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Bastos, H., D. Faria, C. Pesquita, and A. O. Falcao, "Using GO terms to evaluate protein clustering", BioOntologies SIG at ISMB/ECCB-15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), 2007.
Cruz, I. F., C. Stroe, F. Caimi, A. Fabiani, C. Pesquita, F. Couto, and M. Palmonari, "Using AgreementMaker to align ontologies for OAEI 2011", Proceedings of the Sixth International Workshop on Ontology Matching, pp. 114–121, 2011.
Dragisic, Z., V. Ivanova, P. Lambrix, D. Faria, E. Jiménez-Ruiz, and C. Pesquita, "User validation in ontology alignment", International Semantic Web Conference: Springer, pp. 200–217, 2016.
Pesquita, C., D. Faria, T. Grego, F. Couto, and M. J. Silva, "Untangling BioOntologies for Mining Biomedical Information", Handbook of research on text and Web mining technologies: Information Science Reference, 2009.
Silva, M. J., F. Couto, T. Grego, D. Faria, and C. Pesquita, Untangling BioOntologies for Mining Biomedical Information, : Handbook of Research on Text and Web Mining Technologies, IGI Global Publishing, 2008.
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Cheatham, M., I. F. Cruz, J. Euzenat, and C. Pesquita, "Special issue on ontology and linked data matching.", Semantic Web, vol. 8, no. 2, pp. 183–184, 2017.
Pesquita, C., "Semantic similarity in the gene ontology", The Gene Ontology Handbook: Springer, pp. 161–173, 2017.
Pesquita, C., D. Faria, A. O. Falcao, P. Lord, and F. Couto, "Semantic similarity in biomedical ontologies", PLoS computational biology, vol. 5, no. 7: Public Library of Science, pp. e1000443, 2009.
Pesquita, C., D. Faria, A. O. Falcao, P. Lord, F. Couto, and , "Semantic Similarities in Biomedical Ontologies", IMIA Yearbook, vol. 5, pp. 84–84, 2010.
Cheatham, M., and C. Pesquita, "Semantic Data Integration", Handbook of Big Data Technologies: Springer, pp. 263–305, 2017.
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Faria, D., C. Pesquita, F. Couto, and A. O. Falcao, Proteinon: A web tool for protein semantic similarity, : Department of Informatics, University of Lisbon, 2007.
Ivanova, V., T. Kauppinen, S. Lohmann, S. Mazumdar, C. Pesquita, and K. Xu, "Proceedings of the International Workshop on Visualizations and User Interfaces for Knowledge Engineering and Linked Data Analytics", International Workshop on Visualizations and User Interfaces for Knowledge Engineering and Linked Data Analytics: CEUR Workshop Proceedings, 2014.
Pesquita, C., and F. Couto, "Predicting the extension of biomedical ontologies", PLoS computational biology, vol. 8, no. 9: Public Library of Science, pp. e1002630, 2012.
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Oliveira, D., and C. Pesquita, "Improving the interoperability of biomedical ontologies with compound alignments", Journal of biomedical semantics, vol. 9, no. 1: BioMed Central, pp. 1, 2018.
Pesquita, C., Improving semantic similarity for proteins based on the gene ontology, , 2007.
Pesquita, C., T. Grego, and F. Couto, "Identifying Gene Ontology Areas for Automated Enrichment", Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living: Springer, pp. 934–941, 2009.
Couto, F., T. Grego, H. Bastos, C. Pesquita, R. Torres, P. Sánchez, L. Pascual, and C. Blaschke, "Identifying bioentity recognition errors of rule-based text-mining systems", Digital Information Management, 2008. ICDIM 2008. Third International Conference on: IEEE, pp. 733–738, 2008.
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Couto, F., T. Grego, C. Pesquita, and P. Verissimo, Handling self-citations using Google Scholar, : International Journal of Scientometrics, Informetrics and Bibliometrics, 2009.
