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…

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…

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…

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…

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…

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).

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…

For reading, writing, debugging, or extending Soufflé Datalog (`.dl`) programs in this repo — the layered ontology QC program under `src/util/qc/`, the `basic-cycles.tsv` cycle check, taxon-constraint materialization, and the relation-diff CI report. Covers…

For reviewing a pull request against the GO ontology, whether from a local checkout or from the automated reviewer in CI. Covers what to check, how to grade severity, and how to report coverage honestly. Use whenever asked to review, critique, or check a PR…

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

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

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…

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…

Use whenever you need to access existing standard annotations OR bioentities (genes, gene products) in the ID space used by Noctua

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…

Use whenever you need to access the GO-CAM store (Noctua). This is accomplished via an API called barista.

Save a GO-CAM model the user has been working on to the public geneontology/go-cam-drop-box repository as a pull request. Use when the user asks to "save", "submit", "publish", or "keep" a model so it can be reviewed and (later) promoted into GO-CAM. The…

use this skill to walk a user through an exercise

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…

Use whenever you need to access the GO-CAM store (Noctua). This is accomplished via an API called barista.

use this skill to recap an exercise a user has performed

Check whether an announced upstream API change (primarily Alliance/AGR) affects go-fastapi. Use when the user reports an upstream release announcement, forwards a release-notes email, or asks whether an upcoming Alliance/AGR change breaks us.

Generate deployment commands for a production go-fastapi instance

Smoke test a deployed go-fastapi instance