Identifying bioentity recognition errors of rule-based text-mining systems. - Francisco M. Couto; Tiago Grego; Hugo P. Bastos; Catia Pesquita; Rafael P. Torres; Pablo Sanchez; Leandro Pascual; Christian Blaschke (ICDIM, 2008)

BOLOS: BLAST & Ontology Linked-hOmologue Stars. - Hugo P. Bastos; Catia Pesquita; Daniel Faria; André O. Falcão (SAC, 2008)

Metrics for GO based protein semantic similarity: a systematic evaluation. - Catia Pesquita; Daniel Faria; Hugo P. Bastos; António E. N. Ferreira; André O. Falcão; Francisco M. Couto (BMC Bioinform., 2008)

Identifying Gene Ontology Areas for Automated Enrichment. - Catia Pesquita; Tiago Grego; Francisco M. Couto (IWANN (2), 2009)

Measuring coherence between electronic and manual annotations in biological databases. - Catia Pesquita; Daniel Faria; Francisco M. Couto (SAC, 2009)

Semantic Similarity in Biomedical Ontologies. - Catia Pesquita; Daniel Faria; André O. Falcão; Phillip W. Lord; Francisco M. Couto (PLoS Comput. Biol., 2009)

BLOOMS on AgreementMaker: results for OAEI 2010. - Catia Pesquita; Cosmin Stroe; Isabel F. Cruz; Francisco M. Couto (OM, 2010)

Biomedical Ontology Matching Using the AgreementMaker System. - Isabel F. Cruz; Cosmin Stroe; Catia Pesquita; Francisco M. Couto; Valerie Cross (ICBO, 2011)

Where GO is Going and What it Means for Ontology Extension. - Catia Pesquita; Francisco M. Couto (ICBO, 2011)

The Biomedical Ontology Applications (BOA) Framework. - Bruno Tavares; Hugo P. Bastos; Daniel Faria; João D. Ferreira; Tiago Grego; Catia Pesquita; Francisco M. Couto (ICBO, 2011)

Using AgreementMaker to align ontologies for OAEI 2011. - Isabel F. Cruz; Cosmin Stroe; Federico Caimi; Alessio Fabiani; Catia Pesquita; Francisco M. Couto; Matteo Palmonari (OM, 2011)

Bringing epidemiology into the Semantic Web. - João D. Ferreira; Catia Pesquita; Francisco M. Couto; Mário J. Silva (ICBO, 2012)

Testing the AgreementMaker System in the Anatomy Task of OAEI 2012 - Daniel Faria; Catia Pesquita; Emanuel Santos; Francisco M. Couto; Cosmin Stroe; Isabel F. Cruz (CoRR, 2012)

Predicting the Extension of Biomedical Ontologies. - Catia Pesquita; Francisco M. Couto (PLoS Comput. Biol., 2012)

Digital preservation of epidemic resources: coupling metadata and ontologies. - João D. Ferreira; Catia Pesquita; Francisco M. Couto; Mário J. Silva (iPRES, 2013)

The AgreementMakerLight Ontology Matching System. - Daniel Faria; Catia Pesquita; Emanuel Santos; Matteo Palmonari; Isabel F. Cruz; Francisco M. Couto (OTM Conferences, 2013)

AgreementMakerLight results for OAEI 2013. - Daniel Faria; Catia Pesquita; Emanuel Santos; Isabel F. Cruz; Francisco M. Couto (OM, 2013)

To repair or not to repair: reconciling correctness and coherence in ontology reference alignments. - Catia Pesquita; Daniel Faria; Emanuel Santos; Francisco M. Couto (OM, 2013)

What's in a 'nym'? Synonyms in Biomedical Ontology Matching. - Catia Pesquita; Daniel Faria; Cosmin Stroe; Emanuel Santos; Isabel F. Cruz; Francisco M. Couto (ISWC (1), 2013)

Ontology alignment repair through modularization and confidence-based heuristics. - Emanuel Santos; Daniel Faria; Catia Pesquita; Francisco M. Couto (CoRR, 2013)

Towards Visualizing the Alignment of Large Biomedical Ontologies. - Catia Pesquita; Daniel Faria; Emanuel Santos; Jean-Marc Neefs; Francisco M. Couto (DILS, 2014)

Introduction to VISUAL 2014 - Workshop on Visualizations and User Interfaces for Knowledge Engineering and Linked Data Analytics. - Valentina Ivanova; Tomi Kauppinen; Steffen Lohmann; Suvodeep Mazumdar; Catia Pesquita; Kai Xu 003 (EKAW (Satellite Events), 2014)

