Catia Pesquita

141 papers A* 3A 1B 4Misc 3Journal 38Unranked 75

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Agentic Personas for Adaptive Scientific Explanations with Knowledge Graphs. CoRR Susana Nunes, Tiago Guerreiro, Catia Pesquita
2026	J	`jnl`	Exploring the limits of pre-trained embeddings in machine-guided protein design: a case study on predicting AAV vector viability. CoRR Ana F. Rodrigues, Lucas Ferraz, Laura Balbi, Pedro Giesteira Cotovio, Catia Pesquita
2026	J	`jnl`	Reinforcement-guided generative protein language models enable de novo design of highly diverse AAV capsids. CoRR Lucas Ferraz, Ana F. Rodrigues, Pedro Giesteira Cotovio, Mafalda Ventura, Gabriela Silva, Ana Sofia Coroadinha, Miguel Machuqueiro, Catia Pesquita
2025	J	`jnl`	A Systematic Evaluation of Knowledge Graph Embeddings for Gene-Disease Association Prediction. CoRR Catarina Canastra, Catia Pesquita
2025	J	`jnl`	CMOMgen: Complex Multi-Ontology Alignment via Pattern-Guided In-Context Learning. CoRR Marta Contreiras Silva, Daniel Faria, Catia Pesquita
2025	—	`conf`	Can Language Models Align Biomedical Ontologies?: Evaluating Retrieval-Augmented Prompt Strategies in Bio-ML. SeWeBMeDA@ESWC Lucas Ferraz, Pedro Giesteira Cotovio, Catia Pesquita
2025	—	`conf`	Knowledge Graphs for Explainable Scientific Discovery. SeWeBMeDA@ESWC Catia Pesquita
2025	J	`jnl`	Leveraging knowledge for explainable AI in personalized cancer treatment: challenges and future directions. Frontiers Digit. Health Emilia Daghir-Wojtkowiak, Javier Antonio Alfaro, Michele Mastromattei, Aleksander Palkowski, Mark Stares, Ana Roca-Umbert, Andraz Krajnc, Riccardo Leoni, Anne Boland, Aria Nourbaksh, Ashwin Adrian Kallor, Camille Ducki, Davide Venditti, Carla Montesano, Chiara Cipriani, Daniel Faria, Delphine Pflieger, Elisa Zago, Etienne Bardet, Filipa Serrano, Florian Jeanneret, Damien Alouges, Liangwei Yin, Elodine Coquelet, Apolline Bacquet, Francesco Bonchi, Francesco Maiorino, Francesco Torino, Georges Bedran, Jean-Alexandre Long, Laura Balbi, Laurent Guyon, Liana Bevilacqua, Manuel Fiorelli, Marie-Catherine Wagner, Mario Reyes, Mario Roselli, Marta Contreiras Silva, Michal Waleron, Nikolas Dovrolis, Odile Filhol-Cochet, In Hwa Um, Georg Wölflein, Patrícia Eugénio, Pauline Bazelle, Pavlos Golnas, Peter Thorpe, Pierluigi Bove, Piyush Borole, Roberta Bernardini, Rohit Kumar, Rosella Cicconi, Saskia Kaltenbrunner, Saverio Gravina, Simona Brezar, Stefan Symeonides, Steven McGinn, Susana Nunes, Ted Hupp, Yuri G. Gordienko, Dimitrios Varvaras, Sergii G. Stirenko, Luciano Xumerle, Stefania Mariani, Assilah Bouzit, Stéphane Gazut, Heiko Poth, Kyriakos Souliotis, Hector Katifelis, Elena Verzoni, Giuseppe Procopio, Sarah Schoch, Francisco Lupiáñez-Villanueva, Sandra Türk, Katarzyna Barud, Dimitri Koroliouk, Juan Caubet, Yamir Moreno, Jean-Luc Descotes, Christina Golna, Valentina Guadalupi, Paolo Garagnani, Maria Gazouli, Jean-François Deleuze, Frans Folkvord, Nikolaus Forgó, David J. Harrison, Håkan Axelson, Armando Stellato, Maurizio Mattei, Ajitha Rajan, Alexander Laird, Christophe Battail, Catia Pesquita, Fabio Massimo Zanzotto
2025	—	`conf`	Matcha results in OAEI 2025. OM@ISWC Marta Contreiras Silva, Daniel Faria, Pedro Cotovio, Lucas Ferraz, Laura Balbi, Catia Pesquita
2025	—	`conf`	Results of the Ontology Alignment Evaluation Initiative 2025. OM@ISWC Mina Abd Nikooie Pour, Eva Blomqvist, Pedro Giesteira Cotovio, Adrien Coulet, Lucas Ferraz, Sven Hertling, Sarika Jain, Ernesto Jiménez-Ruiz, Felix Kraus, Patrick Lambrix, Huanyu Li, Ying Li, Xianhao Liu, Pierre Monnin, Heiko Paulheim, Catia Pesquita, Abhisek Sharma, Pavel Shvaiko, Marta Contreiras Silva, Guilherme Sousa, Cássia Trojahn, Jana Vatascinová, Beyza Yaman, Ondrej Zamazal, Lu Zhou
2025	A*	`conf`	Rewarding Explainability in Drug Repurposing with Knowledge Graphs. IJCAI Susana Nunes, Samy Badreddine, Catia Pesquita
