Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration.

Journal: Nucleic acids research
Published Date: Jan 4, 2017

Abstract

Linked Data (LD) aims to achieve interconnected data by representing entities using Unified Resource Identifiers (URIs), and sharing information using Resource Description Frameworks (RDFs) and HTTP. Ontologies, which logically represent entities and relations in specific domains, are the basis of LD. Ontobee (http://www.ontobee.org/) is a linked ontology data server that stores ontology information using RDF triple store technology and supports query, visualization and linkage of ontology terms. Ontobee is also the default linked data server for publishing and browsing biomedical ontologies in the Open Biological Ontology (OBO) Foundry (http://obofoundry.org) library. Ontobee currently hosts more than 180 ontologies (including 131 OBO Foundry Library ontologies) with over four million terms. Ontobee provides a user-friendly web interface for querying and visualizing the details and hierarchy of a specific ontology term. Using the eXtensible Stylesheet Language Transformation (XSLT) technology, Ontobee is able to dereference a single ontology term URI, and then output RDF/eXtensible Markup Language (XML) for computer processing or display the HTML information on a web browser for human users. Statistics and detailed information are generated and displayed for each ontology listed in Ontobee. In addition, a SPARQL web interface is provided for custom advanced SPARQL queries of one or multiple ontologies.

Authors

  • Edison Ong
    University of Michigan Medical School, Ann Arbor, MI 48109, USA.
  • Zuoshuang Xiang
    University of Michigan Medical School, Ann Arbor, MI 48109 USA.
  • Bin Zhao
    University of Michigan Medical School, Ann Arbor, MI 48109, USA.
  • Yue Liu
    School of Athletic Performance, Shanghai University of Sport, Shanghai, China.
  • Yu Lin
    Research School of Computer Science, Australian National University, Canberra, 2601, ACT, Australia.
  • Jie Zheng
    State Key Laboratory of Information Engineering in Surveying, Mapping and Remote Sensing, Wuhan University, Wuhan, China.
  • Chris Mungall
    Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Mélanie Courtot
    Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada, Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA, Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, USA, School of Dental Medicine, University at Buffalo, NY 14214-8006, USA, J. Craig Venter Institute, La Jolla, CA 92037, USA, Department of Pathology, University of California, San Diego, CA 92093, USA.
  • Alan Ruttenberg
    School of Dental Medicine, State University of New York at Buffalo, Buffalo, New York, United States of America.
  • Yongqun He
    University of Michigan Medical School, Ann Arbor, MI 48109 USA ; Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, and Comprehensive Cancer Center, University of Michigan Medical School, 1301 MSRB III, 1150 W. Medical Dr., Ann Arbor, MI 48109 USA.

Keywords

External Resources

Popular Topics
Recent Journals