff1ca88b8f153888bd927d": {
"predicate": "biolink:related_to",
"subject": "NCBIGene:367",
"object": "CHEMBL.COMPOUND:1200335",
"attributes": [
{
"attribute_type_id": "moleculeType",
"value": [
"Small molecule"
]
}
],
"sources": []
},
"6e6fd42aa1c78019fa0eb186f9204393": {
"predicate": "biolink:related_to",
"subject": "NCBIGene:367",
"object": "CHEMBL.COMPOUND:1200436",
"attributes": [
{
"attribute_type_id": "moleculeType",
"value": [
"Small molecule"
]
}
],
"sources": []
},
"42f52d8dc57d25bfe8f25a32b1c2f62f": {
"predicate": "biolink:related_to",
"subject": "NCBIGene:367",
"object": "CHEMBL.COMPOUND:139835",
"attributes": [
{
"attribute_type_id": "moleculeType",
"value": [
"Small molecule"
]
}
],
"sources": []
},
"fc656feb2b6a78ff93636ea3acadf280": {
"predicate": "biolink:related_to",
"subject": "NCBIGene:367",
"object": "CHEMBL.COMPOUND:4594417",
"attributes": [
{
"attribute_type_id": "moleculeType",
"value": [
"Small molecule"
]
}
],
"sources": []
},
"5fc30953f738cd61b259a158c04ac490": {
"predicate": "biolink:related_to",
"subject": "NCBIGene:367",
"object": "CHEMBL.COMPOUND:3545333",
"attributes": [
{
"attribute_type_id": "moleculeType",
"value": [
"Small molecule"
]
}
],
"sources": []
},
"5c4445199cadec965126c066c92e3651": {
"predicate": "biolink:related_to",
"subject": "NCBIGene:367",
"object": "CHEMBL.COMPOUND:1479",
"attributes": [
{
"attribute_type_id": "moleculeType",
"value": [
"Small molecule"
]
}
],
"sources": []
},
"fa774f8aef359843492bbcecd4211de1": {
"predicate": "biolink:related_to",
"subject": "NCBIGene:367",
"object": "CHEMBL.COMPOUND:3590187",
"attributes": [
{
"attribute_type_id": "moleculeType",
"value": [
"Small molecule"
]
}
],
"sources": []
}
}
},
"results": [
{
"node_bindings": {
"n0": [
{
"id": "NCBIGene:367"
}
],
"n1": [
{
"id": "CHEMBL.COMPOUND:806"
}
]
},
"analyses": [
{
"resource_id": "infores:biothings-explorer",
"edge_bindings": {
"e0": [
{
"id": "4a259a7adcf6af171acdd155ca4b61f5"
}
]
}
}
]
},
{
"node_bindings": {
"n0": [
{
"id": "NCBIGene:367"
}
],
"n1": [
{
"id": "CHEMBL.COMPOUND:1082407"
}
]
},
"analyses": [
{
"resource_id": "infores:biothings-explorer",
"edge_bindings": {
"e0": [
{
"id": "99a55e0e5dde8e4392ad1015eca3e362"
}
]
}
}
]
},
{
"node_bindings": {
"n0": [
{
"id": "NCBIGene:367"
}
],
"n1": [
{
"id": "CHEMBL.COMPOUND:409"
}
]
},
"analyses": [
{
"resource_id": "infores:biothings-explorer",
"edge_bindings": {
"e0": [
{
"id": "94ebc51a78d8a8b69747275f54937775"
}
]
}
}
]
},
{
"node_bindings": {
"n0": [
{
"id": "NCBIGene:367"
}
],
"n1": [
{
"id": "CHEMBL.COMPOUND:3183409"
}
]
},
"analyses": [
{
"resource_id": "infores:biothings-explorer",
"edge_bindings": {
"e0": [
{
"id": "eb9e71e4de4c781bfd24414ec7f66c6a"
}
]
}
}
]
},
{
"node_bindings": {
"n0": [
{
"id": "NCBIGene:367"
}
],
"n1": [
{
"id": "CHEMBL.COMPOUND:254328"
}
]
},
"analyses": [
{
"resource_id": "infores:biothings-explorer",
"edge_bindings": {
"e0": [
{
"id": "5c6b00df38f2a5b0ff1ab9a63f008d20"
}
]
}
}
]
},
{
"node_bindings": {
"n0": [
{
