Comments (7)
cbizon
commented on June 8, 2024
As an example, once graph coalescence has run in the AnswerCoalesce notebook, I do this:
print( graph_result['knowledge_graph']['nodes'])
Most of the nodes are fine, but there are several that are not:
{'id': 'CHEBI:10545', 'type': 'named_thing'}, {'id': 'CHEBI:24431', 'type': 'named_thing'}, {'id': 'CHEBI:25585', 'type': 'named_thing'}, {'id': 'CHEBI:27594', 'type': 'named_thing'}, {'id': 'CHEBI:33250', 'type': 'named_thing'}, {'id': 'CHEBI:33306', 'type': 'named_thing'}, {'id': 'CHEBI:33318', 'type': 'named_thing'}, {'id': 'CHEBI:33560', 'type': 'named_thing'}, {'id': 'CHEBI:22221', 'type': 'named_thing'}, {'id': 'CHEBI:23004', 'type': 'named_thing'}, {'id': 'CHEBI:27207', 'type': 'named_thing'}, {'id': 'CHEBI:37838', 'type': 'named_thing'}, {'id': 'MEDDRA:10013710', 'type': 'named_thing'}, {'id': 'MEDDRA:10029328', 'type': 'named_thing'}, {'id': 'MONDO:0008889', 'type': 'named_thing'}, {'id': 'CHEBI:23019', 'type': 'named_thing'}, {'id': 'CHEBI:33246', 'type': 'named_thing'}, {'id': 'CHEBI:46629', 'type': 'named_thing'}, {'id': 'CHEBI:51422', 'type': 'named_thing'}, {'id': 'CHEBI:51446', 'type': 'named_thing'}, {'id': 'CHEBI:23367', 'type': 'named_thing'}, {'id': 'CHEBI:24835', 'type': 'named_thing'}, {'id': 'CHEBI:29235', 'type': 'named_thing'}, {'id': 'CHEBI:33249', 'type': 'named_thing'}, {'id': 'CHEBI:33559', 'type': 'named_thing'}, {'id': 'CHEBI:37527', 'type': 'named_thing'}, {'id': 'CHEBI:43176', 'type': 'named_thing'}, {'id': 'CHEBI:46883', 'type': 'named_thing'}, {'id': 'CHEBI:51447', 'type': 'named_thing'}, {'id': 'CHEBI:24433', 'type': 'named_thing'}, {'id': 'CHEBI:24473', 'type': 'named_thing'}, {'id': 'CHEBI:29311', 'type': 'named_thing'}, {'id': 'CHEBI:25555', 'type': 'named_thing'}, {'id': 'CHEBI:33300', 'type': 'named_thing'}, {'id': 'CHEBI:25805', 'type': 'named_thing'}, {'id': 'CHEBI:33247', 'type': 'named_thing'}, {'id': 'CHEBI:26833', 'type': 'named_thing'}
I put some of the chebis into node normalization and they came back fine. This might be a version problem though. Perhaps these didn't get properly normalized in the robokop grpah or some derivative that the service is using?
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PhillipsOwen
commented on June 8, 2024
are we talking a redo of the entire DB or just a targeted normalization sweep of the insufficient ones?
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cbizon
commented on June 8, 2024
First, we need to understand why this is happening, then we can make a decision on how to fix it. In other words, I can't answer your question, because I don't know what/where the problem actually is.
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PhillipsOwen
commented on June 8, 2024
do you know when this was loaded? perhaps there is an old graph backup we can restore to verify.
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cbizon
commented on June 8, 2024
Sorry, I don't know what you're referring to. There are at least 3 databases in play - the robokop graph, the sqlite dbs, and the redis backing nodenormalization. I don't know which, if any, are the reason for the bug.
The first thing to do, I think, is write a simple test verifying the behavior.
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cbizon
commented on June 8, 2024
This is also true of the ontology version.
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cbizon
commented on June 8, 2024
I think that the right idea here is to use node normalization on our output graphs before sending them back. We will soon have a TRAPI nodenorm interface which will simplify this, so once that's done, we'll implement.
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Related Issues (20)
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