A top-level ontology of functions and its application in the Open Biomedical Ontologies. - Patryk Burek; Robert Hoehndorf; Frank Loebe; Johann Visagie; Heinrich Herre; Janet Kelso (ISMB (Supplement of Bioinformatics), 2006)

A Proposal for a Gene Functions Wiki. - Robert Hoehndorf; Kay Prüfer; Michael Backhaus; Heinrich Herre; Janet Kelso; Frank Loebe; Johann Visagie (OTM Workshops (1), 2006)

BOWiki - a Collaborative Annotation and Ontology Curation Framework. - Michael Backhaus; Janet Kelso; Joshua Bacher; Heinrich Herre; Robert Hoehndorf; Frank Loebe; Johann Visagie (CKC, 2007)

Representing default knowledge in biomedical ontologies: application to the integration of anatomy and phenotype ontologies. - Robert Hoehndorf; Frank Loebe; Janet Kelso; Heinrich Herre (BMC Bioinform., 2007)

BOWiki: Ontology-based Semantic Wiki with ABox Reasoning. - Joshua Bacher; Robert Hoehndorf; Janet Kelso (SemWiki, 2008)

GFO-Bio: A biological core ontology. - Robert Hoehndorf; Frank Loebe; Roberto Poli; Heinrich Herre; Janet Kelso (Appl. Ontology, 2008)

Developing Consistent and Modular Software Models with Ontologies. - Robert Hoehndorf; Axel-Cyrille Ngonga Ngomo; Heinrich Herre (SoMeT, 2009)

BOWiki: an ontology-based wiki for annotation of data and integration of knowledge in biology. - Robert Hoehndorf; Joshua Bacher; Michael Backhaus; Sergio E. Gregorio Jr.; Frank Loebe; Kay Prüfer; Alexandr Uciteli; Johann Visagie; Heinrich Herre; Janet Kelso (BMC Bioinform., 2009)

The ontology of biological sequences. - Robert Hoehndorf; Janet Kelso; Heinrich Herre (BMC Bioinform., 2009)

Basic considerations for improving interoperability between ontology based biological information systems. - Robert Hoehndorf (2009)

Realism for scientific ontologies. - Michel Dumontier; Robert Hoehndorf (FOIS, 2010)

Relational Patterns in OWL and Their Application to OBO. - Robert Hoehndorf; Anika Oellrich; Michel Dumontier; Heinrich Herre; Dietrich Rebholz-Schuhmann (OWLED, 2010)

Applying ontology design patterns to the implementation of relations in GENIA. - Robert Hoehndorf; Axel-Cyrille Ngonga Ngomo; Sampo Pyysalo; Tomoko Ohta; Anika Oellrich; Dietrich Rebholz-Schuhmann (Semantic Mining in Biomedicine, 2010)

Interoperability between phenotype and anatomy ontologies. - Robert Hoehndorf; Anika Oellrich; Dietrich Rebholz-Schuhmann (Bioinform., 2010)

Applying the functional abnormality ontology pattern to anatomical functions. - Robert Hoehndorf; Axel-Cyrille Ngonga Ngomo; Janet Kelso (J. Biomed. Semant., 2010)

Relations as patterns: bridging the gap between OBO and OWL. - Robert Hoehndorf; Anika Oellrich; Michel Dumontier; Janet Kelso; Dietrich Rebholz-Schuhmann; Heinrich Herre (BMC Bioinform., 2010)

An Advanced Strategy for Integration of Biological Measurement Data. - Hiroshi Masuya; Georgios V. Gkoutos; Nobuhiko Tanaka; Kazunori Waki; Yoshihiro Okuda; Tatsuya Kushida; Norio Kobayashi; Koji Doi; Kouji Kozaki; Robert Hoehndorf; Shigeharu Wakana; Tetsuro Toyoda; et al. (ICBO, 2011)

Higgs Bosons, Mars Missions, and Unicorn Delusions: How to Deal with Terms of Dubious Reference in Scientific Ontologies. - Stefan Schulz 001; Mathias Brochhausen; Robert Hoehndorf (ICBO, 2011)

