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Consider a non-isomorphic mappings to NCBI Taxon database

Open cmungall opened this issue 3 years ago • 1 comments

The NCBI taxonomy database is a database, not an ontology. As such that automatic translation includes various things that are not ideal from an ontology modeling perspective

If we were to make the OWL non-isomorphic here are some things we might change:

  • change root class name #10
  • depluralize taxa common names "human" not "humans"
  • exclude non-taxon entries, or rewire them to a different hierarchy
    • e.g. https://www.ebi.ac.uk/ols/search?q=sample&ontology=ncbitaxon
    • metagenomes (e.g "soil metagenome")
    • environmental samples, e.g http://purl.obolibrary.org/obo/NCBITaxon_743727 environmental samples <archaea,phylum Candidatus Aenigmarchaeota>
    • random terms like "mixed sample"
    • host samples, e.g. "human sample"

We could also use this as an opportunity to merge into a single ncbitaxon representation see https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1383

cmungall avatar May 11 '21 22:05 cmungall