The BioSample Database (BioSD) at the European Bioinformatics Institute

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

The international Genome sample resource (IGSR): A worldwide collection of genome variation incorporating the 1000 Genomes Project data

“…Clicking on the population name brings up the population page described below. There is also a direct link to the sample in the BioSamples database (5) and to the relevant source, such as the Coriell Institute, where the lymphoblastoid cell line can be purchased. The lower section of the sample page lists all the files available for the sample on the IGSR FTP site.…”

Orchestrating differential data access for translational research: a pilot implementation

“…The Biosamples Database (BioSD [43, 44]) is a public repository focused on biological sample information, which is maintained by the European Bioinformatics Institute (EBI). Its rationale is to provide a single access point to the information about the bio-materials used in biological and/or medical research.…”

The International Nucleotide Sequence Database Collaboration

“…For the convenience of data submitters, EBI (6) and NCBI (7) independently launched BioSample databases to store and provide sample information. The BioSample databases contain descriptions of biological source materials used in experimental assays.…”

“…Routine data exchange, standard formats and the sharing of technology provide global synchrony across the collaboration. In this article, we outline the current status of, and changes to, INSDC including the creation of the BioSample databases (6,7) and some modifications that allow INSDC partners to respond to demands of the research domain.…”