The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data. - Robert Hoehndorf; Colin R. Batchelor; Thomas Bittner; Michel Dumontier; Karen Eilbeck; Rob Knight 001; Chris Mungall; Jane S. Richardson; Jesse Stombaugh; Eric Westhof; Craig L. Zirbel; Neocles Leontis (Appl. Ontology, 2011)

PIDO: the primary immunodeficiency disease ontology. - Nico Adams; Robert Hoehndorf; Georgios V. Gkoutos; Gesine Hansen; Christian Hennig (Bioinform., 2011)

A common layer of interoperability for biomedical ontologies based on OWL EL. - Robert Hoehndorf; Michel Dumontier; Anika Oellrich; Sarala M. Wimalaratne; Dietrich Rebholz-Schuhmann; Paul N. Schofield; Georgios V. Gkoutos (Bioinform., 2011)

OBML - Ontologies in Biomedicine and Life Sciences. - Heinrich Herre; Robert Hoehndorf; Janet Kelso; Frank Loebe; Stefan Schulz 001 (J. Biomed. Semant., 2011)

Ontology design patterns to disambiguate relations between genes and gene products in GENIA. - Robert Hoehndorf; Axel-Cyrille Ngonga Ngomo; Sampo Pyysalo; Tomoko Ohta; Anika Oellrich; Dietrich Rebholz-Schuhmann (J. Biomed. Semant., 2011)

Integrating systems biology models and biomedical ontologies. - Robert Hoehndorf; Michel Dumontier; John H. Gennari; Sarala M. Wimalaratne; Bernard de Bono; Daniel L. Cook; Georgios V. Gkoutos (BMC Syst. Biol., 2011)

Argumentation to Represent and Reason over Biological Systems. - Adam Z. Wyner; Luke Riley; Robert Hoehndorf; Samuel Croset (ITBAM, 2012)

Linking PharmGKB to Phenotype Studies and Animal Models of Disease for Drug Repurposing. - Robert Hoehndorf; Anika Oellrich; Dietrich Rebholz-Schuhmann; Paul N. Schofield; Georgios V. Gkoutos (Pacific Symposium on Biocomputing, 2012)

Profiling of Semantically Annotated Proteins. - Jens Hollunder; Vladimir Mironov; Erick Antezana; Robert Hoehndorf; Martin Kuiper (SWAT4LS, 2012)

The Units Ontology: a tool for integrating units of measurement in science. - Georgios V. Gkoutos; Paul N. Schofield; Robert Hoehndorf (Database J. Biol. Databases Curation, 2012)

Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics. - Robert Hoehndorf; Michel Dumontier; Georgios V. Gkoutos (Bioinform., 2012)

Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology. - Robert Hoehndorf; Midori A. Harris; Heinrich Herre; Gabriella Rustici; Georgios V. Gkoutos (Bioinform., 2012)

An infrastructure for ontology-based information systems in biomedicine: RICORDO case study. - Sarala M. Wimalaratne; Pierre Grenon; Robert Hoehndorf; Georgios V. Gkoutos; Bernard de Bono (Bioinform., 2012)

Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes. - Georgios V. Gkoutos; Robert Hoehndorf (J. Biomed. Semant., 2012)

Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL. - Simon Jupp; Robert Stevens 001; Robert Hoehndorf (J. Biomed. Semant., 2012)

Towards improving phenotype representation in OWL. - Frank Loebe; Frank Stumpf; Robert Hoehndorf; Heinrich Herre (J. Biomed. Semant., 2012)

Quantitative comparison of mapping methods between Human and Mammalian Phenotype Ontology. - Anika Oellrich; Georgios V. Gkoutos; Robert Hoehndorf; Dietrich Rebholz-Schuhmann (J. Biomed. Semant., 2012)

Towards quantitative measures in applied ontology - Robert Hoehndorf; Michel Dumontier; Georgios V. Gkoutos (CoRR, 2012)

Evaluation of research in biomedical ontologies. - Robert Hoehndorf; Michel Dumontier; Georgios V. Gkoutos (Briefings Bioinform., 2013)

Representing physiological processes and their participants with PhysioMaps. - Daniel L. Cook; Maxwell Lewis Neal; Robert Hoehndorf; Georgios V. Gkoutos; John H. Gennari (J. Biomed. Semant., 2013)

Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources. - Dietrich Rebholz-Schuhmann; Senay Kafkas; Jee-Hyub Kim; Chen Li 011; Antonio Jimeno-Yepes; Robert Hoehndorf; Rolf Backofen; Ian Lewin (J. Biomed. Semant., 2013)

Mouse model phenotypes provide information about human drug targets. - Robert Hoehndorf; Tanya Hiebert; Nigel W. Hardy; Paul N. Schofield; Georgios V. Gkoutos; Michel Dumontier (Bioinform., 2014)

The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery. - Michel Dumontier; Christopher J. O. Baker; Joachim Baran; Alison Callahan; Leonid L. Chepelev; Jose Cruz-Toledo; Nicholas R. Del Rio; Geraint Duck; Laura Inés Furlong; Nichealla Keath; Dana Klassen; Jamie P. McCusker; et al. (J. Biomed. Semant., 2014)

Thematic series on biomedical ontologies in JBMS: challenges and new directions. - Robert Hoehndorf; Dietrich Rebholz-Schuhmann; Melissa A. Haendel; Robert Stevens 001 (J. Biomed. Semant., 2014)

Using Aber-OWL for fast and scalable reasoning over BioPortal ontologies. - Luke T. Slater; Georgios V. Gkoutos; Paul N. Schofield; Robert Hoehndorf (ICBO, 2015)

AberOWL: an ontology portal with OWL EL reasoning. - Luke T. Slater; Georgios V. Gkoutos; Paul N. Schofield; Robert Hoehndorf (ICBO, 2015)

Experiences with Aber-OWL, an Ontology Repository with OWL EL Reasoning. - Luke T. Slater; Miguel Ángel Rodríguez-García; Keiron O'Shea; Paul N. Schofield; Georgios V. Gkoutos; Robert Hoehndorf (OWLED, 2015)

Visualising Ontologies with AberOWL. - Miguel Ángel Rodríguez-García; Luke T. Slater; Keiron O'Shea; Paul N. Schofield; Georgios V. Gkoutos; Robert Hoehndorf (SWAT4LS, 2015)

The role of ontologies in biological and biomedical research: a functional perspective. - Robert Hoehndorf; Paul N. Schofield; Georgios V. Gkoutos (Briefings Bioinform., 2015)

Similarity-based search of model organism, disease and drug effect phenotypes. - Robert Hoehndorf; Michael Gruenberger; Georgios V. Gkoutos; Paul N. Schofield (J. Biomed. Semant., 2015)

Aber-OWL: a framework for ontology-based data access in biology. - Robert Hoehndorf; Luke T. Slater; Paul N. Schofield; Georgios V. Gkoutos (BMC Bioinform., 2015)

Large-Scale Reasoning over Functions in Biomedical Ontologies. - Robert Hoehndorf; Liam Mencel; Georgios V. Gkoutos; Paul N. Schofield (FOIS, 2016)

SPARQL2OWL: Towards Bridging the Semantic Gap Between RDF and OWL. - Mona Alshahrani; Hussein Almashouq; Robert Hoehndorf (ICBO/BioCreative, 2016)

FoodON: A Global Farm-to-Fork Food Ontology. - Emma J. Griffiths; Damion M. Dooley; Pier Luigi Buttigieg; Robert Hoehndorf; Fiona S. L. Brinkman; William W. L. Hsiao (ICBO/BioCreative, 2016)

Updates to the AberOWL Ontology Repository. - Miguel Ángel Rodríguez-García; Luke T. Slater; Imane Boudellioua; Paul N. Schofield; Georgios V. Gkoutos; Robert Hoehndorf (ICBO/BioCreative, 2016)

To MIREOT or not to MIREOT? A Case Study of the Impact of Using MIREOT in the Experimental Factor Ontology (EFO). - Luke T. Slater; Georgios V. Gkoutos; Paul N. Schofield; Robert Hoehndorf (ICBO/BioCreative, 2016)

FLOPO - An Ontology for the Integration of Trait Data from Digitized Floras and Plant Image Collections. - Claus Weiland; Robert Hoehndorf; George Gosline; Quentin Groom; Thomas Hamann; Marco Schmidt 003 (SWAT4LS, 2016)

FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation. - Jerven T. Bolleman; Christopher J. Mungall; Francesco Strozzi; Joachim Baran; Michel Dumontier; Raoul Jean Pierre Bonnal; Robert M. Buels; Robert Hoehndorf; Takatomo Fujisawa; Toshiaki Katayama; Peter J. A. Cock (J. Biomed. Semant., 2016)

DermO; an ontology for the description of dermatologic disease. - Hannah M. Fisher; Robert Hoehndorf; Bruno S. Bazelato; Soheil S. Dadras; Lloyd E. King; Georgios V. Gkoutos; John P. Sundberg; Paul N. Schofield (J. Biomed. Semant., 2016)

The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants. - Robert Hoehndorf; Mona Alshahrani; Georgios V. Gkoutos; George Gosline; Quentin Groom; Thomas Hamann; Jens Kattge; Sylvia Mota de Oliveira; Marco Schmidt 003; Soraya Sierra; Erik Smets; Rutger A. Vos; et al. (J. Biomed. Semant., 2016)

Using AberOWL for fast and scalable reasoning over BioPortal ontologies. - Luke T. Slater; Georgios V. Gkoutos; Paul N. Schofield; Robert Hoehndorf (J. Biomed. Semant., 2016)

DESM: portal for microbial knowledge exploration systems. - Adil Salhi; Magbubah Essack; Aleksandar Radovanovic; Benoit Marchand; Salim Bougouffa; André Antunes 001; Marta Filipa Simões; Feras F. Lafi; Olaa A. Motwalli; Ameerah Bokhari; Tariq Malas; Soha Al Amoudi; et al. (Nucleic Acids Res., 2016)

Notions of similarity for systems biology models. - Ron Henkel; Robert Hoehndorf; Tim Kacprowski; Christian Knüpfer; Wolfram Liebermeister; Dagmar Waltemath (Briefings Bioinform., 2017)

Neuro-symbolic representation learning on biological knowledge graphs. - Mona Alshahrani; Mohammad Asif Khan 001; Omar Maddouri; Akira R. Kinjo; Núria Queralt-Rosinach; Robert Hoehndorf (Bioinform., 2017)

Evaluating the effect of annotation size on measures of semantic similarity. - Maxat Kulmanov; Robert Hoehndorf (J. Biomed. Semant., 2017)

Integrating phenotype ontologies with PhenomeNET. - Miguel Ángel Rodríguez-García; Georgios V. Gkoutos; Paul N. Schofield; Robert Hoehndorf (J. Biomed. Semant., 2017)

Usage of cell nomenclature in biomedical literature. - Senay Kafkas; Sirarat Sarntivijai; Robert Hoehndorf (BMC Bioinform., 2017)

Data Science and symbolic AI: Synergies, challenges and opportunities. - Robert Hoehndorf; Núria Queralt-Rosinach (Data Sci., 2017)

Semantic prioritization of novel causative genomic variants. - Imane Boudellioua; Rozaimi B. Mahamad Razali; Maxat Kulmanov; Yasmeen Hashish; Vladimir B. Bajic; Eva Goncalves-Serra; Nadia Schoenmakers; Georgios V. Gkoutos; Paul N. Schofield; Robert Hoehndorf (PLoS Comput. Biol., 2017)

Vec2SPARQL: integrating SPARQL queries and knowledge graph embeddings. - Maxat Kulmanov; Senay Kafkas; Andreas Karwath; Alexander Malic; Georgios V. Gkoutos; Michel Dumontier; Robert Hoehndorf (SWAT4LS, 2018)

The anatomy of phenotype ontologies: principles, properties and applications. - Georgios V. Gkoutos; Paul N. Schofield; Robert Hoehndorf (Briefings Bioinform., 2018)

Semantic Disease Gene Embeddings (SmuDGE): phenotype-based disease gene prioritization without phenotypes. - Mona Alshahrani; Robert Hoehndorf (Bioinform., 2018)

DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier. - Maxat Kulmanov; Mohammad Asif Khan 001; Robert Hoehndorf (Bioinform., 2018)

Ontology-based validation and identification of regulatory phenotypes. - Maxat Kulmanov; Paul N. Schofield; Georgios V. Gkoutos; Robert Hoehndorf (Bioinform., 2018)

Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations. - Fatima Zohra Smaili; Xin Gao 001; Robert Hoehndorf (Bioinform., 2018)

Inferring ontology graph structures using OWL reasoning. - Miguel Ángel Rodríguez-García; Robert Hoehndorf (BMC Bioinform., 2018)

The Flora Phenotype Ontology (FLOPO) and the FLOPO Knowledgebase. - Robert Hoehndorf; Claus Weiland; Marco Schmidt 003; Quentin Groom; George Gosline; Stefan Dressler; Thomas Hamann (Application of Semantic Technology in Biodiversity Science, 2018)

EL Embeddings: Geometric Construction of Models for the Description Logic EL++. - Maxat Kulmanov; Wang Liu-Wei; Yuan Yan; Robert Hoehndorf (IJCAI, 2019)

Semi-Supervised Entity Alignment via Knowledge Graph Embedding with Awareness of Degree Difference. - Shichao Pei; Lu Yu 006; Robert Hoehndorf; Xiangliang Zhang 001 (WWW, 2019)

Ontology based text mining of gene-phenotype associations: application to candidate gene prediction. - Senay Kafkas; Robert Hoehndorf (Database J. Biol. Databases Curation, 2019)

OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction. - Fatima Zohra Smaili; Xin Gao 001; Robert Hoehndorf (Bioinform., 2019)

Ontology based mining of pathogen-disease associations from literature. - Senay Kafkas; Robert Hoehndorf (J. Biomed. Semant., 2019)

BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services. - Toshiaki Katayama; Shuichi Kawashima; Gos Micklem; Shin Kawano; Jin-Dong Kim; Simon Kocbek; Shinobu Okamoto; Yue Wang 040; Hongyan Wu; Atsuko Yamaguchi; Yasunori Yamamoto; Erick Antezana; et al. (F1000Research, 2019)

DeepPVP: phenotype-based prioritization of causative variants using deep learning. - Imane Boudellioua; Maxat Kulmanov; Paul N. Schofield; Georgios V. Gkoutos; Robert Hoehndorf (BMC Bioinform., 2019)

Formal axioms in biomedical ontologies improve analysis and interpretation of associated data. - Fatima Zohra Smaili; Xin Gao 001; Robert Hoehndorf (Bioinform., 2020)

Combining lexical and context features for automatic ontology extension. - Sara Althubaiti; Senay Kafkas; Marwa Abdelhakim; Robert Hoehndorf (J. Biomed. Semant., 2020)

Efficient long-distance relation extraction with DG-SpanBERT. - Jun Chen 021; Robert Hoehndorf; Mohamed Elhoseiny; Xiangliang Zhang 001 (CoRR, 2020)

BioHackathon 2015: Semantics of data for life sciences and reproducible research. - Rutger A. Vos; Toshiaki Katayama; Hiroyuki Mishima; Shin Kawano; Shuichi Kawashima; Jin-Dong Kim; Yuki Moriya; Toshiaki Tokimatsu; Atsuko Yamaguchi; Yasunori Yamamoto; Hongyan Wu; Peter Amstutz; et al. (F1000Research, 2020)

Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies. - Luke T. Slater; Georgios V. Gkoutos; Robert Hoehndorf (BMC Medical Informatics Decis. Mak., 2020)

DeepPheno: Predicting single gene loss-of-function phenotypes using an ontology-aware hierarchical classifier. - Maxat Kulmanov; Robert Hoehndorf (PLoS Comput. Biol., 2020)

Semantic similarity and machine learning with ontologies. - Maxat Kulmanov; Fatima Zohra Smaili; Xin Gao 001; Robert Hoehndorf (Briefings Bioinform., 2021)

Predicting candidate genes from phenotypes, functions and anatomical site of expression. - Jun Chen 021; Azza Althagafi; Robert Hoehndorf (Bioinform., 2021)

DTI-Voodoo: machine learning over interaction networks and ontology-based background knowledge predicts drug-target interactions. - Tilman Hinnerichs; Robert Hoehndorf (Bioinform., 2021)

DeepGOPlus: improved protein function prediction from sequence. - Maxat Kulmanov; Robert Hoehndorf (Bioinform., 2021)

