papers.bib

@book{couto-springer2019,
  author = {F. Couto},
  title = {Data and Text Processing for Health and Life Sciences},
  publisher = {Springer},
  year = {2019},
  series = {Advances in Experimental Medicine and Biology},
  number = {1137},
  isbn = {978-3-030-13845-5},
  doi = {https://doi.org/10.1007/978-3-030-13845-5},
  scholar = {https://scholar.google.com/scholar?cluster=9113948196639339491},
}
@book{couto-gradiva2019,
  author = {F. Couto},
  title = {Introdução à Bioinformática Via Linha de Comando},
  publisher = {Gradiva},
  year = {2019},
  series = {Trajectos / Ciência},
  isbn = {978-989-616-933-6},
  url = {https://www.gradiva.pt/catalogo/46792/introducao-a-bioinformatica-via-linha-de-comando},
}
@incollection{mfernandes-advances2023,
  author = {M. Fernandes and J. Decouchant and F. Couto},
  title = {Security, Privacy and Trust Management in {DNA} Computing},
  booktitle = {Perspective of {DNA} Computing in Computer Science},
  editor = {Suyel Namasudra},
  publisher = {Elsevier},
  issn = {0065-2458},
  volume = {129},
  number = {},
  doi = {https://doi.org/10.1016/bs.adcom.2022.08.009},
  scholar = {https://scholar.google.com/scholar?cluster=10203695993712386087},
  year = {2023},
}
@incollection{dsousa-ann2020,
  author = {D. Sousa and A. Lamurias and F. Couto},
  title = {Using Neural Networks for Relation Extraction from Biomedical Literature},
  booktitle = {Artificial Neural Networks. Methods in Molecular Biology},
  editor = {H. Cartwright},
  publisher = {Humana, New York, NY},
  issn = {978-1-0716-0826-5},
  volume = {2190},
  number = {},
  doi = {https://doi.org/10.1007/978-1-0716-0826-5_14},
  scholar = {https://scholar.google.com/scholar?cluster=9812797563413350432},
  year = {2020},
}
@incollection{jferreira-intechopen2019,
  author = {J. Ferreira and F. Couto},
  title = {Semantic Similarity in Cheminformatics},
  booktitle = {Cheminformatics and its Applications},
  editor = {A. Stefaniu},
  publisher = {IntechOpen},
  issn = {},
  volume = {},
  number = {},
  doi = {https://doi.org/10.5772/intechopen.89032},
  scholar = {https://scholar.google.com/scholar?cluster=2577905030734149447},
  year = {2019},
}
@incollection{alamurias-encyclopedia2019,
  author = {A. Lamurias and F. Couto},
  title = {Text Mining for Bioinformatics using Biomedical Literature},
  booktitle = {Encyclopedia of Bioinformatics and Computational Biology},
  editor = {S. Ranganathan and K. Nakai and C. Schönbach and M. Gribskov},
  publisher = {Oxford: Elsevier},
  issn = {978-0-12-809633-8},
  volume = {1},
  number = {},
  doi = {https://doi.org/10.1016/B978-0-12-809633-8.20409-3},
  scholar = {https://scholar.google.com/scholar?cluster=14948095891339718994},
  year = {2019},
}
@incollection{couto-encyclopedia2019,
  author = {F. Couto and A. Lamurias},
  title = {Semantic similarity definition},
  booktitle = {Encyclopedia of Bioinformatics and Computational Biology},
  editor = {S. Ranganathan and K. Nakai and C. Schönbach and M. Gribskov},
  publisher = {Oxford: Elsevier},
  issn = {978-0-12-809633-8},
  volume = {1},
  number = {},
  doi = {https://doi.org/10.1016/B978-0-12-809633-8.20401-9},
  scholar = {https://scholar.google.com/scholar?cluster=17975789099203629768},
  year = {2019},
}
@incollection{hbastos-mmb2011,
  author = {H. Bastos and B. Tavares and C. Pesquita and D. Faria and F. Couto},
  editor = {Bing Yu and Marcus Hinchcliffe},
  booktitle = {In Silico Tools for Gene Discovery, Methods in Molecular Biology},
  title = {Application of {Gene Ontology} to Gene Identification},
  publisher = {Humana Press},
  year = 2011,
  doi = {http://dx.doi.org/10.1007/978-1-61779-176-5_9},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/21779995},
  scholar = {http://scholar.google.com/scholar?cluster=12643848841912773505},
}
@incollection{pcoutinho-wiley2009,
  author = {P. Coutinho and C. Rancurel and M. Stam and T. Bernard and F. Couto and E. Danchin and B. Henrissat},
  editor = {C. Lieth and T. Lutteke and M. Frank},
  booktitle = {In Bioinformatics for Glycobiology and Glycomics},
  title = { Carbohydrate-Active Enzymes Database: Principles and 
	Classification of Glycosyltransferases},
  publisher = {Wiley},
  year = 2009,
  doi = {http://dx.doi.org/10.1002/9780470029619.ch5},
  scholar = {http://scholar.google.com/scholar?cluster=2290392574016729845},
}
@incollection{fcouto-nlp2009,
  author = {F. Couto and M. Silva and V. Lee and E. Dimmer and E. Camon
	and R. Apweiler and H. Kirsch and D. Rebholz-Schuhmann},
  editor = {V. Prince and M. Roche},
  booktitle = {Information Retrieval in Biomedicine: 
	Natural Language Processing for Knowledge Integration},
  title = {Verification of Uncurated Protein Annotations},
  publisher = {Idea Group Inc},
  year = 2009,
  doi = {http://dx.doi.org/10.4018/978-1-60566-274-9},
  scholar = {http://scholar.google.com/scholar?cluster=18213034071364387405},
}
@incollection{cpesquita-hrtwmt2008,
  author = {C. Pesquita and D. Faria and T. Grego and F. Couto and M. Silva},
  editor = {M. Song and Y. Wu},
  booktitle = {Handbook of Research on Text and Web Mining Technologies},
  title = {Untangling {BioOntologies} for Mining Biomedical Information},
  publisher = {Idea Group Inc.},
  year = 2009,
  doi = {http://dx.doi.org/10.4018/978-1-59904-990-8},
  scholar = {http://scholar.google.com/scholar?cluster=13942401852471990234},
}
@incollection{fcouto-admtbi2006,
  author = {F. Couto and M. Silva},
  editor = {H. Hsu},
  booktitle = {Advanced Data Mining Techonologies in Bioinformatics},
  title = {Mining the {BioLiterature}: towards automatic annotation of genes and proteins},
  publisher = {Idea Group Inc.},
  year = 2006,
  doi = {http://dx.doi.org/10.4018/978-1-59140-863-5},
  scholar = {http://scholar.google.com/scholar?cluster=14676363902212556905},
}
@article{dsousa-bioinf2023,
  author = {D. Sousa and F. Couto},
  title = {{K-RET}: Knowledgeable Biomedical Relation Extraction System},
  journal = {Bioinformatics, Oxford Univ Press},
  issn = {1367-4803},
  volume = {39},
  number = {4},
  doi = {https://doi.org/10.1093/bioinformatics/btad174},
  scholar = {http://scholar.google.com/scholar?cluster=11642374822553271334},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/37018156},
  year = {2023},
  ranking = {Q1 2022 Computer Science Applications|https://www.scimagojr.com/journalsearch.php?q=17945&tip=sid&clean=0},
}
@article{asif-bmcbioinf2023,
  author = {M. Asif and H. Martiniano and A. Lamurias and S. Kausar and F. Couto},
  title = {{DGH‑GO}: dissecting the genetic heterogeneity of complex diseases using {Gene Ontology}},
  journal = {BMC Bioinformatics},
  issn = {1471-2105},
  volume = {24},
  number = {171},
  doi = {https://doi.org/10.1186/s12859-023-05290-4},
  scholar = {https://scholar.google.com/scholar?cluster=7956626234689431398},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/37101154},
  year = {2023},
  ranking = {Q1 2022 Computer Science Applications|https://www.scimagojr.com/journalsearch.php?q=17929&tip=sid&clean=0},
}
@article{dfaria-semanticweb2023,
  author = {D. Faria and E. Santos B. Balasubramani and M. Silva and F. Couto and C. Pesquita},
  title = {{AgreementMakerLight}},
  journal = {Semantic Web, IOS Press},
  issn = {2210-4968},
  volume = {Pre-press},
  number = {Pre-press},
  doi = {https://doi.org/10.3233/SW-233304},
  year = {2023},
  ranking = {Q2 2022 Information Systems|https://www.scimagojr.com/journalsearch.php?q=21100269620&tip=sid&clean=0},
}
@article{mbarros-scidata2022,
  author = {M. Barros and A. Moitinho and F. Couto},
  title = {{SeEn}: Sequential enriched datasets for sequence-aware recommendations},
  journal = {Scientific Data},
  issn = {2052-4463},
  volume = {9},
  number = {1},
  doi = {https://doi.org/10.1038/s41597-022-01598-7},
  scholar = {http://scholar.google.com/scholar?cluster=3028106393498985942},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/35927282},
  year = {2022},
  ranking = {Q1 2021 Information Systems|https://www.scimagojr.com/journalsearch.php?q=21100451321&tip=sid&clean=0},
}
@article{pruas-jbi2022,
  author = {P. Ruas and F. Couto},
  title = {{NILINKER}: Attention-based approach to {NIL} Entity Linking},
  journal = {Journal of Biomedical Informatics},
  issn = {1532-0464},
  volume = {132},
  number = {104137},
  doi = {https://doi.org/10.1016/j.jbi.2022.104137},
  scholar = {https://scholar.google.com/scholar?cluster=795383090980521804},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/35811025},
  year = {2022},
  ranking = {Q1 2021 Computer Science Applications|https://www.scimagojr.com/journalsearch.php?q=23706&tip=sid&clean=0},
}
@article{dsousa-jbhi2022,
  author = {D. Sousa and F. Couto},
  title = {Biomedical Relation Extraction With Knowledge Graph-Based Recommendations},
  journal = {IEEE Journal of Biomedical and Health Informatics},
  issn = {2168-2194},
  volume = {26},
  number = {8},
  doi = {https://doi.org/10.1109/JBHI.2022.3173558},
  scholar = {https://scholar.google.com/scholar?cluster=3374250315703325352},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/35536818},
  year = {2022},
  ranking = {Q1 2021 Computer Science Applications|https://www.scimagojr.com/journalsearch.php?q=21100256982&tip=sid&clean=0},
}
@article{sofia-biomolecules2021,
  author = {S. Conceição and F. Couto},
  title = {Text Mining for Building Biomedical Networks Using Cancer as a Case Study},
  journal = {biomolecules},
  issn = {2218-273X},
  volume = {11},
  number = {10},
  doi = {https://doi.org/10.3390/biom11101430},
  scholar = {https://scholar.google.com/scholar?cluster=17330013652080639438},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/34680062},
  year = {2021},
  ranking = {Q2 2020 Molecular Biology|https://www.scimagojr.com/journalsearch.php?q=21100394188&tip=sid&clean=0},
}
@article{arodrigues-cancers2021,
  author = {A. Rodrigues and J. Santinha and B. Galvão and C. Matos and F. Couto and N. Papanikolaou},
  title = {Prediction of Prostate Cancer Disease Aggressiveness Using Bi-Parametric Mri Radiomics},
  journal = {cancers},
  issn = {2072-6694},
  volume = {13},
  number = {23},
  doi = {https://doi.org/10.3390/cancers13236065},
  scholar = {https://scholar.google.com/scholar?cluster=12780393161387146897},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/34885175},
  year = {2021},
  ranking = {Q1 2020 Oncology|https://www.scimagojr.com/journalsearch.php?q=19700188419&tip=sid&clean=0},
}
@article{mbarros-genomics2021,
  author = {M. Barros and P. Ruas and D. Sousa and A. Bangash and F. Couto},
  title = {{COVID-19} recommender system based on an annotated multilingual corpus},
  journal = {Genomics \& Informatics},
  issn = {2234-0742},
  volume = {19},
  number = {3},
  doi = {https://doi.org/10.5808/gi.21008},
  scholar = {https://scholar.google.com/scholar?cluster=3657838504113523971},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/34638171},
  year = {2021},
  ranking = {Q2 2020 Ecology, Evolution, Behavior and Systematics|https://www.scimagojr.com/journalsearch.php?q=21100945202&tip=sid&clean=0},
}
@article{alamurias-frontiers2021,
  author = {A. Lamurias and S. Jesus and V. Neveu and R. Salek and F. Couto},
  title = {Information Retrieval Using Machine Learning for Biomarker Curation in the Exposome-Explorer},
  journal = {Frontiers in Research Metrics and Analytics},
  issn = {2504-0537},
  volume = {6},
  number = {55},
  doi = {https://doi.org/10.3389/frma.2021.689264},
  scholar = {http://scholar.google.com/scholar?cluster=118642626963647663},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/34490412},
  year = {2021},
}
@article{mbarros-cheminformatics2021,
  author = {M. Barros and A. Moitinho and F. Couto},
  title = {Hybrid semantic recommender system for chemical compounds in large‐scale datasets},
  journal = {Journal of Cheminformatics},
  issn = {1758-2946},
  volume = {13},
  number = {15},
  doi = {https://doi.org/10.1186/s13321-021-00495-2},
  scholar = {http://scholar.google.com/scholar?cluster=10348733191904411550},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/33622374},
  year = {2021},
  ranking = {Q1 2020 Computer Science Applications|https://www.scimagojr.com/journalsearch.php?q=19600157322&tip=sid&clean=0},
}
@article{dsousa-database2020,
  author = {D. Sousa and A. Lamurias and F. Couto},
  title = {A hybrid approach toward biomedical relation extraction training corpora: combining distant supervision with crowdsourcing},
  journal = {Database: The Journal of Biological Databases and Curation},
  publisher = {Oxford University Press},
  issn = {1758-0463},
  volume = {2020},
  number = {baaa104},
  doi = {https://doi.org/10.1093/database/baaa104},
  scholar = {http://scholar.google.com/scholar?cluster=16982016212489131651},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/33258966},
  year = {2020},
  ranking = {Q1 2020 Information Systems|https://www.scimagojr.com/journalsearch.php?q=19700188321&tip=sid&clean=0},
}
@article{pruas-cheminformatics2020,
  author = {P. Ruas and A. Lamurias and F. Couto},
  title = {Linking chemical and disease entities to ontologies by integrating {PageRank} with extracted relations from literature},
  journal = {Journal of Cheminformatics},
  issn = {1758-2946},
  volume = {12},
  number = {57},
  doi = {https://doi.org/10.1186/s13321-020-00461-4},
  scholar = {http://scholar.google.com/scholar?cluster=5949428901936199122},
  pubmed = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7507273/},
  year = {2020},
  ranking = {Q1 2020 Computer Science Applications|https://www.scimagojr.com/journalsearch.php?q=19600157322&tip=sid&clean=0},
}
@article{alamurias-ieeeaccess2020,
  author = {A. Lamurias and D. Sousa and F. Couto},
  title = {Generating Biomedical Question Answering Corpora from {Q\&A} Forums},
  journal = {IEEE Access},
  issn = {2169-3536},
  volume = {8},
  number = {0},
  doi = {https://doi.org/10.1109/ACCESS.2020.3020868},
  scholar = {https://scholar.google.com/scholar?cluster=13154981135367515839},
  year = {2020},
  ranking = {Q1 2020 Computer Science (miscellaneous)|https://www.scimagojr.com/journalsearch.php?q=21100374601&tip=sid&clean=0},
}
@article{sergio-sigirforum2020,
  author = {S. Nunes and S. Little and S. Bhatia and L. Boratto and G. Cabanac and R. Campos and F. Couto and S. Faralli and I. Frommholz and A. Jatowt and A. Jorge and M. Marras and P. Mayr and G. Stilo},
  title = {{ECIR} 2020 Workshops: Assessing the Impact of Going Online},
  journal = {SIGIR Forum},
  issn = {0163-5840},
  volume = {54},
  number = {1},
  doi = {http://sigir.org/wp-content/uploads/2020/06/p09.pdf},
  scholar = {http://scholar.google.com/scholar?cluster=4460945127397842114},
  ranking = {Q1 2006 Management Information Systems|https://www.scimagojr.com/journalsearch.php?q=15745&tip=sid&clean=0},
  year = {2020},
}
@article{dsousa-genomics2020,
  author = {D. Sousa and A. Lamurias and F. Couto},
  title = {Improving accessibility and distinction between negative results in biomedical relation extraction},
  journal = {Genomics \& Informatics},
  issn = {2234-0742},
  volume = {18},
  number = {1},
  doi = {https://doi.org/10.5808/GI.2020.18.2.e20},
  scholar = {https://scholar.google.com/scholar?cluster=18260470397026833028},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/32634874},
  year = {2020},
  ranking = {Q2 2020 Ecology, Evolution, Behavior and Systematics|https://www.scimagojr.com/journalsearch.php?q=21100945202&tip=sid&clean=0},
}
@article{mfernandes-jbhi2020,
  author = {M. Fernandes and J. Decouchant and M. Völp and F. Couto and P. Veríssimo},
  title = {{DNA-SeAl}: Sensitivity Levels to Optimize the Performance of Privacy-Preserving {DNA} Alignment},
  journal = {IEEE Journal of Biomedical and Health Informatics},
  issn = {2168-2194},
  volume = {24},
  number = {3},
  doi = {https://doi.org/10.1109/JBHI.2019.2914952},
  scholar = {https://scholar.google.com/scholar?cluster=12044920287604301732},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/31265423},
  year = {2020},
  ranking = {Q1 2020 Computer Science Applications|https://www.scimagojr.com/journalsearch.php?q=21100256982&tip=sid&clean=0},
