Published September 28, 2022
| Version v1
Conference paper
Open
Ubergraph: integrating OBO ontologies into a unified semantic graph
Creators
- 1. Renaissance Computing Institute, University of North Carolina, Chapel Hill, NC USA
- 2. European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK
- 3. Semanticly, Athens, Greece
- 4. Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley CA, 94720
Description
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.
Notes
Also supported by NIH-NCATS Biomedical Data Translator program, 3OT2TR003449-01S1.
Files
ICBO-2022_paper_5005.pdf
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Additional details
Related works
- Is identical to
- Conference paper: https://icbo-conference.github.io/icbo2022/papers/ICBO-2022_paper_5005.pdf (URL)
Funding
- An Intelligent Concept Agent for Assisting with the Application of Metadata 5U01HG009453-03
- National Institutes of Health