Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Enhancing the quality and trustworthiness of large language model-generated summaries of clinical oncology literature.

JAMIA open·2026
Same author

Effects of Nanosecond Pulsed Laser Cleaning Parameters on the Removal of Thick Paint Coatings from Shipbuilding Steel.

Materials (Basel, Switzerland)·2026
Same author

Odor-specific olfactory stimulation is associated with selective transcriptional changes and partial improvement of stress-evoked bladder overactivity in mice.

Frontiers in neuroscience·2026
Same author

Creating an engine of scientific discovery, an Indo-Japan perspective: learnings from IJNTC 2025 workshop.

NPJ systems biology and applications·2026
Same author

Outplaying elite table tennis players with an autonomous robot.

Nature·2026
Same author

Recurrent Phosphoglyceride Crystal Deposition Disease in the Mandible Mimicked a Malignant Tumor: Insights from a Clinical Case Report and Literature Review.

Diagnostics (Basel, Switzerland)·2026

Related Experiment Video

Updated: Jun 12, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

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

Published on: February 8, 2017

PathText: a text mining integrator for biological pathway visualizations.

Brian Kemper1, Takuya Matsuzaki, Yukiko Matsuoka

  • 1Department of Computer Science, University of Tokyo, Tokyo, Japan. brian@monrovian.com

Bioinformatics (Oxford, England)
|June 10, 2010
PubMed
Summary
This summary is machine-generated.

This study introduces PathText, a system integrating pathway visualization with text mining to link biological pathways directly to scientific literature, streamlining research and curation.

More Related Videos

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information
05:01

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

Published on: July 1, 2020

Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization
03:08

Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization

Published on: October 3, 2025

Related Experiment Videos

Last Updated: Jun 12, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

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

Published on: February 8, 2017

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information
05:01

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

Published on: July 1, 2020

Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization
03:08

Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization

Published on: October 3, 2025

Area of Science:

  • Systems biology
  • Bioinformatics
  • Computational biology

Background:

  • Metabolic and signaling pathways are crucial for organizing knowledge in systems biology.
  • Current pathway models lack direct links to source literature, hindering verification and curation.
  • The rapid expansion of scientific literature complicates pathway model relevance and maintenance.

Purpose of the Study:

  • To present PathText, an integrated system for pathway visualization and text mining.
  • To enable seamless navigation between pathway components and relevant literature sections.
  • To facilitate the identification of relevant scientific papers for pathway construction and validation.

Main Methods:

  • Integration of a pathway visualizer with text mining and annotation tools.
  • Development of a system allowing free movement between pathway elements and article content.
  • Utilizing large text bases for efficient paper retrieval.

Main Results:

  • PathText provides a unified environment for systems biologists.
  • Biologists can efficiently access and verify information from original research articles.
  • The system aids in keeping pathway models up-to-date with scientific advancements.

Conclusions:

  • PathText enhances the efficiency of biological pathway research and knowledge integration.
  • The system addresses the challenge of linking pathway models to supporting literature.
  • Facilitates easier curation and validation of biological pathway knowledge.