Publications

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2017
Barata, A., L. Carvalho, and F. M. Couto, "Anthropometric data analytics: a portuguese case study", International Conference on Practical Applications of Computational Biology & Bioinformatics: Springer, pp. 92–100, 2017.
Ferreira, J. D., B. Inácio, R. M. Salek, and F. M. Couto, "Assessing Public Metabolomics Metadata, Towards Improving Quality", Journal of integrative bioinformatics, vol. 14, no. 4: De Gruyter, 2017.
Fernandes, M., J. Decouchant, F. M. Couto, and P. Esteves-Verissimo, "Cloud-Assisted Read Alignment and Privacy", 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, vol. 616: Springer, pp. 220, 2017.
Lamurias, A., L. A. Clarke, and F. M. Couto, "Extracting microRNA-gene relations from biomedical literature using distant supervision", PloS one, vol. 12, no. 3: Public Library of Science, pp. e0171929, 2017.
Lamurias, A., J. D. Ferreira, L. A. Clarke, and F. M. Couto, "Generating a Tolerogenic Cell Therapy Knowledge Graph from Literature", Frontiers in Immunology, vol. 8: Frontiers, pp. 1656, 2017.
Cogo, V. V., A. Bessani, F. M. Couto, M. Gama-Carvalho, M. Fernandes, and P. Esteves-Verissimo, "How Can Photo Sharing Inspire Sharing Genomes?", 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, vol. 616: Springer, pp. 74, 2017.
Lobo, M., A. Lamurias, and F. M. Couto, "Identifying Human Phenotype Terms by Combining Machine Learning and Validation Rules", BioMed Research International, vol. 2017: Hindawi, 2017.
Campos, L., V. Pedro, and F. Couto, "Impact of translation on named-entity recognition in radiology texts", Database, vol. 2017: Oxford University Press, 2017.
Asif, M., C. Rasga, H. Martiniano, JX. Santos, AR. Marques, FM. Couto, and AM. Vicente, "An integrative system biology approach for dissecting Autism Spectrum Disorder", 2º Dia do Jovem Investigador do Instituto Nacional de Saúde Doutor Ricardo Jorge, 8 maio 2017: Instituto Nacional de Saúde Doutor Ricardo Jorge, IP, 2017.
Asif, M., H. F. Martiniano, C. Rasga, A. R. Marques, J. X. Santos, F. M. Couto, A. M. Vicente, and , "An integrative system biology approach to delineate complex genotype-phenotype associations in Autism Spectrum Disorder", 2nd BioSys Retreat 2017, 6-7 October, 2017: Instituto Nacional de Saúde Doutor Ricardo Jorge, IP, 2017.
Couto, F. M., L. Campos, and A. Lamurias, "MER: a minimal named-entity recognition tagger and annotation server", Proceedings of the BioCreative, Conference: BeCalm challenge evaluation workshop (Biocreative V.5), at Barcelona, Spain, vol. 5, 2017.
Inácio, B., J. D. Ferreira, and F. M. Couto, "Metadata Analyser: measuring metadata quality", International Conference on Practical Applications of Computational Biology & Bioinformatics: Springer, pp. 197–204, 2017.
Rodrigues, M. J., and F. M. Couto, "MoRS at SemEval-2017 task 3: Easy to use SVM in ranking tasks", Proceedings of the 11th International Workshop on Semantic Evaluation (SemEval-2017), pp. 287–291, 2017.
Campos, L., and F. Couto, "MRA-Proof of Concept of a Multilingual Report Annotator Web Application", arXiv preprint arXiv:1704.01748, 2017.
Lamurias, A., D. Sousa, S. Pereira, L. Clarke, and F. M. Couto, "ULISBOA at SemEval-2017 Task 12: Extraction and classification of temporal expressions and events", Proceedings of the 11th International Workshop on Semantic Evaluation (SemEval-2017), pp. 1019–1023, 2017.
2016
Lamurias, A., M. J. Rodrigues, L. A. Clarke, and F. M. Couto, "Extraction of Regulatory Events using Kernel-based Classifiers and Distant Supervision", ACL 2016, pp. 88, 2016.
Gonçalves, D., M. Costa, and F. M. Couto, "A Flexible Recommendation System for Cable TV", arXiv preprint arXiv:1609.02451, 2016.
