Member

Acronym	Title	Funding Entity	Start Date	End Date
HfPT	Health from Portugal	PRR- Portuguese Resilience and Recovery Plan	01/02/2023	31/12/2025
DKG	Distributed Knowledge Graphs	COST ACTION	23/09/2020	22/09/2024

PAST

Acronym	Title	Funding Entity	Start Date	End Date
MarCODE	Development and Application of Biochemical Tools for Seafood Products Traceability	MAR2020 Other	01/07/2020	30/06/2023
CAMELOT	Autonomic platform for Machine Learning using anonymized data	P2020	01/07/2020	01/01/2023
GADgET	Online Gambling Addiction Detection	FCT	10/01/2019	09/07/2022
SMiLax	Semantic Mining with Linked Data	FCT	01/07/2016	31/12/2020
MIMED	Mining the Molecular Metric Space for Drug Design	FCT	01/06/2016	30/11/2019
RESISTIR	Sistema de Informação para controlo de infecção inteligente e antibioterapia personalizada	P2020	01/04/2016	01/04/2019
SOMER	SOMER - Semantic Ontology Matching using External Resources	FCT	19/03/2012	31/10/2014

Rita T. Sousa, Sara Silva, Catia Pesquita. Explainable Representations for Relation Prediction in Knowledge Graphs. In Proceedings of the Twentieth International Conference on Principles of Knowledge Representation and Reasoning. International Joint Conferences on Artificial Intelligence Organization, 2023 [Biblios]

Susana Nunes, Rita T. Sousa, Catia Pesquita. Multi-domain knowledge graph embeddings for gene-disease association prediction. Journal of Biomedical Semantics, 14(1), Springer Science and Business Media LLC, 2023 [Biblios]

Daniel Faria, Emanuel Santos, Booma Sowkarthiga Balasubramani, Marta C. Silva, Francisco M. Couto, Catia Pesquita. AgreementMakerLight. Semantic Web, 1-13, IOS Press, 2023 [Biblios]

Georges Bedran, Hans-Christof Gasser, Kenneth Weke, Tongjie Wang, Dominika Bedran, Alexander Laird, Christophe Battail, Fabio Massimo Zanzotto, Catia Pesquita, Håkan Axelson, Ajitha Rajan, David J. Harrison, Aleksander Palkowski, Maciej Pawlik, Maciej Parys, J. Robert O'Neill, Paul M. Brennan, Stefan N. Symeonides, David R. Goodlett, Kevin Litchfield, Robin Fahraeus, Ted R. Hupp, Sachin Kote, Javier A. Alfaro. The Immunopeptidome from a Genomic Perspective: Establishing the Noncanonical Landscape of MHC Class I–Associated Peptides. Cancer Immunology Research, 11(6):747-762, American Association for Cancer Research (AACR), 2023 [Biblios]

Ricardo M. S. Carvalho, Daniela Oliveira, Catia Pesquita. Knowledge Graph Embeddings for ICU readmission prediction. BMC Medical Informatics and Decision Making, 23(1), Springer Science and Business Media LLC, 2023 [Biblios]

Rodrigues, Hugo Miguel Costa, Barros, Pedro, Pesquita, Cátia. Identification of gene regulation modules that act in the interaction between cork development and environmental variables. Master's dissertation, 2023 [Biblios]

Balbi, Laura de Oliveira Lopes Henchman, Pesquita, Cátia Luísa Santana Calisto. Combining deep learning and knowledge graphs in PPI network prediction tasks. Master's dissertation, 2023 [Biblios]

Rita T. Sousa, Sara Silva, Catia Pesquita. Supervised Biomedical Semantic Similarity. IEEE Access, 11, Institute of Electrical and Electronics Engineers (IEEE), 2023 [Biblios]

Rita T. Sousa, Sara Silva, Heiko Paulheim, Catia Pesquita. Biomedical Knowledge Graph Embeddings with Negative Statements. In The Semantic Web – ISWC 2023,Lecture Notes in Computer Science, pages 428-446. Springer Nature Switzerland, 2023 [Biblios]

Gehmayr, Jonathan, Pesquita, Cátia Luísa Santana Calisto. Automatic task discovery : towards full automation of the machine learning lifecycle. Master's dissertation, 2023 [Biblios]

Rita T. Sousa, Sara Silva, Catia Pesquita. Explaining Protein-Protein Interaction Predictions with Genetic Programming. In Evo* 2022 -- Late-Breaking Abstracts Volume, pages 30-33, 2022 [Biblios]

Ruben Branco, Diogo F. Soares, Andreia S. Martins, Eleonora Auletta, Eduardo N. Castanho, Susana Nunes, Filipa Serrano, Rita T. Sousa, Catia Pesquita, Sara C. Madeira, Helena Aidos. Hierarchical Modelling for ALS Prognosis: Predicting the Progression Towards Critical Events. In Intelligent Disease Progression Prediction (iDPP) at CLEF, pages 1211-1227. CEUR-WS.org, 2022 [Biblios]

Susana Nunes, Rita T. Sousa, Filipa Serrano, Ruben Branco, Diogo F. Soares, Andreia S. Martins, Eleonora Auletta, Eduardo N. Castanho, Sara C. Madeira, Helena Aidos, Catia Pesquita. Explaining Artificial Intelligence Predictions of Disease Progression with Semantic Similarity. In Intelligent Disease Progression Prediction (iDPP) at CLEF 2022. CEUR-WS.org, 2022 [Biblios]

Marta Contreiras Silva, Daniel Faria, Catia Pesquita. Extending AgreementMakerLight to Perform Holistic Ontology Matching. In The Semantic Web: ESWC 2022 Satellite Events,Lecture Notes in Computer Science, pages 31-35. Springer International Publishing, 2022 [Biblios]

Marta Contreiras Silva, Daniel Faria, Catia Pesquita. Matching Multiple Ontologies to Build a Knowledge Graph for Personalized Medicine. In The Semantic Web,Lecture Notes in Computer Science, pages 461-477. Springer International Publishing, 2022 [Biblios]

Rita T. Sousa, Sara Silva, Catia Pesquita. The Supervised Semantic Similarity Toolkit, In The Semantic Web: ESWC 2022 Satellite Events,Lecture Notes in Computer Science, pages 42 - 46. Springer International Publishing, 2022 [Biblios]

Almeida, David Campos, Sá, Joana Gonçalves de, Pesquita, Cátia. PandeMedia: an annotated corpus of digital media for issue salience. Master's dissertation, 2022 [Biblios]

Amorim, Sofia Pessoa de, Pesquita, Cátia. Evaluating Pre-trained Word Embeddings in domain specific Ontology Matching. Master's dissertation, 2022 [Biblios]

Carvalho, Ricardo Miguel Serafim de, Pesquita, Cátia, Oliveira, Daniela Patrícia dos Santos. Linking patient data to scientific knowledge to support contextualized mining. Master's dissertation, 2022 [Biblios]

Aveiro, Lina Andreia Gama, Pesquita, Cátia. To be or NOT to be: The Impact of Negative Annotation in Biomedical Semantic Similarity. Master's dissertation, 2022 [Biblios]

Gonçalves, André Miguel da Costa, Pesquita, Cátia Luísa Santana Calisto, Guerreiro, Tiago João Vieira. Semantic annotation of clinical questionnaires to support personalized medicine. Master's dissertation, 2022 [Biblios]

Eugénio, Patrícia Raquel dos Anjos, Pesquita, Cátia Luísa Santana Calisto, Faria, Daniel Pedro de Jesus. The ImmunoPeptidomics Ontology : design and evaluation. Master's dissertation, 2022 [Biblios]

Ana Rita Pereira Guerreiro, Cátia Luisa Santana Calisto Pesquita, Daniel Pedro de Jesus Faria. Helping scientists integrate and interact with biomedical data. Master's dissertation, 2021 [Biblios]

Beatriz Fonseca de Lima, Cátia Luisa Santana Calisto Pesquita, Daniel Pedro de Jesus Faria. Breaking rules: taking Complex Ontology Alignment beyond rulebased approaches. Master's dissertation, 2021 [Biblios]

