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alfred-GWAS 🧬

An Alfred workflow to browse the GWAS catalog

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Motivation ✅

  • to obtain, without opening websites, a summarized version of all genes associated with a particular trait in the GWAS catalog, or all traits asssociated with a gene or locus.
  • quickly access papers supporting a gene-trait association

Setting up ⚙️

Needed

Basic Usage 📖

Querying by gene 🧬

  • launch with keyword (default: gwg) or custom hotkey, enter a search string. Results will include a gene name, the number of associated traits, and the number of papers.

  • output is sorted by number of traits by default. Adding --p to the search string will sort by number of papers.

  • once a gene is selected, associated traits are shown, including for each trait the range of OR (or beta), minimum p-value, number of papers supporting the association, and number of associated loci. It is possible to refine the list of associated traits by entering an additional search string.

    • ctrl-enter will show the currently selected gene-trait pair in large font, and copy to clipboard
    • cmd-enter will copy the entire gene-trait list to clipboard
    • cmd-option-enter will go back to the previous list
  • once a gene-trait pair is selected, individual associations are shown, with OR min p-value, and source publication.

    • ctrl-enter will show the currently selected association in large font, and copy to clipboard
    • cmd-enter will copy the entire set of associations to clipboard
  • once an individual association is selected, enter will open the supporting publication in Pubmed.

Querying by trait 👤

  • launch with keyword (default: gwt) or custom hotkey. Results will include a gene name, the number of associated traits, and the number of papers.
  • once a gene is selected, associated traits are shown, including for each trait the range of OR (or beta), minimum p-value, number of papers supporting the association, and number of associated loci. Alfred's QuickOutlook (shift) will show the expression profile from GTEx. Hit shift again to close.
  • output is sorted by number of supporting papers. Adding --es to the search string will sort by largest reported effect size (OR or beta).
    • ctrl-enter will show the currently selected gene-trait pair in large font, and copy to clipboard
    • cmd-enter will copy the entire gene-trait list to clipboard
    • cmd-option-enter will go back to the previous list
  • once a gene-trait pair is selected, individual associations are shown, with OR min p-value, and source publication.
    • ctrl-enter will show the currently selected association in large font, and copy to clipboard
    • cmd-enter will copy the entire set of associations to clipboard
  • once an individual association is selected, enter will open the supporting publication in Pubmed.

rebuilding database (optional) 🛠️

  • alfred-GWAS comes with the database derived from version e109_r2023-05-07 of the GWAS catalog (v1.0.2, all associations) available here.
  • the script build-GWAS-index.py can be used to rebuild/update the database. Run with python3 build-GWAS-index.py "path-to-GWAS-file.tsv", or select the file in Finder and use the Universal Action.

Limitations & known issues ⚠️

  • None for now, but I have not done extensive testing, let me know if you see anything!

Acknowledgments 😀

Changelog 🧰

  • 05-17-2023: version 0.4
  • 03-25-2023: version 0.3
  • 05-31-2022: version 0.2
  • 12-12-2020: version 0.1

Feedback 🧐

Feedback welcome! If you notice a bug, or have ideas for new features, please feel free to get in touch either here, or on the Alfred forum.

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An Alfred workflow to browse the GWAS catalog

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