Seminars

  • SOMER Final Workshop, University of Lisbon, April 2014 [ outline ]
  • SOMER OAEI 2013 Preparation Meeting, University of Lisbon, July 2013
  • SOMER Annual Meeting, University of Lisbon, April 2013 [ outline ]
  • SOMER Kick-off Meeting, University of Lisbon, March 2012 [ outline ]

Talks

  • F. Couto, Semantic ontology matching using external resources, in Centro de Ciências e Tecnologias de Computação (CCTC) Seminar, University of Braga, 2012 [ pdf ]

Current Work

  • D. Faria, C. Pesquita, E. Santos, I. Cruz, and F. Couto, , Automatic Background Knowledge Selection for Matching Biomedical Ontologies. PLoS One (In Press), 2014.
  • D. Faria, E. Jimenez, C. Pesquita, E. Santos, and F. Couto, , Towards annotating potential incoherences in BioPortal mappings, in International Semantic Web Conference (ISWC), 2014.
  • D. Faria, C. Martins, A. Nanavaty, A. Taheri, C. Pesquita, E. Santos, I. Cruz, and F. Couto, AgreementMakerLight Results for OAEI 2014, in ISWC Workshop on Ontology Matching, 2014.
  • C. Pesquita, D. Faria, E. Santos, and F. Couto, , Towards visualizing the alignment of large biomedical ontologies, in International Conference on Data Integration in the Life Sciences (DILS), 2014.
  • D. Faria, C. Pesquita, E. Santos, I. Cruz, and F. Couto, AgreementMakerLight Results for OAEI 2013, in ISWC Workshop on Ontology Matching, 2013.
  • C. Pesquita, D. Faria, E. Santos, and F. Couto, To repair or not to repair: reconciling correctness and coherence in ontology reference alignments, in ISWC Workshop on Ontology Matching, 2013.
  • C. Pesquita, D. Faria, C. Stroe, E. Santos, I. Cruz, and F. Couto, What's in a `nym'? synonyms in biomedical ontology matching, in International Semantic Web Conference (ISWC), 2013.
  • D. Faria, C. Pesquita, E. Santos, M. Palmonari, I. Cruz, and F. Couto, The AgreementMakerLight ontology matching system, in The 12th International Conference on Ontologies, DataBases, and Applications of Semantics (ODBASE), 2013.
  • J. Ferreira, J. Hastings, and F. Couto, Exploiting disjointness axioms to improve semantic similarity measures, Bioinformatics, Oxford Univ Press, (in press) 2013. [ bib ]
  • F. Couto and 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.  5 (1371001), pp. 1-12, 2013. [pdf | doi ]
  • D. Faria, C. Pesquita, E. Santos, F. Couto, C. Stroe, and I. Cruz, Testing the AgreementMaker system in the anatomy task of OAEI 2012, Tech. Rep. arXiv:1212.1625 [cs.IR], arXiv.org, December 2012. [pdf | url ]
  • C. Pesquita, Automated Extension of Biomedical Ontologies, Doctoral Thesis, 2012 [ pdf ]

Applied Work

  • J. Ferreira, C. Pesquita, F. Couto, and M. Silva, Digital preservation of epidemic resources: coupling metadata and ontologies, in 10th International Conference on Preservation of Digital Objects, 2013.
  • T. Grego, F. Pinto, and F. Couto, LASIGE: using conditional random fields and chebi ontology, in 7th International Workshop on Semantic Evaluation (SemEval), 2013. [pdf | url ]
  • C. Machado, A. Freitas, and F. Couto, Enrichment analysis applied to disease prognosis, Journal of Biomedical Semantics, vol. in press, 2013. [pdf ]
  • T. Grego and F. Couto, Enhancement of chemical entity identification in text using semantic similarity validation, PLoS ONE, vol. 8, no. 5 (e62984), pp. 1-13, 2013. [doi | pubmed | scholar ]
  • S. Moreira, D. Batista, P. Carvalho, F. Couto, and M. Silva, Tracking politics with POWER, Program: electronic library and information systems, vol. 47, no. 2, pp. 1-18, 2013. [ doi ]
  • J. Ferreira, D. Paolotti, F. Couto, and M. Silva, The usefulness of ontologies in epidemiologic research and practice, Journal of Epidemiology & Community Health, 2012. [doi | pubmed | scholar ]
  • J. Ferreira, C. Pesquita, M. Silva, and F. Couto, Bringing epidemiology into the semantic web, in International Conference on Biomedical Ontologies (ICBO), 2012. [pdf | html | scholar ]
  • T. Grego, F. Pinto, and F. Couto, Identifying chemical entities based on ChEBI, in Software Demonstration at the International Conference on Biomedical Ontologies (ICBO), 2012. [pdf | html ]
  • F. Couto, J. Ferreira, J. Zamite, C. Santos, T. Posse, P. Graça, D. Domingos, and M. Silva, The epidemic marketplace platform: towards semantic characterization of epidemiological resources using biomedical ontologies, in Software Demonstration at the International Conference on Biomedical Ontologies (ICBO), 2012. [pdf | html ]
  • C. Machado, F. Couto, A. Fernandes, S. Santos, and A. Freitas, Toward a translational medicine approach for hypertrophic cardiomyopathy, in International Conference on Information Technology in Bio and Medical Informatics (ITBAM - DEXA), 2012. [pdf | doi | scholar ]
  • C. Machado, A. Freitas, and F. Couto, Enrichment analysis applied to disease prognosis, in Ontologies in Biomedicine and Life Sciences (OBML), 2012. [pdf | html ]

Past Work

  • I. Cruz, C. Stroe, F. Caimi, A. Fabiani, C. Pesquita, F. Couto, and M. Palmonari, Using AgreementMaker to align ontologies for OAEI 2011, in The Sixth International Workshop on Ontology Matching (OM-2011), 2011. [pdf | html ]
  • I. Cruz, C. Stroe, C. Pesquita, F. Couto, and V. Cross, Biomedical ontology matching using the AgreementMaker system, in Software Demonstration at the International Conference on Biomedical Ontologies (ICBO), 2011. [pdf ]
  • C. Pesquita, C. Stroe, I. Cruz, and F. Couto, BLOOMS on AgreementMaker: results for OAEI 2010, in ISWC Workshop on Ontology Matching, 2010. [pdf ]
  • J. Ferreira, D. Batista, F. Couto, and M. Silva, The Geo-Net-PT/Yahoo! GeoPlanet (TM) concordance, DI/FCUL TR 10-05, Department of Informatics, University of Lisbon, September 2010. [pdf | doi ]

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