Updates to BioSamples Database at European Bioinformatics Institute

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2013 Nov 23

PMID 24265224

Citations 22

Authors

Adam Faulconbridge

Tony Burdett

Marco Brandizi

Mikhail Gostev

Rui Pereira

Drashtti Vasant

Ugis Sarkans

Alvis Brazma

Helen Parkinson

Affiliations

Soon will be listed here.

Abstract

The BioSamples database at the EBI (http://www.ebi.ac.uk/biosamples) provides an integration point for BioSamples information between technology specific databases at the EBI, projects such as ENCODE and reference collections such as cell lines. The database delivers a unified query interface and API to query sample information across EBI's databases and provides links back to assay databases. Sample groups are used to manage related samples, e.g. those from an experimental submission, or a single reference collection. Infrastructural improvements include a new user interface with ontological and key word queries, a new query API, a new data submission API, complete RDF data download and a supporting SPARQL endpoint, accessioning at the point of submission to the European Nucleotide Archive and European Genotype Phenotype Archives and improved query response times.

Citing Articles

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Extending the Minimum Information About BIobank Data Sharing Terminology to Describe Samples, Sample Donors, and Events.

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Using association rule mining and ontologies to generate metadata recommendations from multiple biomedical databases.

Martinez-Romero M, OConnor M, Egyedi A, Willrett D, Hardi J, Graybeal J Database (Oxford). 2019; 2019.

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Navigating in vitro bioactivity data by investigating available resources using model compounds.

Ilmjarv S, Augsburger F, Bolleman J, Liechti R, Bridge A, Sandstrom J Sci Data. 2019; 6(1):45.

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The EMBL-EBI search and sequence analysis tools APIs in 2019.

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