Using SPARQL to query bioportal ontologies and metadata

  • Authors:

  • Manuel Salvadores;Matthew Horridge;Paul R. Alexander;Ray W. Fergerson;Mark A. Musen;Natalya F. Noy

  • Affiliations:

  • Stanford Center for Biomedical Informatics Research, Stanford University, US;Stanford Center for Biomedical Informatics Research, Stanford University, US;Stanford Center for Biomedical Informatics Research, Stanford University, US;Stanford Center for Biomedical Informatics Research, Stanford University, US;Stanford Center for Biomedical Informatics Research, Stanford University, US;Stanford Center for Biomedical Informatics Research, Stanford University, US

  • Venue:
  • ISWC'12 Proceedings of the 11th international conference on The Semantic Web - Volume Part II
  • Year:
  • 2012

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Abstract

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 languages, 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 based serializations of all these ontologies and their metadata at sparql.bioontology.org . This dataset contains 203M triples, representing both content and metadata for the 300+ ontologies; and 9M mappings between terms. This endpoint can be queried with SPARQL which opens new usage scenarios for the biomedical domain. This paper presents lessons learned from having redesigned several applications that today use this SPARQL endpoint to consume ontological data.