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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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Ontology no longer builds due to unsatisfiable classes (NCBITaxon) #29301

Open kltm opened 3 days ago

kltm commented 3 days ago

I'm not sure the origin of these changes, but the ontology no longer builds due to a large number of unsatisfiable NCBITaxon classes. Current captured errors at:

http://skyhook.berkeleybop.org/go-ontology-dev/reports/unsatisfiable_explanations.md

Sample:

Tue Nov 26 01:13:58 UTC 2024
3148
## [Scheffersomyces shehatae](http://purl.obolibrary.org/obo/NCBITaxon_45589) SubClassOf [Nothing](http://www.w3.org/2002/07/owl#Nothing) ##

  - [Scheffersomyces shehatae](http://purl.obolibrary.org/obo/NCBITaxon_45589) SubClassOf [Scheffersomyces](http://purl.obolibrary.org/obo/NCBITaxon_766733)
    - [Scheffersomyces](http://purl.obolibrary.org/obo/NCBITaxon_766733) SubClassOf [Debaryomycetaceae](http://purl.obolibrary.org/obo/NCBITaxon_766764)
      - [Debaryomycetaceae](http://purl.obolibrary.org/obo/NCBITaxon_766764) SubClassOf [CUG-Ser1 clade](http://purl.obolibrary.org/obo/NCBITaxon_2916678)
        - [CUG-Ser1 clade](http://purl.obolibrary.org/obo/NCBITaxon_2916678) SubClassOf [Saccharomycetales](http://purl.obolibrary.org/obo/NCBITaxon_4892)
          - [Saccharomycetales](http://purl.obolibrary.org/obo/NCBITaxon_4892) SubClassOf [Saccharomycetes](http://purl.obolibrary.org/obo/NCBITaxon_4891)
        - [CUG-Ser1 clade](http://purl.obolibrary.org/obo/NCBITaxon_2916678) SubClassOf [Pichiomycetes](http://purl.obolibrary.org/obo/NCBITaxon_3239874)
  - [Pichiomycetes](http://purl.obolibrary.org/obo/NCBITaxon_3239874) DisjointWith [Saccharomycetes](http://purl.obolibrary.org/obo/NCBITaxon_4891)

## [Deinococcus maricopensis DSM 21211](http://purl.obolibrary.org/obo/NCBITaxon_709986) SubClassOf [Nothing](http://www.w3.org/2002/07/owl#Nothing) ##

  - [Deinococcus maricopensis DSM 21211](http://purl.obolibrary.org/obo/NCBITaxon_709986) SubClassOf [Deinococcus maricopensis](http://purl.obolibrary.org/obo/NCBITaxon_309887)
    - [Deinococcus maricopensis](http://purl.obolibrary.org/obo/NCBITaxon_309887) SubClassOf [Deinococcus](http://purl.obolibrary.org/obo/NCBITaxon_1298)
      - [Deinococcus](http://purl.obolibrary.org/obo/NCBITaxon_1298) SubClassOf [Deinococcaceae](http://purl.obolibrary.org/obo/NCBITaxon_183710)
        - [Deinococcaceae](http://purl.obolibrary.org/obo/NCBITaxon_183710) SubClassOf [Deinococcales](http://purl.obolibrary.org/obo/NCBITaxon_118964)
          - [Deinococcales](http://purl.obolibrary.org/obo/NCBITaxon_118964) SubClassOf [Deinococci](http://purl.obolibrary.org/obo/NCBITaxon_188787)
            - [Deinococci](http://purl.obolibrary.org/obo/NCBITaxon_188787) SubClassOf [Deinococcota](http://purl.obolibrary.org/obo/NCBITaxon_1297)
              - [Deinococcota](http://purl.obolibrary.org/obo/NCBITaxon_1297) SubClassOf [Terrabacteria group](http://purl.obolibrary.org/obo/NCBITaxon_1783272)
  - [Deinococcota](http://purl.obolibrary.org/obo/NCBITaxon_1297) DisjointWith [Terrabacteria group](http://purl.obolibrary.org/obo/NCBITaxon_1783272)

## [Truepera radiovictrix DSM 17093](http://purl.obolibrary.org/obo/NCBITaxon_649638) SubClassOf [Nothing](http://www.w3.org/2002/07/owl#Nothing) ##

  - [Truepera radiovictrix DSM 17093](http://purl.obolibrary.org/obo/NCBITaxon_649638) SubClassOf [Truepera radiovictrix](http://purl.obolibrary.org/obo/NCBITaxon_332249)
    - [Truepera radiovictrix](http://purl.obolibrary.org/obo/NCBITaxon_332249) SubClassOf [Truepera](http://purl.obolibrary.org/obo/NCBITaxon_332248)
      - [Truepera](http://purl.obolibrary.org/obo/NCBITaxon_332248) SubClassOf [Trueperaceae](http://purl.obolibrary.org/obo/NCBITaxon_332247)
        - [Trueperaceae](http://purl.obolibrary.org/obo/NCBITaxon_332247) SubClassOf [Trueperales](http://purl.obolibrary.org/obo/NCBITaxon_2762275)
          - [Trueperales](http://purl.obolibrary.org/obo/NCBITaxon_2762275) SubClassOf [Deinococci](http://purl.obolibrary.org/obo/NCBITaxon_188787)
            - [Deinococci](http://purl.obolibrary.org/obo/NCBITaxon_188787) SubClassOf [Deinococcota](http://purl.obolibrary.org/obo/NCBITaxon_1297)
              - [Deinococcota](http://purl.obolibrary.org/obo/NCBITaxon_1297) SubClassOf [Terrabacteria group](http://purl.obolibrary.org/obo/NCBITaxon_1783272)
  - [Deinococcota](http://purl.obolibrary.org/obo/NCBITaxon_1297) DisjointWith [Terrabacteria group](http://purl.obolibrary.org/obo/NCBITaxon_1783272)
kltm commented 3 days ago 
# Ontologies used: 
- go-plus.owl (http://purl.obolibrary.org/obo/go/extensions/go-plus.owl)
- taxslim-disjoint-over-in-taxon.owl (http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim-disjoint-over-in-taxon.owl)
- taxslim.owl (http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl)
cmungall commented 3 days ago

there was a release today https://github.com/obophenotype/ncbitaxon/releases/tag/v2024-11-25

unless we are using 100% base we will get superpositions cc @balhoff