Bastos, H. P., L. Sousa, L. A. Clarke, and F. M. Couto, "Functional coherence metrics in protein families", Journal of biomedical semantics, vol. 7, no. 1: BioMed Central, pp. 41, 2016.
Barros, M., F. M. Couto, and , "Knowledge Representation and Management: a linked data perspective", IMIA Yearbook: Schattauer Publishers, pp. 178–183, 2016.
Gonçalves, D., M. Costa, and F. M. Couto, "A Large-Scale Characterization of User Behaviour in Cable TV", arXiv preprint arXiv:1609.02453, 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.
Barros, M., A. Lamurias, G. Figueiró, M. Antunes, J. Teixeira, A. Pinheiro, and F. M. Couto, "ULISBOA at SemEval-2016 Task 12: Extraction of temporal expressions, clinical events and relations using IBEnt.", SemEval@ NAACL-HLT, pp. 1263–1267, 2016.
Rodrigues, M. J., M. Falé, A. Lamurias, and F. M. Couto, "WS4A: a biomedical question and answering system based on public web services and ontologies", arXiv preprint arXiv:1609.08492, 2016.
2015
Groza, T.., S.. Köhler, S.. Doelken, N.. Collier, A.. Oellrich, D.. Smedley, F. Couto, G.. Baynam, A.. Zankl, and P.. Robinson, "Automatic concept recognition using the Human Phenotype Ontology}reference and test suite corpora", Database, vol. 2015, pp. 1-13, 2015.
Krallinger, M.., O.. Rabal, F.. Leitner, M.. Vazquez, D.. Salgado, Z.. Lu, R.. Leaman, Y.. Lu, D.. Ji, D.. Lowe, et al., "The CHEMDNER corpus of chemicals and drugs and its annotation principles", Journal of Cheminformatics, vol. 7, pp. S2, 1-20, 2015.
Bastos, H., L.. Sousa, L.. Clarke, and F. Couto, "GRYFUN: A Web Application for GO Term Annotation Visualization and Analysis in Protein Sets", PLoS ONE, vol. 10, pp. 1-20, 2015.
Cogo, V., A. Bessani, F. Couto, and P. Verissimo, "A High-Throughput Method to Detect Privacy-Sensitive Human Genomic Data", Workshop on Privacy in the Electronic Society (WPES), 2015.
Lamurias, A., M.. Lobo, M.. Antunes, L.. Clarke, and F. Couto, "Identifying chemical entities in patents using brown clustering and semantic similarity", 5th BioCreative Challenge Evaluation, 2015.
Lamurias, A., L.. Clarke, and F. Couto, "IICE: web tool for automatic identification of chemical entities and interactions", European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML-PKDD), Demo Track, 2015.
Lamurias, A., J. Ferreira, and F. Couto, "Improving chemical entity recognition through h-index based semantic similarity", Journal of Cheminformatics, vol. 7, pp. S13, 1-20, 2015.
Leal, A.., B. Martins, and F. Couto, "Recognition and Normalization of Biomedical Entities Based on Ontologies", Bioinformatics Open Days, University of Lisbon, 2015.
Machado, C. M., D. Rebholz-Schuhmann, A. T. Freitas, and F. Couto, "The semantic web in translational medicine: current applications and future directions", Briefings in bioinformatics, vol. 16, no. 1: Oxford University Press, pp. 89–103, 2015.
Barata, C., M. Abreu, P. Torres, J. Teixeira, T. Guerreiro, and F. Couto, "Social Impact-Identifying Quotes of Literary Works in Social Networks", Progress in Artificial Intelligence: Springer, pp. 789–795, 2015.
Leal, A.., B.. Martins, and F. Couto, "ULisboa: Recognition and Normalization of Medical Concepts", 8th International Workshop on Semantic Evaluation (SemEval), 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.
Lamurias, A., J. Ferreira, and F. Couto, "Chemical named entity recognition: Improving recall using a comprehensive list of lexical features", 8th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2014): Springer International Publishing, pp. 253–260, 2014.
Lamurias, A., J. Ferreira, and F. Couto, "Chemical Named Entity Recognition: Improving Recall Using a Comprehensive List of Lexical", Bioinformatics (Pacbb 2014), vol. 294: Springer, pp. 253, 2014.
Silva, L., F. Couto, H.. Manso, and A.. Vicente, "Development of a semantic model for Cerebrovascular Accident (CVA) Patients", Bioinformatics Open Days, University of Braga, 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.
