How to Submit to dbSNP:
I. Submission Quick Start
Version 4.1; December 11, 2015
1. Send a Small Submission to dbSNP
A small submission is defined as a submission of 1-1000 variations per batch at a rate of 1-10 batches per day or <100K of data.
To send a small submission to dbSNP, follow these steps:
1. Look at our lists of acceptable and non-acceptable data types to see if your data can be accepted.
2. Review our Hold Until Published Policies if you need your data witheld from public view after submission.
3. Review the Introduction and Submission Overview documentation for general information about submissions and the data types required in each
submission.
4. Perform the dbSNP Pre-Submission Process
5. Format the Metadata (Meta)files for your submission
6. Format your data for submission
7. Email your small submission to dbSNP via email at snp-sub@ncbi.nlm.nih.gov.
8. Send a separate email to dbSNP at snp-sub@ncbi.nlm.nih.gov to expect your data once you have sent it. Be sure to include your Handle in the text
of the email.
2. Send a Large Submission to dbSNP
A large submission is defined as a submission of >1000 variations/batch or at a rate of > 10 batches/day, or >100K of data. We accept large
submissions to dbSNP in Variant Call Format (VCF) only.
To send a large submission to dbSNP, follow these steps:
1. Look at our lists of acceptable and non-acceptable data types to see if your data can be accepted.
2. Send an email with the subject line “dbSNP FTP account request” to: snp-sub@ncbi.nlm.nih.gov with your handle information. Once we set up the
account, we will send a password for the account to you.
3. Review our Hold Until Published policies if you need your data witheld from public view after submission.
4. Review the Introduction and Submission Overview documentation for general information about submissions and the data types required in each
submission.
5. Perform the dbSNP Pre-Submission Process.
6. Format Metadata (Meta)files for your submission.
7. Format your data for Submission.
8. Login to the FTP account we created for you and upload your dbSNP VCF formatted submission.
9. Send an email to snp-sub@ncbi.nlm.nih.gov , to let us know that you have uploaded to your FTP account.
Remember, in addition to VCF formatted variation files, dbSNP also requires VCF submissions to include separate Metafile(s), that include Publication, Method, Population, and Assay. You may submit the Metafiles separately or combine them into a single text file for submission. See Formatting Metadata (Meta)files for more information.
3. What happens to my data once it's submitted?
Accessions
Once you have either emailed your data to dbSNP or uploaded it to your pre-arranged FTP upload, we will begin to process your submission. When we complete processing and assign ss numbers to your variations, we will send an email containing an attachment listing the ss numbers assigned to the variations in your submission. If we find submitter-based errors in your submission, we will contact you by email. We do not process partial submissions, so if there is a submitter-based error in just one variant of your submission, we will ask you to fix the error or remove the record containing the error before we can process the submission.
Submitted SNP (ss) Number Assignment
Each submission of a variant from independent experiments that used different methods or samples will get a unique number assigned, the "ss number", regardless of whether instances of the submitted variant already exist in dbSNP. Although this may create a redundant set of submitted variants, this redundancy allows dbSNP to aggregate and validate variants across independent experiments, methods and populations. Ultimately, dbSNP creates a non-redundant set of variants (reference variants, rs a.k.a. RefSNP) for annotation and exchange through a process known as clustering. In the clustering process, dbSNP computes and aggregates identical ss and their attributes into a single cluster and then assigns a single unique rs number to represent the cluster of ss numbers.
RefSNP (rs) Number Assignment
We assign RefSNP (rs) numbers only during the dbSNP build clustering process, so rs numbers for your submitted variations will be assigned during the next dbSNP build that follows your submission. As we will not send an email notifying you of the rs number assignments to your submitted variations, you can search dbSNP at https://www.ncbi.nlm.nih.gov/snp/advanced or Batch Query Service at https://www.ncbi.nlm.nih.gov/projects/SNP/batchquery.html using the list of ss numbers we sent to find your assigned rs numbers, or you can find an ss or rs number by using one of dbSNP’s submission searches.
We do not assign reference variant accessions (rs) immediately after your submission; instead, we assign them during the next dbSNP build following your submission. We do not send dbSNP submitters notification emails of rs number assignments, so use the dbSNP search function at https://www.ncbi.nlm.nih.gov/snp/advanced or the dbSNP Batch Query Service at https://www.ncbi.nlm.nih.gov/projects/SNP/batchquery.html to query the database with the list of ss numbers from your submission to find the corresponding rs numbers. dbSNP submission searches at http://www.ncbi.nlm.nih.gov/SNP/snp_tableList.cgi?type=submitter also provide a way for you to find ss or rs numbers.
4. How long will it take dbSNP to send me my ss number(s) or rs number(s)?
SS and RS Turnaround Time
Assuming there are no problems with your submission, your ss numbers will be assigned within approximately two weeks of your submission. rs numbers for your submission will be assigned during the next dbSNP build that follows your submission. Your submission may be delayed if you submitted your data during a major holiday or if we find a problem with your submission.
If you require the ss number(s) by a certain date for publication, contact us and tell us the approximate date you need the ss number(s) when you submit, and we will try to get your SNP(s) processed and the ss number(s) to you by the date specified.
SS and RS Processing Status
Once dbSNP receives your submission, you will receive an email acknowledging the submission within 24 hours. If we find a problem with your submission, we will contact you by email. When we complete processing and assign ss numbers to your variations, we will send an email containing an attachment listing the ss numbers assigned to the variations in your submission. dbSNP does not send emails providing submitted variation rs number assignments. If you have questions regarding the processing status of your submission, contact the dbSNP submission group at snp-sub@ncbi.nlm.nih.gov. Include your submission Handle in the email.
If it has been two weeks since your submission and you have not received email notification of your ss number assignments, contact the dbSNP submission group at snp-sub@ncbi.nlm.nih.gov. Include your submission Handle in the email.
5. What are dbSNP's "Hold Until Published" Policies?
dbSNP will not hold data to be released on a particular date or in a particular dbSNP build for non-clinical variations submitted in dbSNP VCF or Flat File format to dbSNP. However, if your manuscript requires dbSNP accession numbers (ss numbers) for the review process, we can hold the submitted data from public view until the publication is accepted and you have notified us that dbSNP can release the data. Once notification has been given, dbSNP will release the data during the next build release cycle.
6. How do I cite dbSNP in my Paper?
How do I cite dbSNP as a NCBI Resource?
Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11.
How do I cite dbSNP database as a whole for a specific build?
Database of Single Nucleotide Polymorphisms (dbSNP). Bethesda (MD): National Center for Biotechnology Information, National Library of Medicine. (dbSNP Build ID: {build ID}). Available from: http://www.ncbi.nlm.nih.gov/SNP/
How do I cite a single or a range of Submitted SNP (ss) or Reference SNP (rs) entries?
Database of Single Nucleotide Polymorphisms (dbSNP). Bethesda (MD): National Center for Biotechnology Information, National Library of Medicine. dbSNP accession:{ss1 or ss1 – ss100}, (dbSNP Build ID: {build ID}). Available from: http://www.ncbi.nlm.nih.gov/SNP/
Contact dbSNP
If you do not find the answer to your submission questions in any of the titles in the "How to Submit to dbSNP" series of documents, contact dbSNP submissions at snp-sub@ncbi.nlm.nih.gov, and we will do our best to answer your submission question or help you solve a difficult submission problem.
- Send submissions and submission questions to: snp-sub@ncbi.nlm.nih.gov
- Send Submission updates to: snp-update@ncbi.nlm.nih.gov
- Send general inquiries, etc. to: snp-admin@ncbi.nlm.nih.gov
Titles in the How to Submit to dbSNP Series: