OverviewA complete list of publications by members of the Bio-Ontology Research Group (175 entries). By year By topic 2026 Mashkova, Zhapa-Camacho, Hoehndorf. DELE: Deductive EL++ Embeddings for Knowledge Base Completion Neurosymbolic Artificial Intelligence. [live] Zhapa-Camacho, Hoehndorf. Fully Geometric Multi-hop Reasoning on Knowledge Graphs with Transitive Relations The Semantic Web -- ESWC 2026. [live] Alsulami, Lehmann, Daga, Khan et al.. LEP-AD: language embedding of proteins and attention to drugs predicts drug-target interactions Journal of Cheminformatics. [live] Colombo, Salem, Szczepski, Yu et al.. Molecular basis and cellular effects of Janus-class–driven cytoplasmic PYK2 coacervates Communications Biology. [live] Song, Ma, Liu, Luo et al.. Robust Knowledge Graph Embedding via Denoising The Semantic Web -- ESWC 2026. [live] Ashhad, Mashkova, Henao, Hoehndorf. SIDEKICK: A Semantically Integrated Resource for Drug Effects, Indications, and Contraindications The Semantic Web -- ESWC 2026. [live] Guzman-Vega, Cardona-Londono, Gonzalez-Alvarez, Pena-Guerra et al.. VarLand: A pipeline to map the structural landscape of missense variants at the proteome scale Journal of Biological Chemistry. [live] 2025 Gomez, Al Mahri, Abdullah, Malik et al.. Age-related differences in gene expression and pathway activation following heatstroke Physiological Genomics. [live] Tawfiq, Niu, Kulmanov, Hoehndorf. Annotating genomes with DeepGO protein function prediction tools Protein Function Prediction. [live] Aspromonte, Del Conte, Zhu, Tan et al.. CAGI6 ID panel challenge: assessment of phenotype and variant predictions in 415 children with neurodevelopmental disorders (NDDs) Human Genetics. [live] Toonsi, Schofield, Hoehndorf. Causal knowledge graph analysis identifies adverse drug effects Bioinformatics. [live] Kulmanov, Hoehndorf. Computational prediction of protein functional annotations Protein Function Prediction. [live] Alarawi, Altammami, Abutarboush, Kulmanov et al.. Genomic diversity and antimicrobial resistance of Staphylococcus aureus in Saudi Arabia: a nationwide study using whole-genome sequencing Microbial Genomics. [live] Maktabi, Liu, Almesfer, Abdelhakim et al.. Genomic landscape of retinoblastoma: Insights into risk stratification and precision pediatric Neuro-Oncology Neuro-Oncology Pediatrics. [live] Zhapa-Camacho, Mashkova, Hoehndorf, Kulmanov. LLM Agent Based Protein Function Prediction Biocomputing 2026. [live] Rios Zertuche, Kafkas, Renn, Rueping et al.. Nanodesigner: resolving the complex-CDR interdependency with iterative refinement Journal of Cheminformatics. [live] Hoehndorf, Pesquita, Zhapa-Camacho. Neuro-Symbolic AI in Life Sciences Handbook on Neurosymbolic AI and Knowledge Graphs. [live] Chen, Mashkova, Zhapa-Camacho, Hoehndorf et al.. Ontology Embedding: A Survey of Methods, Applications and Resources IEEE Transactions on Knowledge and Data Engineering. [live] Kulmanov, Ashouri, Liu, Abdelhakim et al.. Phased genome assemblies and pangenome graphs of human populations of Japan and Saudi Arabia Scientific Data. [live] Alhattab, Barakeh, Khoja, Elhadi et al.. Sa1216: Development of colorectal cancer and matched healthy organoids from Saudi patients: a case study Gastroenterology. [live] Alhattab, Barakeh, Khoja, Elhadi et al.. Su1295: Chemically defined peptide-based matrices enabling the development of colorectal organoid models for therapeutic applications and disease modeling Gastroenterology. [live] Kafkas, Abdelhakim, Althagafi, Toonsi et al.. The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients Scientific Reports. [live] Schofield, Hoehndorf, Gkoutos, Smith. The informatics of developmental phenotypes Kaufman’s Atlas of Mouse Development Supplement. [live] Bouchama, Gomez, Abdullah, Al Mahri et al.. Whole genome transcriptomic profiling reveals distinct sex-specific responses to heat stroke Journal of Applied Physiology. [live] 2024 Kulmanov, Tawfiq, Liu, Al Ali et al.. A reference quality, fully annotated diploid genome from a Saudi individual Scientific Data. [live] Callahan, Tripodi, Stefanski, Cappelletti et al.. An open source knowledge graph ecosystem for the life sciences Scientific Data. [live] Toonsi, Gauran, Ombao, Schofield et al.. Causal relationships between diseases mined from the literature improve the use of polygenic risk scores Bioinformatics. [live] Stenton, O’Leary, Lemire, VanNoy et al.. Critical assessment of variant prioritization methods for rare disease diagnosis within the rare genomes project Human Genomics. [live] Tawfiq, Niu, Hoehndorf, Kulmanov. DeepGOMeta for functional insights into microbial communities using deep learning-based protein function prediction Scientific Reports. [live] Mashkova, Zhapa-Camacho, Hoehndorf. Enhancing Geometric Ontology Embeddings for ^++ with Negative Sampling and Deductive Closure Filtering Neural-Symbolic Learning and Reasoning. [live] Ghunaim, Hoehndorf. Large-Scale Knowledge Integration for Enhanced Molecular Property Prediction Neural-Symbolic Learning and Reasoning. [live] Zhapa-Camacho, Hoehndorf. Lattice-Preserving ALC Ontology Embeddings Neural-Symbolic Learning and Reasoning. [live] Zhapa-Camacho, Tang, Kulmanov, Hoehndorf. Predicting protein functions using positive-unlabeled ranking with ontology-based priors Bioinformatics. [live] Althagafi, Zhapa-Camacho, Hoehndorf. Prioritizing genomic variants through neuro-symbolic, knowledge-enhanced learning Bioinformatics. [live] Vogt, Kuhn, Hoehndorf. Semantic units: organizing knowledge graphs into semantically meaningful units of representation Journal of Biomedical Semantics. [live] 2023 Fernando Zhapa-Camacho, Robert Hoehndorf. Evaluating Different Methods for Semantic Reasoning Over Ontologies Joint Proceedings of Scholarly QALD 2023 and SemREC 2023 co-located with 22nd International Semantic Web Conference ISWC 2023, Athens, Greece, November 6-10, 2023. Sumyyah Toonsi, Senay Kafkas, Robert Hoehndorf. Exploring the Use of Ontology Components for Distantly-Supervised Disease and Phenotype Named Entity Recognition Proceedings of the International Conference on Biomedical Ontologies 2023 together with the Workshop on Ontologies for Infectious and Immune-Mediated Disease Data Science (OIIDDS 2023) and the FAIR Ontology Harmonization and TRUST Data Interoperability Workshop (FOHTI 2023), Bras\', Brazil, August 28 - September 1, 2023. Fernando Zhapa-Camacho, Robert Hoehndorf. From Axioms over Graphs to Vectors, and Back Again: Evaluating the Properties of Graph-based Ontology Embeddings Proceedings of the 17th International Workshop on Neural-Symbolic Learning and Reasoning, La Certosa di Pontignano, Siena, Italy, July 3-5, 2023. Mazen Hassanain, Yang Liu, Weam Hussain, Albandri Binowayn et al.. Genomic landscape in Saudi patients with hepatocellular carcinoma using whole-genome sequencing: a pilot study Frontiers in Gastroenterology. [live] Sarah M. Alghamdi, Robert Hoehndorf. Improving the classification of cardinality phenotypes using collections Journal of Biomedical Semantics. [live] Luke T. Slater, John A. Williams, Paul N. Schofield, Sophie Russell et al.. Klarigi: Characteristic explanations for semantic biomedical data Computers in Biology and Medicine. [live] Fernando Zhapa-Camacho, Maxat Kulmanov, Robert Hoehndorf. mOWL: Python library for machine learning with biomedical ontologies Bioinformatics. [live] Senay Kafkas, Marwa Abdelhakim, Mahmut Uludag, Azza Althagafi et al.. Starvar: symptom-based tool for automatic ranking of variants using evidence from literature and genomes BMC Bioinformatics. [live] Sherin Abdelrahman, Rui Ge, Hepi H. Susapto, Yang Liu et al.. The Impact of Mechanical Cues on the Metabolomic and Transcriptomic Profiles of Human Dermal Fibroblasts Cultured in Ultrashort Self-Assembling Peptide 3D Scaffolds ACS Nano. [live] Nuria Queralt-Rosinach, Paul N. Schofield, Marco Roos, Robert Hoehndorf. Updating the CEMO ontology for future epidemiological challenges 14th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4HCLS 2023), Basel, Switzerland, February 13-16, 2023. 2022 Yongqun He, Hong Yu, Anthony Huffman, Asiyah Yu Lin et al.. A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology Journal of Biomedical Semantics. [live] Mona Alshahrani, Abdullah Almansour, Asma Alkhaldi, Maha A. Thafar et al.. Combining biomedical knowledge graphs and text to improve predictions for drug-target interactions and drug-indications PeerJ. [live] Sarah Alghamdi, Paul N. Schofield, Robert Hoehndorf. Contribution of model organism phenotypes to the computational identification of human disease genes Disease Models & Mechanisms. [live] Maxat Kulmanov, Robert Hoehndorf. DeepGOZero: improving protein function prediction from sequence and zero-shot learning based on ontology axioms Bioinformatics. [live] Azza Althagafi, Lamia Alsubaie, Nagarajan Kathiresan, Katsuhiko Mineta et al.. DeepSVP: integration of genotype and phenotype for structural variant prioritization using deep learning Bioinformatics. [live] Luke T. Slater, Sophie Russell, Silver Makepeace, Alexander Carberry et al.. Evaluating semantic similarity methods for comparison of text-derived phenotype profiles BMC Medical Informatics and Decision Making. [live] Zhenwei Tang, Shichao Pei, Zhao Zhang, Yongchun Zhu et al.. Positive-Unlabeled Learning with Adversarial Data Augmentation for Knowledge Graph Completion Proceedings of the Thirty-First International Joint Conference on Artificial Intelligence. [live] Ali Syed, Senay Kafkas, Maxat Kulmanov, Robert Hoehndorf. Using SPARQL to Unify Queries over Data, Ontologies, and Machine Learning Models in the PhenomeBrowser Knowledgebase Proceedings of the 13th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences, SWAT4HCLS 2022. 2021 Maxat Kulmanov, Fernando Zhapa-Camacho, Robert Hoehndorf. DeepGOWeb: fast and accurate protein function prediction on the (Semantic) Web Nucleic Acids Research. [live] Liu-Wei, Kafkas, Chen, Dimonaco et al.. DeepViral: prediction of novel virus–host interactions from protein sequences and infectious disease phenotypes Bioinformatics. [live] Tilman Hinnerichs, Robert Hoehndorf. DTI-Voodoo: machine learning over interaction networks and ontology-based background knowledge predicts drug interactions Bioinformatics. [live] Luke T. Slater, Andreas Karwath, Robert Hoehndorf, Georgios V. Gkoutos. Effects of Negation and Uncertainty Stratification on Text-Derived Patient Profile Similarity Frontiers in Digital Health. [live] Luke T. Slater, William Bradlow, Simon Ball, Robert Hoehndorf et al.. Improved characterisation of clinical text through ontology-based vocabulary expansion Journal of Biomedical Semantics. [live] Luke T. Slater, John A. Williams, Andreas Karwath, Hilary Fanning et al.. Multi-faceted semantic clustering with text-derived phenotypes Computers in Biology and Medicine. [live] Jun Chen, Azza Althagafi, Robert Hoehndorf. Predicting candidate genes from phenotypes, functions and anatomical site of expression Bioinformatics. [live] 2020 Rutger A. Vos, Toshiaki Katayama, Hiroyuki Mishima, Shin Kawano et al.. BioHackathon 2015: Semantics of data for life sciences and reproducible research F1000Research. [live] Sara Althubaiti, Senay Kafkas, Marwa Abdelhakim, Robert Hoehndorf. Combining lexical and context features for automatic ontology extension Journal of Biomedical Semantics. Marwa Abdelhakim, Eunice McMurray, Ali Raza Syed, Senay Kafkas et al.. DDIEM: drug database for inborn errors of metabolism Orphanet Journal of Rare Diseases. [live] Kulmanov, Hoehndorf. DeepGOPlus: improved protein function prediction from sequence Bioinformatics. Kulmanov, Hoehndorf. DeepPheno: Predicting single gene loss-of-function phenotypes using an ontology-aware hierarchical classifier PLOS Computational Biology. [live] Muhammad Umair, Mariam Ballow, Abdulaziz Asiri, Yusra Alyafee et al.. EMC10 homozygous variant identified in a family with global developmental delay, mild intellectual disability, and speech delay Clinical Genetics. [live] Smaili, Gao, Hoehndorf. Formal axioms in biomedical ontologies improve analysis and interpretation of associated data Bioinformatics. JOWO 2020: The Joint Ontology Workshops : Proceedings of the Joint Ontology Workshops co-located with the Bolzano Summer of Knowledge (BOSK 2020) CEUR-WS. Kulmanov, Smaili, Gao, Hoehndorf. Semantic similarity and machine learning with ontologies Briefings in Bioinformatics. [live] Luke T. Slater, Georgios V. Gkoutos, Robert Hoehndorf. Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies BMC Medical Informatics and Decision Making. [live] Ahmed Alfares, Lamia Alsubaie, Taghrid Aloraini, Aljoharah Alaskar et al.. What is the right sequencing approach? Solo VS extended family analysis in consanguineous populations BMC Medical Genomics. [live] 2019 Claus Weiland, Maxat Kulmanov, Marco Schmidt, Robert Hoehndorf. A Machine Learning Based Approach for Similarity Search on Biodiversity Knowledge Graphs Biodiversity Information Science and Standards. Katayama, Kawashima, Micklem, Kawano et al.. BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services F1000Research. Boudellioua, Kulmanov, Schofield, Gkoutos et al.. DeepPVP: phenotype-based prioritization of causative variants using deep learning BMC Bioinformatics. Maxat Kulmanov, Wang Liu-Wei, Yuan Yan, Robert Hoehndorf. EL Embeddings: Geometric construction of models for the Description Logic EL++ Proceedings of IJCAI 2019. Timothy K. Cooper, Kathleen A. Silva, Victoria E. Kennedy, Sarah M. Alghamdi et al.. Hyaline Arteriolosclerosis in 30 Strains of Aged Inbred Mice Veterinary Pathology. [live] Linn, Mustonen, Silva, Kennedy et al.. Nail abnormalities identified in an ageing study of 30 inbred mouse strains Experimental Dermatology. [live] Senay Kafkas, Robert Hoehndorf. Ontology based mining of pathogen--disease associations from literature Journal of Biomedical Semantics. Kafkas, Hoehndorf. Ontology based text mining of gene-phenotype associations: application to candidate gene prediction Database. Althubaiti, Karwath, Dallol, Noor et al.. Ontology-based prediction of cancer driver genes Scientific Reports. Kafkas, Abdelhakim, Hashish, Kulmanov et al.. PathoPhenoDB: linking human pathogens to their disease phenotypes in support of infectious disease research Scientific Data. [live] Sarah M. Alghamdi, Beth A. Sundberg, John P. Sundberg, Paul N. Schofield et al.. Quantitative evaluation of ontology design patterns for combining pathology and anatomy ontologies Scientific Reports. Pei, Yu, Hoehndorf, Zhang. Semi-Supervised Entity Alignment via Knowledge Graph Embedding with Awareness of Degree Difference The World Wide Web Conference. [live] Zhou, Jiang, Bergquist, Lee et al.. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens Genome Biology. 2018 Keenan, McKerlie, Gkoutos, Ward et al.. A Review of Current Standards and the Evolution of Histopathology Nomenclature for Laboratory Animals ILAR Journal. Damion M. Dooley, Emma J. Griffiths, Gurinder S. Gosal, Pier L. Buttigieg et al.. FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration Science of Food. Othoum, Bougouffa, Razali, Bokhari et al.. In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters BMC Genomics. Ron Henkel, Robert Hoehndorf, Tim Kacprowski, Christian Knupfer et al.. Notions of similarity for systems biology models Briefings in Bioinformatics. Boudellioua, Kulmanov, Schofield, Gkoutos et al.. OligoPVP: Phenotype-driven analysis of individual genomic information to prioritize oligogenic disease variants Scientific Reports. Smaili, Gao, Hoehndorf. Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations Bioinformatics. Senay Kafkas, Robert Hoehndorf. Ontology based mining of pathogen-disease associations from literature Bio-Ontologies COSI. Sara Althubaiti, Senay Kafkas, Robert Hoehndorf. Ontology-Based Concept Recognition by Using Word Embeddings Bio-Ontologies COSI. Kulmanov, Schofield, Gkoutos, Hoehndorf. Ontology-based validation and identification of regulatory phenotypes Bioinformatics. Smaili, Gao, Hoehndorf. OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction Bioinformatics. [live] Alshahrani, Hoehndorf. Semantic Disease Gene Embeddings (SmuDGE): phenotype-based disease gene prioritization without phenotypes Bioinformatics. Sohaib Younis, Claus Weiland, Robert Hoehndorf, Stefan Dressler et al.. Taxon and trait recognition from digitized herbarium specimens using deep convolutional neural networks Botany Letters. Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf. The anatomy of phenotype ontologies: principles, properties and applications Briefings in Bioinformatics. [live] Maxat Kulmanov, Senay Kafkas, Andreas Karwath, Alexander Malic et al.. Vec2SPARQL: integrating SPARQL queries and knowledge graph embeddings Proceedings of the 11th International Conference Semantic Web Applications and Tools for Life Sciences, SWAT4LS 2018, Antwerp, Belgium, December 3-6, 2018.. 2017 Hoehndorf, Queralt-Rosinach. Data science and symbolic AI: Synergies, challenges and opportunities Data Science. [live] Kulmanov, Khan, Hoehndorf. DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier Bioinformatics. Salhi, Negrao, Essack, Morton et al.. DES-TOMATO: A Knowledge Exploration System Focused On Tomato Species Scientific Reports. Kulmanov, Hoehndorf. Evaluating the effect of annotation size on measures of semantic similarity Journal of Biomedical Semantics. [live] Motwalli, Essack, Jankovic, Ji et al.. In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria BMC Genomics. [live] Maha Alrashed, Lujain Alharbi, Omamah Talal Al-Muhammadi, Salha Bahadiq et al.. Interactively Exploring Graph Coloring Algorithms in a Bilingual Web Platform with Gamification Proceedings of EdMedia: World Conference on Educational Media and Technology 2017. Alshahrani, Khan, Maddouri, Kinjo et al.. Neuro-symbolic representation learning on biological knowledge graphs Bioinformatics. Imane Boudellioua, Maxat Kulmanov, Paul N Schofield, Georgios V Gkoutos et al.. Phenotype-driven discovery of digenic variants in personal genome sequences Proceedings of VarI-SIG. Boudellioua, Mahamad Razali, Kulmanov, Hashish et al.. Semantic prioritization of novel causative genomic variants PLOS Computational Biology. [live] Kafkas, Sarntivijai, Hoehndorf. Usage of cell nomenclature in biomedical literature BMC Bioinformatics. [live] 2016 Hoehndorf, Gkoutos, Schofield. Datamining with Ontologies Data Mining Techniques for the Life Sciences. [live] Fisher, Hoehndorf, Bazelato, Dadras et al.. DermO; an ontology for the description of dermatologic disease Journal of Biomedical Semantics. [live] Salhi, Essack, Radovanovic, Marchand et al.. DESM: portal for microbial knowledge exploration systems Nucleic Acids Research. [live] Maxat Kulmanov, Robert Hoehndorf. Evaluating the effect of annotation size on measures of semantic similarity Proceedings of Bio-Ontologies SIG. Slater, Rodriguez-Garcia, O'Shea, Schofield et al.. Experiences with Aber-OWL, an Ontology Repository with OWL EL Reasoning Ontology Engineering: 12th International Experiences and Directions Workshop on OWL, OWLED 2015, co-located with ISWC 2015, Bethlehem, PA, USA, October 9-10, 2015, Revised Selected Papers. [live] Bolleman, Mungall, Strozzi, Baran et al.. FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation Journal of Biomedical Semantics. [live] Miguel Rodriguez-Garcia, Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf. Integrating phenotype ontologies with PhenomeNET Proceedings of Ontology Matching Workshop 2016. Robert Hoehndorf, Liam Mencel, Georgios V. Gkoutos, Paul N. Schofield. Large-Scale Reasoning over Functions in Biomedical Ontologies Formal Ontology in Information Systems. Boudellioua, Saidi, Hoehndorf, Martin et al.. Prediction of Metabolic Pathway Involvement in Prokaryotic UniProtKB Data by Association Rule Mining PLoS ONE. [live] Mona Alshahrani, Hussein Almashouq, Robert Hoehndorf. SPARQL2OWL: Towards Bridging the Semantic Gap Between RDF and OWL Proceedings of the Joint International Conference on Biological Ontology and BioCreative, Corvallis, Oregon, United States, August 1-4, 2016.. Hoehndorf, Alshahrani, Gkoutos, Gosline et al.. The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants Journal of Biomedical Semantics. [live] Luke Slater, Georgios V. Gkoutos, Paul N Schofield, Robert Hoehndorf. To MIREOT or not to MIREOT? A case study of the impact of using MIREOT in the Experimental Factor Ontology (EFO) International Conference on Biomedical Ontology and BioCreative (ICBO BioCreative 2016). 2015 Robert Hoehndorf, Luke Slater, Paul N Schofield, Georgios V Gkoutos. Aber-OWL: a framework for ontology-based data access in biology BMC Bioinformatics. Luke Slater, Georgios Gkoutos, Paul N. Schofield, Robert Hoehndorf. AberOWL: an ontology portal with OWL EL reasoning Proceedings of International Conference on Biomedical Ontologies (ICBO). Oellrich, Walls, Cannon, Cannon et al.. An ontology approach to comparative phenomics in plants Plant Methods. [live] Martin Hrabe de Angelis, George Nicholson, Mohammed Selloum, Jacqueline K White et al.. Analysis of mammalian gene function through broad-based phenotypic screens across a consortium of mouse clinics Nature Genetics. Robert Hoehndorf, Paul N Schofield, Georgios V Gkoutos. Analysis of the human diseasome using phenotype similarity between common, genetic, and infectious diseases Scientific Reports. Gkoutos, Hoehndorf, Tsaprouni, Schofield. Best behaviour? Ontologies and the formal description of animal behaviour Mammalian Genome. [live] Baran, Durgahee, Eilbeck, Antezana et al.. GFVO: the Genomic Feature and Variation Ontology PeerJ. [live] Gottlieb, Hoehndorf, Dumontier, Altman. Ranking Adverse Drug Reactions With Crowdsourcing J Med Internet Res. [live] Hoehndorf, Gruenberger, Gkoutos, Schofield. Similarity-based search of model organism, disease and drug effect phenotypes Journal of Biomedical Semantics. [live] Hoehndorf, Schofield, Gkoutos. The role of ontologies in biological and biomedical research: a functional perspective Briefings in Bioinformatics. Luke Slater, Georgios Gkoutos, Paul N. Schofield, Robert Hoehndorf. Using Aber-OWL for fast and scalable reasoning over BioPortal ontologies Proceedings of International Conference on Biomedical Ontologies (ICBO). 2014 Hoehndorf, Hancock, Hardy, Mallon et al.. Analyzing gene expression data in mice with the Neuro Behavior Ontology Mamm Genome. Rutger Vos, Jordan Biserkov, Bachir Balech, Niall Beard et al.. Enriched biodiversity data as a resource and service Biodiversity Data Journal. [live] Dumontier, Baker, Baran, Callahan et al.. The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery Journal of Biomedical Semantics. Hoehndorf, Haendel, Stevens, Rebholz-Schuhmann. Thematic series on biomedical ontologies in JBMS: challenges and new directions Journal of Biomedical Semantics. 2013 Hoehndorf, Schofield, Gkoutos. An integrative, translational approach to understanding rare and orphan genetically based diseases Interface Focus. [live] Rebholz-Schuhmann, Kafkas, Kim, Li et al.. Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources Journal of Biomedical Semantics. Dietrich Rebholz-Schuhmann, Jee-Hyub Kim, Ying Yan, Abhishek Dixit et al.. Evaluation and Cross-Comparison of Lexical Entities of Biological Interest (LexEBI) PLoS ONE. Hoehndorf, Hiebert, Hardy, Schofield et al.. Mouse model phenotypes provide information about human drug targets Bioinformatics. Cook, Neal, Hoehndorf, Gkoutos et al.. Representing physiological processes and their participants with PhysioMaps Journal of Biomedical Semantics. [live] Dumontier, Chepelev, Hoehndorf. Semantic Systems Biology: Formal Knowledge Representation in Systems Biology for Model Construction, Retrieval, Validation and Discovery Systems Biology. Hoehndorf, Hardy, Osumi-Sutherland, Tweedie et al.. Systematic Analysis of Experimental Phenotype Data Reveals Gene Functions PLoS ONE. 2012 Robert Hoehndorf, Georgios V. Gkoutos. A translational medicine approach to orphan diseases Proceedings of the Virtual Physiological Human Conference 2012 (VPH2012). Adam Wyner, Luke Riley, Robert Hoehndorf, Samuel Croset. Argumentation to Represent and Reason over Biological Systems Proceedings of the 3rd International Conference on Information Technology in Bio- and Medical Informatics (ITBAM 2012). Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf. Chapter Four - The Neurobehavior Ontology: An Ontology for Annotation and Integration of Behavior and Behavioral Phenotypes Bioinformatics of Behavior: Part 1. [live] Hoehndorf, Dumontier, Gkoutos. Evaluation of research in biomedical ontologies Briefings in Bioinformatics. Hoehndorf, Dumontier, Gkoutos. Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics Bioinformatics. Robert Hoehndorf, Michel Dumontier, Georgios V. Gkoutos. Integration of knowledge for personalized medicine: a pharmacogenomics case-study Proceedings of the Virtual Physiological Human Conference 2012 (VPH2012). Gkoutos, Hoehndorf. Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes Journal of Biomedical Semantics. Oellrich, Gkoutos, Hoehndorf, Rebholz-Schuhmann. Quantitative comparison of mapping methods between Human and Mammalian Phenotype Ontology Journal of Biomedical Semantics. Hoehndorf, Harris, Herre, Rustici et al.. Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology Bioinformatics. [live] Dietrich Rebholz-Schuhmann, Anika Oellrich, Robert Hoehndorf. Text-mining solutions for biomedical research: enabling integrative biology Nature Reviews Genetics. Gkoutos, Schofield, Hoehndorf. The Units Ontology: a tool for integrating units of measurement in science Database. Loebe, Stumpf, Hoehndorf, Herre. Towards improving phenotype representation in OWL Journal of Biomedical Semantics. 2011 Simon Jupp, Robert Stevens, Robert Hoehndorf. Exploring Gene Ontology Annotations with OWL Proceedings of the 13th Bio-Ontology Meeting. Stefan Schulz, Mathias Brochhausen, Robert Hoehndorf. Higgs bosons, mars missions, and unicorn delusions: How to deal with terms of dubious reference in scientific ontologies Proceedings of the Second International Conference on Biomedical Ontology. Hiroshi Masuya, Georgios V. Gkoutos, Nobuhiko Tanaka, Kazunori Waki et al.. Investigation of the fundamental strategy for interoperability of description of biological measurements Proceedings of the Second International Conference on Biomedical Ontology. Georgios V. Gkoutos, Robert Hoehndorf. Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes Proceedings of the 3rd Workshop for Ontologies in Biomedicine and Life sciences (OBML). Anika Oellrich, Robert Hoehndorf, Georgios V. Gkoutos, Dietrich Rebholz-Schuhmann. Quantitative comparison of mapping methods between Human and Mammalian Phenotype Ontology Proceedings of the 3rd Workshop for Ontologies in Biomedicine and Life sciences (OBML). Frank Loebe, Frank Stumpf, Robert Hoehndorf, Heinrich Herre. Towards Improving Phenotype Representation in OWL Proceedings of the 3rd Workshop for Ontologies in Biomedicine and Life sciences (OBML). 0 Robert Hoehndorf, Michel Dumontier, Anika Oellrich, Sarala Wimalaratne et al.. A common layer of interoperability for biomedical ontologies based on OWL EL Bioinformatics. Wimalaratne, Grenon, Hoehndorf, Gkoutos et al.. An infrastructure for ontology-based information systems in biomedicine: RICORDO case study Bioinformatics. Robert Hoehndorf, Michel Dumontier, Anika Oellrich, Dietrich Rebholz-Schuhmann et al.. Interoperability between biomedical ontologies through relation expansion, upper-level ontologies and automatic reasoning PLOS ONE. Hoehndorf, Oellrich, Rebholz-Schuhmann. Interoperability between phenotype and anatomy ontologies Bioinformatics. Robert Hoehndorf, Anika Oellrich, Dietrich Rebholz-Schuhmann, Paul N. Schofield et al.. Linking PharmGKB to phenotype studies and animal models of disease for drug repurposing Pacific Symposium on Biocomputing (PSB). Jupp, Stevens, Hoehndorf. Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL Journal of Biomedical Semantics. Schofield, Hoehndorf, Gkoutos. Mouse genetic and phenotypic resources for human genetics Human Mutation. Tang, Pei, Peng, Zhuang et al.. Neural Multi-hop Logical Query Answering with Concept-Level Answers The Semantic Web – ISWC 2023. Schofield, Sundberg, Hoehndorf, Gkoutos. New approaches to the representation and analysis of phenotype knowledge in human diseases and their animal models Briefings in Functional Genomics. Herre, Hoehndorf, Kelso, Loebe et al.. OBML - Ontologies in Biomedicine and Life Sciences Journal of Biomedical Semantics. [live] Hoehndorf, Ngonga Ngomo, Pyysalo, Ohta et al.. Ontology design patterns to disambiguate relations between genes and gene products in GENIA Journal of Biomedical Semantics. [live] Hoehndorf, Schofield, Gkoutos. PhenomeNET: a whole-phenome approach to disease gene discovery Nucleic Acids Research. Adams, Hoehndorf, Gkoutos, Hansen et al.. PIDO: The Primary Immunodeficiency Disease Ontology Bioinformatics. de Bono, Hoehndorf, Wimalaratne, Gkoutos et al.. The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions. BMC Research Notes. Robert Hoehndorf, Colin Batchelor, Thomas Bittner, Michel Dumontier et al.. The RNA Ontology (RNAO): An Ontology for Integrating RNA Sequence and Structure Data Applied Ontology. Neuro-symbolic AI (34) (2026) Alsulami, Lehmann, Daga, Khan et al.. LEP-AD: language embedding of proteins and attention to drugs predicts drug-target interactions Journal of Cheminformatics. [live] (2026) Mashkova, Zhapa-Camacho, Hoehndorf. DELE: Deductive EL++ Embeddings for Knowledge Base Completion Neurosymbolic Artificial Intelligence. [live] (2026) Ashhad, Mashkova, Henao, Hoehndorf. SIDEKICK: A Semantically Integrated Resource for Drug Effects, Indications, and Contraindications The Semantic Web -- ESWC 2026. [live] (2026) Song, Ma, Liu, Luo et al.. Robust Knowledge Graph Embedding via Denoising The Semantic Web -- ESWC 2026. [live] (2026) Zhapa-Camacho, Hoehndorf. Fully Geometric Multi-hop Reasoning on Knowledge Graphs with Transitive Relations The Semantic Web -- ESWC 