, Volume 16, Issue 3, pp 195–205 | Cite as

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

  • Naouel Karam
  • Claudia Müller-Birn
  • Maren Gleisberg
  • David Fichtmüller
  • Robert Tolksdorf
  • Anton Güntsch


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.


Research data infrastructure Interoperability Data discovery Terminology repository Ontology-based data access Ontologies Taxonomies 


  1. 1.
    WoRMS Editorial Board (2016) World Register of Marine Specie. Accessed 2016-04-25Google Scholar
  2. 2.
    Adamusiak T, Burdett T, Kurbatova N, Joeri van der Velde K, Abeygunawardena N, Antonakaki D, Kapushesky M, Parkinson H, Swertz MA (2011) Ontocat – Simple Ontology Search and Integration in Java, R and Rest/Javascript. BMC Bioinformatics 12(1):1–12CrossRefGoogle Scholar
  3. 3.
    Atkins D, Droegemeier K, Feldman S, Garcia-Molina H, Klein M, Messerschmitt D, Messina P, Ostriker J, Wright M (2003) Revolutionizing Science and Engineering Through Cyberinfrastructure: Report of the Blue-Ribbon Advisory Panel on Cyberinfrastructure. National Science Foundation, Washington, DCGoogle Scholar
  4. 4.
    Authmann C, Beilschmidt C, Drönner J, Mattig M, Seeger B (2015) VAT: A System for Visualizing, Analyzing and Transforming Spatial Data in Science. Datenbank-Spektrum 15(3):175–184CrossRefGoogle Scholar
  5. 5.
    Baader F, Lutz C, Suntisrivaraporn B (2006) CEL – A Polynomial-Time Reasoner for Life Science Ontologies. Springer, Berlin, HeidelbergCrossRefGoogle Scholar
  6. 6.
    Berendsohn W, Döring M, Geoffroy M, Glück K, Güntsch A, Hahn A, Kusber WH, Li J, Röpert D, Specht F (2003) The berlin model: a concept-based taxonomic information model. In: MoReTax – Handling Factual Information Linked to Taxonomic Concepts in Biology. BfN, Schriftenreihe Vegetationskunde, vol 39Google Scholar
  7. 7.
    Ciardelli P, Kelbert P, Kohlbecker A, Hoffmann N, Güntsch A, Berendsohn WG (2009) The EDIT Cyberplatform for Taxonomy and the Taxonomic Workflow: Selected Components. In 39. Jahrestagung der Gesellschaft für Informatik e.V. (GI). GI, Lübeck, Germany, pp 625–638Google Scholar
  8. 8.
    Deegan (née Clark) JI, Dimmer EC, Mungall CJ (2010) Formalization of Taxon-Based Constraints to Detect Inconsistencies in Annotation and Ontology Development. BMC Bioinformatics 11(1):1–10CrossRefGoogle Scholar
  9. 9.
    Côté RG, Jones P, Apweiler R, Hermjakob H (2006) The Ontology Lookup Service, a Lightweight Cross-Platform Tool for Controlled Vocabulary Queries. BMC Bioinformatics 7(1):1–7CrossRefGoogle Scholar
  10. 10.
    Diepenbroek M, Glöckner FO, Grobe P, Güntsch A, Huber R, König-Ries B, Kostadinov I, Nieschulze J, Seeger B, Tolksdorf R, Triebel D (2014) Towards an Integrated Biodiversity and Ecological Research Data Management and Archiving Platform: The German Federation for the Curation of Biological Data (gfbio). 44. Jahrestagung der Gesellschaft für Informatik. GI, Stuttgart, GermanyGoogle Scholar
  11. 11.
    Euzenat J, Shvaiko P (2013) Ontology Matching, 2nd edn. Springer-Verlag, Heidelberg (DE)zbMATHCrossRefGoogle Scholar
  12. 12.
    Federhen S (2012) The NCBI Taxonomy Database. Nucleic Acids Res 40(Database issue):D136–D143CrossRefGoogle Scholar
  13. 13.
    Franz N (2011) Biological Taxonomy and Ontology Development: Scope and Limitations. Biodivers Informatics. doi: 10.17161/bi.v7i1.3927 Google Scholar
  14. 14.
    Gerlach R, Blaa D, Chamanara J, Hohmuth M, Navabpour N, Thiel S, König-Ries B (2015) Bexis 2 – A Platform for Managing Heterogeneous Biodiversity Data and Projects. TDWG Annual ConferenceGoogle Scholar
  15. 15.
    Hevner AR, March ST, Park J, Ram S (2004) Design Science in Information Systems Research. Mis Q 28(1):75–105Google Scholar
  16. 16.
    Hey T, Tansley S, Tolle KM et al (2009) The Fourth Paradigm: Data-Intensive Scientific Discovery vol. 1. Microsoft research, Redmond, WAGoogle Scholar
  17. 17.
    Hoehndorf R, Dumontier M, Oellrich A, Rebholz-Schuhmann D, Schofield PN, Gkoutos GV (2011) Interoperability Between Biomedical Ontologies Through Relation Expansion, Upper-Level Ontologies and Automatic Reasoning. PLOS ONE 6(7):1–9CrossRefGoogle Scholar
  18. 18.
    Hoehndorf R, Slater L, Schofield PN, Gkoutos GV (2015) Aber-Owl: A Framework for Ontology-Based Data Access in Biology. BMC Bioinformatics 16(1):1–9CrossRefGoogle Scholar
  19. 19.
