dbVar Submission Guidelines
Welcome to the dbVar Submission Guidelines page.
IMPORTANT, PLEASE READ: SV data can be complex to represent. We ask that all submitters read this primer on popular methods for generating SV data. It addresses details we expect to receive in your submission - such as when to provide outer start and stop coordinates, allele length, etc. - based on the experimental methods you used. Even if you think your data is straightforward, please read and follow the guidelines included in the primer, to avoid additional work and processing delays later. Thank you for you cooperation.
Below you will find tips and instructions to help you navigate the submission process and make it as quick and painless as possible. dbVar accepts data in three formats: Excel, tab-delimited text, and XML. Pre-defined templates are provided for each format. The Excel template contains detailed information describing required fields and dependencies; this information is not present in the templates for other formats. Most submitters will choose to use Excel; however, even if you plan to submit in either the tab-delimited or XML format, you may still wish to download a copy of the Excel spreadsheet and keep it open for reference while you complete your submission.
Note 1: Data Embargo
Some users may want dbVar to withhold public release of their data until after a specific date (e.g., the anticipated publication of a manuscript). If you wish, we will process your data on our normal schedule but not release it on our public pages until a date you specify. Please provide a date in the Study section of your submission after which we may share your data with the public.
Note 2: Genotyping Data
NCBI is currently constructing a "Genotype Server" to store genetic variation data for both SNPs and Structural Variation. The outcome of that project will determine the details of the exact data format dbVar will eventually request for the submission of genotyping data. Therefore, although the current dbVar Submission Template does not have a section for accepting genotyping data, we are currently accepting genotyping data and ask that you contact us to facilitate your submission.
Submitting Your Data in Four Easy Steps
Step One.
There are a few things you should do before you begin your submission.
- (Required) Raw sequence and aCGH data must be deposited in a public database, e.g.,GenBank, GEO, dbGaP, SRA or Trace.
- (Required) If your data contains clinically sensitive information or is from patients who have not fully consented to having their genetic information displayed on a public website, you must first submit it to NCBI's Genotypes and Phenotypes database, dbGaP. There, sensitive information will be kept behind controlled access while anonymized structural variation data will be forwarded directly to dbVar. NOTE: When submitting structural variation data to dbGaP, you must still use the VARIANT CALLS and VARIANT REGIONS sections of the dbVar submission template to define your variants, since the dbVar template is specially designed to capture specific information about structural variation that is not defined in dbGaP's submission process.
- (Optional) If you do not already have one, you may request a PDA Login. The PDA login system enables NCBI to better keep track of your data and make it accessible via addtiional NCBI resources. Obtaining a PDA login is not required for submission to dbVar, but it is strongly encouraged.
- (Optional) If your submission is part of a larger project or initiative that has been assigned an NCBI Entrez Project ID, please indicate this in your submission (in the STUDY section, see below). If you do not have one, we encourage you to request an NCBI Entrez Project ID to include in your submission. This will facilitate searching and retrieval of your data across all NCBI databases.
Step Two.
Choose a format for your submission - Excel, Tab-delimited, or XML - and download the appropriate pre-defined template here. In addition to the primer mentioned at the top of this page, you can find details on the use of individual template formats here: Excel, Tab-delimited, XML. Use whichever format best suits your needs. Many important details and instructions are found only in the Excel template - please use it as a reference guide, whichever format you select for your submission.
Step Three.
Populate the template with your data and associated information, using these pages and the notes in the Excel template as guides. dbVar has fairly well-defined criteria for the type of data you may enter; however, we are flexible and can add additional fields or requirements as needed. If you are unsure about how to complete a section, or if you need additional guidance, we are available to assist with your submission. Simply email us at dbvar@ncbi.nlm.nih.gov.
Step Four.
Email your completed submission to dbvar@ncbi.nlm.nih.gov. You should receive a response within 24 hours confirming receipt of your submission. If this confirmation does not arrive, please contact us again by email or notify the NIH Help Desk.
Congratulations! You have completed the submission of your data to dbVar. We release data to the public on a monthly cycle. Barring any unforeseen delays in processing, your data should be available on the public dbVar website within three to six weeks from the date of submission (sometimes sooner). Thank you for sharing your data!