BioSamples database: an updated sample metadata hub. Issue Volume 47:Issue D1(2019) (8th November 2018)

• Record Type: Journal Article
• Authors: Courtot, Mélanie; Cherubin, Luca; Faulconbridge, Adam; Vaughan, Daniel; Green, Matthew; Richardson, David; Harrison, Peter; Whetzel, Patricia L; Parkinson, Helen; Burdett, Tony
• Is Part Of: Nucleic acids research. Volume 47:Issue D1(2019)
• Page Start: D1172
• Page End: D1178
• Publication Date: 2018-11-08
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gky1061
• Languages: English
• ISSNs: 0305-1048

Abstract

Abstract: The BioSamples database at EMBL-EBI provides a central hub for sample metadata storage and linkage to other EMBL-EBI resources. BioSamples has recently undergone major changes, both in terms of data content and supporting infrastructure. The data content has more than doubled from around 2 million samples in 2014 to just over 5 million samples in 2018. Fast, reciprocal data exchange was fully established between sister Biosample databases and other INSDC partners, enabling a worldwide common representation and centralization of sample metadata. The BioSamples platform has been upgraded to accommodate anticipated increases in the number of submissions via GA4GH driver projects such as the Human Cell Atlas and the EGA, as well as from mirroring of NCBI dbGaP data. The BioSamples database is now the authoritative repository for all INSDC sample metadata, an ELIXIR Deposition Database for Biomolecular Data and the EMBL-EBI sample metadata hub. To support faster turnaround for sample submission, and to increase scalability and resilience, we have upgraded the BioSamples database backend storage, APIs and user interface. Finally, the website has been redesigned to allow search and retrieval of records based on specific filters, such as 'disease' or 'organism'. These changes are targeted at answering current use cases as well as providing functionalities for future emerging and anticipated developments. Availability: The BioSamples database is freely available at http://www.ebi.ac.uk/biosamples . Content is distributed under the EMBL-EBI Terms of Use available at https://www.ebi.ac.uk/about/terms-of-use .