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 where I lead the Research Line of Excellence in Health and Biomedical Informatics. 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 Mining.

Selected Publications

Sousa RT, Silva S, Pesquita C. Evolving knowledge graph similarity for supervised learning in complex biomedical domains. BMC bioinformatics. 2020 Dec 1;21(1):6.

Oliveira D, Pesquita C. Improving the interoperability of biomedical ontologies with compound alignments. Journal of biomedical semantics. 2018 Dec;9(1):1.

Pesquita C. Semantic similarity in the gene ontology. In The Gene Ontology Handbook 2017 (pp. 161-173). Humana Press, New York, NY.

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.

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.

Selected Projects

2021-2024: KATY- Knowledge At the Tip of Your fingers: Clinical Knowledge for Humanity
An H2020 funded project on AI-Empowered Personalised Medicine System to Improve Cancer Treatments
(Team Leader, WP co-lead)

2021-2024: BRAINTEASER - BRinging Artificial INTelligencE home for a better cAre of amyotrophic lateral sclerosis and multiple SclERosis
An H2020 funded project on AI for patient stratification and disease progression models for Amyotrophic Lateral Sclerosis (ALS) and Multiple Sclerosis (MS)

2016-2020: SMiLaX - Semantic Mining with Linked Data
FCT funded project on novel data mining approaches embedded with semantics (Principal Investigator)

Tools, Software and Ontologies

KGsim-benchmark, a benchmark for Biomedical Knowledge Graph-based semantic similarity Github

AML, an ontology matching system. Available on GitHub

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

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

superseded by KGsim-benchmark



Rita Sousa (PhD in Informatics)

Marta Silva (PhD in Informatics)

Ana Guerreiro (MSc in Bioinformatics)

André Gonçalves(MSc in Bioinformatics)

Beatriz Lima (MSc in Data Science)

Susana (MSc in Bioinformatics)

Susana Sousa (MSc in Bioinformatics)

Ricardo Carvalho (MSc in Bioinformatics)

Anna Laura Souza (BSc in Computer Science and Engineering)



Marzieh Bakshandeh (PhD)

Carlos Alexandre Lourenço (PhD)

Carlota Branco (MSc in Bioinformatics)

Diogo Pereira (MSc in Informatics Engineering)

Liliana Veríssimo (MSc in Informatics)

Madalena Guerra(MSc in Data Science)

Pedro Ladino (MSc in Bioinformatics)

Rodrigo Neves (MSc in Data Science)

Teemu Tervo (MSc in Data Science)

David C. Teixeira (junior researcher, pre-PhD)

Kornelia Ufniarz (junior researcher)

Isabela Mott Silva (MSc)

Madalena Pavão (MSc)

João Rebelo (MSc)

Catarina Martins (MSc)

Daniela Olveira (MSc)


Advanced Databases, Data Integration and Processing, Bioinformatics and Big Data.


February, 2021: Honoured to have been the Program Chair of the 14th HealthInf conference.

January, 2021: The KATY project has kicked-off!

June, 2020: Our work in Benchmarks for KG-based semantic similarity in the biomedical domain was co-awarded the Best Poster Paper Award at ESWC2020

May, 2020: Our position paper Towards Evaluating Complex Ontology Alignments was published in the Knowledge Engineering Review

August, 2019: I am honored to join BMC Bioinformatics as Associate Editor.

I was an invited keynote at the Bio-Ontologies COSI in ISMB/ECCB 2017, in Prague.

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.