Fraunhofer FOKUS, Berlin, Germany e-mail: naouel.karam@fokus.fraunhofer.de"/> Fraunhofer IAIS, Sankt Augustin, Germany e-mail: abderrahmane.khiat@iais.fraunhofer.de"/> Friedrich-Schiller University of Jena, Germany e-mail: alsayed.algergawy@uni-jena.de"/> MARUM, University of Bremen, Germany e-mail: mbuss@marum.de"/> Senckenberg Biodiversity and Climate Research Center, Frankfurt, Germany e-mail: claus.weiland@senckenberg.de"/> Palmengarten der Stadt Frankfurt, Germany e-mail: marco.schmidt@stadt-frankfurt.de"/>
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2020 Volume 35
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RESEARCH ARTICLE   Open Access    

Matching biodiversity and ecology ontologies: challenges and evaluation results

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  • Abstract: Biodiversity research studies the variability and diversity of organisms, including variability within and between species with particular focus on the functional diversity of traits and their relationship to environment. Managing biodiversity data implies dealing with its heterogeneous nature using semantics and tailored ontologies. These are themselves differently conceived, and combining them in semantically enabled applications necessitates an effective alignment between their concepts. This paper describes the ontology matching of biodiversity- and ecology-related ontologies. We illustrate diverse challenges introduced by this kind of ontologies to ontology matching in general. Real use cases requiring pairwise alignments between environment and trait ontologies are introduced. We describe our experience creating a new track at the Ontology Alignment Evaluation Initiative designed for this specific domain and report on the results obtained by state-of-the-art participating systems. The biodiversity and ecology use case turns out to be a strong one for ontology matching, introducing new interesting challenges. Even if most of the matching systems perform relatively well in the proposed matching tasks, there is still room for improvement. We highlight possible directions in that matter and elaborate on our plan to further progress with the track.
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  • Cite this article

    Naouel Karam, Abderrahmane Khiat, Alsayed Algergawy, Melanie Sattler, Claus Weiland, Marco Schmidt. 2020. Matching biodiversity and ecology ontologies: challenges and evaluation results. The Knowledge Engineering Review 35(1), doi: 10.1017/S0269888920000132
    Naouel Karam, Abderrahmane Khiat, Alsayed Algergawy, Melanie Sattler, Claus Weiland, Marco Schmidt. 2020. Matching biodiversity and ecology ontologies: challenges and evaluation results. The Knowledge Engineering Review 35(1), doi: 10.1017/S0269888920000132
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RESEARCH ARTICLE   Open Access    

Matching biodiversity and ecology ontologies: challenges and evaluation results

  • Received: 14 December 2018
  • Revised: 27 January 2020
  • Accepted: 05 February 2020
  • Published online: 09 March 2020
The Knowledge Engineering Review  35,  2020, 35(1)  |  Cite this article

Abstract: Abstract: Biodiversity research studies the variability and diversity of organisms, including variability within and between species with particular focus on the functional diversity of traits and their relationship to environment. Managing biodiversity data implies dealing with its heterogeneous nature using semantics and tailored ontologies. These are themselves differently conceived, and combining them in semantically enabled applications necessitates an effective alignment between their concepts. This paper describes the ontology matching of biodiversity- and ecology-related ontologies. We illustrate diverse challenges introduced by this kind of ontologies to ontology matching in general. Real use cases requiring pairwise alignments between environment and trait ontologies are introduced. We describe our experience creating a new track at the Ontology Alignment Evaluation Initiative designed for this specific domain and report on the results obtained by state-of-the-art participating systems. The biodiversity and ecology use case turns out to be a strong one for ontology matching, introducing new interesting challenges. Even if most of the matching systems perform relatively well in the proposed matching tasks, there is still room for improvement. We highlight possible directions in that matter and elaborate on our plan to further progress with the track.

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    Acknowledgments

    • This work was partially funded by the German Research Foundation in the context of the GFBio Project (grant no. SE 553/7-1) and the CRC 1076 AquaDiva, the German Federal Ministry of Education and Research (BMBF) through the project QURATOR (grant no. 03WKDA1A), the Leitprojekt der Fraunhofer Gesellschaft in the context of the MED2ICIN project (grant no. 600628), and the German Network for Bioinformatics Infrastructure—de.NBI (grant no. 031A539B). We would like to thank Ernesto Jiménez-Ruiz and the organizers and participants of the OAEI campaign.

    • www.gfbio.org.

    • www.aquadiva.uni-jena.de.

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    Naouel Karam, Abderrahmane Khiat, Alsayed Algergawy, Melanie Sattler, Claus Weiland, Marco Schmidt. 2020. Matching biodiversity and ecology ontologies: challenges and evaluation results. The Knowledge Engineering Review 35(1), doi: 10.1017/S0269888920000132
    Naouel Karam, Abderrahmane Khiat, Alsayed Algergawy, Melanie Sattler, Claus Weiland, Marco Schmidt. 2020. Matching biodiversity and ecology ontologies: challenges and evaluation results. The Knowledge Engineering Review 35(1), doi: 10.1017/S0269888920000132
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