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Review
. 2022:2443:511-525.
doi: 10.1007/978-1-0716-2067-0_27.

Plant Reactome and PubChem: The Plant Pathway and (Bio)Chemical Entity Knowledgebases

Parul Gupta  1 , Sushma Naithani  1 , Justin Preece  1 , Sunghwan Kim  2 , Tiejun Cheng  2 , Peter D'Eustachio  3 , Justin Elser  1 , Evan E Bolton  2 , Pankaj Jaiswal  4
Affiliations
Review

Plant Reactome and PubChem: The Plant Pathway and (Bio)Chemical Entity Knowledgebases

Parul Gupta et al. Methods Mol Biol. 2022.

Abstract

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.

Keywords: Biochemical entities; Comparative pathway analysis; Developmental pathway; Gene–gene interaction; Gramene; Metabolic Pathway; Plant Reactome; Plant pathway database; PubChem; Regulatory pathway; Small molecules; Transcriptional network.

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