}
@article{asif-transpsychiatry2020,
  author = {M. Asif and H. Martiniano and A. Marques and J. Santos and J. Vilela and C. Rasga and G. Oliveira and F. Couto and A. Vicente},
  title = {Identification of biological mechanisms underlying a multidimensional {ASD} phenotype using machine learning},
  journal = {Translational Psychiatry},
  issn = {2158-3188},
  volume = {10},
  number = {43},
  doi = {https://doi.org/10.1038/s41398-020-0721-1},
  scholar = {https://scholar.google.com/scholar?cluster=3018038020149462839},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/32066720},
  year = {2020},
  ranking = {Q1 2020 Biological Psychiatry|https://www.scimagojr.com/journalsearch.php?q=19900191866&tip=sid&clean=0},
}
@article{mbarros-ieeeaccess2019,
  author = {M. Barros and A. Moitinho and F. Couto},
  title = {Using research literature to generate datasets of implicit feedback for recommending scientific items},
  journal = {IEEE Access},
  issn = {2169-3536},
  volume = {7},
  number = {0},
  doi = {https://doi.org/10.1109/ACCESS.2019.2958002},
  scholar = {https://scholar.google.com/scholar?cluster=7813997720593140840},
  year = {2019},
  ranking = {Q1 2019 Engineering (miscellaneous)|https://www.scimagojr.com/journalsearch.php?q=21100374601&tip=sid&clean=0},
}
@article{pruas-bmcbioinf2019,
  author = {A. Lamurias and P. Ruas and F. Couto},
  title = {{PPR-SSM}: personalized {PageRank} and semantic similarity measures for entity linking},
  journal = {BMC Bioinformatics},
  issn = {1471-2105},
  volume = {20},
  number = {534},
  doi = {https://doi.org/10.1186/s12859-019-3157-y},
  scholar = {https://scholar.google.com/scholar?cluster=10809403692248160012},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/31664891},
  year = {2019},
  ranking = {Q1 2019 Computer Science Applications|https://www.scimagojr.com/journalsearch.php?q=17929&tip=sid&clean=0},
}
@article{asif-jbi2019,
  author = {M. Asif and A. Vicente and F. Couto},
  title = {FunVar: A Systematic Pipeline to Unravel the Convergence Patterns of Genetic Variants in {ASD}, a Paradigmatic Complex Disease},
  journal = {Journal of Biomedical Informatics},
  issn = {1532-0464},
  volume = {},
  number = {},
  doi = {https://doi.org/10.1016/j.jbi.2019.103273},
  scholar = {https://scholar.google.com/scholar?cluster=12549731118347754136},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/31454647},
  year = {2019},
  ranking = {Q1 2019 Computer Science Applications|https://www.scimagojr.com/journalsearch.php?q=23706&tip=sid&clean=0},
}
@article{jferreira-bmcbioinf2019,
  author = {J. Ferreira and F. Couto},
  title = {Multi-domain semantic similarity in biomedical research},
  journal = {BMC Bioinformatics},
  issn = {1471-2105},
  volume = {20},
  number = {246},
  doi = {https://doi.org/10.1186/s12859-019-2810-9},
  scholar = {https://scholar.google.com/scholar?cluster=4084066250393649896},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/31138117},
  year = {2019},
  ranking = {Q1 2019 Computer Science Applications|https://www.scimagojr.com/journalsearch.php?q=17929&tip=sid&clean=0},
}
@article{alamurias-bmcbioinf2019,
  author = {A. Lamurias and Diana Sousa and L. Clarke and F. Couto},
  title = {{BO-LSTM}: classifying relations via long short-term memory networks along biomedical ontologies},
  journal = {BMC Bioinformatics},
  issn = {1471-2105},
  volume = {20},
  number = {10},
  doi = {https://doi.org/10.1186/s12859-018-2584-5},
  scholar = {https://scholar.google.com/scholar?cluster=846578847271646360},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/30616557},
  year = {2019},
  ranking = {Q1 2019 Computer Science Applications|https://www.scimagojr.com/journalsearch.php?q=17929&tip=sid&clean=0},
}
@article{fcouto-cheminformatics2018,
  author = {F. Couto and A. Lamurias},
  title = {{MER}: a Shell Script and Annotation Server for Minimal Named Entity Recognition and Linking},
  journal = {Journal of Cheminformatics},
  issn = {1758-2946},
  volume = {10},
  number = {58},
  doi = {https://doi.org/10.1186/s13321-018-0312-9},
  scholar = {http://scholar.google.com/scholar?cluster=15497062409518618912},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/30519990},
  year = {2018},
  ranking = {Q1 2018 Computer Science Applications|https://www.scimagojr.com/journalsearch.php?q=19600157322&tip=sid&clean=0},
}
@article{asif-plos2018,
  author = {M. Asif and H. Martiniano and A. Vicente and F. Couto},
  title = {Identifying disease genes using machine learning and gene functional similarities, assessed through {Gene Ontology}},
  journal = {PLoS ONE},
  issn = {1932-6203},
  volume = {13},
  number = {12},
  doi = {https://doi.org/10.1371/journal.pone.0208626},
  scholar = {https://scholar.google.com/scholar?cluster=12948580205243375809},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/30532199},
  year = {2018},
  ranking = {Q1 2018 Biochemistry, Genetics and Molecular Biology (miscellaneous)|https://www.scimagojr.com/journalsearch.php?q=10600153309&tip=sid&clean=0},
}
@article{santana-bmc2018,
  author = {J. Santana and K. Gramacho and K. Ferreira and R. Rezende and P. Mangabeira and R. Dias and F. Couto and C. Pirovani},
  title = {Witches' broom resistant genotype {CCN51} shows greater diversity of symbiont bacteria in its phylloplane than susceptible genotype catongo},
  journal = {BMC Microbiology},
  issn = {1471-2180},
  volume = {18},
  number = {1},
  doi = {https://doi.org/10.1186/s12866-018-1339-9},
  scholar = {https://scholar.google.com/scholar?cluster=10382797770818647901},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/30470193},
  year = {2018},
  ranking = {Q2 2018 Microbiology|https://www.scimagojr.com/journalsearch.php?q=19633&tip=sid&clean=0},
}
@article{jeremie-jbi2018,
  author = {J. Decouchant and M. Fernandes and M. Völp and F. Couto and P. Veríssimo},
  title = {Accurate Filtering of Privacy-Sensitive Information in Raw Genomic Data},
  journal = {Journal of Biomedical Informatics},
  issn = {1532-0464},
  volume = {82},
  number = {},
  doi = {https://doi.org/10.1016/j.jbi.2018.04.006},
  scholar = {https://scholar.google.com/scholar?cluster=17691955303609776476},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/29660494},
  year = {2018},
  ranking = {Q1 2018 Computer Science Applications|https://www.scimagojr.com/journalsearch.php?q=23706&tip=sid&clean=0},
}
@article{dfaria-jbs2018,
  author = {D. Faria and C. Pesquita and I. Mott and C. Martins and F. Couto and I. Cruz},
  title = {Tackling the Challenges of Matching Biomedical Ontologies},
  journal = {Journal of Biomedical Semantics},
  issn = {2041-1480},
  volume = {9},
  number = {4},
  doi = {https://doi.org/10.1186/s13326-017-0170-9},
  scholar = {http://scholar.google.com/scholar?cluster=5686839660215807872},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/29335022},
  year = {2018},
  ranking = {Q1 2018 Computer Science Applications|https://www.scimagojr.com/journalsearch.php?q=21100316001&tip=sid&clean=0},
}
@article{alamurias-frontiers2017,
  author = {A. Lamurias and J. Ferreira and L. Clarke and F. Couto},
  title = {Generating a Tolerogenic Cell Therapy Knowledge Graph from Literature},
  journal = {Frontiers in Immunology},
  issn = {1664-3224},
  volume = {8},
  number = {1656},
  doi = {https://doi.org/10.3389/fimmu.2017.01656},
  scholar = {https://scholar.google.com/scholar?cluster=14098381561814812459},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/29238346},
  year = {2017},
  ranking = {Q1 2017 Immunology|https://www.scimagojr.com/journalsearch.php?q=21100229161&tip=sid&clean=0},
}
@article{jferreira-jib2017,
  author = {J. Ferreira and B. Inácio and R. Salek and F. Couto},
  title = {Assessing public metabolomics metadata, towards improving quality},
  journal = {Journal of Integrative Bioinformatics},
  issn = {1613-4516},
  volume = {14},
  number = {4},
  doi = {https://doi.org/10.1515/jib-2017-0054},
  scholar = {http://scholar.google.com/scholar?cluster=10121317516803272610},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/29236679},
  year = {2017},
  ranking = {Q3 2017 Medicine (miscellaneous)|https://www.scimagojr.com/journalsearch.php?q=19700170615&tip=sid&clean=0},
}
@article{lobo-bri2017,
  author = {M. Lobo and A. Lamurias and F. Couto},
  title = {Identifying Human Phenotype Terms by Combining Machine Learning and Validation Rules},
  journal = {BioMed Research International},
  issn = {2314-6133},
  volume = {2017},
  doi = {https://doi.org/10.1155/2017/8565739},
  scholar = {https://scholar.google.com/scholar?cluster=4869642720799292513},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/29250549},
  year = {2017},
  ranking = {Q1 2017 Biochemistry, Genetics and Molecular Biology (miscellaneous)|https://www.scimagojr.com/journalsearch.php?q=21100230018&tip=sid&clean=0},
}
@article{lcampos-database2017,
  author = {L. Campos and V. Pedro and F. Couto},
  title = {Impact of translation on named-entity recognition in radiology texts},
  journal = {Database: The Journal of Biological Databases and Curation},
  publisher = {Oxford University Press},
  issn = {1758-0463},
  volume = {2017},
  number = {bax064},
  doi = {https://doi.org/10.1093/database/bax064},
  scholar = {http://scholar.google.com/scholar?cluster=3941214383333093090},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/29220455},
  year = {2017},
  ranking = {Q1 2017 Information Systems|https://www.scimagojr.com/journalsearch.php?q=19700188321&tip=sid&clean=0},
}
@article{alamurias-plos2017,
  author = {A. Lamurias and L. Clarke and F. Couto},
  title = {Extracting Micro{RNA}-Gene Relations from Biomedical Literature using Distant Supervision},
  journal = {PLoS ONE},
  issn = {1932-6203},
  volume = {12},
  number = {3},
  doi = {https://doi.org/10.1371/journal.pone.0171929},
  scholar = {https://scholar.google.com/scholar?cluster=11355153884256199712},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/28263989},
  year = {2017},
  ranking = {Q1 2017 Biochemistry, Genetics and Molecular Biology (miscellaneous)|https://www.scimagojr.com/journalsearch.php?q=10600153309&tip=sid&clean=0},
}
@article{marcia-imia2016,
  author = {M. Barros and F. Couto},
  title = {Knowledge Representation and Management: a linked data perspective},
  journal = {IMIA Yearbook of Medical Informatics},
  issn = {0943-4747},
  volume = {},
  number = {},
  doi = {https://doi.org/10.15265/IY-2016-022},
  scholar = {http://scholar.google.com/scholar?cluster=15641593609834120828},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/27830248},
  year = {2016},
  ranking = {Q2 2016 Medicine (miscellaneous)|https://www.scimagojr.com/journalsearch.php?q=11400153302&tip=sid&clean=0},
}
@article{hbastos-jbs2016,
  author = {H. Bastos and L. Sousa and L. Clarke and F. Couto},
  title = {Functional Coherence Metrics in Protein Families},
  journal = {Journal of Biomedical Semantics},
  issn = {2041-1480},
  volume = {7},
  number = {1},
  doi = {https://doi.org/10.1186/s13326-016-0076-y},
  scholar = {http://scholar.google.com/scholar?cluster=1295068287268556422},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/27338101},
  year = {2016},
  ranking = {Q1 2016 Computer Science Applications|https://www.scimagojr.com/journalsearch.php?q=21100316001&tip=sid&clean=0},
}
@article{esantos-plos2015,
  author = {E. Santos and D. Faria and C. Pesquita and F. Couto},
  title = {Ontology alignment repair through modularization and confidence-based heuristics},
  journal = {PLoS ONE},
  issn = {1932-6203},
  volume = {10},
  number = {12},
  doi = {https://doi.org/10.1371/journal.pone.0144807},
  scholar = {http://scholar.google.com/scholar?cluster=4482331533431326630},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/26710335},
  year = {2015},
  ranking = {Q1 2015 Biochemistry, Genetics and Molecular Biology (miscellaneous)|https://www.scimagojr.com/journalsearch.php?q=10600153309&tip=sid&clean=0},
}
@article{hbastos-plos2015,
  author = {H. Bastos and L. Sousa and L. Clarke and F. Couto},
  title = {{GRYFUN}: A Web Application for {GO} Term Annotation Visualization and Analysis in Protein Sets},
  journal = {PLoS ONE},
  issn = {1932-6203},
  volume = {10},
  number = {3},
  doi = {https://doi.org/10.1371/journal.pone.0119631},
  scholar = {http://scholar.google.com/scholar?cluster=15572209849553074224},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/25794277},
  ranking = {Q1 2015 Biochemistry, Genetics and Molecular Biology (miscellaneous)|https://www.scimagojr.com/journalsearch.php?q=10600153309&tip=sid&clean=0},
  year = {2015},
}
@article{tudor-database2015,
  author = {T. Groza and S. K{\"o}hler and S. Doelken and N. Collier and A. Oellrich and D. Smedley and F. Couto and G. Baynam and A. Zankl and P. Robinson},
  title = {Automatic concept recognition using the {Human Phenotype Ontology} reference and test suite corpora},
  journal = {Database: The Journal of Biological Databases and Curation},
  publisher = {Oxford University Press},
  issn = {1758-0463},
  volume = {2015},
  number = {bav005},
  doi = {https://doi.org/10.1093/database/bav005},
  scholar = {http://scholar.google.com/scholar?cluster=1564163549171586954},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/25725061},
  year = {2015},
  ranking = {Q1 2015 Information Systems|https://www.scimagojr.com/journalsearch.php?q=19700188321&tip=sid&clean=0},
}
@article{alamurias-cheminformatics2015,
  author = {A. Lamurias and J. Ferreira and F. Couto},
  title = {Improving chemical entity recognition through h-index based semantic similarity},
  journal = {Journal of Cheminformatics},
  issn = {1758-2946},
  volume = {7},
  number = {Suppl 1},
  doi = {https://doi.org/10.1186/1758-2946-7-S1-S13},
  scholar = {http://scholar.google.com/scholar?cluster=6836896844438242588},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/25810770},
  year = {2015},
  ranking = {Q1 2015 Computer Science Applications|https://www.scimagojr.com/journalsearch.php?q=19600157322&tip=sid&clean=0},
}
@article{krallinger-cheminformatics2015,
  author = {M. Krallinger and O. Rabal and F. Leitner and M. Vazquez and D. Salgado and Z. Lu and R. Leaman and Y. Lu and D. Ji and D. Lowe and R. Sayle and R. Batista-Navarro and R. Rak and T. Huber and T. Rocktaschel and S. Matos and D. Campos and B. Tang and H. Xu and T. Munkhdalai and K. Ryu and S. Ramanan and S. Nathan and S. Zitnik and M. Bajec and L. Weber and M. Irmer and S. Akhondi and J. Kors and S. Xu and X. An and U. Sikdar and A. Ekbal and M. Yoshioka and T. Dieb and M. Choi and K. Verspoor and M. Khabsa and C. Giles and H. Liu and K. Ravikumar and A. Lamurias and F. Couto and H. Dai and R. Tsai and C. Ata and T. Can and A. Usié and R. Alves and I. Segura-Bedmar and P. Martínez and J. Oryzabal and A. Valencia},
  title = {The {CHEMDNER} corpus of chemicals and drugs and its annotation principles},
  journal = {Journal of Cheminformatics},
  issn = {1758-2946},
  volume = {7},
  number = {Suppl 1},
  doi = {https://doi.org/10.1186/1758-2946-7-S1-S2},
  scholar = {http://scholar.google.com/scholar?cluster=16243593868952519643},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/25810773},
  year = {2015},
  ranking = {Q1 2015 Computer Science Applications|https://www.scimagojr.com/journalsearch.php?q=19600157322&tip=sid&clean=0},
}
@article{cmachado-briefings2015,
  author = {C. Machado and D. Rebholz-Schuhmann and A. Freitas and F. Couto},
  title = {The semantic web in translational medicine: current applications and future directions},
  journal = {Briefings in Bioinformatics, Oxford University Press},
  issn = {1477-4054},
  volume = {16},
  number = {1},
  doi = {https://doi.org/10.1093/bib/bbt079},
  scholar = {http://scholar.google.com/scholar?cluster=13751739436555389157},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/24197933},
  year = {2015},
  ranking = {Q1 2015 Information Systems|https://www.scimagojr.com/journalsearch.php?q=17956&tip=sid&clean=0},
}
@article{dfaria-plos2014,
  author = {D. Faria and C. Pesquita and E. Santos and I. Cruz and F. Couto},
