Guide to Taxon Restrictions¶
What are taxon restrictions?¶
Taxon restrictions are a formalised way of to record what species a term applies to - something crucial in multi-species ontologies.
Even species neutral ontologies (eg GO) have classes that have implicit taxon restriction.
Eg GO:0007595 ! Lactation - defined as “The secretion of milk by the mammary gland.”
Why restrict taxon?¶
- Finding inconsistencies Taxon restriction use NCBITaxon which have pairwise disjointness between species (eg Nothing is both an insect and a rodent and a primate) When addint taxon constraints, a reasoner can check for inconsistencies.
E.g. when GO implemented taxon restrictions, they found 5874 errors PMID:20973947
Creating SLIMs Allows for use of reasoner to generate taxon related SLIMs
Querying E.g. in Brain Data Standards, in_taxon axioms that allow faceting cell types by species. (note: there are limitations on this and may be incomplete)
How to add taxon restrictions:¶
Please see how-to guide on adding taxon restrictions
Why annotation for some taxon restrictions?¶
Annotations for taxon restrictions are used as a shortcut. These are used to more simply represent complex description. Shortcuts work as a macro that is expanded out (see this document for technical details):
Eg C never_in_taxon T -> C disjointWith in-taxon some T