Claude Skills by geneontology

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.

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 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 or a diff to go-edit.obo.

For working with any terms in the catalytic activity branch; these often correspond to RHEA or EC terms

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 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 the RDF fact-file format these programs consume, this repo's Soufflé conventions, the check registry, and the required control-ontology self-test for any new or changed rule.

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