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Automate UMLS data download and artifact build pipeline #61

Description

@AlexMikhalev

Summary

Script to authenticate with UMLS API, download release files, filter to relevant subsets, and rebuild automata artifacts.

Details

  • Replaces manual download process
  • Complements/supersedes feat: Python backup script to download SNOMED CT without UMLS API key #35 (Python SNOMED download script)
  • UMLS API supports programmatic access with API key authentication
  • Key files to download: MRCONSO.RRF, MRREL.RRF, MRSTY.RRF
  • Filter to relevant SABs (SNOMEDCT_US, RXNORM, NCI, NDFRT, ICD11)
  • Rebuild umls_automata.bin.zst artifact after download
  • Should be runnable in CI for periodic updates

Acceptance Criteria

  • Script authenticates with UMLS API using stored credentials
  • Downloads and extracts required RRF files
  • Filters to relevant vocabularies
  • Rebuilds automata artifact
  • Can run headless in CI environment
  • Documented in README

See also: #35

Priority: P3

Activity

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