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BioPortal as a Dataset of Linked Biomedical Ontologies and Terminologies in RDF.
Manuel Salvadores1, Paul R Alexander1, Mark A Musen1
1Stanford Center for Biomedical Informatics Research Stanford University, US.
Semantic Web
|September 13, 2014
Summary
BioPortal offers a vast collection of over 300 biomedical ontologies and medical terminologies. Its RDF dataset provides uniform access to ontology content and metadata, including cross-ontology mappings.
Area of Science:
- Biomedical Informatics
- Knowledge Representation
- Data Management
Background:
- BioPortal serves as a leading repository for biomedical ontologies.
- It houses over 300 ontologies in various formats (OWL, OBO) and NLM medical terminologies.
- Existing access methods may lack uniformity for diverse ontology data.
Purpose of the Study:
- To publish a comprehensive RDF dataset of biomedical ontologies from BioPortal.
- To enable uniform access to ontology content and metadata.
- To facilitate the use of cross-ontology mappings.
Main Methods:
- All BioPortal ontologies were converted to RDF format.
- Ontology metadata and content were integrated into a large RDF dataset (190M triples).
- Simple RDFS reasoning was applied to standardize access to key properties.
Main Results:
- A publicly accessible RDF dataset of 300 biomedical ontologies is now available at http://sparql.bioontology.org.
- The dataset includes 190 million triples of ontology metadata and content.
- Over 9.8 million cross-ontology mappings with associated metadata are provided.
Conclusions:
- The RDF dataset enhances accessibility and usability of biomedical ontologies.
- Uniform access to ontology data and mappings supports biomedical research and data integration.
- This resource empowers users with standardized access to a critical biomedical knowledge base.
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