"id": "NCBIGene:367"
}
],
"n1": [
{
"id": "CHEMBL.COMPOUND:1274"
}
]
},
"analyses": [
{
"resource_id": "infores:biothings-explorer",
"edge_bindings": {
"e0": [
{
"id": "ac9449e3fde58d443d3ab417251b49d7"
}
]
}
}
]
},
{
"node_bindings": {
"n0": [
{
"id": "NCBIGene:367"
}
],
"n1": [
{
"id": "CHEMBL.COMPOUND:4297185"
}
]
},
"analyses": [
{
"resource_id": "infores:biothings-explorer",
"edge_bindings": {
"e0": [
{
"id": "d33ab0ff3ec2b1d83b5254dfad027801"
}
]
}
}
]
},
{
"node_bindings": {
"n0": [
{
"id": "NCBIGene:367"
}
],
"n1": [
{
"id": "CHEMBL.COMPOUND:2107067"
}
]
},
"analyses": [
{
"resource_id": "infores:biothings-explorer",
"edge_bindings": {
"e0": [
{
"id": "09f70c7b2623b22b445d9550b9ef0f26"
}
]
}
}
]
},
{
"node_bindings": {
"n0": [
{
"id": "NCBIGene:367"
}
],
"n1": [
{
"id": "CHEMBL.COMPOUND:386630"
}
]
},
"analyses": [
{
"resource_id": "infores:biothings-explorer",
"edge_bindings": {
"e0": [
{
"id": "0c49f94ed6ade3405f748d53e5afbfe8"
}
]
}
}
]
},
{
"node_bindings": {
"n0": [
{
"id": "NCBIGene:367"
}
],
"n1": [
{
"id": "CHEMBL.COMPOUND:1201101"
}
]
},
"analyses": [
{
"resource_id": "infores:biothings-explorer",
"edge_bindings": {
"e0": [
{
"id": "30aeac2469d218b2352d7ab0169155a8"
}
]
}
}
]
},
{
"node_bindings": {
"n0": [
{
"id": "NCBIGene:367"
}
],
"n1": [
{
"id": "CHEMBL.COMPOUND:1445"
}
]
},
"analyses": [
{
"resource_id": "infores:biothings-explorer",
"edge_bindings": {
"e0": [
{
"id": "5bbac1295b807766b57836d899f621b5"
}
]
}
}
]
},
{
"node_bindings": {
"n0": [
{
"id": "NCBIGene:367"
}
],
"n1": [
{
"id": "CHEMBL.COMPOUND:1395"
}
]
},
"analyses": [
{
"resource_id": "infores:biothings-explorer",
"edge_bindings": {
"e0": [
{
"id": "dba5a64d63473662cb8d61f390649c4e"
}
]
}
}
]
},
{
"node_bindings": {
"n0": [
{
"id": "NCBIGene:367"
}
],
"n1": [
{
"id": "CHEMBL.COMPOUND:1200335"
}
]
},
"analyses": [
{
"resource_id": "infores:biothings-explorer",
"edge_bindings": {
"e0": [
{
"id": "ea3009bf1aff1ca88b8f153888bd927d"
}
]
}
}
]
},
{
"node_bindings": {
"n0": [
{
"id": "NCBIGene:367"
}
],
"n1": [
{
"id": "CHEMBL.COMPOUND:1200436"
}
]
},
"analyses": [
{
"resource_id": "infores:biothings-explorer",
"edge_bindings": {
"e0": [
{
"id": "6e6fd42aa1c78019fa0eb186f9204393"
}
]
}
}
]
},
{
"node_bindings": {
"n0": [
{
"id": "NCBIGene:367"
}
],
"n1": [
{
"id": "CHEMBL.COMPOUND:139835"
}
]
},
"analyses": [
{
"resource_id": "infores:biothings-explorer",
"edge_bindings": {
"e0": [
{
"id": "42f52d8dc57d25bfe8f25a32b1c2f62f"
}
]
}
}
]
},
{
"node_bindings": {
"n0": [
{
"id": "NCBIGene:367"
}
],
"n1": [
{
"id": "CHEMBL.COMPOUND:4594417"
}
]
},
"analyses": [
{
"resource_id": "infores:biothings-explorer",
"edge_bindings": {
"e0": [
{
"id": "fc656feb2b6a78ff93636ea3acadf280"
}
]
}
}
]
},
{
"node_bindings": {
"n0": [
{
"id": "NCBIGene:367"
}
],
"n1": [
{
"id": "CHEMBL.COMPOUND:3545333"
}
]
},
"analyses": [
{
"resource_id": "infores:biothings-explorer",
"edge_bindings": {
"e0": [
{
"id": "5fc30953f738cd61b259a158c04ac490"
}
]
}
}
]
},
{
"node_bindings": {
"n0": [
{
