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SNP FAQ Archive [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2005-.

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SNP FAQ Archive [Internet].

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dbSNP Data Origins

Where does the data in dbSNP come from?

dbSNP accepts submissions from academic research laboratories as well as from private research companies. Currently, the major contributors to dbSNP include laboratories associated with the National Human Genome Research Institute (NHGRI) grants program. Although NHGRI’s SNP initiative for human is essentially complete, there may be further SNP submissions generated for other organisms in the future as more genomes are completed. NHGRI grant recipients continuing SNP work include genome centers, private, extra-mural research labs, and private businesses. While research groups under the NHGRI grant umbrella will be submitting new SNPs to dbSNP, the majority of new submissions to dbSNP will be genotype, frequency, and haplotype data for existing SNPs.(04/05/06)

Does dbSNP gather data exclusively from researchers, or do you also get it from other SNP databases?

Our data comes from researchers and other SNP databases.

Does dbSNP collect SNPs using automated SNP detection and external submissions, or do you also collect SNPs from peer-reviewed literature?

Currently, dbSNP does not have the staff to mine literature citations for new variation records, so we rely on the authors and editors involved in the publication process to submit their data to dbSNP.

Given the current levels of funding for dbSNP, I do not expect this policy to change in the near future. I would point out that other groups, such as the Cardiff Human Gene Mutation Database, have been actively compiling lists of variations from the literature for many years. The Cardiff dataset, however, is protected by copyright; therefore, Cardiff refuses permission to migrate the data to dbSNP.

Is the rice reference sequence from the IRGSP sequence, or is it from the TIGR assembly of the IRGSP sequence?

Check the Oryza sativa (rice) Genome Resource page. (8/9/05)

Data Exchange/Data Synchronization with other SNP Databases/Resources

Is dbSNP’s dataset the same as SNP500 CANCER or do you cover more SNPs then they do?

Although SNP500 CANCER is one of the major submitters to dbSNP,dbSNP still covers more SNPs. You can see dbSNP’s content statistics on our build summary page (10/02/08)

Does NCBI exchange information with EMBL and DDBJ on a daily basis? If so, does this mean that NCBI’s data are updated every day?

No, dbSNP does not exchange information with EMBL and DDBJ on a daily basis. dbSNP is updated every 4 to 8 weeks, and the data are available to everyone via FTP.

We do have links to some of the submitter databases. This information is available in the XML dump on the FTP site. Search the XML for the tag “NSE-ss_linkout-url”. The XML dump also contains a list of dbSNP’s contributors called “submitterlist.xml.gz”.

Does dbSNP contain all the SNPs found in JSNP, the SNP consortium, the UCSC Genome Browser, and in the HapMap project?

Although dbSNP synchronizes each new build with the resources you mentioned, you should note that the JSNP resource only periodically synchronizes to our site; UCSC downloads its SNP data from us, and the SNP Consortium is no longer growing. dbSNP, however, should contain all of their SNPs. HapMap contains SNPs found in dbSNP only (refSNP numbers). Exceptions to the above mentioned synchronizations may occur in between builds. Any SNP that is identified by a refSNP(rs) number originated in dbSNP, as dbSNP assigns rs numbers. (3/17/06)

Is dbSNP in synch with the Seattle SNP database?

Seattle SNP submits data to dbSNP on a regular basis. Recent submissions will be available with the next dbSNP build release in about a month. (6/22/07)

Are all of the SNPs provided by The SNP Consortium (TSC) available in dbSNP?

All of the SNPs from the TSC should be in dbSNP. You can search for them using Entrez SNP using the handle "TSC-CSHL"

You can also see a history of TSC’s submissions to dbSNP (with links to the data) by entering "TSC-CSHL" in the text box at the top of the dbSNP Submitter Page.

You can access the dbSNP Submitter page by going to the dbSNP home page, scrolling down to the “Submission Information” Section, and clicking on the words “By Submitter”. (7/5/07)

Does dbSNP contain all of the ESTs found in GenBank?

No, only the ESTs and STSs that contain SNPs are submitted to dbSNP.

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