Towards Annotating Potential Incoherences in BioPortal Mappings. - Daniel Faria; Ernesto Jiménez-Ruiz; Catia Pesquita; Emanuel Santos; Francisco M. Couto (ISWC (2), 2014)

AgreementMakerLight results for OAEI 2014. - Daniel Faria; Catarina Martins; Amruta Nanavaty; Aynaz Taheri; Catia Pesquita; Emanuel Santos; Isabel F. Cruz; Francisco M. Couto (OM, 2014)

AgreementMakerLight 2.0: Towards Efficient Large-Scale Ontology Matching. - Daniel Faria; Catia Pesquita; Emanuel Santos; Isabel F. Cruz; Francisco M. Couto (ISWC (Posters & Demos), 2014)

Building reference alignments for compound matching of multiple ontologies using OBO cross-products. - Catia Pesquita; Michelle Cheatham; Daniel Faria; Joana Barros; Emanuel Santos; Francisco M. Couto (OM, 2014)

The epidemiology ontology: an ontology for the semantic annotation of epidemiological resources. - Catia Pesquita; João D. Ferreira; Francisco M. Couto; Mário J. Silva (J. Biomed. Semant., 2014)

The Process Model Matching Contest 2015. - Gonçalo Antunes; Marzieh Bakhshandeh; José Borbinha; João Cardoso 002; Sharam Dadashnia; Chiara Di Francescomarino; Mauro Dragoni; Peter Fettke; Avigdor Gal; Chiara Ghidini; Philip Hake; Abderrahmane Khiat; et al. (EMISA, 2015)

Visualization and editing of biomedical ontology alignments in AgreementMakerLight. - Catarina Martins; Daniel Faria; Catia Pesquita (ICBO, 2015)

Towards visualizing the mapping incoherences in Bioportal. - Catarina Martins; Ernesto Jiménez-Ruiz; Emanuel Santos; Catia Pesquita (ICBO, 2015)

Compound matching of biomedical ontologies. - Daniela Oliveira 002; Catia Pesquita (ICBO, 2015)

Inferring logical definitions using compound ontology matching. - Daniela Oliveira 002; Catia Pesquita (ICBO, 2015)

Ontology matching techniques for enterprise architecture models. - Marzieh Bakhshandeh; Catia Pesquita; José Borbinha (OM, 2015)

Results of the Ontology Alignment Evaluation Initiative 2015. - 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; et al. (OM, 2015)

AML results for OAEI 2015. - Daniel Faria; Catarina Martins; Amruta Nanavaty; Daniela Oliveira 002; Booma Sowkarthiga; Aynaz Taheri; Catia Pesquita; Francisco M. Couto; Isabel F. Cruz (OM, 2015)

An Ontological Matching Approach for Enterprise Architecture Model Analysis. - Marzieh Bakhshandeh; Catia Pesquita; José Borbinha (BIS, 2016)

Ontology-Based Approach for Heterogeneity Analysis of EA Models. - João Cardoso 002; Marzieh Bakhshandeh; Daniel Faria; Catia Pesquita; José Borbinha (Business Process Management Workshops, 2016)

Results of the Ontology Alignment Evaluation Initiative 2016. - 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; et al. (OM@ISWC, 2016)

User Validation in Ontology Alignment. - Zlatan Dragisic; Valentina Ivanova; Patrick Lambrix; Daniel Faria; Ernesto Jiménez-Ruiz; Catia Pesquita (ISWC (1), 2016)

OAEI 2016 results of AML. - Daniel Faria; Catia Pesquita; Booma S. Balasubramani; Catarina Martins; João Cardoso 002; Hugo Curado; Francisco M. Couto; Isabel F. Cruz (OM@ISWC, 2016)

Workshop Summary. - Valentina Ivanova; Patrick Lambrix; Steffen Lohmann; Catia Pesquita (VOILA@ISWC, 2016)

Semantic Data Integration. - Michelle Cheatham; Catia Pesquita (Handbook of Big Data Technologies, 2017)

Results of the Ontology Alignment Evaluation Initiative 2017. - 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; et al. (OM@ISWC, 2017)

Results of AML in OAEI 2017. - Daniel Faria; Booma S. Balasubramani; Vivek R. Shivaprabhu; Isabela Mott; Catia Pesquita; Francisco M. Couto; Isabel F. Cruz (OM@ISWC, 2017)

Special issue on ontology and linked data matching. - Michelle Cheatham; Isabel F. Cruz; Jérôme Euzenat; Catia Pesquita (Semantic Web, 2017)

