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OpenTreeOfLife / reference-taxonomy

Open Tree Reference Taxonomy (OTT) tools
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Escherichia not in OTT #327

Open mtholder opened 7 years ago

mtholder commented 7 years ago

Escherichia-Shigella is See https://tree.opentreeoflife.org/taxonomy/browse?id=5248878 It would be nice to be able to find Escherichia

mtholder commented 7 years ago

find in the taxonomy browser that is.

TonyRees commented 7 years ago

Hi Mark - from perusing the literature it appears that Escherichia and Shigella are separately defined genera however Shigella species including the type species, S. dysenteriae, nest inside Escherichia, see http://www.sciencedirect.com/science/article/pii/S167202291200112X . So the genera are synonyms but until someone synonymizes the species names the Shigella species should remain in that genus. A parent name such as "Escherichia-Shigella" has no standing in nomenclature even though the intention is apparent. So in these situations I am guessing that OTT should maintain both genus names, with children as assigned, until relevant species transfers are done?

jar398 commented 7 years ago

It's not in SILVA at all, and whatever NCBI has for the genus is paraphyletic with respect to SILVA. E.g. (Escherichia sp. 7CR ncbi:370987) is in (Escherichia-Shigella 5248878=silva:U88546/#6+632) while (Escherichia sp. CPD32 ncbi:332031) is in (Enterobacter 424061=silva:U33121/#6+5007)

FWIW. This is from the conflicts.tsv file in the OTT dump. When this happens we kick the record (and name) out of OTT, but it might be better to keep it as a synonym. In this case, the smallest taxon that contains all of NCBI Escherichia is Enterobacteriaceae, so it would be synonymized with that.

TonyRees commented 7 years ago

Escherichia and Shigella are both in IRMNG as valid genera, if that helps. Escherichia is parent to all E. spp. and Shigella is parent to all S. spp. (funny, that...), with both in family Enterobacteriaceae.

jar398 commented 7 years ago

So should Escherichia just be made a synonym (of some kind) of SILVA's Escherichia-Shigella ? Would that solve the problem, @mtholder ?

mtholder commented 7 years ago

I did just find it at: https://tree.opentreeoflife.org/taxonomy/browse?id=474503 Perhaps we need a more general issue of how to sort the list children suppressed at the bottom of the page. I probably mistyped it in the search and didn't find it in a page search, so thought it was not browsable. Sorry for the static. I do think linking it in some way to the E-S group would be nice, but there may not be a general way to do that.

jar398 commented 7 years ago

Definitely agree about the sort order. Maybe that should be its own issue (in opentree repo, which is where the browser is found).