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dbSNP in SRS

Heikki Lehvaslaiho heikki at ebi.ac.uk
Fri Nov 17 10:20:37 EST 2000


Dear all,

There have been quite a lot of interest in getting dbSNP into SRS.
I've now written the first version of parsers for the new dbSNP
distribution
(XML) format. Since the XML support for SRS is not yet ready and I had
parsing code for it anyway, I created three flat files from XML and
wrote parsers for them; quick and easy. Note that the XML will be
change and have richer representation of dbSNP relational database
schema in near future. Also, note that current dump in the NCBI ftp
server contains data submitted before September 5th, only. 

The URLs:

The EBI SRS server:
	http://srs.ebi.ac.uk/

dbSNP disribution files:
	ftp://ftp.ncbi.nlm.nih.gov/snp/pc_compressed/XML_exchange/

Perl XML parser (needs XML::Parser and XML::Node) and icarus files:
	http://www.ebi.ac.uk/mutations/progs/dbsnp.tar.gz


  -Heikki

-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki at ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________








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