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News
January 2009: Addition of SEGUIDs

We have implemented the SEGUID algorithm to generate sequence-based unique identifiers, as described in Babnigg, 2006.

January 2009: New databases and bugfixes

We have added the KIPO database as well as several ENSEMBL genome databases to the mapping algorithm. We have also improved the PICR codebase to make it more robust. PICR has been the victim of its own success in recent months and has had problems coping with the demands put on the web application. These problems should now be resolved.

July 2007: Updated CSV and XLS formats

The CSV and XLS output formats have been improved to be more usable and to fit into size restrictions imposed by the Microsoft Excel format. If you are submitting large data sets to be mapped, we recommend choosing the XLS format for batch downloads.

June 2007: Added functionality

We have added a new output format for mapping results. You may now save your results as a Microsoft Excel workbook (XLS file). This fine can be opened in MS Excel or Open Office. This is still experimental, so please contact us if you are experiencing problems.

June 2007: Added functionality

You may now submit an unilmited number of protein identifiers or sequences. Please be aware that if you submit more than 500 items at one time, you will be prompted to enter your email address and a notification will be emailed to you when your job is done. You will then be able to download a CSV file containing your results.

April 2007: BETA Release

A BETA version of the Protein Identifier Cross-Referencing (PICR) service has now been released and we invite your feedback! Please email us any questions or comments you may have.

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PICR - Protein Identifier Cross-Reference Service


Input Data
Output Parameters
View results as:


Enter one or more valid protein accessions (one per line) and click on on submit. Alternatively, enter one or more protein sequences in FASTA format and select "Protein Sequence" as input type. You may also upload a file that contains either protein identifiers (one per line) or protein sequences in FASTA format. The file must be less than 2MB in size.
Input Parameters
If you wish to limit your query to an organism that is not in the menu above, enter a partial organism name to query the OLS:


Mapping Databases Include mappings to the following databases (if available):

   


Project description

  • 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.

    The Protein Identifier Cross-Reference (PICR) service is 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 84 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.

Documentation: Downloads:
  • The PICR software and the SOAP webservice are both freely available for use. If you find them useful for your own applications, we would be grateful for a mention similar to the following:

    "Uses the EBI PICR <http://www.ebi.ac.uk/Tools/picr>."

    where both the image and URL are hyperlinked to the PICR homepage.


  • Java code examples are available to download here: http://www.ebi.ac.uk/Tools/picr/client/picr_demo.zip
Mailing lists, bug reports
Acknowledgements:

  • PICR is supported through BBSRC iSPIDER.
iSPIDER BBSRC
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