4 research outputs found
Using the relation ontology Metarel for modelling Linked Data as multi-digraphs
The Semantic Web standards OWL and RDF are often used to represent biomedical information as Linked Data; however, the OWL/RDF syntax, which combines both, was never optimised for querying. By combining two formal paradigms for modelling Linked Data, namely multi-digraphs and Description Logic, many precise terms for relations have emerged that are defined in the Metarel relation ontology. They are especially useful in Linked Data and RDF knowledge bases that 1) rely on SPARQL querying and 2) require semantic support for chains of relations.
Metarel-described multi-digraphs were used for knowledge integration and reasoning in three RDF knowledge bases in the domain of genome biology: BioGateway, Cell Cycle Ontology and Gene Expression Knowledge Base. These knowledge bases integrate both data, like KEGG, and ontologies, like Gene Ontology, in the same RDF graphs. Their libraries with biomedically relevant SPARQL queries show the practical benefits of this semantic paradigm. In addition to the management of RDF stores, this paper describes how Metarel can be used for remodelling Linked Data as SPARQL-friendly and semantically rich multi-digraphs
Metarel, an ontology facilitating advanced querying of biomedical knowledge
Knowledge management has become indispensible in the Life Sciences for integrating and querying the enormous amounts of detailed knowledge about genes, organisms, diseases, drugs, cells, etc. Such detailed knowledge is continuously generated in bioinformatics via both hardware (e.g. raw data dumps from microâarrays) and software (e.g. computational analysis of data). Wellâknown frameworks for managing knowledge are relational databases and spreadsheets. The doctoral dissertation describes knowledge management in two more recentlyâinvestigated frameworks: ontologies and the Semantic Web. Knowledge statements like âlions live in Africaâ and âgenes are located in a cell nucleusâ are managed with the use of URIs, logics and the ontological distinction between instances and classes. Both theory and practice are described. Metarel, the core subject of the dissertation, is an ontology describing relations that can bridge the mismatch between networkâbased relations that appeal to internet browsing and logicâbased relations that are formally expressed in Description Logic. Another important subject of the dissertation is BioGateway, which is a knowledge base that has integrated biomedical knowledge in the form of hundreds of millions of networkâbased relations in the RDF format. Metarel was used to upgrade the logical meaning of these relations towards Description Logic. This has enabled to build a computer reasoner that could run over the knowledge base and derive new knowledge statements