Microorganisms source isolation

Question

[Giulia.cosenza]

Hi, I was told that there is a way on NCBI nucleotides to get, for each microbial taxonomy ID, metadata such as info about the source of isolation .

I'm looking for such information but can't find it.

I was also wandering if there is a way to get a data frame (txt format) with all the Taxon IDs and the metadata info, because it would take ages to look for metadata of all microorganisms one by one.

Thank you so much!! Giulia

[GenoMax]

NCBI hosts all kinds of data and it is possible to get taxonomic info for some of it. Information about source of isolation is only going to be available for a smaller set of that data. So it would be useful to further clarify what data type (accessions) are you interested in getting this information for.

[Giulia.cosenza]

Basically I would need a file containing all taxaIDs of all bacteria and all associated metadata

Answer 1

[GenoMax]

NCBI makes taxonomy dump files available on their FTP site. You can parse out bacterial entries from that as needed. Taxonomy classification would be standalone and will not have source of isolation. Take a look at the taxdump_readme.txt to see the data options available.

[Giulia.cosenza]

Thank you! And do you know where I can find the "isolated from" data in NCBI?