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Explanatory Agent returns blank knowledge graph on example query
When given the example query provided in the apidoc, explanatory agent returns no results.
{
"message": {
"query_graph": {
"edges": [
{
"id": "e00",
"source_id": "n00",
"target_id": "n01",
"type": "associated"
}
],
"nodes": [
{
"curie": "EFO:0004465",
"id": "n00",
"type": "disease"
},
{
"id": "n01",
"type": "gene"
}
]
}
}
}
{
"query_graph": {
"edges": [
{
"id": "e00",
"source_id": "n00",
"target_id": "n01",
"type": "associated"
}
],
"nodes": [
{
"curie": "EFO:0004465",
"id": "n00",
"type": "disease"
},
{
"id": "n01",
"type": "gene"
}
]
},
"knowledge_graph": {
"edges": [],
"nodes": []
},
"results": []
}
Review 0 Results from today's Standup
Thousands of requests from Explanatory agent to RTX-KG2
Recently, there appears to be thousands of requests from Explanatory Agent hitting ARAX's RTX-KG2:
It appears that these are a ton of one-hop queries, with an example such as:
{
"message": {
"query_graph": {
"edges": {
"e00": {
"object": "n01",
"predicates": [
"biolink:produces"
],
"subject": "n00"
}
},
"nodes": {
"n00": {
"categories": [
"biolink:ChemicalEntity"
],
"ids": [
"PUBCHEM.COMPOUND:3926"
]
},
"n01": {
"categories": [
"biolink:NamedThing"
]
}
}
}
},
"remote_address": "52.149.163.31",
"submitter": "infores:explanatory-agent"
}
I wanted to make you aware of this in case this behavior is unintentional. Our system is currently handling the load, but we'd appreciate your:
- Making sure this isn't some runaway process
- Implementing batching/bundling to decrease the number of requests. For example, there are a bunch of one hop (drug X)-[r]-(category Y) queries where the only thing that changes is the predicate r. These can be combined since TRAPI can handle multiple predicates, so (drug X)-[r1, r2, r3]-(category Y). Similarly, the categories of the unpinned nodes can be bundled, so (drug X)-[r1, r2, r3]-(category Y1, Y2, Y3). In addition, you could try not specifying the predicate or category of the un-pinned node, and then post processing the results (equivalent to the query "get me all the neighbors of X".
Deploy TRAPI 1.3
https://arax.ncats.io/?smartapi=1 shows that Explanatory Agent API has 1.2 in development (infores:explanatory-agent)
Please deploy 1.3 of this tool into development ASAP.
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