News:NCBI is going to eliminate GI identifiers
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5.9 years ago
Anima Mundi ★ 2.9k

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

GI number identifier ncbi News • 1.8k views
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would all existing entries change or only the new submissions?

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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.

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

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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..

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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.

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

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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.

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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

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