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Cátia Pesquita is an Associate Professor at Departamento de Informática, Faculdade de Ciências, Universidade de Lisboa. She is an integrated member of the LASIGE research unit where she leads the Research Line of Excellence in Health and Biomedical Informatics and is also a Member of the Executive Commission. Her research work is dedicated to knowledge engineering and data mining, particularly in the biomedical and clinical domains, supported by her multidisciplinary background (degree in Biology (2005), an MSc in Bioinformatics (2008) and a PhD in Computer Science(2012)). She is also the Vice-President of the Biodata.pt Association that manages the Portuguese biological data infrastructure. She has made significant contributions to the area of knowledge graphs and ontology-based semantic similarity, producing highly cited publications in PLoS Computational Biology, BMC Bioinformatics, the International Semantic Web Conference and the Extended Semantic Web Conference. She has led and collaborated in multiple research projects including more recently, an H2020 funded project for Knowledge Graphs and Explainable AI in Oncology. She has supervised over 30 MSc and PhD theses, and is also an Associate Editor at BMC Bioinformatics. Throughout her career, she has established international collaborations with multiple institutions, including University of Illinois (USA), Oxford University (UK), Linkoping University (Sweden), Fondazione Bruno Kessler (Italy), University Milano-Bicocca (Italy), Fraunhofer Institute (Germany), University of Bonn (Germany), UniHospital Charite (Germany), University of Rome Tor Vergata (Italy) and INRIA (France). She has given more than 30 invited talks and keynotes, including keynotes at the International Conference of Conceptual Modeling (2023) and the BioOntologies track of ISMB/ECCB 2017 (the most renowned conference in Bioinformatics). In 2022, she was recognized as AI 2000 Most Influential Scholars Honorable Mention in Knowledge Engineering, ranking 16th in the world. She was listed as a Top 2% Scientist by Stanford University in the field of Artificial Intelligence and Bioinformatics since 2020. Her research team and collaborators develop AML, an award-winning software for ontology matching used at Jansen Pharmaceuticals, NASA and FAO among others. Lab: https://liseda-lab.github.io/ Google Scholar: https://scholar.google.com/citations?user=8nGYegMAAAAJ Bibliometrics: Citations: >5200 h-index:36 (Google Scholar).
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Identification

Personal identification

Full name
Cátia Luísa Santana Calisto Pesquita

Citation names

  • Pesquita, Cátia

Author identifiers

Ciência ID
3B1B-7244-4EB4
ORCID iD
0000-0002-1847-9393

Knowledge fields

  • Exact Sciences - Computer and Information Sciences
  • Exact Sciences - Computer and Information Sciences - Bioinformatics

Languages

Language Speaking Reading Writing Listening Peer-review
English Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2)
French Intermediate (B1) Advanced (C1) Intermediate (B1) Intermediate (B1)
Spanish; Castilian Intermediate (B1) Advanced (C1) Intermediate (B1) Intermediate (B1)
Education
Degree Classification
2012
Concluded
 Doutoramento em Informática - Ramo Bioinformática (Doutoramento)
Universidade de Lisboa Faculdade de Ciências, Portugal
"Automated Extension of Biomedical Ontologies" (THESIS/DISSERTATION)
 Distinção e Louvor por Unanimidade
2007
Concluded
 Mestrado em Bioinformática (Mestrado)
Universidade de Lisboa Faculdade de Ciências, Portugal
"Improving Semantic Similarity for Proteins based on the Gene Ontology" (THESIS/DISSERTATION)
 Muito Bom
2006
Concluded
 Bioinformática (Especialização pós-licenciatura)
Universidade de Lisboa Faculdade de Ciências, Portugal
2005
Concluded
 Biologia Celular e Biotecnologia (Licenciatura)
Universidade de Lisboa Faculdade de Ciências, Portugal
Affiliation

Teaching in Higher Education

Category
Host institution 		Employer
2022/11/21 - Current Associate Professor (University Teacher) Universidade de Lisboa Faculdade de Ciências, Portugal
2016/02/16 - 2022/11/20 Assistant Professor (University Teacher) Universidade de Lisboa Faculdade de Ciências, Portugal
2012/09/01 - 2016/02/15 Invited Assistant Professor (University Teacher) Universidade de Lisboa Faculdade de Ciências, Portugal

Positions / Appointments

Category
Host institution 		Employer
2022 - Current Member of the Scientific Council of Faculdade de Ciências UL Universidade de Lisboa Faculdade de Ciências, Portugal
2021 - Current Representante da Faculdade de Ciências (UL) junto do LxDataLab (Câmara Municipal de Lisboa) Universidade de Lisboa Faculdade de Ciências, Portugal
2019/07/25 - Current Member of Ciências's Ethics Committee for Data Collection and Protection Universidade de Lisboa Faculdade de Ciências, Portugal

Others

Category
Host institution 		Employer
2022 - Current Member of the Executive Commission of LASIGE (direction of the research unit) Universidade de Lisboa Laboratório de Sistemas Informáticos de Grande Escala, Portugal
2021 - Current Vice-President of the Association BioData.pt - Infraestrutura Portuguesa para os Dados Biológicos Universidade de Lisboa Faculdade de Ciências, Portugal
BioData.pt, Portugal
2015/09/01 - Current Public Relations Committee of the Informatics Departmanent/Comissão de Relações Externas do Departamento de Informática Universidade de Lisboa Faculdade de Ciências, Portugal
2013/01/01 - Current Researcher/Investigadora Universidade de Lisboa Laboratório de Sistemas Informáticos de Grande Escala, Portugal
2013/01/01 - Current Member of Scientific Council /Membro do Conselho Científico Universidade de Lisboa Laboratório de Sistemas Informáticos de Grande Escala, Portugal
2006/09/01 - 2012/12/31 Junior Researcher/Investigadora Júnior Universidade de Lisboa Laboratório de Sistemas Informáticos de Grande Escala, Portugal
Projects

Grant

Designation Funders
2023 - Current Knowledge Graph-based Explanations for Biomedical Artificial Intelligence
2023.00653.BD
Supervisor
Universidade de Lisboa Laboratório de Sistemas Informáticos de Grande Escala, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2022 - Current Holistic Biomedical Knowledge Graph Integration
2022.11895.BD
Supervisor
Universidade de Lisboa Laboratório de Sistemas Informáticos de Grande Escala, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2022 - Current Learning and Explaining Knowledge Graph Alignment
2022.10557.BD
Supervisor
Universidade de Lisboa Laboratório de Sistemas Informáticos de Grande Escala, Portugal
 Fundação para a Ciência e a Tecnologia
2022 - Current Time and Knowledge-Aware Clinical Graph Data Mining
2022.10769.BD
Supervisor
Universidade de Lisboa Laboratório de Sistemas Informáticos de Grande Escala, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2019 - Current Evolving meaning for supervised learning in complex biomedical domains using knowledge graphs
SFRH/BD/145377/2019
Supervisor
Fundação para a Ciência e a Tecnologia
Ongoing
2008/07 - 2012/08 Automated extension of Biomedical Ontologies
SFRH / BD / 42481 / 2007
 Fundação para a Ciência e a Tecnologia

Contract

Designation Funders
2023/11/02 - Current TrustAI4Sci: Trustworthy Artificial Intelligence for Science
CPCA-IAC/AV/594790/2023
Principal investigator
FCiênciasID Associação para a Investigação e Desenvolvimento de Ciências, Portugal
 Google Inc
Ongoing
2021/03/01 - Current AIpALS - Modelos Avançados de aprendIzagem para a Previsão do prognóstico na ELA usando perfis de doentes e padrões de progressão da doença
PTDC/CCI-CIF/4613/2020
Researcher
FCiênciasID Associação para a Investigação e Desenvolvimento de Ciências, Portugal

Universidade de Lisboa Laboratório de Sistemas Informáticos de Grande Escala, Portugal

Associação Fraunhofer Portugal Research, Portugal

Universidade de Lisboa Instituto de Medicina Molecular João Lobo Antunes, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2021/01/01 - Current Knowledge At the Tip of Your fingers: Clinical Knowledge for Humanity (KATY)
GA101017453
Principal investigator
FCiênciasID Associação para a Investigação e Desenvolvimento de Ciências, Portugal
 European Commission