"id": "NCBIGene:367"
}
],
"n1": [
{
"id": "CHEMBL.COMPOUND:1479"
}
]
},
"analyses": [
{
"resource_id": "infores:biothings-explorer",
"edge_bindings": {
"e0": [
{
"id": "5c4445199cadec965126c066c92e3651"
}
]
}
}
]
},
{
"node_bindings": {
"n0": [
{
"id": "NCBIGene:367"
}
],
"n1": [
{
"id": "CHEMBL.COMPOUND:3590187"
}
]
},
"analyses": [
{
"resource_id": "infores:biothings-explorer",
"edge_bindings": {
"e0": [
{
"id": "fa774f8aef359843492bbcecd4211de1"
}
]
}
}
]
}
]
},
"logs": [
{
"timestamp": "2023-06-03T00:11:00.510Z",
"level": "INFO",
"message": "Expanded ids for node n0: (1 ids -> 1 ids)",
"code": null
},
{
"timestamp": "2023-06-03T00:11:00.992Z",
"level": "INFO",
"message": "Node n0 with id [ENSEMBL:ENSG00000169083] assigned category [biolink:BiologicalEntity] inferred from id.",
"code": null
},
{
"timestamp": "2023-06-03T00:11:00.999Z",
"level": "DEBUG",
"message": "BTE identified 2 qNodes from your query graph",
"code": null
},
{
"timestamp": "2023-06-03T00:11:00.999Z",
"level": "DEBUG",
"message": "BTE identified 1 qEdges from your query graph",
"code": null
},
{
"timestamp": "2023-06-03T00:11:01.005Z",
"level": "DEBUG",
"message": "Edge manager is managing 1 qEdges.",
"code": null
},
{
"timestamp": "2023-06-03T00:11:01.005Z",
"level": "DEBUG",
"message": "Edge manager is sending next qEdge 'e0' for execution.",
"code": null
},
{
"timestamp": "2023-06-03T00:11:01.005Z",
"level": "INFO",
"message": "Executing e0: n0 --> n1",
"code": null
},
{
"timestamp": "2023-06-03T00:11:01.287Z",
"level": "DEBUG",
"message": "REDIS cache is not enabled.",
"code": null
},
{
"timestamp": "2023-06-03T00:11:01.291Z",
"level": "DEBUG",
"message": "BTE is trying to find metaKG edges (smartAPI registry, x-bte annotation) connecting from BiologicalProcessOrActivity,MolecularActivity,BiologicalProcess,Pathway,PhysiologicalProcess,Behavior,PathologicalProcess,GeneticInheritance,OrganismalEntity,Virus,CellularOrganism,LifeStage,IndividualOrganism,Case,PopulationOfIndividualOrganisms,StudyPopulation,Cohort,AnatomicalEntity,CellularComponent,Cell,GrossAnatomicalStructure,PathologicalAnatomicalStructure,CellLine,DiseaseOrPhenotypicFeature,Disease,PhenotypicFeature,BehavioralFeature,ClinicalFinding,Gene,MacromolecularComplex,NucleosomeModification,Genome,Polypeptide,Protein,ProteinIsoform,ProteinDomain,PosttranslationalModification,ProteinFamily,NucleicAcidSequenceMotif,GeneFamily,Genotype,Haplotype,SequenceVariant,Snv,ReagentTargetedGene,BiologicalEntity to Attribute,ChemicalRole,BiologicalSex,PhenotypicSex,GenotypicSex,SeverityValue,OrganismAttribute,PhenotypicQuality,Zygosity,ClinicalAttribute,ClinicalMeasurement,ClinicalModifier,ClinicalCourse,Onset,SocioeconomicAttribute,GenomicBackgroundExposure,PathologicalProcessExposure,PathologicalAnatomicalExposure,DiseaseOrPhenotypicFeatureExposure,ChemicalExposure,DrugExposure,DrugToGeneInteractionExposure,ComplexChemicalExposure,BioticExposure,EnvironmentalExposure,GeographicExposure,BehavioralExposure,SocioeconomicExposure,OrganismTaxon,Event,AdministrativeEntity,Agent,InformationContentEntity,StudyResult,ConceptCountAnalysisResult,ObservedExpectedFrequencyAnalysisResult,RelativeFrequencyAnalysisResult,TextMiningResult,ChiSquaredAnalysisResult,Study,StudyVariable,CommonDataElement,Dataset,DatasetDistribution,DatasetVersion,DatasetSummary,ConfidenceLevel,EvidenceType,InformationResource,Publication,Book,BookChapter,Serial,Article,PhysicalEntity,MaterialSample,Activity,Procedure,Phenomenon,Device,PlanetaryEntity,EnvironmentalProcess,EnvironmentalFeature,GeographicLocation,GeographicLocationAtTime,BiologicalEntity,BiologicalProcessOrActivity,MolecularActivity,BiologicalProcess,Pathway,PhysiologicalProcess,Behavior,PathologicalProcess,GeneticInheritance,OrganismalEntity,Virus,CellularOrganism,LifeStage,IndividualOrganism,Case,PopulationOfIndividualOrganisms,StudyPopulation,Cohort,AnatomicalEntity,CellularComponent,Cell,GrossAnatomicalStructure,PathologicalAnatomicalStructure,CellLine,DiseaseOrPhenotypicFeature,Disease,PhenotypicFeature,BehavioralFeature,ClinicalFinding,Gene,MacromolecularComplex,NucleosomeModification,Genome,Polypeptide,Protein,ProteinIsoform,ProteinDomain,PosttranslationalModification,ProteinFamily,NucleicAcidSequenceMotif,GeneFamily,Genotype,Haplotype,SequenceVariant,Snv,ReagentTargetedGene,ChemicalEntity,MolecularEntity,SmallMolecule,NucleicAcidEntity,Exon,Transcript,RnaProduct,RnaProductIsoform,NoncodingRnaProduct,MicroRna,SiRna,CodingSequence,ChemicalMixture,MolecularMixture,Drug,ComplexMolecularMixture,ProcessedMaterial,Food,EnvironmentalFoodContaminant,FoodAdditive,ClinicalEntity,ClinicalTrial,ClinicalIntervention,Hospitalization,Treatment,NamedThing with predicate undefined",
"code": null
},
{
"timestamp": "2023-06-03T00:11:01.291Z",
"level": "DEBUG",
"message": "BTE found 1 metaKG edges corresponding to e0. These metaKG edges comes from 1 unique APIs. They are OpenTarget API",
"code": null
},
{
"timestamp": "2023-06-03T00:11:01.292Z",
"level": "DEBUG",
"message": "BTE found 3 metaKG for this batch.",
"code": null
},
{
"timestamp": "2023-06-03T00:11:01.294Z",
"level": "DEBUG",
"message": "Resolving ID feature is turned on",
"code": null
},
{
"timestamp": "2023-06-03T00:11:01.294Z",
"level": "DEBUG",
"message": "call-apis: 3 planned queries for edge e0",
"code": null
},
{
"timestamp": "2023-06-03T00:11:01.866Z",
"level": "ERROR",
"message": "call-apis: Failed GET https://api.platform.opentargets.org/api/v4 (1 ID): Gene > related_to > SmallMolecule: (TypeError: Cannot read properties of null (reading 'associatedDiseases'))",
"code": null
},
{
"timestamp": "2023-06-03T00:11:01.916Z",
"level": "ERROR",
"message": "call-apis: Failed GET https://api.platform.opentargets.org/api/v4 (1 ID): Gene > related_to > SmallMolecule: (TypeError: Cannot read properties of null (reading 'associatedDiseases'))",
"code": null
},
{
"timestamp": "2023-06-03T00:11:03.084Z",
"level": "DEBUG",
