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Summary

  • Remove built-in xenbase and zfin transforms from monarch-ingest
  • Update ingests.yaml to use pass-through URLs pointing to:
  • Update README with consolidated documentation and modular ingest table
  • Update docs/Sources/xenbase.md and docs/Sources/zfin.md to redirect to modular repos

Future Work

All internal koza ingests are expected to be migrated to modular repositories in the same pattern. This PR establishes the approach:

  1. Create standalone <source>-ingest repository with justfile-based workflow
  2. Configure GitHub Actions to create releases with KGX edge/node TSV artifacts
  3. Update ingests.yaml to reference the release artifacts as pass-through URLs
  4. Remove the built-in transform code from monarch-ingest
  5. Update documentation to point to the modular repository

Remaining ingests to migrate:

  • bgee
  • ctd
  • dictybase
  • flybase (if not already in Alliance)
  • hgnc
  • mgi (if not already in Alliance)
  • pombase
  • reactome
  • rgd (if not already in Alliance)
  • sgd (if not already in Alliance)
  • string

Related Changes

Test plan

  • Verify xenbase-ingest and zfin-ingest releases exist and are accessible
  • Run monarch-ingest download/transform to confirm pass-through URLs work
  • Verify no regressions in KG build output

🤖 Generated with Claude Code

- Remove built-in xenbase and zfin transforms
- Update ingests.yaml to use xenbase-ingest and zfin-ingest releases
- Update README with consolidated documentation
- Update source docs to point to modular repositories

Co-Authored-By: Claude Opus 4.5 <[email protected]>
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2 participants