A Framework to Conduct and Report on Empirical User Studies in Semantic Web Contexts. - Catia Pesquita; Valentina Ivanova; Steffen Lohmann; Patrick Lambrix (EKAW, 2018)

Results of the Ontology Alignment Evaluation Initiative 2018. - 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 001; et al. (OM@ISWC, 2018)

Results of AML participation in OAEI 2018. - Daniel Faria; Catia Pesquita; Booma Sowkarthiga Balasubramani; Teemu Tervo; David Carriço; Rodrigo Garrilha; Francisco M. Couto; Isabel F. Cruz (OM@ISWC, 2018)

Complex matching for multiple ontologies: an exploratory study. - Madalena Pavão; Catia Pesquita (OM@ISWC, 2018)

Tackling the challenges of matching biomedical ontologies. - Daniel Faria; Catia Pesquita; Isabela Mott; Catarina Martins; Francisco M. Couto; Isabel F. Cruz (J. Biomed. Semant., 2018)

Improving the interoperability of biomedical ontologies with compound alignments. - Daniela Oliveira 002; Catia Pesquita (J. Biomed. Semant., 2018)

The properties of property alignment on the semantic web. - Michelle Cheatham; Catia Pesquita; Daniela Oliveira 002; Helena B. McCurdy (Int. J. Metadata Semant. Ontologies, 2018)

Results of the Ontology Alignment Evaluation Initiative 2019. - Alsayed Algergawy; Daniel Faria; Alfio Ferrara; Irini Fundulaki; Ian Harrow; Sven Hertling; Ernesto Jiménez-Ruiz; Naouel Karam; Abderrahmane Khiat; Patrick Lambrix; Huanyu Li 001; Stefano Montanelli; et al. (OM@ISWC, 2019)

AML and AMLC Results for OAEI 2019. - Daniel Faria; Catia Pesquita; Teemu Tervo; Francisco M. Couto; Isabel F. Cruz (OM@ISWC, 2019)

User validation in ontology alignment: functional assessment and impact. - Huanyu Li 001; Zlatan Dragisic; Daniel Faria; Valentina Ivanova; Ernesto Jiménez-Ruiz; Patrick Lambrix; Catia Pesquita (Knowl. Eng. Rev., 2019)

Visualization and interaction for ontologies and linked data - Editorial. - Valentina Ivanova; Patrick Lambrix; Steffen Lohmann; Catia Pesquita (J. Web Semant., 2019)

Learning reference alignments for ontology matching within and across domains. - Beatriz Lima; Ruben Branco; João Castanheira; Gustavo Fonseca; Catia Pesquita (OM@ISWC, 2020)

OAEI 2020 results for AML and AMLC. - Beatriz Lima; Daniel Faria; Francisco M. Couto; Isabel F. Cruz; Catia Pesquita (OM@ISWC, 2020)

Results of the Ontology Alignment Evaluation Initiative 2020. - 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; et al. (OM@ISWC, 2020)

A Collection of Benchmark Data Sets for Knowledge Graph-based Similarity in the Biomedical Domain. - Carlota Cardoso; Rita Torres Sousa; Sebastian Köhler; Catia Pesquita (Database J. Biol. Databases Curation, 2020)

Evolving knowledge graph similarity for supervised learning in complex biomedical domains. - Rita Torres Sousa; Sara Silva; Catia Pesquita (BMC Bioinform., 2020)

Crowd-assessing quality in uncertain data linking datasets. - Daniel Faria; Alfio Ferrara; Ernesto Jiménez-Ruiz; Stefano Montanelli; Catia Pesquita (Knowl. Eng. Rev., 2020)

Towards evaluating complex ontology alignments. - Lu Zhou 005; Élodie Thiéblin; Michelle Cheatham; Daniel Faria; Catia Pesquita; Cássia Trojahn dos Santos; Ondrej Zamazal (Knowl. Eng. Rev., 2020)

Towards Semantic Integration for Explainable Artificial Intelligence in the Biomedical Domain. - Catia Pesquita (HEALTHINF, 2021)

evoKGsim+: A Framework for Tailoring Knowledge Graph-Based Similarity for Supervised Learning. - Rita Torres Sousa; Sara Silva; Catia Pesquita (ESWC (Satellite Events), 2021)

Results of SemTab 2021. - Vincenzo Cutrona; Jiaoyan Chen 001; Vasilis Efthymiou; Oktie Hassanzadeh; Ernesto Jiménez-Ruiz; Juan Sequeda; Kavitha Srinivas; Nora Abdelmageed; Madelon Hulsebos; Daniela Oliveira 002; Catia Pesquita (SemTab@ISWC, 2021)

