Preamble¶
Originally the BioSamples database was where metadata describing sequence data submitted to ENA was stored. Today it is a standalone repository where sample metadata can be accessioned even if not associated with sequence data. Indeed, you can still obtain a new BioSamples accession by submitting sample metadata in conjuction with sequence data to ENA. However, we recommend registering BioSamples accesssion(s) first and referencing the accession number when submitting derived sequence data to ENA, or data to any of the other data repositories.
Because of it’s origins and wide range of potential metadata than can be included to describe a sample - note that a sample may be many different types of artefact, not just DNA samples - data submitted to BioSamples must be in the form of a spreadsheet of values with each row being a separate sample. That is to say, there is no online form where you can fill in data values, rather you create the spreadsheet of data offline then drop the file into the submission box. There is also an extensive API for submitting sample records programmatically - a guide can be found here.
How to register one or many BioSamples accessions¶
The Biosamples step-by-step guide can be found here.
The BioSamples submission data are based on a number of checklists that define mandatory data fields for different data, and project data types. These checklists are described here. For EUREMAP projects, we recommend you use this checklist template that is based on the ENA default sample checklist (ERC000011). You can of course add additional fields to the submission if necessary, but you should understand what you are doing.
In the checklist template spreadsheet, the term in the columns labeled “Characteristic[term]” are the “Field Name” identified in the checklist e.g. ERC000011. From the checklist you can identifiy which fields are mandatory. Each “Characteristic[term]” column is followed by two further columns labeled “Term Source REF” and “Term Accession Number”. If you don’t know what these mean, leave them blank - BUT they must still be included in the submission spreadsheet.
Please note that the spreadsheet must be in tab-separated format (TSV) and all columns in the template should be included even if left blank.