TY - JOUR KW - Computational Biology KW - Databases, Genetic KW - Gene Regulatory Networks KW - Genomics KW - Humans KW - Metabolic Networks and Pathways KW - Metabolomics KW - Plants KW - Proteomics KW - Signal Transduction KW - Web Browser AU - Sushma Naithani AU - Parul Gupta AU - Justin Preece AU - Peter D'Eustachio AU - Justin Elser AU - Priyanka Garg AU - Daemon Dikeman AU - Jason Kiff AU - Justin Cook AU - Andrew Olson AU - Sharon Wei AU - Marcela Tello-Ruiz AU - Antonio Mundo AU - Alfonso Munoz-Pomer AU - Suhaib Mohammed AU - Tiejun Cheng AU - Evan Bolton AU - Irene Papatheodorou AU - Lincoln Stein AU - Doreen Ware AU - Pankaj Jaiswal AB -

Plant Reactome (https://plantreactome.gramene.org) is an open-source, comparative plant pathway knowledgebase of the Gramene project. It uses Oryza sativa (rice) as a reference species for manual curation of pathways and extends pathway knowledge to another 82 plant species via gene-orthology projection using the Reactome data model and framework. It currently hosts 298 reference pathways, including metabolic and transport pathways, transcriptional networks, hormone signaling pathways, and plant developmental processes. In addition to browsing plant pathways, users can upload and analyze their omics data, such as the gene-expression data, and overlay curated or experimental gene-gene interaction data to extend pathway knowledge. The curation team actively engages researchers and students on gene and pathway curation by offering workshops and online tutorials. The Plant Reactome supports, implements and collaborates with the wider community to make data and tools related to genes, genomes, and pathways Findable, Accessible, Interoperable and Re-usable (FAIR).

BT - Nucleic Acids Res DA - 2020 Jan 08 DO - 10.1093/nar/gkz996 IS - D1 J2 - Nucleic Acids Res LA - eng N2 -

Plant Reactome (https://plantreactome.gramene.org) is an open-source, comparative plant pathway knowledgebase of the Gramene project. It uses Oryza sativa (rice) as a reference species for manual curation of pathways and extends pathway knowledge to another 82 plant species via gene-orthology projection using the Reactome data model and framework. It currently hosts 298 reference pathways, including metabolic and transport pathways, transcriptional networks, hormone signaling pathways, and plant developmental processes. In addition to browsing plant pathways, users can upload and analyze their omics data, such as the gene-expression data, and overlay curated or experimental gene-gene interaction data to extend pathway knowledge. The curation team actively engages researchers and students on gene and pathway curation by offering workshops and online tutorials. The Plant Reactome supports, implements and collaborates with the wider community to make data and tools related to genes, genomes, and pathways Findable, Accessible, Interoperable and Re-usable (FAIR).

PY - 2020 SP - D1093 EP - D1103 T2 - Nucleic Acids Res TI - Plant Reactome: a knowledgebase and resource for comparative pathway analysis. VL - 48 SN - 1362-4962 ER -