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Updated: Mar 31, 2026

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 Pathway Databases.

Pankaj Jaiswal¹, Björn Usadel^2,3

¹Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR, 97331-2902, USA. jaiswalp@science.oregonstate.edu.

Methods in Molecular Biology (Clifton, N.J.)

|November 1, 2015

Summary

This summary is machine-generated.

This chapter reviews online databases for plant pathways, detailing their use for understanding plant biological processes and gene functions. It highlights resources like WikiPathways, MapMan, RiceCyc, and MaizeCyc for exploring plant science.

Keywords:

Biological pathway s Comparative pathway analysis Gramene database MaizeCyc MapMan Metabolic Pathways Molecular interaction s Plant pathway database s Regulatory pathway s RiceCyc Signaling pathway s Transport pathway s WikiPathways

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Area of Science:

Plant Biology
Bioinformatics
Systems Biology

Background:

Pathway databases integrate data on chemicals, genes, and gene products.
These databases elucidate metabolic, transport, regulatory, and signaling reactions.
Pathways are constructed by linking reactions based on inputs and outputs.

Purpose of the Study:

To provide a comprehensive list of online databases for plant pathways.
To offer a guide on utilizing these plant pathway databases.
To introduce specific databases such as WikiPathways Plants Portal, MapMan, RiceCyc, and MaizeCyc.

Main Methods:

Compilation of relevant online plant pathway databases.
Description of the functionalities and data organization within each database.
Illustrative examples of database navigation and information retrieval.

Main Results:

A curated list of accessible plant pathway databases is presented.
Key features and usability of WikiPathways Plants Portal, MapMan, RiceCyc, and MaizeCyc are detailed.
Guidance on accessing and interpreting pathway information is provided.

Conclusions:

Online pathway databases are essential resources for plant science research.
Effective utilization of these databases enhances the understanding of plant biological systems.
Databases like RiceCyc and MaizeCyc, developed with Pathway Tools, offer specialized insights into cereal crops.