Ubergraph: integrating OBO ontologies into a unified semantic graph

descriptionPublicationkeyboard_double_arrow_right Article , Conference object 28 Sep 2022Publisher:ZenodoFunded by:NIH | A Common Dialect for Infr..., WT | unidentified, NIH | An Intelligent Concept Ag...

Authors: Balhoff, James P.; Bayindir, Ugur; Caron, Anita R.; Matentzoglu, Nicolas; Osumi-Sutherland, David; Mungall, Christopher J.;

doi: 10.5281/zenodo.7249758 , 10.5281/zenodo.7249759

Ubergraph: integrating OBO ontologies into a unified semantic graph

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Abstract

OBO library ontologies include a wealth of inter-ontology semantic links, which require OWL reasoning to utilize fully. Merging and reasoning over a large suite of ontologies is resource intensive, and challenging for many users. Here we present Ubergraph, an RDF triplestore and public SPARQL query endpoint, which includes a novel approach to precomputing OWL inferences, stored in a readily traversable knowledge graph. Ubergraph’s “relation graphs” allow users to perform SPARQL queries which make use of the semantics of the included ontologies. Ubergraph currently includes 39 OBO library ontologies. We describe several use cases enabled by Ubergraph such as ontology browsing and entailment validation.

Also supported by NIH-NCATS Biomedical Data Translator program, 3OT2TR003449-01S1.

Related Organizations

University of North Carolina at Greensboro
United States
Lawrence Berkeley National Laboratory
United States
University of North Carolina at Chapel Hill
United States
European Bioinformatics Institute
United Kingdom
Renaissance Computing Institute
United States

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Keywords

semantic web, knowledge graph, reasoning, ontology, SPARQL, OWL, RDF

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