DeepGOWeb: fast and accurate protein function prediction on the (Semantic) Web. - Maxat Kulmanov; Fernando Zhapa-Camacho; Robert Hoehndorf (Nucleic Acids Res., 2021)

A-LIOn - alignment learning through inconsistency negatives of the aligned ontologies. - Sarah M. Alghamdi; Fernando Zhapa-Camacho; Robert Hoehndorf (OM@ISWC, 2022)

From Axioms over Graphs to Vectors, and Back Again: Evaluating the Properties of Graph-based Ontology Embeddings. - Fernando Zhapa-Camacho; Robert Hoehndorf (NeSy, 2023)

Evaluating Different Methods for Semantic Reasoning Over Ontologies. - Fernando Zhapa-Camacho; Robert Hoehndorf (QALD/SemREC@ISWC, 2023)

CatE: Embedding ALC ontologies using category-theoretical semantics. - Fernando Zhapa-Camacho; Robert Hoehndorf (CoRR, 2023)

mOWL: Python library for machine learning with biomedical ontologies. - Fernando Zhapa-Camacho; Maxat Kulmanov; Robert Hoehndorf (Bioinform., 2023)

Enhancing Geometric Ontology Embeddings for Eℒ++ with Negative Sampling and Deductive Closure Filtering. - Olga Mashkova; Fernando Zhapa-Camacho; Robert Hoehndorf (NeSy (1), 2024)

Lattice-Preserving ALC Ontology Embeddings. - Fernando Zhapa-Camacho; Robert Hoehndorf (NeSy (1), 2024)

Predicting protein functions using positive-unlabeled ranking with ontology-based priors. - Fernando Zhapa-Camacho; Zhenwei Tang; Maxat Kulmanov; Robert Hoehndorf (Bioinform., 2024)

Enhancing Geometric Ontology Embeddings for ℰℒ++ with Negative Sampling and Deductive Closure Filtering. - Olga Mashkova; Fernando Zhapa-Camacho; Robert Hoehndorf (CoRR, 2024)

DELE: Deductive ℰℒ++ Embeddings for Knowledge Base Completion. - Olga Mashkova; Fernando Zhapa-Camacho; Robert Hoehndorf (CoRR, 2024)

Fully Geometric Multi-Hop Reasoning on Knowledge Graphs with Transitive Relations. - Fernando Zhapa-Camacho; Robert Hoehndorf (CoRR, 2025)

Ontology Embedding: A Survey of Methods, Applications and Resources. - Jiaoyan Chen 001; Olga Mashkova; Fernando Zhapa-Camacho; Robert Hoehndorf; Yuan He 008; Ian Horrocks 001 (IEEE Trans. Knowl. Data Eng., 2025)