"message": "Successful GET https://api.platform.opentargets.org/api/v4 (1 ID): Gene > related_to > SmallMolecule (obtained 233 records, took 2s)",
"code": null
},
{
"timestamp": "2023-06-03T00:11:03.085Z",
"level": "DEBUG",
"message": "call-apis: Total number of records returned for this query is 233",
"code": null
},
{
"timestamp": "2023-06-03T00:11:04.010Z",
"level": "DEBUG",
"message": "call-apis: qEdge queries complete in 2s",
"code": null
},
{
"timestamp": "2023-06-03T00:11:04.012Z",
"level": "INFO",
"message": "e0 execution: 3 queries (1 success/2 fail) and (0) cached qEdges return (233) records",
"code": null
},
{
"timestamp": "2023-06-03T00:11:04.056Z",
"level": "DEBUG",
"message": "'e0' kept (233) / dropped (0) records.",
"code": null
},
{
"timestamp": "2023-06-03T00:11:04.092Z",
"level": "INFO",
"message": "'e0' keeps (233) records!",
"code": null
},
{
"timestamp": "2023-06-03T00:11:04.092Z",
"level": "DEBUG",
"message": "Edge manager collected (233) records!",
"code": null
},
{
"timestamp": "2023-06-03T00:11:04.185Z",
"level": "DEBUG",
"message": "Scoring/PFOCR figures disabled for KP endpoints; results not scored. Use ARA endpoints (/v1/query or /v1/asyncquery) for scoring/PFOCR figures.",
"code": null
},
{
"timestamp": "2023-06-03T00:11:04.191Z",
"level": "WARNING",
"message": "Edge 4a259a7adcf6af171acdd155ca4b61f5 (APIs: OpenTarget API) is missing a primary knowledge source",
"code": null
},
{
"timestamp": "2023-06-03T00:11:04.191Z",
"level": "WARNING",
"message": "Edge 99a55e0e5dde8e4392ad1015eca3e362 (APIs: OpenTarget API) is missing a primary knowledge source",
"code": null
},
{
"timestamp": "2023-06-03T00:11:04.191Z",
"level": "WARNING",
"message": "Edge 94ebc51a78d8a8b69747275f54937775 (APIs: OpenTarget API) is missing a primary knowledge source",
"code": null
},
{
"timestamp": "2023-06-03T00:11:04.191Z",
"level": "WARNING",
"message": "Edge eb9e71e4de4c781bfd24414ec7f66c6a (APIs: OpenTarget API) is missing a primary knowledge source",
"code": null
},
{
"timestamp": "2023-06-03T00:11:04.191Z",
"level": "WARNING",
"message": "Edge 5c6b00df38f2a5b0ff1ab9a63f008d20 (APIs: OpenTarget API) is missing a primary knowledge source",
"code": null
},
{
"timestamp": "2023-06-03T00:11:04.191Z",
"level": "WARNING",
"message": "Edge ac9449e3fde58d443d3ab417251b49d7 (APIs: OpenTarget API) is missing a primary knowledge source",
"code": null
},
{
"timestamp": "2023-06-03T00:11:04.191Z",
"level": "WARNING",
"message": "Edge d33ab0ff3ec2b1d83b5254dfad027801 (APIs: OpenTarget API) is missing a primary knowledge source",
"code": null
},
{
"timestamp": "2023-06-03T00:11:04.191Z",
"level": "WARNING",
"message": "Edge 09f70c7b2623b22b445d9550b9ef0f26 (APIs: OpenTarget API) is missing a primary knowledge source",
"code": null
},
{
"timestamp": "2023-06-03T00:11:04.191Z",
"level": "WARNING",
"message": "Edge 0c49f94ed6ade3405f748d53e5afbfe8 (APIs: OpenTarget API) is missing a primary knowledge source",
"code": null
},
{
"timestamp": "2023-06-03T00:11:04.191Z",
"level": "WARNING",