2025	J	`jnl`	Rewarding Explainability in Drug Repurposing with Knowledge Graphs. CoRR Susana Nunes, Samy Badreddine, Catia Pesquita
2025	J	`jnl`	Towards leveraging explicit negative statements in knowledge graph embeddings. J. Web Semant. Rita T. Sousa, Catia Pesquita, Heiko Paulheim
2024	—	`conf`	Building a Temporal Knowledge Graph for Electronic Health Records. DAO-XAI@ECAI Ricardo Miguel Serafim de Carvalho, Catia Pesquita, Andreia Sofia Teixeira
2024	A	`conf`	Complex Multi-Ontology Alignment Through Geometric Operations on Language Embeddings. ECAI Marta Contreiras Silva, Daniel Faria, Catia Pesquita
2024	—	`conf`	Drug Repurposing Hypothesis Validation with Knowledge-infused Explanations. DAO-XAI@ECAI Susana Nunes, Catia Pesquita
2024	J	`jnl`	Editorial: Special issue on Interactive Semantic Web. Semantic Web Bo Fu, Patrick Lambrix, Catia Pesquita
2024	J	`jnl`	Explaining protein-protein interactions with knowledge graph-based semantic similarity. Comput. Biol. Medicine Rita T. Sousa, Sara Silva, Catia Pesquita
2024	J	`jnl`	Guest Editorial Selected Papers From BIOKDD 2022. IEEE ACM Trans. Comput. Biol. Bioinform. Da Yan, Catia Pesquita, Carsten Görg, Jake Y. Chen
2024	—	`ed.`	Proceedings of the 9th International Workshop on the Visualization and Interaction for Ontologies, Linked Data and Knowledge Graphs co-located with the 23rd International Semantic Web Conference (ISWC 2024), Baltimore, USA, November 12, 2024. VOILA@ISWC Bo Fu, Patrick Lambrix, Huanyu Li, Susana Nunes, Catia Pesquita
2024	—	`conf`	Results in OAEI 2024 for Matcha. OM@ISWC Daniel Faria, Marta Contreiras Silva, Pedro Cotovio, Lucas Ferraz, Laura Balbi, Catia Pesquita
2024	—	`conf`	Results of the Ontology Alignment Evaluation Initiative 2024. OM@ISWC Mina Abd Nikooie Pour, Alsayed Algergawy, Eva Blomqvist, Patrice Buche, Jiaoyan Chen, Adrien Coulet, Julien Cufi, Hang Dong, Daniel Faria, Lucas Ferraz, Pedro Giesteira Cotovio, Yuan He, Sven Hertling, Ian Horrocks, Liliana Ibanescu, Sarika Jain, Ernesto Jiménez-Ruiz, Naouel Karam, Felix Kraus, Patrick Lambrix, Huanyu Li, Ying Li, Pierre Monnin, Heiko Paulheim, Catia Pesquita, Abhisek Sharma, Pavel Shvaiko, Marta Contreiras Silva, Guilherme Sousa, Cássia Trojahn, Jana Vatascinová, Beyza Yaman, Ondrej Zamazal, Lu Zhou
2024	J	`jnl`	The Immunopeptidomics Ontology (ImPO). Database J. Biol. Databases Curation Daniel Faria, Patrícia Eugénio, Marta Contreiras Silva, Laura Balbi, Georges Bedran, Ashwin Adrian Kallor, Susana Nunes, Aleksander Palkowski, Michal Waleron, Javier Antonio Alfaro, Catia Pesquita
2023	—	`conf`	Benchmark Datasets for Biomedical Knowledge Graphs with Negative Statements. SeWeBMeDA@ESWC Rita T. Sousa, Sara Silva, Catia Pesquita
2023	J	`jnl`	Benchmark datasets for biomedical knowledge graphs with negative statements. CoRR Rita T. Sousa, Sara Silva, Catia Pesquita
2023	Misc	`conf`	Biomedical Knowledge Graph Embeddings with Negative Statements. ISWC Rita T. Sousa, Sara Silva, Heiko Paulheim, Catia Pesquita
2023	J	`jnl`	Biomedical Knowledge Graph Embeddings with Negative Statements. CoRR Rita T. Sousa, Sara Silva, Heiko Paulheim, Catia Pesquita
2023	A*	`conf`	Explainable Representations for Relation Prediction in Knowledge Graphs. KR Rita T. Sousa, Sara Silva, Catia Pesquita
2023	J	`jnl`	Explainable Representations for Relation Prediction in Knowledge Graphs. CoRR Rita T. Sousa, Sara Silva, Catia Pesquita
2023	—	`ed.`	Joint Proceedings of the ESWC 2023 Workshops and Tutorials co-located with 20th European Semantic Web Conference (ESWC 2023), Hersonissos, Greece, May 28-29, 2023. ESWC Workshops Mehwish Alam, Cássia Trojahn, Sven Hertling, Catia Pesquita, Christian Aebeloe, Hidir Aras, Amr Azzam, Juan Cano, John Domingue, Simon Gottschalk, Olaf Hartig, Katja Hose, Sabrina Kirrane, Pasquale Lisena, Francesco Osborne, Philipp D. Rohde, Luc Steels, Ruben Taelman, Aisling Third, Ilaria Tiddi, Rima Türker
2023	J	`jnl`	Knowledge Graph Embeddings for ICU readmission prediction. BMC Medical Informatics Decis. Mak. Ricardo M. S. Carvalho, Daniela Oliveira, Catia Pesquita