  title = {Automatic Background Knowledge Selection for Matching Biomedical Ontologies},
  journal = {PLoS ONE},
  issn = {1932-6203},
  volume = {9},
  number = {11},
  doi = {https://doi.org/10.1371/journal.pone.0111226},
  scholar = {http://scholar.google.com/scholar?cluster=1817323375490171503},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/25379899},
  year = {2014},
  ranking = {Q1 2014 Biochemistry, Genetics and Molecular Biology (miscellaneous)|https://www.scimagojr.com/journalsearch.php?q=10600153309&tip=sid&clean=0},
}
@article{alamurias-jib2014,
  author = {A. Lamurias and J. Ferreira and F. Couto},
  title = {Identifying interactions between chemical entities in biomedical text},
  journal = {Journal of Integrative Bioinformatics},
  issn = {1613-4516},
  volume = {11},
  number = {3},
  doi = {https://doi.org/10.2390/biecoll-jib-2014-247},
  scholar = {http://scholar.google.com/scholar?cluster=13824906094288677336},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/25339081},
  year = {2014},
  ranking = {Q2 2014 Medicine (miscellaneous)|https://www.scimagojr.com/journalsearch.php?q=19700170615&tip=sid&clean=0},
}
@article{cpesquita-jbs2014,
  author = {C. Pesquita and J. Ferreira and F. Couto and M. Silva},
  title = {The epidemiology ontology: an ontology for the semantic annotation of epidemiological resources},
  journal = {Journal of Biomedical Semantics},
  issn = {2041-1480},
  volume = {5},
  number = {4},
  doi = {https://doi.org/10.1186/2041-1480-5-4},
  scholar = {http://scholar.google.com/scholar?cluster=13824906094288677336},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/24438387},
  year = {2014},
  ranking = {Q1 2014 Information Systems|https://www.scimagojr.com/journalsearch.php?q=21100316001&tip=sid&clean=0},
}
@article{jferreira-bioinf2013,
  author = {J. Ferreira and J. Hastings and F. Couto},
  title = {Exploiting disjointness axioms to improve semantic similarity measures},
  journal = {Bioinformatics, Oxford Univ Press},
  issn = {1367-4803},
  volume = {29},
  number = {21},
  doi = {https://doi.org/10.1093/bioinformatics/btt491},
  scholar = {http://scholar.google.com/scholar?cluster=492087266593442408},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/24002110},
  year = {2013},
  ranking = {Q1 2013 Computational Mathematics|https://www.scimagojr.com/journalsearch.php?q=17945&tip=sid&clean=0},
}
@article{hbastos-frontiers2013,
  author = {H. Bastos and L. Clarke and F. Couto},
  title = {Annotation extension through protein family annotation coherence metrics},
  journal = {Frontiers in Genetics},
  issn = {1664-8021},
  volume = {4},
  number = {201},
  doi = {https://doi.org/10.3389/fgene.2013.00201},
  scholar = {http://scholar.google.com/scholar?cluster=16238363730320670477},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/24130572},
  year = {2013},
  ranking = {Q2 2013 Genetics|https://www.scimagojr.com/journalsearch.php?q=21100236803&tip=sid&clean=0},
}
@article{fcouto-jbcb2013,
  author = {F. Couto and H. Pinto},
  title = {The Next Generation of Similarity Measures that fully explore the Semantics in Biomedical Ontologies},
  journal = {Journal of Bioinformatics and Computational Biology},
  issn = {0219-7200},
  volume = {11},
  number = {1371001},
  doi = {https://doi.org/10.1142/S0219720013710017},
  scholar = {http://scholar.google.com/scholar?cluster=5948470332995099947},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/24131058},
  year = {2013},
  ranking = {Q2 2013 Computer Science Applications|https://www.scimagojr.com/journalsearch.php?q=29556&tip=sid&clean=0},
}
@article{cmachado-jbs2013,
  author = {C. Machado and A. Freitas and F. Couto},
  title = {Enrichment analysis applied to disease prognosis},
  journal = {Journal of Biomedical Semantics},
  issn = {2041-1480},
  volume = {4},
  number = {21},
  doi = {https://doi.org/10.1186/2041-1480-4-21},
  scholar = {http://scholar.google.com/scholar?cluster=7313889795461083872},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/24103636},
  year = {2013},
  ranking = {Q1 2013 Information Systems|https://www.scimagojr.com/journalsearch.php?q=21100316001&tip=sid&clean=0},
}
@article{tgrego-plos2013,
  author = {T. Grego and F. Couto},
  title = {Enhancement of Chemical Entity Identification in Text using Semantic Similarity Validation},
  journal = {PLoS ONE},
  issn = {1932-6203},
  volume = {8},
  number = {5 (e62984)},
  doi = {https://doi.org/10.1371/journal.pone.0062984},
  scholar = {http://scholar.google.com/scholar?cluster=5498993661040753768},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/23658791},
  year = {2013},
  ranking = {Q1 2013 Biochemistry, Genetics and Molecular Biology (miscellaneous)|https://www.scimagojr.com/journalsearch.php?q=10600153309&tip=sid&clean=0},
}
@article{silvio-program2013,
  author = {S. Moreira and D. Batista and P. Carvalho and F. Couto and M. Silva},
  title = {Tracking Politics with {POWER}},
  journal = {Program: electronic library and information systems},
  issn = {0033-0337},
  volume = {47},
  number = {2},
  doi = {https://doi.org/10.1108/00330331311313708},
  scholar = {http://scholar.google.com/scholar?q=%22Tracking+Politics+with+POWER%22},
  year = {2013},
  ranking = {Q2 2013 Information Systems|https://www.scimagojr.com/journalsearch.php?q=15511&tip=sid&clean=0},
}
@article{jferreira-jech2013,
  author = {J. Ferreira and D. Paolotti and F. Couto and M. Silva},
  title = {On the usefulness of ontologies in epidemiologic research and practice},
  journal = {Journal of Epidemiology and Community Health},
  issn = {0143-005X},
  volume = {67},
  number = {},
  year = {2013},
  ranking = {Q1 2013 Epidemiology|https://www.scimagojr.com/journalsearch.php?q=15896&tip=sid&clean=0},
  doi = {https://doi.org/10.1136/jech-2012-201142},
  scholar = {http://scholar.google.com/scholar?cluster=16216998847028123238},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/23155060},
}
@article{cpesquita-plos2012,
  author = {C. Pesquita and F. Couto},
  title = {Predicting the Extension of Biomedical Ontologies},
  journal = {PLoS Computational Biology},
  issn = {1553-734X},
  volume = {8},
  number = {9 (e1002630)},
  year = {2012},
  ranking = {Q1 2012 Computational Theory and Mathematics|https://www.scimagojr.com/journalsearch.php?q=4000151810&tip=sid&clean=0},
  doi = {https://doi.org/10.1371/journal.pcbi.1002630},
  scholar = {http://scholar.google.com/scholar?cluster=15303723571879668877},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/23028267},
}
@article{tgrego-isrn2012,
  author = {T. Grego and C. Pesquita and H. Bastos and F. Couto},
  title = {Chemical Entity Recognition and Resolution to {ChEBI}},
  journal = {ISRN Bioinformatics},
  volume = {2012},
  number = {619427},
  issn = {2090-7346},
  year = {2012},
  doi = {https://doi.org/10.5402/2012/619427},
  scholar = {http://scholar.google.com/scholar?cluster=17744788220172259679},
}
@article{fcouto-jbs2011,
  author = {F. Couto and M. Silva},
  title = {Disjunctive Shared Information between Ontology Concepts: application to {Gene Ontology}},
  journal = {Journal of Biomedical Semantics},
  issn = {2041-1480},
  volume = {2},
  number = {5},
  year = {2011},
  ranking = {Q1 2011 Information Systems|https://www.scimagojr.com/journalsearch.php?q=21100316001&tip=sid&clean=0},
  doi = {https://doi.org/10.1186/2041-1480-2-5},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/21884591},
  code = {files/DiShIn-201111.sql.gz},
  scholar = {http://scholar.google.com/scholar?cluster=8083957960311555429},
  pt = {files/journal fcouto-jbs2011-pt.pdf},
}
@article{simoes-jp2011,
  author = {T. Simões and N. Charro and J. Blonder and D. Faria and F. Couto and
	K. Chan and T. Waybright and H. Isaaq and T. Veenstra and D. Penque},
  title = {Molecular profiling of the human nasal epithelium: A proteomics approach},
  journal = {Journal of Proteomics},
  issn = {1874-3919},
  volume = {75},
  number = {1},
  year = {2011},
  ranking = {Q1 2011 Biophysics|https://www.scimagojr.com/journalsearch.php?q=11700154304&tip=sid&clean=0},
  doi = {https://doi.org/10.1016/j.jprot.2011.05.012},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/21621024},
  scholar = {http://scholar.google.com/scholar?cluster=10109268632749114689},
}
@article{charro-jp2011,
  author = {N. Charro and B. Hood and D. Faria and P. Pacheco and P. Azevedo 
	and C. Lopes and A. Almeida and F. Couto and T. Conrads and D. Penque},
  title = {Serum proteomics signature of {Cystic Fibrosis} patients: 
	A complementary {2-DE} and {LC-MS}/{MS} approach},
  journal = {Journal of Proteomics},
  issn = {1874-3919},
  volume = {74},
  number = {1},
  year = {2011},
  ranking = {Q1 2011 Biophysics|https://www.scimagojr.com/journalsearch.php?q=11700154304&tip=sid&clean=0},
  doi = {https://doi.org/10.1016/j.jprot.2010.10.001},
  scholar = {http://scholar.google.com/scholar?cluster=11970956521982542823},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/20950718},
}
@article{ferreira-plos2010,
  author = {J. Ferreira and F. Couto},
  title = {Semantic Similarity for Automatic Classification of Chemical Compounds},
  journal = {PLoS Computational Biology},
  issn = {1553-734X},
  volume = {6},
  number = {9 (e1000937)},
  year = {2010},
  ranking = {Q1 2010 Computational Theory and Mathematics|https://www.scimagojr.com/journalsearch.php?q=4000151810&tip=sid&clean=0},
  doi = {https://doi.org/10.1371/journal.pcbi.1000937},
  scholar = {http://scholar.google.com/scholar?cluster=18022949035302963388},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/20885779},
}
@article{alves-biochimica2010,
  author = {P. Gomes-Alves and F. Couto and C. Pesquita and A. Coelho and D. Penque},
  title = {Rescue of {F508del-CFTR} by {RXR} motif inactivation triggers proteome 
	modulation associated with the unfolded protein response},
  journal = {Biochimica et Biophysica Acta, Proteins and Proteomics},
  issn = {1570-9639},
  volume = {1804},
  number = {4},
  year = {2010},
  ranking = {Q1 2010 Biophysics|https://www.scimagojr.com/journalsearch.php?q=16832&tip=sid&clean=0},
  doi = {https://doi.org/10.1016/j.bbapap.2009.12.013},
  scholar = {http://scholar.google.com/scholar?cluster=7320108195716105712},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/20044041},
}
@article{couto-plos2009,
  author = {C. Pesquita and D. Faria and A. Falcão and P. Lord and F. Couto},
  title = {Semantic Similarity in Biomedical Ontologies},
  journal = {PLoS Computational Biology},
  issn = {1553-734X},
  volume = {5},
  number = {7 (e1000443)},
  year = {2009},
  ranking = {Q1 2009 Computational Theory and Mathematics|https://www.scimagojr.com/journalsearch.php?q=4000151810&tip=sid&clean=0},
  doi = {https://doi.org/10.1371/journal.pcbi.1000443},
  scholar = {http://scholar.google.com/scholar?cluster=4114755091410814806},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/19649320},
}
@article{couto-cybermetrics2009,
  author = {F. Couto and C. Pesquita and T. Grego and P. Verissimo},
  title = {Handling Self-citations using {Google Scholar}},
  journal = {Cybermetrics},
  issn = {1137-5019},
  volume = {13},
  number = {1},
  year = {2009},
  ranking = {Q1 2009 Library and Information Sciences|https://www.scimagojr.com/journalsearch.php?q=145507&tip=sid&clean=0},
  doi = {https://doi.org/10451/14427},
  scholar = {http://scholar.google.com/scholar?cluster=10434027016596126591},
}
@article{cpesquita-bmc2008,
  author = {C. Pesquita and D. Faria and A. Ferreira and A. Falcão and F. Couto},
  title = {Metrics for {GO} based protein semantic similarity: a systematic evaluation},
  journal = {BMC Bioinformatics},
  volume = {9},
  number = {5 (S4)},
  issn = {1471-2105},
  doi = {https://doi.org/10.1186/1471-2105-9-S5-S4},
  scholar = {http://scholar.google.com/scholar?cluster=4993473811464216221},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/18460186},
  year = {2008},
  ranking = {Q1 2008 Computer Science Applications|https://www.scimagojr.com/journalsearch.php?q=17929&tip=sid&clean=0},
}
@article{fcouto-dke2007,
  author = {F. Couto and M. Silva and P. Coutinho},
  title = {Measuring Semantic Similarity between {Gene Ontology} Terms},
  journal = {Data and Knowledge Engineering},
  volume = {61},
  number = {1},
  issn = {0169-023X},
  year = {2007},
  ranking = {Q2 2007 Information Systems and Management|https://www.scimagojr.com/journalsearch.php?q=24437&tip=sid&clean=0},
  doi = {https://doi.org/10.1016/j.datak.2006.05.003},
  scholar = {http://scholar.google.com/scholar?cluster=17406369667746632778},
}
@article{fcouto-jbdc2006,
  author = {F. Couto and M. Silva and V. Lee and E. Dimmer and E. Camon and R. Apweiler
            and H. Kirsch and D. Rebholz-Schuhmann},
  title = {{GOAnnotator}: linking electronic protein {GO} annotation to evidence text},
  journal = {Journal of Biomedical Discovery and Collaboration},
  volume = {19},
  number = {1},
  doi = {https://doi.org/10.1186/1747-5333-1-19},
  scholar = {http://scholar.google.com/scholar?cluster=10681658035466703036},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/17181854},
  issn = {1747-5333},
  year = {2006},
  ranking = {Q2 2007 History and Philosophy of Science|https://www.scimagojr.com/journalsearch.php?q=5800179621&tip=sid&clean=0},
}
@article{fcouto-bmc2005,
  author = {F. Couto and M. Silva and P. Coutinho},
  title = {Finding Genomic Ontology Terms in Text using Evidence Content},
  journal = {BMC Bioinformatics},
  issn = {1471-2105},
  volume = {6},
  number = {S1( S21)},
  year = {2005},
  ranking = {Q1 2005 Computer Science Applications|https://www.scimagojr.com/journalsearch.php?q=17929&tip=sid&clean=0},
  doi = {https://doi.org/10.1186/1471-2105-6-S1-S21},
  scholar = {http://scholar.google.com/scholar?cluster=2638531050205218786},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/15960834},
}
@article{dietrich-plos2005,
  author = {D. Rebholz-Schuhmann and H. Kirsch and F. Couto},
  title = {Facts from text - Is Text Mining ready to deliver?},
  journal = {PLoS Biology},
  issn = {1545-7885},
  volume = {3},
  number = {2 (e65)},
  year = {2005},
  ranking = {Q1 2005 Biochemistry, Genetics and Molecular Biology (miscellaneous)|https://www.scimagojr.com/journalsearch.php?q=12977&tip=sid&clean=0},
  doi = {https://doi.org/10.1371/journal.pbio.0030065},
  scholar = {http://scholar.google.com/scholar?cluster=7235717651467416540},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/15719064},
}
@inproceedings{west-www2021,
  author = { R. West and  S. Bhagat and  P. Groth and  M. Zitnik and  F. M. Couto and  P. Lisena and  A. Mero\~{n}o-Pe\~{n}uela and  X. Zhao and  W. Fan and  D. Yin and  J. Tang and  L. Shou and  M. Gong and  J. Pei and  X. Geng and  X. Zhou and  D. Jiang and  B. Ricaud and  N. Aspert and  V. Miz and  J. Dy and  S. Ioannidis and  I. Y\i{}ld\i{}z and  R. Rezapour and  S. Aref and  L. Dinh and  J. Diesner and  A. Drutsa and  D. Ustalov and  N. Popov and  D. Baidakova and  S. Mishra and  A. Gopalan and  D. Juan and  C. Ilharco Magalhaes and  C. Ferng and  A. Heydon and  C. Lu and  P. Pham and  G. Yu and  Y. Fan and  Y. Wang and  F. Laurent and  Y. Schraner and  C. Scheller and  S. Mohanty and  J. Chen and  X. Wang and  F. Feng and  X. He and  I. Teinemaa and  J. Albert and  D. Goldenberg and  F. Vasile and  D. Rohde and  O. Jeunen and  A. Benhalloum and  O. Sakhi and  Y. Rong and  W. Huang and  T. Xu and  Y. Bian and  H. Cheng and  F. Sun and  J. Huang and  S. Fakhraei and  C. Faloutsos and  O. \c{C}elebi and  M. M\"{u}ller and  M. Schneider and  O. Altunina and  W. Wingerath and  B. Wollmer and  F. Gessert and  S. Succo and  N. Ritter and  E. Courdier and  T. Mihai Avram and  D. Cvetinovic and  L. Tsinadze and  J. Jose and  R. Howell and  M. Koenig and  M. Defferrard and  K. Kenthapadi and  B. Packer and  M. Sameki and  N. Sephus},
  title = {Summary of Tutorials at {The Web Conference} 2021},
  booktitle = {Companion Proceedings of the Web Conference 2021},
  volume = {},
  url = {https://doi.org/10.1145/3442442.3453701},
  scholar = {https://scholar.google.com/scholar?cites=18276910064050392996},
  year = 2021,
