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kate dreher curator PMN/TAIR

PlantCyc, AraCyc, PoplarCyc and more . . . Building databases and connecting to researchers at the Plant Metabolic Network. kate dreher curator PMN/TAIR. Introducing the PMN. The PMN is a network of plant metabolic pathway databases and researchers

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kate dreher curator PMN/TAIR

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  1. PlantCyc, AraCyc, PoplarCyc and more . . . Building databases and connecting to researchers at the Plant Metabolic Network kate dreher curator PMN/TAIR

  2. Introducing the PMN • The PMN is a network of plant metabolic pathway databases and researchers • Funded by the National Science Foundation • Major goals: • Create metabolic pathway databases • for individual plant species • e.g. AraCyc (Arabidopsis thaliana) • combining data for all plant species - PlantCyc • Create a computational prediction “pipeline”: • Start with protein sequences for a specific plant species . . . • End with a comprehensive set of predicted metabolic pathways • Create a website for researchers working on plant metabolism • PMN website: www.plantcyc.org

  3. PMN databases • Current PMN databases: PlantCyc, AraCyc, PoplarCyc • Coming soon: databases for wine grape, maize, cassava, Selaginella, and more . . . • Other plant databases accessible from the PMN: ** Significant numbers of genes from these databases have been integrated into PlantCyc P60. Connecting the Solaneceae genome to the metabolic networks via SolCyc and MetaCyc. Anuradha Pujar

  4. PMN data types

  5. PMN data types Evidence Codes Upstream pathway Reaction Regulation Pathway Enzyme Gene Compound

  6. PMN database content statistics • New PMN release . . . almost here! • Increased data content • shhh . . . sneak preview at pmn.plantcyc.org! • Upgraded Pathway Tools software (version 12.5 -> version 14.0)

  7. Searching in PMN databases • PMN quick search bar • Pathway Tools quick search bar choline choline

  8. Searching in PMN databases

  9. Specific search pages

  10. Additional search options

  11. Comparing across species • Use general Comparative Analyses tools

  12. Visualizing OMICs data • Overlay “pre-cleaned” data sets on a metabolic map • Gene transcription data • Proteomic data • Metabolomic data • Only available for single-species databases, not PlantCyc • Demonstrations available at conference . . . please see me! Upload a data file

  13. Visualizing OMICs data

  14. Visualizing OMICs data

  15. Data and software downloads • Install a local copy of the Pathway Tools software

  16. Pathway Tools – desktop version • Desktop version offers additional features • Create new pathways • Modify existing pathways • Generate and work with groups of items • Perform metabolite tracing on metabolic map • See Omics Viewer results on pathway pages • Demonstrations available throughout the conference

  17. PMN data • The PMN houses a large quantity of data, • Numerous previously identified enzymes and pathways are missing • Exciting new discoveries are continuously made • Plant genome sequence data is becoming available at a rapid rate • How do we bring this information in? but . . .

  18. You! You! Database growth at the PMN • Manual curation • Curators read and enter information from published journal articles • Researchers contact the PMN directly • Computational database generation • Automated pipeline • Predicted protein sequences for species X -> Predict enzymatic functions • Predicted enzymatic functions -> Map to reactions and pathways in PlantCyc • Predict an overall set of metabolic pathways with associated enzymes for species X • Manual validation • Remove incorrectly predicted pathways • Create or import relevant pathways that were not predicted • Add references, data, and evidence codes

  19. Building better databases together • To submit data, report an error, or volunteer to help validate . . . • Send an e-mail: curator@plantcyc.org • Use data submission “tools” • Meet with me individually at this conference • P2,4,12,14,18,20,22,24,26,30,34,36,38,40,44,48,50,54,56,62,74,84,92,9,21,25,29,31,33,39,41,43,5157,59,63,65,75,81,87,89,91,93 • CS30,15,32,27,28,13,14,7,4,12, 31, 35, 18, 36, 21, 1, 16, 11, 6, • PS IVb, Vb, VIa, VIIa, VIIIa, VIIIb

  20. Building better databases together • Details are very, very welcome!! • Reactions: • All co-factors, co-substrates, etc. • EC suggestions – partial or full • Compounds • Structure – visual representation / compound file (e.g. mol file) • Synonyms • Unique IDs (e.g. ChEBI, CAS, KEGG) • Enzymes • Unique IDs (e.g. At2g46480, UniProt, Genbank) • Specific reactions catalyzed

  21. Community gratitude • We thank you publicly!

  22. Plant metabolic NETWORKING • Please use our data • Please use our tools • Please help us to improve our databases! • Please contact us if we can be of any help! curator@plantcyc.org www.plantcyc.org special pre-release sneak preview: pmn.plantcyc.org

  23. Sue Rhee (PI) Peifen Zhang (Director) PMN Acknowledgements Peifen Zhang (Director) Sue Rhee (PI) Eva Huala (Co-PI) Current Curators: kate dreher Curators: recent alumni: - A. S. Karthikeyan (curator) - Christophe Tissier (curator) - Hartmut Foerster (curator) Collaborators: - Peter Karp (SRI) - Ron Caspi (SRI) - Suzanne Paley (SRI) - SRI Tech Team - Lukas Mueller (SGN) - Anuradha Pujar (SGN) - Gramene and MedicCyc Current Tech Team Members: - Bob Muller (Manager) - Larry Ploetz (Sys. Administrator) - Cynthia Lee - Shanker Singh - Chris Wilks Tech Team: recent alumni - Raymond Chetty - Anjo Chi - Vanessa Kirkup - Tom Meyer

  24. Data and software downloads • Desktop version offers additional features • Create new pathways • Modify existing pathways

  25. arogenate dehydratase prephenate aminotransferase chorismate mutase 5.4.99.5 4.2.1.91 2.6.1.79 chorismate prephenate L-arogenate L-phenylalanine chorismate mutase Pv1234.56.a How does the PMN acquire new data? Phaseolus vulgaris MetaCyc / PlantCyc ANNOTATED GENOME DNA sequences Gene calls Pv1234.56.a PathoLogic Gene functions chorismate mutase Single species database PhaseolusCyc

  26. Additional search options • experimental support • all kingdoms • experimental or computational support • plants only

  27. How can you put the PMN to work for you? • Learn background information about particular metabolic pathways • Create customized metabolic data sets • Compare metabolism across plant species • Analyze experimental OMICs data in a metabolic context • Manipulate and study data offline • Create new metabolic pathway databases

  28. Community data submission

  29. Comparing across species • Use Metabolic Map

  30. Comparing across species

  31. Additional search options

  32. Data and software downloads • Get pathway data sets from pathway pages

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