Susana Nunes, Rita Sousa, Catia Pesquita. Predicting Gene-Disease Associations with Knowledge Graph Embeddings over Multiple Ontologies. In European Conference on Computational Biology, 2021 [Biblios]

Lima, Beatriz Fonseca de, Pesquita, Cátia, Faria, Daniel Pedro de Jesus. Breaking rules: taking Complex Ontology Alignment beyond rulebased approaches. Master's dissertation, 2021 [Biblios]

Nunes, Susana Catarina Plácido, Pesquita, Cátia. Predicting Gene-Disease Associations with Knowledge Graph Embeddings over Multiple Ontologies. Master's dissertation, 2021 [Biblios]

Catia Pesquita, Viatlis Wiens, Patrick Lambrix. Proceedings of the Sixth International Workshop on the Visualization and Interaction for Ontologies and Linked Data co-located with the 20th International Semantic Web Conference (ISWC 2021), International Semantic Web Conference, 2021 [Biblios]

Ana Guerreiro, Catia Pesquita, Daniel Faria. VOWLMap: Graph-based Ontology Alignment Visualization and Editing. In VOILA! 2021 Visualization and Interaction for Ontologies and Linked Data, 2021 [Biblios]

Beatriz Lima, Daniel Faria, Catia Pesquita. Challenges of evaluating complex alignments. In Ontology Matching Workshop co-located wth ISWC, 2021 [Biblios]

Catia Pesquita. Towards Semantic Integration for Explainable Artificial Intelligence in the Biomedical Domain. In Proceedings of the 14th International Joint Conference on Biomedical Engineering Systems and Technologies. SCITEPRESS - Science and Technology Publications, 2021 [Biblios]

Rita T Sousa, Sara Silva, Catia Pesquita. evoKGsim+: a framework for tailoring Knowledge Graph-based similarity for supervised learning. In Extended Semantic Web Conference, 2021 [Biblios]

Rita T. Sousa, Sara Silva, Catia Pesquita. Evolving knowledge graph similarity for supervised learning in complex biomedical domains. BMC Bioinformatics, 21(1), Springer Science and Business Media LLC, 2020 [Biblios]

Carlota Cardoso, Rita T. Sousa, Sebastian Köhler, Catia Pesquita. A Collection of Benchmark data sets for Knowledge Graph-based Similarity in the Biomedical Domain. In Extended Semantic Web Conference, 2020 [Biblios]

Carlota Cardoso, Rita T Sousa, Sebastian Köhler, Catia Pesquita. A Collection of Benchmark Data Sets for Knowledge Graph-based Similarity in the Biomedical Domain. Database, 2020, Oxford University Press (OUP), 2020 [Biblios]

Pedro Miguel Oliveira Ladino, Cátia Pesquita, Maria Cristina Duarte. Building a Portal for Scientific Collections at the University of Lisbon. Master's dissertation, 2020 [Biblios]

Rodrigo David Rodrigues Neves, Cátia Luísa Santana Calisto Pesquita. Matching Biomedical Knowledge Graphs with Neural Embeddings. Master's dissertation, 2020 [Biblios]

Diogo Miguel Soares Pereira, Cátia Pesquita. Solução mobile para serviço de atendimento à distância. Master's dissertation, 2020 [Biblios]

Carlota Maria Alegre Branco Ferreira Cardoso, Cátia Luísa Santana Calisto Pesquita. A Benchmark for Biomedical Knowledge Graph based Similarity. Master's dissertation, 2020 [Biblios]

Madalena da Costa França Ribeiro Guerra, Cátia Luísa Santana Calisto Pesquita. Internal Hacking Detection using Machine Learning. Master's dissertation, 2020 [Biblios]

João D. Ferreira, David C. Teixeira, Catia Pesquita. Biomedical Ontologies: Coverage, Access and Use, In Systems Medicine, pages 382 - 395. Elsevier, 2020 [Biblios]

Lu Zhou, Elodie Thiéblin, Michelle Cheatham, Daniel Faria, Catia Pesquita, Cassia Trojahn, Ond?ej Zamazal. Towards evaluating complex ontology alignments. The Knowledge Engineering Review, 35, Cambridge University Press (CUP), 2020 [Biblios]

