title: The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases.
abstract: BACKGROUND
  Each major protein database uses its own conventions when assigning protein identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins is a major challenge. This is a common problem when attempting to unify datasets that have been annotated with proteins from multiple data sources or querying data providers with one flavour of protein identifiers when the source database uses another. Partial solutions for protein identifier mapping exist but they are limited to specific species or techniques and to a very small number of databases. As a result, we have not found a solution that is generic enough and broad enough in mapping scope to suit our needs.
  
  
  RESULTS
  We have created the Protein Identifier Cross-Reference (PICR) service, a web application that provides interactive and programmatic (SOAP and REST) access to a mapping algorithm that uses the UniProt Archive (UniParc) as a data warehouse to offer protein cross-references based on 100% sequence identity to proteins from over 70 distinct source databases loaded into UniParc. Mappings can be limited by source database, taxonomic ID and activity status in the source database. Users can copy/paste or upload files containing protein identifiers or sequences in FASTA format to obtain mappings using the interactive interface. Search results can be viewed in simple or detailed HTML tables or downloaded as comma-separated values (CSV) or Microsoft Excel (XLS) files suitable for use in a local database or a spreadsheet. Alternatively, a SOAP interface is available to integrate PICR functionality in other applications, as is a lightweight REST interface.
  
  
  CONCLUSIONS
  We offer a publicly available service that can interactively map protein identifiers and protein sequences to the majority of commonly used protein databases. Programmatic access is available through a standards-compliant SOAP interface or a lightweight REST interface. The PICR interface, documentation and code examples are available at http://www.ebi.ac.uk/Tools/picr.
authors.affiliation: European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1QY, UK. rcote@ebi.ac.uk
authors.forename: Richard G
authors.initials: RG
authors.lastname: Côté
authors.forename: Philip
authors.initials: P
authors.lastname: Jones
authors.forename: Lennart
authors.initials: L
authors.lastname: Martens
authors.forename: Samuel
authors.initials: S
authors.lastname: Kerrien
authors.forename: Florian
authors.initials: F
authors.lastname: Reisinger
authors.forename: Quan
authors.initials: Q
authors.lastname: Lin
authors.forename: Rasko
authors.initials: R
authors.lastname: Leinonen
authors.forename: Rolf
authors.initials: R
authors.lastname: Apweiler
authors.forename: Henning
authors.initials: H
authors.lastname: Hermjakob
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D003628:Database Management Systems; D030562:Databases, Protein; D016247:Information Storage and Retrieval / Q000379:methods; D020407:Internet; D008969:Molecular Sequence Data; D011506:Proteins / Q000737:chemistry* / Q000145:classification*; D016415:Sequence Alignment / Q000379:methods; D020539:Sequence Analysis, Protein / Q000379:methods*; D014584:User-Computer Interface
chemical_list: D011506:Proteins