From 268b095409d2b83c85ad8637752519067d43fb03 Mon Sep 17 00:00:00 2001 From: David Osumi-Sutherland Date: Wed, 16 Jun 2021 16:36:56 +0100 Subject: [PATCH] Update taxon_constraints.md Attempted to make more accessible on CL editor's call. --- docs/key-topics/taxon_constraints.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/key-topics/taxon_constraints.md b/docs/key-topics/taxon_constraints.md index 72e3f24..7db0975 100644 --- a/docs/key-topics/taxon_constraints.md +++ b/docs/key-topics/taxon_constraints.md @@ -3,14 +3,14 @@ There are, in essence, three categories of taxon-specific knowledge we use across OBO ontologies. Given a class `C`, which could be anything from an anatomical entity to a biological process, we have the following categories: -1. The ALL-IN restriction: "C in-taxon T" -2. The NOT-IN restriction: "C never-in-taxon T" -2. The SOME-IN restriction: "C present-in-taxon T" +1. The ALL-IN restriction: "C in-taxon T". Use this when the entity (e.g. anatomical structures, cell types or biological processes) is only found in the taxon specified. +2. The NOT-IN restriction: "C never-in-taxon T". Use this when the entity is never found in the taxon specified +2. The SOME-IN restriction: "C present-in-taxon T". Use this when the entity is found in the taxon specified, but may also be found in other taxa. ## The ALL-IN restriction: "in-taxon some T" - _Meaning_: "_All_ instances of `C` are in taxon `T`" -- _Canonical logical representation_: `C SubClassOf: in-taxon some T` +- _Canonical logical representation_: `C SubClassOf: in-taxon some T` # Editors should use this one. - Comment: no need for only-in-taxon if in-taxon is functional - _Alternative representations_: None - _Editor guidance_: Editors use the Cannonical logical representation in subClassOf or simple (non-nested) EquivalentClass axioms. @@ -18,11 +18,11 @@ There are, in essence, three categories of taxon-specific knowledge we use acros ## The NOT-IN restriction: "C SubClassOf: not (in_taxon some T)" - _Meaning_: "_No_ instances of `C` are in taxon `T`" -- _Canonical logical representation_: `C SubClassOf: not (in_taxon some T)` +- _Canonical logical representation_: `C SubClassOf: not (in_taxon some T)` - _Alternative representations_: - Alternative EL logical representation: `C disjointWith in-taxon some T` - Comment: depends on injecting GCIs into NCBITaxon - - Canonical Shortcut: AnnotationAssertion: `C never-in-taxon T` + - Canonical Shortcut: AnnotationAssertion: `C never-in-taxon T` # - _Editor guidance_: Editors use cannonical logical representation, only in simple subClassOf axioms. ## The SOME-IN restriction: "a ClassAssertion: `C` and in-taxon some `T`"