European Union
Ongoing
2021/01/01 - Current Brainteaser
GA101017598
Researcher
FCiênciasID Associação para a Investigação e Desenvolvimento de Ciências, Portugal
 European Commission
Ongoing
2021 - Current WideHealth: Widening Research on Pervasive and eHealth
GA952279
Researcher
European Union
2020 - Current MARCODE - Desenvolvimento e Aplicação de Ferramentas Bioquímicas de Rastreamento de Produtos Comerciais Marinhos
MARCODE
 MAR2020
2019/01 - Current GADgET - Online Gambling Addiction Detection
DSAIPA/DS/0022/2018
 Fundação para a Ciência e a Tecnologia
2015/07 - 2020/12/31 SMILAX: Semantic Mining with Linked Data
PTDC/EEI-ESS/4633/2014
Principal investigator
FCiênciasID Associação para a Investigação e Desenvolvimento de Ciências, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2016/04 - 2019/09 RESISTIR: Intelligent Systems for Personalized Antibiotherapy and Infection Control
POCI-01-0247-FEDER-003379
Researcher
European Commission
Concluded
2015/06 - 2019 MIMED: Mining the Molecular Metric Space for Drug Design
PTDC/EEI-ESS/4923/2014
 Fundação para a Ciência e a Tecnologia
2012/03/19 - 2014/10/31 SOMER: Emparelhamento Semântico de Ontologias usando Recursos Externos
PTDC/EIA-EIA/119119/2010
Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal

Universidade de Lisboa Laboratório de Sistemas Informáticos de Grande Escala, Portugal

Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2008/07/01 - 2012/10/31 EXTENSÃO E ENRIQUECIMENTO AUTOMATIZADO DE BIOONTOLOGIAS
SFRH/BD/42481/2007
Universidade de Lisboa Faculdade de Ciências, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded

Other

Designation Funders
2021 - Current Distributed Knowledge Graphs COST Action
CA19134
Researcher
Outputs

