How to Submit to dbSNP:
IV. BioProject, BioSample and dbSNP
Version 4.1; December 11, 2015
We encourage our submitters to submit their project and sample metadata to BioProject and BioSample prior to submitting a variation to dbSNP. Those variations submitted with with a BioProject and BioSample accession numbers contain links directly to the metadata collected by BioProject and BioSample from dbSNP submitters. The information stored in these resources will be broad in scope, and in the case of BioSample data, will contain structured and consistent data descriptions. See Figure 1 for a diagrammatic representation of the links between dbSNP, BioProject and BioSample.
BioProject
A BioProject is a collection of biological data related to a single initiative, originating from a single organization or from a consortium.
NIH-funded projects must be registered in BioProject with the assigned BioProject accession associated with the grant number for compliance with the NIH Genomic Data Sharing (GDS) Policy. If your data is not already associated with an NCBI BioProject accession, request one via the NCBI Submission Portal.You can reuse BioProject accession registered for the same NIH-funded project for submission to other NCBI databases including GenBank, SRA, and dbSNP.
The BioProject database is a flexible framework where you describe a project's scope and objectives and group related projects and sub-projects. The data collected in a BioProject submission includes:
- Structured information about the type of research investigation (e.g. genome sequencing, gene expression),
- Project title and goals
- The submitting group
- Environmental sample label or organism
- Project data type attributes for sample scope, target and method
Once you have your BioProject Accession number, you can reference it in your dbSNP submission so that users can easily link from the dbSNP record of your submitted variant to the detailed information you provided to BioProject, which will allow investigators studying your variant to see how the experiment that generated the variant fits in to your overall research goals. if you have questions regarding BioProject, contact [email protected].
BioSample
A BioSample is a description of the biological source materials used in experimental assays.
The BioSample database provides a dedicated area where a submitter describes the biological materials under investigation in a project. The BioSample submissions process guides the submitter to use structured and consistent sample descriptions of sample charactersitics and provides the opportunity to supply custom-descriptive attributes. For example, if you specify that your sample is a pathogen, you will be prompted to provide information about collection locality, date, host (if applicable), and isolation source (food, faeces, etc.). BioSample will also prompt you to describe the host, disease state, etc. Biosample also has a batch submission option that uses spreadsheets tailored for a particular sample type. if you have questions regarding BioSample, contact [email protected].
Because sample descriptions are often dependent on the context of the study, the definition of what a BioSample represents is deliberately flexible, but typical examples of a BioSample include: a cell line, a primary tissue biopsy, an individual organism or an environmental isolate. Descriptions of your sample can include the following if they are applicable:
- cell type
- collection site
- disease state
Once you have your BioSample Accession number, reference it in your dbSNP submission so that users can easily link from the dbSNP record of your submitted variant to the detailed information you provided to BioSample about the characteristics of the sample used to generate the variant.
If you are working with a pure source of any of the commonly used commercial cell lines that are re-used over and over again by the research community, you may be able to bypass Biosample submission and use a "Reference Biosample" accession in your dbSNP submission instead. A "Reference Biosample" is an official representation of these common and highly referenced samples or cell lines that was developed by BioSample in collaboration with major cell line vendors, including ATCC and Coriell. Before you start your submission to BioSample, search the BioSample Authenticated Cell Line Profiles to see if your cell line already exists as a "Reference BioSample".
Figure 1: Linking between dbSNP, BioProject and BioSample
Contact dbSNP
If you do not find the answer to your submission questions in the How to Submit to dbSNP document series, contact dbSNP submissions at [email protected], 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: [email protected]
- Send submission updates to: [email protected]
- Send general inquiries, etc. to: [email protected]
Titles in the How to Submit to dbSNP Series: