What should be submitted to BioSamples Database?

BioSamples Database is a suitable repository for pre-registering multi-omic submissions (e.g. http://www.hipsci.org/).

Samples that do not have associated data in other EBI databases may also be appropriate to submit to BioSamples Database.

When submitting to other EBI databases (e.g. ENA or ArrayExpress), please note that these share sample information with BioSamples Database. Therefore sample information from submitters may be present in BioSamples Database even if the information was not submitted directly to BioSamples Database.

How to submit BioSamples Database?

Submissions to BioSamples Database should be in SampleTab file format. This is a tab-separated spreadsheet-like text format compatible with popular office tools.

All of the existing samples in the BioSamples database is available in SampleTab format as examples at http://ftp.ebi.ac.uk/pub/databases/biosamples/

Once you have a SampleTab file, you can use the online validation service to ensure it is correct. This will also apply common corrections and ontology mappings that are used to standardize the data.

You can send the validated and corrected SampleTab file by email to biosamples@ebi.ac.uk. We aim to respond to submissions within one working day.

What is a BioSample?

The definition of a BioSample is deliberately flexible in order to accommodate a wide range of uses. Typically each BioSample corresponds to a discrete physical object that is composed of live biological material.

In most cases BioSample entities are self-evident; such as a blood sample, cell culture or an individual organism. However, a BioSample can also be an environmental sample (e.g. for meta-genomic analysis), a hybrid between two species, parasite infected cell culture, etc.

Some highly-curated and highly-referenced submissions may become part of the reference layer, for example ENCODE and 1000 Genomes Project. These are BioSamples that are of significant interest and value.

How are BioSamples described?

The basic structure for describing BioSamples is an attribute which is composed of a key and a value (a key/value pair), as well as optional modifiers.

A BioSample is described by a set of attributes. BioSamples are collected together into one or more Groups(s), which may also have attributes.

A SampleTab file contains one or more Groups, any BioSamples contained in those groups, and the attributes describing those BioSamples and Groups. A SampleTab file also contains general information, such as contact information and any publications related to the BioSamples.