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A Terminology Service Supporting Semantic Annotation, Integration, Discovery and Analysis of Interdisciplinary Research Data

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Abstract

Research has become more data-intensive over the last few decades. Sharing research data is often a challenge, especially for interdisciplinary collaborative projects. One primary goal of a research infrastructure for data management should be to enable efficient data discovery and integration of heterogeneous data. In order to enable such interoperability, a lot of effort has been undertaken by scientists to develop standards and characterize their domain knowledge in the form of taxonomies and formal ontologies. However, these knowledge models are often disconnected and distributed. The work presented here provides a promising approach for integrating and harmonizing terminological resources to serve as a backbone for a platform. The component developed, called the GFBio Terminology Service, acts as a semantic platform for access, development and reasoning over internally and externally maintained terminological resources within the biological and environmental domain. We highlight the utility of the Terminology Service by practical use cases of semantically enhanced components. We show how the Terminology Service enables applications to add meaning to their data by giving access to the knowledge that can be derived from the terminologies and data annotated by them.

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Notes

  1. www.gfbio.org

  2. The European Bioinformatics Institute (www.ebi.ac.uk)

  3. Data Publisher for Earth & Environmental Science (www.pangaea.de)

  4. Natural History Museum (www.naturkundemuseum.berlin)

  5. German Collection of Microorganisms and Cell Cultures (www.dsmz.de)

  6. The Bavarian Natural History Collections (www.snsb.mwn.de)

  7. The complete list of involved archives and data centers is available on the GFBio website.

  8. bioportal.bioontology.org

  9. www.finto.fi

  10. www.ebi.ac.uk/ols

  11. www.ontobee.org

  12. www.aber-owl.net

  13. www.molgenis.org/wiki/OntocatStart

  14. virtuoso.openlinksw.com

  15. www.w3.org/TR/rdf-sparql-query

  16. The NCBI taxonomy is a curated classification and nomenclature for all of the organisms in the public sequence databases

  17. Web Ontology Language, www.w3.org/OWL

  18. build.berkeleybop.org/job/build-ncbitaxon

  19. JavaScript Object Notation (www.w3.org/TR/html-json-forms/)

  20. Extensible Markup Language (www.w3.org/XML/)

  21. Comma Separated Values (tools.ietf.org/html/rfc4180)

  22. JSON for Linking Data (www.w3.org/TR/json-ld/)

  23. terminologies.gfbio.org

  24. www.diversitymobile.net/wiki/DTN_Taxon_Lists_Services

  25. abcd.biowikifarm.net

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Authors and Affiliations

  1. Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany

    Naouel Karam, Claudia Müller-Birn & Robert Tolksdorf

  2. Botanic Garden and Botanical Museum Berlin, Freie Universität Berlin, Berlin, Germany

    Maren Gleisberg, David Fichtmüller & Anton Güntsch

Authors
  1. Naouel Karam
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  3. Maren Gleisberg
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Correspondence to Naouel Karam or Maren Gleisberg.

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Karam, N., Müller-Birn, C., Gleisberg, M. et al. A Terminology Service Supporting Semantic Annotation, Integration, Discovery and Analysis of Interdisciplinary Research Data. Datenbank Spektrum 16, 195–205 (2016). https://doi.org/10.1007/s13222-016-0231-8

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