2023	J	`jnl`	Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities. CoRR Jiaoyan Chen, Hang Dong, Janna Hastings, Ernesto Jiménez-Ruiz, Vanessa López, Pierre Monnin, Catia Pesquita, Petr Skoda, Valentina Tamma
2023	J	`jnl`	Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities. TGDK Jiaoyan Chen, Hang Dong, Janna Hastings, Ernesto Jiménez-Ruiz, Vanessa López, Pierre Monnin, Catia Pesquita, Petr Skoda, Valentina Tamma
2023	J	`jnl`	Multi-domain knowledge graph embeddings for gene-disease association prediction. J. Biomed. Semant. Susana Nunes, Rita T. Sousa, Catia Pesquita
2023	—	`ed.`	Proceedings of the 8th International Workshop on the Visualization and Interaction for Ontologies, Linked Data and Knowledge Graphs co-located with the 22nd International Semantic Web Conference (ISWC 2023), Athens, Greece, November 6, 2023. VOILA@ISWC Bo Fu, Patrick Lambrix, Huanyu Li, Susana Nunes, Catia Pesquita
2023	—	`conf`	Results for Matcha and Matcha-DL in OAEI 2023. OM@ISWC Daniel Faria, Marta Contreiras Silva, Pedro Cotovio, Lucas Ferraz, Laura Balbi, Catia Pesquita
2023	—	`conf`	Results of the Ontology Alignment Evaluation Initiative 2023. OM@ISWC Mina Abd Nikooie Pour, Alsayed Algergawy, Patrice Buche, Leyla Jael Castro, Jiaoyan Chen, Adrien Coulet, Julien Cufi, Hang Dong, Omaima Fallatah, Daniel Faria, Irini Fundulaki, Sven Hertling, Yuan He, Ian Horrocks, Martin Huschka, Liliana Ibanescu, Sarika Jain, Ernesto Jiménez-Ruiz, Naouel Karam, Patrick Lambrix, Huanyu Li, Ying Li, Pierre Monnin, Engy Nasr, Heiko Paulheim, Catia Pesquita, Tzanina Saveta, Pavel Shvaiko, Guilherme Sousa, Cássia Trojahn, Jana Vatascinová, Mingfang Wu, Beyza Yaman, Ondrej Zamazal, Lu Zhou
2023	J	`jnl`	Supervised Biomedical Semantic Similarity. IEEE Access Rita T. Sousa, Sara Silva, Catia Pesquita
2023	B	`ed.`	The Semantic Web - 20th International Conference, ESWC 2023, Hersonissos, Crete, Greece, May 28 - June 1, 2023, Proceedings ESWC Catia Pesquita, Ernesto Jiménez-Ruiz, Jamie P. McCusker, Daniel Faria, Mauro Dragoni, Anastasia Dimou, Raphaël Troncy, Sven Hertling
2023	—	`ed.`	The Semantic Web: ESWC 2023 Satellite Events - Hersonissos, Crete, Greece, May 28 - June 1, 2023, Proceedings ESWC (Satellite Events) Catia Pesquita, Hala Skaf-Molli, Vasilis Efthymiou, Sabrina Kirrane, Axel Ngonga, Diego Collarana, Renato Cerqueira, Mehwish Alam, Cássia Trojahn, Sven Hertling
2023	J	`jnl`	What can knowledge graph alignment gain with Neuro-Symbolic learning approaches? CoRR Pedro Giesteira Cotovio, Ernesto Jiménez-Ruiz, Catia Pesquita
2022	A*	`conf`	21th International Workshop on Data Mining in Bioinformatics (BIOKDD 2022). KDD Da Yan, Catia Pesquita, Carsten Görg, Jake Y. Chen, Mohammed J. Zaki
2022	—	`ed.`	Biomedical Engineering Systems and Technologies - 14th International Joint Conference, BIOSTEC 2021, Virtual Event, February 11-13, 2021, Revised Selected Papers BIOSTEC (Selected Papers) Claudine Géhin, Bruno Wacogne, Alexandre Douplik, Ronny Lorenz, Bethany K. Bracken, Catia Pesquita, Ana Fred, Hugo Gamboa
2022	—	`conf`	Explaining Artificial Intelligence Predictions of Disease Progression with Semantic Similarity. CLEF (Working Notes) 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
2022	—	`conf`	Extending AgreementMakerLight to Perform Holistic Ontology Matching. ESWC (Satellite Events) Marta Contreiras Silva, Daniel Faria, Catia Pesquita
2022	—	`conf`	Hierarchical Modelling for ALS Prognosis: Predicting the Progression Towards Critical Events. CLEF (Working Notes) 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
2022	—	`conf`	Matcha and Matcha-DL results for OAEI 2022. OM@ISWC Daniel Faria, Marta Contreiras Silva, Pedro Cotovio, Patrícia Eugénio, Catia Pesquita
2022	B	`conf`	Matching Multiple Ontologies to Build a Knowledge Graph for Personalized Medicine. ESWC Marta Contreiras Silva, Daniel Faria, Catia Pesquita
