The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases

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.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 webcite.Biological data is being generated at an unparalleled rate and data analysis is becoming a key challenge in bioinformatics and systems biology. Two common tasks that are more difficult than they should be are identifier unification, where datasets from various sources must be merged together for analysis and identifier translation, where identifiers from one source (e.g. NCBI gi number) need to be converted to those from another source (e.g. Ensembl) so that they can be used in database specific tools and queries. A major hindrance to the effective implementation of those tasks is that data comes from multiple sources, each using a proprietary identifier sc