dbVar News and Announcements

Added study nstd16 Korbel et al 2007

Thu, 05 Nov 2009 16:00:00 EST

New human study.

Added study nstd17 Conrad et al 2006

Thu, 05 Nov 2009 16:00:00 EST

New human study.

dbVar FTP files updated

Thu, 05 Nov 2009 16:00:00 EST

The following change affect all studies: all variant.tab and supportingvariant.tab files have been updated to change the columns related to flanking sequences. Previous files have been moved to ARCHIVE directories.

dbVar Submission files and documentation updated.

Mon, 02 Nov 2009 10:00:00 EST

The Excel and XML submission forms and guidelines have been updated. Changes include: 1. Removal of controlled vocabulary for Method platform and Analysis detection method. These are now free-text fields. 2. Addition of 'sex' to Sampleset 3. Change of 'hapmap' to 'repository' in Sample 4. Addition of array experiment ID to Validation 4. Addition of fields to describe inner and outer probes for aCGH variant placements.

Added new study nstd15_Cutler_et_al_2007

Wed, 28 Oct 2009 14:00:00 EST

http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=search&term=17989247

dbVar FTP files updated.

Thu, 22 Oct 2009 10:00:00 EST

The following changes affect all studies: 1) all structvar.xml files have been updated to report chromosome name in "chr" and chromosome accession in "accession. 2) all .gff files have been updated to correct assembly names in the ##genome-build line. 3) all variant.tab and supportingvariant.tab files have been updated to correct assembly names and to remove build column. 4) all analysis.xml files have been updated to correct GENOME assembly name and to remove build attribute (only Kidd, Mills, and Tuzun have GENOME assembly names). 5) all analysis.tab files have been updated to correct ref_assembly and to remove ref_build (only Kidd, Mills, and Tuzun have ref_assembly). 6) all method.tab files have been updated to change seq_platform to platform. 7) all method.xml files have been updated to remove ARRAY and SEQUENCING levels. Previous files have been moved to ARCHIVE directories.

Added new study nstd13_Chen_et_al_2009

Thu, 22 Oct 2009 09:00:00 EST

http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=search&term=19015322

Added new study nstd14_Cooper_et_al_2008

Thu, 22 Oct 2009 09:00:00 EST

http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=search&term=18776910

dbVar FTP files updated.

Tue, 13 Oct 2009 15:00:00 EST

The following changes affect all studies: 1) remove date from all FTP filenames. 2) All structvar.xml files have been updated to report chromosomes as accession.version instead of chromosome names. 3) All variant.tab and supportingvariant.tab files have been updated to add chromosome accession.version in addition to chromosome names. 4) All analysis.tab files have been updated to include “ref_” in reference field labels, to remove software* fields and to add detection_method and detection_parameters. 5) All analysis.xml files have been updated to replace ALGORITHM and SOFTWARE with DETECTION. Previous files have been moved to ARCHIVE directories.

nstd10_Nicholas_et_al_2009 FTP files updated

Tue, 13 Oct 2009 15:00:00 EST

FTP files have been updated to correct placement errors due to submission file being 0-based and contig conversion file being 1-based. Previous files have been moved to ARCHIVE directories.

nstd2_Kidd_et_al_2008 FTP files updated

Tue, 13 Oct 2009 15:00:00 EST

FTP files have been updated to correct placement errors due to contig conversion file being 0-based. Previous files have been moved to ARCHIVE directories.

nstd11_Walter_et_al_2009 FTP files updated

Tue, 13 Oct 2009 15:00:00 EST

Method.xml FTP file updated to include platform name. Previous file has been moved to ARCHIVE directories.

nstd9_Perry_et_al_2006 FTP files updated

Tue, 13 Oct 2009 15:00:00 EST

Method.xml FTP file has been updated to include platform name. Previous file has been moved to ARCHIVE directories.

nstd8_Perry_et_al_2008b FTP files updated

Tue, 13 Oct 2009 15:00:00 EST

FTP files in Homo_sapiens/nstd8_Perry_et_al_2008b and Pan_troglodytes/nstd8_Perry_et_al_2008b have been updated to correct sex for 2 subjects, to report HGDP samples with repository="HGDP", and to correct the HGDP subject ethnicity. Previous files have been moved to ARCHIVE directories.

dbVar is accepting submissions

Fri, 24 Jul 2009 15:00:00 EST

dbVar is now open and accepting submissions. We accept submissions as either an XML file or a Microsoft Excel file. For more information, see our submissions page.