2022	—	`conf`	Powering Biomedical Artificial Intelligence with a Holistic Knowledge Graph (invited talk). SeWeBMeDA@ESWC Catia Pesquita
2022	—	`ed.`	Proceedings of the Semantic Web Challenge on Tabular Data to Knowledge Graph Matching co-located with the 20th International Semantic Web Conference (ISWC 2021), Virtual conference, October 27, 2021. SemTab@ISWC Ernesto Jiménez-Ruiz, Vasilis Efthymiou, Jiaoyan Chen, Vincenzo Cutrona, Oktie Hassanzadeh, Juan Sequeda, Kavitha Srinivas, Nora Abdelmageed, Madelon Hulsebos, Daniela Oliveira, Catia Pesquita
2022	—	`ed.`	Proceedings of the Seventh International Workshop on the Visualization and Interaction for Ontologies and Linked Data co-located with the 21st International Semantic Web Conference (ISWC 2022), Virtual Event, Hangzhou, China, October 23, 2022. VOILA@ISWC Bo Fu, Patrick Lambrix, Catia Pesquita
2022	—	`conf`	Results of the Ontology Alignment Evaluation Initiative 2022. OM@ISWC Mina Abd Nikooie Pour, Alsayed Algergawy, Patrice Buche, Leyla Jael Castro, Jiaoyan Chen, Hang Dong, Omaima Fallatah, Daniel Faria, Irini Fundulaki, Sven Hertling, Yuan He, Ian Horrocks, Martin Huschka, Liliana Ibanescu, Ernesto Jiménez-Ruiz, Naouel Karam, Amir Laadhar, Patrick Lambrix, Huanyu Li, Ying Li, Franck Michel, Engy Nasr, Heiko Paulheim, Catia Pesquita, Tzanina Saveta, Pavel Shvaiko, Cássia Trojahn, Chantelle Verhey, Mingfang Wu, Beyza Yaman, Ondrej Zamazal, Lu Zhou
2022	B	`ed.`	The Semantic Web - 19th International Conference, ESWC 2022, Hersonissos, Crete, Greece, May 29 - June 2, 2022, Proceedings ESWC Paul Groth, Maria-Esther Vidal, Fabian M. Suchanek, Pedro A. Szekely, Pavan Kapanipathi, Catia Pesquita, Hala Skaf-Molli, Minna Tamper
2022	—	`conf`	The Supervised Semantic Similarity Toolkit. ESWC (Satellite Events) Rita T. Sousa, Sara Silva, Catia Pesquita
2022	—	`conf`	Towards Supervised Biomedical Semantic Similarity. SeWeBMeDA@ESWC Rita T. Sousa, Sara Silva, Catia Pesquita
2022	—	`conf`	VOWLExplain: Knowledge Graph visualization for Explainable Artificial Intelligence. VOILA@ISWC Filipa Serrano, Susana Nunes, Catia Pesquita
2021	—	`conf`	AML and AMLC results for OAEI 2021. OM@ISWC Daniel Faria, Beatriz Lima, Marta Contreiras Silva, Francisco M. Couto, Catia Pesquita
2021	—	`conf`	Challenges of evaluating complex alignments. OM@ISWC Beatriz Lima, Daniel Faria, Catia Pesquita
2021	—	`conf`	Integrating knowledge graphs for explainable artificial intelligence in biomedicine. OM@ISWC Marta Contreiras Silva, Daniel Faria, Catia Pesquita
2021	—	`conf`	Is there data leakage in protein-protein interaction prediction using knowledge graphs? ISWC (Posters/Demos/Industry) Rita T. Sousa, Sara Silva, Catia Pesquita
2021	—	`conf`	Pattern-Guided Association Rule Mining for Complex Ontology Alignment. ISWC (Posters/Demos/Industry) Beatriz Lima, Daniel Faria, Catia Pesquita
2021	J	`jnl`	Predicting Gene-Disease Associations with Knowledge Graph Embeddings over Multiple Ontologies. CoRR Susana Nunes, Rita T. Sousa, Catia Pesquita
2021	—	`ed.`	Proceedings of the 14th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2021, Volume 5: HEALTHINF, Online Streaming, February 11-13, 2021. HEALTHINF Catia Pesquita, Ana Fred, Hugo Gamboa
2021	—	`ed.`	Proceedings of the ISWC 2021 Posters, Demos and Industry Tracks: From Novel Ideas to Industrial Practice co-located with 20th International Semantic Web Conference (ISWC 2021), Virtual Conference, October 24-28, 2021. ISWC (Posters/Demos/Industry) Oshani Seneviratne, Catia Pesquita, Juan Sequeda, Lorena Etcheverry
2021	—	`ed.`	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), Virtual Conference, 2021. VOILA@ISWC Patrick Lambrix, Catia Pesquita, Vitalis Wiens
2021	—	`conf`	Results of SemTab 2021. SemTab@ISWC Vincenzo Cutrona, Jiaoyan Chen, Vasilis Efthymiou, Oktie Hassanzadeh, Ernesto Jiménez-Ruiz, Juan Sequeda, Kavitha Srinivas, Nora Abdelmageed, Madelon Hulsebos, Daniela Oliveira, Catia Pesquita