    Holetschek J, Dröge G, Güntsch A, Berendsohn WG (2012) The ABCD of Primary Biodiversity Data Access. Plant Biosyst 146(4):771–779CrossRefGoogle Scholar
  20. 20.
    Isaac A, Haslhofer B (2013) Europeana Linked Open Data – Semant Web 4(3):291–297Google Scholar
  21. 21.
    de Jong Y, Kouwenberg J, Boumans L et al (2015) Pesi – A Taxonomic Backbone for Europe. Biodivers Data J 3:e5848CrossRefGoogle Scholar
  22. 22.
    Köhler S, Bauer S, Mungall CJ, Carletti G, Smith CL, Schofield P, Gkoutos GV, Robinson PN (2011) Improving Ontologies by Automatic Reasoning and Evaluation of Logical Definitions. BMC Bioinformatics 12(1):1–8CrossRefGoogle Scholar
  23. 23.
    Kuśnierczyk W (2008) Taxonomy-Based Partitioning of the Gene Ontology. J Biomed Inform 41(2):282–292CrossRefGoogle Scholar
  24. 24.
    Leibniz Institute DSMZ (2016) Prokaryotic Nomenclature Up-To-Date. Google Scholar
  25. 25.
    Löffler F, Sateli B, Witte R, König-Ries B (2014) Towards semantic recommendation of biodiversity datasets based on linked open data. In: Proceedings of the 26th GI-Workshop Grundlagen von Datenbanken, vol. 1313. Bozen-Bolzano, Italy, pp 65–70Google Scholar
  26. 26.
    Meyer ET, Schroeder R (2015) Knowledge Machines: Digital Transformations of the Sciences and Humanities. MIT Press, Cambridge, MAGoogle Scholar
  27. 27.
    Noy NF, Shah NH, Whetzel PL, Dai B, Dorf M, Griffith N, Jonquet C, Rubin DL, Storey MD, Chute CG, Musen MA (2009) Bioportal: Ontologies and Integrated Data Resources at the Click of a Mouse. Nucleic Acids Res 37(Web-Server-Issue):170–173CrossRefGoogle Scholar
  28. 28.
    Roskov Y, Abucay L, Orrell T, Nicolson D, Flann C, Bailly N, Kirk P, Bourgoin T, DeWalt R, Decock W, De~Wever A (eds) (2016) Species 2000 & ITIS Catalogue of Life, 25th March 2016. (Species 2000: Naturalis, Leiden, the Netherlands. ISSN 2405-8858)
  29. 29.
    Schulz S, Stenzhorn H, Boeker M (2008) The ontology of biological taxa. In: Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB) Toronto, Canada, July 19–23, 2008. pp 313–321Google Scholar
  30. 30.
    Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S (2007) The Obo Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration. Nat Biotechnol 25(11):1251–1255CrossRefGoogle Scholar
  31. 31.
    Suominen O, Pessala S, Tuominen J, Lappalainen M, Nykyri S, Ylikotila H, Frosterus M, Hyvönen E (2014) Deploying national ontology services: From onki to finto. In: Proceedings of the Industry Track at the International Semantic Web Conference 2014. CEUR Workshop ProceedingsGoogle Scholar
  32. 32.
    Thau D, Ludäscher B (2007) Reasoning About Taxonomies in First-Order Logic. Ecol Inform 2(3):195–209 (Meta-information systems and ontologies. A Special Feature from the 5th International Conference on Ecological Informatics ISEI5, Santa Barbara, CA, Dec. 4–7, 2006 Novel Concepts of Ecological Data Management S.I.)CrossRefGoogle Scholar
  33. 33.
    Triebel D, Hagedorn G, Jablonski S, Rambold G (eds) (1999) Diversity Workbench – A virtual research environment for building and accessing biodiversity and environmental data.
  34. 34.
    Tuominen J, Laurenne N, Hyvönen E (2011) Biological names and taxonomies on the semantic web – managing the change in scientific conception. In: The Semanic Web: Research and Applications – 8th Extended Semantic Web Conference, ESWC 2011, Heraklion, Crete, Greece, Proceedings, Part II. pp 255–269Google Scholar
  35. 35.
    Viljanen K, Tuominen J, Hyvönen E (2009) Ontology libraries for production use: The finnish ontology library service onki. In: Proceedings of the 6th European Semantic Web ConferenceGoogle Scholar
  36. 36.
    Viljanen K, Tuominen J, Mäkelä E, Hyvönen E (2012) Normalized access to ontology repositories. In: Proceedings of the Sixth International Conference on Semantic Computing (IEEE ICSC 2012). IEEE Press, Washington, DCGoogle Scholar
  37. 37.
    Xiang Z, Mungall C, Ruttenberg A, He Y (2011) Ontobee: A linked data server and browser for ontology terms. In: Proceedings of the 2nd International Conference on Biomedical Ontology Buffalo, NY, USA, July 26–30, 2011Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  1. 1.Department of Mathematics and Computer ScienceFreie Universität BerlinBerlinGermany
  2. 2.Botanic Garden and Botanical Museum BerlinFreie Universität BerlinBerlinGermany

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