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Document | BibTeX source
Marcia Barros, Andre Lamurias, Goncalo Figueiro, Marta Antunes, Joana Teixeira, Alexandre Pinheiro, Francisco M Couto, ULISBOA at SemEval-2016 Task 12: Extraction of temporal expressions, clinical events and relations using IBEnt.9th International Workshop on Semantic Evaluation (SemEval) 2016.

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Catia Pesquita, João D Ferreira, Francisco M Couto, Mário J Silva 2014: The epidemiology ontology: an ontology for the semantic annotation of epidemiological resources. Journal of biomedical semantics.

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Lara Silva, Francisco Couto, Helena Manso, Astrid Vicente, Development of a semantic model for Cerebrovascular Accident (CVA) Patients.Bioinformatics Open Days, Universidade do Minho Braga, Portugal, February, 2014.

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Marques, AF, Rosset, C., Rasinmaki, J., Vacik, H., Gordon, S., Nobre, S., Andre Falcao, Weber, D., Granitzer, M., Eriksson, LO 2013: Collaborative development of a semantic wiki on forest management decision support. Scandinavian Journal of Forest Research (), 1-14.

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D. Batista, J. Ferreira, Francisco Couto, M. Silva, Toponym Disambiguation using Ontology-based Semantic Similarity.Computational Processing of the Portuguese Language (PROPOR) 2012.

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D. Faria, C. Pesquita, E. Santos, M. Palmonari, I. Cruz, Francisco Couto, The AgreementMakerLight Ontology Matching System.The 12th International Conference on Ontologies, DataBases, and Applications of Semantics (ODBASE) 2013.

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C. Machado, A. Freitas, Francisco Couto 2013: Enrichment analysis applied to disease prognosis. Journal of Biomedical Semantics.

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Francisco Couto, H. Pinto 2013: The Next Generation of Similarity Measures that fully explore the Semantics in Biomedical Ontologies. Journal of Bioinformatics and Computational Biology.

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C. Machado, D. Rebholz-Schuhmann, A. Freitas, Francisco Couto 2013: The semantic web in translational medicine: current applications and future directions. Briefings in Bioinformatics, Oxford Univ Press.

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Catia Pesquita, Daniel Faria, Cosmin Stroe, Emanuel Santos, Isabel F Cruz, Francisco M Couto, What's in a 'nym'? Synonyms in Biomedical Ontology Matching.International Semantic Web Conference p. 526-541, 2013. Springer Berlin Heidelberg.

Document | BibTeX source
Andre Lamurias, Tiago Grego, Francisco Couto, Chemical compound and drug name recognition using CRFs and semantic similarity based on ChEBI.Proceedings of the fourth BioCreative challenge evaluation workshop 2013.

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João D Ferreira, Janna Hastings, Francisco M Couto 2013: Exploiting disjointness axioms to improve semantic similarity measures. Oxford Bioinformatics (), btt491.

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Tiago Grego, Francisco Pinto, Francisco Couto, LASIGE: using Conditional Random Fields and ChEBI ontology.Proceedings of the International Workshop on Semantic Evaluation (SemEval2013) 2013.

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Tiago Grego, Francisco Couto 2013: Enhancement of Chemical Entity Identification in Text Using Semantic Similarity Validation. PLOS ONE 5(8), e62984.

Poster | BibTeX source
João D. Ferreira, Francisco M. Couto, Semantic Similarity in the Biomedical Domain. Braga, Portugal. Poster @ Bioinformatics Open Days 2012. 2012

Presentation | BibTeX source
Francisco M. Couto, João D. Ferreira, João Zamite, Carlos Santos, Tiago Posse, Paulo Graça, Dulce Domingos, Mário J. Silva, The Epidemic Marketplace Platform: towards semantic characterization of epidemiological resources using biomedical ontologies.International Conference on Biomedical Ontologies (ICBO) 2012.

Document | Presentation | BibTeX source
João D. Ferreira, Catia Pesquita, Francisco M. Couto, Mário J. Silva, Bringing epidemiology into the Semantic Web.International Conference on Biomedical Ontologies (ICBO) 2012.