Leitão, N., J.. Leitão, and F. Couto, "Expansão do Espaço de Procura em Mapeamento Genómico de Alto Rendimento", INForum - Simp{ó}sio de Inform{á}tica, 2014.
Mendes, T.., B.. Rodrigues, A.. Moitinho, M.. Gomes, F. Couto, T. Guerreiro, and A.. Krone-Martins, "Exploração Visual Online de Bases de Dados Astronómicas", INForum - Simpósio de Informática, 2014.
Martins, J., J. Carilho, O. Schnell, C. Duarte, F. Couto, L. Carriço, and T. Guerreiro, "Friendsourcing the unmet needs of people with dementia", Proceedings of the 11th Web for All Conference: ACM, pp. 35, 2014.
Ferreira, J., B.. Bono, and F. Couto, "From data to knowledge: a tool for clustering multi-scale resources for physiology research", Virtual Physiological Human (VPH), 2014.
Lamurias, A., J. Ferreira, and F. Couto, "Identifying interactions between chemical entities in biomedical text", Journal of integrative bioinformatics, vol. 11, no. 3, pp. 247, 2014.
Lamurias, A., and F. Couto, "Identifying Interactions Between Chemical Entities in Text", Bioinformatics Open Days, University of Braga, 2014.
Costa, M., F. Couto, and M. J. Silva, "Learning temporal-dependent ranking models", Proceedings of the 37th international ACM SIGIR conference on Research & development in information retrieval: ACM, pp. 757–766, 2014.
Leitão, N., J.. Leitão, and F. Couto, "LLC-GNUMAP: Scalable, Precise, and High-Coverage Genomics Mapping", Bioinformatics Open Days, University of Braga, 2014.
Carilho, J.., O.. Schnell, J.. Martins, L. Carriço, C. Duarte, F. Couto, and T. Guerreiro, "Predicting Relevant Events in the Life of a Person with Alzheimer", Bioinformatics Open Days, University of Braga, 2014.
Couto, F., "Rating, recognizing and rewarding metadata integration and sharing on the semantic web", 10th International Workshop on Uncertainty Reasoning for the Semantic Web (URSW 2014), pp. 67, 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.
Leal, A., D. Gonçalves, B. Martins, and F. Couto, "ULisboa: Identification and Classification of Medical Concepts", SemEval 2014, pp. 711, 2014.
Asif, M., I.. Conceição, C.. Café, J.. Almeida, S.. Mouga, G.. Oliveira, F. Couto, and A.. Vicente, "Use of machine learning approaches to explore genetic and phenotypic associations for Autism Spectrum Disorder", 18th Meeting of The Portuguese Society of Human Genetics (SPGH), 2014.
Norman, R., and F. Couto, "Using Google Scholar to predict self citation: A case study in Health Economics", arXiv preprint arXiv:1406.5241, 2014.
Moitinho, A.., T.. Mendes, B.. Rodrigues, M.. Gomes, A.. Krone-Martins, and F. Couto, "VEJA - Visual Exploration Just Anywhere", International Astronomical Union Symposium (IAUS), 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", 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.
Bastos, H., L. A. Clarke, and F. Couto, "Annotation extension through protein family annotation coherence metrics", Frontiers in genetics, vol. 4: Frontiers Media SA, 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.
Lamurias, A., T. Grego, and F. Couto, "Chemical compound and drug name recognition using CRFs and semantic similarity based on ChEBI", BioCreative Challenge Evaluation Workshop, vol. 2, pp. 75, 2013.
Couto, F., "CIDS country rankings: comparing documents and citations of USA, UK and China top researchers", arXiv preprint arXiv:1310.5597, 2013.
Grego, T., and F. Couto, "Enhancement of chemical entity identification in text using semantic similarity validation", PloS one, vol. 8, no. 5: Public Library of Science, pp. e62984, 2013.
Machado, C. M., A. T. Freitas, and F. Couto, "Enrichment analysis applied to disease prognosis.", J. Biomedical Semantics, vol. 4, pp. 21, 2013.
Ferreira, J., J. Hastings, and F. Couto, "Exploiting disjointness axioms to improve semantic similarity measures", Bioinformatics, vol. 29, no. 21: Oxford University Press, pp. 2781–2787, 2013.
Grego, T., F. Pinto, and F. Couto, "LASIGE: using conditional random fields and chebi ontology", Proceedings of SemEval, pp. 660–666, 2013.
Couto, F., and S. H Pinto, "The next generation of similarity measures that fully explore the semantics in biomedical ontologies", Journal of bioinformatics and computational biology, vol. 11, no. 05: The Authors, 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.
Moreira, S., J. Filgueiras, B. Martins, F. Couto, and M. J. Silva, "Reaction: A naive machine learning approach for sentiment classification", Second Joint Conference on Lexical and Computational Semantics (* SEM), vol. 2, pp. 490–494, 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.
Moreira, S., D. S. Batista, P. Carvalho, F. Couto, and M. J. Silva, "Tracking politics with POWER", Program, vol. 47, no. 2: Emerald Group Publishing Limited, pp. 120–135, 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
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.
Couto, F., J. Ferreira, J. Zamite, C. Santos, T. Posse, P. Graça, D. Domingos, and M. J. Silva, "The Epidemic Marketplace Platform: towards semantic characterization of epidemiological resources using biomedical ontologies", International Conference on Biomedical Ontologies, 2012.
Couto, F., J. Ferreira, J. Zamite, C. Santos, T. Posse, P. Graça, D. Domingos, and M. J. Silva, "The Epidemic Marketplace Platform: towards semantic characterization of epidemiological resources using biomedical ontologies.", ICBO, 2012.
Grego, T., F. R. Pinto, and F. Couto, "Identifying Chemical Entities based on ChEBI.", ICBO, 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.
Batista, D. S., J. Ferreira, F. Couto, and M. J. Silva, "Toponym disambiguation using ontology-based semantic similarity", Computational Processing of the Portuguese Language: Springer Berlin Heidelberg, pp. 179–185, 2012.
Machado, C. M., F. Couto, A. R. Fernandes, S. Santos, and A. T. Freitas, "Toward a translational medicine approach for hypertrophic cardiomyopathy", Information Technology in Bio-and Medical Informatics: Springer Berlin Heidelberg, pp. 151–165, 2012.
Ferreira, J., D. Paolotti, F. Couto, and M. J. Silva, "On the usefulness of ontologies in epidemiology research and practice", Journal of epidemiology and community health: BMJ Publishing Group Ltd, pp. jech–2012, 2012.
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.
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.
Cruz, I. F., C. Stroe, C. Pesquita, F. Couto, and V. Cross, "Biomedical Ontology Matching Using the AgreementMaker System.", ICBO, 2011.
Couto, F., and E. Santos, Desenvolvimento de Sistemas de Informação baseados em PHP e MySQL, e Java e Oracle, : DI-FCUL, 2011.
Couto, F., M. J. Silva, and , "Disjunctive shared information between ontology concepts: application to Gene Ontology.", J. Biomedical Semantics, vol. 2, pp. 5, 2011.
Ferreira, J., and F. Couto, "Generic Semantic Relatedness Measure for Biomedical Ontologies.", ICBO, vol. 833, 2011.
Zamite, J., F. Silva, F. Couto, and M. J. Silva, "MEDCollector: Multisource epidemic data collector", Transactions on large-scale data-and knowledge-centered systems IV: Springer Berlin Heidelberg, pp. 40–72, 2011.
Simões, T., N. Charro, J. Blonder, D. Faria, F. Couto, K. C. Chan, T. Waybright, H. J. Isaaq, T. D. Veenstra, and D. Penque, "Molecular profiling of the human nasal epithelium: A proteomics approach", Journal of proteomics, vol. 75, no. 1: Elsevier, pp. 56–69, 2011.
Moreira, S., D. S. Batista, P. Carvalho, F. Couto, and M. J. Silva, "POWER-Politics Ontology for Web Entity Retrieval", Advanced Information Systems Engineering Workshops: Springer Berlin Heidelberg, pp. 489–500, 2011.
Charro, N., B. L. Hood, D. Faria, P. Pacheco, P. Azevedo, C. Lopes, A. Bugalho de Almeida, F. Couto, T. P. Conrads, and D. Penque, "Serum proteomics signature of Cystic Fibrosis patients: A complementary 2-DE and LC–MS/MS approach", Journal of proteomics, vol. 74, no. 1: Elsevier, pp. 110–126, 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.", ICBO, 2011.

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