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Comprehensive Guide to PSICQUIC Data Integration

Explore PSICQUIC, a standardized query interface for molecular interaction data integration. Learn about the simplified tabular format MITAB 2.5, PSICQUIC Query Language (MIQL), SOAP and REST interfaces, and more. Discover how to access and leverage molecular interactions from various databases easily.

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Comprehensive Guide to PSICQUIC Data Integration

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  1. Data Integration:PSICQUIC Henning Hermjakob May 2010

  2. Client PSICQUIC servers PSICQUIC PSICQUIC PSICQUIC Interaction databases Annotation ….…. …..... ….…. …..... Publications Observation Sample

  3. MITAB • The PSI MI XML format is full-featured, but complex • On frequent user request, we developed a simplified tabular format, MITAB 2.5 • 15 well-defined columns to represent a molecular interaction in a database independent manner • Now widely implemented http://www.psidev.info/MI

  4. PSICQUIC:The PSI Common Query InterfaCe • Common computational interface for querying molecular interaction databases • Widely implemented by independent interaction data resources • Simple interface, open source server implementation exists, can be “fed” from a tab-delimited file => easy to provide data • Not limited to protein-protein interactions, also e.g. • Drug-target interactions • Simplified pathway data

  5. PSICQUIC:Simple PSICQUIC viewer http://www.ebi.ac.uk/Tools/webservices/psicquic/view

  6. PSICQUIC: Pointing to other resources http://www.ebi.ac.uk/intact

  7. PSICQUIC: Pointing to other resources http://www.ebi.ac.uk/intact

  8. PSICQUIC:Overlay of molecular interactions on Reactome pathways (beta)

  9. Integrating standards into EnCore/EnVision Molecular interactions service Preview

  10. PSICQUIC Query Language:MIQL • Based on Lucene, with specific field names • Example: ppx AND species:"Escherichia coli" • Precise field query: taxidA, taxidB • Order-independent: • species == taxidA OR taxidB • species:9606 • returns interactions with at least one human protein • (taxidA:9606 AND NOT taxidB:9606) OR (taxidB:9606 AND NOT taxidA:9606) • returns all mixed species interactions (mostly experimental rather than biological)

  11. PSICQUIC Query Language:MIQL

  12. PSICQUIC: SOAP and REST interfaces http://code.google.com/p/psicquic/

  13. PSICQUIC: The challenge FROM: TO:

  14. Thank you! Questions? • ALL PSI CONTRIBUTORS! • ENFIN partners: • Bernd Brandt (IBIVU) • Christine Orengo (UCL) • Andrew Clegg (UCL) • Ioannis Xenarios (SIB) • Heinz Stockinger (SIB) • Jaak Vilo (QURETEC) • Jüri Reimand (QURETEC) • Gianni Cesareni (UNITOR) • Arnaud Ceol (UNITOR) • James Procter (UNIVDUN) • Ana Rojas Mendoza (CNIO) Funding • EU FW6 Enfin • EU FW7 PSIMEx

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