2021	—	`conf`	Results of the Ontology Alignment Evaluation Initiative 2021. OM@ISWC Mina Abd Nikooie Pour, Alsayed Algergawy, Florence Amardeilh, Reihaneh Amini, Omaima Fallatah, Daniel Faria, Irini Fundulaki, Ian Harrow, Sven Hertling, Pascal Hitzler, Martin Huschka, Liliana Ibanescu, Ernesto Jiménez-Ruiz, Naouel Karam, Amir Laadhar, Patrick Lambrix, Huanyu Li, Ying Li, Franck Michel, Engy Nasr, Heiko Paulheim, Catia Pesquita, Jan Portisch, Catherine Roussey, Tzanina Saveta, Pavel Shvaiko, Andrea Splendiani, Cássia Trojahn, Jana Vatascinová, Beyza Yaman, Ondrej Zamazal, Lu Zhou
2021	—	`conf`	Towards Semantic Integration for Explainable Artificial Intelligence in the Biomedical Domain. HEALTHINF Catia Pesquita
2021	—	`conf`	VOWLMap: Graph-based Ontology Alignment Visualization and Editing. VOILA@ISWC Ana Guerreiro, Catia Pesquita, Daniel Faria
2021	—	`conf`	VOWLMap: graph-based ontology alignment visualization and editing. ISWC (Posters/Demos/Industry) Ana Guerreiro, Catia Pesquita, Daniel Faria
2021	—	`conf`	evoKGsim+: A Framework for Tailoring Knowledge Graph-Based Similarity for Supervised Learning. ESWC (Satellite Events) Rita Torres de Sousa, Sara Silva, Catia Pesquita
2020	—	`conf`	A Collection of Benchmark Data Sets for Knowledge Graph-Based Similarity in the Biomedical Domain. ESWC (Satellite Events) Carlota Cardoso, Rita T. Sousa, Sebastian Köhler, Catia Pesquita
2020	J	`jnl`	A Collection of Benchmark Data Sets for Knowledge Graph-based Similarity in the Biomedical Domain. Database J. Biol. Databases Curation Carlota Cardoso, Rita T. Sousa, Sebastian Köhler, Catia Pesquita
2020	J	`jnl`	Crowd-assessing quality in uncertain data linking datasets. Knowl. Eng. Rev. Daniel Faria, Alfio Ferrara, Ernesto Jiménez-Ruiz, Stefano Montanelli, Catia Pesquita
2020	J	`jnl`	Evolving knowledge graph similarity for supervised learning in complex biomedical domains. BMC Bioinform. Rita T. Sousa, Sara Silva, Catia Pesquita
2020	—	`conf`	Learning reference alignments for ontology matching within and across domains. OM@ISWC Beatriz Lima, Ruben Branco, João Castanheira, Gustavo Fonseca, Catia Pesquita
2020	—	`conf`	OAEI 2020 results for AML and AMLC. OM@ISWC Beatriz Lima, Daniel Faria, Francisco M. Couto, Isabel F. Cruz, Catia Pesquita
2020	—	`ed.`	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), Virtual Conference (originally planned in Athens, Greece), November 02, 2020. VOILA@ISWC Valentina Ivanova, Patrick Lambrix, Catia Pesquita, Vitalis Wiens
2020	—	`conf`	Results of the Ontology Alignment Evaluation Initiative 2020. OM@ISWC Mina Abd Nikooie Pour, Alsayed Algergawy, Reihaneh Amini, Daniel Faria, Irini Fundulaki, Ian Harrow, Sven Hertling, Ernesto Jiménez-Ruiz, Clément Jonquet, Naouel Karam, Abderrahmane Khiat, Amir Laadhar, Patrick Lambrix, Huanyu Li, Ying Li, Pascal Hitzler, Heiko Paulheim, Catia Pesquita, Tzanina Saveta, Pavel Shvaiko, Andrea Splendiani, Élodie Thiéblin, Cássia Trojahn, Jana Vatascinová, Beyza Yaman, Ondrej Zamazal, Lu Zhou
2020	J	`jnl`	Towards evaluating complex ontology alignments. Knowl. Eng. Rev. Lu Zhou, Élodie Thiéblin, Michelle Cheatham, Daniel Faria, Catia Pesquita, Cássia Trojahn dos Santos, Ondrej Zamazal
2019	—	`conf`	AML and AMLC Results for OAEI 2019. OM@ISWC Daniel Faria, Catia Pesquita, Teemu Tervo, Francisco M. Couto, Isabel F. Cruz
2019	—	`conf`	Results of the Ontology Alignment Evaluation Initiative 2019. OM@ISWC Alsayed Algergawy, Daniel Faria, Alfio Ferrara, Irini Fundulaki, Ian Harrow, Sven Hertling, Ernesto Jiménez-Ruiz, Naouel Karam, Abderrahmane Khiat, Patrick Lambrix, Huanyu Li, Stefano Montanelli, Heiko Paulheim, Catia Pesquita, Tzanina Saveta, Pavel Shvaiko, Andrea Splendiani, Élodie Thiéblin, Cássia Trojahn, Jana Vatascinová, Ondrej Zamazal, Lu Zhou
2019	J	`jnl`	User validation in ontology alignment: functional assessment and impact. Knowl. Eng. Rev. Huanyu Li, Zlatan Dragisic, Daniel Faria, Valentina Ivanova, Ernesto Jiménez-Ruiz, Patrick Lambrix, Catia Pesquita