Publications

Book chapter
  1. Pesquita, Cátia; David Teixeira Carriço; João D. Ferreira. "Biomedical ontologies: Coverage, access and use". In Systems Medicine: Integrative, Qualitative and Computational Approaches. Elsevier, 2020.
    In press
  2. Pesquita, Catia. "Semantic Similarity in the Gene Ontology". In Methods in Molecular Biology, 161-173. Springer New York, 2017.
    10.1007/978-1-4939-3743-1_12
  3. Cheatham, Michelle; Pesquita, Catia. "Semantic Data Integration". In Handbook of Big Data Technologies, 263-305. Springer International Publishing, 2017.
    10.1007/978-3-319-49340-4_8
  4. Bastos, Hugo P.; Tavares, Bruno; Pesquita, Catia; Faria, Daniel; Couto, Francisco M.. "Application of Gene Ontology to Gene Identification". In In Silico Tools for Gene Discovery, 141-157. Humana Press, 2011.
    10.1007/978-1-61779-176-5_9
  5. Pesquita, Catia; Grego, Tiago; Couto, Francisco. "Identifying Gene Ontology Areas for Automated Enrichment". In Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living, 934-941. Springer Berlin Heidelberg, 2009.
    10.1007/978-3-642-02481-8_143
  6. Pesquita, Catia. "Untangling BioOntologies for Mining Biomedical Information". In Handbook of Research on Text and Web Mining Technologies, 314-330. IGI Global, 2008.
    10.4018/978-1-59904-990-8.ch019
Conference paper
  1. Faria, Daniel; Silva, Marta Contreiras; Giesteira Cotovio, Pedro; Lucas Ferraz; Laura Balbi; Pesquita, Cátia. "Results for Matcha and Matcha-DL in OAEI 2023". Paper presented in OM 2023: The 18th International Workshop on Ontology Matching collocated with the 22nd International Semantic Web Conference ISWC-2023, Athens, 2023.
    Published
  2. Rita T. Sousa; Sara Silva; Heiko Paulheim; Catia Pesquita. "Biomedical Knowledge Graph Embeddings with Negative Statements". Paper presented in International Semantic Web Conference, 2023.
    10.1007/978-3-031-47240-4_23
  3. Sousa, Rita T.; Silva, Sara; Pesquita, Cátia. "Explainable Representations for Relation Prediction in Knowledge Graphs". Paper presented in International Conference on Principles of Knowledge Representation and Reasoning, 2023.
    Accepted • 10.24963/kr.2023/62
  4. Serrano, Filipa; Nunes, Susana; Pesquita, Cátia. "VOWLExplain: Knowledge Graph Visualization for Explainable Artificial Intelligence". Paper presented in VOILA@ISCW, 2022.
  5. Branco, Ruben; Diogo F. Soares; Andreia S. Martins; Auletta, Eleonora; Eduardo N. Castanho; Nunes, Susana; Serrano, Filipa; et al. "Hierarchical modelling for ALS prognosis: predicting the progression towards critical events". Paper presented in iDPP@CLEF 2022, 2022.
    Published
  6. Nunes, Susana; Rita T. Sousa; Serrano, Filipa; Branco, Ruben; Diogo F. Soares; Andreia S. Martins; Auletta, Eleonora; et al. "Explaining artificial intelligence predictions of disease progression with semantic similarity". Paper presented in iDPP@CLEF 2022, Bologna, 2022.
    Published
  7. Marta Contreiras Silva; Daniel Faria; Catia Pesquita. "Matching Multiple Ontologies to Build aKnowledge Graph for Personalized Medicine". Paper presented in Extended Semantic Web Conference (CORE A), 2022.
    Accepted
  8. Rita Sousa; Sara Silva; Catia Pesquita. "Towards Supervised Biomedical Semantic Similarity". Paper presented in SeWebMeDa: Semantic Web solutions for large-scale biomedical data analytics, 2022.
    Accepted
  9. Susana Nunes; Rita Torres Sousa; Pesquita, Cátia. "Predicting Gene-Disease Associations with Knowledge Graph Embeddings over Multiple Ontologies". Paper presented in International Conference on Intelligent Systems for Molecular Biology (ISMB/ECCB) BioOntologies COSI, 2021.
  10. Rita Torres Sousa; Sara Silva; Pesquita, Cátia. "evoKGsim+: a framework for tailoring Knowledge Graph-based similarity for supervised learning". Paper presented in Extended Semantic Web Conference, 2021.
    Published
  11. Pesquita, Cátia. "Towards Semantic Integration for Explainable Artificial Intelligence in the Biomedical Domain". 2021.
    DOI: 10.5220/0010389707470753
  12. "VOWLMap: Graph-based Ontology Alignment Visualization and Editing". 2021.
  13. Beatriz Lima; Daniel Faria; Catia Pesquita. "Challenges of evaluating complex alignments". Paper presented in Ontology Matching Workshop (co-located with ISWC), 2021.
  14. Pesquita, Cátia. "Proceedings of the Fifth International Workshop on Visualization and Interaction for Ontologies and Linked Data: co-located with the 19th International Semantic Web Conference (ISWC 2020)". 2020.
  15. Daniel Faria; Pesquita, Cátia; Teemu Tervo; Isabel F. Cruz; Francisco M. Couto. "AML and AMLC Results for OAEI 2019". Paper presented in Ontology Matching Workshop (co-located with ISWC), 2019.
  16. Pesquita, Cátia. "Results of AML participation in OAEI 2018". Paper presented in Ontology Matching Workshop (co-located with ISWC), 2018.
  17. "A framework to conduct and report on empirical user studies in semantic web contexts". 2018.
    https://doi.org/10.1007/978-3-030-03667-6_36
  18. Faria, D.; Balasubramani, B.S.; Shivaprabhu, V.R.; Mott, I.; Pesquita, C.; Couto, F.M.; Cruz, I.F.. "Results of AML in OAEI 2017". Paper presented in Ontology Matching Workshop (co-located with ISWC), 2017.
  19. Achichi, M.; Cheatham, M.; Dragisic, Z.; Euzenat, J.; Faria, D.; Ferrara, A.; Flouris, G.; et al. "Results of the ontology alignment evaluation initiative 2017". Paper presented in Ontology Matching Workshop (ISWC), 2017.
  20. Cardoso, João; Bakhshandeh, Marzieh; Faria, Daniel; Pesquita, Cátia; Borbinha, José. "Ontology-Based Approach for Heterogeneity Analysis of EA Models". Paper presented in International Conference on Business Process Management, 2016.
    10.1007/978-3-319-58457-7_10
  21. Faria, D.; Pesquita, C.; Balasubramani, B.S.; Martins, C.; Cardoso, J.; Curado, H.; Couto, F.M.; Cruz, I.F.. "OAEI 2016 results of AML". Paper presented in Ontology Matching Workshop (co-located with ISWC), 2016.
  22. Achichi, M.; Cheatham, M.; Dragisic, Z.; Euzenat, J.; Faria, D.; Ferrara, A.; Flouris, G.; et al. "Results of the Ontology Alignment Evaluation Initiative 2016". Paper presented in Ontology Matching Workshop (co-located with ISWC), 2016.
  23. Bakhshandeh, M.; Pesquita, C.; Borbinha, J.. "An ontological matching approach for enterprise architecture model analysis". Paper presented in International Conference on Business Information Systems, 2016.
    10.1007/978-3-319-39426-8_25
  24. Dragisic, Z.; Ivanova, V.; Lambrix, P.; Faria, D.; Jiménez-Ruiz, E.; Pesquita, C.. "User validation in ontology alignment". Paper presented in International Semantic Web Conference, 2016.
    10.1007/978-3-319-46523-4_13
  25. Ivanova, V.; Lambrix, P.; Lohmann, S.; Pesquita, C.. "VOILA 2016 - editorial". Paper presented in 2nd International Workshop on Visualization and Interaction for Ontologies and Linked Data, 2016.
  26. Ivanova, V.; Lambrix, P.; Lohmann, S.; Pesquita, C.. "Preface to VOILA 2018". Paper presented in VOILA 2018 : 4th International Workshop on Visualization and Interaction for Ontologies and Linked Data, 2016.
  27. Antunes, G.; Bakhshandeh, M.; Borbinha, J.; Cardoso, J.; Dadashnia, S.; Di Francescomarino, C.; Dragoni, M.; et al. "The process model matching contest 2015". Paper presented in 6th International Workshop on Enterprise Modelling and Information Systems Architectures., 2015.
  28. Oliveira, D.; Pesquita, C.. "Inferring logical definitions using compound ontology matching". Paper presented in International Conference in Biomedical Ontology, 2015.
  29. Cheatham, M.; Dragisic, Z.; Euzenat, J.; Faria, D.; Ferrara, A.; Flouris, G.; Fundulaki, I.; et al. "Results of the ontology alignment evaluation initiative 2015". Paper presented in Ontology Matching Workshop (co-located with ISWC), 2015.
  30. Bakhshandeh, M.; Pesquita, C.; Borbinha, J.. "Ontology matching techniques for enterprise architecture models". Paper presented in Ontology Matching Workshop (co-located with ISWC), 2015.
  31. Martins, C.; Jimenez-Ruiz, E.; Santos, E.; Pesquita, C.. "Towards visualizing the mapping incoherences in BioPortal". Paper presented in International Conference in Biomedical Ontology, 2015.
  32. Faria, D.; Martins, C.; Nanavaty, A.; Oliveira, D.; Balasubramani, B.S.; Taheri, A.; Pesquita, C.; Couto, F.M.; Cruz, I.F.. "AML results for OAEI 2015". Paper presented in Ontology Matching Workshop (co-located with ISWC), 2015.
  33. Oliveira, D.; Pesquita, C.. "Compound matching of biomedical ontologies". Paper presented in International Conference on Biomedical Ontology, 2015.