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Isabel F. Cruz, Cosmin Stroe, Federico Caimi, Alessio Fabiani, Catia Pesquita, Francisco M. Couto, Matteo Palmonari, Using AgreementMaker to Align Ontologies for OAEI 2011.Ontology Matching Workshop at the 10th International Semantic Web Conference 2011.

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Francisco Couto, Mário J. Silva 2011: Disjunctive Shared Information between Ontology Concepts: application to Gene Ontology. Journal of Biomedical Semantics.

Document | BibTeX source
João D. Ferreira, Francisco Couto, Generic semantic relatedness measure for biomedical ontologies.Proceedings of ICBO 2011.

Document | BibTeX source
Hugo Bastos, Bruno Tavares, Catia Pesquita, Daniel Faria, Francisco Couto: Application of Gene Ontology to Gene Identification. In Silico Tools for Gene Discovery: Methods in Molecular Biology. Springer, 2011.

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Nuno Cardoso, Iustin Dornescu, Sven Hartrumpf, Johannes Leveling, Revamping Question Answering with a Semantic Approach over World Knowledge.Multiple Language Question Answering 2010 (MLQA10), wokshop at CLEF 2010 Padua, Italy, 22-23 September,

Document | Poster | Presentation | BibTeX source
Nuno Cardoso, Mário J. Silva, Experiments with Semantic-flavored Query Reformulation of Geo-Temporal Queries.Working Notes of the 8th NTCIR Workshop Tokyo, Japan, Juno 15--18, 2010.

Document | BibTeX source
Catia M. Machado, Francisco Couto, Alexandra R. Fernandes, Susana Santos, Nuno Cardim, Ana T. Freitas, Semantic Characterization of Hypertrophic Cardiomyopathy Disease.First Workshop on Knowledge Engineering, Discovery and Dissemination in Health (KEDDH10), held in conjunction with The IEEE International Conference on Bioinformatics % Biomedicine (BIBM 2010) 2010.

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Daniel Amoedo, Medidas de Semelhança Semântica Aplicadas às Ontologias Geográficas Master Thesis, University of Lisbon, Faculty of Sciences, September 2010.

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João D. Ferreira, Francisco Couto 2010: Semantic Similarity for Automatic Classification of Chemical Compounds. PLoS Computational Biology 9(6), e1000937.

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Francisco J. Lopez-Pellicer, Mário J. Silva, Marcirio Chaves, F. Javier Zarazaga-Soria, Pedro R. Muro-Medrano, Geo Linked Data.Proceedings of DEXA 2010 LNCS 6261/2011, p. 495-502, August, 2010. Springer. DOI:10.1007/978-3-642-15364-8A42.

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Tiago Grego, João D. Ferreira, Catia Pesquita, Hugo Bastos, Diogo Vila Viçosa, João Freire, Francisco Couto, Chemical and Metabolic Pathway Semantic Similarity Technical Report. TR 2010-01. University of Lisbon, Faculty of Sciences, LASIGE, March 2010.

Document | Presentation | BibTeX source
David Batista, Mário J. Silva, Francisco Couto, Bibek Behera, Geographic Signatures for Semantic Retrieval.6th Workshop on Geographic Information Retrieval Zurich, Switzerland, 18-19 February, 2010.

Document | Presentation | BibTeX source
Nuno Cardoso, Mário J. Silva, A GIR Architecture with Semantic-flavored Query Reformulation.6th Workshop on Geographic Information Retrieval Zurich, Switzerland, 18-19 February, 2010.

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Catia Pesquita, Delphine Pessoa, Daniel Faria, Francisco Couto, CESSM : Collaborative Evaluation of Semantic Similarity Measures.JB2009: Challenges in Bioinformatics November, 2009.

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Catia Pesquita, Daniel Faria, Andre O Falcao, Philip Lord, Francisco Couto 2009: Semantic Similarity in Biomedical Ontologies. PLoS Computational Biology.

