Access dbSNP via the IUSM MSSQL server

Test access of dbSNP via CGI, Java and JDBC

This form will set up a script to submit an SQL command to the dbSNP database running at IUSM via a CGI interface to a Java program using JDBC. This web interface is NOT "productional," but rather an experimental interface to help consider alternative approaches to integrating dbSNP services with other systems.

This page has been moved to:

http://discern.uits.iu.edu:8421/dbSNP/access-dbSNP.html

and will be retired from service sometime after Jan 1, 2008.

For help composing queries see Using dbSNP via SQL queries.

Choose which dbSNP database to query:

Display up to rows beginning with row

Enter the SQL command here.

Account name: Password:

Here are some example commands you may use if you don't have one at hand:

To get a list of all tables in one of the dbSNPdatabases: Choose one of the dbSNP databases, and
To get a list of the first 4 rows in the table of dbSNPdatabases: Choose one of the dbSNP databases, and
To get all columns of the alleles table of schema dbSNP127: Choose the dbSNP127_shared database, and
To count the number of entries in an allele database: Choose one of the dbSNP "shared" databases, and
To get the dbSNP variations composed of the largest number of alleles: Chose dbSNP127_shared, sort in descending order on the magnitude of the allele_cnt field (and show only the top 500 rows in the table):
To combine information from tables in different databases, you can build queries that specify table names in the following format: For example, you could join the allele table in dbSNP126_shared with the allele table in dbSNP127_shared via the following query:
This explicit database specification will override the select made in the pulldown option on the web form above.
To see the entire HapMap classification code table (9 entries): Choose one of the dbSNP "human" databases, and
To get a list of just the codes and their abbreviations: Choose one of the dbSNP "human" databases, and
To get a list of genes containing "brain" in their LOCUS_NAME: Choose one of the dbSNP "human" or "mouse" databases, and Note that "brain" IS case specific.
To get a list of ALL SNPs reported on a reference contig that have any mapping to a location on human chromosome 1 within 10000 positions from the beginning: Choose one of the dbSNP "human" databases, and use a command LIKE: Remember, however, that the full names for the "snpcontigloc" and "contiginfo" tables include different SNP and genome build information.
To get the same list, but for SNPs that map to exactly one position on the current Build, OR map to more than one position on the same chromosome, add "and weight < 3" to the command above. Note that this SHOULD match what is returned from NCBI Entrez queries.
To get the same list, but for only those SNPs that map to exactly one position on the current Build, add "and weight < 2" to the command above. Note that this should NOT match what is returned from NCBI Entrez queries.
To get a list of all columns on every table in one of the dbSNP databases: Choose one of the dbSNP databases, and
Likewise, to get a list of all tables with the number of columns included in each:
To get a list of all views defined in a database:
To find other INFORMATION_SCHEMA tables, you can consult this primer from aspfree.com.

If you have questions about this script, please contact Michael Grobe of the Biomedical Applications Group within Research Technologies at Indiana University.