Current Database Content

14 studies from the following diseases/disorders:

Click here for the full list of studies.

Marker data from dbSNP build 129 (18,045,285 entries)

Data Mining via HGVmart

For power users, advanced queries to HGVbaseG2P will be possible via the HGVmart system.
Initially, we will offer two entry points: a G2P study focus and a marker focus.. See our How to.. guide for a quick introduction to using HGVmart

We will shortly post information on how to use HGVmart web services from data mining tools such as myGrid's Taverna workbench and Galaxy.

Bulk Downloads

Text dumps of HGVbaseG2P data content are available on our FTP downloads area.

Distributed Annotation System (DAS)

The Distributed Annotation System (DAS) is a standard technology by which datasets can be transferred to remote sites to be integrated with other datasets and visualised on a genome browser. HGVbaseG2P uses this system to enable datasets of interest to be viewed in the Ensembl Browser, or in any other DAS compatible browser. Follow this link to see the full list of DAS sources available from HGVbaseG2P.

Data Release History

HGVbaseG2P


Release 18.0 - August 20th 2008:
  8 new genome-wide association studies added.
  HGVmart data mining service enabled.
  New genome viewer and analysis tool for G2P datasets.
  DAS support enabled.

Release 17.0 - July 1st 2008:
  Database and website completely redesigned to incorporate G2P data
  18,045,285 total marker records (update to dbSNP b129)
  GWA data for 5 disease phenotypes imported from 6 G2P studies

HGVbase

Release 16.0 - January 2004: 8,924,237 records
  Over 6,000,000 new records added
  New datasets - SNP data from dbSNP119

Release 15.0 - July 23rd 2003: 2,859,130 records
  Over 1,150,000 new records added 
  New datasets - SNP data from dbSNP111 and co-ordinate information uses NCBI 33 assembly

Release 14.0 - December 17th 2002: 1,702,845 records
  Over 251,000 new records added.
  Output enhanced with haplotype data.
  Functional predictions for non synonymous (ns) SNPs.
  Warnings of "low quality" data (Duplicon, Repeat, MultiplyMapped).

Release 13.0 - March 27th 2002: 1,451,426 records
  Over 467,000 new records added.
  Output enhanced with additional gene co-ordinate information from Ensembl

Release 12.0 - November 2nd 2001: 984,093 records
  Over 238,000 new records added.

HGBASE

Release 11.0 - October 5th 2001: 746,006 records
  Over 214,000 new records added.
  Output format enhanced with MESH terms and links to Pubmed abstracts for all records with a literature source.

Release 10.0 - July 12th 2001: 531,850 records
  Over 6100 new records added.
  Output format enhanced with additional hotlinks.

Release 9.0 - May 11th 2001: 525,690 records
  Many new records including initial exchange with dbSNP.

Release 8.0 - November 1st 2000: 62907 records
  Over 1300 new records added

Release 7.3 - May 19th 2000: 61598 records
  Corrected the way variation type 'Tandem Repeat' is treated. The fix affects DTD, XML, FASTA and DAT files. 

Release 7.2 - May 15th 2000: 61598 records
  Corrected minor bugs in XML file element names. A bug affecting allele frequency values was corrected and 
  more comments were added into the downloadable flat-file.

Release 7.1 - May 12th 2000: 61598 records
  Corrected wrongly ordered allele data in the downloadable flat-file.

Release 7.0 - May 10th 2000: 61598 records
  Over 54000 new records added
  Curation information added for each record

Release 6.0 - February 7th 2000: 6688 records
  First release by the new KI/EBI/EMBL HGVbase consortium
  Database completely redesigned, 100 new records added, redundancy eliminated

Release 5.0 - September 10th 1999: 6974 records
  Over 2000 new records added

Release 4.0 - July 13th 1999: 4522 records
  Over 1200 new records added

  Release 3.1 - May 7th 1999: 3220 records
  Missing and additional population sample sizes added

Release 3.0 - March 3rd 1999: 3220 records
Over 600 new records added, some redundancy removed

Release 2.1 - February 12th 1999: 2617 records
  PCR related data removed

Release 2.0 - January 20th 1999: 2617 records
  Over 250 new records added, some redundancy removed

Release 1.0 - August 25th: 1998: 2349 records