go-cam-drop-box

A staging "drop box" where GO curators submit complete, production-worthy GO-CAM models as pull requests. Every submission is validated by CI before a maintainer merges it. Validated models are intended to flow into the main GO-CAM / Noctua workflows by a mechanism that is still to be designed (see "Status" below).

Status: early / forming. The contract and the CI gates below are real and working, but the promotion path into production is not yet built, and details may still change.

What a submission looks like

• Format: a GO-CAM model serialized as gocam-py YAML (the LinkML data model for GO-CAMs).
• Identifier: the model id is in the gomodel: namespace with a drop-box-specific internal id: gomodel:gcdb-<UUID>.
• Filename: the file lives at models/gcdb-<UUID>.yaml and its name must match the model id.

You mint the gcdb-<UUID> yourself (a UUID guarantees it can never collide with a production model id — those are hex, minted by Noctua/minerva). See CONTRIBUTING.md.

What CI checks (the merge gates)

A PR can only be merged once all of these pass on each added/changed model:

1. Identifier & filename. id matches gomodel:gcdb-<UUID> (valid UUID), the filename matches the id, and the id is unique within models/.
2. LinkML schema conformance. The model validates against the pinned gocam-py GO-CAM LinkML schema.
3. "True GO-CAM" semantics. The model is complete and production-worthy — production status, a connected causal graph (no orphan activities), and evidence. These criteria live in validation/criteria.yaml and are intentionally modular so the bar can be loosened later.
4. Ontology-term validity. Every ontology term used (GO, RO, ECO, CHEBI, NCBITaxon, …) exists and is not obsolete, checked with oaklib.

Run all four locally before opening a PR:

pip install -r validation/requirements.txt
python validation/validate_model.py models/gcdb-<UUID>.yaml

Who can contribute

GitHub organization members. Anyone can technically open a PR on a public repo, but merge is gated on the CI checks above and a maintainer's review; we only support submissions from GO-org members at this time.

Layout

Path	What
models/	Submitted models, gcdb-<UUID>.yaml each
examples/	Reference model(s) that demonstrate the format and pass all gates
validation/	The validator (validate_model.py) + the modular criteria + pinned deps
.github/workflows/validate.yml	The CI that runs the four gates on each PR
CLAUDE.md	Instructions for AI agents that author/submit models on a curator's behalf