Semantic Similarity for Automatic Classification of Chemical Compounds. - João D. Ferreira; Francisco M. Couto (PLoS Comput. Biol., 2010)

Generic Semantic Relatedness Measure for Biomedical Ontologies. - João D. Ferreira; Francisco M. Couto (ICBO, 2011)

The Biomedical Ontology Applications (BOA) Framework. - Bruno Tavares; Hugo P. Bastos; Daniel Faria; João D. Ferreira; Tiago Grego; Catia Pesquita; Francisco M. Couto (ICBO, 2011)

The Epidemic Marketplace Platform: towards semantic characterization of epidemiological resources using biomedical ontologies. - Francisco M. Couto; João D. Ferreira; João Zamite; Carlos Santos; Tiago Posse; Paulo M. L. A. Graça; Dulce Domingos; Mário J. Silva (ICBO, 2012)

Bringing epidemiology into the Semantic Web. - João D. Ferreira; Catia Pesquita; Francisco M. Couto; Mário J. Silva (ICBO, 2012)

Toponym Disambiguation Using Ontology-Based Semantic Similarity. - David S. Batista; João D. Ferreira; Francisco M. Couto; Mário J. Silva (PROPOR, 2012)

Digital preservation of epidemic resources: coupling metadata and ontologies. - João D. Ferreira; Catia Pesquita; Francisco M. Couto; Mário J. Silva (iPRES, 2013)

Exploiting disjointness axioms to improve semantic similarity measures. - João D. Ferreira; Janna Hastings; Francisco M. Couto (Bioinform., 2013)

Chemical Named Entity Recognition: Improving Recall Using a Comprehensive List of Lexical Features. - Andre Lamurias; João D. Ferreira; Francisco M. Couto (PACBB, 2014)

The epidemiology ontology: an ontology for the semantic annotation of epidemiological resources. - Catia Pesquita; João D. Ferreira; Francisco M. Couto; Mário J. Silva (J. Biomed. Semant., 2014)

Identifying interactions between chemical entities in biomedical text. - Andre Lamurias; João D. Ferreira; Francisco M. Couto (J. Integr. Bioinform., 2014)

Improving chemical entity recognition through h-index based semantic similarity. - Andre Lamurias; João D. Ferreira; Francisco M. Couto (J. Cheminformatics, 2015)

Metadata Analyser: Measuring Metadata Quality. - Bruno Inácio; João D. Ferreira; Francisco M. Couto (PACBB, 2017)

Assessing Public Metabolomics Metadata, Towards Improving Quality. - João D. Ferreira; Bruno Inácio; Reza M. Salek; Francisco M. Couto (J. Integr. Bioinform., 2017)

Multi-domain semantic similarity in biomedical research. - João D. Ferreira; Francisco M. Couto (BMC Bioinform., 2019)