02363nas a2200301   4500000000100000000000100001008004100002260000900043653002300052653002000075653003600095653001100131653001300142100001600155700002000171700001800191700001700209700001700226700002200243700001700265700001600282700001900298245009100317300001200408490000900420520161800429022001402047       2022                            d  c202210aDatabases, Factual10aKnowledge Bases10aMetabolic Networks and Pathways10aPlants10aProteins1 aParul Gupta1 aSushma Naithani1 aJustin Preece1 aSunghwan Kim1 aTiejun Cheng1 aPeter D'Eustachio1 aJustin Elser1 aEvan Bolton1 aPankaj Jaiswal00aPlant Reactome and PubChem: The Plant Pathway and (Bio)Chemical Entity Knowledgebases.  a511-5250 v24433 a<p>Plant Reactome (https://plantreactome.gramene.org) and PubChem ( https://pubchem.ncbi.nlm.nih.gov ) are two reference data portals and resources for curated plant pathways, small molecules, metabolites, gene products, and macromolecular interactions. Plant Reactome knowledgebase, a conceptual plant pathway network, is built by biocuration and integrating (bio)chemical entities, gene products, and macromolecular interactions. It provides manually curated pathways for the reference species Oryza sativa (rice) and gene orthology-based projections that extend pathway knowledge to 106 plant species. Currently, it hosts 320 reference pathways for plant metabolism, hormone signaling, transport, genetic regulation, plant organ development and differentiation, and biotic and abiotic stress responses. In addition to the pathway browsing and search functions, the Plant Reactome provides the analysis tools for pathway comparison between reference and projected species, pathway enrichment in gene expression data, and overlay of gene-gene interaction data on pathways. PubChem, a popular reference database of (bio)chemical entities, provides information on small molecules and other types of chemical entities, such as siRNAs, miRNAs, lipids, carbohydrates, and chemically modified nucleotides. The data in PubChem is collected from hundreds of data sources, including Plant Reactome. This chapter provides a brief overview of the Plant Reactome and the PubChem knowledgebases, their association to other public resources providing accessory information, and how users can readily access the contents.</p>
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