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Updated: Jun 20, 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

SimCT: a generic tool to visualize ontology-based relationships for biological objects.

Carl Herrmann¹, Sèverine Bérard, Laurent Tichit

¹TAGC-U928 Inserm, Faculté des Sciences, Université de la Méditerranée, Campus de Luminy Case 928, Marseille, France. carl.herrmann@univmed.fr

Bioinformatics (Oxford, England)

|September 25, 2009

Summary

SimCT is a web-based service that graphically displays relationships between biological objects using biomedical ontologies. It simplifies complex biological data into an explorable tree format for easier understanding.

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Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

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Published on: August 15, 2019

Area of Science:

Bioinformatics
Computational Biology
Systems Biology

Background:

Biological object relationships are complex and difficult to visualize.
Existing tools often focus on overrepresented terms, not simplified representations.
Annotation data linked to biomedical ontologies is widely available.

Purpose of the Study:

To present SimCT, a novel web-based service for visualizing biological object relationships.
To provide an intuitive and easy-to-use tool for exploring biological data.
To offer an alternative to existing methods by simplifying term representation.

Main Methods:

Development of a web-based service named SimCT.
Graphical display of relationships between biological objects (genes, proteins) based on ontology annotations.
Utilization of a Java applet for interactive viewing and exploration of the resulting object tree.

Main Results:

SimCT generates a simplified tree representation of biological terms within a set of objects.
The service can be applied to any ontology with available annotation data.
The web-based nature eliminates the need for prior installation.

Conclusions:

SimCT offers a user-friendly and accessible method for visualizing complex biological relationships.
The tool simplifies biological term representation, aiding in data interpretation.
It serves as a valuable resource for researchers working with annotated biological data.