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A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
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WormPaths: Caenorhabditis elegans metabolic pathway annotation and visualization
Melissa D Walker1, Gabrielle E Giese1, Amy D Holdorf1
1Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America.
Biorxiv : the Preprint Server for Biology
|January 5, 2021
Summary
WormPaths offers detailed metabolic pathway maps for Caenorhabditis elegans, aiding research during COVID-19 lockdowns. These resources facilitate easy navigation and analysis of gene expression data.
Area of Science:
- * Molecular biology and systems biology research.
- * Utilizing the nematode *Caenorhabditis elegans* as a model organism.
Background:
- * The COVID-19 pandemic necessitated a pause in experimental research, prompting alternative productive activities.
- * A critical need existed for comprehensive, annotated metabolic pathway data in *C. elegans*.
Approach:
- * Developed WormPaths, a resource featuring manually annotated metabolic genes and 66 detailed pathway maps.
- * Maps include metabolites, structures, genes, reactions, and inter-map connections, accessible via the WormFlux website.
Key Points:
- * WormPaths provides user-friendly, navigable maps of *C. elegans* metabolism.
- * The hierarchical structure of WormPaths enables metabolic pathway enrichment analysis of transcriptomic data.
Conclusions:
- * WormPaths serves as a valuable tool for understanding *C. elegans* metabolism and gene expression.
- * Future development aims for more interactive, mobile-friendly pathway maps.
