News:NCBI is going to eliminate GI identifiers

Question

[Anima Mundi]

NCBI gets rid of the old GI identifiers for sequence records by September 2016, see here.

[Naren]

would all existing entries change or only the new submissions?

[GenoMax]

Appears to be all entries. GI's may still be used internally at NCBI but they will not be visible/included in GenBank, GenPept, and FASTA records.

[Anima Mundi]

Indeed, as far as I understood is going to be eliminated from all entries.

[5heikki]

Although they now provide accession2taxid map files, these do not work with makeblastdb -taxid_map option even if you parse columns 2 and 3 (accession.version & taxid) into their own file. It's relatively painless to join the taxids to tabular blast output, but it gets less convenient if you also want to see e.g. "sscinames" ;-( There should really be taxid2alltaxinfo map files..

[GenoMax]

I suggest that you send that request in to BLAST help email address. Perhaps NCBI will start making that file available by the time GI gets phased out in September 2016.

[5heikki]

I did that yesterday. At least right now there is no solution and you have to do post processing yourself.

[bedeabc]

This. It's crazy how many slow API alls are required to extract meaningful taxonomic information from BLAST results. It's hilariously user unfriendly. Thanks for making the request.

[bedeabc]

So it looks like we'll soon have to do this to get any meangful info from BLAST results:

• GI -> accession.version
• accession.version > taxid
• taxid > taxonomy

Someone please tell me there's a better solution