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omim-cli v2.1.0

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@Liozhang Liozhang released this 17 Jul 17:48
· 9 commits to master since this release
v2.1.0
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omim-cli v2.1.0

A client for OMIM (Online Mendelian Inheritance in Man) that obtains data
exclusively through official, legal channels — the OMIM REST API and the
official text-file downloads. No HTML scraping, no bundled/redistributed data.

Highlights

  • Official data sources. mim2gene.txt / mimTitles.txt / genemap2.txt /
    morbidmap.txt provide structured data; the API provides text sections,
    clinical synopsis (with HPO/SNOMED/ICD ontology IDs), allelic variants,
    references, and 30+ external cross-references.
  • Store everything. All source-provided fields are persisted (status,
    external_links, full gene record, dates, contributors, edit history, etc.).
  • Incremental by design.
    • text import is skipped when files are unchanged
    • --with-api only enriches entries not yet enriched
    • --refresh probes dateUpdated in batches of 20 (include=dates) and
      re-fetches only entries OMIM has updated
  • Commands: download, update, query, stats, faq, api
    (entry/search/gene-map/clinical-synopsis/allelic-variants/
    references/batch/config/status).
  • Configurable DB path via OMIM_DB env var or --dbfile.

Install

pip install -U omim-cli          # Python ≥ 3.8
omim-cli api config --set-key YOUR_KEY   # free key from https://omim.org/downloads
omim-cli download
omim-cli update                  # add --with-api for deep content
omim-cli stats

Data & license

  • Code: MIT (see LICENSE). Copyright © suqingdong (original omim) and Liozhang (omim-cli fork).
  • OMIM data is copyrighted by Johns Hopkins University and is not
    redistributed by this package — each user downloads their own copy. Use of
    OMIM data is governed by the OMIM User Agreement.
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