From 1948d458e9e304a47fcb96a4e0abf94f01ec5975 Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Thu, 18 Aug 2022 18:25:01 -0700 Subject: [PATCH] Eliminating ncbitaxon:root and instead bridging to true organism subclasses **please read closely and read the related issue before commenting** This PR removed the statement that COB:organism = NCBITaxon:root Rationale: root includes non-organisms such as samples See https://github.com/obophenotype/ncbitaxon/issues/10 This PR replaces that link with two subClassOf axioms * COB:organism * NCBITaxon:Viruses * NCBITaxon:cellular organisms Note that if this were merged, then the union of NCBITaxon and COB would have a lattice at the top. However, it would be trivial to add NCBITaxon:1 to an anti-slim and filter it out, resulting in a tree with COB:organism as the single MRCA of all organism classes Merging this PR has some advantages such as obviating the need to rename NCBITaxon:1, since we instead simply inject our own true parent. It leaves the structure of labeling of NCBITaxon intact **Important** please refrain from discussing the definition of organism here, specifically whether it includes viruses. For COB purposes, this is a closed issue. See: #6 --- src/ontology/components/cob-to-external.tsv | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/ontology/components/cob-to-external.tsv b/src/ontology/components/cob-to-external.tsv index 5f5d5b0..fc70787 100644 --- a/src/ontology/components/cob-to-external.tsv +++ b/src/ontology/components/cob-to-external.tsv @@ -57,7 +57,8 @@ COB:0000019 cell in vitro owl:equivalentClass CL:0001034 cell in vitro . HumanCu COB:0000020 subcellular structure rdfs:subClassOf owl:Thing owl:Thing Chris will follow up HumanCurated COB:0000021 gross anatomical part owl:equivalentClass CARO:0001008 gross anatomical part . HumanCurated COB:0000021 gross anatomical part sssom:superClassOf UBERON:0010000 multicellular anatomical structure . HumanCurated -COB:0000022 organism owl:equivalentClass NCBITaxon:1 root . HumanCurated +COB:0000022 organism sssom:superClassOf NCBITaxon:10239 Viruses . HumanCurated +COB:0000022 organism sssom:superClassOf NCBITaxon:131567 cellular organisms . HumanCurated COB:0000022 organism owl:equivalentClass OBI:0100026 organism . HumanCurated COB:0000022 organism owl:equivalentClass CARO:0001010 organism or virus or viroid . HumanCurated COB:0000025 organization owl:equivalentClass OBI:0000245 organization . HumanCurated