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Eliminating ncbitaxon:root and instead bridging to true organism subc…
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…lasses

**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 obophenotype/ncbitaxon#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
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cmungall authored Aug 19, 2022
1 parent 5066c5e commit 1948d45
Showing 1 changed file with 2 additions and 1 deletion.
3 changes: 2 additions & 1 deletion src/ontology/components/cob-to-external.tsv
Original file line number Diff line number Diff line change
Expand Up @@ -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
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