News: NCBI is going to eliminate GI identifiers
6
gravatar for Anima Mundi
5.0 years ago by
Anima Mundi2.8k
Italy
Anima Mundi2.8k wrote:

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

number news gi identifier ncbi • 1.5k views
ADD COMMENTlink written 5.0 years ago by Anima Mundi2.8k

would all existing entries change or only the new submissions?

ADD REPLYlink written 5.0 years ago by Nari880
1

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.

ADD REPLYlink written 5.0 years ago by GenoMax96k
1

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

ADD REPLYlink written 5.0 years ago by Anima Mundi2.8k
1

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..

ADD REPLYlink modified 5.0 years ago • written 5.0 years ago by 5heikki9.3k
2

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.

ADD REPLYlink written 5.0 years ago by GenoMax96k
2

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

ADD REPLYlink written 5.0 years ago by 5heikki9.3k

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.

ADD REPLYlink written 4.9 years ago by bedeabc110

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

ADD REPLYlink modified 4.9 years ago • written 4.9 years ago by bedeabc110
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