Cátia Pesquita

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2018
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.
Faria, D., C. Pesquita, I. Mott, C. Martins, F. M. Couto, and I. F. Cruz, "Tackling the challenges of matching biomedical ontologies", Journal of biomedical semantics, vol. 9, no. 1: BioMed Central, pp. 4, 2018.
Ivanova, V., P. Lambrix, S. Lohmann, and C. Pesquita, "Visualization and interaction for ontologies and linked data", Journal of Web Semantics, 2018.
Ivanova, V., P. Lambrix, S. Lohmann, and C. Pesquita, "VOILA 2018 Visualization and Interaction for Ontologies and Linked Data: Proceedings of the Fourth International Workshop on Visualization and Interaction for Ontologies and Linked Data co-located with the 17th International Semantic Web Conference (ISWC ", Fourth International Workshop on Visualization and Interaction for Ontologies and Linked Data: CEUR Workshop Proceedings, 2018.
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.
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.
Cheatham, M., and C. Pesquita, "Semantic Data Integration", Handbook of Big Data Technologies: Springer, pp. 263–305, 2017.
Pesquita, C., "Semantic similarity in the gene ontology", The Gene Ontology Handbook: Springer, pp. 161–173, 2017.
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.
2016
Faria, D., C. Pesquita, B. S. Balasubramani, C. Martins, J. Cardoso, H. Curado, F. M. Couto, and I. F. Cruz, "OAEI 2016 results of AML.", OM@ ISWC, pp. 138–145, 2016.
Bakhshandeh, M., C. Pesquita, and J. Borbinha, "An Ontological Matching Approach for Enterprise Architecture Model Analysis", International Conference on Business Information Systems: Springer, pp. 315–326, 2016.
Cardoso, J., M. Bakhshandeh, D. Faria, C. Pesquita, and J. Borbinha, "Ontology-Based Approach for Heterogeneity Analysis of EA Models", International Conference on Business Process Management: Springer, pp. 131–142, 2016.
Achichi, M., M. Cheatham, Z. Dragisic, J. Euzenat, D. Faria, A. Ferrara, G. Flouris, I. Fundulaki, I. Harrow, V. Ivanova, et al., "Results of the ontology alignment evaluation initiative 2016", CEUR workshop proceedings, vol. 1766: RWTH, pp. 73–129, 2016.
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.
Ivanova, V., P. Lambrix, S. Lohmann, and C. Pesquita, "VOILA! 2016: Proceedings of the 2nd International Workshop on Visualization and Interaction for Ontologies and Linked Data, Co-located with ISWC 2016, Kobe, Japan, October 17, 2016", 2nd International Workshop on Visualization and Interaction for Ontologies and Linked Data, Kobe, Japan, October 17: CEUR Workshop Proceedings, 2016.
2015
Serrazina, S., C. Santos, H. Machado, C. Pesquita, R. Vicentini, M. Salomé Pais, M. Sebastiana, and R. Costa, "Castanea root transcriptome in response to Phytophthora cinnamomi challenge", Tree Genetics & Genomes, vol. 11, no. 1: Springer Berlin Heidelberg, pp. 1–19, 2015.
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.
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. 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, "Automatic Background Knowledge Selection for Matching Biomedical Ontologies", PloS one, vol. 9, no. 11: Public Library of Science, pp. e111226, 2014.
Pesquita, C., M. Cheatham, D. Faria, J. Barros, E. Santos, and F. Couto, "Building reference alignments for compound matching of multiple ontologies using OBO cross-products", Ontology Matching Workshop at ISWC 2014, 2014.
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.
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.
Faria, D., E. Jiménez-Ruiz, C. Pesquita, E. Santos, and F. Couto, "Towards annotating potential incoherences in BioPortal mappings", International Semantic Web Conference, 2014.
Pesquita, C., D. Faria, E. Santos, J-M. Neefs, and F. Couto, "Towards visualizing the alignment of large biomedical ontologies", Data Integration in the Life Sciences (DILS), 2014.
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 results for OAEI 2013.", OM, pp. 101–108, 2013.
Faria, D., C. Pesquita, E. Santos, I. F. Cruz, and F. Couto, "AgreementMakerLight Results for OAEI 2013", Ontology Matching, pp. 101, 2013.
Santos, E., D. Faria, C. Pesquita, and F. Couto, "Ontology alignment repair through modularization and confidence-based heuristics", arXiv preprint arXiv:1307.5322, 2013.
Pesquita, C., D. Faria, E. Santos, and F. Couto, "To repair or not to repair: reconciling correctness and coherence in ontology reference alignments.", OM, pp. 13–24, 2013.
Pesquita, C., D. Faria, E. Santos, and F. Couto, "To repair or not to repair: reconciling correctness and coherence in ontology reference alignments", Ontology Matching, pp. 13, 2013.
Pesquita, C., D. Faria, C. Stroe, E. Santos, I. F. Cruz, and F. Couto, "What's in a 'nym'? Synonyms in Biomedical Ontology Matching", The Semantic Web–ISWC 2013: Springer Berlin Heidelberg, pp. 526–541, 2013.