2019	J	`jnl`	Visualization and interaction for ontologies and linked data - Editorial. J. Web Semant. Valentina Ivanova, Patrick Lambrix, Steffen Lohmann, Catia Pesquita
2018	B	`conf`	A Framework to Conduct and Report on Empirical User Studies in Semantic Web Contexts. EKAW Catia Pesquita, Valentina Ivanova, Steffen Lohmann, Patrick Lambrix
2018	—	`conf`	Complex matching for multiple ontologies: an exploratory study. OM@ISWC Madalena Pavão, Catia Pesquita
2018	J	`jnl`	Improving the interoperability of biomedical ontologies with compound alignments. J. Biomed. Semant. Daniela Oliveira, Catia Pesquita
2018	—	`ed.`	Proceedings of the Fourth International Workshop on Visualization and Interaction for Ontologies and Linked Data co-located with the 17th International Semantic Web Conference, VOILA@ISWC 2018, Monterey, CA, USA, October 8, 2018. VOILA@ISWC Valentina Ivanova, Patrick Lambrix, Steffen Lohmann, Catia Pesquita
2018	—	`conf`	Results of AML participation in OAEI 2018. OM@ISWC Daniel Faria, Catia Pesquita, Booma Sowkarthiga Balasubramani, Teemu Tervo, David Carriço, Rodrigo Garrilha, Francisco M. Couto, Isabel F. Cruz
2018	—	`conf`	Results of the Ontology Alignment Evaluation Initiative 2018. OM@ISWC Alsayed Algergawy, Michelle Cheatham, Daniel Faria, Alfio Ferrara, Irini Fundulaki, Ian Harrow, Sven Hertling, Ernesto Jiménez-Ruiz, Naouel Karam, Abderrahmane Khiat, Patrick Lambrix, Huanyu Li, Stefano Montanelli, Heiko Paulheim, Catia Pesquita, Tzanina Saveta, Daniela Schmidt, Pavel Shvaiko, Andrea Splendiani, Élodie Thiéblin, Cássia Trojahn, Jana Vatascinová, Ondrej Zamazal, Lu Zhou
2018	J	`jnl`	Tackling the challenges of matching biomedical ontologies. J. Biomed. Semant. Daniel Faria, Catia Pesquita, Isabela Mott, Catarina Martins, Francisco M. Couto, Isabel F. Cruz
2018	J	`jnl`	The properties of property alignment on the semantic web. Int. J. Metadata Semant. Ontologies Michelle Cheatham, Catia Pesquita, Daniela Oliveira, Helena B. McCurdy
2017	—	`ed.`	Proceedings of the Third International Workshop on Visualization and Interaction for Ontologies and Linked Data co-located with the 16th International Semantic Web Conference (ISWC 2017), Vienna, Austria, October 22, 2017. VOILA@ISWC Valentina Ivanova, Patrick Lambrix, Steffen Lohmann, Catia Pesquita
2017	—	`conf`	Results of AML in OAEI 2017. OM@ISWC Daniel Faria, Booma S. Balasubramani, Vivek R. Shivaprabhu, Isabela Mott, Catia Pesquita, Francisco M. Couto, Isabel F. Cruz
2017	—	`conf`	Results of the Ontology Alignment Evaluation Initiative 2017. OM@ISWC Manel Achichi, Michelle Cheatham, Zlatan Dragisic, Jérôme Euzenat, Daniel Faria, 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, Stefano Montanelli, Catia Pesquita, Tzanina Saveta, Pavel Shvaiko, Andrea Splendiani, Heiner Stuckenschmidt, Élodie Thiéblin, Konstantin Todorov, Cássia Trojahn, Ondrej Zamazal
2017	—	`ch.`	Semantic Data Integration. Handbook of Big Data Technologies Michelle Cheatham, Catia Pesquita
2017	J	`jnl`	Special issue on ontology and linked data matching. Semantic Web Michelle Cheatham, Isabel F. Cruz, Jérôme Euzenat, Catia Pesquita
2016	—	`conf`	An Ontological Matching Approach for Enterprise Architecture Model Analysis. BIS Marzieh Bakhshandeh, Catia Pesquita, José Borbinha
2016	—	`conf`	OAEI 2016 results of AML. OM@ISWC Daniel Faria, Catia Pesquita, Booma S. Balasubramani, Catarina Martins, João Cardoso, Hugo Curado, Francisco M. Couto, Isabel F. Cruz
2016	—	`conf`	Ontology-Based Approach for Heterogeneity Analysis of EA Models. Business Process Management Workshops João Cardoso, Marzieh Bakhshandeh, Daniel Faria, Catia Pesquita, José Borbinha
2016	—	`ed.`	Proceedings of the Second International Workshop on Visualization and Interaction for Ontologies and Linked Data co-located with the 15th International Semantic Web Conference, VOILA@ISWC 2016, Kobe, Japan, October 17, 2016. VOILA@ISWC Valentina Ivanova, Patrick Lambrix, Steffen Lohmann, Catia Pesquita
