The RDF Foundry: Call for an initiative to build enhanced RDF resources for biological data integration (original) (raw)
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LexRDF Model: An RDF-based Unified Model for Heterogeneous Biomedical Ontologies
The Lexical Grid (LexGrid) project is an on-going community-driven initiative coordinated by the Mayo Clinic Division of Biomedical Statistics and Informatics (BSI). It provides a common terminology model to represent multiple vocabulary and ontology sources as well as a scalable and robust API for accessing such information. While successfully used and adopted in the biomedical and clinical community, an important requirement is to align the existing LexGrid model with emerging Semantic Web standards and specifications. This paper introduces the LexRDF model, which maps the LexGrid model elements to corresponding constructs in W3C specifications such as RDF, OWL, and SKOS. Our mapping specification successfully used W3C standards to represent most of the existing LexGrid components, and those that did not map point out issues in the existing specifications that the W3C may want to consider in future work. With LexRDF, the terminological information represented in LexGrid can be tra...
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BioPortal as a Dataset of Linked Biomedical Ontologies and Terminologies in RDF
Semantic web, 2013
BioPortal is a repository of biomedical ontologies-the largest such repository, with more than 300 ontologies to date. This set includes ontologies that were developed in OWL, OBO and other formats, as well as a large number of medical terminologies that the US National Library of Medicine distributes in its own proprietary format. We have published the RDF version of all these ontologies at http://sparql.bioontology.org. This dataset contains 190M triples, representing both metadata and content for the 300 ontologies. We use the metadata that the ontology authors provide and simple RDFS reasoning in order to provide dataset users with uniform access to key properties of the ontologies, such as lexical properties for the class names and provenance data. The dataset also contains 9.8M cross-ontology mappings of different types, generated both manually and automatically, which come with their own metadata.
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OBO and OWL: Leveraging semantic web technologies for the life sciences
2007
OBO is an ontology language that has often been used for modeling ontologies in the life sciences. Its definition is relatively informal, so, in this paper, we provide a clear specification for OBO syntax and semantics via a mapping to OWL. This mapping also allows us to apply existing Semantic Web tools and techniques to OBO. We show that Semantic Web reasoners can be used to efficiently reason with OBO ontologies.
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