Abstract
To successfully integrate biomedical data it is crucial to establish meaningful relationships between the ontologies used to annotate this data. Recent developments in ontology alignment techniques, including our AgreementMakerLight system, have been successful in matching very large biomedical ontologies. However the visualization of these alignments is still a challenge.
We have developed a graphical user interface for AgreementMakerLight that follows its core focus on computational efficiency and the handling of very large ontologies. It allows non-expert users to easily align biomedical ontologies, offering a wide selection of matching strategies and algorithms, with a particular focus on the use of external background knowledge. The visualization of the resulting alignment is based on linked subgraphs which are generated according to search queries over the full graph composed by the matched ontologies and the mappings between them. This strategy decreases the need for computational resources and improves the visualization experience, by letting the user focus on selected areas of the alignment.
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References
Euzenat, J., Shvaiko, P.: Ontology matching, vol. 18. Springer, Berlin (2007)
Smith, B., Ashburner, M., Rosse, C., Bard, J., Bug, W., Ceusters, W., Goldberg, L., Eilbeck, K., Ireland, A., Mungall, C., et al.: The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nature Biotechnology 25(11), 1251–1255 (2007)
Kocbek, S., Perret, J.L., Kim, J.D.: Visual presentation of mappings between biomedical ontologies. In: SWAT4LS (2012)
Jiménez-Ruiz, E., Grau, B.C., Zhou, Y., Horrocks, I.: Large-scale interactive ontology matching: Algorithms and implementation. In: ECAI, vol. 242, pp. 444–449 (2012)
Faria, D., Pesquita, C., Santos, E., Palmonari, M., Cruz, I.F., Couto, F.M.: The agreementMakerLight ontology matching system. In: Meersman, R., Panetto, H., Dillon, T., Eder, J., Bellahsene, Z., Ritter, N., De Leenheer, P., Dou, D. (eds.) ODBASE 2013. LNCS, vol. 8185, pp. 527–541. Springer, Heidelberg (2013)
Cheatham, M., Hitzler, P.: String similarity metrics for ontology alignment. In: Alani, H., Kagal, L., Fokoue, A., Groth, P., Biemann, C., Parreira, J.X., Aroyo, L., Noy, N., Welty, C., Janowicz, K. (eds.) ISWC 2013, Part II. LNCS, vol. 8219, pp. 294–309. Springer, Heidelberg (2013)
Pesquita, C., Faria, D., Stroe, C., Santos, E., Cruz, I.F., Couto, F.M.: What’s in a ‘nym’? Synonyms in Biomedical Ontology Matching. In: Alani, H., Kagal, L., Fokoue, A., Groth, P., Biemann, C., Parreira, J.X., Aroyo, L., Noy, N., Welty, C., Janowicz, K. (eds.) ISWC 2013, Part I. LNCS, vol. 8218, pp. 526–541. Springer, Heidelberg (2013)
Hartung, M., Gross, A., Kirsten, T., Rahm, E.: Effective mapping composition for biomedical ontologies. In: Semantic Interoperability in Medical Informatics (SIMI-2012), Workshop at ESWC, vol. 12 (2012)
Paulheim, H., Hertling, S., Ritze, D.: Towards evaluating interactive ontology matching tools. In: Cimiano, P., Corcho, O., Presutti, V., Hollink, L., Rudolph, S. (eds.) ESWC 2013. LNCS, vol. 7882, pp. 31–45. Springer, Heidelberg (2013)
Cruz, I.F., Stroe, C., Palmonari, M.: Interactive user feedback in ontology matching using signature vectors. In: 2012 IEEE 28th International Conference on Data Engineering (ICDE), pp. 1321–1324. IEEE (2012)
Granitzer, M., Sabol, V., Onn, K.W., Lukose, D., Tochtermann, K.: Ontology alignmenta survey with focus on visually supported semi-automatic techniques. Future Internet 2(3), 238–258 (2010)
Fu, B., Noy, N.F., Storey, M.-A.: Indented tree or graph? A usability study of ontology visualization techniques in the context of class mapping evaluation. In: Alani, H., Kagal, L., Fokoue, A., Groth, P., Biemann, C., Parreira, J.X., Aroyo, L., Noy, N., Welty, C., Janowicz, K. (eds.) ISWC 2013, Part I. LNCS, vol. 8218, pp. 117–134. Springer, Heidelberg (2013)
Cruz, I.F., Sunna, W.: Structural Alignment Methods with Applications to Geospatial Ontologies. Transactions in GIS, Special Issue on Semantic Similarity Measurement and Geospatial Applications 12(6), 683–711 (2008)
Massmann, S., Raunich, S., Aumüller, D., Arnold, P., Rahm, E.: Evolution of the COMA match system. Ontology Matching 49 (2011)
Ngo, D., Bellahsene, Z.: YAM++: A multi-strategy based approach for ontology matching task. In: ten Teije, A., Völker, J., Handschuh, S., Stuckenschmidt, H., d’Acquin, M., Nikolov, A., Aussenac-Gilles, N., Hernandez, N. (eds.) EKAW 2012. LNCS, vol. 7603, pp. 421–425. Springer, Heidelberg (2012)
Thayasivam, U., Doshi, P.: Optima results for oaei 2011. In: Proc. of 6th OM Workshop, pp. 204–211 (2011)
Grau, B.C., Dragisic, Z., Eckert, K., Euzenat, J., Ferrara, A., Granada, R., Ivanova, V., Jiménez-Ruiz, E., Kempf, A.O., Lambrix, P., et al.: Results of the ontology alignment evaluation initiative 2013. In: Proc. 8th ISWC workshop on ontology matching (OM), pp. 61–100 (2013)
Santos, E., Faria, D., Pesquita, C., Couto, F.: Ontology alignment repair through modularization and confidence-based heuristics. arXiv preprint arXiv:1307.5322 (2013)
Bastian, M., Heymann, S., Jacomy, M.: Gephi: an open source software for exploring and manipulating networks. In: ICWSM, pp. 361–362 (2009)
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Pesquita, C., Faria, D., Santos, E., Neefs, JM., Couto, F.M. (2014). Towards Visualizing the Alignment of Large Biomedical Ontologies. In: Galhardas, H., Rahm, E. (eds) Data Integration in the Life Sciences. DILS 2014. Lecture Notes in Computer Science(), vol 8574. Springer, Cham. https://doi.org/10.1007/978-3-319-08590-6_10
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DOI: https://doi.org/10.1007/978-3-319-08590-6_10
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