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UMLS - HPO Mappings #20

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matentzn opened this issue Jan 9, 2023 · 1 comment
Open

UMLS - HPO Mappings #20

matentzn opened this issue Jan 9, 2023 · 1 comment
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@hrshdhgd

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@matentzn
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matentzn commented Jan 9, 2023

  1. Get UMLS key and download UMLS
  2. Read this: https://www.ncbi.nlm.nih.gov/books/NBK9685/ and make sure all we need is in MRCONSO, and not MRMAP.RRF and MRSMAP.RRF
  3. Obtain MRCONSO.RRF (schema)
  4. Make sure this file covers all "UMLS-HPO" mappings. What is the % of all HPO terms in that file?
  5. Filter MRCONSO.RFF to only HP relevant (grep)
  6. Add UMLS parser to sssom py to read MRCONSO.RRF and convert into SSSOM. The parser should have a switch to distinguish between MRCONSO and MRMAP files (both are needed, MRMAP has ID to ID mappings from sources, and MRCONSO the UMLS to SOURCE "mappings")
  7. Make PR here with a pipeline using SSSOM PY to extract hp-umls.sssom.tsv from MRCONSO.RFF.
@hrshdhgd
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See umls-ingest.

Also ticket opened at pyobo to correct CURIEs in object_id.

@matentzn matentzn mentioned this issue Nov 20, 2023
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