A Roadmap for Navigating the Life Sciences Linked Open Data Cloud

  • Ali Hasnain
  • Syeda Sana e Zainab
  • Maulik R. Kamdar
  • Qaiser Mehmood
  • Claude N. WarrenJr.
  • Qurratal Ain Fatimah
  • Helena F. Deus
  • Muntazir Mehdi
  • Stefan Decker
Conference paper

DOI: 10.1007/978-3-319-15615-6_8

Part of the Lecture Notes in Computer Science book series (LNCS, volume 8943)
Cite this paper as:
Hasnain A. et al. (2015) A Roadmap for Navigating the Life Sciences Linked Open Data Cloud. In: Supnithi T., Yamaguchi T., Pan J., Wuwongse V., Buranarach M. (eds) Semantic Technology. JIST 2014. Lecture Notes in Computer Science, vol 8943. Springer, Cham

Abstract

Multiple datasets that add high value to biomedical research have been exposed on the web as a part of the Life Sciences Linked Open Data (LSLOD) Cloud. The ability to easily navigate through these datasets is crucial for personalized medicine and the improvement of drug discovery process. However, navigating these multiple datasets is not trivial as most of these are only available as isolated SPARQL endpoints with very little vocabulary reuse. The content that is indexed through these endpoints is scarce, making the indexed dataset opaque for users. In this paper, we propose an approach for the creation of an active Linked Life Sciences Data Roadmap, a set of configurable rules which can be used to discover links (roads) between biological entities (cities) in the LSLOD cloud. We have catalogued and linked concepts and properties from 137 public SPARQL endpoints. Our Roadmap is primarily used to dynamically assemble queries retrieving data from multiple SPARQL endpoints simultaneously. We also demonstrate its use in conjunction with other tools for selective SPARQL querying, semantic annotation of experimental datasets and the visualization of the LSLOD cloud. We have evaluated the performance of our approach in terms of the time taken and entity capture. Our approach, if generalized to encompass other domains, can be used for road-mapping the entire LOD cloud.

Keywords

Linked Data (LD) SPARQL Life Sciences (LS) Semantic web Query federation 

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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Ali Hasnain
    • 1
  • Syeda Sana e Zainab
    • 1
  • Maulik R. Kamdar
    • 1
  • Qaiser Mehmood
    • 1
  • Claude N. WarrenJr.
    • 2
  • Qurratal Ain Fatimah
    • 1
    • 2
    • 3
  • Helena F. Deus
    • 3
  • Muntazir Mehdi
    • 1
  • Stefan Decker
    • 1
  1. 1.Insight Center for Data AnalyticsNational University of IrelandGalwayIreland
  2. 2.Xenei.comDenverUSA
  3. 3.Foundation Medicine Inc.CambridgeUSA

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