Daniel Faria, Alfio Ferrara, Ernesto Jiménez-ruiz, Stefano Montanelli, Catia Pesquita. Crowd-assessing quality in uncertain data linking datasets. The Knowledge Engineering Review, 35, Cambridge University Press (CUP), 2020 [Biblios]

Teixeira, David Carriço, Pesquita, Cátia, Madeira, Sara Alexandra Cordeiro. Understanding ALS patients using semantic similarity. Master's dissertation, 2019 [Biblios]

Maria Madalena Ervedosa de Lacerda Pavão, Pesquita, Cátia. Compound Matching for Multiple Ontologies. Master's dissertation, 2019 [Biblios]

Rita Isabel Torres de Sousa, Pesquita, Cátia, Silva, Sara Guilherme Oliveira da. Evolving meaning: using Genetic Programming to learn similarity perspectives for mining biomedical data. Master's dissertation, 2019 [Biblios]

Huanyu Li, Zlatan Dragisic, Daniel Faria, Valentina Ivanova, Ernesto Jiménez-Ruiz, Patrick Lambrix, Catia Pesquita. User validation in ontology alignment: functional assessment and impact. The Knowledge Engineering Review, 34, Cambridge University Press (CUP), 2019 [Biblios]

Isabela Mott Silva, Cátia Pesquita, João Ferreira. Investigating Semantic Similarity for Biomedical Ontology Alignment. Master's dissertation, 2018 [Biblios]

Daniel Faria, Catia Pesquita, Isabela Mott, Catarina Martins, Francisco M. Couto, Isabel F. Cruz. Tackling the challenges of matching biomedical ontologies. Journal of Biomedical Semantics, 9(1), Springer Nature, 2018 [Biblios]

Daniela Oliveira, Catia Pesquita. Improving the interoperability of biomedical ontologies with compound alignments. Journal of Biomedical Semantics, 9(1), Springer Nature, 2018 [Biblios]

Michelle Cheatham, Catia Pesquita, Daniela Oliveira, Helena B. McCurdy. The properties of property alignment on the semantic web. International Journal of Metadata, Semantics and Ontologies, 13(1), Inderscience Publishers, 2018 [Biblios]

Catia Pesquita, Daniel Faria, Alsayed Algergawy, Michelle Cheatham, Alfio Ferrara, Irina Fundulaki, Ian Harrow, Sven Hertling, Ernesto Jimenez-Ruiz, Naouel Karam, Abderrahman Khiat, Patrick Lambrix, Huanyu Li, Stefano Montanelli, Heiko Paulheim, Tzanina Saveta, Daniela Schmidt, Pavel Shvaiko, Andrea Splendiani, Elodie Thiéblin, Cassia Trojahn, Jana Vatascinova, Ondrej Zamazal, Lu Zhou. Results of the Ontology Alignment Evaluation Initiative 2018. In 13th International Workshop on Ontology Matching, 2018 [Biblios]

Valentina Ivanova, Patrick Lambrix, Steffen Lohmann, Catia Pesquita. Visualization and interaction for ontologies and linked data. Journal of Web Semantics, 55, Elsevier BV, 2018 [Biblios]

Catia Pesquita, Valentina Ivanova, Steffen Lohmann, Patrick Lambrix. A Framework to Conduct and Report on Empirical User Studies in Semantic Web Contexts. In European Knowledge Acquisition Workshop Conference (Lecture Notes in Computer Science,Knowledge Engineering and Knowledge Management), pages 567-583. Springer International Publishing, 2018 [Biblios]

R. Dias, C. Pesquita, J. Rebelo, A. Pedrosa, C. Santos, J. Adonis, V. Mendes, F. Couto, R. Tenreiro. RESISTIR – intelligent decision support systems for personalized prevention and clinical management of infectious diseases. In Ciência 2018 - Encontro com a Ciência e Tecnologia em Portugal, 2018 [Biblios]

D. Faria, C. Pesquita, B. Balasubramani, T. Tervo, D. Carriço, R. Garrilha, F. Couto, I. Cruz. Results of AML in OAEI 2018. In The Thirteen International Workshop on Ontology Matching (OM-2018), 2018 [Biblios]

