[Biopython-dev] [Bug 2535] Support for PIR / NBRF format in Bio.SeqIO

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2535





------- Comment #3 from biopython-bugzilla at maubp.freeserve.co.uk  2008-08-08 07:09 EST -------
NBRF = National Biomedical Research Foundation
PIR = Protein Information Resource, a major project of the NBRF.

See http://pir.georgetown.edu/pirwww/dbinfo/pir_psd.shtml
> Database Description for PIR-PSD
>
> Release 80.00 (31 Dec 2004) is the final release for the
> PIR-International Protein Sequence Database (PIR-PSD), the
> world's first database of classified and functionally
> annotated protein sequences that grew out of the Atlas of
> Protein Sequence and Structure (1965-1978) edited by
> Margaret Dayhoff. Produced and distributed by the Protein
> Information Resource in collaboration with MIPS (Munich
> Information Center for Protein Sequences) and JIPID (Japan
> International Protein Information Database), PIR-PSD has
> been the most comprehensive and expertly-curated protein
> sequence database in the public domain for over 20 years.
> In 2002, PIR joined EBI (European Bioinformatics Institute)
> and SIB (Swiss Institute of Bioinformatics) to form the
> UniProt consortium. PIR-PSD sequences and annotations have
> been integrated into UniProt Knowledgebase. Bi-directional
> cross-references between UniProt (UniProt Knowledgebase
> and/or UniParc) and PIR-PSD are established to allow easy
> tracking of former PIR-PSD entries. PIR-PSD unique
> sequences, reference citations, and experimentally-verified
> data can now be found in the relevant UniProt records.

Given the PIR database itself is now part of UniProt, I wonder if there is
actually much need for the PIR/NBRF format any more?

Perhaps reading PIR files might still be useful, but I doubt there is any need
to support writing PIR files with Bio.SeqIO now.


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