alfred-GWAS 🧬

An Alfred workflow to browse the GWAS catalog

• Motivation
• Setting up
• Basic Usage
• Known Issues
• Acknowledgments
• Changelog
• Feedback

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

• Alfred 5 with Powerpack license

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 😀

• Icons from Flaticon

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.