AML and AMLC results for OAEI 2021. - Daniel Faria; Beatriz Lima; Marta Contreiras Silva; Francisco M. Couto; Catia Pesquita (OM@ISWC, 2021)

VOWLMap: Graph-based Ontology Alignment Visualization and Editing. - Ana Guerreiro; Catia Pesquita; Daniel Faria (VOILA@ISWC, 2021)

Pattern-Guided Association Rule Mining for Complex Ontology Alignment. - Beatriz Lima; Daniel Faria; Catia Pesquita (ISWC (Posters/Demos/Industry), 2021)

Challenges of evaluating complex alignments. - Beatriz Lima; Daniel Faria; Catia Pesquita (OM@ISWC, 2021)

Results of the Ontology Alignment Evaluation Initiative 2021. - 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; et al. (OM@ISWC, 2021)

Integrating knowledge graphs for explainable artificial intelligence in biomedicine. - Marta Contreiras Silva; Daniel Faria; Catia Pesquita (OM@ISWC, 2021)

Is there data leakage in protein-protein interaction prediction using knowledge graphs? - Rita Torres Sousa; Sara Silva; Catia Pesquita (ISWC (Posters/Demos/Industry), 2021)

Predicting Gene-Disease Associations with Knowledge Graph Embeddings over Multiple Ontologies. - Susana Nunes; Rita Torres Sousa; Catia Pesquita (CoRR, 2021)

Hierarchical Modelling for ALS Prognosis: Predicting the Progression Towards Critical Events. - Ruben Branco; Diogo F. Soares; Andreia S. Martins; Eleonora Auletta; Eduardo N. Castanho; Susana Nunes; Filipa Serrano; Rita Torres Sousa; Catia Pesquita; Sara C. Madeira; Helena Aidos (CLEF (Working Notes), 2022)

Explaining Artificial Intelligence Predictions of Disease Progression with Semantic Similarity. - Susana Nunes; Rita Torres Sousa; Filipa Serrano; Ruben Branco; Diogo F. Soares; Andreia S. Martins; Eleonora Auletta; Eduardo N. Castanho; Sara C. Madeira; Helena Aidos; Catia Pesquita (CLEF (Working Notes), 2022)

Matching Multiple Ontologies to Build a Knowledge Graph for Personalized Medicine. - Marta Contreiras Silva; Daniel Faria; Catia Pesquita (ESWC, 2022)

Extending AgreementMakerLight to Perform Holistic Ontology Matching. - Marta Contreiras Silva; Daniel Faria; Catia Pesquita (ESWC (Satellite Events), 2022)

The Supervised Semantic Similarity Toolkit. - Rita Torres Sousa; Sara Silva; Catia Pesquita (ESWC (Satellite Events), 2022)

21th International Workshop on Data Mining in Bioinformatics (BIOKDD 2022). - Da Yan 001; Catia Pesquita; Carsten Görg; Jake Y. Chen; Mohammed J. Zaki (KDD, 2022)

Matcha and Matcha-DL results for OAEI 2022. - Daniel Faria; Marta Contreiras Silva; Pedro Cotovio; Patrícia Eugénio; Catia Pesquita (OM@ISWC, 2022)

Results of the Ontology Alignment Evaluation Initiative 2022. - Mina Abd Nikooie Pour; Alsayed Algergawy; Patrice Buche; Leyla Jael Castro; Jiaoyan Chen 001; Hang Dong 002; Omaima Fallatah; Daniel Faria; Irini Fundulaki; Sven Hertling; Yuan He 008; Ian Horrocks 001; et al. (OM@ISWC, 2022)

VOWLExplain: Knowledge Graph visualization for Explainable Artificial Intelligence. - Filipa Serrano; Susana Nunes; Catia Pesquita (VOILA@ISWC, 2022)

Powering Biomedical Artificial Intelligence with a Holistic Knowledge Graph (invited talk). - Catia Pesquita (SeWeBMeDA@ESWC, 2022)

Towards Supervised Biomedical Semantic Similarity. - Rita Torres Sousa; Sara Silva; Catia Pesquita (SeWeBMeDA@ESWC, 2022)

Benchmark Datasets for Biomedical Knowledge Graphs with Negative Statements. - Rita Torres Sousa; Sara Silva; Catia Pesquita (SeWeBMeDA@ESWC, 2023)

Explainable Representations for Relation Prediction in Knowledge Graphs. - Rita Torres Sousa; Sara Silva; Catia Pesquita (KR, 2023)

