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Prediction and curation of missing biomedical identifier mappings with Biomappings
Charles Tapley Hoyt1, Amelia L Hoyt2, Benjamin M Gyori1
1Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, United States.
Bioinformatics (Oxford, England)
|March 14, 2023
Summary
Biomappings semi-automates the creation of missing links between biomedical data resources. This improves data integration and knowledge discovery by providing thousands of new mappings for key biological concepts.
Area of Science:
- Biomedical Informatics
- Data Integration
- Knowledge Management
Background:
- Biomedical identifier resources (ontologies, taxonomies, vocabularies) often overlap and contain equivalent entries with different identifiers.
- Maintaining mappings between these resources is vital for data interoperability and integration.
- Existing mappings have substantial gaps, necessitating semi-automated curation methods.
Purpose of the Study:
- To develop and implement a semi-automated workflow for curating missing mappings between biomedical identifier resources.
- To enhance data interoperability and facilitate knowledge integration through improved mapping availability.
Main Methods:
- Biomappings employs a curation workflow combining automated prediction with human-in-the-loop review.
- It supports multiple prediction approaches and includes a web-based interface for mapping validation.
- Automated consistency checking is integrated into the curation process.
Main Results:
- Biomappings has curated 9,274 mappings and predicted 40,691 new ones.
- These mappings bridge gaps between widely used resources for small molecules, cell lines, and diseases.
- Case studies demonstrated value in cancer cell line and clinical trial small molecule data integration.
- Curated mappings were contributed back to community ontologies.
Conclusions:
- Biomappings effectively addresses the need for missing mappings in biomedical identifier resources.
- The developed workflow enhances data interoperability and supports biomedical research.
- The publicly available resource facilitates broader adoption and contribution.
