02583nas a2200457   4500000000100000000000100001008004100002260001600043653002600059653002300085653001300108653003600121653001100157653001800168653002400186653002000210653002800230653001600258100002000274700001800294700002200312700001600334700002400350700002700374700001600401700002100417700001700438700001600455700001600471700002000487700002100507700001800528700001600546700001900562245007600581856003900657300001600696490000700712520139200719022001402111       2018                            d  c2017 Jan 0410aComputational Biology10aDatabases, Genetic10aGenomics10aMetabolic Networks and Pathways10aPlants10aSearch Engine10aSignal Transduction10aSystems Biology10aUser-Computer Interface10aWeb Browser1 aSushma Naithani1 aJustin Preece1 aPeter D'Eustachio1 aParul Gupta1 aVindhya Amarasinghe1 aPalitha Dharmawardhana1 aGuanming Wu1 aAntonio Fabregat1 aJustin Elser1 aJoel Weiser1 aMaria Keays1 aAlfonso Fuentes1 aRobert Petryszak1 aLincoln Stein1 aDoreen Ware1 aPankaj Jaiswal00aPlant Reactome: a resource for plant pathways and comparative analysis.  uhttps://doi.org/10.1093/nar/gkw932  aD1029-D10390 v453 aPlant Reactome (http://plantreactome.gramene.org/) is a free, open-source, curated plant pathway database portal, provided as part of the Gramene project. The database provides intuitive bioinformatics tools for the visualization, analysis and interpretation of pathway knowledge to support genome annotation, genome analysis, modeling, systems biology, basic research and education. Plant Reactome employs the structural framework of a plant cell to show metabolic, transport, genetic, developmental and signaling pathways. We manually curate molecular details of pathways in these domains for reference species Oryza sativa (rice) supported by published literature and annotation of well-characterized genes. Two hundred twenty-two rice pathways, 1025 reactions associated with 1173 proteins, 907 small molecules and 256 literature references have been curated to date. These reference annotations were used to project pathways for 62 model, crop and evolutionarily significant plant species based on gene homology. Database users can search and browse various components of the database, visualize curated baseline expression of pathway-associated genes provided by the Expression Atlas and upload and analyze their Omics datasets. The database also offers data access via Application Programming Interfaces (APIs) and in various standardized pathway formats, such as SBML and BioPAX.  a1362-4962