  ranking = {Core2021 A* (companion)|http://portal.core.edu.au/conf-ranks/1548/},
}
@inproceedings{fabio-recsys2020,
  author = {F. Colaço and M. Barros and F. Couto},
  title = {{DRecPy}: A Python Framework for Developing Deep Learning-Based Recommenders},
  booktitle = {14th ACM Conference on Recommender Systems (RECSYS 2020) (Late-breaking results)},
  volume = {},
  url = {https://doi.org/10.1145/3383313.3418483},
  scholar = {https://scholar.google.com/scholar?cluster=12647422680977593822},
  year = 2020,
  ranking = {Core2020 B|http://portal.core.edu.au/conf-ranks/28/},
}
@inproceedings{mbarros-ecir2020,
  author = {M. Barros and A. Moitinho and F. Couto},
  title = {Hybrid Semantic Recommender System for Chemical Compounds},
  booktitle = {42nd European Conference on Information Retrieval (ECIR 2020)},
  volume = {12036},
  url = {https://doi.org/10.1007/978-3-030-45442-5_12},
  scholar = {https://scholar.google.com/scholar?cluster=7117884713876834347},
  year = 2020,
  ranking = {Core2020 A|http://portal.core.edu.au/conf-ranks/483/},
}
@inproceedings{dsousa-ecir2020,
  author = {D. Sousa and F. Couto},
  title = {{BiOnt}: Deep Learning using Multiple Biomedical Ontologies for Relation Extraction},
  booktitle = {42nd European Conference on Information Retrieval (ECIR 2020)},
  volume = {12036},
  url = {https://doi.org/10.1007/978-3-030-45442-5_46},
  scholar = {https://scholar.google.com/scholar?cluster=15323912899745798453},
  year = 2020,
  ranking = {Core2020 A|http://portal.core.edu.au/conf-ranks/483/},
}
@inproceedings{fcouto-ecir2020,
  author = {F. Couto and M. Krallinger},
  title = {Proposal of the First International Workshop on Semantic Indexing and Information Retrieval for Health from heterogeneous content types and languages {(SIIRH)}},
  booktitle = {42nd European Conference on Information Retrieval (ECIR 2020)},
  volume = {12036},
  url = {https://doi.org/10.1007/978-3-030-45442-5_87},
  scholar = {https://scholar.google.com/scholar?cluster=608581979891058841},
  year = 2020,
  ranking = {Core2020 A|http://portal.core.edu.au/conf-ranks/483/},
}
@inproceedings{dsousa-naacl2019,
  author = {D. Sousa and A. Lamurias and F. Couto},
  title = {A Silver Standard Corpus of Human Phenotype-Gene Relations},
  booktitle = {Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies (NAACL 2019)},
  volume = {N19-1152},
  url = {https://www.aclweb.org/anthology/N19-1152},
  scholar = {https://scholar.google.com/scholar?cluster=15690562588439326838},
  year = 2019,
  ranking = {Core2018 A|http://portal.core.edu.au/conf-ranks/1648/},
}
@inproceedings{mfernandes-pacbb2017,
  author = {M. Fernandes and J. Decouchant and F. Couto and P. Verissimo},
  title = {Cloud-Assisted Read Alignment and Privacy},
  booktitle = {Practical Applications of Computational Biology and Bioinformatics (PACBB)},
  volume = {},
  doi = {https://doi.org/10.1007/978-3-319-60816-7_27},
  scholar = {https://scholar.google.com/scholar?cluster=4046435247671139835},
  year = 2017,
}
@inproceedings{binacio-pacbb2017,
  author = {B. Inácio and J. Ferreira and F. Couto},
  title = {Metadata Analyser: measuring metadata quality},
  booktitle = {Practical Applications of Computational Biology and Bioinformatics (PACBB)},
  volume = {},
  doi = {https://doi.org/10.1007/978-3-319-60816-7_24},
  scholar = {http://scholar.google.com/scholar?cluster=12175273002811620336},
  year = 2017,
}
@inproceedings{abarata-pacbb2017,
  author = {A. Barata and L. Carvalho and F. Couto},
  title = {Anthropometric Data Analytics: a Portuguese Case Study},
  booktitle = {Practical Applications of Computational Biology and Bioinformatics (PACBB)},
  volume = {},
  doi = {https://doi.org/10.1007/978-3-319-60816-7_12},
  scholar = {https://scholar.google.com/scholar?cluster=12843768395974103201},
  year = 2017,
}
@inproceedings{vcogo-pacbb2017,
  author = {V. Cogo and A. Bessani and F. Couto and M. Gama-Carvalho and M. Fernandes and P. Verissimo},
  title = {How can photo sharing inspire sharing genomes?},
  booktitle = {Practical Applications of Computational Biology and Bioinformatics (PACBB)},
  volume = {},
  doi = {https://doi.org/10.1007/978-3-319-60816-7_10},
  scholar = {https://scholar.google.com/scholar?cluster=14767115946407042751},
  year = 2017,
}
@inproceedings{alamurias-pkdd2015,
  title = {{IICE}: web tool for automatic identification of chemical entities and interactions},
  author = {A. Lamurias and L. Clarke and F. Couto},
  booktitle = {European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML-PKDD), Demo Track},
  year = 2015,
  ranking = {Core2014 A|http://portal.core.edu.au/conf-ranks/491/},
  doi = {https://doi.org/10.1007/978-3-319-23461-8_31},
  scholar = {http://scholar.google.com/scholar?cluster=16535448753528616589},
  url = {https://books.google.com/books?id=o111CgAAQBAJ&pg=PA285},
}
@inproceedings{alamurias-icbo2015,
  title = {Annotating biomedical terms in electronic health records using crowd-sourcing},
  author = {A. Lamurias and V. Pedro and L. Clarke and F. Couto},
  booktitle = {International Conference on Biomedical Ontologies (ICBO), Early Career},
  year = 2015,
  url = {http://ceur-ws.org/Vol-1515/early1.pdf},
  scholar = {http://scholar.google.com/scholar?cluster=13685801770975361327},
}
@inproceedings{barata-epia2015,
  author = {C. Barata and M. Abreu and P. Torres and J. Teixeira and T. Guerreiro and F. Couto},
  title = {Social Impact - Identifying Quotes of Literary Works in Social Networks },
  booktitle = {17th Portuguese Conference on Artificial Intelligence (EPIA)},
  year = {2015},
  doi = {https://doi.org/10.1007/978-3-319-23485-4_79},
  scholar = {http://scholar.google.com/scholar?cluster=5963693185755264807},
}
@inproceedings{dfaria-iswc2014,
  author = {D. Faria and Ernesto Jim\'enez-Ruiz and C. Pesquita and E. Santos and I. Cruz and F. Couto},
  title = {Towards annotating potential incoherences in {BioPortal} mappings},
  booktitle = {International Semantic Web Conference (ISWC)},
  year = {2014},
  ranking = {Core2014 A|http://portal.core.edu.au/conf-ranks/1338/},
  doi = {https://doi.org/10.1007/978-3-319-11915-1_2},
  scholar = {http://scholar.google.com/scholar?cluster=4087739904693348966},
}
@inproceedings{mcosta-sigir2014,
  author = {M. Costa and F. Couto and M. Silva},
  title = {Learning Temporal-Dependent Ranking Models},
  booktitle = {The 37th annual international ACM Special Interest Group On Information Retrieval conference (ACM SIGIR)},
  year = {2014},
  ranking = {Core2014 A*|http://portal.core.edu.au/conf-ranks/29/},
  doi = {https://doi.org/10.1145/2600428.2609619},
  scholar = {http://scholar.google.com/scholar?cluster=7354367069945128468},
  url = {http://sigir.org/sigir2014/finalfullpapers.php},
}
@inproceedings{cpesquita-dils2014,
  author = {C. Pesquita and D. Faria and E. Santos and J. Neefs and F. Couto},
  title = {Towards visualizing the alignment of large biomedical ontologies},
  booktitle = {The 10th International Conference on Data Integration in the Life Sciences (DILS) (short paper)},
  year = {2014},
  doi = {https://doi.org/10.1007/978-3-319-08590-6_10},
  scholar = {http://scholar.google.com/scholar?cluster=8398776852474835365},
}
@inproceedings{alamurias-pacbb2014,
  author = {A. Lamurias and J. Ferreira and F. Couto},
  title = {Chemical Named Entity Recognition: Improving Recall Using a Comprehensive List of Lexical Features},
  booktitle = {Practical Applications of Computational Biology and Bioinformatics (PACBB)},
  publisher = {Lecture Notes in Computer Science},
  volume = 294,
  doi = {https://doi.org/10.1007/978-3-319-07581-5_30},
  scholar = {http://scholar.google.com/scholar?cluster=17060406327099918028},
  year = 2014,
}
@inproceedings{jmartins-w4a2014,
  author = {J. Martins and J. Carilho and O. Schnell and C. Duarte and F. Couto and L. Carriço and T. Guerreiro},
  title = {Friendsourcing the Unmet Needs of People with Dementia},
  booktitle = {The 11th Web for All Conference (W4A)},
  year = {2014},
  doi = {https://doi.org/10.1145/2596695.2596716},
  scholar = {http://scholar.google.com/scholar?cluster=2993455842048304596},
}
@inproceedings{dfaria-odbase2013,
  author = {D. Faria and C. Pesquita and E. Santos and M. Palmonari and I. Cruz and F. Couto},
  title = {The {AgreementMakerLight} Ontology Matching System},
  booktitle = {The 12th International Conference on Ontologies, DataBases, and Applications of Semantics (ODBASE)},
  year = {2013},
  doi = {https://doi.org/10.1007/978-3-642-41030-7_38},
  scholar = {http://scholar.google.com/scholar?cluster=11348944698436252059},
}
@inproceedings{cpesquita-iswc2013,
  author = {C. Pesquita and D. Faria and C. Stroe and E. Santos and I. Cruz and F. Couto},
  title = {What's in a `nym'? Synonyms in Biomedical Ontology Matching},
  booktitle = {International Semantic Web Conference (ISWC)},
  year = {2013},
  ranking = {Core2013 A|http://portal.core.edu.au/conf-ranks/1338/},
  doi = {https://doi.org/10.1007/978-3-642-41335-3_33},
  scholar = {http://scholar.google.com/scholar?cluster=17671538620882011761},
}
@inproceedings{cmachado-itbam2012,
  author = {C. Machado and F. Couto and A. Fernandes and S. Santos and A. Freitas},
  title = {Toward a Translational Medicine Approach for Hypertrophic Cardiomyopathy},
  booktitle = {International Conference on Information Technology in Bio and Medical Informatics (ITBAM - DEXA)},
  year = {2012},
  ranking = {Core2010 B|http://portal.core.edu.au/conf-ranks/987/},
  doi = {https://doi.org/10.1007/978-3-642-32395-9_12},
  scholar = {http://scholar.google.com/scholar?cluster=8769330970233833400},
}
@inproceedings{ferreira-icbo2012,
  author = {J. Ferreira and C. Pesquita and M. Silva and F. Couto},
  title = {Bringing epidemiology into the Semantic Web},
  booktitle = {International Conference on Biomedical Ontologies (ICBO)},
  year = 2012,
  url = {http://ceur-ws.org/Vol-897/session1-paper02.pdf},
  scholar = {http://scholar.google.com/scholar?cluster=13950847390330365317},
}
@inproceedings{dbatista-propor2012,
  author = {D. Batista and J. Ferreira and F. Couto and M. Silva},
  title = {Toponym Disambiguation using Ontology-based Semantic Similarity},
  booktitle = {Computational Processing of the Portuguese Language (PROPOR)},
  year = {2012},
  doi = {https://doi.org/10.1007/978-3-642-28885-2_20},
  scholar = {http://scholar.google.com/scholar?cluster=143194817580493938},
}
@inproceedings{ferreira-icbo2011,
  author = {J. Ferreira and F. Couto},
  title = {Generic semantic relatedness measure for biomedical ontologies},
  booktitle = {International Conference on Biomedical Ontologies (ICBO)},
  year = 2011,
  url = {http://ceur-ws.org/Vol-833/paper16.pdf},
  scholar = {http://scholar.google.com/scholar?cluster=17067037268222458310},
}
@inproceedings{cpesquita-icbo2011,
  author = {C. Pesquita and F. Couto},
  title = {Where {GO} is going and what it means for ontology extension},
  booktitle = {International Conference on Biomedical Ontologies (ICBO)},
  year = 2011,
  url = {http://ceur-ws.org/Vol-833/paper1.pdf},
  scholar = {http://scholar.google.com/scholar?cluster=834567132010429390},
}
@inproceedings{lopes-itbam2010,
  author = {L. Lopes and F. Silva and F. Couto and J. Zamite and H. Ferreira and C. Sousa and M. Silva},
  title = {Epidemic Marketplace: An Information Management System for Epidemiological Data},
  booktitle = {International Conference on Information Technology in Bio and Medical Informatics (ITBAM - DEXA)},
  year = 2010,
  ranking = {Core2010 B|http://portal.core.edu.au/conf-ranks/987/},
  doi = {https://doi.org/10.1007/978-3-642-15020-3_3},
  scholar = {http://scholar.google.com/scholar?cluster=14180276948836474886},
}
@inproceedings{zamite-itbam2010,
  author = {J. Zamite and F. Silva and F. Couto and M. Silva},
  title = {{MEDCollector}: Multisource Epidemic Data Collector},
  booktitle = {International Conference on Information Technology in Bio and Medical Informatics (ITBAM - DEXA)},
  year = {2010},
  ranking = {Core2010 B|http://portal.core.edu.au/conf-ranks/987/},
  doi = {https://doi.org/10.1007/978-3-642-15020-3_2},
}
@inproceedings{mjs-icdl2010,
  author = {M. Silva and F. Silva and L. Lopes and F. Couto},
  title = {Building a Digital Library for Epidemic Modelling},
  booktitle = {The International Conference on Digital Libraries (ICDL)},
  year = 2010,
  scholar = {http://scholar.google.com/scholar?cluster=268386023296566408},
}
@inproceedings{fcouto-icdim2008,
  author = {F. Couto and T. Grego and C. Pesquita and H. Bastos and R. Torres and P. Sanchez and L. Pascual and C. Blaschke},
  title = {Identifying Bioentity Recognition Errors of Rule-Based Text-Mining Systems},
  booktitle = {IEEE Third International Conference on Digital Information Management (ICDIM)},
  year = 2008,
  doi = {https://doi.org/10.1109/ICDIM.2008.4746791},
  scholar = {http://scholar.google.com/scholar?cluster=7894029173146046374},
}
@inproceedings{fcouto-cikm2006,
  author = {F. Couto and M. Silva and P. Coutinho},
  title = {Validating Associations in Biological Databases},
  booktitle = {ACM Conference in Information 
               and Knowledge Management (CIKM)},
  ranking = {Core2008 A|http://portal.core.edu.au/conf-ranks/25/},
  year = 2006,
  doi = {https://doi.org/10.1145/1183614.1183639},
  scholar = {http://scholar.google.com/scholar?cluster=576692722105021963},
}
@inproceedings{fcouto-cikm2005,
  author = {F. Couto and M. Silva and P. Coutinho},
  title = {Semantic Similarity over the Gene Ontology: 
           Family Correlation and Selecting Disjunctive Ancestors},
  booktitle = {ACM Conference in Information 
               and Knowledge Management (CIKM) (as a short paper)},
  ranking = {Core2008 A|http://portal.core.edu.au/conf-ranks/25/},
  year = 2005,
  doi = {https://doi.org/10.1145/1099554.1099658},
  scholar = {http://scholar.google.com/scholar?cluster=2944142862198883776},
}
@inproceedings{fcouto-sac2004,
  author = {F. Couto and B. Martins and M. Silva},
  title = {Classifying biological articles using web resources},
  booktitle = {2004 ACM Symposium on Applied Computing (SAC)},
  year = {2004},
  ranking = {Core2008 B|http://portal.core.edu.au/conf-ranks/59/},
  doi = {https://doi.org/10.1145/967900.967925},
  scholar = {http://scholar.google.com/scholar?cluster=3385704427349463965},
}
@inproceedings{fcouto-jisbd2003,
  author = {F. Couto and M. Silva and P. Coutinho},
  title = {{ProFAL}: Protein Functional Annotation through Literature},
  booktitle = {8th Conference on Software Engineering 
               and Databases (JISBD)},
  year = 2003,
  scholar = {http://scholar.google.com/scholar?cluster=10263935717386785253},
}
@inproceedings{sconceicao-biocreative2023,
  author = {S. Conceicao and D. Sousa and P. Silvestre and F. Couto},
  title = {{BioRED} track {lasigeBioTM} submission: Relation extraction
using Domain Ontologies with {BioRED}},
  booktitle = {BioCreative VIII Challenge Evaluation},
  year = 2023,
  url = {https://www.researchgate.net/profile/Sofia-Conceicao-2/publication/375861723_BioRED_track_lasigeBioTM_submission_Relation_Extraction_using_Domain_Ontologies_with_BioRED/links/655f7b8db1398a779dab8deb/BioRED-track-lasigeBioTM-submission-Relation-Extraction-using-Domain-Ontologies-with-BioRED.pdf},
}
@inproceedings{sofia-semeval2023,
  author = {S. Conceicao and D. Sousa and P. Silvestre and F. Couto},
  title = {{lasigeBioTM} at {SemEval-2023} {Task} 7: Improving Natural Language Inference Baseline Systems with Domain Ontologies},
  booktitle = {17th International Workshop on Semantic Evaluation (SemEval)},
  year = 2023,
  url = {https://aclanthology.org/2023.semeval-1.2/},
}
@inproceedings{dfaria-om2021,
  author = {D. Faria and B. Lima and M. Silva and F. Couto and C. Pesquita},
  title = {{AML} and {AMLC} results for {OAEI} 2021},
  booktitle = {16th International Workshop on Ontology Matching (OM-2021)},
  year = 2021,
  url = {http://disi.unitn.it/~pavel/om2021/papers/oaei21_paper4.pdf},
}
@inproceedings{dsousa-biocreative2021,
  author = {D. Sousa and R. Cassanheira and F. Couto},
  title = {{lasigeBioTM} at {BioCreative VII Track} 1: Text mining drug and chemical-protein interactions using biomedical ontologies},
  booktitle = {BioCreative VII Challenge Evaluation},
  year = 2021,
  url = {https://biocreative.bioinformatics.udel.edu/media/store/files/2021/Track1_pos_18_BC7_submission_174.pdf},
}
@inproceedings{mbarros-emnlp2020,
  author = {M. Barros and A. Lamurias and D. Sousa and P. Ruas and F. Couto},
  title = {{COVID-19}: A Semantic-Based Pipeline for Recommending Biomedical Entities},
  booktitle = {1st Workshop on NLP for COVID-19 (Part 2) at EMNLP 2020},
  year = 2020,
  url = {https://www.aclweb.org/anthology/2020.nlpcovid19-2.20.pdf},
}
@inproceedings{mcampos-bioasq2021,
  author = {M. Campos and F. Couto},
  title = {Post-processing {BioBERT} And Using Voting Methods for Biomedical Question Answering},
  booktitle = {9th edition of BioASQ: Large-scale Biomedical Semantic Indexing and Question Answering (CLEF 2021 Working Notes)},
  year = 2021,
  url = {http://ceur-ws.org/Vol-2936/paper-19.pdf},
}
@inproceedings{pruas-bioasq2021,
  author = {P. Ruas and V. Andrade and F. Couto},
  title = {{LASIGE-BioTM} at {MESINESP2}: entity linking with semantic similarity and extreme multi-label classification on Spanish biomedical documents},
  booktitle = {9th edition of BioASQ: Large-scale Biomedical Semantic Indexing and Question Answering (CLEF 2021 Working Notes)},
  year = 2021,
  url = {http://ceur-ws.org/Vol-2936/paper-24.pdf},
}
@inproceedings{pruas-profner2021,
  author = {P. Ruas and V. Andrade and F. Couto},
  title = {{Lasige-BioTM} at {ProfNER}: {BiLSTM-CRF} and contextual Spanish embeddings for Named Entity Recognition and Tweet Binary Classification},
  booktitle = {6th Social Media Mining for Health Workshop},
  year = 2021,
  url = {https://www.aclweb.org/anthology/2021.smm4h-1.21.pdf},
}
@inproceedings{dfaria-om2020,
  author = {B. Lima and D. Faria and F. Couto and I. Cruz and C. Pesquita},
  title = {{OAEI} 2020 results for {AML} and {AMLC}},
  booktitle = {15th International Workshop on Ontology Matching (OM-2020)},
  year = 2020,
  url = {http://ceur-ws.org/Vol-2788/oaei20_paper3.pdf},
}
@inproceedings{aneves-bioasq2020,
  author = {A. Neves and A. Lamurias and F. Couto},
  title = {Biomedical Question Answering using Extreme Multi-Label Classification and Ontologies in the Multilingual Panorama},
  booktitle = {8th edition of BioASQ: Large-scale Biomedical Semantic Indexing and Question Answering (CLEF 2020 Working Notes)},
  year = 2020,
  url = {http://ceur-ws.org/Vol-2696/paper_67.pdf},
}
@inproceedings{pruas-chemu2020,
  author = {P. Ruas and A. Lamurias and F. Couto},
  title = {{LasigeBioTM} Team at {CLEF2020} {ChEMU} Evaluation Lab: Named Entity Recognition and Event extraction from chemical reactions described in patents using {BioBERT} {NER} and {RE}},
  booktitle = {The workshop ChEMU: Named Entity Recognition and Event Extraction of Chemical Reactions from Patents (CLEF 2020 Working Notes)},
  year = 2020,
  url = {http://ceur-ws.org/Vol-2696/paper_175.pdf},
}
@inproceedings{aneves-chemu2020,
  author = {J. He and D. Nguyen and S. Akhondi and C. Druckenbrodt and C. Thorne and R. Hoessel and Z. Afzal and Z. Zhai and B. Fang and H. Yoshikawa and A. Albahem and J. Wang and Y. Ren and Z. Zhang and Y. Zhang and M. Dao and P. Ruas and A. Lamurias and F. Couto and J. Copara and N. Naderi and J. Knafou and P. Ruch and D. Teodoro and D. Lowe and J. Mayfield and A. Köksal and H. Dönmez and E. Özkırımlı and A. Özgür and D. Mahendran and G. Gurdin and N. Lewinski and C. Tang and B. McInnes and M. C.S. and P. Rao and S. Devi and L. Cavedon and T. Cohn and T. Baldwin and K. Verspoor},
  title = {An Extended Overview of the {CLEF} 2020 {ChEMU} Lab: Information Extraction of Chemical Reactions from Patents},
  booktitle = {The workshop ChEMU: Named Entity Recognition and Event Extraction of Chemical Reactions from Patents (CLEF 2020 Working Notes)},
  year = 2020,
  url = {http://ceur-ws.org/Vol-2696/paper_254.pdf},
}
@inproceedings{pruas-cantemist2020,
  author = {P. Ruas and A. Neves and V. Andrade and F. Couto},
  title = {{LasigeBioTM} at {CANTEMIST}: Named Entity Recognition and Normalization of Tumour Morphology Entities and Clinical Coding of Spanish Health-related Documents},
  booktitle = {The Iberian Languages Evaluation Forum (IberLEF 2020)},
  year = 2020,
  url = {http://ceur-ws.org/Vol-2664/cantemist_paper11.pdf},
}
@inproceedings{aneves-siirh2020,
  author = {A. Neves and A. Lamurias and F. Couto},
  title = {Biomedical Question Answering using Extreme Multi-Label Classification and Ontologies in the Multilingual Panorama},
  booktitle = {1st International Workshop on Semantic Indexing and Information Retrieval for Health from heterogeneous content types and languages (SIIRH)},
  year = 2020,
  url = {http://ceur-ws.org/Vol-2619/short2.pdf},
}
@inproceedings{pruas-siirh2020,
  author = {P. Ruas and A. Lamurias and F. Couto},
  title = {Towards a Multilingual Corpus for Named Entity Linking Evaluation in the Clinical Domain},
  booktitle = {1st International Workshop on Semantic Indexing and Information Retrieval for Health from heterogeneous content types and languages (SIIRH)},
  year = 2020,
  url = {http://ceur-ws.org/Vol-2619/short3.pdf},
}
@inproceedings{fcouto-siirh2020,
  author = {F. Couto and M. Krallinger},
  title = {Report of the First International Workshop on Semantic Indexing and Information Retrieval for Health from heterogeneous content types and languages},
  booktitle = {1st International Workshop on Semantic Indexing and Information Retrieval for Health from heterogeneous content types and languages (SIIRH)},
  year = 2020,
  url = {http://ceur-ws.org/Vol-2619/paper4.pdf},
}
@inproceedings{mfernandes-genopri2019,
  author = {M. Fernandes and J. Decouchant and M. Volp and F. Couto and P. Veríssimo},
  title = {Privacy-Preserving Processing of Filtered {DNA} Reads},
  booktitle = {6th International Workshop on Genome Privacy and Security (GenoPri-2019)},
  year = 2019,
  url = {https://www.genopri.org/},
}
@inproceedings{dfaria-om2019,
  author = {D. Faria and C. Pesquita and T. Tervo and F. Couto and I. Cruz},
  title = {{AML} and {AMLC} Results for {OAEI} 2019},
  booktitle = {14th International Workshop on Ontology Matching (OM-2019)},
  year = 2019,
  url = {http://ceur-ws.org/Vol-2536/oaei19_paper3.pdf},
}
@inproceedings{alamurias-bionlp2019,
  title = {{LasigeBioTM} at {MEDIQA} 2019: Biomedical Question Answering using Bidirectional Transformers and Named Entity Recognition},
  author = {A. Lamurias and F. Couto},
  booktitle = {18th ACL Workshop on Biomedical Natural Language Processing (BioNLP 2019)},
  year = 2019,
  url = {https://www.aclweb.org/anthology/W19-5057/},
}
@inproceedings{jferreira-dtmbio2018,
  author = {J. Ferreira and F. Couto},
  title = {Multi-domain Semantic Similarity in Biomedical Research},
  booktitle = {12th Data and Text Mining in Biomedical Informatics (DTMBIO 2018)},
  year = 2018,
  url = {http://web.archive.org/web/20220929122301/http://dtmbio.net/dtmbio2018/?page_id=155},
}
@inproceedings{dfaria-om2018,
  author = {D. Faria and C. Pesquita and B. Balasubramani and T. Tervo and D. Carriço and R. Garrilha and F. Couto and I. Cruz},
  title = {Results of {AML} in {OAEI} 2018},
  booktitle = {13th International Workshop on Ontology Matching (OM-2018)},
  year = 2018,
  url = {http://ceur-ws.org/Vol-2788/oaei20_paper3.pdf},
}
@inproceedings{mfernandes-eurodw2018,
  author = {M. Fernandes and J. Decouchant and F. Couto and P. Veríssimo},
  title = {Privacy-preserving algorithms and workflows for next-generation genomics},
  booktitle = {The Twelfth EuroSys Doctoral Workshop (EuroDW 2018)},
  year = 2018,
  url = {http://conferences.inf.ed.ac.uk/EuroDW2018/papers/eurodw18-Fernandes.pdf},
}
@inproceedings{dfaria-om2017,
  author = {D. Faria and B. Balasubramani and V. Shivaprabhu and I. Mott and C. Pesquita and F. Couto and I. Cruz},
  title = {Results of {AML} in {OAEI} 2017},
  booktitle = {12th International Workshop on Ontology Matching (OM-2017)},
  year = 2017,
  url = {http://ceur-ws.org/Vol-2032/oaei17_paper2.pdf},
}
@inproceedings{lcampos-inforum2017,
  author = {L. Campos and A. Lamurias and F. Couto},
  title = {Can the Wisdom of the Crowd Be Used to Improve the Creation of Gold-standard for Text Mining applications?},
  booktitle = {INForum - Simp{ó}sio de Inform{á}tica},
  year = 2017,
}
@inproceedings{fcouto-biocreative2017,
  author = {F. Couto and L. Campos and A. Lamurias},
  title = {{MER}: a Minimal Named-Entity Recognition Tagger and Annotation Server},
  booktitle = {BioCreative V.5 Challenge Evaluation},
  year = 2017,
  url = {http://www.biocreative.org/media/store/files/2017/BioCreative_V5_paper18.pdf},
}
@inproceedings{alamurias-biocreative2017,
  author = {A. Lamurias and L. Campos and F. Couto},
  title = {{IBEnt}: Chemical Entity Mentions in Patents using {ChEBI}},
  booktitle = {BioCreative V.5 Challenge Evaluation},
  year = 2017,
  url = {http://www.biocreative.org/media/store/files/2017/BioCreative_V5_paper12.pdf},
}
@inproceedings{mrodrigues-semeval2017,
  author = {M. Rodrigues and F. Couto},
  title = {{MoRS} At {SemEval-2017} Task 3: Easy To Use {SVM} In Ranking Tasks},
  booktitle = {10th International Workshop on Semantic Evaluation (SemEval)},
  year = 2017,
  url = {https://www.aclweb.org/anthology/S17-2046.pdf},
}
@inproceedings{alamurias-semeval2017,
  author = {A. Lamurias and D. Sousa and S. Pereira and L. Clarke and F. Couto},
  title = {{ULISBOA at SemEval-2017 Task 12}: Extraction and classification of
temporal expressions and events},
  booktitle = {10th International Workshop on Semantic Evaluation (SemEval)},
  year = 2017,
  url = {https://www.aclweb.org/anthology/S17-2179.pdf},
}
@inproceedings{dfaria-om2016,
  author = {D. Faria and C. Pesquita and B. Balasubramani and C. Martins and J. Cardoso and H. Curado and F. Couto and I. Cruz},
  title = {{OAEI} 2016 Results of {AML}},
  booktitle = {The Eleventh International Workshop on Ontology Matching (OM-2016)},
  year = 2016,
  url = {http://ceur-ws.org/Vol-1766/oaei16_paper2.pdf},
}
@inproceedings{diogo-studyrecsystv2016,
  author = {D. Goncalves and M. Costa and F. Couto},
  title = {A Large-Scale Characterization of User Behaviour in Cable {TV}},
  booktitle = {3rd Workshop on Recommendation Systems for Television and online Video (RecSysTV)},
  year = 2016,
}
@inproceedings{diogo-systemrecsystv2016,
  author = {D. Goncalves and M. Costa and F. Couto},
  title = {A Flexible Recommendation System for Cable {TV}},
  booktitle = {3rd Workshop on Recommendation Systems for Television and online Video (RecSysTV)},
  year = 2016,
}
@inproceedings{marcia-inforum2016,
  author = {M. Barros and F. Couto and H. Savietto and C. Barata and M. Domingos and A. Krone-Martins and A. Moitinho},
  title = {A pipeline for producing a scientifically accurate visualisation of the {Milky Way}},
  booktitle = {INForum - Simp{ó}sio de Inform{á}tica},
  year = 2016,
}
@inproceedings{lamurias-bionlp2016,
  title = {Extraction of Regulatory Events using Kernel-based Classifiers and Distant Supervision},
  author = {A. Lamurias and M. Rodrigues and L. Clarke and F. Couto},
  booktitle = {ACL proceedings of the 4th BioNLP Shared Task Workshop},
  year = 2016,
  url = {https://aclweb.org/anthology/W/W16/W16-3011.pdf},
}
@inproceedings{marcia-semeval2016,
  author = {M. Barros and A. Lamurias and G. Figueiro and M. Antunes and J. Teixeira and A. Pinheiro and F. Couto},
  title = {{ULISBOA} at {SemEval-2016} Task 12: Extraction of temporal expressions, clinical events and relations using {IBEnt}},
  booktitle = {9th International Workshop on Semantic Evaluation (SemEval)},
  year = 2016,
  url = {http://www.aclweb.org/anthology/S/S16/S16-1196.pdf},
}
@inproceedings{dfaria-om2015,
  author = {D. Faria and C. Martins and A. Nanavaty and D. Oliveira and B. Sowkarthiga and A. Taheri and C. Pesquita and F. Couto and I. Cruz},
  title = {{AgreementMakerLight} results for {OAEI} 2015},
  booktitle = {The Tenth International Workshop on Ontology Matching (OM-2015)},
  year = 2014,
  url = {http://ceur-ws.org/Vol-1545/oaei15_paper1.pdf},
}
@inproceedings{cogo-wpes2015,
  author = {V. Cogo and A. Bessani and F. Couto and P. Verissimo},
  title = {A High-Throughput Method to Detect Privacy-Sensitive Human Genomic Data},
  booktitle = {Workshop on Privacy in the Electronic Society (WPES)},
  year = 2015,
  url = {http://dl.acm.org/citation.cfm?doid=2808138.2808139},
}
@inproceedings{alamurias-biocreative2015,
  author = {A. Lamurias and M. Lobo and M. Antunes and L. Clarke and F. Couto},
  title = {Identifying chemical entities in patents using brown clustering and semantic similarity},
  booktitle = {5th BioCreative Challenge Evaluation},
  year = 2015,
  url = {http://www.biocreative.org/media/store/files/2015/BCV2015_paper_58.pdf},
}
@inproceedings{aleal-semeval2015,
  author = {A. Leal and B. Martins and F. Couto},
  title = {{ULisboa}: Recognition and Normalization of Medical Concepts},
  booktitle = {8th International Workshop on Semantic Evaluation (SemEval)},
  year = 2015,
  url = {http://alt.qcri.org/semeval2015/cdrom/pdf/SemEval070.pdf},
}
@inproceedings{dfaria-om2014,
  author = {D. Faria and C. Martins and A. Nanavaty and A. Taheriand and C. Pesquita and E. Santos and I. Cruz and F. Couto},
  title = {{AgreementMakerLight} results for {OAEI} 2014},
  booktitle = {The Ninth International Workshop on Ontology Matching (OM-2014)},
  year = 2014,
  url = {http://ceur-ws.org/Vol-1317/oaei14_paper1.pdf},
}
@inproceedings{fcouto-method2014,
  author = {F. Couto},
  title = {Rating, recognizing and rewarding metadata integration and sharing on the semantic web},
  booktitle = {3rd International Workshop on Methods for Establishing Trust of (Open) Data (METHOD)},
  year = 2014,
  url = {http://dl.acm.org/citation.cfm?id=2878922},
}
@inproceedings{tmendes-inforum2014,
  author = {T. Mendes and B. Rodrigues and A. Moitinho and M. Gomes and F. Couto and T. Guerreiro and A. Krone-Martins},
  title = {Exploração Visual Online de Bases de Dados Astronómicas},
  booktitle = {INForum - Simp{ó}sio de Inform{á}tica},
  year = 2014,
}
@inproceedings{aleal-semeval2014,
  author = {A. Leal and D. Gonçalves and B. Martins and F. Couto},
  title = {{ULisboa}: Identification and Classification of Medical Concepts},
  booktitle = {7th International Workshop on Semantic Evaluation (SemEval)},
  year = 2014,
  url = {http://alt.qcri.org/semeval2014/cdrom/pdf/SemEval127.pdf},
}
@inproceedings{cpesquita-om2013,
  author = {C. Pesquita and D. Faria and E. Santos and F. Couto},
  title = {To repair or not to repair: reconciling correctness and coherence in ontology reference alignments},
  booktitle = {The Eighth International Workshop on Ontology Matching (OM-2013)},
  year = 2013,
  url = {http://ceur-ws.org/Vol-1111/om2013_Tpaper2.pdf},
}
@inproceedings{dfaria-om2013,
  author = {D. Faria and C. Pesquita and E. Santos and I. Cruz and F. Couto},
  title = {{AgreementMakerLight} results for {OAEI} 2013},
  booktitle = {The Eighth International Workshop on Ontology Matching (OM-2013)},
  year = 2013,
  url = {http://ceur-ws.org/Vol-1111/oaei13_paper1.pdf},
}
@inproceedings{alamurias-biocreative2013,
  author = {A. Lamurias and T. Grego and F. Couto},
  title = {Chemical compound and drug name recognition using {CRFs} and semantic similarity based on {ChEBI}},
  booktitle = {4th BioCreative Challenge Evaluation},
  year = 2013,
  url = {http://www.biocreative.org/media/store/files/2013/ProceedingsBioCreativeIV_vol2.pdf},
}
@inproceedings{mcosta-tempweb2013,
  author = {M. Costa and D. Gomes and F. Couto and M. Silva},
  title = {A survey of web archive search architectures},
  booktitle = {3rd Temporal Web Analytics Workshop (TempWeb)},
  year = 2013,
  url = {http://sobre.arquivo.pt/sobre-o-arquivo/a-survey-of-web-archive-search-architectures},
}
@inproceedings{tgrego-semeval2013,
  author = {T. Grego and F. Pinto and F. Couto},
  title = {{LASIGE}: using Conditional Random Fields and {ChEBI} ontology},
  booktitle = {7th International Workshop on Semantic Evaluation (SemEval)},
  year = 2013,