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Gaspar, D., C. Trindade, A. Usié, B. Meireles, P. Barbosa, A. M. Fortes, C. Pesquita, R. L. Costa, and A. M. Ramos, "Expression Profiling in Pinus pinaster in Response to Infection with the Pine Wood Nematode Bursaphelenchus xylophilus", Forests, vol. 8, no. 8: Multidisciplinary Digital Publishing Institute, pp. 279, 2017.
Gaspar, D., C. Trindade, A. Usié, B. Meireles, P. Barbosa, A. M. Fortes, C. Pesquita, R. L. Costa, and A. M. Ramos, "Expression profiling in Pinus pinaster in response to infection with the pine wood nematode Bursaphelenchus xylophilus", Forests, vol. 8, no. 8: Multidisciplinary Digital Publishing Institute, pp. 279, 2017.
Pesquita, C., D. Faria, H. Bastos, A. O. Falcao, and F. Couto, "Evaluating GO-based Semantic Similarity Measures. ISMB/ECCB 2007 SIG Meeting Program Materials", International Society for Computational Biology, 2007.
Pesquita, C., D. Faria, H. Bastos, A. O. Falcao, and F. Couto, "Evaluating gobased semantic similarity measures", Proc. 10th Annual Bio-Ontologies Meeting, vol. 2007, pp. 37–40, 2007.
Pesquita, C., D. Faria, H. Bastos, A. O. Falcao, and F. Couto, "Evaluating go-based semantic similarity measures", Proc. 10th Annual Bio-Ontologies Meeting, vol. 37, no. 40, pp. 38, 2007.
Pesquita, C., J. Ferreira, F. Couto, and M. J. Silva, "The epidemiology ontology: an ontology for the semantic annotation of epidemiological resources", Journal of biomedical semantics, vol. 5: BioMed Central, pp. 4, 2014.
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Faria, D., C. Pesquita, E. Santos, I. F. Cruz, and F. Couto, "Automatic Background Knowledge Selection for Matching Biomedical Ontologies", PloS one, vol. 9, no. 11: Public Library of Science, pp. e111226, 2014.
Pesquita, C., Automated extension of biomedical ontologies, , 2012.
Bastos, H., B. Tavares, C. Pesquita, D. Faria, and F. Couto, "Application of Gene Ontology to gene identification", In Silico Tools for Gene Discovery: Humana Press, pp. 141–157, 2011.
Bastos, H., B. Tavares, C. Pesquita, D. Faria, and F. Couto, "Application of gene ontology to gene identification.", Methods in molecular biology (Clifton, NJ), vol. 760: Springer, pp. 141–157, 2011.
Faria, D., C. Martins, A.. Nanavaty, A.. Taheriand, C. Pesquita, E. Santos, I.. Cruz, and F. Couto, "AgreementMakerLight results for OAEI 2014", The Ninth International Workshop on Ontology Matching (OM-2013), 2014.
Faria, D., C. Pesquita, E. Santos, I. F. Cruz, and F. Couto, "AgreementMakerLight Results for OAEI 2013", Ontology Matching, pp. 101, 2013.
Faria, D., C. Pesquita, E. Santos, I. F. Cruz, and F. Couto, "AgreementMakerLight results for OAEI 2013.", OM, pp. 101–108, 2013.
Faria, D., C. Pesquita, E. Santos, M. Palmonari, I. F. Cruz, and F. Couto, "The agreementmakerlight ontology matching system", On the Move to Meaningful Internet Systems: OTM 2013 Conferences: Springer Berlin Heidelberg, pp. 527–541, 2013.
Faria, D., C. Pesquita, E. Santos, I. F. Cruz, and F. Couto, "AgreementMakerLight: A Scalable Automated Ontology Matching System", DILS 2014, pp. 29, 2014.
Faria, D., C. Pesquita, E. Santos, I.. Cruz, and F. Couto, "AgreementMakerLight 2.0: Towards Efficient Large-Scale Ontology Matching", International Semantic Web Conference (ISWC), 2014.