Update/Replace missing NCBITaxon terms

[allenbaron]

Four terms used in DO have been removed from NCBITaxon. They're listed in #946. I'm opening a new issue because these are not new terms to be added but instead terms that have been removed.

obophenotype/ncbitaxon#33 lists some files I might use to find out what happened to these terms.

[allenbaron]

Copying the four terms from ncbitaxon_terms.txt that are no longer in NCBITaxon from #946:

id	label
NCBITaxon:12461	Hepatitis E virus
NCBITaxon:1535326	Candida
NCBITaxon:27317	Galactomyces geotrichum
NCBITaxon:489714	Microsporum gypseum

Only the first two are currently in use in doid-edit.owl. At a minimum these will have to be fixed before the next release if import versioning (#1052) is to be implemented.

[allenbaron]

merged.dmp from NCBI taxonomy's ftp site dated 2022-07-14 lists each of these as merged into a new ID:

id	merged to id	merged id label	merger type
12461	1678143	Paslahepevirus balayani	heterotypic synonym
1535326	5475	Candida
27317	1173061	Geotrichum candidum	homotypic synonym of Endomyces geotrichum (heterotypic synonym)
489714	63402	Nannizzia gypsea	homotypic synonym

[allenbaron]

Publications supporting name changes and describing diseases

• Hepatitis E virus >> Paslahepevirus balayani
  • https://talk.ictvonline.org/ictv-reports/ictv_online_report/positive-sense-rna-viruses/w/hepeviridae/728/genus-paslahepevirus
• Galactomyces geotrichum (teleomorph) >> Geotrichum candidum (anamorph)
  • https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7470357/
  • See https://en.wikipedia.org/wiki/Teleomorph,_anamorph_and_holomorph to understand fungal nomenclature changes.
• Microsporum gypseum >> Nannizzia gypsea
  • https://pubmed.ncbi.nlm.nih.gov/28840426/
  • https://pubmed.ncbi.nlm.nih.gov/30148055/

Looking at these in DO:

• Hepatitis E virus is used for hepatitis E (DOID:4411).
• Candida is used for candidiasis (DOID:1508).
• Microsporum gypseum, as requested in Terms to add to imports #946, is not used yet and will be available as Nannizzia gypsea.
• Geotrichum candidum is already in ncbitaxon_terms.txt and used for geotrichosis (DOID:2832), so Galactomyces geotrichum (NCBITaxon:27317), which is not used, will be removed.

[lschriml]

Looks good.
Have the ncbi taxon updates been completed ?

Cheers,
Lynn

[allenbaron]

Yes. The NCBITaxon updates for #946 and this issue are available in the pull request that establishes versioning of imports (PR #1052). I updated them there as a second test to ensure the refresh_<import> commands were working correctly. Aside from merging that PR nothing else needs to be done and this issue should close automatically.