  url = {https://aclanthology.org/S13-2109.pdf},
}
@inproceedings{filgueiras-semeval2013,
  author = {S. Moreira and J. Filgueiras and B. Martins and F. Couto and M. Silva},
  title = {{REACTION}: A naive machine learning approach for sentiment classification},
  booktitle = {7th International Workshop on Semantic Evaluation (SemEval)},
  year = 2013,
  url = {https://aclanthology.org/S13-2081.pdf},
}
@inproceedings{cmachado-obml2012,
  author = {C. Machado and A. Freitas and F. Couto},
  title = {Enrichment analysis applied to disease prognosis},
  booktitle = {Ontologies in Biomedicine and Life Sciences (OBML)},
  year = 2012,
  url = {https://web.archive.org/web/20150421125319/http://www.onto-med.de/obml/ws2012/obml2012report.pdf},
}
@inproceedings{tgrego-icbo2012,
  author = {T. Grego and F. Pinto and F. Couto},
  title = {Identifying Chemical Entities based on {ChEBI}},
  booktitle = {Software Demonstration at the International Conference on Biomedical Ontologies (ICBO)},
  year = 2012,
  url = {http://ceur-ws.org/Vol-897/demo_8.pdf},
}
@inproceedings{fcouto-icbo2012,
  author = {F. Couto and J. Ferreira and J. Zamite and C. Santos and T. Posse and P. Gra{\c{c}}a and D. Domingos and M. Silva},
  title = {The Epidemic Marketplace Platform: towards semantic characterization of epidemiological resources using biomedical ontologies},
  booktitle = {Software Demonstration at the International Conference on Biomedical Ontologies (ICBO)},
  year = 2012,
  url = {http://ceur-ws.org/Vol-897/demo_1.pdf},
}
@inproceedings{cosmin-oaei2011,
  author = {I. Cruz and C. Stroe and F. Caimi and A. Fabiani and C. Pesquita and F. Couto and M. Palmonari},
  title = {Using {AgreementMaker} to Align Ontologies for {OAEI} 2011},
  booktitle = {The Sixth International Workshop on Ontology Matching (OM-2011)},
  year = 2011,
  url = {http://ceur-ws.org/Vol-814/oaei11_paper1.pdf},
}
@inproceedings{sara-inforum2011,
  author = {S. Domingos and C. Pesquita and F. Couto and L. Goulao and C. Oliveira and F. Couto},
  title = {Improving Gene Functional Analysis in Ethylene-induced Leaf Abscission using {GO} and {ProteInOn}},
  booktitle = {INForum - Simp{ó}sio de Inform{á}tica},
  year = 2011,
}
@inproceedings{btavares-icbo2011,
  author = {B. Tavares and H. Bastos and D. Faria and J. Ferreira and T. Grego and C. Pesquita and F. Couto},
  title = {The Biomedical Ontology Applications {(BOA)} framework},
  booktitle = {Software Demonstration at the International Conference on Biomedical Ontologies (ICBO)},
  year = 2011,
  url = {http://ceur-ws.org/Vol-833/paper56.pdf},
}
@inproceedings{cruz-icbo2011,
  author = {I. Cruz and C. Stroe and C. Pesquita and F. Couto and V. Cross},
  title = {Biomedical Ontology Matching Using the {AgreementMaker} System},
  booktitle = {Software Demonstration at the International Conference on Biomedical Ontologies (ICBO)},
  year = 2011,
  url = {http://ceur-ws.org/Vol-833/paper51.pdf},
}
@inproceedings{silvio-ontose2011,
  author = {S. Moreira and D. Batista and P. Carvalho and F. Couto and M. Silva},
  title = {{POWER}: Politics Ontology for Web Entity Retrieval},
  booktitle = {5th International Workshop on Ontology, Models, Conceptualization and Epistemology in Social, Artificial and Natural Systems (ONTOSE)},
  year = 2011,
}
@inproceedings{cmachado-keddh2010,
  author = {C. Machado and F. Couto and A. Fernandes and S. Santos and N. Cardim and A. Freitas},
  title = {Semantic Characterization of Hypertrophic Cardiomyopathy Disease},
  booktitle = {First Workshop on Knowledge Engineering, Discovery and Dissemination in Health (KEDDH)},
  year = 2010,
}
@inproceedings{cpesquita-iswc2010,
  author = {C. Pesquita and C. Stroe and I. Cruz and F. Couto},
  title = {{BLOOMS} on {AgreementMaker}: results for {OAEI} 2010},
  booktitle = {ISWC Workshop on Ontology Matching},
  year = 2010,
}
@inproceedings{dbatista-gir2010,
  author = {D. Batista and M. Silva and F. Couto and B. Behera},
  title = {Geographic Signatures for Semantic Retrieval},
  booktitle = {6th Workshop on Geographic Information Retrieval (GIR)},
  year = 2010,
}
@inproceedings{dfaria-ismb2009,
  author = {D. Faria and C. Pesquita and F. Couto and A. Falcão},
  title = {{GOclasses}: molecular function as viewed by proteins},
  booktitle = {The 12th Annual Bio-Ontologies Meeting at ISMB/ECCB},
  year = 2009,
}
@inproceedings{pesquita-ismb2009:,
  author = {C. Pesquita and F. Couto},
  title = {Taking {GO} where we need it to go: focused automated enrichment of the Gene Ontology},
  booktitle = {Student Council Symposium at ISMB/ECCB},
  year = 2009,
}
@inproceedings{cpesquita-jb2009,
  author = {C. Pesquita and D. Pessoa and D. Faria and F. Couto},
  title = {{CESSM}: Collaborative Evaluation of Semantic Similarity Measures},
  booktitle = {Jornadas em Bioinformatica},
  year = 2009,
}
@inproceedings{hbastos-jb2009,
  author = {H. Bastos and T. Grego and F. Couto and P. Coutinho},
  title = {Enzyme family coherence assessment: validation and prediction},
  booktitle = {Jornadas em Bioinformatica},
  year = 2009,
}
@inproceedings{ateixeira-inforum2009,
  author = {A. Teixeira and R. Santos and F. Couto},
  title = {{ThermInfo}: Collecting and Presenting Thermochemical Properties},
  booktitle = {INForum - Simp{ó}sio de Inform{á}tica},
  year = 2009,
}
@inproceedings{lopes-inforum2009,
  author = {L. Filipe Lopes and J. Zamite and B. Tavares and F. Couto and F. Silva and M. Silva},
  title = {Automated Social Network Epidemic Data Collector},
  booktitle = {INForum - Simp{ó}sio de Inform{á}tica},
  year = 2009,
}
@inproceedings{cpesquita-iwpacbb2009,
  author = {C. Pesquita and T. Grego and F. Couto},
  title = {Identifying Gene Ontology Areas for Automated Enrichment},
  booktitle = {Workshop on Practical Applications of Computational Biology and Bioinformatics ({IWPACBB})},
  publisher = {Lecture Notes in Computer Science},
  volume = 5518,
  year = 2009,
}
@inproceedings{tgrego-iwpacbb2009,
  author = {T. Grego and P. Pezik and F. Couto and D. Rebholz-Schuhmann},
  title = {Identification of Chemical Entities in Patent Documents},
  booktitle = {Workshop on Practical Applications of Computational Biology and Bioinformatics ({IWPACBB})},
  publisher = {Lecture Notes in Computer Science},
  volume = 5518,
  year = 2009,
}
@inproceedings{cmachado-iwpacbb2009,
  author = {C. Machado and H. Bastos and F. Couto},
  title = {{GREAT}: Gene Regulation EvAluation Tool},
  booktitle = {Workshop on Practical Applications of Computational Biology and Bioinformatics ({IWPACBB})},
  publisher = {Lecture Notes in Computer Science},
  volume = 5518,
  year = 2009,
}
@inproceedings{cpesquita-ismb2007,
  title = {Evaluating {GO}-based Semantic Similarity Measures},
  year = {2007},
  author = {C. Pesquita and D. Faria and H. Bastos and A. Falcão and F. Couto},
  booktitle = {BioOntologies SIG co-located with 
               Internacional Conference on Intelligent 
               Systems for Molecular Biology (ISMB)},
}
@inproceedings{fcouto-ismb2007,
  title = {Filtering Bioentity Recognition Errors in Bioliterature using a Case-based Approach},
  year = 2007,
  author = {F. Couto and T. Grego and R. Torres and P. Sanchez and L. Pascual and C. Blaschke},
  booktitle = {BioLINK SIG co-located with co-located with 
               Internacional Conference on Intelligent 
               Systems for Molecular Biology (ISMB)},
}
@inproceedings{pooja-bkdb2005,
  author = {P. Jain and F. Couto and M. Silva and J. Becker},
  title = {Literature Based Functional Annotation of Genes},
  booktitle = {Bioinformatics: Knowledge Discovery in Biology Workshop (BKDB)},
  year = 2005,
  annote = {June, Lisbon, Portugal},
}
@inproceedings{fcouto-biocreative2004,
  author = {F. Couto and M. Silva and P. Coutinho},
  title = {{FiGO}: Finding {GO} terms in unstructured text},
  booktitle = {{BioCreAtIvE} Challenge Evaluation Workshop},
  year = 2004,
  annote = {March, Granada, Spain},
}
@inproceedings{fcouto-pkdd2003,
  author = {F. Couto and M. Silva and P. Coutinho},
  title = {Improving Information Extraction 
           through Biological Correlation},
  booktitle = { Data Mining and Text Mining for Bioinformatics 
               Workshop co-located with 7th European Conference 
               on Principles and Practice of Knowledge Discovery 
               in Databases (PKDD)},
  year = 2003,
  annote = {September, Dubrovnik-Cavtat, Croatia},
}
@inproceedings{fcouto-ismb2003,
  author = {F. Couto and M. Silva and P. Coutinho},
  title = {Curating Extracted Information 
           through the Correlation between
           Structure and Function},
  booktitle = {Text Data Mining SIG co-located with 
               Internacional Conference on Intelligent 
               Systems for Molecular Biology (ISMB)},
  year = 2003,
  annote = {June, Brisbane, Australia},
}
@inproceedings{fcouto-fme2001,
  author = {F. Couto},
  title = {The Development of a Computer Application that
                  Identifies Reusable Components through Formal
                  Specifications},
  year = 2001,
  annote = {Humboldt-Universit{\"a}t zu Berlin, Germany, March},
  booktitle = { 1st International Workshop on Automated
                  Verification of Infinite-State Systems (AVIS'01)
                  co-located with the 10th European Conference 
                  organised by Formal Methods Europe (FME)},
}
@proceedings{fcouto-proceedingssiirh2020,
  title = {First International Workshop on Semantic Indexing and Information Retrieval for Health from heterogeneous content types and languages ({SIIRH})},
  year = {2020},
  editor = {F. Couto and M. Krallinger},
  volume = {2619},
  publisher = {CEUR Workshop Proceedings (CEUR-WS.org)},
  url = {http://ceur-ws.org/Vol-2619/},
}
@proceedings{fcouto-icbo2015,
  title = {The Sixth International Conference on Biomedical Ontologies ({ICBO})},
  year = {2015},
  editor = {F. Couto and J. Hastings},
  volume = {1515},
  publisher = {CEUR Workshop Proceedings (CEUR-WS.org)},
  url = {http://ceur-ws.org/Vol-1515/},
}
@article{asif-boletimepidemiologico2018,
  author = {M. Asif and H. Martiniano and F. Couto and A. Vicente},
  title = {Associação entre variantes genéticas e perfil clínico multidimensional de doentes com perturbação do espetro do autismo: uma abordagem integrativa},
  journal = {Observações Boletim Epidemiológico},
  year = 2018,
  url = {http://www.insa.min-saude.pt/category/informacao-e-cultura-cientifica/publicacoes/boletim-epidemiologico-observacoes-numero-22/},
}
@article{fcouto-atomiumculture2011,
  author = {F. Couto},
  title = {Exploiting Biomedical Information through Literature and Ontologies},
  journal = {El País - Sociedad},
  year = 2011,
  url = {http://sociedad.elpais.com/sociedad/2011/11/07/actualidad/1320620406_850215.html},
}
@article{cmachado-ercim2010,
  author = {C. Machado and F. Couto and A. Fernandes and S. Santos and N. Cardim and A. Freitas},
  title = {Unraveling Hypertrophic Cardiomyopathy Variability},
  journal = {ERCIM News 82 - Special Theme: Computational Biology},
  year = 2010,
  url = {http://ercim-news.ercim.eu/en82/special/unraveling-hypertrophic-cardiomyopathy-variability},
}
@article{fabricio-ercim2010,
  author = {F. Silva and M. Silva and F. Couto},
  title = {Epidemic Marketplace: an e-Science Platform for Epidemic Modelling and Analysis},
  journal = {ERCIM News 82 - Special Theme: Computational Biology},
  year = {2010},
  url = {http://ercim-news.ercim.eu/en82/special/epidemic-marketplace-an-e-science-platform-for-epidemic-modelling-and-analysis},
}
@article{fcouto-centroatl2003,
  author = {F. Couto and M. Silva},
  title = {Bioinform{á}tica - Exploração da Informação},
  journal = {centroatlantico.pt magazine},
  year = 2003,
  volume = 3,
  annote = {October},
}
@inproceedings{fcouto-increase2023,
  author = {F. Couto},
  title = {Data and Text Processing for Sustainability},
  booktitle = {2nd edition of the INternational CongRess on Engineering and Sustainability in the XXI cEntury (INCREaSE)},
  year = 2023,
}
@inproceedings{fcouto-frm2023,
  author = {F. Couto},
  title = {Data and Text Processing for Development and Stem Cells},
  booktitle = {FENS Regional Meeting (FRM)},
  year = 2023,
}
@inproceedings{fcouto-proteo2022,
  author = {F. Couto},
  title = {{DeST}: Deep Semantic Tagger},
  booktitle = {2nd Joint Meeting of Spanish, French and Portuguese Proteomics Societies (ProteoVilamoura 2022)},
  year = 2022,
}
@inproceedings{asif-eshg2022,
  author = {M. Asif and H. Martiniano and F. Couto},
  title = {{DGH-GO} Dissecting the Genetic Heterogeneity of complex diseases using {Gene Ontology}, an interactive and user-friendly web application},
  booktitle = {55th European Society of Human Genetics Conference (ESHG)},
  year = 2022,
}
@inproceedings{mbarros-ida2021,
  author = {M. Barros and A. Moitinho and F. Couto},
  title = {Recommender Systems for Scientific Fields},
  booktitle = {19th International Symposium on Intelligent Data Analysis (IDA)},
  year = 2021,
}
@inproceedings{ilheu-eshg2019,
  author = {A. Ilhéu and M. Asif and F. Couto},
  title = {Establishing genotype-phenotype associations for {ASD}},
  booktitle = {52nd European Society of Human Genetics Conference (ESHG)},
  year = 2019,
}
@inproceedings{asif-eshg2018,
  author = {M. Asif and H. Martiniano and C. Rasga and A. Marques and J. Santo and G. Oliveira and F. Couto and A. Vicente},
  title = {An integrative approach to correlate clinical presentation patterns in Autism Spectrum Disorder with biological processes disrupted by {Copy Number Variants (CNV)} in brain genes},
  booktitle = {51st European Society of Human Genetics Conference (ESHG)},
  year = 2018,
}
@inproceedings{rdias-encontrociencia2018,
  author = {R. Dias and C. Pesquita and J. Rebelo and A. Pedrosa and C. Santos and J. Adonis and V. Mendes and F. Couto and R. Tenreiro and P. Sousa},
  title = {{RESISTIR} - Intelligent Decision Support Systems for personalized prevention and clinical management of infectious diseases},
  booktitle = {Ciência 2018 - Encontro com a Ciência e Tecnologia em Portugal},
  year = 2018,
}
@inproceedings{asif-embl2017,
  author = {M. Asif and H. Martiniano and C. Rasga and A. Marques and J. Santos and F. Couto and A. Vicente},
  title = {An integrative system biology approach to delineate complex genotype phenotype associations in {Autism Spectrum Disorder}},
  booktitle = {EMBO EMBL Symposia - From Single to Multiomics: Applications and Challenges in Data Integration},
  year = 2017,
}
@inproceedings{asif-insar2017,
  author = {M. Asif and H. Martiniano and C. Rasga and A. Marques and J. Santos and G. Oliveira and F. Couto and A. Vicente},
  title = {Translating the complex {ASD} genetic architecture into clinical phenotype using an integrative system biology approach},
  booktitle = {Annual meeting of the International Society for Autism Research (INSAR 2017)},
  year = 2017,
}
@inproceedings{asif-insa2017,
  author = {M. Asif and C. Rasga and H. Martiniano and J. Santos and A. Marques and F. Couto and A. Vicente},
  title = {An integrative system biology approach for dissecting Autism Spectrum Disorder},
  booktitle = {2º Dia do Jovem Investigador do Instituto Nacional de Saúde Doutor Ricardo Jorge},
  year = 2017,
}
@inproceedings{lcampos-bod2017,
  title = {Semantic annotation of electronic health records in a
multilingual environment},
  author = {L. Campos and V. Pedro and F. Couto},
  booktitle = {Bioinformatics Open Days, University of Minho},
  year = 2017,
}
@inproceedings{alamurias-bod2017,
  title = {Development of a Text Mining Framework for Systems
Biology},
  author = {A. Lamurias and L. Clarke and F. Couto},
  booktitle = {Bioinformatics Open Days, University of Minho},
  year = 2017,
}
@inproceedings{gfigueiro-bod2017,
  title = {{3D} Identification of clusters: a cancer cell case-study},
  author = {G. Figueiró and F. Couto and A. Moitinho},
  booktitle = {Bioinformatics Open Days, University of Minho},
  year = 2017,
}
@inproceedings{rodrigues-bioasq2016,
  author = {M. Rodriques and M. Fale and F. Couto},
  title = {{WS4A}: a Biomedical Question and Answering System based on public
