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Inconsistent results with merged NCBI TaxIDs #707

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lm-jkominek opened this issue Sep 11, 2023 · 0 comments
Open

Inconsistent results with merged NCBI TaxIDs #707

lm-jkominek opened this issue Sep 11, 2023 · 0 comments
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@lm-jkominek
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lm-jkominek commented Sep 11, 2023

Hi, I run into some consistency issues while working with TaxIDs that have been merged on NCBI's end. Le's take 2074836 and 2588313 as an example of what I mean.

1/ When I run ncbi.get_lineage(), I get back 2074836's lineage in both cases:
[1, 131567, 2759, 33154, 4751, 451864, 4890, 716545, 147538, 716546, 715989, 147550, 222544, 5139, 35718, 2382315, 2074836]

2/ When I run ncbi.get_taxid_translator(), I get back both TaxID's in results:
{2074836: 'Arxotrichum gangligerum'}
{2588313: 'Arxotrichum gangligerum'}

3/ Finally, when I run ncbi.get_rank(), I get back the proper result for 2074836 but an empty dict for 2588313.
{2074836: 'species'}
{}

So, depending on the function call, the results can lead to different conclusions - (1) indicates they are the same species, (2) indicates that they might be different strains of the same species (due to different IDs) and (3) that one of the IDs is completely invalid.

So, I was hoping for some clarity on that, and perhaps some streamlining too, in order to avoid the confusing results?

@dengzq1234 dengzq1234 self-assigned this Sep 11, 2023
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