geneontology

This skill should be used when creating, editing, or validating GO-CAM (Gene Ontology Causal Activity Model) models. It provides comprehensive annotation guidelines for molecular functions, biological processes, cellular components, and causal relationships following GO Consortium standards.

Search GO bioentities (genes, gene products, complexes) and their GO annotations directly from the GO database. Use to resolve MGI/MOD/ComplexPortal IDs, cross-check GO annotations independently of gocam search, or find MOD-specific gene product IDs needed in Noctua models.

Independent blind evaluation of GO-CAM claims documents using Claude Explore subagents to read the PDFs. Reads expert_validation_claims.md and verifies every claim against primary PDFs from scratch, producing a structured evaluation report. Use after gocam-claims-pipeline has generated its output. Always run in a fresh session — never in the same session as the pipeline. For a Gemini-powered alternative, see /blind-review-gemini.

Independent blind evaluation of GO-CAM claims documents using Gemini. One Gemini instance per primary PDF reads the paper directly and returns PASS/FLAG/FAIL verdicts on every claim citing it. Use after gocam-claims-pipeline has generated its output. Always run in a fresh session — never in the same session as the pipeline. For a Claude-engine alternative, see /blind-review-claude.

Generate a .drawio pathway diagram from a GO-CAM claims document. Use after completing the annotation pipeline (Phase 7) to produce agent-output/pathway_sketch.drawio. Reads shape styles and the Shape Palette page from workflow/network_template_draw.drawio.

Launches two parallel Gemini instances per paper to review GO-CAM claims from two complementary perspectives — a peer reviewer (scientific accuracy) and a GO-CAM curator (annotation correctness). Each receives the full claim in claims_template format and responds as an expert with OK/WRONG/UNCERTAIN plus a corrected claim where needed. Collects both outputs into peer_review_claims.md alongside the original claim.

Run the full GO-CAM literature-backed annotation pipeline. Reads GO-CAM models (OWL/TTL), verifies all claims against primary research PDFs, and produces expert validation documents. Use when starting or continuing a GO-CAM curation project folder.

Fetch full-text articles and metadata from PubMed/PMC. Use when a PDF is missing from literature/ and you need the article text or abstract to verify a claim. Full text is only available for open-access PMC articles (~6 million).

For working with GO taxon constraints (TCs) using onlyin:/neverin: superclass assertions

Use whenever you run a Makefile target (e.g. `make travis_build`, `make test`, `make reasoned.ofn`) or any one-off ROBOT / owltools / dosdp-tools / scala-cli command derived from a Makefile recipe. These must run inside the pinned ODK Docker image, not against host tools. Covers validation, reasoning, imports, and release builds in src/ontology.

For handling the process around obsoleting GO terms. This is a complex process involving substantial analysis of impact, both on existing terms that reference to the to-be-obsoleted term, and on annotations

Use the /research skill when performing background research from the literature or the web to create a RESEARCH.md file; also covers use of `deep-research-client`

For working with any terms referencing chemical entities (CHEBI). CHEBI has some unusual properties that are counter-intuitive, so always use this skill to plan or check work that involves a chemical entity or CHEBI IDs, whether a new term, or significant alteration of existing terms

Use this skill when planning to create new ontology terms or modify existing ones to ensure proper design pattern compliance. This skill should be used proactively during issue planning to identify appropriate design patterns before term creation begins. No intersection_of tags should be added without using this skill.

Use this to search for relevant terms in external ontologies. NEVER guess ontology terms or term IDs, always confirm using this skill. The general methodology is to use `obo-grep.pl`

For working with mappings (dbxrefs) in GO.

Generate deployment commands for a production go-fastapi instance

Smoke test a deployed go-fastapi instance