clpesquita [at]

+351 217500846 (ext.26314)

I am an Assistant Professor at the Department of Informatics of the Faculty of Sciences of the University of Lisbon and a researcher at LASIGE. I have a PhD in Computer Science - Bioinformatics (2012), an MSc in Bioinformatics (2008) and a degree in Biology (2005).

My main research interest is how we can turn data, of which we have more and more each day, into meaningful and purposeful knowledge. My research areas include Biomedical Ontologies, Semantic Web, Ontology Matching, Semantic Similarity, Ontology Evolution, Knowledge Management and Data and Text Mining.

Selected Publications

Cheatham M, Pesquita C. Semantic Data Integration. In Handbook of Big Data Technologies 2017 (pp. 263-305). Springer International Publishing.

Dragisic Z, Ivanova V, Lambrix P, Faria D, Jiménez-Ruiz E, Pesquita C. User validation in ontology alignment. In International Semantic Web Conference 2016 Oct 17 (pp. 200-217). Springer International Publishing.

Santos E, Faria D, Pesquita C, Couto FM. Ontology alignment repair through modularization and confidence-based heuristics. PLoS ONE. 2015;10(12).

Pesquita C, Faria D, Stroe C, Santos E, Cruz IF, Couto FM. What’s in a ‘nym’? Synonyms in Biomedical Ontology Matching. In The Semantic Web–ISWC 2013 2013 Oct 21 (pp. 526-541). Springer Berlin Heidelberg.

Pesquita C, Couto FM.Predicting the Extension of Biomedical Ontologies. PLoS Computational Biology. 2012.

Pesquita C, Faria D, Falcao AO, Lord P, Couto FM. Semantic similarity in biomedical ontologies. PLoS Comput Biol. 2009 Jul 31;5(7):e1000443.



SOMER (Semantic Ontology Matching using External Resources)

Turning Big Data into Smart Data

BOA (BioOntologies Applications)

AEB (Automated Extension of Biomedical Ontologies) completed

Epiwork (Developing the framework for an epidemic forecast infrastructure) completed

Tools, Software and Ontologies

AML, an ontology matching system. Available on GitHub

The Epidemiology Ontology, dedicated to epidemiologically relevant parameters and metrics. Available on Google Code

CESSM, an online tool for evaluation of semantic similarity measures for the Gene Ontology

Proteinon, an online tool for calculating GO-based semantic similarity.



Carlos Alexandre Lourenço (PhD)

Isabela Mott Silva (MSc)

Madalena Pavão (MSc)



João Rebelo (MSc)

Carlos Alexandre Lourenço (MSc)

Marzieh Bakshandeh (PhD)

Catarina Martins

Daniela Olveira (MSc)


In 2015/2016 I am teaching Bases de Dados/Databases, Big Data, Bioinformática, Conceção de Produto/Porduct Design, Introdução às Tecnologias Web/Introduction to Web Technologies, Tecnologia de Bases de Dados/Database Technologies (advanced).


AML was awarded the IBM Research prize at OAEI 2017.

Our ontology matching system, AML, placed first (f-measure) in 7 out of 9 tracks we entered at OAEI 2017.

My student, Daniela Oliveira, successfully defended her MSc dissertation and has been accepted for a PhD at the Insight Centre for Data Analytics, NUI Galway, Ireland

AML-EA, a flavour of AML geared for Enterprise Architechture matching developed in collaboration with INESC-ID ranked first in the Asset Management Matching task at the Process Model Matching Contest at EMISA 2015.

Our ontology matching system, AML, placed first (f-measure) in 6 out of 7 tracks we entered at OAEI 2015.

My student's paper won Best Early Career Paper Award at ICBO 2015. Congratulations, Catarina!

Faculdade de Ciências is hosting ICBO 2015, and I am the local organizer. Welcome to Lisbon!

Our paper The epidemiology ontology: an ontology for the semantic annotation of epidemiological resources is out on JBMS.