2012
Pesquita, C., Automated extension of biomedical ontologies, , 2012.
Ferreira, J., C. Pesquita, F. Couto, and M. J. Silva, "Bringing epidemiology into the Semantic Web.", ICBO, 2012.
Grego, T., C. Pesquita, H. Bastos, and F. Couto, "Chemical entity recognition and resolution to ChEBI", International Scholarly Research Notices, vol. 2012: Hindawi Publishing Corporation, 2012.
Faria, D., A. Schlicker, C. Pesquita, H. Bastos, A. E. N. Ferreira, M. Albrecht, and A. O. Falcao, "Mining GO annotations for improving annotation consistency", PloS one, vol. 7, no. 7: Public Library of Science, pp. e40519, 2012.
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.
Faria, D., C. Pesquita, E. Santos, F. Couto, C. Stroe, and I. F. Cruz, "Testing the AgreementMaker System in the Anatomy Task of OAEI 2012", arXiv preprint arXiv:1212.1625, 2012.
2011
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.
Cruz, I. F., C. Stroe, C. Pesquita, F. Couto, and V. Cross, "Biomedical Ontology Matching Using the AgreementMaker System.", ICBO, 2011.
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.
Pesquita, C., and F. Couto, "Where GO is going and what it means for ontology extension", International Conference on Biomedical Ontology, 2011.
Pesquita, C., and F. Couto, "Where GO is Going and What it Means for Ontology Extension.", ICBO, 2011.
2010
Pesquita, C., C. Stroe, I. F. Cruz, and F. Couto, "BLOOMS on AgreementMaker: results for OAEI 2010", Ontology Matching, pp. 134, 2010.
Grego, T., J. Ferreira, C. Pesquita, H. Bastos, D. Vila Viçosa, J. Freire, and F. Couto, Chemical and Metabolic Pathway Semantic Similarity, , 2010.
Gomes-Alves, P., F. Couto, C. Pesquita, A. V. Coelho, and D. Penque, "Rescue of F508del-CFTR by RXR motif inactivation triggers proteome modulation associated with the unfolded protein response", Biochimica et Biophysica Acta (BBA)-Proteins & Proteomics, vol. 1804, no. 4: Elsevier, pp. 856–865, 2010.
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.
2009
Pesquita, C., D. Pessoa, D. Faria, and F. Couto, "CESSM: collaborative evaluation of semantic similarity measures", JB2009: Challenges in Bioinformatics, 2009.
Pesquita, C., D. Pessoa, D. Faria, and F. Couto, Collaborative Evaluation of GO-based Similarity Measures, : 12th Annual Bio-Ontologies Meeting at ISMB/ECCB 2009, 2009.
Taylor, I. W., R. Linding, D. Warde-Farley, Y. Liu, C. Pesquita, D. Faria, S. Bull, T. Pawson, Q. Morris, and J. L. Wrana, "Dynamic modularity in protein interaction networks predicts breast cancer outcome", Nature biotechnology, vol. 27, no. 2: Nature Publishing Group, pp. 199–204, 2009.
Pesquita, C., and F. Couto, GO where we need it to go: focused automated enrichment of the Gene Ontology. Student Council Symposium, : Student Council Symposium at ISMB/ECCB 2009, 2009.
Faria, D., C. Pesquita, F. Couto, and A. O. Falcao, "GOclasses: molecular function as viewed by proteins", The 12th Annual Bio-Ontologies, 2009.
Couto, F., T. Grego, C. Pesquita, and P. Verissimo, Handling self-citations using Google Scholar, : International Journal of Scientometrics, Informetrics and Bibliometrics, 2009.
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.
Pesquita, C., D. Faria, and F. Couto, "Measuring coherence between electronic and manual annotations in biological databases", Proceedings of the 2009 ACM symposium on Applied Computing: ACM, pp. 806–807, 2009.
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, 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.
2008
Tavares, B., H. Bastos, D. Faria, J. Ferreira, T. Grego, C. Pesquita, and F. Couto, "The Biomedical Ontology Applications (BOA) framework", evaluation, vol. 9, no. S5, pp. S4, 2008.
Bastos, H., C. Pesquita, D. Faria, and A. O. Falcao, "BOLOS: BLAST & Ontology Linked-hOmologue Stars", Proceedings of the 2008 ACM symposium on Applied computing: ACM, pp. 1278–1281, 2008.
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.
Pesquita, C., D. Faria, H. Bastos, A. Ferreira, A. O. Falcao, and F. Couto, "Metrics for GO based protein semantic similarity: a systematic evaluation", BMC bioinformatics, vol. 9, no. Suppl 5: BioMed Central Ltd, pp. S4, 2008.
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.
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., 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. ISMB/ECCB 2007 SIG Meeting Program Materials", International Society for Computational Biology, 2007.
Pesquita, C., Improving semantic similarity for proteins based on the gene ontology, , 2007.
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.
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.