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. 2019 Jan 8;47(D1):D1172-D1178.
doi: 10.1093/nar/gky1061.

BioSamples database: an updated sample metadata hub

Mélanie Courtot  1 , Luca Cherubin  1 , Adam Faulconbridge  1 , Daniel Vaughan  1 , Matthew Green  1 , David Richardson  1 , Peter Harrison  1 , Patricia L Whetzel  1 , Helen Parkinson  1 , Tony Burdett  1
Affiliations

BioSamples database: an updated sample metadata hub

Mélanie Courtot et al. Nucleic Acids Res. .

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.

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Figures

Figure 1.
Figure 1.
A search query for ‘Homo sapiens’ samples with ‘disease state’ associated metadata and links to external database visualized in the new BioSamples user interface. https://www.ebi.ac.uk/biosamples/samples?filter=attr:Organism:Homo+sapiens&filter=attr:disease+state&filter=attr:external+reference.
Figure 2.
Figure 2.
An example of user-supplied JSON block representing AMR data. On the left hand side the JSON file and on the right side the rendering in the BioSamples UI. The block boxes contain the attribute name/value pairs, the orange boxes frame the AMR data Some attributes omitted from for clarity.
Figure 3.
Figure 3.
Users can submit and search the BioSamples database via APIs. The BioSamples services perform required operations including data persistence using a MongoDB, indexing via Apache Solr, and curation using external EMBL-EBI services OLS and Zooma. BioSamples are exchanged with INSDC partners and exported in multiple formats. The application also provides links to EMBl-EBI archives (blue circle are established links, grey circles are under development).
See this image and copyright information in PMC

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