  34. Pesquita, C.; Faria, D.; Santos, E.; Neefs, J.-M.; Couto, F.M.. "Towards visualizing the alignment of large biomedical ontologies". Paper presented in International Conference on Data Integration in the Life Sciences, 2015.
    10.1007/978-3-319-08590-6_10
  35. Pesquita, C.; Cheatham, M.; Faria, D.; Barros, J.; Santos, E.; Couto, F.M.. "Building reference alignments for compound matching of multiple ontologies using OBO cross-products". Paper presented in Ontology Matching Workshop (co-located with ISWC), 2014.
  36. Faria, D.; Martins, C.; Nanavaty, A.; Taheri, A.; Pesquita, C.; Santos, E.; Cruz, I.F.; Couto, F.M.. "Agreementmakerlight results for OAEI 2014". Paper presented in Ontology Matching Workshop (co-located with ISWC), 2014.
  37. Faria, D.; Jiménez-Ruiz, E.; Pesquita, C.; Santos, E.; Couto, F.M.. "Towards annotating potential incoherences in bioportal mappings". Paper presented in International Semantic Web Conference, 2014.
  38. Pesquita, Cátia. "AgreementMakerLight 2.0: Towards Efficient Large-Scale Ontology Matching.". 2014.
  39. Pesquita, C.; Faria, D.; Santos, E.; Couto, F.M.. "To repair or not to repair: Reconciling correctness and coherence in ontology reference alignments". Paper presented in Ontology Matching Workshop (co-located with ISWC), 2013.
  40. Faria, D.; Pesquita, C.; Santos, E.; Cruz, I.F.; Couto, F.M.. "AgreementMakerLight results for OAEI 2013". Paper presented in Ontology Matching Workshop (co-located with ISWC), 2013.
  41. Faria, Daniel; Pesquita, Catia; Santos, Emanuel; Palmonari, Matteo; Cruz, Isabel F.; Couto, Francisco M.. "The AgreementMakerLight Ontology Matching System". Paper presented in On the Move to Meaningful Internet Systems: OTM 2013 Conferences, 2013.
    10.1007/978-3-642-41030-7_38
  42. Pesquita, Catia; Faria, Daniel; Stroe, Cosmin; Santos, Emanuel; Cruz, Isabel F.; Couto, Francisco M.. "What’s in a ‘nym’? Synonyms in Biomedical Ontology Matching". Paper presented in International Semantic Web Conference, 2013.
    10.1007/978-3-642-41335-3_33
  43. Ferreira, J.D.; Pesquita, C.; Couto, F.M.; Silva, M.J.. "Bringing epidemiology into the semantic web". Paper presented in International Conference on Biomedical Ontology, 2012.
  44. Cruz, I.F.; Stroe, C.; Pesquita, C.; Couto, F.M.; Cross, V.. "Biomedical ontology matching using the agreementmaker system". Paper presented in International Conference on Biomedical Ontology, 2011.
  45. Pesquita, C.; Couto, F.M.. "Where GO is going and what it means for ontology extension". Paper presented in International Conference on Biomedical Ontology, 2011.
  46. Tavares, B.; Bastos, H.P.; Faria, D.; Ferreira, J.D.; Grego, T.; Pesquita, C.; Couto, F.M.. "The biomedical ontology applications (BOA) framework". Paper presented in International Conference on Biomedical Ontology, 2011.
  47. Cruz, I.F.; Stroe, C.; Caimi, F.; Fabiani, A.; Pesquita, C.; Couto, F.M.; Palmonari, M.. "Using agreementmaker to align ontologies for OAEI2011". Paper presented in Ontology Matching Workshop (co-located with ISWC), 2011.
  48. Pesquita, C.; Stroe, C.; Cruz, I.F.; Couto, F.M.. "BLOOMS on AgreementMaker: Results for OAEI 2010". Paper presented in Ontology Matching Workshop (co-located with ISWC), 2010.
  49. Pesquita, Catia; Faria, Daniel; Couto, Francisco M.. "Measuring coherence between electronic and manual annotations in biological databases". Paper presented in ACM symposium on Applied Computing - SAC '09, 2009.
    10.1145/1529282.1529452
  50. Pesquita, Cátia; Francisco M. Couto. "CESSM: collaborative evaluation of semantic similarity measures". Paper presented in JB2009: Challenges in Bioinformatics, 2009.
  51. Bastos, Hugo P.; Pesquita, Catia; Faria, Daniel; Falcão, André O.. "BOLOS: BLAST & Ontology Linked-hOmologue Stars". Paper presented in 2008 ACM symposium on Applied computing - SAC '08, 2008.
    10.1145/1363686.1363982
  52. Couto, Francisco M.; Grego, Tiago; Bastos, Hugo P.; Pesquita, Catia; Torres, Rafael; Sanchez, Pablo; Pascual, Leandro; Blaschke, Christian. "Identifying bioentity recognition errors of rule-based text-mining systems". Paper presented in Third International Conference on Digital Information Management, 2008.
    10.1109/icdim.2008.4746791
Conference poster
  1. Silva, Marta Contreiras; Faria, Daniel; Pesquita, Cátia. "Extending AgreementMakerLight to Perform Holistic Ontology Matching". Paper presented in 19th Extended Semantic Web Conference, 2022.
  2. Silva, Marta Contreiras; Faria, Daniel; Pesquita, Cátia. "Integrating knowledge graphs for explainable artificial intelligence in biomedicine". Paper presented in 16th International Workshop on Ontology Matching, 2021.
  3. Beatriz Lima; Daniel Faria; Pesquita, Cátia. "Pattern-Guided Association Rule Mining for Complex Ontology Alignment". Paper presented in International Semantic Web Conference, 2021.
  4. Ana Guerreiro; Daniel Faria; Pesquita, Cátia. "VOWLMap: graph-based ontology alignmentvisualization and editing". Paper presented in International Semantic Web Conference, 2021.
  5. Rita Torres Sousa; Sara Silva; Pesquita, Cátia. "Is there Data Leakage in Protein-ProteinInteraction Prediction using Knowledge Graphs?". Paper presented in International Semantic Web Conference, 2021.
  6. Nunes, Susana; Rita T. Sousa; Pesquita, Cátia. "Prediction of Gene-Disease Associations through Knowledge Graph Mining". Paper presented in Bioinformatics Opens Days, 2021.
  7. Pesquita, Cátia. "A Collection of Benchmark data sets for Knowledge Graph-based Similarity in the Biomedical Domain". 2020.
    https://doi.org/10.1007/978-3-030-62327-2_9
  8. Martins, C.; Faria, D.; Pesquita, C.. "Visualization and editing of biomedical ontology alignments in AgreementMakerLight". Paper presented in Data Integration in the Life Sciences, 2015.
  9. Faria, D.; Pesquita, C.; Santos, E.; Cruz, I.F.; Couto, F.M.. "AgreementMakerLight 2.0: Towards efficient large-scale ontology matching". Paper presented in International Semantic Web Conference, 2014.
Edited book
  1. Ivanova, V.; Lambrix, P.; Lohmann, S.; Pesquita, C.. VOILA! 2018: Proceedings of the Fourth International Workshop on Visualization and Interaction for Ontologies and Linked Data. CEUR Workshop Proceedings, CEUR-WS. 2018.
    Editor
  2. Ivanova, Valentina; Lambrix, Patrick; Lohmann, Steffen; Pesquita, Catia. VOILA! 2017: Proceedings of the Third International Workshop on Visualization and Interaction for Ontologies and Linked Data. CEUR WS Proceedings. 2017.
    Editor
  3. VOILA! 2017: Proceedings of the Third International Workshop on Visualization and Interaction for Ontologies and Linked Data: co-located with the 16th International Semantic Web Conference, Vienna, Austria, October 22, 2017.. 2017.
  4. Pesquita, Cátia. VOILA! 2016: Proceedings of the 2nd International Workshop on Visualization and Interaction for Ontologies and Linked Data, Co-located with ISWC 2016, Kobe, Japan, October 17, 2016. 2016.
  5. Ivanova, V.; Kauppinen, T.; Lohmann, S.; Mazumdar, S.; Pesquita, C.; Xu, K.. Introduction to VISUAL 2014 - workshop on visualizations and user interfaces for knowledge engineering and linked data analytics. 2015.
    10.1007/978-3-319-17966-7_8 • Editor
  6. Pesquita, Cátia. VOILA 2015 Visualizations and User Interfaces for Ontologies and Linked Data: Proceedings of the International Workshop on Visualizations and User Interfaces for Ontologies and Linked Data. 2015.
Journal article
  1. Rita T. Sousa; Sara Silva; Catia Pesquita. "Explaining protein–protein interactions with knowledge graph-based semantic similarity". Computers in Biology and Medicine (2024): https://doi.org/10.1016/j.compbiomed.2024.108076.
    10.1016/j.compbiomed.2024.108076
  2. Nunes, Susana; Sousa, Rita T.; Pesquita, Cátia. "Multi-domain knowledge graph embeddings for gene-disease association prediction". Journal of Biomedical Semantics 14 1 (2023): http://dx.doi.org/10.1186/s13326-023-00291-x.
    10.1186/s13326-023-00291-x
  3. Faria, Daniel; Santos, Emanuel; Balasubramani, Booma Sowkarthiga; Silva, Marta C.; Couto, Francisco M.; Pesquita, Cátia. Corresponding author: Pesquita, Cátia. "AgreementMakerLight". Semantic Web (2023): 1-13. http://dx.doi.org/10.3233/sw-233304.
    10.3233/sw-233304
  4. Georges Bedran; Hans-Christof Gasser; Kenneth Weke; Tongjie Wang; Dominika Bedran; Alexander Laird; Christophe Battail; et al. "The Immunopeptidome from a Genomic Perspective: Establishing the Noncanonical Landscape of MHC Class I–Associated Peptides". Cancer Immunology Research (2023): https://doi.org/10.1158/2326-6066.CIR-22-0621.
