IGVF Catalog Documentation

Documentation for the IGVF Catalog data model, UI, REST API, and data provenance.

Published site: https://igvf-dacc.github.io/igvf-catalog-docs/

Contents

• Nodes & regions — genes, variants, proteins, transcripts, diseases, ontologies, and UI guides
• API Reference — auto-generated from the development Catalog OpenAPI spec
• Data Sources — IGVF/ENCODE portal file metadata and field lineage (portal → adapter → API)

API environment

Documentation currently targets the development API:

• Base URL: https://catalog-api-dev.demo.igvf.org/api
• Swagger UI: https://catalog-api-dev.demo.igvf.org/

Configuration: openapi/config.json

Local development

Install the Mintlify CLI:

npm install -g mintlify

Refresh generated content and preview:

python3 scripts/fetch_openapi.py
python3 scripts/build_source_index.py
python3 scripts/build_field_lineage.py
mintlify dev

Open http://localhost:3000

Configuration lives in docs.json (Mintlify v4). Site-wide styling overrides are in custom.css.

GitHub Pages serves this repo at /igvf-catalog-docs/; the deploy workflow runs scripts/patch_github_pages_basepath.py after export so Mintlify asset URLs resolve correctly.

Build scripts

Script	Purpose
scripts/fetch_openapi.py	Download OpenAPI from dev Swagger UI
scripts/build_source_index.py	Resolve IGVF/ENCODE file metadata + format specs
scripts/build_field_lineage.py	Adapter → field mapping docs
scripts/sample_responses.py	Store example API responses
scripts/catalog_per_example_audit.py	Validate doc examples against live API

Deployment

Pushes to main trigger .github/workflows/deploy-pages.yml, which exports Mintlify HTML and deploys to GitHub Pages.

Repository Settings → Pages → Source: GitHub Actions (one-time setup).

License

Documentation content follows the IGVF Catalog project licenses (CC BY 4.0 for data; MIT for software where applicable).