Daniel Gaspar, Cândida Trindade, Ana Usié, Brígida Meireles, Pedro Barbosa, Ana Fortes, Cátia Pesquita, Rita Costa, António Ramos. Expression Profiling in Pinus pinaster in Response to Infection with the Pine Wood Nematode Bursaphelenchus xylophilus. Forests, 8(8), MDPI AG, 2017 [Biblios]

Pedro Miguel Rodrigues De Barros, Cátia Pesquita, Marcos Ramos. Alternative splicing detection across different tissues in cork oak. Master's dissertation, 2017 [Biblios]

C Pesquita, Daniel Faria, Manel Achichi, Michelle Cheatham, Zlatan Dragisic, Jérôme Euzenat, Alfio Ferrara, Giorgos Flouris, Irini Fundulaki, Ian Harrow, Valentina Ivanova, Ernesto Jiménez-Ruiz, Kristian Kolthoff, Elena Kuss, Patrick Lambrix, Henrik Leopold, Huanyu Li, Christian Meilicke, Majid Mohammadi, T Saveta, P Shvaiko, A Splendiani, H Stuckenschmidt, E Thieblin, K Todorov, C Trojahn, O Zamazal. Results of the ontology alignment evaluation initiative 2017. In 12th International Workshop on Ontology Matching co-located with the 16th International Semantic Web Conference, 2017 [Biblios]

Catia Pesquita. Semantic Similarity in the Gene Ontology, In Methods in Molecular Biology,The Gene Ontology Handbook, pages 161 - 173. Springer New York, 2017 [Biblios]

Michelle Cheatham, Catia Pesquita. Semantic Data Integration, In Handbook of Big Data Technologies, pages 263 - 305. Springer International Publishing, 2017 [Biblios]

D. Faria, B. Balasubramani, V. Shivaprabhu, I. Mott, C. Pesquita, F. Couto, I. Cruz. Results of AML in OAEI 2017. In The Twelfth International Workshop on Ontology Matching (OM-2017), 2017 [Biblios]

Guilherme, Fábio André da Cunha, Pesquita, Cátia. Extracção de informação de registos electrónicos de saúde. Master's dissertation, 2016 [Biblios]

Carlos Alexandre Lourenço Dos Santos, Pesquita, Cátia. SESAME: Clustering with Semantic Similarity based on Multiple Ontologies. Master's dissertation, 2016 [Biblios]

Gaspar, Daniel Filipe Branco, Ramos, António Marcos Costa do Amaral, Pesquita, Cátia. Transcriptomic analysis of maritime pine response to infection with Bursaphelenchus Xylophilus, the causing agent of pine wilt disease. Master's dissertation, 2016 [Biblios]

Silva, Ana Cristina Antunes da, Pesquita, Cátia, Sousa, Lisete Maria Ribeiro de. Análise por prospeção de dados de registos eletrónicos de saúde de pacientes com cancro do pulmão. Master's dissertation, 2016 [Biblios]

Martins, Catarina Tavares, Pesquita, Cátia. Visualization for Biomedical Ontologies Alignment. Master's dissertation, 2016 [Biblios]

Michelle Cheatham, Catia Pesquita, Jerome Euzenat, Isabel F. Cruz. Special Issue on Ontology and Linked Data Matching. Semantic Web Journal, 2016 [Biblios]

Zlatan Dragisic, Valentina Ivanova, Patrick Lambrix, Daniel Faria, Ernesto Jiménez-Ruiz, Catia Pesquita. User Validation in Ontology Alignment. In International Semantic Web Conference (Lecture Notes in Computer Science,The Semantic Web – ISWC 2016), pages 200-217. Springer International Publishing, 2016 [Biblios]

Marzieh Bakhshandeh, Catia Pesquita, José Borbinha. An Ontological Matching Approach for Enterprise Architecture Model Analysis. In International Conference on Business Information Systems (Lecture Notes in Business Information Processing), pages 315-326. Springer International Publishing, 2016 [Biblios]

D. Faria, C. Pesquita, B. Balasubramani, C. Martins, J. Cardoso, H. Curado, F. Couto, I. Cruz. OAEI 2016 results of AML. In The Eleventh International Workshop on Ontology Matching (OM-2016), 2016 [Biblios]

