{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,5]],"date-time":"2026-01-05T18:28:45Z","timestamp":1767637725134,"version":"3.48.0"},"reference-count":62,"publisher":"Maximum Academic Press","license":[{"start":{"date-parts":[[2020,3,9]],"date-time":"2020-03-09T00:00:00Z","timestamp":1583712000000},"content-version":"unspecified","delay-in-days":68,"URL":"https:\/\/www.cambridge.org\/core\/terms"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["The Knowledge Engineering Review"],"published-print":{"date-parts":[[2020]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>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.<\/jats:p>","DOI":"10.1017\/s0269888920000132","type":"journal-article","created":{"date-parts":[[2020,3,9]],"date-time":"2020-03-09T07:06:16Z","timestamp":1583737576000},"source":"Crossref","is-referenced-by-count":15,"title":["Matching biodiversity and ecology ontologies: challenges and evaluation results"],"prefix":"10.48130","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6762-6417","authenticated-orcid":false,"given":"Naouel","family":"Karam","sequence":"first","affiliation":[]},{"given":"Abderrahmane","family":"Khiat","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8550-4720","authenticated-orcid":false,"given":"Alsayed","family":"Algergawy","sequence":"additional","affiliation":[]},{"given":"Melanie","family":"Sattler","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0351-6523","authenticated-orcid":false,"given":"Claus","family":"Weiland","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6087-6117","authenticated-orcid":false,"given":"Marco","family":"Schmidt","sequence":"additional","affiliation":[]}],"member":"27968","published-online":{"date-parts":[[2020,3,9]]},"reference":[{"key":"S0269888920000132_ref59","doi-asserted-by":"publisher","DOI":"10.3897\/biss.3.37048"},{"key":"S0269888920000132_ref58","unstructured":"Wang, P. , Zhou, Y. & Xu, B. 2011. 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Jahrestagung der Gesellschaft f\u00fcr Informatik, Informatik 2014, Big Data - Komplexit\u00c4t meistern, September 22\u201326, 2014, Stuttgart, Deutschland, pp. 1711\u20131721."},{"key":"S0269888920000132_ref26","unstructured":"Fichtm\u00fcller, D. , Gleisberg, M. , Karam, N. , M\u00fcller-Birn, C. & G\u00fcntsch, A. 2017. Terminologies as a neglected part of research data: making supplementary research data available through the GFBio terminology service. In Proceedings of the 2nd International Workshop on Semantics for Biodiversity Co-located with 16th International Semantic Web Conference (ISWC \u201917), Vienna, Austria, October 22, 2017."},{"key":"S0269888920000132_ref62","unstructured":"Yilmaz, P. , Kottmann, R. , Field, D. , Knight, R. & al. 2011. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (mixs) specifications. 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Ontology matching: State of the art and future challenges. IEEE Transactions on Knowledge and Data Engineering 25(1), 158\u2013176."},{"key":"S0269888920000132_ref7","doi-asserted-by":"publisher","DOI":"10.1186\/2041-1480-4-43"},{"key":"S0269888920000132_ref33","first-page":"107","volume-title":"Application of Semantic Technology in Biodiversity Science","author":"Hoehndorf","year":"2018"},{"key":"S0269888920000132_ref20","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-662-49534-6_5"},{"key":"S0269888920000132_ref4","doi-asserted-by":"publisher","DOI":"10.1016\/j.datak.2014.07.001"},{"key":"S0269888920000132_ref36","unstructured":"Jim\u00e9nez-Ruiz, E. , Grau, B. C. & Horrocks, I. 2013. Is my ontology matching system similar to yours? In Proceedings of the 8th International Workshop on Ontology Matching Co-located with the 12th International Semantic Web Conference (ISWC 2013), Sydney, Australia, October 21, 2013, Shvaiko, P., Euzenat, J., Srinivas, K., Mao, M. & Jim\u00e9nez-Ruiz, E. (eds), CEUR Workshop Proceedings 1111. CEUR-WS.org, pp. 229\u2013230."},{"key":"S0269888920000132_ref61","unstructured":"Wilkinson, M. D. , Dumontier, M. , Aalbersberg & al. 2016. The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data 3, 160018+."},{"key":"S0269888920000132_ref37","unstructured":"Kalfoglou, Y. & Schorlemmer, W. M. 2005. Ontology mapping: the state of the art. In Semantic Interoperability and Integration."},{"key":"S0269888920000132_ref3","article-title":"Towards a reference plant trait ontology for modeling knowledge of plant traits and phenotypes.","volume":"1","author":"Arnaud.","year":"2012","journal-title":"Proceedings of the International Conference on Knowledge Engineering and Ontology Development"},{"key":"S0269888920000132_ref34","unstructured":"IPBES 2018. The IPBES assessment report on land degradation and restoration."},{"key":"S0269888920000132_ref45","unstructured":"Melnik, S. , Garcia-Molina, H. & Rahm, E. 2002. Similarity flooding: a versatile graph matching algorithm and its application to schema matching. In ICDE \u201902."},{"key":"S0269888920000132_ref22","unstructured":"Ehrig, M. 2007. Ontology Alignment: Bridging the Semantic Gap, Semantic Web and Beyond: Computing for Human Experience 4, Springer."},{"key":"S0269888920000132_ref35","unstructured":"Jim\u00e9nez-Ruiz, E. & Grau, B. C. 2011. LogMap: logic-based and scalable ontology matching. In 10th International Semantic Web Conference, ISWC \u201911, pp. 273\u2013288."},{"key":"S0269888920000132_ref53","unstructured":"Stevens, P. F. Glossary of the angiosperm phylogeny website, New York Botanical Garden. https:\/\/sweetgum.nybg.org\/science\/glossary\/glossary-checklist\/"},{"key":"S0269888920000132_ref11","doi-asserted-by":"publisher","DOI":"10.1093\/database\/bay110"},{"key":"S0269888920000132_ref39","unstructured":"Kattge, J. , Ogle, K. , Bnisch, G. , Daz, S. , Lavorel, S. , Madin, J. , Nadrowski, K. , Nllert, S. , Sartor, K. & Wirth, C. 2011. A generic structure for plant trait databases. Methods in Ecology and Evolution 2(2), 202\u2013213."},{"key":"S0269888920000132_ref52","doi-asserted-by":"publisher","DOI":"10.1007\/s10115-016-0983-3"},{"key":"S0269888920000132_ref42","unstructured":"Laadhar, A. , Ghozzi, F. , Megdiche, I. , Ravat, F. , Teste, O. & Gargouri, F. 2017. 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