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Training Meeting Microme – Marseilles - 28/03/2012.

Web Service Dedicated to Metabolism. Training Meeting Microme – Marseilles - 28/03/2012. David Vallenet , François Le Fèvre , Damien Mornico , Maria Jose Lopez, Eugenio Belda , Claudine Médigue. Laboratory of Bioinformatic Analysis in Genomic and Metabolism (LABGeM team)

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Training Meeting Microme – Marseilles - 28/03/2012.

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  1. Web Service Dedicated to Metabolism Training Meeting Microme – Marseilles - 28/03/2012. David Vallenet, François Le Fèvre, Damien Mornico, Maria Jose Lopez, Eugenio Belda, Claudine Médigue Laboratory of Bioinformatic Analysis in Genomic and Metabolism (LABGeM team) CEA/DSV/IG/Genoscope & CNRS UMR8030

  2. Some of the Microme‘s needs WEB SERVICE CEA / LABGeM partner - Microme Training

  3. CEA Accessible Data / Information • & EXPERT CURATION • PREDICTED CEA / LABGeM partner - Microme Training

  4. GPR USE CASE Web service to retrieve the Gene Protein Relationship CEA / LABGeM partner - Microme Training

  5. Metabolic Workflow Automatic pipeline pkgdb PathoLogic Formatter Complexes Generator MicroDB Generator MicroCyc PGDB Expert validation MicroDb CEA / LABGeM partner - Microme Training

  6. Data Retrieval Layer MicroScope PkGDB MicroDb MicroScope Web Service MicroCyc Web CEA / LABGeM partner - Microme Training

  7. Application Design • UML specification • Automatic generation • Back end • Persistence • Entity • Services • Technologies • Java (Hibernate/Spring) • Maven • AndroMDA http://www.andromda.org/docs/index.html CEA / LABGeM partner - Microme Training

  8. From PGDB to reaction CEA / LABGeM partner - Microme Training

  9. Gene Protein Relationship CEA / LABGeM partner - Microme Training

  10. Protein Reaction Relationship CEA / LABGeM partner - Microme Training

  11. Available Service 1.0 CEA / LABGeM partner - Microme Training

  12. Accessible Genomes Hamap code Microscope id BioCyc version CEA / LABGeM partner - Microme Training

  13. Gene Details Id MicroScope Id MicroCyc Id UniProt Id RefSeq • Evidence Genomic • Automatic: Transfert of annotation • Validated: Human Expert Curation CEA / LABGeM partner - Microme Training

  14. Complex Encoding <ns:gprSimpleVOxsi:type="ns:GprSimpleVO"> <ns:associatedGenes> <ns:geneSimpleVOxsi:type="ns:GeneSimpleVO"><ns:accession1>GO145023</ns:accession1> <ns:frame>G2NI-1492</ns:frame> <ns:id>14363</ns:id> <ns:shortName>linC</ns:shortName> </ns:geneSimpleVO> <ns:geneSimpleVOxsi:type="ns:GeneSimpleVO"> <ns:accession1>GO145024</ns:accession1> <ns:frame>G2NI-1493</ns:frame> <ns:id>14364</ns:id> <ns:shortName>linD</ns:shortName> </ns:geneSimpleVO></ns:associatedGenes> <ns:catalyzedReactionCommonName>ACIAD1575_linCD</ns:catalyzedReactionCommonName><ns:ecNumber>1.14.99.28</ns:ecNumber><ns:frameReaction>LINALOOL-8-MONOOXYGENASE-RXN</ns:frameReaction><ns:gpr>G2NI-1492</ns:gpr><ns:gprEvidence>validated</ns:gprEvidence><ns:reactionCommonName>linalool 8-monooxygenase</ns:reactionCommonName></ns:gprSimpleVO> Id MicroCyc G(P)R Evidence GO145023 RXN0-2606 GO145024 CEA / LABGeM partner - Microme Training

  15. Isozyme Encoding or putative Complex? <ns:gprSimpleVOxsi:type="ns:GprSimpleVO"> <ns:ecNumber>NIL</ns:ecNumber> <ns:frameReaction>DISULFOXRED-RXN</ns:frameReaction> <ns:gpr>GEL-4936@EB7Av1_1080005_dsbA$GO3290285</ns:gpr> <ns:gprEvidence>predicted</ns:gprEvidence></ns:gprSimpleVO><ns:gprSimpleVOxsi:type="ns:GprSimpleVO"> <ns:ecNumber>NIL</ns:ecNumber> <ns:frameReaction>DISULFOXRED-RXN</ns:frameReaction> <ns:gpr>GEL-1163@EB7Av1_90089_dsbC$GO3286552</ns:gpr> <ns:gprEvidence>predicted</ns:gprEvidence></ns:gprSimpleVO><ns:gprSimpleVOxsi:type="ns:GprSimpleVO"> <ns:ecNumber>NIL</ns:ecNumber> <ns:frameReaction>DISULFOXRED-RXN</ns:frameReaction> <ns:gpr>GEL-2576@EB7Av1_290029_dsbG$GO3287959</ns:gpr> <ns:gprEvidence>predicted</ns:gprEvidence></ns:gprSimpleVO> GO3290285 DISULFOXRED-RXN GO3286552 GO3286297 GO3290285 DISULFOXRED-RXN GO3286552 GO3286297 CEA / LABGeM partner - Microme Training

  16. BIOLOG DATA Storing and managing growth phenotype CEA / LABGeM partner - Microme Training

  17. Growth phenotype CEA / LABGeM partner - Microme Training

  18. Experiment CEA / LABGeM partner - Microme Training

  19. Growth Phenotype CEA / LABGeM partner - Microme Training

  20. Medium CEA / LABGeM partner - Microme Training

  21. Strain CEA / LABGeM partner - Microme Training

  22. OUTLINE CEA / LABGeM partner - Microme Training

  23. Other projects in development CEA / LABGeM partner - Microme Training

  24. Main Entry point http://www.genoscope.cns.fr/microme/ CEA / LABGeM partner - Microme Training

  25. Interactions Outlook & Open Questions MicroScope Microme Web Service Update Frequency? Integration Process ? GPRs Integration Process ? Partner Tools CEATools WebService / UI / Web CEA / LABGeM partner - Microme Training

  26. Training with webservice CEA / LABGeM partner - Microme Training

  27. Thanks for Interaction • ULB partner • Jacques van Helden • Didier Croes • Quentin Dacosta • Jonathan Verneau • CERTH partner • Christos Ouzounis • FotisPsomopoulos CEA / LABGeM partner - Microme Training

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