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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.
Dragisic, Z., K. Eckert, J. Euzenat, D. Faria, A. Ferrara, R. Granada, V. Ivanova, E. Jiménez-Ruiz, A. Kempf, P. Lambrix, et al., "Results of theOntology Alignment Evaluation Initiative 2014", International Workshop on Ontology Matching, pp. 61–104, 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.
Couto, F., D. Faria, B. Tavares, P. Gonçalves, and P. Verissimo, "Benchmarking some Portuguese S&T system research units", arXiv preprint arXiv:1302.0420, 2013.
Couto, F., D. Faria, B. Tavares, P. Gonçalves, and P. Verissimo, "Benchmarking some Portuguese S&T system research units: 2nd Edition", arXiv preprint arXiv:1302.0420, 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.
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.
Faria, D., A. E. N. Ferreira, and A. O. Falcao, "Enzyme classification with peptide programs: a comparative study", BMC bioinformatics, vol. 10, no. 1: BioMed Central Ltd, pp. 231, 2009.
Faria, D., C. Pesquita, F. Couto, and A. O. Falcao, "GOclasses: molecular function as viewed by proteins", The 12th Annual Bio-Ontologies, 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.
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.
Falcao, A. O., D. Faria, and A. Ferreira, "Peptide programs: applying fragment programs to protein classification", Proceedings of the 2nd international workshop on Data and text mining in bioinformatics: ACM, pp. 37–44, 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 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., 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.
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.