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Updated: Jun 3, 2025
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A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
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A general strategy for generating expert-guided, simplified views of ontologies
Anita R Caron1, Aleix Puig-Barbe1, Ellen M Quardokus2
1European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Biorxiv : the Preprint Server for Biology
|January 7, 2025
Summary
Researchers can now simplify complex ontologies for FAIR data using new validation tools. These tools help create tailored ontology views and improve data organization for atlases.
Area of Science:
- Bioinformatics
- Data Science
- Genomics and Proteomics
Background:
- Ontologies are crucial for Findable, Accessible, Interoperable, and Reusable (FAIR) data through standardized terms and structure.
- Complexity of general ontologies poses a barrier to adoption by researchers and resource developers.
- Existing manual simplifications of ontologies for specific applications often use unsuitable relationship types.
Purpose of the Study:
- To present a suite of tools for validating user-created hierarchies against established ontology structures.
- To generate graphical reports and tailored ontology views for specific atlas projects.
- To address the complexity barrier and improve ontology adoption for FAIR data principles.
Main Methods:
- Development of software tools to validate user hierarchies against ontology structure.
- Generation of graphical reports to facilitate discussion and identify discrepancies.
- Creation of customized ontology views for projects like the HuBMAP Human Reference Atlas and Human Developmental Cell Atlas.
Main Results:
- The validation process identified corrections and content for both ontologies and user-generated hierarchies.
- Tailored ontology views were successfully generated for specific atlas needs.
- The tools facilitate a more efficient and accurate use of ontologies in biological data annotation.
Conclusions:
- The developed tools effectively validate user hierarchies against ontology structures, simplifying complex ontologies.
- This approach aids in the creation of FAIRer datasets by improving ontology application in biological atlases.
- Validation serves as a mechanism for iterative improvement of both ontologies and their specialized applications.
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