1 / 27

Metabolism Training Web Service for Microme: CEA/LABGeM Partnership Meeting

A dedicated web service for metabolism training by the LABGeM team, focusing on gene-protein relationships, metabolic workflows, data retrieval, and more. Explore various tools and services offered, including automated pipelines, complex generators, and genome interactions. Stay updated with the latest integration processes and partner tools. Join this training session to enhance your knowledge in genomics and metabolism. Interact with experts like David Vallenet, François Le Fèvre, and Maria Jose Lopez, among others. Visit the main entry point at http://www.genoscope.cns.fr/microme/ for more details.

nimrod
Download Presentation

Metabolism Training Web Service for Microme: CEA/LABGeM Partnership Meeting

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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. MicromePartners’s needs WEB SERVICE CEA / LABGeM partner - Microme Training

  3. CEA Accessible Data / Information Old Current Next 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 Genomic MicroScope Proteomic PkGDB MicroDb Metabolic Modelic Phenotypic MicroScope Web Service MicroCyc Web CEA / LABGeM partner - Microme Training

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

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

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

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

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

  12. 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

  13. 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

  14. 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

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

  16. Growth phenotype CEA / LABGeM partner - Microme Training

  17. Experiment CEA / LABGeM partner - Microme Training

  18. Growth Phenotype CEA / LABGeM partner - Microme Training

  19. Medium CEA / LABGeM partner - Microme Training

  20. Strain CEA / LABGeM partner - Microme Training

  21. OUTLINE CEA / LABGeM partner - Microme Training

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

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

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

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

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

  27. Training Synthesis Gene Prediction G Operon Prediction Pathway Evol P GPR BBH Patho Logic C Generator GAP Filing GPR Validator Micro Reactor P C E M C Validator Model Generator GPR CANOE Pathway Validator R Retro BioZ C Pathway Discovery

More Related