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]

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]

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 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]

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]

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]

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]

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]

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]

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. 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. CEUR-WS.org, 2022 [Biblios]

Marta Contreiras Silva, Patrícia Eugénio, Daniel Faria, Catia Pesquita. Ontologies and Knowledge Graphs in Oncology Research. Cancers, 14(8), MDPI AG, 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]

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]

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]

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]