Accessing information in plant metabolic pathway databases at the PMN, Gramene, and SGN Part I: Contents, Search Strategies, and Data Sharing Opportunities kate dreher, PMN / TAIR - www.plantcyc.org Part II: Pathway Networks for Cereals Palitha Dharmawardhana, Gramene - www.gramene.org/pathway Part III: Using the desktop version of the Pathway Tools software Lukas Mueller, SGN – solcyc.solgenomics.net
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Accessing information in plant metabolic pathway databases ...€¦ · BioCyc / Pathway Tools databases pMultiple data providers: nSRI International nPlant Metabolic Network (PMN)
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Accessing information inplant metabolic pathway databases at
the PMN, Gramene, and SGN
Part I: Contents, Search Strategies, and Data Sharing Opportunitieskate dreher, PMN / TAIR - www.plantcyc.org
Part II: Pathway Networks for CerealsPalitha Dharmawardhana, Gramene - www.gramene.org/pathway
Part III: Using the desktop version of the Pathway Tools softwareLukas Mueller, SGN – solcyc.solgenomics.net
Part I overviewp Introduction
p Data
p Search tools
p Data submissions
p Acknowledgments
p More examples
Plant metabolism
p Plants provide crucial benefits to the ecosystem and humanity
p A better understanding of plant metabolism may contribute to:
n More nutritious foodsn New medicinesn More pest-resistant plantsn Higher photosynthetic capacity and yield in cropsn Better biofuel feedstocksn Improved industrial inputs (e.g. oils, fibers, etc.)n . . . many more applications
p These efforts require access to high quality plant metabolism data
Plant metabolic databases
p Capture and organize published data
p Make metabolic predictions for “new” species
p Facilitate data analysis
p Focus on different aspects of metabolismn Pathways
p KEGGp Reactomep BioCyc / Pathway tools family
BioCyc / Pathway Tools databases
p Multiple data providers:n SRI Internationaln Plant Metabolic Network (PMN)n Gramenen Sol Genomics Network (SGN)
p One software package:n Pathway Toolsn SRI International
p Common set of data typesp Common toolsp Common display modes
n Predict plant metabolic pathways for many species with sequence data
n Solicit help from experts who work on different species for pathway validation
p Remove mis-predictionsp Add missed pathways
n Potential candidates:p wine grapep cassavap Selaginella moellendorfiip moss p eucalyptusp sunflowerp apple p cowpea p ice plantp papayap YOUR FAVORITE SPECIES??