Here you can consult: Journal Articles, Conference Papers, Posters, and Book Chapters.
Complex multi-ontology alignment through geometric operations on language embeddings M.C.Silva, D.Faria, C.Pesquita |
Drug Repurposing Hypothesis Validation with Knowledge-infused Explanations S.Nunes, C.Pesquita |
Building a Temporal Knowledge Graph for Electronic Health Records R.M.S. Carvalho, A.S.Teixeira, C.Pesquita |
Injecting domain knowledge into graph neural networks for protein-protein interactions L.Balbi, R.T.Sousa, P.G.Cotovio, C.Pesquita |
Matcha-DL a tool for supervised ontology alignment P.G.Cotovio, L.Ferraz, D.Faria, L.Balbi, M.C.Silva, C.Pesquita |
The Immunopeptidomics Ontology (ImPO) D.Faria, P.Eugénio, M.C.Silva, L.Balbi, G.Bedran, A.A.Kallor, S.Nunes, A.Palkowski, M.Waleron, J.A.Alfaro, C.Pesquita |
Explaining protein–protein interactions with knowledge graph-based semantic similarity Rita T. Sousa, Sara Silva, Heiko Paulheim, Catia Pesquita |
Multi-domain Knowledge Graph Embeddings for Gene-Disease Association Prediction Susana Nunes, Rita T. Sousa, Catia Pesquita |
Results for Matcha and Matcha-DL in OAEI 2023 D. Faria, M.C. Silva, P. Cotovio, L. Ferraz, L. Balbi, C. Pesquita |
Biomedical Knowledge Graph Embeddings with Negative Statements Rita T. Sousa, Heiko Paulheim, Sara Silva, Catia Pesquita |
Explainable representations for relation prediction in knowledge graphs Rita T. Sousa, Sara Silva, Catia Pesquita |
Supervised Biomedical Semantic Similarity Rita T. Sousa, Sara Silva, Catia Pesquita |
Benchmark datasets for biomedical knowledge graphs with negative statements Rita T. Sousa, Sara Silva, Catia Pesquita |
Matching Multiple Ontologies to Build a Knowledge Graph for Personalized Medicine M.C. Silva, D. Faria, C. Pesquita |
Explaining artificial intelligence predictions of disease progression with semantic similarity 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 |
Towards supervised biomedical semantic similarity Rita T. Sousa, Sara Silva, Catia Pesquita |
The supervised semantic similarity toolkit Rita T. Sousa, Sara Silva, Catia Pesquita |
Extending AgreementMakerLight to Perform Holistic Ontology Matching M.C. Silva, D. Faria, C. Pesquita |
Explaining protein-protein interaction predictions with genetic programming Rita T. Sousa, Sara Silva, Catia Pesquita |
Linking Patient Data to Ontologies to Support Semantic Mining R.M.S Carvalho, D. Oliveira, C. Pesquita |
Ontologies and Knowledge Graphs in Oncology Research M.C. Silva, P. Eugénio, D. Faria, C. Pesquita |
Challenges of evaluating complex alignments B. Lima, D. Faria, C. Pesquita |
VOWLMap: Graph-based Ontology Alignment Visualization and Editing A. Guerreiro, C. Pesquita, D. Faria |
Pattern-Guided Association Rule Mining for Complex Ontology Alignment B. Lima, D. Faria, C. Pesquita |
VOWLMap: graph-based ontology alignment visualization and editing A. Guerreiro, C. Pesquita, D. Faria |
Is there data leakage in protein-protein interaction prediction using knowledge graphs? R.T. Sousa, S. Silva, C. Pesquita |
Integrating knowledge graphs for explainable artificial intelligence in biomedicine M.C. Silva, D. Faria, C. Pesquita |
Predicting Gene-Disease Associations with Knowledge Graph Embeddings over Multiple Ontologies S. Nunes, R.T. Sousa, C. Pesquita |
evoKGsim+: a framework for tailoring Knowledge Graph-based similarity for supervised learning R.T. Sousa, S. Silva, C. Pesquita |
Towards Semantic Integration for Explainable Artificial Intelligence in the Biomedical Domain C. Pesquita |
Learning reference alignments for ontology matching within and across domains B. Lima, R. Branco, J. Castanheira, G. Fonseca, C. Pesquita |
Evolving knowledge graph similarity for supervised learning in complex biomedical domains R.T. Sousa, S. Silva, C. Pesquita |
A Collection of Benchmark data sets for Knowledge Graph-based Similarity in the Biomedical Domain C. Cardoso, R.T. Sousa, S. Köhler, C. Pesquita |