DeepViral: prediction of novel virus-host interactions from protein sequences and infectious disease phenotypes. - Wang Liu-Wei; Senay Kafkas; Jun Chen 021; Nicholas J. Dimonaco; Jesper Tegnér; Robert Hoehndorf (Bioinform., 2021)

Linking common human diseases to their phenotypes; development of a resource for human phenomics. - Senay Kafkas; Sara Althubaiti; Georgios V. Gkoutos; Robert Hoehndorf; Paul N. Schofield (J. Biomed. Semant., 2021)

Improved characterisation of clinical text through ontology-based vocabulary expansion. - Luke T. Slater; William Bradlow; Simon Ball; Robert Hoehndorf; Georgios V. Gkoutos (J. Biomed. Semant., 2021)

A fast, accurate, and generalisable heuristic-based negation detection algorithm for clinical text. - Luke T. Slater; William Bradlow; Dino FA. Motti; Robert Hoehndorf; Simon Ball; Georgios V. Gkoutos (Comput. Biol. Medicine, 2021)

Towards similarity-based differential diagnostics for common diseases. - Luke T. Slater; Andreas Karwath; John A. Williams 002; Sophie Russell; Silver Makepeace; Alexander Carberry; Robert Hoehndorf; Georgios V. Gkoutos (Comput. Biol. Medicine, 2021)

Multi-faceted semantic clustering with text-derived phenotypes. - Luke T. Slater; John A. Williams 002; Andreas Karwath; Hilary Fanning; Simon Ball; Paul N. Schofield; Robert Hoehndorf; Georgios V. Gkoutos (Comput. Biol. Medicine, 2021)

Effects of Negation and Uncertainty Stratification on Text-Derived Patient Profile Similarity. - Luke T. Slater; Andreas Karwath; Robert Hoehndorf; Georgios V. Gkoutos (Frontiers Digit. Health, 2021)

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

Ontological Analysis of Collection Improves Classification of Cardinality Phenotypes. - Sarah M. Alghamdi; Robert Hoehndorf (ICBO, 2022)

The Coevolution of Ontologies and Knowledge-based Analytics in Bioinformatics. - Robert Hoehndorf (ICBO, 2022)

Positive-Unlabeled Learning with Adversarial Data Augmentation for Knowledge Graph Completion. - Zhenwei Tang; Shichao Pei; Zhao Zhang 011; Yongchun Zhu; Fuzhen Zhuang; Robert Hoehndorf; Xiangliang Zhang 001 (IJCAI, 2022)

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

Using SPARQL to Unify Queries over Data, Ontologies, and Machine Learning Models in the PhenomeBrowser Knowledgebase. - Ali Syed; Senay Kafkas; Maxat Kulmanov; Robert Hoehndorf (SWAT4HCLS, 2022)

DeepSVP: integration of genotype and phenotype for structural variant prioritization using deep learning. - Azza Althagafi; Lamia Alsubaie; Nagarajan Kathiresan; Katsuhiko Mineta; Taghrid Aloraini; Fuad Al Mutairi; Majid Alfadhel; Takashi Gojobori; Ahmad Alfares; Robert Hoehndorf (Bioinform., 2022)

DeepGOZero: improving protein function prediction from sequence and zero-shot learning based on ontology axioms. - Maxat Kulmanov; Robert Hoehndorf (Bioinform., 2022)

A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology. - Yongqun He; Hong Yu 014; Anthony Huffman; Asiyah Yu Lin; Darren A. Natale; John Beverley; Ling Zheng; Yehoshua Perl; Zhigang Wang; Yingtong Liu; Edison Ong; Yang Wang; et al. (J. Biomed. Semant., 2022)

Description Logic EL++ Embeddings with Intersectional Closure. - Xi Peng; Zhenwei Tang; Maxat Kulmanov; Kexin Niu; Robert Hoehndorf (CoRR, 2022)

Joint Abductive and Inductive Neural Logical Reasoning. - Zhenwei Tang; Shichao Pei; Xi Peng; Fuzhen Zhuang; Xiangliang Zhang 001; Robert Hoehndorf (CoRR, 2022)

