clpesquita [at] fc.ul.pt

+351 217500846 (ext.26314)

Catia Pesquita is an Associate Professor in Computer Science at the Department of Informatics of the Faculty of Sciences of the University of Lisbon and a senior researcher at LASIGE where she leads the Health and Biomedical Informatics Research Line.

She has a multidisciplinary background in Biology and Computer Science, and together with her research group, LiSeDa Lab, she does research at the intersection between Artificial Intelligence and Data Science, focusing on applications in the life and health sciences. She is also vice-president of the Biodata.pt association devoted to the valorisation of the biological data generated by Portuguese Science, and is involved in activities to promote computer science career paths to young women.

Her research areas include Semantic Web, Biomedical Ontologies, Knowledge Graphs, Ontology Matching, Semantic Similarity, Explainable Artificial Intelligence.

Selected Publications

Sousa RT, Silva S, Paulheim H, Pesquita C. Biomedical Knowledge Graph Embeddings with Negative Statements Internatinal Semantic Web Conference (ISWC2023), Greece, 2023

Sousa RT, Silva S, Pesquita C. Explainable Representations for Relation Prediction in Knowledge Graphs. International Conference on Principles of Knowledge Representation and Reasoning (KR2023), Greece, 2023

Silva MC, Faria D, Pesquita C. Matching multiple ontologies to build a knowledge graph for personalized medicine. In European Semantic Web Conference 2022

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.

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.

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)
(Researcher)

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

Students

Current

Ricardo Carvalho (PhD in Computer Science)

Pedro Cotovio (PhD in Computer Science)

Susana Nunes (PhD in Computer Science)

Marta Silva (PhD in Computer Science)

Rita Sousa (PhD in Computer Science)

Laura Balbi (MSc in Bioinformatics)

José Oliveira (MSc in Bioinformatics)

Filipe Paulino (MSc in Data Science)

Catarina Canastra (MSc in Data Science)

Natércia Soeiro (MSc in Computer Science and Engineering)

Susana Sousa (MSc in Bioinformatics)

Past

Marzieh Bakshandeh (PhD)

Carlos Alexandre Lourenço (PhD)

Filipa Serrano (MSc in Data Science)

Patrícia Eugénio (MSc in Bioinformatics)

Ana Guerreiro (MSc in Bioinformatics)

André Gonçalves(MSc in Bioinformatics)

Beatriz Lima (MSc in Data Science)

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)

Teaching

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