2016	—	`conf`	Results of the Ontology Alignment Evaluation Initiative 2016. OM@ISWC Manel Achichi, Michelle Cheatham, Zlatan Dragisic, Jérôme Euzenat, Daniel Faria, Alfio Ferrara, Giorgos Flouris, Irini Fundulaki, Ian Harrow, Valentina Ivanova, Ernesto Jiménez-Ruiz, Elena Kuss, Patrick Lambrix, Henrik Leopold, Huanyu Li, Christian Meilicke, Stefano Montanelli, Catia Pesquita, Tzanina Saveta, Pavel Shvaiko, Andrea Splendiani, Heiner Stuckenschmidt, Konstantin Todorov, Cássia Trojahn dos Santos, Ondrej Zamazal
2016	—	`conf`	User Validation in Ontology Alignment. ISWC (1) Zlatan Dragisic, Valentina Ivanova, Patrick Lambrix, Daniel Faria, Ernesto Jiménez-Ruiz, Catia Pesquita
2016	—	`conf`	Workshop Summary. VOILA@ISWC Valentina Ivanova, Patrick Lambrix, Steffen Lohmann, Catia Pesquita
2015	—	`conf`	AML results for OAEI 2015. OM Daniel Faria, Catarina Martins, Amruta Nanavaty, Daniela Oliveira, Booma Sowkarthiga, Aynaz Taheri, Catia Pesquita, Francisco M. Couto, Isabel F. Cruz
2015	—	`conf`	Compound matching of biomedical ontologies. ICBO Daniela Oliveira, Catia Pesquita
2015	—	`conf`	Inferring logical definitions using compound ontology matching. ICBO Daniela Oliveira, Catia Pesquita
2015	—	`conf`	Ontology matching techniques for enterprise architecture models. OM Marzieh Bakhshandeh, Catia Pesquita, José Borbinha
2015	—	`ed.`	Proceedings of the International Workshop on Visualizations and User Interfaces for Ontologies and Linked Data co-located with 14th International Semantic Web Conference (ISWC 2015), Bethlehem, Pennsylvania, USA, October 11, 2015. VOILA@ISWC Valentina Ivanova, Patrick Lambrix, Steffen Lohmann, Catia Pesquita
2015	—	`conf`	Results of the Ontology Alignment Evaluation Initiative 2015. OM Michelle Cheatham, Zlatan Dragisic, Jérôme Euzenat, Daniel Faria, Alfio Ferrara, Giorgos Flouris, Irini Fundulaki, Roger Granada, Valentina Ivanova, Ernesto Jiménez-Ruiz, Patrick Lambrix, Stefano Montanelli, Catia Pesquita, Tzanina Saveta, Pavel Shvaiko, Alessandro Solimando, Cássia Trojahn dos Santos, Ondrej Zamazal
2015	—	`conf`	The Process Model Matching Contest 2015. EMISA Gonçalo Antunes, Marzieh Bakhshandeh, José Borbinha, João Cardoso, Sharam Dadashnia, Chiara Di Francescomarino, Mauro Dragoni, Peter Fettke, Avigdor Gal, Chiara Ghidini, Philip Hake, Abderrahmane Khiat, Christopher Klinkmüller, Elena Kuss, Henrik Leopold, Peter Loos, Christian Meilicke, Tim Niesen, Catia Pesquita, Timo Péus, Andreas Schoknecht, Eitam Sheetrit, Andreas Sonntag, Heiner Stuckenschmidt, Tom Thaler, Ingo Weber, Matthias Weidlich
2015	—	`conf`	Towards visualizing the mapping incoherences in Bioportal. ICBO Catarina Martins, Ernesto Jiménez-Ruiz, Emanuel Santos, Catia Pesquita
2015	—	`conf`	Visualization and editing of biomedical ontology alignments in AgreementMakerLight. ICBO Catarina Martins, Daniel Faria, Catia Pesquita
2014	—	`conf`	AgreementMakerLight 2.0: Towards Efficient Large-Scale Ontology Matching. ISWC (Posters & Demos) Daniel Faria, Catia Pesquita, Emanuel Santos, Isabel F. Cruz, Francisco M. Couto
2014	—	`conf`	AgreementMakerLight results for OAEI 2014. OM Daniel Faria, Catarina Martins, Amruta Nanavaty, Aynaz Taheri, Catia Pesquita, Emanuel Santos, Isabel F. Cruz, Francisco M. Couto
2014	—	`conf`	Building reference alignments for compound matching of multiple ontologies using OBO cross-products. OM Catia Pesquita, Michelle Cheatham, Daniel Faria, Joana Barros, Emanuel Santos, Francisco M. Couto
2014	—	`conf`	Introduction to VISUAL 2014 - Workshop on Visualizations and User Interfaces for Knowledge Engineering and Linked Data Analytics. EKAW (Satellite Events) Valentina Ivanova, Tomi Kauppinen, Steffen Lohmann, Suvodeep Mazumdar, Catia Pesquita, Kai Xu
2014	—	`ed.`	Proceedings of the International Workshop on Visualizations and User Interfaces for Knowledge Engineering and Linked Data Analytics co-located with 19th International Conference on Knowledge Engineering and Knowledge Management, VISUAL@EKAW 2014, Linköping, Sweden, November 24, 2014. VISUAL@EKAW Valentina Ivanova, Tomi Kauppinen, Steffen Lohmann, Suvodeep Mazumdar, Catia Pesquita, Kai Xu