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Cláudia Freitas, Diana Santos, Cristina Mota, Hugo Gonçalo Oliveira, Paula Carvalho, Detection of relations between named entities: report of a shared task.EW-2009 - Semantic Evaluations: Recent Achievements and Future Directions (NAACL-HLT 2009 Workshop) Colorado, USA, 2009.

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Cláudia Freitas, Diana Santos, Hugo Gonçalo Oliveira, Paula Carvalho, Cristina Mota 2008: Relações semânticas do ReRelEM: além das entidades no Segundo HAREM. in: Cristina Mota, Diana Santos (Eds.) : Desafios na avaliação conjunta do reconhecimento de entidades mencionadas: O Segundo HAREM. Linguateca.

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Catia Pesquita, Daniel Faria, Hugo Bastos, António Ferreira, Andre O Falcao, Francisco Couto 2008: Metrics for GO based protein semantic similarity: a systematic evaluation. BMC Bioinformatics Suppl 5(9), S4.

Document | BibTeX source
Catia Pesquita, Improving semantic similarity for proteins based on the Gene Ontology Master Thesis, University of Lisbon, Faculty of Sciences, December 2007.

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Nuno Cardoso, Diana Santos: Directivas para a identificação e classificação semântica na colecção dourada do HAREM. 16. in: Nuno Cardoso, Diana Santos (Eds.) : Reconhecimento de entidades mencionadas em português: Documentação e actas do HAREM, a primeira avaliação conjunta na área. Linguateca., 211--238, 2007.

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Catia Pesquita, Daniel Faria, Hugo Bastos, Andre O. Falcao, Francisco Couto, Evaluating GO-based Semantic Similarity Measures.BioOntologies SIG at ISMB/ECCB - 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) July, 2007.

Poster | BibTeX source
Daniel Faria, Catia Pesquita, Francisco Couto, Andre O. Falcao, ProteinOn: Web Tool for Protein Semantic Similarity.Poster at ISMB/ECCB 2007 July, 2007.

DOI | | BibTeX source
Francisco Couto, Mário J. Silva, Pedro M. Coutinho 2007: Measuring Semantic Similarity between Gene Ontology Terms. Data and Knowledge Engineering, Elsevier.

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Daniel Faria, Catia Pesquita, Francisco Couto, Andre O. Falcao, ProteInOn: A Web Tool for Protein Semantic Similarity Technical Report. TR 07-6. DI FCUL, March 2007.

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Nuno Cardoso, Diana Santos, Directivas para identificação e classificação semântica na colecção dourada do HAREM Technical Report. DI/FCUL TR-06-18. Faculty of Sciences, University of Lisbon, November 2006.

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Francisco Couto, Mário J. Silva, Pedro Coutinho, Semantic Similarity over the Gene Ontology: Family Correlation and Selecting Disjunctive Ancestors.ACM CIKM - Conference in Information and Knowledge Management October, 2005.

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Marcirio Chaves, Mário J. Silva, Bruno Martins, A Geographic Knowledge Base for Semantic Web Applications.20th Brazilian Symposium on Databases - SBBD Uberlândia, Minas Gerais, Brazil, October, 2005.

Paper | Presentation | BibTeX source
Norman Noronha, Mário J. Silva, Using the Semantic Web for Web Searches.INTERACÇÃO 2004 - 1ª Conferência Nacional em Interacção Pessoa-Máquina Lisbon, Portugal, July, 2004.

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Norman Noronha, Request: Validating Semantic Searches Master Thesis, University of Lisbon, Faculty of Sciences, May 2004. Also available as Technical Report DI/FCUL TR 4-9

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Francisco Couto, Mário J. Silva, Implementation of a Functional Semantic Similarity Measure between Gene-Products Technical Report. DI/FCUL TR 3-29. FCUL, November 2003.

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Paulo Carreira, Helena Galhardas, Efficient development of data migration transformations.Semantic Integration Workshop October, 2003. In conjunction with The Second Int'l Semantic Web Conference and Demo Paper.

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