go-ontology

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.

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