web services and ontologies},
  booktitle = {ACL proceedings of the 4th BioASQ Workshop},
  year = 2016,
  url = {https://www.aclweb.org/anthology/W/W16/W16-3108.pdf},
}
@inproceedings{asif-eshg2016,
  author = {M. Asif and I. Conceição and K. Kwiatkowska and C. Rasga and C. Café and L. Sousa and G. Oliveira and F. Couto and A. Vicente},
  title = {Increased frequency of the autism broader phenotype in mothers transmitting etiological {CNVs} to sons affected by {Autism Spectrum Disorder (ASD)}},
  booktitle = {49th European Human Genetics Conference (ESHG)},
  year = 2016,
}
@inproceedings{asif-icgh2016,
  author = {M. Asif and I. Conceição and K. Kwiatkowska and C. Rasga and F. Couto and A. Vicente},
  title = {Maternal Copy Number Variants {(CNV)} transmission to their {Autism Spectrum Disorder (ASD)} sons correlates with phenotypic traits},
  booktitle = {The 13th International Congress of Human Genetics (ICHG)},
  year = 2016,
}
@inproceedings{hcurado-bod2016,
  title = {A proposal for Allele Validation Tool {(AVT)} for whole genome Multilocus Sequence Typing {(wgMLST)} schemas},
  author = {H. Curado and M. Cândido and M. Silva and J. Carriço and F. Couto},
  booktitle = {Bioinformatics Open Days,  University of Minho},
  year = 2016,
}
@inproceedings{mlobo-bod2016,
  title = {Identifying human phenotype terms in text using a machine learning approach},
  author = {M. Lobo and A. Lamurias and F. Couto},
  booktitle = {Bioinformatics Open Days,  University of Minho},
  year = 2016,
}
@inproceedings{rflorencio-bod2016,
  title = {Radiation Monitoring System in Clinical Imaging},
  author = {R. Florencio and F. Couto and N. Matela and J. Afonso},
  booktitle = {Bioinformatics Open Days,  University of Minho},
  year = 2016,
}
@inproceedings{pmartins-bod2016,
  title = {Exploring Machine Learning Algorithms to predict subcellular localizations},
  author = {P. Martins and L. Clarke and M. Amaral and F. Couto},
  booktitle = {Bioinformatics Open Days,  University of Minho},
  year = 2016,
}
@inproceedings{mbarros-bod2016,
  title = {Extraction of temporal expressions and clinical events from clinical notes},
  author = {M. Barros and A. Lamúrias and M. Antunes and J. Teixeira and G. Figueiró and A. Pinheiro and F. Couto},
  booktitle = {Bioinformatics Open Days,  University of Minho},
  year = 2016,
}
@inproceedings{abarata-bod2016,
  title = {Anthropometric Data Analytics: Portuguese case-study},
  author = {A. Barata and F. Couto and L. Carvalho},
  booktitle = {Bioinformatics Open Days, University of Minho},
  year = 2016,
}
@inproceedings{fcouto-edf2015,
  title = {{METARATE} - incentivize data integration and sharing by rating and rewarding metadata annotation},
  author = {F. Couto},
  booktitle = {European Data Forum (EDF)},
  year = 2015,
}
@inproceedings{aleal-bod2015,
  title = {Recognition and Normalization of Biomedical Entities Based on Ontologies},
  author = {A. Leal and B. Martins and F. Couto},
  booktitle = {Bioinformatics Open Days, University of Lisbon},
  year = 2015,
}
@inproceedings{asif-spgh2014,
  author = {M. Asif and I. Conceição and C. Café and J. Almeida and S. Mouga and G. Oliveira and F. Couto and A. Vicente},
  title = {Use of machine learning approaches to explore genetic and phenotypic associations for {Autism Spectrum Disorder}},
  booktitle = {18th Meeting of The Portuguese Society of Human Genetics (SPGH)},
  year = 2014,
}
@inproceedings{jferreira-vph2014,
  author = {J. Ferreira and B. Bono and F. Couto},
  title = {From data to knowledge: a tool for clustering multi-scale resources for physiology research},
  booktitle = {Virtual Physiological Human (VPH)},
  year = 2014,
}
@inproceedings{cpesquita-om2014,
  author = {C. Pesquita and M. Cheatham and D. Faria and J. Barros and E. Santos and F. Couto},
  title = {Building reference alignments for compound matching of multiple ontologies using {OBO} cross-products},
  booktitle = {The Ninth International Workshop on Ontology Matching (OM-2014)},
  year = 2014,
  url = {http://ceur-ws.org/Vol-1317/om2014_poster2.pdf},
}
@inproceedings{dfaria-dils2014,
  title = {{AgreementMakerLight}: A Scalable Automated Ontology Matching System},
  author = {D. Faria and C. Pesquita and E. Santos and I. Cruz and F. Couto},
  booktitle = {The 10th International Conference on Data Integration in the Life Sciences (DILS)},
  year = 2014,
  url = {http://dbs.uni-leipzig.de/file/dils14-posters.pdf},
}
@inproceedings{natacha-inforum2014,
  title = {Expansão do Espaço de Procura em Mapeamento Genómico de Alto Rendimento},
  author = {N. Leitão and J. Leitão and F. Couto},
  booktitle = {INForum - Simp{ó}sio de Inform{á}tica},
  year = 2014,
}
@inproceedings{dfaria-iswcposter2014,
  title = {{AgreementMakerLight 2.0}: Towards Efficient Large-Scale Ontology Matching},
  author = {D. Faria and C. Pesquita and E. Santos and I. Cruz and F. Couto},
  booktitle = {International Semantic Web Conference (ISWC)},
  year = 2014,
}
@inproceedings{moitinho-iaus2014,
  title = {{VEJA} - Visual Exploration Just Anywhere},
  author = {A. Moitinho and T. Mendes and B. Rodrigues and M. Gomes and A. Krone-Martins and F. Couto},
  booktitle = {International Astronomical Union Symposium (IAUS)},
  year = 2014,
}
@inproceedings{lsilva-bod2014,
  title = {Development of a semantic model for Cerebrovascular Accident ({CVA}) Patients},
  author = {L. Silva and F. Couto and H. Manso and A. Vicente},
  booktitle = {Bioinformatics Open Days, University of Minho},
  year = 2014,
}
@inproceedings{carilho-bod2014,
  title = {Predicting Relevant Events in the Life of a Person with Alzheimer},
  author = {J. Carilho and O. Schnell and J. Martins and L. Carriço and C. Duarte and F. Couto and T. Guerreiro},
  booktitle = {Bioinformatics Open Days,  University of Minho},
  year = 2014,
}
@inproceedings{nleitao-bod2014,
  title = {{LLC-GNUMAP}: Scalable, Precise, and High-Coverage Genomics Mapping},
  author = {N. Leitão and J. Leitão and F. Couto},
  booktitle = {Bioinformatics Open Days,  University of Minho},
  year = 2014,
}
@inproceedings{alamurias-bod2014,
  title = {Identifying Interactions Between Chemical Entities in Text},
  author = {A. Lamurias and F. Couto},
  booktitle = {Bioinformatics Open Days,  University of Minho},
  year = 2014,
}
@inproceedings{cmachado-nips2013,
  author = {C. Machado and F. Couto and A. Freitas},
  title = {Exploring ontological knowledge for translational medicine},
  booktitle = {Workshop on Machine Learning for Clinical Data Analysis and Healthcare (NIPS)},
  year = 2013,
}
@inproceedings{jferreira-ipres2013,
  author = {J. Ferreira and C. Pesquita and F. Couto and M. Silva},
  title = {Digital preservation of epidemic resources: coupling metadata and ontologies},
  booktitle = {10th International Conference on Preservation of Digital Objects},
  year = 2013,
}
@inproceedings{cpesquita-epiwork2013,
  author = {C. Pesquita and J. Ferreira and F. Couto and M. Silva},
  title = {Semi-automated Annotation of Epidemiological Resources},
  booktitle = {Epiwork International Workshop on Digital Epidemiology, Turin},
  year = 2013,
}
@inproceedings{mickael-embl2013,
  author = {M. Silva and C. Vaz and A. Francisco and M. Ramirez and F. Couto and J. Carriço},
  title = {{NGSOnto} - keeping track of the NGS pipeline process using an ontological approach and its application on molecular epidemiology},
  booktitle = {Molecular Biology in Portugal and EMBL (and EMBL Alumni), FCUL},
  year = 2013,
}
@inproceedings{jferreira-embl2013,
  author = {J. Ferreira and F. Couto},
  title = {Semantic Similarity in the Biomedical Domain},
  booktitle = {Molecular Biology in Portugal and EMBL (and EMBL Alumni), FCUL},
  year = 2013,
}
@inproceedings{calonso-embl2013,
  author = {C. Alonso and F. Couto and R. Dias},
  title = {Comparative Genomics of Bacillus spp.: can core genome be the key for new therapeutics? Assessment of the core genome of Bacillus spp. and its stability},
  booktitle = {Molecular Biology in Portugal and EMBL (and EMBL Alumni), FCUL},
  year = 2013,
}
@inproceedings{tgrego-bragaworkshop2012,
  author = {T. Grego and F. Couto},
  title = {Recognition and resolution of chemical entities to {ChEBI}},
  booktitle = {Bioinformatics Open Days, University of Minho},
  year = 2012,
}
@inproceedings{jferreira-bragaworkshop2012,
  author = {J. Ferreira and F. Couto},
  title = {Semantic Similarity in the Biomedical Domain},
  booktitle = {Bioinformatics Open Days, University of Minho},
  year = 2012,
}
@inproceedings{hbastos-cmb2011,
  author = {H. Bastos and F. Couto and P. Coutinho},
  title = {Exploring Gene Ontology relationships in Enzyme Families: An application to Polysaccharide Lyases},
  booktitle = {9th Carbohydrate Bioengineering Meeting (CBM9)},
  year = 2011,
}
@inproceedings{cpesquita-vph2010,
  author = {C. Pesquita and J. Ferreira and F. Couto},
  title = {{FLORAL}: Semantic and Lexical Matching of Biomedical Ontologies},
  booktitle = {1st Virtual Physiological Human Conference (VPH)},
  year = 2010,
}
@inproceedings{cpesquita-ismb2009,
  author = {C. Pesquita and D. Pessoa and D. Faria and F. Couto},
  title = {Collaborative Evaluation of {GO-based} Similarity Measures},
  booktitle = {The 12th Annual Bio-Ontologies Meeting at ISMB/ECCB},
  year = 2009,
}
@inproceedings{cpesquita-sac2009,
  author = {C. Pesquita and D. Faria and R. Lopes and F. Couto},
  title = {Measuring coherence between electronic and manual annotations in biological databases},
  booktitle = {SAC '09: Proceedings of the 2009 ACM Symposium on Applied Computing},
  year = 2009,
}
@inproceedings{palves-hupo2008,
  author = {P. Gomes-Alves and A.V. Coelho and F. Couto and P. Nogueira and D. Penque},
  title = {Proteins potentially involved in {F508del-CFTR} trafficking restoration process},
  booktitle = {HUPO 7th Annual World Congress},
  year = 2008,
  annote = {Amsterdam},
}
@inproceedings{cpesquita-fpbc2008,
  author = {C. Pesquita and F. Couto and M. Silva},
  title = {Automated Enrichment of {BioOntologies}},
  booktitle = {First Portuguese Forum on Computational Biology},
  year = 2008,
  annote = {IGC, Portugal},
}
@inproceedings{hbastos-fpbc2008,
  author = {H. Bastos and C. Machado and A. Freitas and F. Couto},
  title = {Retrieving Relevant Documents from {BioLiterature} for the Curation of Yeast Gene Regulatory Networks},
  booktitle = {First Portuguese Forum on Computational Biology},
  year = 2008,
  annote = {IGC, Portugal},
}
@inproceedings{dfaria-ismb2007,
  author = {D. Faria and C. Pesquita and F. Couto and A. Falcão},
  title = {{ProteInOn}: Web Tool for Protein Semantic Similarity},
  booktitle = { 15th Internacional Conference 
               on Intelligent Systems for 
               Molecular Biology (ISMB) as a poster},
  year = 2007,
  annote = {June, Austria},
}
@inproceedings{fcouto-procura2004,
  author = {F. Couto},
  title = {{ReBIL}: Relating Biological Information through Literature},
  booktitle = { I Annual Meeting of Portuguese Proteomic Network - 
               ProCura: Functional Genomics And Proteomics},
  year = 2003,
  annote = {Inst. Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal},
}
@inproceedings{fcouto-abstractismb2003,
  author = {F. Couto and M. Silva and P. Coutinho},
  title = {{ReBIL}: Relating Biological Information through Literature},
  booktitle = { 11th Internacional Conference 
               on Intelligent Systems for 
               Molecular Biology (ISMB) as a poster},
  year = 2003,
  annote = {June, Brisbane, Australia},
}
@inproceedings{fcouto-ecdl2001,
  author = {F. Couto},
  title = {Category theory based Identification of reusable 
                  components through formal specifications},
  booktitle = { 5th European Conference on Research and Advanced 
	         Technology for Digital Libraries as a poster},
  annote = {September, Darmstadt, Germany},
  year = 2001,
}
@techreport{dsousa-arxiv2023,
  author = {P. Ruas and D. Sousa and A. Neves and C. Cruz and F. Couto},
  title = {{LASIGE} and {UNICAGE} at {NASA LitCoin NLP Competition}},
  institution = {arXiv.org},
  year = {2023},
  month = {Aug},
  number = {arXiv:2308.05609 [cs.CL]},
  url = {https://arxiv.org/abs/2308.05609},
}
@techreport{lcampos-arxiv2017,
  author = {L. Campos and F. Couto},
  title = {{MRA} - Proof of Concept of a Multilingual Report Annotator Web Application},
  institution = {arXiv.org},
  year = {2017},
  month = {April},
  number = {arXiv:1704.01748 [cs.DL]},
  url = {https://arxiv.org/abs/1704.01748},
}
@techreport{camila-arxiv2016,
  author = {C. Ramos and M. Louro and M. Santos and F. Couto},
  title = {Knowledge Ratings in {MetaboLights}},
  institution = {arXiv.org},
  year = {2016},
  month = {April},
  number = {arXiv:1604.07997 [cs.DL]},
  url = {https://arxiv.org/abs/1604.07997},
}
@techreport{richard-arxiv2014,
  author = {R. Norman and F. Couto},
  title = {Using {Google Scholar} to Predict Self-Citation: A Case Study in Health Economics},
  institution = {arXiv.org},
  year = {2014},
  month = {July},
  number = {arXiv:1406.5241 [stat.OT]},
  url = {https://arxiv.org/abs/1406.5241},
}
@techreport{fcouto-arxiv2013,
  author = {F. Couto},
  title = {{CIDS} country rankings: comparing documents and citations of {USA}, {UK} and {China} top researchers},
  institution = {arXiv.org},
  year = {2013},
  month = {July},
  number = {arXiv:1310.5597 [cs.DL]},
  url = {https://arxiv.org/abs/1310.5597},
}
@techreport{emanuel-arxiv2013,
  author = {E. Santos and D. Faria and C. Pesquita and F. Couto},
  title = {Ontology alignment repair through modularization and confidence-based heuristics},
  institution = {arXiv.org},
  year = {2013},
  month = {July},
  number = {arXiv:1307.5322 [cs.AI]},
  url = {https://arxiv.org/abs/1307.5322v1},
}
@techreport{fcouto-tr2013,
  author = {F. Couto and D. Faria and B. Tavares and P. Gonçalves and P. Verissimo},
  title = {Benchmarking some Portuguese {S\&T} system research units: 2nd Edition},
  institution = {Department of Informatics, University of Lisbon},
  year = {2013},
  month = {February},
  type = {DI/FCUL TR},
  number = {13-03},
  doi = {https://doi.org/10451/14123},
}
@techreport{dfaria-tr2012,
  author = {D. Faria and C. Pesquita and E. Santos and F. Couto and C. Stroe and I. Cruz},
  title = {Testing the {AgreementMaker} System in the Anatomy Task of {OAEI} 2012},
  institution = {arXiv.org},
  year = {2012},
  month = {December},
  number = {arXiv:1212.1625 [cs.IR]},
  url = {https://arxiv.org/abs/1212.1625},
}
@techreport{ferreira-tr2010,
  author = {J. Ferreira and D. Batista and F. Couto and M. Silva},
  title = {The {Geo-Net-PT/Yahoo! GeoPlanet (TM)} concordance},
  institution = {Department of Informatics, University of Lisbon},
  year = {2010},
  month = {September},
  type = {DI/FCUL TR},
  number = {10-05},
  doi = {https://doi.org/10451/14174},
}
@techreport{tgrego-tr2010,
  author = {T. Grego and J. Ferreira and C. Pesquita and H. Bastos and D. Viçosa and J. Freire and F. Couto},
  title = {Chemical and Metabolic Pathway Semantic Similarity},
  institution = {Department of Informatics, University of Lisbon},
  year = {2010},
  month = {March},
  type = {DI/FCUL TR},
  number = {10-01},
  doi = {https://doi.org/10451/14249},
}
@techreport{fcouto-tr2010,
  author = {F. Couto and I. Andrade and P. Gonçalves and P. Verissimo},
  title = {Benchmarking some Portuguese {S\&T} system research units},
  institution = {Department of Informatics, University of Lisbon},
  year = {2010},
  month = {March},
  type = {DI/FCUL TR},
  number = {10-07},
  doi = {https://doi.org/10451/14175},
}
@techreport{fmartins-tr2007,
  author = {F. Martins and A. Falcão and F. Couto},
  title = {Semantic Similarity Match for Data Quality},
  institution = {Department of Informatics, University of Lisbon},
  year = {2007},
  month = {October},
  type = {DI/FCUL TR},
  number = {07-25},
  doi = {https://doi.org/10451/14158},
}
@techreport{dfaria-tr2007,
  author = {D. Faria and C. Pesquita and F. Couto and A. Falcão},
  title = {{ProteInOn}: a Web Tool for Protein Semantic Similarity},
  institution = {Department of Informatics, University of Lisbon},