Results for Matcha and Matcha-DL in OAEI 2023. - Daniel Faria; Marta Contreiras Silva; Pedro Cotovio; Lucas Ferraz; Laura Balbi; Catia Pesquita (OM@ISWC, 2023)

Results of the Ontology Alignment Evaluation Initiative 2023. - Mina Abd Nikooie Pour; Alsayed Algergawy; Patrice Buche; Leyla Jael Castro; Jiaoyan Chen 001; Adrien Coulet; Julien Cufi; Hang Dong 002; Omaima Fallatah; Daniel Faria; Irini Fundulaki; Sven Hertling; et al. (OM@ISWC, 2023)

Biomedical Knowledge Graph Embeddings with Negative Statements. - Rita Torres Sousa; Sara Silva; Heiko Paulheim; Catia Pesquita (ISWC, 2023)

Supervised Biomedical Semantic Similarity. - Rita Torres Sousa; Sara Silva; Catia Pesquita (IEEE Access, 2023)

What can knowledge graph alignment gain with Neuro-Symbolic learning approaches? - Pedro Giesteira Cotovio; Ernesto Jiménez-Ruiz; Catia Pesquita (CoRR, 2023)

Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities. - Jiaoyan Chen 001; Hang Dong 002; Janna Hastings; Ernesto Jiménez-Ruiz; Vanessa López; Pierre Monnin; Catia Pesquita; Petr Skoda 001; Valentina Tamma (TGDK, 2023)

Multi-domain knowledge graph embeddings for gene-disease association prediction. - Susana Nunes; Rita Torres Sousa; Catia Pesquita (J. Biomed. Semant., 2023)

Knowledge Graph Embeddings for ICU readmission prediction. - Ricardo M. S. Carvalho; Daniela Oliveira 002; Catia Pesquita (BMC Medical Informatics Decis. Mak., 2023)

Building a Temporal Knowledge Graph for Electronic Health Records. - Ricardo Miguel Serafim de Carvalho; Catia Pesquita; Andreia Sofia Teixeira (DAO-XAI@ECAI, 2024)

Drug Repurposing Hypothesis Validation with Knowledge-infused Explanations. - Susana Nunes; Catia Pesquita (DAO-XAI@ECAI, 2024)

Complex Multi-Ontology Alignment Through Geometric Operations on Language Embeddings. - Marta Contreiras Silva; Daniel Faria; Catia Pesquita (ECAI, 2024)

Results in OAEI 2024 for Matcha. - Daniel Faria; Marta Contreiras Silva; Pedro Cotovio; Lucas Ferraz; Laura Balbi; Catia Pesquita (OM@ISWC, 2024)

Results of the Ontology Alignment Evaluation Initiative 2024. - Mina Abd Nikooie Pour; Alsayed Algergawy; Eva Blomqvist; Patrice Buche; Jiaoyan Chen 001; Adrien Coulet; Julien Cufi; Hang Dong 002; Daniel Faria; Lucas Ferraz; Pedro Giesteira Cotovio; Yuan He 008; et al. (OM@ISWC, 2024)

Editorial: Special issue on Interactive Semantic Web. - Bo Fu 005; Patrick Lambrix; Catia Pesquita (Semantic Web, 2024)

Guest Editorial Selected Papers From BIOKDD 2022. - Da Yan 001; Catia Pesquita; Carsten Görg; Jake Y. Chen (IEEE ACM Trans. Comput. Biol. Bioinform., 2024)

The Immunopeptidomics Ontology (ImPO). - 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 (Database J. Biol. Databases Curation, 2024)

Explaining protein-protein interactions with knowledge graph-based semantic similarity. - Rita Torres Sousa; Sara Silva; Catia Pesquita (Comput. Biol. Medicine, 2024)

Can Language Models Align Biomedical Ontologies?: Evaluating Retrieval-Augmented Prompt Strategies in Bio-ML. - Lucas Ferraz; Pedro Giesteira Cotovio; Catia Pesquita (SeWeBMeDA@ESWC, 2025)

Knowledge Graphs for Explainable Scientific Discovery. - Catia Pesquita (SeWeBMeDA@ESWC, 2025)

Towards leveraging explicit negative statements in knowledge graph embeddings. - Rita Torres Sousa; Catia Pesquita; Heiko Paulheim (J. Web Semant., 2025)

A Systematic Evaluation of Knowledge Graph Embeddings for Gene-Disease Association Prediction. - Catarina Canastra; Catia Pesquita (CoRR, 2025)