How to unifying the alternative names for different taxonomy databases (e.g. Acidobacteriota vs. Acidobacteria in SILVA vs. GreenGenes)

General Discussion
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Dear friends,

Have any of you encountered the issues in naming conventions while working with taxonomy assignment with different reference database (SILVA vs. GreenGenes vs. RDP). I recently compared the output results and noticed some discrepancied in naming converntions, especially for SILVA as compared to others. For instance, Acidobacteria is assigned to Acidobacteriota, and Gemmatimonadetes is assigned to Gemmatimonadota.

I'm struggling to find resources like handbooks or notes that provide the alternative names for different databases. I've already searched online but failed to get a clear idea. Has anyone come across such resources or have any tips to share? Your insights would be greatly appreciated. Thank you very much in advance!

Sirong

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Hi @ZhangSR,

There is quite a lot of changes happening in the world of microbial taxonomy. Also, the rate at which the different databases can keep up, is getting ever more difficult. Additionally, not all databases curate their data the same way or follow varying nomenclatural rules & schemas.

The following post provides some links about the renaming scheme:

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Got it. Thank you~ @SoilRotifer
I've read the papers you recommended. Although there were still no solutions to keep the same taxonomic name for different databases, it's much clearer for me to understand the differences across different databases.

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Hi @ZhangSR ,

Sadly, it is up to the researcher at this point on how they'd like to pick and choose which taxonomy they'd like to use, and curate.

You could probably leverage RESCRIPts merge-taxa and edit-taxonomy, actions to help curate your taxonomy.

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