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Data Integration: PSICQUIC

Data Integration: PSICQUIC. Henning Hermjakob May 2010. Client. PSICQUIC servers. PSICQUIC. PSICQUIC. PSICQUIC. Interaction databases. Annotation. ….…. …. ….…. …. Publications. Observation. Sample. MITAB. The PSI MI XML format is full-featured, but complex

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Data Integration: PSICQUIC

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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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