2014	J	`jnl`	The epidemiology ontology: an ontology for the semantic annotation of epidemiological resources. J. Biomed. Semant. Catia Pesquita, João D. Ferreira, Francisco M. Couto, Mário J. Silva
2014	—	`conf`	Towards Annotating Potential Incoherences in BioPortal Mappings. ISWC (2) Daniel Faria, Ernesto Jiménez-Ruiz, Catia Pesquita, Emanuel Santos, Francisco M. Couto
2014	—	`conf`	Towards Visualizing the Alignment of Large Biomedical Ontologies. DILS Catia Pesquita, Daniel Faria, Emanuel Santos, Jean-Marc Neefs, Francisco M. Couto
2013	—	`conf`	AgreementMakerLight results for OAEI 2013. OM Daniel Faria, Catia Pesquita, Emanuel Santos, Isabel F. Cruz, Francisco M. Couto
2013	—	`conf`	Digital preservation of epidemic resources: coupling metadata and ontologies. iPRES João D. Ferreira, Catia Pesquita, Francisco M. Couto, Mário J. Silva
2013	J	`jnl`	Ontology alignment repair through modularization and confidence-based heuristics. CoRR Emanuel Santos, Daniel Faria, Catia Pesquita, Francisco M. Couto
2013	—	`conf`	The AgreementMakerLight Ontology Matching System. OTM Conferences Daniel Faria, Catia Pesquita, Emanuel Santos, Matteo Palmonari, Isabel F. Cruz, Francisco M. Couto
2013	—	`conf`	To repair or not to repair: reconciling correctness and coherence in ontology reference alignments. OM Catia Pesquita, Daniel Faria, Emanuel Santos, Francisco M. Couto
2013	—	`conf`	What's in a 'nym'? Synonyms in Biomedical Ontology Matching. ISWC (1) Catia Pesquita, Daniel Faria, Cosmin Stroe, Emanuel Santos, Isabel F. Cruz, Francisco M. Couto
2012	—	`conf`	Bringing epidemiology into the Semantic Web. ICBO João D. Ferreira, Catia Pesquita, Francisco M. Couto, Mário J. Silva
2012	J	`jnl`	Predicting the Extension of Biomedical Ontologies. PLoS Comput. Biol. Catia Pesquita, Francisco M. Couto
2012	J	`jnl`	Testing the AgreementMaker System in the Anatomy Task of OAEI 2012 CoRR Daniel Faria, Catia Pesquita, Emanuel Santos, Francisco M. Couto, Cosmin Stroe, Isabel F. Cruz
2011	—	`conf`	Biomedical Ontology Matching Using the AgreementMaker System. ICBO Isabel F. Cruz, Cosmin Stroe, Catia Pesquita, Francisco M. Couto, Valerie Cross
2011	—	`conf`	The Biomedical Ontology Applications (BOA) Framework. ICBO Bruno Tavares, Hugo P. Bastos, Daniel Faria, João D. Ferreira, Tiago Grego, Catia Pesquita, Francisco M. Couto
2011	—	`conf`	Using AgreementMaker to align ontologies for OAEI 2011. OM Isabel F. Cruz, Cosmin Stroe, Federico Caimi, Alessio Fabiani, Catia Pesquita, Francisco M. Couto, Matteo Palmonari
2011	—	`conf`	Where GO is Going and What it Means for Ontology Extension. ICBO Catia Pesquita, Francisco M. Couto
2010	—	`conf`	BLOOMS on AgreementMaker: results for OAEI 2010. OM Catia Pesquita, Cosmin Stroe, Isabel F. Cruz, Francisco M. Couto
2009	—	`conf`	Identifying Gene Ontology Areas for Automated Enrichment. IWANN (2) Catia Pesquita, Tiago Grego, Francisco M. Couto
2009	Misc	`conf`	Measuring coherence between electronic and manual annotations in biological databases. SAC Catia Pesquita, Daniel Faria, Francisco M. Couto
2009	J	`jnl`	Semantic Similarity in Biomedical Ontologies. PLoS Comput. Biol. Catia Pesquita, Daniel Faria, André O. Falcão, Phillip W. Lord, Francisco M. Couto
2008	Misc	`conf`	BOLOS: BLAST & Ontology Linked-hOmologue Stars. SAC Hugo P. Bastos, Catia Pesquita, Daniel Faria, André O. Falcão
2008	—	`conf`	Identifying bioentity recognition errors of rule-based text-mining systems. ICDIM Francisco M. Couto, Tiago Grego, Hugo P. Bastos, Catia Pesquita, Rafael P. Torres, Pablo Sanchez, Leandro Pascual, Christian Blaschke
2008	J	`jnl`	Metrics for GO based protein semantic similarity: a systematic evaluation. BMC Bioinform. Catia Pesquita, Daniel Faria, Hugo P. Bastos, António E. N. Ferreira, André O. Falcão, Francisco M. Couto