João Nascimento, Cátia Luísa Santana Calisto Pesquita. RESIST: An intelligent system to predict antibiotic resistance. Master's dissertation, 2015 [Biblios]

Marzieh Bakhshandeh, Cátia Pesquita, José Luis Borbinha. Ontology matching techniques for enterprise architecture models. In Ontology Matching 2015, 2015 [Biblios]

Catarina Martins, Daniel Faria, Cátia Pesquita. Visualization and editing of biomedical ontology alignments in AgreementMakerLight. In ICBO 2015, 2015 [Biblios]

Catarina Martins, Ernesto Jimenez-Ruiz, Emanuel Santos, Cátia Pesquita. Towards visualizing the mapping incoherences in Bioportal. In ICBO 2015, 2015 [Biblios]

Emanuel Santos, Daniel Faria, Cátia Pesquita, Francisco Couto. Ontology alignment repair through modularization and confidence-based heuristics. PLOS ONE, 10(12):1-19, 2015 [Biblios]

Susana Serrazina, Carmen Santos, Helena Machado, Catia Pesquita, Renato Vicentini, Maria Salomé Pais, Mónica Sebastiana, Rita Costa. Castanea root transcriptome in response to Phytophthora cinnamomi challenge. TREE GENETICS & GENOMES, 11, 2015 [Biblios]

Daniel Faria, Ernesto Jiménez-Ruiz, Catia Pesquita, Emanuel Santos, Francisco M. Couto. Towards Annotating Potential Incoherences in BioPortal Mappings. In The Semantic Web – ISWC 2014,Lecture Notes in Computer Science, pages 17-32. Springer International Publishing, 2014 [Biblios]

Santos, Luís Duarte de Jesus, Pesquita, Cátia, Brás, Abílio Neves. Desenvolvimento de soluções mobile para o Banco de Portugal. Master's dissertation, 2014 [Biblios]

Abrantes, Anabela Rolo, Pesquita, Cátia, Pedro, Neuza Sofia Guerreiro. Aprendizagem da usabilidade e prototipagem e a sua aplicação no desenho de um museu virtual. Master's dissertation, 2014 [Biblios]

Daniel Faria, Cátia Pesquita, Emanuel Santos, Isabel Cruz, Francisco Couto. Automatic Background Knowledge Selection for Matching Biomedical Ontologies. PLOS ONE, 9(11), 2014 [Biblios]

Catia Pesquita, Michelle Cheatham, Daniel Faria, Joana Barros, Emanuel Santos, Francisco M. Couto. Building reference alignments for compound matching of multiple ontologies using obo cross-products. In The Ninth International Workshop on Ontology Matching (OM-2014), 2014 at ISWC 2014, 2014 [Biblios]

Daniel Faria, Cátia Pesquita, Emanuel Santos, Isabel Cruz, Francisco Couto. AgreementMakerLight: A Scalable Automated Ontology Matching System. In DILS 2014, 2014 [Biblios]

Emanuel Santos, Daniel Faria, Cátia Pesquita, Francisco Couto. Ontology alignment repair through modularization and confidence-based heuristics, 2013 [Biblios]

Daniel Faria, Cátia Pesquita, Emanuel Santos, M. Palmonari, I. Cruz, Francisco Couto. The AgreementMakerLight ontology matching system. In On The Move (OTM) Federated International Conference, pages 527-541, 2013 [Biblios]

Cátia Pesquita, Daniel Faria, Emanuel Santos, Francisco Couto. To repair or not to repair: reconciling correctness and coherence in ontology reference alignments. In The Eighth International Workshop on Ontology Matching (OM-2013), 2013 [Biblios]

Cátia Pesquita, Daniel Faria, C. Stroe, Emanuel Santos, I. Cruz, Francisco Couto. What's in a `nym'? synonyms in biomedical ontology matching. In 12th International Semantic Web Conference (ISWC), pages 526-541, 2013 [Biblios]

Daniel Faria, Catia Pesquita, Francisco Couto, André Falcão. GOclasses: molecular function as viewed by proteins. In BioOntologies SIG at ISMB/ECCB - 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) , 2009 [Biblios]