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Gupta P, Naithani S, Preece J, et al. Plant Reactome and PubChem: The Plant Pathway and (Bio)Chemical Entity Knowledgebases. Methods Mol Biol. 2022;2443:511-525doi: 10.1007/978-1-0716-2067-0_27.
Gupta, P., Naithani, S., Preece, J., Kim, S., Cheng, T., D'Eustachio, P., Elser, J., Bolton, E. E., & Jaiswal, P. (2022). Plant Reactome and PubChem: The Plant Pathway and (Bio)Chemical Entity Knowledgebases. Methods in molecular biology (Clifton, N.J.), 2443511-525. https://doi.org/10.1007/978-1-0716-2067-0_27
Gupta, Parul, et al. "Plant Reactome and PubChem: The Plant Pathway and (Bio)Chemical Entity Knowledgebases." Methods in molecular biology (Clifton, N.J.) vol. 2443 (2022): 511-525. doi: https://doi.org/10.1007/978-1-0716-2067-0_27
Gupta P, Naithani S, Preece J, Kim S, Cheng T, D'Eustachio P, Elser J, Bolton EE, Jaiswal P. Plant Reactome and PubChem: The Plant Pathway and (Bio)Chemical Entity Knowledgebases. Methods Mol Biol. 2022;2443:511-525. doi: 10.1007/978-1-0716-2067-0_27. PMID: 35037224.
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Methods Mol Biol. 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.

Methods in molecular biology (Clifton, N.J.)

Parul Gupta, Sushma Naithani, Justin Preece, Sunghwan Kim, Tiejun Cheng, Peter D'Eustachio, Justin Elser, Evan E Bolton, Pankaj Jaiswal

Affiliations

  1. Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA.
  2. National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
  3. NYU Grossman School of Medicine, New York, NY, USA.
  4. Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA. [email protected].

PMID: 35037224 DOI: 10.1007/978-1-0716-2067-0_27

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.

© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

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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