dbSNP

dbSNP: Single Nucleotide Polymorphism database

dbSNP comes from the National Center for Biotechnology Information, and is described by its creators thusly:

SNP stands for "single nucleotide polymorphism". SNPs are the most common genetic variations and occur once every 100 to 300 bases. A key aspect of research in genetics is the association of sequence variation with heritable phenotypes. It is expected that SNPs will accelerate the identification of disease genes by allowing researchers to look for associations between a disease and specific differences (SNPs) in a population. This differs from the more typical approach of pedigree analysis which tracks transmission of a disease through a family. It is much easier to obtain DNA samples from a random set of individuals in a population than it is to obtain them from every member of a family over several generations. Once discovered, these polymorphisms can be used by additional laboratories, using the sequence information around the polymorphism and the specific experimental conditions.
[online; accessed 1/2/03; http://www.ncbi.nlm.nih.gov/SNP/]

dbSNP tables within CLSD

dbSNP is stored at the NCBI in a MicroSoft SQL Server database. Copies of recent releases are maintained in a local MS SQL Server database by the Information Services & Technology Management group in the IU School of Medicine. UITS and ISTM work together to make this database accessible via CLSD.

Beginning with Release 125 SNP data for each organism were separated into two components:
  • tables shared by all organisms, and
  • tables representing each organism.
Release 128 of the Human_9606 and Mouse_10090 data are the most recent organism versions available within CLSD as of February 2008.

Here are the SQL table definition commands for the Build 127 versions of the:

You can access the PDF version of the ER diagram for the combined set of tables .

Using dbSNP within CLSD

Within CLSD tables are grouped together into "schemas". For example, all of the tables distributed as Build 128 of the Human_9606 data, will appear within the schema "DBSNP128_HUMAN".

A table will then be referenced as DBSNP128_HUMAN.table_name, as in 

      select * from DBSNP128_HUMAN.SNP
which will display all columns within the SNP table distributed with Build 128.

You can reference the mouse and shared tables likewise, as in: 

       select * from DBSNP128_MOUSE.SNP
and 
       select * from DBSNP128_SHARED.ALLELE



For more information about using SNP data within CLSD see the tutorial "Using dbSNP via SQL queries".

For assistance using SNP data from within CLSD please contact Scientific Data Services via data @ iupui.edu.