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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

Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API.

Nobuaki Kono¹, Kazuharu Arakawa, Ryu Ogawa

¹Institute for Advanced Biosciences, Keio University, Fujisawa, Japan.

|November 13, 2009

Summary

This summary is machine-generated.

Pathway Projector offers an integrated pathway browser with comprehensive search and data mapping for multi-omics experiments. This web-based tool facilitates post-genomic research by providing scalable, zoomable pathway maps for academic users.

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An Integrated Approach for Microprotein Identification and Sequence Analysis

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Published on: July 12, 2022

Area of Science:

Systems Biology
Bioinformatics
Genomics

Background:

Biochemical pathways are crucial for understanding cellular functions and experimental data.
Existing online pathway maps often lack comprehensiveness and user-friendly interfaces for general use.
Genome browsers have significantly advanced genomics research, highlighting the need for similar tools in pathway analysis.

Purpose of the Study:

To address the limitations of current pathway databases and tools.
To develop a comprehensive and user-friendly online pathway browser.
To facilitate post-genomic research by integrating diverse biological data.

Main Methods:

Identified five key requirements for an effective pathway browser: integrated maps, comprehensive search, data mapping and annotation, data exchange, and intuitive user experience.
Evaluated existing pathway databases and tools against these requirements.
Implemented a web-based pathway browser named Pathway Projector.

Main Results:

Pathway Projector integrates large pathway maps (based on KEGG Atlas) with genes, enzymes, and metabolites.
It offers robust search capabilities (keywords, molecular/nucleotide/amino acid sequences) and data mapping for transcriptomic, proteomic, and metabolomic experiments.
The browser is implemented as a scalable, zoomable map using the Google Maps API, allowing map editing and annotation.

Conclusions:

Pathway Projector provides a solution meeting the identified requirements for a pathway browser.
It enables efficient searching and visualization of pathway data and experimental results.
The tool is freely available to academic users, promoting broader access to advanced pathway analysis.