R package to link NCBI taxonomy ID to bacterial properties (Gram stain, aerobe/anaerobe, etc)
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11 months ago
predeus ★ 2.0k

Hi all,

I wonder if you know of an R package that would allow linking a bacterial species (e.g. by NCBI taxonomy ID, or by a full species name) to a selection of properties. I am currently interested in Gram status and aerobe/anaerobe growth requirements, but other properties (e.g. whether it's cultureable, etc) would be neat to have as well.

Thank you, as always.

R NCBI bacteria taxonomy • 810 views
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Entering edit mode
11 months ago

BacDive has an API (free registration required) with a REST-R client: https://r-forge.r-project.org/R/?group_id=1573 More examples here: https://api.bacdive.dsmz.de/

It's a shame how the other efforts to unify similar databases seem to have disappeared. The Microbe Directory's web page is gone, but it seems like you can pull out the tables on Github: https://github.com/dcdanko/MD2 BactoTraits seems to have also disappeared.

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