"message": "Edge 30aeac2469d218b2352d7ab0169155a8 (APIs: OpenTarget API) is missing a primary knowledge source",
"code": null
},
{
"timestamp": "2023-06-03T00:11:04.192Z",
"level": "WARNING",
"message": "Edge 5bbac1295b807766b57836d899f621b5 (APIs: OpenTarget API) is missing a primary knowledge source",
"code": null
},
{
"timestamp": "2023-06-03T00:11:04.192Z",
"level": "WARNING",
"message": "Edge dba5a64d63473662cb8d61f390649c4e (APIs: OpenTarget API) is missing a primary knowledge source",
"code": null
},
{
"timestamp": "2023-06-03T00:11:04.192Z",
"level": "WARNING",
"message": "Edge ea3009bf1aff1ca88b8f153888bd927d (APIs: OpenTarget API) is missing a primary knowledge source",
"code": null
},
{
"timestamp": "2023-06-03T00:11:04.192Z",
"level": "WARNING",
"message": "Edge 6e6fd42aa1c78019fa0eb186f9204393 (APIs: OpenTarget API) is missing a primary knowledge source",
"code": null
},
{
"timestamp": "2023-06-03T00:11:04.192Z",
"level": "WARNING",
"message": "Edge 42f52d8dc57d25bfe8f25a32b1c2f62f (APIs: OpenTarget API) is missing a primary knowledge source",
"code": null
},
{
"timestamp": "2023-06-03T00:11:04.192Z",
"level": "WARNING",
"message": "Edge fc656feb2b6a78ff93636ea3acadf280 (APIs: OpenTarget API) is missing a primary knowledge source",
"code": null
},
{
"timestamp": "2023-06-03T00:11:04.192Z",
"level": "WARNING",
"message": "Edge 5fc30953f738cd61b259a158c04ac490 (APIs: OpenTarget API) is missing a primary knowledge source",
"code": null
},
{
"timestamp": "2023-06-03T00:11:04.192Z",
"level": "WARNING",
"message": "Edge 5c4445199cadec965126c066c92e3651 (APIs: OpenTarget API) is missing a primary knowledge source",
"code": null
},
{
"timestamp": "2023-06-03T00:11:04.192Z",
"level": "WARNING",
"message": "Edge fa774f8aef359843492bbcecd4211de1 (APIs: OpenTarget API) is missing a primary knowledge source",
"code": null
},
{
"timestamp": "2023-06-03T00:11:04.205Z",
"level": "INFO",
"message": "Execution Summary: (20) nodes / (19) edges / (19) results; (1/3) queries returned results from (1) unique APIs ",
"code": null
},
{
"timestamp": "2023-06-03T00:11:04.205Z",
"level": "INFO",
"message": "APIs: OpenTarget API",
"code": null
}
]
} |
|
Also, just wondering why Pharos was mentioned in the original issue when there seems to be a trapi API (https://smart-api.info/registry?q=pharos). Is there any benefit that could be gained by using the GraphQL one? |
That registered TRAPI API is dependent on automat periodically updating their data ingestion. By directly annotating the Pharos API, no data updates are required since it always hits the latest API. Let's pause further work on this pending review and merge of biothings/api-respone-transform.js#51 |
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This issue will track discussion related to the potential annotation and ingestion of GraphQL endpoints in BTE. There are a few public GraphQL endpoints that would be useful to query in BTE:
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