Studying the Reuse of Content in Biomedical Ontologies: An Axiom-Based Approach

  • Manuel Quesada-Martínez
  • Jesualdo Tomás Fernández-BreisEmail author
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10259)


The biomedical community has developed many ontologies in the last years, which may follow a set of community accepted principles for ontology development such as the ones proposed by the OBO Foundry. One of such principles is the orthogonality of biomedical ontologies, which should be based on the reuse of existing content. Previous works have studied how ontology matching techniques help to increase the number of terms reused. In this paper we investigate to what extent the reuse of terms also mean reuse of logical axioms. For this purpose, our method identifies two different ways of reusing terms, reuse of URIs (implicit reuse) and reuse of concepts (explicit reuse). The method is also able of detecting hidden axioms, that is, axioms associated with a reused term but that are not actually reused. We have developed and applied our method to a corpus of 144 OBO Foundry ontologies. The results show that 75 ontologies implicitly reuse terms, 50% of which also explicitly does it. The characterisation based on reuse enables the visualisation of the corpus as a dependency graph that can be clustered for grouping ontologies by their reuse profile. Finally, the application of a locality-based module extractor reveals that roughly 2 000 terms and 20 000 hidden axioms, on average, could be automatically reused.


Biomedical ontologies Ontology axiomatisation Reuse 



This work has been partially funded by to the Spanish Ministry of Economy, Industry and Competitiveness, the FEDER Programme and by the Fundación Séneca through grants TIN2014-53749-C2-2-R and 19371/PI/14.


  1. 1.
    Courtot, M., Gibson, F., Lister, A.L., Malone, J., Schober, D., Brinkman, R.R., Ruttenberg, A.: MIREOT: the minimum information to reference an external ontology term. Appl. Ontol. 6(1), 23–33 (2011)Google Scholar
  2. 2.
    Delbru, R., Tummarello, G., Polleres, A.: Context-dependent OWL reasoning in sindice - experiences and lessons learnt. In: Rudolph, S., Gutierrez, C. (eds.) RR 2011. LNCS, vol. 6902, pp. 46–60. Springer, Heidelberg (2011). doi: 10.1007/978-3-642-23580-1_5 CrossRefGoogle Scholar
  3. 3.
    Ghazvinian, A., Noy, N.F., Musen, M.A.: How orthogonal are the OBO foundry ontologies? J. Biomed. Semant. 2(2), S2 (2011)CrossRefGoogle Scholar
  4. 4.
    Grau, B.C., Horrocks, I., Kazakov, Y., Sattler, U.: Modular reuse of ontologies: theory and practice. J. Artif. Int. Res. 31(1), 273–318 (2008)MathSciNetzbMATHGoogle Scholar
  5. 5.
    Horridge, M., Bechhofer, S.: The OWL API: a JAVA API for OWL ontologies. Semant. Web 2(1), 11–21 (2011)Google Scholar
  6. 6.
    Jiménez-Ruiz, E., Grau, B.C., Sattler, U., Schneider, T., Berlanga, R.: Safe and economic re-use of ontologies: a logic-based methodology and tool support. In: Bechhofer, S., Hauswirth, M., Hoffmann, J., Koubarakis, M. (eds.) ESWC 2008. LNCS, vol. 5021, pp. 185–199. Springer, Heidelberg (2008). doi: 10.1007/978-3-540-68234-9_16 CrossRefGoogle Scholar
  7. 7.
    Kamdar, M., Tudorache, T., Musen, M.A.: A systematic analysis of term reuse and term overlap across biomedical ontologies. Semant. Web, 1–19 (2016).
  8. 8.
    Quesada-Martínez, M., Mikroyannidi, E., Fernández-Breis, J.T., Stevens, R.: Approaching the axiomatic enrichment of the gene ontology from a lexical perspective. Artif. Intell. Med. 65(1), 35–48 (2015)CrossRefGoogle Scholar
  9. 9.
    Simperl, E.: Reusing ontologies on the semantic web: a feasibility study. Data Knowl. Eng. 68(10), 905–925 (2009)CrossRefGoogle Scholar
  10. 10.
    Smith, B., Ashburner, M., Rosse, C., Bard, J., Bug, W., Ceusters, W., Goldberg, L.J., Eilbeck, K., Ireland, A., Mungall, C.J., et al.: The OBO foundry: coordinated evolution of ontologies to support biomedical data integration. Nat. Biotechnol. 25(11), 1251–1255 (2007)CrossRefGoogle Scholar
  11. 11.
    Whetzel, P.L., Noy, N.F., Shah, N.H., Alexander, P.R., Nyulas, C., Tudorache, T., Musen, M.A.: BioPortal: enhanced functionality via new web services from the national center for biomedical ontology to access and use ontologies in software applications. Nucleic Acids Res. 39(Suppl 2), W541–W545 (2011)CrossRefGoogle Scholar
  12. 12.
    Xiang, Z., Courtot, M., Brinkman, R.R., Ruttenberg, A., He, Y.: OntoFox: web-based support for ontology reuse. BMC Res. Notes 3(1), 175 (2010)CrossRefGoogle Scholar
  13. 13.
    Znaidi, E., Tamine, L., Latiri, C.: Answering PICO clinical questions: a semantic graph-based approach. In: Holmes, J.H., Bellazzi, R., Sacchi, L., Peek, N. (eds.) AIME 2015. LNCS, vol. 9105, pp. 232–237. Springer, Cham (2015). doi: 10.1007/978-3-319-19551-3_30 CrossRefGoogle Scholar

Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  • Manuel Quesada-Martínez
    • 1
  • Jesualdo Tomás Fernández-Breis
    • 1
    Email author
  1. 1.Facultad de InformáticaUniversidad de Murcia, IMIB-ArrixacaMurciaSpain

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