// 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`
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.
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
For working with GO taxon constraints (TCs), i.e never_in_taxon and only_in_taxon relationships
| name | external-term-lookup |
| description | 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` |
obo-grep.pl --noheader -r cysteine src/ontology/imports/chebi_import.oboYou can use OAK commands with local obo files:
runoak -i simpleobo:src/ontology/go-edit.obo tree -p i GO:0160022
Use runoak on the command line using the OLS adapter plus the ontology
runoak -i ols:chebi search cysteine