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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?

  1. 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

  1. Creating SLIMs Allows for use of reasoner to generate taxon related SLIMs

  2. 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