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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 samples. Physical samples may also be available for further study from suppliers.

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.

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)
  • direct submissions (2,344 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
Parent Organization: Resource:European Bioinformatics Institute
Supporting Agency: Resource:European Molecular Biology Laboratory; Heidelberg; Germany, European Commission, (CAGEKID, ENGAGE from FP7 program)
Related to: Resource:NCBI BioSample, Resource:European Nucleotide Archive, Resource:PRIDE, Resource:ArrayExpress Archive, 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, Resource:OMICtools
Resource Type(s): Database, Biomaterial supply resource, Cell repository, Biospecimen repository
Keywords: Cell line, Cell, Nucleotide, Sequencing, Proteomics, Peptide, Protein, Genomics, Gene expression, Biological sample, Molecular, Gold standard or authority, sequence, structure, Cell line, Topical portal, aggregator
Grant: HEALTH-F4-2010-241669, HEALTH-F4-2007-201413
Abbreviation: BioSD
Resource: Resource
URL: http://www.ebi.ac.uk/biosamples/
PMID: PMID 22096232
Publication link: http://nar.oxfordjournals.org/content/40/D1/D64.abstract?ijkey=374e1923695afc02d016814b186e42cd500c3cc5&keytype2=tf_ipsecsha
Related application: Research
Availability: The community can contribute to this resource
Id: nlx_143930
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

This page uses this default form:Resource

Xref: OMICS_01025

Contributors

Aarnaud, Akash, Ccdbuser



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Facts about Resource:BioSample Database at EBIRDF feed
AbbrevBioSD  +
AvailabilityThe community can contribute to this resource  +
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 samples. Physical samples may also be available for further study from suppliers.

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.

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)
  • direct submissions (2,344 samples) ples)
  • direct submissions (2,344 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  +, Biomaterial supply resource  +, Cell repository  +, and Biospecimen repository  +
Idnlx_143930  +
Is part ofResource:European Bioinformatics Institute  +
KeywordsCell line  +, Cell  +, Nucleotide  +, Sequencing  +, Proteomics  +, Peptide  +, Protein  +, Genomics  +, Gene expression  +, Biological sample  +, Molecular  +, Gold standard or authority  +, Sequence  +, Structure  +, Topical portal  +, and Aggregator  +
LabelResource:BioSample Database at EBI  +
ModifiedDate1 April 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  +, Resource:European Nucleotide Archive  +, Resource:PRIDE  +, Resource:ArrayExpress Archive  +, 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  +, and Resource:OMICtools  +
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  +