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Resource:BioSample Database at EBI

Name: Resource:BioSample Database at EBI
Description: Database that aggregates sample information for reference samples (e.g. Coriell Cell lines) and samples for which data exist in one of the EBI's assay databases such as ArrayExpress, the European Nucleotide Archive or PRoteomics Identificates DatabasE. It provides links to assays for specific samples, and accepts direct submissions of sample information.

The goals of the BioSample Database include:

  1. recording and linking of sample information consistently within EBI databases such as ENA, ArrayExpress and PRIDE;
  2. 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
  3. supporting cross database queries by sample characteristics.

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 (at) ebi.ac.uk. Current data sources:

  • European Nucleotide Archive (424,811 samples)
  • PRIDE (17,001 samples)
  • ArrayExpress (1,187,884 samples)
  • ENCODE cell lines (119 samples)
  • CORIELL cell lines (27,002 samples)
  • Thousand Genome (2,628 samples)
  • HapMap (1,417 samples)
  • IMSR (248,660 samples)[1]
Other Name(s): BioSample Database at the EBI, BioSample Database, BioSD - BioSample Database, BioSD at EBI, BioSamples database, BioSamples Database at EBI, EBI BioSample Database, BioSamples
Abbreviation: BioSD
Parent Organization: Resource:European Bioinformatics Institute
Supporting Agency: Resource:European Molecular Biology Laboratory; Heidelberg; Germany, European Commission, (CAGEKID, ENGAGE from FP7 program)
Grant: HEALTH-F4-2010-241669, HEALTH-F4-2007-201413
Resource Type(s): Database
Resource: Resource
URL: http://www.ebi.ac.uk/biosamples/
*Id: nlx_143930
Alternate Id(s): OMICS_01025
PMID: PMID 22096232
Publication link: http://nar.oxfordjournals.org/content/40/D1/D64.abstract?ijkey=374e1923695afc02d016814b186e42cd500c3cc5&keytype2=tf_ipsecsha
Related application: Research
Related to: Resource:NCBI BioSample
Uses: Resource:European Nucleotide Archive, Resource:PRIDE, Resource:ArrayExpress, Resource:ENCODE: Encyclopedia of DNA Elements, Resource:Coriell Institute for Medical Research, Resource:1000 Genomes: A Deep Catalog of Human Genetic Variation, Resource:International HapMap Project, Resource:International Mouse Strain Resource
Listed By: Resource:OMICtools
Availability: The community can contribute to this resource, Acknowledgement requested
Keywords: Cell line, Cell, Nucleotide, Sequencing, Proteomics, Peptide, Protein, Genomics, Gene expression, Biological sample, Molecular, sequence, structure, Cell line, Topical portal, aggregator, Gold standard
Link to OWL / RDF: Download this content as OWL/RDF

Curation status: Curated

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References

  1. Gostev M et al. (2012) The BioSample Database (BioSD) at the European Bioinformatics Institute. Nucleic Acids Res 40: D64-70 PubMed

Notes

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Facts about Resource:BioSample Database at EBIRDF feed
AbbrevBioSD  +
AvailabilityThe community can contribute to this resource  +, and Acknowledgement requested  +
CommentSample type: Cell line, etc.
CurationStatuscurated  +
DefiningCitationhttp://www.ebi.ac.uk/biosamples/  +
DefinitionDatabase that aggregates sample informatio Database that aggregates sample information for reference samples (e.g. Coriell Cell lines) and samples for which data exist in one of the EBI's assay databases such as ArrayExpress, the European Nucleotide Archive or PRoteomics Identificates DatabasE. It provides links to assays for specific samples, and accepts direct submissions of sample information.

The goals of the BioSample Database include:

  1. recording and linking of sample information consistently within EBI databases such as ENA, ArrayExpress and PRIDE;
  2. 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
  3. supporting cross database queries by sample characteristics.

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 (at) ebi.ac.uk. Current data sources:

  • European Nucleotide Archive (424,811 samples)
  • PRIDE (17,001 samples)
  • ArrayExpress (1,187,884 samples)
  • ENCODE cell lines (119 samples)
  • CORIELL cell lines (27,002 samples)
  • Thousand Genome (2,628 samples)
  • HapMap (1,417 samples)
  • IMSR (248,660 samples) p (1,417 samples)
  • IMSR (248,660 samples)
ExampleImageBioSD.PNG  +
GrantCategory:HEALTH-F4-2010-241669   +, and Category:HEALTH-F4-2007-201413   +
Has default formThis property is a special property in this wiki.Resource  +
Has roleDatabase  +
Idnlx_143930  +
Is part ofResource:European Bioinformatics Institute  +
KeywordsCell line  +, Cell  +, Nucleotide  +, Sequencing  +, Proteomics  +, Peptide  +, Protein  +, Genomics  +, Gene expression  +, Biological sample  +, Molecular  +, Sequence  +, Structure  +, Topical portal  +, Aggregator  +, and Gold standard  +
LabelResource:BioSample Database at EBI  +
ListedbyResource:OMICtools  +
ModifiedDate15 October 2014  +
PMID22096232  +
Page has default formThis property is a special property in this wiki.Resource  +
PublicationLinkhttp://nar.oxfordjournals.org/content/40/D1/D64.abstract?ijkey=374e1923695afc02d016814b186e42cd500c3cc5&keytype2=tf_ipsecsha  +
RelatedToResource:NCBI BioSample  +
Related applicationResearch  +
SuperCategoryResource  +
Supporting AgencyResource:European Molecular Biology Laboratory; Heidelberg; Germany  +, European Commission  +, (CAGEKID  +, and ENGAGE from FP7 program)  +
SynonymBioSample Database at the EBI  +, BioSample Database  +, BioSD - BioSample Database  +, BioSD at EBI  +, BioSamples database  +, BioSamples Database at EBI  +, EBI BioSample Database  +, and BioSamples  +
UsesResource:European Nucleotide Archive  +, Resource:PRIDE  +, Resource:ArrayExpress  +, Resource:ENCODE: Encyclopedia of DNA Elements  +, Resource:Coriell Institute for Medical Research  +, Resource:1000 Genomes: A Deep Catalog of Human Genetic Variation  +, Resource:International HapMap Project  +, and Resource:International Mouse Strain Resource  +
XrefOMICS_01025  +