FALCON: Sound and Complete Neural Semantic Entailment over ALC Ontologies. - Zhenwei Tang; Tilman Hinnerichs; Xi Peng; Xiangliang Zhang 001; Robert Hoehndorf (CoRR, 2022)

Evaluating semantic similarity methods for comparison of text-derived phenotype profiles. - Luke T. Slater; Sophie Russell; Silver Makepeace; Alexander Carberry; Andreas Karwath; John A. Williams 002; Hilary Fanning; Simon Ball; Robert Hoehndorf; Georgios V. Gkoutos (BMC Medical Informatics Decis. Mak., 2022)

Exploring the Use of Ontology Components for Distantly-Supervised Disease and Phenotype Named Entity Recognition. - Sumyyah Toonsi; Senay Kafkas; Robert Hoehndorf (ICBO, 2023)

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

Neural Multi-hop Logical Query Answering with Concept-Level Answers. - Zhenwei Tang; Shichao Pei; Xi Peng; Fuzhen Zhuang; Xiangliang Zhang 001; Robert Hoehndorf (ISWC, 2023)

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

Updating the CEMO ontology for future epidemiological challenges. - Núria Queralt-Rosinach; Paul N. Schofield; Marco Roos; Robert Hoehndorf (SWAT4HCLS, 2023)

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

An Open-Source Knowledge Graph Ecosystem for the Life Sciences. - Tiffany J. Callahan; Ignacio J. Tripodi; Adrianne L. Stefanski; Luca Cappelletti; Sanya Bathla Taneja; Jordan M. Wyrwa; Elena Casiraghi; Nicolas A. Matentzoglu; Justin T. Reese; Jonathan C. Silverstein; Charles Tapley Hoyt; Richard D. Boyce; et al. (CoRR, 2023)

Stylized Projected GAN: A Novel Architecture for Fast and Realistic Image Generation. - Md Nurul Muttakin; Malik Shahid Sultan; Robert Hoehndorf; Hernando Ombao (CoRR, 2023)

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

Klarigi: Characteristic explanations for semantic biomedical data. - Luke T. Slater; John A. Williams 002; Paul N. Schofield; Sophie Russell; Samantha C. Pendleton; Andreas Karwath; Hilary Fanning; Simon Ball; Robert Hoehndorf; Georgios V. Gkoutos (Comput. Biol. Medicine, 2023)

Improving the classification of cardinality phenotypes using collections. - Sarah M. Alghamdi; Robert Hoehndorf (J. Biomed. Semant., 2023)

Starvar: symptom-based tool for automatic ranking of variants using evidence from literature and genomes. - Senay Kafkas; Marwa Abdelhakim; Mahmut Uludag; Azza Althagafi; Malak Alghamdi; Robert Hoehndorf (BMC Bioinform., 2023)

Large-Scale Knowledge Integration for Enhanced Molecular Property Prediction. - Yasir Ghunaim; Robert Hoehndorf (NeSy (2), 2024)

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)

Towards Automated Functional Equation Proving: A Benchmark Dataset and A Domain-Specific In-Context Agent. - Mahdi Buali; Robert Hoehndorf (CoRR, 2024)

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

Protein function prediction as approximate semantic entailment. - Maxat Kulmanov; Francisco J. Guzmán-Vega; Paula Duek Roggli; Lydie Lane; Stefan T. Arold; Robert Hoehndorf (Nat. Mac. Intell., 2024)

Semantic units: organizing knowledge graphs into semantically meaningful units of representation. - Lars Vogt; Tobias Kuhn; Robert Hoehndorf (J. Biomed. Semant., 2024)

Correction to: Semantic units: organizing knowledge graphs into semantically meaningful units of representation. - Lars Vogt; Tobias Kuhn; Robert Hoehndorf (J. Biomed. Semant., 2024)

Causal knowledge graph analysis identifies adverse drug effects. - Sumyyah Toonsi; Paul N. Schofield; Robert Hoehndorf (CoRR, 2025)

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)

Nanodesigner: resolving the complex-CDR interdependency with iterative refinement. - Melissa Maria Rios Zertuche; Senay Kafkas; Dominik Renn; Magnus Rueping; Robert Hoehndorf (J. Cheminformatics, 2025)