How to map SILVA and GG 13_8 ids to NCBI or IMG ids?

[ecolog]

If I have a SILVA latest release (132?) or GG 13_8 taxonomy Ids how can I get the corresponding match to NCBI or IMG databases? I don’t want to rely only in the taxonomy per se.

I found a GG 13_5 file “gg_13_5_accessions.txt” (see below) with exactly what I was looking for, but unfortunately not for the other two databases. Did I miss it? Is this accession files from 13_5 same for 13_8?

I appreciate any guidance,
Ecolog

#gg_id accession_type accession
4 Genbank AB019749.1
7 Genbank AB019734.1
…
4486071 IMG 2505119043
4486072 IMG 2515154082
4486073 IMG 2513237099

[Nicholas_Bokulich]

Hi @ecolog,

@ecolog

If I have a SILVA latest release (132?) or GG 13_8 taxonomy Ids how can I get the corresponding match to NCBI or IMG databases?

It looks like this paper might provide what you are looking for.

I hope that helps!

[ecolog]

Hi Nicholas,
Thanks so much paper, it does illustrate several interesting points of using these different taxonomies however their analysis relies on mapping the taxa names so it seems that there is not an id mapping across them.
An alternative that comes to mind is to contact the authors if they share their named mapped results across taxonomies, that could be used as a mapping file from one taxonomy to another.

Thanks, @ecolog

[Nicholas_Bokulich]

Hi @ecolog,

@ecolog

An alternative that comes to mind is to contact the authors if they share their named mapped results across taxonomies, that could be used as a mapping file from one taxonomy to another.

That sounds like a good way forward. Please share any information that you find — other users of this forum may have similar questions in the future!

[ecolog]

After further looking the authors do have a tool that could do the id mapping (via name mapping described on the paper)
https://bitbucket.org/mokana/crossclassify/wiki/Home
While I still would like to have access to their curated database, this seems to answer my original question.
Thanks!