ranking-agent / strider

A TRAPI-compliant component of ARAGORN that queries distributed KPs and assembles answers to user questions.
MIT License
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Results from SRI KG not in answer #169

Closed cbizon closed 3 years ago

cbizon commented 3 years ago

Possibly a repeat of #165

Query:

{
    "message": {
        "query_graph": {
            "nodes": {
                "n0": {
                    "id": "NCBIGene:1017",
                    "category": "biolink:Gene"
                },
                "n1": {
                    "category": "biolink:Pathway"
                }
            },
            "edges": {
                "e01": {
                    "subject": "n0",
                    "object": "n1"
                }
            }
        }
    }
}

Returns no results from strider. But in the logs in the response we see:

{'message': 'Received response from KP', 'url': 'https://trapi.monarchinitiative.org/query', 'request': {'message': {'query_graph': {'nodes': {'n0': {'category': 'biolink:Gene', 'is_set': False, 'id': 'NCBIGene:1017'}, 'n1': {'category': 'biolink:Pathway', 'is_set': False}}, 'edges': {'e01': {'subject': 'n0', 'object': 'n1', 'predicate': 'biolink:actively_involved_in'}}}}}, 'response': {'message': {'query_graph': {'nodes': {'n0': {'id': 'NCBIGene:1017', 'category': 'biolink:Gene', 'is_set': False}, 'n1': {'id': None, 'category': 'biolink:Pathway', 'is_set': False}}, 'edges': {'e01': {'subject': 'n0', 'object': 'n1', 'predicate': 'biolink:actively_involved_in', 'relation': None}}}, 'knowledge_graph': {'nodes': {'GO:0006977': {'category': ['biolink:NamedThing', 'biolink:BiologicalProcess', 'biolink:Occurrent', 'biolink:Pathway'], 'name': 'DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest', 

i.e. the KP is returning some results and GO terms mapped to the pathway.

cbizon commented 3 years ago

After talking to @patrickkwang I don't think that this observation is related, but I'll mention that the things being returned bound to n1 are GO terms that we don't usually consider Pathways (i.e. the node normalizer will not call them pathways)

patrickkwang commented 3 years ago

May be fixed by #166. Please confirm.

cbizon commented 3 years ago

We're now getting results from REF KG for this query.