// For working with GO taxon constraints (TCs), i.e never_in_taxon and only_in_taxon relationships
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
| name | taxon-constraint |
| description | For working with GO taxon constraints (TCs), i.e never_in_taxon and only_in_taxon relationships |
These live in src/taxon_constraints
never_in_taxon.tsvonly_in_taxon.tsvTaxon constraints don't get added in the main go-edit.obo file.
These should generally be done under instruction. You should balance following user instructions with parsimony. Sometimes it is better to:
However, great care can be taken. Don't assume TCs based just on the GO name. Sometimes GO will use terms like "heart development" in a very general way (encompassing insect 'hearts'), and someimes in a more specific way.
Remember, if a term references an external ontology like CL and UBERON, it's likely these ontologies will have the appropriate TC, which is inherted. No need for duplication.
Use OAK with the OLS adapter:
runoak -i ols:ncbitaxon info Mammalia
Although there is no place to put evidence for TCs, you should do due diligence and research - both phylogenetic, and on the usage of the GO term. Report this when you communicate back to the issue/PR using gh.
When obsoleting a term, you may need to remove the taxon constraint, as these should never point to obsoletes