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PMID: 21785143 Published · epublish English Journal Article Research Support, Non-U.S. Gov't

The InterPro BioMart: federated query and web service access to the InterPro Resource.

Database : the journal of biological databases and curation ·Vol. 2011 ·2011-00-00 ·Pages bar033

Jones P, Binns D, McMenamin C, McAnulla C, Hunter S

Abstract

The InterPro BioMart provides users with query-optimized access to predictions of family classification, protein domains and functional sites, based on a broad spectrum of integrated computational models ('signatures') that are generated by the InterPro member databases: Gene3D, HAMAP, PANTHER, Pfam, PIRSF, PRINTS, ProDom, PROSITE, SMART, SUPERFAMILY and TIGRFAMs. These predictions are provided for all protein sequences from both the UniProt Knowledge Base and the UniParc protein sequence archive. The InterPro BioMart is supplementary to the primary InterPro web interface (http://www.ebi.ac.uk/interpro), providing a web service and the ability to build complex, custom queries that can efficiently return thousands of rows of data in a variety of formats. This article describes the information available from the InterPro BioMart and illustrates its utility with examples of how to build queries that return useful biological information. Database URL: http://www.ebi.ac.uk/interpro/biomart/martview.

MeSH Terms
Access to Information Databases, Protein Humans Internet Metabolic Networks and Pathways Search Engine
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Jones Philip
EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. pjones@ebi.ac.uk
Binns David
McMenamin Conor
McAnulla Craig
Hunter Sarah
References (22)
22 references, click to expand
  1. TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D260-4 PMID: 17151080
  2. The Pfam protein families database.
    Nucleic Acids Res. 2010 Jan;38(Database issue):D211-22 PMID: 19920124
  3. InterPro: the integrative protein signature database.
    Nucleic Acids Res. 2009 Jan;37(Database issue):D211-5 PMID: 18940856
  4. Integrating biological data--the Distributed Annotation System.
    BMC Bioinformatics. 2008 Jul 22;9 Suppl 8:S3 PMID: 18673527
  5. The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases.
    BMC Bioinformatics. 2007 Oct 18;8:401 PMID: 17945017
  6. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
    Nat Genet. 2000 May;25(1):25-9 PMID: 10802651
  7. SMART 6: recent updates and new developments.
    Nucleic Acids Res. 2009 Jan;37(Database issue):D229-32 PMID: 18978020
  8. HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot.
    Nucleic Acids Res. 2009 Jan;37(Database issue):D471-8 PMID: 18849571
  9. Gene3D: merging structure and function for a Thousand genomes.
    Nucleic Acids Res. 2010 Jan;38(Database issue):D296-300 PMID: 19906693
  10. BioMart: a data federation framework for large collaborative projects.
    Database (Oxford). 2011 Sep 19;2011:bar038 PMID: 21930506
  11. PROSITE, a protein domain database for functional characterization and annotation.
    Nucleic Acids Res. 2010 Jan;38(Database issue):D161-6 PMID: 19858104
  12. Ongoing and future developments at the Universal Protein Resource.
    Nucleic Acids Res. 2011 Jan;39(Database issue):D214-9 PMID: 21051339
  13. SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny.
    Nucleic Acids Res. 2009 Jan;37(Database issue):D380-6 PMID: 19036790
  14. ProDom: automated clustering of homologous domains.
    Brief Bioinform. 2002 Sep;3(3):246-51 PMID: 12230033
  15. PANTHER: a library of protein families and subfamilies indexed by function.
    Genome Res. 2003 Sep;13(9):2129-41 PMID: 12952881
  16. Ensembl BioMarts: a hub for data retrieval across taxonomic space.
    Database (Oxford). 2011 Jul 23;2011:bar030 PMID: 21785142
  17. BioMart Central Portal: an open database network for the biological community.
    Database (Oxford). 2011 Sep 18;2011:bar041 PMID: 21930507
  18. PIRSF: family classification system at the Protein Information Resource.
    Nucleic Acids Res. 2004 Jan 1;32(Database issue):D112-4 PMID: 14681371
  19. Reactome: a database of reactions, pathways and biological processes.
    Nucleic Acids Res. 2011 Jan;39(Database issue):D691-7 PMID: 21067998
  20. The Reactome BioMart.
    Database (Oxford). 2011 Oct 19;2011:bar031 PMID: 22012987
  21. BioMart--biological queries made easy.
    BMC Genomics. 2009 Jan 14;10:22 PMID: 19144180
  22. Ensembl 2011.
    Nucleic Acids Res. 2011 Jan;39(Database issue):D800-6 PMID: 21045057
Article Info
Journal
Database : the journal of biological databases and curation
Abbr.
Database (Oxford)
ISSN
1758-0463
DOI
10.1093/database/bar033
Email
pjones@ebi.ac.uk
Published
2011-00-00
Epub
2011-00-23
Pages
bar033
Language
English
Region
England
NLM ID
101517697
PMCID
PMC3170169
Subset
IM
Grants
Biotechnology and Biological Sciences Research Council · BB/F010508/1 · United Kingdom
External Links
PubMed source DOI: 10.1093/database/bar033 PMC Full Text View journal details
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