    10.1158/2326-6066.CIR-22-0621
  5. Kallor, Ashwin Adrian; Waleron, Michal; Bedran, Georges; Eugénio, Patrícia; Pesquita, Catia; Pesquita, Cátia; Zanzotto, Fabio Massimo; et al. "Abstract 6577: CARMEN: A pan-HLA and pan-cancer proteogenomic database on antigen presentation to support cancer immunotherapy". Cancer Research 83 7_Suppleme (2023): 6577-6577. http://dx.doi.org/10.1158/1538-7445.am2023-6577.
    10.1158/1538-7445.am2023-6577
  6. Jiaoyan Chen; Hang Dong; Janna Hastings; Jiménez-Ruiz, Ernesto; Vanessa López; Pierre Monnin; Pesquita, Cátia; Petr Škoda; Valentina Tamma. "Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities". Transactions on Graph Data and Knowledge (2023): https://drops.dagstuhl.de/entities/document/10.4230/TGDK.1.1.5.
    10.4230/TGDK.1.1.5
  7. Marta Contreiras Silva; Eugénio, Patrícia; Daniel Faria; Catia Pesquita. "Ontologies in oncology: a review of semantic technology applications in cancer research". Cancers MDPI (2022):
    Accepted
  8. Rita Torres Sousa; Sara Silva; Catia Pesquita. "Explainable Semantic Similarity for Biomedical Supervised Learning". Knowledge Based Systems (2022):
    Submitted
  9. Sousa, Rita T.; Silva, Sara; Pesquita, Catia. "Evolving knowledge graph similarity for supervised learning in complex biomedical domains". BMC Bioinformatics 21 1 (2020): http://dx.doi.org/10.1186/s12859-019-3296-1.
    10.1186/s12859-019-3296-1
  10. Pesquita, Cátia. "A Collection of Benchmark data sets for Knowledge Graph-based Similarity in the Biomedical Domain". Database 2020 (2020):
    https://doi.org/10.1093/database/baaa078
  11. Pesquita, Cátia. "Crowd-assessing quality in uncertain data linking datasets". The Knowledge Engineering Review 35 (2020): e33-e33.
    https://doi.org/10.1017/S0269888920000363
  12. Pesquita, Cátia. "Towards evaluating complex ontology alignments". The Knowledge Engineering Review 35 (2020):
    https://doi.org/10.1017/S0269888920000168
  13. Ivanova, Valentina; Lambrix, Patrick; Lohmann, Steffen; Pesquita, Catia. "Visualization and interaction for ontologies and linked data—Editorial". Journal of Web Semantics 55 (2019): 145-149. http://dx.doi.org/10.1016/j.websem.2018.10.001.
    10.1016/j.websem.2018.10.001
  14. Li, Huanyu; Dragisic, Zlatan; Faria, Daniel; Ivanova, Valentina; Jiménez-Ruiz, Ernesto; Lambrix, Patrick; Pesquita, Catia. "User validation in ontology alignment: functional assessment and impact". The Knowledge Engineering Review 34 (2019): http://dx.doi.org/10.1017/s0269888919000080.
    10.1017/s0269888919000080
  15. Pesquita, Cátia. "User validation in ontology alignment: functional assessment and impact". The Knowledge Engineering Review 34 (2019):
    https://doi.org/10.1017/S0269888919000080
  16. Faria, D.; Pesquita, C.; Mott, I.; Martins, C.; Couto, F.M.; Cruz, I.F.. "Tackling the challenges of matching biomedical ontologies". Journal of Biomedical Semantics 9 1 (2018): http://www.scopus.com/inward/record.url?eid=2-s2.0-85040717454&partnerID=MN8TOARS.
    10.1186/s13326-017-0170-9
  17. Oliveira, D.; Pesquita, C.. "Improving the interoperability of biomedical ontologies with compound alignments". Journal of Biomedical Semantics 9 1 (2018): http://www.scopus.com/inward/record.url?eid=2-s2.0-85040355501&partnerID=MN8TOARS.
    10.1186/s13326-017-0171-8
  18. Pesquita, Cátia; Pesquita, Catia; McCurdy, Helena B.; Oliveira, Daniela; Cheatham, Michelle. "The properties of property alignment on the semantic web.". IJMSO 13 1 (2018): 42-56. http://dx.doi.org/10.1504/ijmso.2018.10017850.
    10.1504/IJMSO.2018.10017850
  19. Gaspar, D.; Trindade, C.; Usié, A.; Meireles, B.; Barbosa, P.; Fortes, A.M.; Pesquita, C.; Costa, R.L.; Ramos, A.M.. "Expression profiling in Pinus pinaster in response to infection with the pine wood nematode Bursaphelenchus xylophilus". Forests 8 8 (2017): http://www.scopus.com/inward/record.url?eid=2-s2.0-85027470017&partnerID=MN8TOARS.
    10.3390/f8080279
  20. Cheatham, M.; Cruz, I.; Euzenat, J.; Pesquita, C.; Cheatham, Michelle; Cruz, Isabel; Euzenat, Jérôme; Pesquita, Catia. "Special issue on ontology and linked data matching". Semantic Web 8 2 (2017): 183-184. http://www.scopus.com/inward/record.url?eid=2-s2.0-85004011297&partnerID=MN8TOARS.
    10.3233/SW-160251
  21. Santos, E.; Faria, D.; Pesquita, C.; Couto, F.M.. "Ontology alignment repair through modularization and confidence-based heuristics". PLoS ONE 10 12 (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84957588757&partnerID=MN8TOARS.
    10.1371/journal.pone.0144807
  22. Serrazina, S.; Santos, C.; Machado, H.; Pesquita, C.; Vicentini, R.; Pais, M.S.; Sebastiana, M.; Costa, R.. "Castanea root transcriptome in response to Phytophthora cinnamomi challenge". Tree Genetics and Genomes 11 1 (2015): 1-19. http://www.scopus.com/inward/record.url?eid=2-s2.0-84921420915&partnerID=MN8TOARS.
    10.1007/s11295-014-0829-7
  23. Pesquita, C.; Ferreira, J.D.; Couto, F.M.; Silva, M.J.. "The epidemiology ontology: An ontology for the semantic annotation of epidemiological resources". Journal of Biomedical Semantics 5 1 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84926282839&partnerID=MN8TOARS.
    10.1186/2041-1480-5-4
  24. Faria, D.; Pesquita, C.; Santos, E.; Cruz, I.F.; Couto, F.M.. "Automatic background knowledge selection for matching biomedical ontologies". PLoS ONE 9 11 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84915758310&partnerID=MN8TOARS.
    10.1371/journal.pone.0111226
  25. Faria, D.; Schlicker, A.; Pesquita, C.; Bastos, H.; FerreiraAntó, A.E.N.; Albrecht, M.; Falcão, A.O.. "Mining GO annotations for improving annotation consistency". PLoS ONE 7 7 (2012): http://www.scopus.com/inward/record.url?eid=2-s2.0-84864674779&partnerID=MN8TOARS.
    10.1371/journal.pone.0040519
  26. Pesquita, C.; Couto, F.M.. "Predicting the Extension of Biomedical Ontologies". PLoS Computational Biology 8 9 (2012): http://www.scopus.com/inward/record.url?eid=2-s2.0-84866932669&partnerID=MN8TOARS.
    10.1371/journal.pcbi.1002630
  27. Grego, Tiago; Pesquita, Catia; Bastos, Hugo P.; Couto, Francisco M.. "Chemical Entity Recognition and Resolution to ChEBI". ISRN Bioinformatics 2012 (2012): 1-9. http://dx.doi.org/10.5402/2012/619427.
    10.5402/2012/619427
  28. Gomes-Alves, P.; Couto, F.; Pesquita, C.; Coelho, A.V.; Penque, D.. "Rescue of F508del-CFTR by RXR motif inactivation triggers proteome modulation associated with the unfolded protein response". Biochimica et Biophysica Acta - Proteins and Proteomics 1804 4 (2010): 856-865. http://www.scopus.com/inward/record.url?eid=2-s2.0-76849090407&partnerID=MN8TOARS.
    10.1016/j.bbapap.2009.12.013
  29. Pesquita, Catia; Faria, Daniel; Falcão, André O.; Lord, Phillip; Couto, Francisco M.. "Semantic Similarity in Biomedical Ontologies". PLoS Computational Biology 5 7 (2009): e1000443. http://dx.doi.org/10.1371/journal.pcbi.1000443.
    10.1371/journal.pcbi.1000443
  30. Taylor, Ian W; Linding, Rune; Warde-Farley, David; Liu, Yongmei; Pesquita, Catia; Faria, Daniel; Bull, Shelley; et al. "Dynamic modularity in protein interaction networks predicts breast cancer outcome". Nature Biotechnology 27 2 (2009): 199-204. http://dx.doi.org/10.1038/nbt.1522.
    10.1038/nbt.1522
  31. Couto, F.M.; Pesquita, C.; Grego, T.; Veríssimo, P.. "Handling self-citations using Google Scholar". Cybermetrics 13 1 (2009): http://www.scopus.com/inward/record.url?eid=2-s2.0-67650320533&partnerID=MN8TOARS.
  32. Pesquita, C.; Faria, D.; Bastos, H.; Ferreira, A.E.N.; Falcão, A.O.; Couto, F.M.. "Metrics for GO based protein semantic similarity: A systematic evaluation". BMC Bioinformatics 9 SUPPL. 5 (2008): http://www.scopus.com/inward/record.url?eid=2-s2.0-47149083877&partnerID=MN8TOARS.
    10.1186/1471-2105-9-S5-S4
Journal issue
  1. Ivanova, Valentina; Lambrix, Patrick; Lohmann, Steffen; Pesquita, Catia. "Special issue on Visualization and Interaction for Ontologies and Linked Data". Journal of Web Semantics (2018):
    10.1016/j.websem.2018.10.001
Newspaper article
  1. Pesquita, Cátia. "Precisamos de mais mulheres nas tecnologias de informação", Público, 2015, http://www.publico.pt/tecnologia/noticia/precisamos-de-mais-mulheres-nas-tecnologias-de-informacao-1693251.
Preprint
  1. Rita T. Sousa; Sara Silva; Catia Pesquita. "Supervised Semantic Similarity". 2021. https://doi.org/10.1101/2021.02.16.431402.
    10.1101/2021.02.16.431402

