Peptide programs: applying fragment programs to protein classification. - André O. Falcão; Daniel Faria; António E. N. Ferreira (DTMBIO, 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)

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

Enzyme classification with peptide programs: a comparative study. - Daniel Faria; António E. N. Ferreira; André O. Falcão (BMC Bioinform., 2009)

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

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)

The OCRC Fuel Cell Lab Safety System: A Self-Stabilizing Safety-Critical System. - William Leal; Micah McCreery; Daniel Faria (SSS, 2011)

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)

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)

Benchmarking some Portuguese S&T system research units - Francisco M. Couto; Daniel Faria; Bruno Tavares; Pedro Gonçalves; Paulo Veríssimo (CoRR, 2013)

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

Results of the Ontology Alignment Evaluation Initiative 2014. - Zlatan Dragisic; Kai Eckert 001; Jérôme Euzenat; Daniel Faria; Alfio Ferrara; Roger Granada; Valentina Ivanova; Ernesto Jiménez-Ruiz; Andreas Oskar Kempf; Patrick Lambrix; Stefano Montanelli; Heiko Paulheim; et al. (OM, 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)

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

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)

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)

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)

Introducing the HOBBIT platform into the ontology alignment evaluation campaign. - Ernesto Jiménez-Ruiz; Tzanina Saveta; Ondrej Zamazal; Sven Hertling; Michael Röder; Irini Fundulaki; Axel-Cyrille Ngonga Ngomo; Mohamed Ahmed Sherif; Amina Annane; Zohra Bellahsene; Sadok Ben Yahia; Gayo Diallo; et al. (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)

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)

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)

CorkOakDB - The Cork Oak Genome Database Portal. - Cirenia Arias-Baldrich; Marta Contreiras Silva; Filippo Bergeretti; Inês Chaves; Célia Miguel; Nelson J. M. Saibo; Daniel Sobral; Daniel Faria; Pedro M. Barros (Database J. Biol. Databases Curation, 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)

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)

Blockchain Analytics - Real-time Log Management in Healthcare. - Tiago Guimarães; Ricardo Duarte; Bruno Pinheiro; Daniel Faria; Paulo Gomes; Manuel Filipe Santos (ANT/EDI40, 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)

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)

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)

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)

Upgrade of Lark Compiler Generator to Support Attribute Grammars. - Daniel Faria; Tiago João Baptista; Pedro Rangel Henriques (SLATE, 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)