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feat: process ontology bridge terms #239

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merged 11 commits into from
Oct 31, 2024

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nayib-jose-gloria
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@nayib-jose-gloria nayib-jose-gloria commented Oct 25, 2024

Reason for Change

Changes

  • update schemas to support specifying ontology term 'cross ontology mapping' files that map cross-ontology equivalent terms
  • update ontology asset builder to download these files---assume SSSOM.TSV format for now
  • function to map cross-ontology terms from SSSOM and add to ontology asset files

Testing steps

  • Either list QA steps or reasoning you feel QA is unnecessary
  • Describe how you made sure to know that your changes worked. Should allow someone else to go verify your code without in depth knowledge.

Notes for Reviewer

  • TODO: API support for getting bridge terms given an ontology term ID, where applicable
  • TODO: leverage new functions in cellxgene-schema to map organism_cell_type and organism_tissue terms to CL and UBERON terms respectively for experimental organisms
  • TODO: long-term--consider whether to be prescriptive about cross-ontology-mapping filetype (we only accept SSSOM), or be robust to other options (parse xref in ontology JSONs directly, accept bridge files, or something else that emerges)

@nayib-jose-gloria nayib-jose-gloria marked this pull request as ready for review October 28, 2024 16:06
@nayib-jose-gloria nayib-jose-gloria merged commit 48a3080 into 2024-q4/experimental-species Oct 31, 2024
@nayib-jose-gloria nayib-jose-gloria deleted the nayib/bridge-terms branch October 31, 2024 20:59
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2 participants