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dbSNP 134 Downloads

Here we provide resources for creating your own local MySQL implementation of the database. This is the recommended method of working with large amounts of data, such as genome-wide analysis, if fast programmatic access to this database is required.

Documentation | Query

Contents

Table downloads

The following section allows you to download individual tables from the database in various formats.

Installing table dumps

MySQL dumps and tab-delimited text files are compressed using the program gzip. The MySQL dump files have the form "table.sql.gz" and contain both schema information and data. They may be downloaded by clicking the MySQL buttons in the section below, or retrieved in Linux directly using the wget command. The following example shows how, in Linux, to download the compressed MySQL dump file Allele.sql.gz of the table Allele (line 1), and how to load it into the local MySQL database named bioq_dbsnp_human_132 (line 2):

wget -O Allele.sql.gz 'http://bioq.saclab.net/query/download_table.php?db=bioq_dbsnp_human_132&table=Allele&format=mysql'
gunzip --to-stdout Allele.sql.gz | mysql bioq_dbsnp_human_132

This is assuming MySQL has been configured properly and login information is securely stored in the option file ~/.my.cnf as explained here. Please refer to the general MySQL documentation site for more information. Note that views, which typically end in "_v", are references to other tables and therefore should be loaded last.

Text Dumps and schema files

The tab delimited text files contain only the data, and the schema files contain only the MySQL schemas describing the columns and their data types. These can be used to load the database into database management systems other than MySQL. In the table below the column "Size (Kb)" refers to the size of the table in megabytes when implemented in MySQL. Note that in the tab delimited files, the MySQL convention is to use the escape sequence "\N" for NULL; that is, for missing data.

Verifying downloads

Please verify the integrity of your downloads by using the file md5sum.txt. In Linux use the command

md5sum -c md5sum.txt

in the directory containing your downloaded files. This will print a the message "OK" for each file that appears to have downloaded successfully. If you only download a subset of files you may want modify md5sum.txt so it contains only the lines corresponding to the files you downloaded, otherwise md5sum will print error messages for the files that were not downloaded.