Other

Dataset
  1. Benchmark data sets for knowledge graph-based similarity in the biomedical domain. https://github.com/liseda-lab/kgsim-benchmark.
  2. Pesquita, Cátia; Faria, Daniel; Marta Contreiras Silva; Laura Balbi; Patrícia Eugénio. ImPO: Immunopeptidomics Ontology. 2023.
    10.5281/zenodo.8048222
Other output
  1. AgreementMakerLight - Ontology and Knowledge Graph Alignment Tool. Citations to associated publications: >700 AML is an open-source ontology matching system, currently one of the top ontology and knowledge graph matching systems consistently placing in the top tier of all tracks at the Ontology Alignment Evaluation Initiative (http://oaei.ontologymatching.org/). It has been used by NASA, Jansen Pharmaceuticals and FAO (United Nations) among others.. 2022. Pesquita, Cátia; Faria, Daniel. https://github.com/AgreementMakerLight.
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2024 INIVTED TALK: The impact of negative knowledge in biomedical artificial intelligence Knowledge Graphs Interest Group
The Alan Turing Institute (United Kingdom)
2023 INVITED KEYNOTE: “True or False? The impact of negative knowledge in biomedical artificial intelligence” International Conference on Conceptual Modeling (CORE A)
2022 INVITED TALK: More is better: how integrating multiple biomedical ontologies can unlock artificial intelligence applications International Society for Computational Biology Academy
2022 INVITED TALK: Explaining AI biomedical applications with Knowledge Graphs
Aston University (United Kingdom)
2022 INVITED SEMINAR: Holistic Knowledge Graphs for AI in biomedicine
City University of London (United Kingdom)
2022 INVITED SEMINAR: Biomedical Semantic Similarity for Humans and Machines
Harvard Medical School Center for Computational Biomedicine (CCB) (United States)
2022 INVITED TALK: Unlocking biomedical artificial intelligence with multiple integrated ontologies
Universidade do Minho (Portugal)
2022 INVITED KEYNOTE: Powering Biomedical Artificial Intelligence with a Holistic Knowledge Graph 5th Workshop on Semantic Web solutions for large-scale biomedical data analytics
Extended Semantic Web Conference (Greece)
2021 INVITED TALK: Pandemics have no borders: Why Open Data is essential for pandemic preparedness 2nd Lisbon Living+ Conference
2021 Building a Knowledge Graph for Explainable AI in Healthcare U. Mannheim, Germany
2021 Explainable Artificial Intelligence in Personalised Oncology RedeSaude Oncology
2021 INVITED TALK: Artificial Intelligence and Personalized Medicine in Uro-Oncology New Frontiers in Uro-Oncology
2018 Invited Keynote: Matching Biomedical Ontologies for Semantic Data Integration. Data Integration in the Life Sciences (DILS2018) Conference in Hannover, Germany, November 2018.
2018 A framework to conduct and report on empirical user studies in semantic web contexts EKAW - International Conference on Knowledge Engineering and Knowledge Management
2018 Keynote: Conducting and Reporting on Empirical User Studies in Semantic Web Contexts International workshop on Visualization and Interaction for Ontologies and Linked Data
2017 Invited Keynote: Sense and similarity: making sense of similarity for ontologies. Bio-Ontologies COSI (ISMB/ECCB 2017) in Prague, Czech Republic, July 2017
2013 What’s in a ‘nym’? Synonyms in Biomedical Ontology Matching International Semantic Web Conference
(Sydney, Australia)
2013 To repair or not to repair: reconciling correctness and coherence in ontology reference alignments Ontology Matching Workshop (co-located with ISWC)
(Sydney, Australia)
2011 Where GO is going and what it means for ontology extension International Conference in Biomedical Ontology
(Buffalo, United States)
2007 Evaluating GO-based semantic similarity measures Bio-Ontologies Meeting at Intelligent Systems in Molecular Biology Conference
(Vienna, Austria)

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2023 - Current Machine learning-based viral design for bioengineering
Supervisor
Universidade de Lisboa Faculdade de Ciências, Portugal
2023 - Current Exploring neuro-symbolic methods to boost graph neural networks with knowledge
Supervisor
2023 - Current Learning with uncertainty: improving supervised learning of protein-protein interactions with lower quality examples
Supervisor
2023 - Current Deep learning to optimize lentiviral vector production for human gene therapy
Supervisor
 Engenharia Informática (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2023 - Current Link Prediction for Gene-Disease Association
Supervisor
 Ciência de Dados (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2022/11/01 - Current Learning and Explaining Knowledge Graph Alignment
Supervisor
 Informática (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2022 - Current Time and Knowledge-aware Clinical Graph Data Mining
Supervisor
 Informática (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2022 - Current Combining network biology and artificial intelligence to improve cancer drugs synergy predictions
Co-supervisor
Universidade de Coimbra Faculdade de Ciencias e Tecnologia, Portugal
2022 - Current Explaining Knowledge Graph-based Machine Learning
Supervisor
 Ciência de Dados (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2022 - Current Knowledge Graph Alignment with Implicit and Explicit Semantics
Supervisor
 Engenharia Informática (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2021 - Current Distributed Knowledge Graphs for Biomedical Explainable Artificial Intelligence
Supervisor
 Informática (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2021 - Current Knowledge Graph-based Explanations for Biomedical Artificial Intelligence
Supervisor
 Informática (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2021 - Current Explainable AI for understanding associations between disease-related genes
Supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2020 - Current Automatic animal recognition in wildlife conservation programmes with Deep Convolutional Neural Networks
Supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2020 - Current Follow the (scientific) leader: the impact of crisis ontrust in scientific authorities
Co-supervisor
 Ciência de Dados (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2019 - Current Evolving meaning for supervised learning in complex biomedical domains using knowledge graphs
Supervisor of Rita Sousa
 Doutoramento em Informática (PhD)
2021 - 2023 Explaining clinical artificial intelligence predictions with Knowledge Graph visualization
Supervisor
 Ciência de Dados (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2021 - 2023 Combining Deep Learning and Knowledge Graphs in protein-protiein interaction network prediction tasks
Supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2021 - 2023 Semantic data integration for explainable artificial intelligence in personalized medicine
Supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2020 - 2022 Linking patient data to scientific knowledge to support contextualized mining
Supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2020 - 2021 Breaking rules: taking Complex Ontology Alignment beyond rule-based approaches
Co-supervisor
 Ciência de Dados (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2020 - 2021 Helping scientists integrate and interact with biomedical data
Supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2020 - 2021 Prediction of Gene-Disease Associations through Knowledge Graph Mining
Supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2020 - 2021 Semantic annotation of clinical questionnaires to support personalized medicine
Supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2020 - 2021 To be or not to be: impact of negative annotations in the comparison of ALS patients
Supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2019 - 2021 Building a Portal for the Scientific Collections at the University of Lisbon
Supervisor of Pedro Ladino
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2019 - 2020 A Benchmark for Biomedical Knowledge Graph based Similarity
Supervisor of Carlota Cardoso
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2019 - 2020 Matching Biomedical Knowledge Graphs with Neural Embeddings
Supervisor of Rodrigo Neves
 Ciência de Dados (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2019 - 2020 Internal Hacking Detection using Machine Learning (project conducted at Altice Portugal)
Supervisor of Madalena Guerra
 Ciência de Dados
Universidade de Lisboa Faculdade de Ciências, Portugal
2018 - 2019 Understanding ALS Patients using Semantic Similarity
Supervisor of David C. Teixeira
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2018 - 2019 Evolving meaning: using Genetic Programming to learn similarity perspectives for mining biomedical data
Supervisor of Rita Sousa
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2017 - 2019 Complex matching for multiple ontologies
Supervisor of Madalena Pavão
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2016 - 2017 Alternative splicing detection across different tissues in cork oak
Co-supervisor of Pedro Barros
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2016 - 2017 Investigating Semantic Similarity for Biomedical Ontology Alignment
Supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2016 - 2017 SWDM: Data Mining with Semantic Web
Supervisor of João Rebelo
 Engenharia Informática (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2015 - 2016 Optimizing 16S Sequencing Analysis Pipelines
Supervisor of Samuel Viana
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2015 - 2016 SESAME: Clustering with semantic similarity based on multiple ontologies
Supervisor
 Engenharia Informática (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2015 - 2016 Transcriptomic analysis of maritime pine response to infection with Bursaphelenchus xylophilus, the causing agent of pine wilt disease
Co-supervisor of Daniel Gaspar
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2015 - 2016 Extracção de Informação de Registos Electrónicos de Saúde
Supervisor of Fábio Guilherme
 Engenharia Informática (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2014 - 2016 Ontology-driven Analysis of Enterprise Architecture Models
Co-supervisor of Marzieh Bakhshandeh
 Doutoramento (PhD)
Universidade de Lisboa, Portugal
2014 - 2015 Análise por prospecção de dados de registos electrónicos de saúde de pacientes com cancro do pulmão
Supervisor of Ana Cristina Silva
 Gestão de Informação
Universidade de Lisboa Faculdade de Ciências, Portugal
2014 - 2015 Visualization for Biomedical Ontologies Alignment
Supervisor of Catarina Martins
 Bioinformática (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2014 - 2015 Compound Matching of Biomedical Ontologies
Supervisor of Daniela Oliveira
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2013 - 2015 Validation of candidate genes for resistance to Phytophthora cinnamomi in progenies of controlled crosses between Castanea sativa and Castanea crenata
Co-supervisor of Ana Sofia Duarte
 Biologia Molecular e Genética (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2013 - 2014 Desenvolvimento de Soluções Mobile para o Banco de Portugal
Supervisor
 Engenharia Informática (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2013 - 2014 Ensino da Usabilidade e Prototipagem e da Aplicação no desenho de um Museu Virtual
Co-supervisor of Anabela Rolo-Abrantes
 Ensino de Informática (Master)
Universidade de Lisboa Instituto da Educação, Portugal

