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Including historical homologs for post-composed entity terms can change count from zero to many #200

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hlapp opened this issue Feb 19, 2020 · 0 comments
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hlapp commented Feb 19, 2020

This may be related to #198 (which states the behavior for upper ontology terms, which ought to subsume all homologs, hence the surprise there). This case differs in two ways:

  1. The entity query term is a pre-generated post-composition.
  2. The expression uses a UBERON term that conceivably does have homologs.

However, even though the term conceivably has homologs, it's much less clear why only its homologs have matching annotations.

The example is "has_part some paired fin skeleton" (http://purl.org/phenoscape/expression?value=%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000051%3E+some+%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0010713%3E):

curl -X GET "https://kb.phenoscape.org/api/taxon/annotations?entity=http%3A%2F%2Fpurl.org%2Fphenoscape%2Fexpression%3Fvalue%3D%253Chttp%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FBFO_0000051%253E%2Bsome%2B%253Chttp%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FUBERON_0010713%253E&total=true" -H "accept: application/json"

without homologs (gives zero count), with historical homologs:

curl -X GET "https://kb.phenoscape.org/api/taxon/annotations?entity=http%3A%2F%2Fpurl.org%2Fphenoscape%2Fexpression%3Fvalue%3D%253Chttp%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FBFO_0000051%253E%2Bsome%2B%253Chttp%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FUBERON_0010713%253E&historical_homologs=true&total=true" -H "accept: application/json"

gives a count of 3546.

@hlapp hlapp added the question label Feb 19, 2020
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