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A Web Tool for Generating High Quality Machine-readable Biological Pathways

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

Plant Reactome: a knowledgebase and resource for comparative pathway analysis.

Sushma Naithani¹, Parul Gupta¹, Justin Preece¹

¹Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR, USA.

Nucleic Acids Research

|November 5, 2019

Summary

This summary is machine-generated.

Plant Reactome is a comprehensive plant pathway knowledgebase curating 298 pathways for rice and 82 other species. It enables omics data analysis and community collaboration for FAIR data principles in plant biology.

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Area of Science:

Plant biology
Bioinformatics
Systems biology

Background:

Plant Reactome is an open-source, comparative plant pathway knowledgebase developed by the Gramene project.
It utilizes Oryza sativa (rice) as a reference species for manual pathway curation.
Pathway knowledge is extended to 82 additional plant species through gene-orthology projection.

Purpose of the Study:

To provide a comprehensive resource for plant pathways, including metabolic, transport, transcriptional, and signaling pathways.
To enable users to upload and analyze their omics data, such as gene-expression data.
To foster community engagement and collaboration in gene and pathway curation.

Main Methods:

Manual curation of pathways using rice as a reference species.
Gene-orthology projection based on the Reactome data model and framework.
Integration of omics data analysis and gene-gene interaction data visualization.

Main Results:

Hosts 298 curated reference pathways across various biological processes.
Supports pathway knowledge extension to 82 diverse plant species.
Facilitates omics data analysis and visualization of gene-gene interactions.

Conclusions:

Plant Reactome serves as a valuable, FAIR-compliant resource for plant pathway exploration and analysis.
It actively engages the research community through workshops and tutorials to enhance data and tools.
The knowledgebase supports collaborative efforts to advance plant biology research.