taxon-constraint

Taxon constraints are edited directly in src/ontology/go-edit.obo.

A GO term gets a taxon constraint by asserting is_a to one of these materialized classes:

is_a: onlyin:33213
is_a: neverin:4896
is_a: onlyin:4952 {source="PMID:10629216", source="PMID:14504266"}

The class labels are "only in " and "never in ". OBO comments after ! are helpful when present, but do not rely on them being preserved by serialization for these internal idspaces.

Creating new taxon constraints

These should generally be done under instruction. You should balance following user instructions with parsimony. Sometimes it is better to:

• make neverin: constraints to a more general clade than requested
• make onlyin: constraints to a more general clade than requested

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 sometimes 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 inherited. No need for duplication.

Choosing the class

Use onlyin:<taxon_id> for only_in_taxon constraints and neverin:<taxon_id> for never_in_taxon constraints. The local ID is the NCBITaxon local ID with the NCBITaxon: prefix removed:

• NCBITaxon:33213 becomes onlyin:33213
• NCBITaxon:4896 becomes neverin:4896
• NCBITaxon_Union:0000023 becomes onlyin:Union_0000023

Union/grouping taxa are only used for onlyin: constraints. Do not create neverin:Union_* constraints. Prefer multiple separate neverin: constraints when multiple taxa are needed.

If the needed atomic taxon class does not exist, add the taxon to src/ontology/imports/taxon_constraints_seed.txt and regenerate src/ontology/imports/go-taxon-constraint-classes.ofn. Union classes come from src/ontology/imports/go-taxon-groupings-edit.owl.

Check whether a class exists before using it:

rg "only-in/NCBITaxon_33213|never-in/NCBITaxon_4896" src/ontology/imports/go-taxon-constraint-classes.ofn

Evidence

Put evidence on the is_a axiom as source annotations. Multiple sources are multiple annotations on the same axiom:

is_a: onlyin:4952 {source="PMID:10629216", source="PMID:14504266"}

Use the same care as before: research both phylogeny and GO term usage, and report the evidence when communicating on the issue or PR.

Querying NCBITaxon

Use OAK with the OLS adapter:

runoak -i ols:ncbitaxon info Mammalia

Validation

For ordinary term edits, validate the ontology as usual. The old only_in_taxon.tsv / never_in_taxon.tsv column checks no longer apply.

Useful targeted checks:

cd src/ontology && make check_all_taxon_constraints_columns
cd src/ontology && make imports/go-taxon-constraint-classes.ofn

Run the import regeneration target when you change taxon_constraints_seed.txt or taxon grouping definitions. Otherwise, adding an is_a: onlyin: or is_a: neverin: axiom in go-edit.obo should not require regenerating the class import.

Taxon constraints and obsoletion

When obsoleting a term, you may need to remove the taxon constraint, as these should never point to obsoletes