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. 2012 Jan;40(Database issue):D64-70.
doi: 10.1093/nar/gkr937. Epub 2011 Nov 16.

The BioSample Database (BioSD) at the European Bioinformatics Institute

Mikhail Gostev  1 , Adam Faulconbridge, Marco Brandizi, Julio Fernandez-Banet, Ugis Sarkans, Alvis Brazma, Helen Parkinson
Affiliations

The BioSample Database (BioSD) at the European Bioinformatics Institute

Mikhail Gostev et al. Nucleic Acids Res. 2012 Jan.

Abstract

The BioSample Database (http://www.ebi.ac.uk/biosamples) is a new database at EBI that stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics. The goals of the BioSample Database include: (i) recording and linking of sample information consistently within EBI databases such as ENA, ArrayExpress and PRIDE; (ii) minimizing data entry efforts for EBI database submitters by enabling submitting sample descriptions once and referencing them later in data submissions to assay databases and (iii) supporting cross database queries by sample characteristics. Each sample in the database is assigned an accession number. The database includes a growing set of reference samples, such as cell lines, which are repeatedly used in experiments and can be easily referenced from any database by their accession numbers. Accession numbers for the reference samples will be exchanged with a similar database at NCBI. The samples in the database can be queried by their attributes, such as sample types, disease names or sample providers. A simple tab-delimited format facilitates submissions of sample information to the database, initially via email to biosamples@ebi.ac.uk.

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Figures

Figure 1.
Figure 1.
Example of the MSI section of a SampleTab file.
Figure 2.
Figure 2.
Example of the SCD section of a SampleTab file.
Figure 3.
Figure 3.
Example of search results in BioSD web interface.
Figure 4.
Figure 4.
Overview of future integration between BioSD and other EBI databases.
See this image and copyright information in PMC

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