1. The Protein Identifier Cross-Reference (PICR) service

2. Overview • The problem… • What is PICR? • Access via web and web services

3. -No direct comparison of the results can be done. -Both groups used different Protein DB to report their results. The problem… • Protein list A • (DB Search vs. IPI) • IPI000001 • IPI000002 • IPI000003 • … • Protein list B • (DB Search vs. UniProt) • P00001 • P00002 • P00003 • …

4. The problem… • -No direct comparison of the results can be done. • -Both groups used different Protein DB to report their results. • Protein list A • (DB Search vs. IPI) • IPI000001 • IPI000002 • IPI000003 • … • Protein list B • (DB Search vs. UniProt) • P00001 • P00002 • P00003 • … We would need to use the PICR tool to be able to make a direct comparison

5. Databases are all different

6. Databases evolve

7. Merging datasets to a common identifier space Finding all aliases/synonyms for an identifier (data integration – submissions!) Mapping from secondary IDs to more recent primary IDs (data “freshness”) Preparing data sets for specific tools Querying in various primary databases (data format requirements) Why do you need ID mapping

8. The basic problem: the same protein sequence is referred to by multiple accession numbers assigned by multiple databases. No universal identifier scheme Redundant databases – multiple identifiers for the same sequence in the same database Unstable identifiers (ex: gi numbers) Obsolete and deleted identifiers (hypothetical proteins) Different production cycles for major databases Tools exist, but are limited in important their database and species coverage and in their usability and availability. Protein identifier mapping is hard

9. PICR Home Page BLAST functionality for protein fragments Limit search by taxonomy (pessimistic) Submit accessions OR sequences (FASTA) with 500 entry interactive limit (no batch limit) Choose to return all mappings or only active ones Select output format Select one or many databases to map to in one request Run search

10. Logical xref (hyperlinked) Secondary Identifier Active xref (hyperlinked) Inactive xref PICR Result Page – simple view

11. PICR Result Page – detailed view

12. PICR Result Page – XLS view

13. PICR services • PICR offers both SOAP and REST web service interfaces. • Documentation is available online: • SOAP: http://www.ebi.ac.uk/Tools/picr/WSDLDocumentation.do • REST: http://www.ebi.ac.uk/Tools/picr/RESTDocumentation.do • Sample client code and URL examples are provided from the PICR website.

14. Do you want to know more? Wein et al., NAR, 2012

15. Questions?