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store edge attributes as arrays, convert to set later if needed #220

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merged 2 commits into from
Oct 20, 2024

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rjawesome
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@colleenXu
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colleenXu commented Oct 18, 2024

@rjawesome @tokebe

I think this PR is working. I was able to get an evidence_count of 80, as described in the first paragraph here. This involves a simple addition of the record pmid_counts together, no custom parsing of PMIDs and removing duplicates.

Saved response for CHEBI:45713 -> Gene (semmeddb only), covers Examples 1-2: counting-testing.json

How I tested this: it's convoluted!

  1. Make a modified copy of the semmeddb yaml
    1. Take the master branch yaml
    2. find # publication_count: pmid_count, replace with "biolink:evidence_count": pmid_count
    3. find predication.pmid,predication.sentence, replace with predication.pmid,predication.sentence,pmid_count
  2. In local BTE, adjust override to use that local copy of semmeddb yaml
  3. In local BTE, go to api-response-transform module and reset to d24c07a (before modifications to semmeddb post-processing)
  4. Checkout this branch in query_graph_handler module
  5. Local BTE: build + smartapi-sync (with API_OVERRIDE=true)
  6. Then start up local instance and run Example 1. The edge will have evidence_count = 80, as expected

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