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RDFIO: extending Semantic MediaWiki for interoperable biomedical data management
Samuel Lampa1, Egon Willighagen2, Pekka Kohonen3,4
1Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, SE-751 24, Sweden. samuel.lampa@farmbio.uu.se.
Journal of Biomedical Semantics
|September 6, 2017
Summary
A new tool, RDFIO, enables importing and exporting RDF data into Semantic MediaWiki, facilitating collaborative biological data integration and analysis for researchers.
Area of Science:
- Biological sciences
- Bioinformatics
- Data science
Background:
- Biological data is complex and increasing, requiring efficient integration methods.
- Collaborative data organization is crucial for understanding biological systems.
- Semantic MediaWiki facilitates collaborative data editing and machine-readability but lacks direct RDF import.
Purpose of the Study:
- To address the lack of RDF import functionality in Semantic MediaWiki.
- To enable seamless data exchange between Semantic MediaWiki and Semantic Web formats.
- To enhance collaborative biological data management and analysis.
Main Methods:
- Development of the RDFIO suite of tools for Semantic MediaWiki.
- Implementation of metadata handling for round-tripping RDF data.
- Demonstration using drug discovery data from Orphanet and chemical data from Wikidata.
Main Results:
- RDFIO successfully imports RDF data into Semantic MediaWiki.
- The tool supports exporting data back to RDF or ontology formats.
- Automated data imports can be combined with manual data presentations for flexible analysis.
Conclusions:
- RDFIO enhances Semantic MediaWiki's interoperability with the Semantic Web.
- The tool provides a flexible platform for exploring and managing biomedical datasets.
- Biomedical demonstrators showcase diverse usage scenarios for integrated data exploration.
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