OAEI 2020 results for AML and AMLC B. Lima, D. Faria, F. M. Couto, I. F. Cruz, C. Pesquita |
Crowd-assessing quality in uncertain data linking datasets D. Faria, A. Ferrara, E. Jiménez-Ruiz, S. Montanelli, C. Pesquita |
Biomedical Ontologies: Coverage, Access and Use J.D. Ferreira, D.C. Teixeira, C. Pesquita |
Towards evaluating complex ontology alignments L. Zhou, E. Thiéblin, M. Cheatham, D. Faria, C. Pesquita, C. Trojahn, O. Zamaza |
A Collection of Benchmark data sets for Knowledge Graph-based Similarity in the Biomedical Domain C. Cardoso, R.T. Sousa, S. Köhler, C. Pesquita |
User validation in ontology alignment: functional assessment and impact L. Huanyu, Z. Dragisic, D. Faria, V. Ivanova, E. Jimenez-Ruiz, P. Lambrix, C. Pesquita |
AML and AMLC results for OAEI 2019 D. Faria, C. Pesquita, T. Tervo, F.M. Couto, I.F. Cruz |
Visualization and interaction for ontologies and linked data V. Ivanova, P. Lambrix, S. Lohmann, C. Pesquita |
User validation in ontology alignment: functional assessment and impact H. Li, Z. Dragisic, D. Faria, V. Ivanova, E. Jiménez-Ruiz, P. Lambrix, C. Pesquita |
Evolving meaning: Using genetic Programming to learn similarity perspectives for mining biomedical data R.T. Sousa, S. Silva, C. Pesquita |
Tackling the challenges of matching biomedical ontologies D. Faria, C. Pesquita, I. Mott, C. Martins, F.M. Couto, I.F. Cruz |
The properties of property alignment on the semantic web M. Cheatham, C. Pesquita, D. Oliveira, H.B. McCurdy |
A framework to conduct and report on empirical user studies in semantic web contexts C. Pesquita, V. Ivanova, S. Lohmann, P. Lambrix |
Improving the interoperability of biomedical ontologies with compound alignments D. Oliveira, C. Pesquita |
Results of AML participation in OAEI 2018 D. Faria, C. Pesquita, B. Balasubramani, T. Tervo, D. Carriço, R. Garrilha, F. Couto, I.F. Cruz |
Complex matching for multiple ontologies: an exploratory study M. Pavão, C. Pesquita |
Results of AML in OAEI 2017 D. Faria, B.S. Balasubramani, V.R. Shivaprabhu, I. Mott, C. Pesquita, F.M. Couto, I.F. Cruz |
Expression profiling in Pinus pinaster in response to infection with the pine wood nematode Bursaphelenchus xylophilus D. Gaspar, C. Trindade, A. Usié, B. Meireles, P. Barbosa, A.M. Fortes, C. Pesquita, R.L. Costa, A.M. Ramos |
Semantic Data Integration M. Cheatham, C. Pesquita |
Semantic Similarity in the Gene Ontology C. Pesquita |
User validation in ontology alignment Z. Dragisic, V. Ivanova, P. Lambrix, D. Faria, E. Jiménez-Ruiz, C. Pesquita |
Optimizing 16S Analysis Pipelines S. Viana, C. Pesquita, D. Sobral, D. Faria |
An ontological matching approach for enterprise architecture model analysis M. Bakhshandeh, C. Pesquita, J. Borbinha |
Ontology-Based Approach for Heterogeneity Analysis of EA Models J. Cardoso, M. Bakhshandeh, D. Faria, C. Pesquita, J. Borbinha |
OAEI 2016 results of AML D. Faria, C. Pesquita, B.S. Balasubramani, C. Martins, J. Cardoso, H. Curado, F.M. Couto, I.F. Cruz |
Ontology alignment repair through modularization and confidence-based heuristics E. Santos, D. Faria, C. Pesquita, F.M. Couto |
Compound Matching of Biomedical Ontologies D. Oliveira, C. Pesquita |
Towards visualizing the mapping incoherences in Bioportal C. Martins, E. Jimenez-Ruiz, E. Santos, C. Pesquita |
Visualization and editing of biomedical ontology alignments in AgreementMakerLight C. Martins, D. Faria, C. Pesquita |
Inferring logical definitions using compound ontology matching D. Oliveira, C. Pesquita |
AML results for OAEI 2015 D. Faria, C. Martins, A. Nanavaty, D. Oliveira, B. Sowkarthiga, A. Taheri, C. Pesquita, F.M. Couto, I.F. Cruz |
Ontology matching techniques for enterprise architecture models M. Bakhshandeh, C. Pesquita, J.L. Borbinha |
Castanea root transcriptome in response to Phytophthora cinnamomi challenge S. Serrazina, C. Santos, H. Machado, C. Pesquita, R. Vicentini, M.S. Pais, M. Sebastiana, R. Costa |