  month = {March},
  year = {2007},
  type = {DI/FCUL TR},
  number = {07-6},
  doi = {https://doi.org/10451/14140},
}
@techreport{fcouto-goannotatortr2005,
  author = {F. Couto and M. Silva and V. Lee and E. Dimmer and E. Camon and R. Apweiler
            and H. Kirsch and D. Rebholz-Schuhmann},
  title = {{GOAnnotator}: linking electronic protein {GO} annotation to evidence text},
  institution = {Department of Informatics, University of Lisbon},
  month = {December},
  year = {2005},
  type = {DI/FCUL TR},
  number = {05-25},
  doi = {https://doi.org/10451/14956},
}
@techreport{fcouto-cactr2005,
  author = {F. Couto and M. Silva and P. Coutinho},
  title = {Validation of Automated Protein Annotation},
  institution = {Department of Informatics, University of Lisbon},
  month = {December},
  year = {2005},
  type = {DI/FCUL TR},
  number = {05-24},
  doi = {https://doi.org/10451/14744},
}
@techreport{fcouto-ssmtr2005,
  author = {F. Couto and M. Silva and P. Coutinho},
  title = {Implementation of a Functional Semantic 
             Similarity Measure between Gene-Products},
  institution = {Department of Informatics, University of Lisbon},
  month = {November},
  year = {2003},
  type = {DI/FCUL TR},
  number = {03-29},
  doi = {https://doi.org/10451/14410},
}
@techreport{fcouto-webtctr2005,
  author = {F. Couto and B. Martins and M. Silva and P. Coutinho},
  title = {Classifying Biomedical Articles using Web Resources: application to {KDD Cup} 02},
  institution = {Department of Informatics, University of Lisbon},
  month = {July},
  year = {2003},
  type = {DI/FCUL TR},
  number = {03-24},
  doi = {https://doi.org/10451/14322},
}
@techreport{fcouto-tr2000,
  author = {F. Couto},
  title = {Representação Categorial de Especificações de Espécie Única},
  institution = {Instituto Superior Técnico da Universidade Técnica de Lisboa},
  type = {Trabalho Final de Curso},
  month = {July},
  year = {2000},
}
@mastersthesis{fcouto-master2001,
  author = {F. Couto},
  title = {Identificação de Componentes Reutilizáveis através
                  de Especificações Formais},
  school = {Instituto Superior Técnico da Universidade Técnica de Lisboa},
  year = 2001,
  month = {July},
}
@phdthesis{fcouto-phd2006,
  author = {F. Couto},
  title = {{ReBIL}: Relating Biological Information through Literature},
  school = {Faculdade de Ciências da Universidade de Lisboa},
  year = 2006,
  month = {January},
  doi = {https://doi.org/10451/14312},
}
@techreport{couto-web2010,
  author = {F. Couto},
  title = {Desenvolvimento de Aplicações Web baseadas em {SOA} e {AJAX}},
  institution = {Department of Informatics, University of Lisbon},
  year = {2010},
  month = {March},
  type = {DI/FCUL LO},
  doi = {https://doi.org/10451/15279},
}
@techreport{couto-si2011,
  author = {F. Couto and E. Santos},
  title = {Desenvolvimento de Sistemas de Informação baseados em {PHP} e {MySQL}, e {Java} e {Oracle}},
  institution = {Department of Informatics, University of Lisbon},
  year = {2011},
  month = {December},
  type = {DI/FCUL LO},
  doi = {https://doi.org/10451/15281},
}
@unpublished{fcouto-isa2022,
  title = {Interpretação de dados biológicos},
  year = {2022},
  month = {March},
  author = {F. Couto},
  note = {Tutorial nas Jornadas de Biologia do Instituto Superior de Agronomia, Lisboa},
}
@unpublished{fcouto-ist2022,
  title = {Bioinformatics: interpretation of biological data},
  year = {2022},
  month = {March},
  author = {F. Couto},
  note = {Tutorial na Semana da Bioengenharia no Instituto Superior Técnico, Lisboa},
}
@unpublished{barros-kdd2021,
  title = {Creating Recommender Systems Datasets in Scientific Fields},
  year = {2021},
  month = {August},
  author = {M. Barros and F. Couto and M. Pato and P. Ruas},
  note = {Tutorial at the 30th The Web Conference (KDD2021), Singapore},
}
@unpublished{fcouto-www2021,
  title = {Exploring Biomedical Web Resources using Shell Scripting},
  year = {2021},
  month = {April},
  author = {F. Couto},
  note = {Tutorial at the 30th The Web Conference (WWW2021), Ljubljana, Slovenia},
}
@unpublished{fcouto-ecir2021,
  title = {Biomedical Text Processing using Semantics},
  year = {2021},
  month = {March},
  author = {F. Couto},
  note = {Tutorial at the 43rd European Conference on Information Retrieval (ECIR2021), Lucca, Italy},
}
@unpublished{fcouto-mcdc2020,
  title = {Why analyze biomedical text if we have data?},
  year = {2020},
  month = {December},
  author = {F. Couto},
  note = {Talk at Data Science Seminars, Universidade de Lisboa},
}
@unpublished{fcouto-mbbc2020,
  title = {Biomedical Text Mining: exploring semantic resources},
  year = {2020},
  month = {October},
  author = {F. Couto},
  note = {Talk at Bioinformatics and Computational Biology Seminars, Universidade de Lisboa},
}
@unpublished{fcouto-bioasq2020,
  title = {Multilingual Resources and Community {Q\&A} Forums},
  year = {2020},
  month = {September},
  author = {F. Couto},
  note = {Participation in the Discussion Panel of the 8th BioASQ 2020 Workshop},
}
@unpublished{fcouto-eccb2020,
  title = {Biomedical Data and Text Processing using Shell Scripting},
  year = {2020},
  month = {September},
  author = {F. Couto},
  note = {Tutorial at the 19th European Conference on Computational Biology (ECCB2020), Barcelona, Spain},
}
@unpublished{fcouto-sembio2020,
  title = {Bioinformática: processamento de dados e texto biológico via linha de comando},
  year = {2020},
  month = {September},
  author = {F. Couto},
  note = {Palestra na II Semana de Biologia da Universidade Federal do Sul da Bahia, Brazil},
}
@unpublished{fcouto-muclin2020,
  title = {Multilingual Text Mining: Overcoming the lack of clinical {NLP} resources},
  year = {2020},
  month = {July},
  author = {F. Couto},
  note = {Talk at the First Multilingual clinical NLP workshop (MUCLIN), Geneva, Switzerland},
}
@unpublished{fcouto-fct2019,
  title = {Introdução à Bioinformática Via Linha de Comando},
  year = {2019},
  author = {F. Couto},
  month = {December},
  note = {Tutorial na Faculdade de Ciências e Tecnologias da Universidade Nova de Lisboa, Caparica},
}
@unpublished{fcouto-ucoimbra2019,
  title = {Introdução à Bioinformática Via Linha de Comando},
  year = {2019},
  month = {November},
  author = {F. Couto},
  note = {Tutorial no V Encontro de Ecologia, Universidade de Coimbra},
}
@unpublished{fcouto-ualgarve2019,
  title = {Data and Text Processing in Health and Life Sciences: an example driven workshop using shell scripting},
  year = {2019},
  month = {July},
  author = {F. Couto},
  note = {Tutorial na Universidade do Algarve, Faro},
}
@unpublished{fcouto-um2019,
  title = {Data and Text Processing in Health and Life Sciences: an example driven workshop using shell scripting},
  year = {2019},
  month = {February},
  author = {F. Couto},
  note = {Tutorial at the Bioinformatics Open Days, Universidade do Minho, Braga},
}
@unpublished{fcouto-fismed2017,
  title = {Exploration, sharing and privacy of data: Linked Data - challenges for Imagiology and Radiology},
  year = {2017},
  author = {F. Couto},
  note = {Palestra no Encontro Nacional de Física Médica, FISMED2017, Coimbra},
}
@unpublished{fcouto-imm2016,
  title = {Towards a privacy-preserving environment for genomic data analysis},
  year = {2016},
  author = {F. Couto},
  note = {Talk at the Computational Biology and Bioinformatics Seminar, IMM, Lisboa},
}
@unpublished{fcouto-bod2016,
  title = {Master in Bioinformatics and Computational Biology},
  year = {2016},
  author = {F. Couto},
  note = {Talk at the Bioinformatics Open Days, Braga},
}
@unpublished{fcouto-eit2015,
  title = {Identifying Interactions between Chemical Entities In Text},
  year = {2015},
  author = {F. Couto},
  note = {Talk at the Innovation and Business Creation Pitch Session, EIT Health, Lisboa},
}
@unpublished{fcouto-bod2015,
  title = {Master in Bioinformatics and Computational Biology},
  year = {2015},
  author = {F. Couto},
  note = {Talk at the Bioinformatics Open Days, Lisboa},
}
@unpublished{fcouto-peere2015,
  title = {Recognizing and rewarding data sharing through {KnowldegeCoins}},
  year = {2015},
  author = {F. Couto},
  note = {Talk at the Data sharing in peer review, PEERE workshop, Lisboa},
}
@unpublished{fcouto-isa2014,
  title = {Biomedical Ontologies and optimization challenges},
  year = {2014},
  author = {F. Couto},
  note = {Palestra no 3º workshop em bio-optimização, Instituto Superior de Agronomia},
}
@unpublished{fcouto-ist2014,
  title = {Current Research Themes on the Area of Information Systems: The Case of Biomedical Text Mining},
  year = {2014},
  author = {F. Couto},
  note = {Talk at the Research Topics Class, IST},
}
@unpublished{fcouto-rda2014,
  title = {Rewarding and recognizing metadata sharing and integration on the semantic web using ontologies},
  year = {2014},
  author = {F. Couto},
  note = {Talk at the RDA Europe Workshop about Data Sharing and Interoperability, Brussels},
}
@unpublished{fcouto-sapo2014b,
  title = {{KnowledgeCoin (KC)}: a reward and recognition mechanism to incentivize proper data integration and sharing},
  year = {2014},
  author = {F. Couto},
  note = {Talk at the SAPO Labs, Lisboa},
}
@unpublished{fcouto-biobankcloud2014,
  title = {The {BiobankCloud}},
  year = {2014},
  author = {F. Couto},
  note = {Talk at the Meeting on IT/Informatics BBMRI-ERIC, Austria},
}
@unpublished{fcouto-biosys2014,
  title = {How can Biomedical Ontologies assist Biological Systems, Functional \& Integrative Genomics research?},
  year = {2014},
  author = {F. Couto},
  note = {Talk at the BioSys/BioFIG Research Seminar, University of Lisbon},
}
@unpublished{fcouto-sapo2014,
  title = {O {Mundo em Pessoa} 2.0},
  year = {2014},
  author = {F. Couto},
  note = {Talk at the SAPO Labs, Lisboa},
}
@unpublished{fcouto-bod2014,
  title = {Master in Bioinformatics and Computational Biology at {FCUL}},
  year = {2014},
  author = {F. Couto},
  note = {Talk at the Bioinformatics Open Days, University of Minho},
}
@unpublished{fcouto-flash2013,
  title = {O {Mundo em Pessoa}},
  year = {2014},
  author = {F. Couto},
  note = {Palestra na 1ª Semana Ciências em Movimento, FCUL},
}
@unpublished{fcouto-biobank2013,
  title = {Privacy-preserving Genome Annotation},
  year = {2013},
  author = {F. Couto},
  note = {Talk at the 3rd Biobank Technical Meeting, University of Lisbon},
}
@unpublished{fcouto-igc2013,
  title = {How Biomedical Ontologies can assist Computational and Theoretical Biology research?},
  year = {2013},
  author = {F. Couto},
  note = {Talk at the Seminars on Computational and Theoretical Biology, Instituto Gulbenkian de Ciência},
}
@unpublished{fcouto-ibeb2013,
  title = {Biomedical Ontologies: semantic annotation and similarity},
  year = {2013},
  author = {F. Couto},
  note = {Palestra no Instituto de Biofísica e Engenharia Biomédica (IBEB)},
}
@unpublished{fcouto-obml2012,
  title = {Semantic Similarity in Biomedical Ontologies: Measurement, Assessment and Applications},
  year = {2012},
  author = {F. Couto},
  note = {Talk at the Workshop on Ontologies in Biomedicine and Life Sciences (OBML), Dresden, Germany},
}
@unpublished{fcouto-bragaseminar2012,
  title = {Semantic Ontology Matching using External Resources},
  year = {2012},
  author = {F. Couto},
  note = {Palestra no Centro de Ciências e Tecnologias de Computação (CCTC) Seminar, University of Minho},
}
@unpublished{fcouto-braga2012,
  title = {Exploring the Semantics of Biomedical Ontologies},
  year = {2012},
  author = {F. Couto},
  note = {Talk at the Bioinformatics Open Days, University of Minho},
}
@unpublished{fcouto-acores2011,
  title = {Bioinformática},
  year = {2011},
  author = {F. Couto},
  note = {Palestra no Ciclo de Seminários Web, Universidade dos Açores},
}
@unpublished{fcouto-fcul2011,
  title = {Untangling Biomedical Ontologies},
  year = {2011},
  author = {F. Couto},
  note = {Talk at the Workshop on Bioinformatics and Systems Modelling, University of Lisbon},
}
@unpublished{fcouto-ebi2011,
  title = {Exploring the Semantics of Biomedical Ontologies},
  year = {2011},
  author = {F. Couto},
  note = {Talk at the External Seminar at European Bioinformatics Institute, Hinxton, UK},
}
@unpublished{fcouto-trans2010,
  title = {Biomedical Informatics},
  year = {2010},
  author = {F. Couto},
  note = {Talk at the Translational Bioinformatics, IGC, Oeiras},
}
@unpublished{fcouto-imm2010,
  title = {Untangling {BioOntologies} for Effectively Exploring Biomedical Information},
  year = {2010},
  author = {F. Couto},
  note = {Talk at the IMM Bioinformatics nanocourse, Lisboa},
}
@unpublished{fcouto-flup2010,
  title = {Gene Ontology},
  year = {2010},
  author = {F. Couto},
  note = {Talk at the FLUP Escola de Verão, Lisboa},
}
@unpublished{fcouto-interac2008,
  title = {Biomedical Research Line},
  year = {2008},
  author = {F. Couto},
  note = {Talk at the First INTERAC workshop, Braga},
}
@unpublished{fcouto-igc2008,
  title = {Untangling {BioOntologies} for Mining Biomedical Information},
  year = {2008},
  author = {F. Couto},
  note = {Talk at the First Portuguese forum on computational biology, IGC, Oeiras},
}
@unpublished{fcouto-porto2008,
  title = {{ReBIL}: Relating Biological Information through Literature},
  year = {2008},
  author = {F. Couto},
  note = {Talk at the Workshop: Algoritmos de bioinformatica na Faculdade de Medicina da Universidade do Porto},
}
@unpublished{fcouto-tomar2006,
  title = {Bioinformática - exploração da informação genómica},
  year = {2006},
  author = {F. Couto},
  note = {Palestra no Instituto Politécnico de Tomar},
}
@unpublished{fcouto-bioalma2006,
  title = {Machine Learning},
  year = {2006},
  author = {F. Couto},
  note = {Talk at the BioAlma Seminar, Madrid},
}
@unpublished{fcouto-talkordeng:2005,
  author = {F. Couto},
  title = {Identificação Automática de Evidências que suportem Anotações de Proteínas na Literatura Científica},
  note = {Palestra na Entrega do Prémio Inovação Jovem Engenheiro 2004, Ordem dos Engenheiros, Lisboa, Portugal},
  year = 2005,
  month = {October},
}
@unpublished{fcouto-talkenebioq:2005,
  author = {F. Couto},
  title = {Caracterização Bioquímica de Genes e Proteínas: Bases de Dados e Ferramentas de Anotação Automática},
  note = {Palestra no II Encontro Nacional de Estudantes Bioquímicos (II ENeBIOQ), Faculdade de Ciências da Universidade de Lisboa, Portugal},
  year = 2005,
  month = {April},
}
@unpublished{fcouto-talkigc2005,
  author = {F. Couto},
  title = {{ReBIL}: Relating Biological Information through Literature},
  note = {Palestra no Seminário do Programa Estudos Avançados de Oeiras (EAO seminar), IGC, Oeiras},
  year = 2005,
}
@unpublished{fcouto-talkprocura2004,
  author = {F. Couto},
  title = {{ReBIL}: Relating Biological Information through Literature},
  note = { II Annual Meeting of Portuguese Proteomic Network (ProCura) Functional Genomics And Proteomics, Inst. Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal},
  year = 2004,
  month = {November},
}
@unpublished{fcouto-talkebi2004,
  author = {F. Couto},
  title = {Automatic identification in literature of evidences that support electronic {GOA} annotations},
  note = {Talk at the Seminary of the Sequence Database Group, European Bioinformatics Institute, Hinxton, UK},
  month = {October},
  year = 2004,
}
@unpublished{fcouto-talkafmb2003,
  author = {F. Couto},
  title = {{ReBIL} : Relating Biological Information through Literature},
  note = {Talk at the Seminary of the AFMB laboratory, AFMB-CNRS, Marseille, France},
  month = {December},
  year = 2003,
}
@unpublished{fcouto-talkinesc2003,
  author = {F. Couto},
  title = {Extracção de Informação da Literatura Biológica},
  note = {Talk at the ALGOS Seminars, INESC, Lisboa, Portugal}
}
@unpublished{fcouto-talkigc2002,
  author = {F. Couto},
  title = {Extracting biological information through literature: automatic annotation of {FlyBase} and {CAZy} databases},
  note = {Talk at the Scientific Meeting on Bioinformatics (satellite to the EMBnet AGM02), Instituto Gulbenkian de Ciência, Oeiras, Portugal},
  month = {September},
  year = 2002,
}