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TogoID: an exploratory ID converter to bridge biological datasets
Shuya Ikeda1, Hiromasa Ono1, Tazro Ohta1
1Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, University of Tokyo Kashiwanoha-campus Station Satellite 6F, Kashiwa, Chiba 277-0871, Japan.
Bioinformatics (Oxford, England)
|July 8, 2022
Summary
TogoID is a new service that converts biological database identifiers (IDs), overcoming limitations of existing tools. It supports numerous datasets and provides an ontology for interpreting biological relationships during multi-step conversions.
Area of Science:
- Bioinformatics
- Computational Biology
- Life Sciences
Background:
- Biological data is essential for understanding life but is fragmented across diverse databases.
- Identifier (ID) conversion is crucial for integrating this scattered biological data.
- Existing ID conversion services have limitations in database coverage, update frequency, and interpretability of multi-step conversions.
Purpose of the Study:
- To introduce TogoID, a novel ID conversion service designed to address the shortcomings of existing tools.
- To provide a comprehensive solution for seamless biological data integration through robust ID conversion.
- To enhance the interpretability of biological data by defining dataset relationships semantically.
Main Methods:
- Developed TogoID with an intuitive web interface and an application programming interface (API).
- Integrated 65 diverse biological datasets, covering a wide range of biological categories.
- Created a semantic ontology to define relationships between datasets, aiding in the interpretation of conversion paths.
- Enabled exploratory multi-step ID conversions for users to discover connections between different biological IDs.
Main Results:
- TogoID successfully supports 65 datasets, offering broad coverage for biological ID conversion.
- The service facilitates multi-step ID conversions, allowing users to navigate complex data relationships.
- An accompanying ontology enhances the understanding of biological meanings derived from ID conversions.
- TogoID provides both a user-friendly web interface and an API for flexible access.
Conclusions:
- TogoID offers a significant improvement over existing ID conversion services by providing extensive dataset support and enhanced interpretability.
- The service facilitates the seamless integration and analysis of fragmented biological data.
- TogoID's open development model encourages community contribution, promoting continuous improvement and expansion of supported datasets.
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