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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

Ontodog: a web-based ontology community view generation tool.

Jie Zheng¹, Zuoshuang Xiang, Christian J Stoeckert

¹Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 and Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.

Bioinformatics (Oxford, England)

|January 14, 2014

Summary

Ontodog simplifies biomedical ontology use by generating custom subsets with community-preferred labels. This web-based tool requires no programming, making ontology customization accessible to all users.

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Area of Science:

Biomedical Informatics
Bioinformatics
Ontology Engineering

Background:

Biomedical ontologies are large and complex, often requiring tailored subsets for specific applications.
End users benefit from community-driven labels over developer-generated ones for improved usability.
Existing ontology tools may demand significant technical expertise or programming skills.

Purpose of the Study:

To introduce Ontodog, a web-based system for generating customized ontology subsets and community views.
To enable users to create ontology views with preferred labels and annotations without programming knowledge.
To provide access to over 100 ontologies, including all OBO Foundry ontologies, for view generation.

Main Methods:

Ontodog utilizes Excel input to define the desired ontology subset.
The system supports the creation of 'community views' with user-specified annotations and labels.
Web-based accessibility requires no installation or programming skills.

Main Results:

Ontodog successfully generates ontology subsets and community views based on user-defined requirements.
The system demonstrates ease of use for individuals with minimal ontology expertise.
A practical application using the Ontology for Biomedical Investigations showcases its utility.

Conclusions:

Ontodog effectively addresses the need for customized biomedical ontology subsets and community-driven labeling.
It democratizes ontology customization, making complex resources more accessible to a broader user base.
The tool enhances the practical application of biomedical ontologies in diverse research and community settings.