Event organisation

Event name
Type of event (Role) 		Institution / Organization
2022 - Current Program Chair of the Extended Semantic Web Conference (CORE A) (2022)
2015 - Current Girls in ICT @ Ciências.ULisboa. Evento para promover as tecnologias da informação junto das raparigas e jovens mulheres. (2015, 2016, 2017, 2018, 2019) (2015)
Meeting (Co-organisor)
 Universidade de Lisboa Faculdade de Ciências, Portugal
2023 - 2023 General Chair of Extended Semantic Web Conference 2023 (CORE A) (2023 - 2023)
Conference (President of the Organising Committee)
2016 - 2023 International Workshop on Visualization and Interaction for Ontologies and Linked Data, co-located with ISWC (VOILA 2016, 2017, 2018, 2020, 2021, 2022, 2023) (2016/10)
Workshop (Co-organisor)
2022 - 2022 Semantic Web Challenge Track Chair at International Semantic Web Conference 2022 (CORE A) (2022 - 2022)
2020 - 2021 Program Chair for HEALTHINF 14th International Conference on Health Informatics (2021) (2020)
Conference (President of the Organising Committee)
2020 - 2021 Track Chair for Matching, Integration and Fusion at the Extended Semantic Web Conference (2021 - 2021)
Conference (Member of the Organising Committee)
2020 - 2021 Poster and Demos Track Chair at the International Semantic Web Conference (CORE A) (2021 - 2021)
Conference (Member of the Organising Committee)
2019 - 2019 Tutorial: Ontology Matching in the Biomedical Domain – Challenges, Solutions and Applications (Semantic Web Applications and Tools for Healthcare and Life Sciences Conference) (2019)
Workshop (Co-organisor)
2019 - 2019 "Oportunidades e desafios na gestão de precisão e prevenção inteligente das doenças infecciosas" com divulgação e demonstração em tempo real da plataforma RESISTIR junto do público alvo na área (especialistas e decisores). (2019 - 2019)
Meeting (Co-organisor)
 Universidade de Lisboa Faculdade de Ciências, Portugal
2015 - 2015 International Conference on Biomedical Ontology (2015)
Conference (Member of the Organising Committee)

Event participation

Activity description
Type of event 		Event name
Institution / Organization
2021 - Current SWSA Panel: "20 years into ISWC: What's next beyond Knowledge Graphs?" (Moderator) A panel with Jim Handler (SWSA president), Natasha Noy (Google) and Rudi Studer (Karlsruhe Institute of Technology ) https://www.youtube.com/watch?v=ns7qIrNCpNo&ab_channel=COSTDKG SWSA Panel: "20 years into ISWC: What's next beyond Knowledge Graphs?"
2022/01/16 - 2022/01/21 Dagstuhl seminar: Bringing Graph Databases and Network Visualization Together
Seminar
 Dagstuhl seminar: Bringing Graph Databases and Network Visualization Together
Schloss Dagstuhl Leibniz-Zentrum für Informatik GmbH, Germany
2019 - 2019 Integração de informação clínica, demográfica, científica e meteorológica para o controlo inteligente de doenças infeciosas (Case study Projeto RESISTIR)
Conference
 Conferência "Saúde e Inovação Digital"

Jury of academic degree

Topic
Role 		Candidate name (Type of degree)
Institution / Organization
2023 Representing Health Data and Medical Knowledge for Deep Learning
(Thesis) Main arguer
 Emil Riis Hansen (PhD)
Aalborg Universitet, Denmark
2023 Bridging the Knowledge Gap in Multigenic Pathogenicity Predictions
(Thesis) Main arguer
 Alexandre RENAUX (PhD)
Université Libre de Bruxelles, Belgium
2022 Assessing, Creating and Using Knowledge Graph Restrictions
(Thesis) Main arguer
 Sven Lieber (PhD)
Universiteit Gent, Belgium
2022 Machine Learning Models for Predicting Disease-related Biological Interactions
(Thesis) Arguer
 Iván Marcelo Carrera Izurieta (PhD)
Universidade do Porto Faculdade de Ciências, Portugal
2022 Exploiting General-Purpose Background Knowledge for Automated SchemaMatching
(Thesis) Main arguer
 Jan Philipp Portisch (PhD)
Universität Mannheim, Germany
2022 Integration as a solution: A multi-omic approach to cancer diseases
(Thesis) Arguer
 Marcos Yébenes Mayordomo (PhD)
Miedzyuczelniany Wydzial Biotechnologii Uniwersytetu Gdanskiego i Gdanskiego Uniwersytetu Medycznego, Poland
2021 Modelling and interpreting the impact of splicing variants on human health
(Thesis) Arguer
 Pedro Barbosa (Other)
Universidade de Lisboa Faculdade de Ciências, Portugal
2021 User Interaction Patterns for Linked Data
(Thesis) Main arguer
 Mariana Aguiar (Master)
Universidade do Porto, Portugal
2019 Towards Complex Ontology Alignment (Phd Dissertation Committee; supervisor: Pascal Hitzler)
(Thesis) Main arguer
 Lu Zhou (Other)
Wright State University, United States
2019 Computational approaches to virtual screening in human central nervous system therapeutic targets
(Thesis) Arguer
 Samina Kausar (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2019 Gestão Automática de Dadores, Transfusões e Banco de Sangue
(Thesis) Main arguer
 Ana Raquel Alqueidão (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2017 Combining metric and vector space data mining methods for screening CFTR rescuers in cystic fybrosis
(Thesis) Main arguer
 Inês Ferreira (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2016 Deep Generative Semantic Grounding (Proposta de Tese)
(Thesis) Arguer
 Davide Nunes (Other)
Universidade de Lisboa Faculdade de Ciências, Portugal
2016 SPARQL Query FORMULATION AND Execution through Visual Interface (supervisor: Dietrich Rebholz-Schuhmann, director of Insight Centre)
(Thesis) Main arguer
 Syeda Sana E Zainab (Master)
National University of Ireland, Ireland
2016 Cross-Lingual Mapping of Lexical Ontologies with Automatic Translation (supervisor: Matteo Palmonari)
(Thesis) Arguer
 Mamoun Abu Helou (PhD)
Università degli Studi di Milano-Bicocca, Italy
2015 Open-source intelligence em sistemas SIEM.
(Thesis) Main arguer
 Bernardo Rodrigues. (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2015 Adapting State-of-the-Art Named Entity Recognition and Disambiguation Frameworks for Handling Clinical Text
(Thesis) Main arguer
 Rodrigo Rodrigues (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2014 Towards an Intelligente biographical Cognitive Prosthesis.
(Thesis) Main arguer
 José Carilho (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2013 Avatares em Língua Gestual Portuguesa
(Thesis) Main arguer
 José Bento (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2013 Avaliação do Desempenho em contexto organizacional utilizando o método Balanced Scorecard.
(Thesis) Main arguer
 Marco Barros (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2013 Aplicação Web Inovadora para a Saúde.
(Thesis) Main arguer
 Bruno Ferreira (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal

Committee member

Activity description
Role 		Institution / Organization
2019 - Current Associate Editor: BMC Bioinformatics
2019 - Current Comissão de Ética para Recolha e Proteção de Dados de Ciências
Member
 Universidade de Lisboa Faculdade de Ciências, Portugal
2019 - Current Leader of the LASIGE Research Line of Excellence in Health and Biomedical Informatics Universidade de Lisboa Laboratório de Sistemas Informáticos de Grande Escala, Portugal
2016 - Current Editorial board: Journal of Privacy and Health Information Management
2015 - Current Steering Committee of the International Conference in Biomedical Ontology
Member
2019 - 2022 Comissão Científica do Doutoramento em Informática
Member
 Universidade de Lisboa Faculdade de Ciências, Portugal

Conference scientific committee

Conference name Conference host
2022 - Current TheWebConf
2018 - 2023 Extended Semantic Web Conference
2016 - 2023 International Semantic Web Conference
2015 - 2023 AAAI CONFERENCE ON ARTIFICIAL INTELLIGENCE (2015-2020)
2020 - 2022 15TH INTERNATIONAL WORKSHOP ON NEURAL-SYMBOLIC LEARNING AND REASONING
2019 - 2022 SEMANTICS
2018 - 2020 ISMB Intelligent Systems in Molecular Biology (Bio-ontologies COSI) 2018,2020
2018 - 2019 Intelligent Systems for Molecular Biology

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2021 - Current Integração e Processamento Analítico de Informação (regente 2020/2021)
2019 - Current Bioinformática (regente 2018/2019, 2019/2020, 2020/2021) (Mestrado) Universidade de Lisboa Faculdade de Ciências, Portugal
2018 - Current Concepção de Produto (regente 2018/2019, 2019/2020) Tecnologias de Informação (Licenciatura) Universidade de Lisboa Faculdade de Ciências, Portugal
2015 - Current Grandes Dados (regente) 2015/2016, 2017/2018, 2018/2019, 2019/2020) Informática (Doutoramento) Universidade de Lisboa Faculdade de Ciências, Portugal
2015 - Current Tecnologia de Bases de Dados (regente 2015/2016, 2017/2018, 2018/2019, 2019/2020, 2020/2021) (Mestrado) Universidade de Lisboa Faculdade de Ciências, Portugal
2013 - Current Análise e Design de Sistemas de Informação (regente: 2013/2014, 2014/2015, 2018/2019, 2019/2020) Engenharia Informática (Licenciatura) Universidade de Lisboa Faculdade de Ciências, Portugal
2012 - Current Bioinformática (2012/2013, 2013/2014, 2014/2015, 2015/2016) Ciências da Saúde (Licenciatura) Universidade de Lisboa Faculdade de Medicina, Portugal
2018 - 2019 Prospecção de Dados (Mestrado) Universidade de Lisboa Faculdade de Ciências, Portugal
2018 - 2019 Seminário em Ciência de Dados (regente 2018/2019) Ciência de Dados (Mestrado integrado) Universidade de Lisboa Faculdade de Ciências, Portugal
2017 - 2018 Introdução às Tecnologias Web (regente: 2017/2018) Tecnologias de Informação (Licenciatura) Universidade de Lisboa Faculdade de Ciências, Portugal
2012 - 2018 Análise e Design de Sistemas de Informação (2012/2013, 2017/2018) Engenharia Informática (Licenciatura) Universidade de Lisboa Faculdade de Ciências, Portugal
2012 - 2018 Concepção de Produto (2012/2013, 2013/2014, 2014/2015, 2015/2016, 2017/2018) Tecnologias de Informação (Licenciatura) Universidade de Lisboa Faculdade de Ciências, Portugal
2015 - 2016 Bases de Dados (2015/2016) Tecnologias de Informação (Licenciatura) Universidade de Lisboa Faculdade de Ciências, Portugal
2014 - 2016 Introdução às Tecnologias Web (2014/2015, 2015/2016) Tecnologias de Informação (Licenciatura) Universidade de Lisboa Faculdade de Ciências, Portugal
2014 - 2015 Projecto em Sistemas de Informação (2014/2015) Engenharia Informática (Licenciatura) Universidade de Lisboa Faculdade de Ciências, Portugal
2013 - 2014 Interação com Computadores (2013/2014) Tecnologias de Informação (Licenciatura) Universidade de Lisboa Faculdade de Ciências, Portugal
2009 - 2011 Bioinformática (monitora 2009/2010, 2010/2011) (Mestrado) Universidade de Lisboa Faculdade de Ciências, Portugal
2007 - 2008 Tecnologias de Informação e Comunicação (monitora) (Licenciatura) Universidade de Lisboa Faculdade de Ciências, Portugal

Interview (newspaper / magazine)

Activity description Newspaper / Forum
2023 O que falta à IA para ser útil à Ciência? Exame Informática

Interview (tv / radio show)

Program Topic
2023 - Current Entrevista na TSF Notícias Artificial Intelligence
2023 - Current 90 segundos com Ciência Inteligência Artificial na Medicina Personalizada
2018 - Current Geração Digital Girls in ICT na FCUL: promover as tecnologias da informação junto das jovens

Journal scientific committee

Journal title (ISSN) Publisher
2018 - 2023 Journal of Web Semantics
2018 - 2023 Semantic Web (2210-4968) IOS Press
2015 - 2020 Nucleic Acids Research (1362-4962) Oxford University Press
2011 - 2020 BMC Bioinformatics (1471-2105) Springer (Biomed Central Ltd.)
2015 - 2019 Bioinformatics (1460-2059) Oxford University Press
2014 - 2019 Journal of Biomedical Semantics (2041-1480) Springer (Biomed Central Ltd.)
2009 - 2009 Briefings in Bioinformatics (1477-4054) Oxford University Press
Distinctions

Award

2022 Best Paper Award
2021 Best Poster Award - Extended Semantic Web Conference
2020 Best Poster Award - Extended Semantic Web Conference
2019 Best Outreach Initiative Award (runner-up)
Universidade de Lisboa Laboratório de Sistemas Informáticos de Grande Escala, Portugal
2017 IBM Research Instance Matching Prize
IBM Research, United States
2016 Pistoia Alliance Ontology Matching Prize
2015 Best Sudent Paper Award (as supervisor)
International Conference on Biomedical Ontology, United States

Title

2022 AI 2000 Most Influential Scholar Award Honorable Mention (#16 in Knowledge Engineering - world wide)
2021 AI 2000 Most Influential Scholar Award Honorable Mention (#37 in Knowledge Engineering - world wide)
2020 AI 2000 Most Influential Scholar Award Honorable Mention (#54 in Knowledge Engineering - world wide)
AMiner , China

Other distinction

2023 Top 2% Scientist in Artificial Intelligence and Bioinformatics 2022 (Stanford Study)
2022 H-INNOVA Projects Awards (Top 5) - Innovation in Healthcare Technology
2022 Top 2% Scientist in Artificial Intelligence 2021 (Stanford Study)
2022 Ontology Alignment Evaluation Initiative top performing system
2021 Top 2% Scientist in Artificial Intelligence 2020 (Stanford Study)
2021 Ontology Alignment Evaluation Initiative top performing system
2020 Ontology Alignment Evaluation Initiative top performing system
2019 Ontology Alignment Evaluation Initiative top performing system
2018 Ontology Alignment Evaluation Initiative top performing system
2017 Ontology Alignment Evaluation Initiative top performing system
2016 Ontology Alignment Evaluation Initiative top performing system
2015 Ontology Alignment Evaluation Initiative top performing system
2014 Ontology Alignment Evaluation Initiative top performing system
2013 FLAD/NSF award: "Portugal - EUA: Parcerias e Redes para Investigação 2013"
2013 Ontology Alignment Evaluation Initiative top performing system