2026. [live] (2025) Hoehndorf, Pesquita, Zhapa-Camacho. Neuro-Symbolic AI in Life Sciences Handbook on Neurosymbolic AI and Knowledge Graphs. [live] (2025) Chen, Mashkova, Zhapa-Camacho, Hoehndorf et al.. Ontology Embedding: A Survey of Methods, Applications and Resources IEEE Transactions on Knowledge and Data Engineering. [live] (2024) Ghunaim, Hoehndorf. Large-Scale Knowledge Integration for Enhanced Molecular Property Prediction Neural-Symbolic Learning and Reasoning. [live] (2024) Zhapa-Camacho, Tang, Kulmanov, Hoehndorf. Predicting protein functions using positive-unlabeled ranking with ontology-based priors Bioinformatics. [live] (2024) Althagafi, Zhapa-Camacho, Hoehndorf. Prioritizing genomic variants through neuro-symbolic, knowledge-enhanced learning Bioinformatics. [live] (2024) Mashkova, Zhapa-Camacho, Hoehndorf. Enhancing Geometric Ontology Embeddings for ^++ with Negative Sampling and Deductive Closure Filtering Neural-Symbolic Learning and Reasoning. [live] (2024) Zhapa-Camacho, Hoehndorf. Lattice-Preserving ALC Ontology Embeddings Neural-Symbolic Learning and Reasoning. [live] (2023) Fernando Zhapa-Camacho, Maxat Kulmanov, Robert Hoehndorf. mOWL: Python library for machine learning with biomedical ontologies Bioinformatics. [live] (2023) Fernando Zhapa-Camacho, Robert Hoehndorf. From Axioms over Graphs to Vectors, and Back Again: Evaluating the Properties of Graph-based Ontology Embeddings Proceedings of the 17th International Workshop on Neural-Symbolic Learning and Reasoning, La Certosa di Pontignano, Siena, Italy, July 3-5, 2023. (2022) Mona Alshahrani, Abdullah Almansour, Asma Alkhaldi, Maha A. Thafar et al.. Combining biomedical knowledge graphs and text to improve predictions for drug-target interactions and drug-indications PeerJ. [live] (2022) Maxat Kulmanov, Robert Hoehndorf. DeepGOZero: improving protein function prediction from sequence and zero-shot learning based on ontology axioms Bioinformatics. [live] (2022) Zhenwei Tang, Shichao Pei, Zhao Zhang, Yongchun Zhu et al.. Positive-Unlabeled Learning with Adversarial Data Augmentation for Knowledge Graph Completion Proceedings of the Thirty-First International Joint Conference on Artificial Intelligence. [live] (2021) Tilman Hinnerichs, Robert Hoehndorf. DTI-Voodoo: machine learning over interaction networks and ontology-based background knowledge predicts drug interactions Bioinformatics. [live] (2020) Kulmanov, Hoehndorf. DeepGOPlus: improved protein function prediction from sequence Bioinformatics. (2020) Kulmanov, Smaili, Gao, Hoehndorf. Semantic similarity and machine learning with ontologies Briefings in Bioinformatics. [live] (2020) Kulmanov, Hoehndorf. DeepPheno: Predicting single gene loss-of-function phenotypes using an ontology-aware hierarchical classifier PLOS Computational Biology. [live] (2019) Boudellioua, Kulmanov, Schofield, Gkoutos et al.. DeepPVP: phenotype-based prioritization of causative variants using deep learning BMC Bioinformatics. (2019) Claus Weiland, Maxat Kulmanov, Marco Schmidt, Robert Hoehndorf. A Machine Learning Based Approach for Similarity Search on Biodiversity Knowledge Graphs Biodiversity Information Science and Standards. (2019) Maxat Kulmanov, Wang Liu-Wei, Yuan Yan, Robert Hoehndorf. EL Embeddings: Geometric construction of models for the Description Logic EL++ Proceedings of IJCAI 2019. (2019) Pei, Yu, Hoehndorf, Zhang. Semi-Supervised Entity Alignment via Knowledge Graph Embedding with Awareness of Degree Difference The World Wide Web Conference. [live] (2018) Maxat Kulmanov, Senay Kafkas, Andreas Karwath, Alexander Malic et al.. Vec2SPARQL: integrating SPARQL queries and knowledge graph embeddings Proceedings of the 11th International Conference Semantic Web Applications and Tools for Life Sciences, SWAT4LS 2018, Antwerp, Belgium, December 3-6, 2018.. (2018) Smaili, Gao, Hoehndorf. Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations Bioinformatics. (2018) Smaili, Gao, Hoehndorf. OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction Bioinformatics. [live] (2018) Alshahrani, Hoehndorf. Semantic Disease Gene Embeddings (SmuDGE): phenotype-based disease gene prioritization without phenotypes Bioinformatics. (2018) Sara Althubaiti, Senay Kafkas, Robert Hoehndorf. Ontology-Based Concept Recognition by Using Word Embeddings Bio-Ontologies COSI. (2017) Alshahrani, Khan, Maddouri, Kinjo et al.. Neuro-symbolic representation learning on biological knowledge graphs Bioinformatics. (2017) Hoehndorf, Queralt-Rosinach. Data science and symbolic AI: Synergies, challenges and opportunities Data Science. [live] (2017) Kulmanov, Khan, Hoehndorf. DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier Bioinformatics. Tang, Pei, Peng, Zhuang et al.. Neural Multi-hop Logical Query Answering with Concept-Level Answers The Semantic Web – ISWC 2023. Ontology engineering (45) (2026) Mashkova, Zhapa-Camacho, Hoehndorf. DELE: Deductive EL++ Embeddings for Knowledge Base Completion Neurosymbolic Artificial Intelligence. [live] (2026) Song, Ma, Liu, Luo et al.. Robust Knowledge Graph Embedding via Denoising The Semantic Web -- ESWC 2026. [live] (2026) Zhapa-Camacho, Hoehndorf. Fully Geometric Multi-hop Reasoning on Knowledge Graphs with Transitive Relations The Semantic Web -- ESWC 2026. [live] (2024) Callahan, Tripodi, Stefanski, Cappelletti et al.. An open source knowledge graph ecosystem for the life sciences Scientific Data. [live] (2023) Luke T. Slater, John A. Williams, Paul N. Schofield, Sophie Russell et al.. Klarigi: Characteristic explanations for semantic biomedical data Computers in Biology and Medicine. [live] (2023) Fernando Zhapa-Camacho, Robert Hoehndorf. Evaluating Different Methods for Semantic Reasoning Over Ontologies Joint Proceedings of Scholarly QALD 2023 and SemREC 2023 co-located with 22nd International Semantic Web Conference ISWC 2023, Athens, Greece, November 6-10, 2023. (2022) Ali Syed, Senay Kafkas, Maxat Kulmanov, Robert Hoehndorf. Using SPARQL to Unify Queries over Data, Ontologies, and Machine Learning Models in the PhenomeBrowser Knowledgebase Proceedings of the 13th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences, SWAT4HCLS 2022. (2021) Maxat Kulmanov, Fernando Zhapa-Camacho, Robert Hoehndorf. DeepGOWeb: fast and accurate protein function prediction on the (Semantic) Web Nucleic Acids Research. [live] (2020) Sara Althubaiti, Senay Kafkas, Marwa Abdelhakim, Robert Hoehndorf. Combining lexical and context features for automatic ontology extension Journal of Biomedical Semantics. (2020) Smaili, Gao, Hoehndorf. Formal axioms in biomedical ontologies improve analysis and interpretation of associated data Bioinformatics. (2020) Luke T. Slater, Georgios V. Gkoutos, Robert Hoehndorf. Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies BMC Medical Informatics and Decision Making. [live] (2020) Rutger A. Vos, Toshiaki Katayama, Hiroyuki Mishima, Shin Kawano et al.. BioHackathon 2015: Semantics of data for life sciences and reproducible research F1000Research. [live] (2020) JOWO 2020: The Joint Ontology Workshops : Proceedings of the Joint Ontology Workshops co-located with the Bolzano Summer of Knowledge (BOSK 2020) CEUR-WS. (2019) Sarah M. Alghamdi, Beth A. Sundberg, John P. Sundberg, Paul N. Schofield et al.. Quantitative evaluation of ontology design patterns for combining pathology and anatomy ontologies Scientific Reports. (2019) Katayama, Kawashima, Micklem, Kawano et al.. BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services F1000Research. (2018) Maxat Kulmanov, Senay Kafkas, Andreas Karwath, Alexander Malic et al.. Vec2SPARQL: integrating SPARQL queries and knowledge graph embeddings Proceedings of the 11th International Conference Semantic Web Applications and Tools for Life Sciences, SWAT4LS 2018, Antwerp, Belgium, December 3-6, 2018.. (2018) Damion M. Dooley, Emma J. Griffiths, Gurinder S. Gosal, Pier L. Buttigieg et al.. FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration Science of Food. (2018) Keenan, McKerlie, Gkoutos, Ward et al.. A Review of Current Standards and the Evolution of Histopathology Nomenclature for Laboratory Animals ILAR Journal. (2017) Alshahrani, Khan, Maddouri, Kinjo et al.. Neuro-symbolic representation learning on biological knowledge graphs Bioinformatics. (2017) Salhi, Negrao, Essack, Morton et al.. DES-TOMATO: A Knowledge Exploration System Focused On Tomato Species Scientific Reports. (2017) Kafkas, Sarntivijai, Hoehndorf. Usage of cell nomenclature in biomedical literature BMC Bioinformatics. [live] (2016) Bolleman, Mungall, Strozzi, Baran et al.. FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation Journal of Biomedical Semantics. [live] (2016) Salhi, Essack, Radovanovic, Marchand et al.. DESM: portal for microbial knowledge exploration systems Nucleic Acids Research. [live] (2016) Slater, Rodriguez-Garcia, O'Shea, Schofield et al.. Experiences with Aber-OWL, an Ontology Repository with OWL EL Reasoning Ontology Engineering: 12th International Experiences and Directions Workshop on OWL, OWLED 2015, co-located with ISWC 2015, Bethlehem, PA, USA, October 9-10, 2015, Revised Selected Papers. [live] (2016) Robert Hoehndorf, Liam Mencel, Georgios V. Gkoutos, Paul N. Schofield. Large-Scale Reasoning over Functions in Biomedical Ontologies Formal Ontology in Information Systems. (2016) Luke Slater, Georgios V. Gkoutos, Paul N Schofield, Robert Hoehndorf. To MIREOT or not to MIREOT? A case study of the impact of using MIREOT in the Experimental Factor Ontology (EFO) International Conference on Biomedical Ontology and BioCreative (ICBO BioCreative 2016). (2016) Mona Alshahrani, Hussein Almashouq, Robert Hoehndorf. SPARQL2OWL: Towards Bridging the Semantic Gap Between RDF and OWL Proceedings of the Joint International Conference on Biological Ontology and BioCreative, Corvallis, Oregon, United States, August 1-4, 2016.. (2015) Robert Hoehndorf, Luke Slater, Paul N Schofield, Georgios V Gkoutos. Aber-OWL: a framework for ontology-based data access in biology BMC Bioinformatics. (2015) Luke Slater, Georgios Gkoutos, Paul N. Schofield, Robert Hoehndorf. Using Aber-OWL for fast and scalable reasoning over BioPortal ontologies Proceedings of International Conference on Biomedical Ontologies (ICBO). (2015) Luke Slater, Georgios Gkoutos, Paul N. Schofield, Robert Hoehndorf. AberOWL: an ontology portal with OWL EL reasoning Proceedings of International Conference on Biomedical Ontologies (ICBO). (2014) Dumontier, Baker, Baran, Callahan et al.. The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery Journal of Biomedical Semantics. (2013) Hoehndorf, Schofield, Gkoutos. An integrative, translational approach to understanding rare and orphan genetically based diseases Interface Focus. [live] (2012) Hoehndorf, Harris, Herre, Rustici et al.. Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology Bioinformatics. [live] (2012) Gkoutos, Hoehndorf. Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes Journal of Biomedical Semantics. (2012) Gkoutos, Schofield, Hoehndorf. The Units Ontology: a tool for integrating units of measurement in science Database. (2012) Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf. Chapter Four - The Neurobehavior Ontology: An Ontology for Annotation and Integration of Behavior and Behavioral Phenotypes Bioinformatics of Behavior: Part 1. [live] (2012) Robert Hoehndorf, Michel Dumontier, Georgios V. Gkoutos. Integration of knowledge for personalized medicine: a pharmacogenomics case-study Proceedings of the Virtual Physiological Human Conference 2012 (VPH2012). (2011) Hiroshi Masuya, Georgios V. Gkoutos, Nobuhiko Tanaka, Kazunori Waki et al.. Investigation of the fundamental strategy for interoperability of description of biological measurements Proceedings of the Second International Conference on Biomedical Ontology. Hoehndorf, Oellrich, Rebholz-Schuhmann. Interoperability between phenotype and anatomy ontologies Bioinformatics. Robert Hoehndorf, Michel Dumontier, Anika Oellrich, Sarala Wimalaratne et al.. A common layer of interoperability for biomedical ontologies based on OWL EL Bioinformatics. Robert Hoehndorf, Michel Dumontier, Anika Oellrich, Dietrich Rebholz-Schuhmann et al.. Interoperability between biomedical ontologies through relation expansion, upper-level ontologies and automatic reasoning PLOS ONE. de Bono, Hoehndorf, Wimalaratne, Gkoutos et al.. The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions. BMC Research Notes. Hoehndorf, Ngonga Ngomo, Pyysalo, Ohta et al.. Ontology design patterns to disambiguate relations between genes and gene products in GENIA Journal of Biomedical Semantics. [live] Jupp, Stevens, Hoehndorf. Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL Journal of Biomedical Semantics. Wimalaratne, Grenon, Hoehndorf, Gkoutos et al.. An infrastructure for ontology-based information systems in biomedicine: RICORDO case study Bioinformatics. Applied Ontology (65) (2026) Mashkova, Zhapa-Camacho, Hoehndorf. DELE: Deductive EL++ Embeddings for Knowledge Base Completion Neurosymbolic Artificial Intelligence. [live] (2026) Zhapa-Camacho, Hoehndorf. Fully Geometric Multi-hop Reasoning on Knowledge Graphs with Transitive Relations The Semantic Web -- ESWC 2026. [live] (2024) Vogt, Kuhn, Hoehndorf. Semantic units: organizing knowledge graphs into semantically meaningful units of representation Journal of Biomedical Semantics. [live] (2023) Sumyyah Toonsi, Senay Kafkas, Robert Hoehndorf. Exploring the Use of Ontology Components for Distantly-Supervised Disease and Phenotype Named Entity Recognition Proceedings of the International Conference on Biomedical Ontologies 2023 together with the Workshop on Ontologies for Infectious and Immune-Mediated Disease Data Science (OIIDDS 2023) and the FAIR Ontology Harmonization and TRUST Data Interoperability Workshop (FOHTI 2023), Bras\', Brazil, August 28 - September 1, 2023. (2023) Sarah M. Alghamdi, Robert Hoehndorf. Improving the classification of cardinality phenotypes using collections Journal of Biomedical Semantics. [live] (2023) Nuria Queralt-Rosinach, Paul N. Schofield, Marco Roos, Robert Hoehndorf. Updating the CEMO ontology for future epidemiological challenges 14th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4HCLS 2023), Basel, Switzerland, February 13-16, 2023. (2022) Ali Syed, Senay Kafkas, Maxat Kulmanov, Robert Hoehndorf. Using SPARQL to Unify Queries over Data, Ontologies, and Machine Learning Models in the PhenomeBrowser Knowledgebase Proceedings of the 13th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences, SWAT4HCLS 2022. (2022) Yongqun He, Hong Yu, Anthony Huffman, Asiyah Yu Lin et al.. A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology Journal of Biomedical Semantics. [live] (2020) Smaili, Gao, Hoehndorf. Formal axioms in biomedical ontologies improve analysis and interpretation of associated data Bioinformatics. (2020) Kulmanov, Smaili, Gao, Hoehndorf. Semantic similarity and machine learning with ontologies Briefings in Bioinformatics. [live] (2020) Luke T. Slater, Georgios V. Gkoutos, Robert Hoehndorf. Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies BMC Medical Informatics and Decision Making. [live] (2020) JOWO 2020: The Joint Ontology Workshops : Proceedings of the Joint Ontology Workshops co-located with the Bolzano Summer of Knowledge (BOSK 2020) CEUR-WS. (2019) Sarah M. Alghamdi, Beth A. Sundberg, John P. Sundberg, Paul N. Schofield et al.. Quantitative evaluation of ontology design patterns for combining pathology and anatomy ontologies Scientific Reports. (2019) Althubaiti, Karwath, Dallol, Noor et al.. Ontology-based prediction of cancer driver genes Scientific Reports. (2019) Senay Kafkas, Robert Hoehndorf. Ontology based mining of pathogen--disease associations from literature Journal of Biomedical Semantics. (2018) Damion M. Dooley, Emma J. Griffiths, Gurinder S. Gosal, Pier L. Buttigieg et al.. FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration Science of Food. (2018) Ron Henkel, Robert Hoehndorf, Tim Kacprowski, Christian Knupfer et al.. Notions of similarity for systems biology models Briefings in Bioinformatics. (2018) Keenan, McKerlie, Gkoutos, Ward et al.. A Review of Current Standards and the Evolution of Histopathology Nomenclature for Laboratory Animals ILAR Journal. (2018) Smaili, Gao, Hoehndorf. Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations Bioinformatics. (2018) Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf. The anatomy of phenotype ontologies: principles, properties and applications Briefings in Bioinformatics. [live] (2018) Kulmanov, Schofield, Gkoutos, Hoehndorf. Ontology-based validation and identification of regulatory phenotypes Bioinformatics. (2018) Senay Kafkas, Robert Hoehndorf. Ontology based mining of pathogen-disease associations from literature Bio-Ontologies COSI. (2017) Salhi, Negrao, Essack, Morton et al.. DES-TOMATO: A Knowledge Exploration System Focused On Tomato Species Scientific Reports. (2017) Kulmanov, Hoehndorf. Evaluating the effect of annotation size on measures of semantic similarity Journal of Biomedical Semantics. [live] (2016) Hoehndorf, Alshahrani, Gkoutos, Gosline et al.. The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants Journal of Biomedical Semantics. [live] (2016) Bolleman, Mungall, Strozzi, Baran et al.. FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation Journal of Biomedical Semantics. [live] (2016) Fisher, Hoehndorf, Bazelato, Dadras et al.. DermO; an ontology for the description of dermatologic disease Journal of Biomedical Semantics. [live] (2016) Robert Hoehndorf, Liam Mencel, Georgios V. Gkoutos, Paul N. Schofield. Large-Scale Reasoning over Functions in Biomedical Ontologies Formal Ontology in Information Systems. (2016) Luke Slater, Georgios V. Gkoutos, Paul N Schofield, Robert Hoehndorf. To MIREOT or not to MIREOT? A case study of the impact of using MIREOT in the Experimental Factor Ontology (EFO) International Conference on Biomedical Ontology and BioCreative (ICBO BioCreative 2016). (2016) Maxat Kulmanov, Robert Hoehndorf. Evaluating the effect of annotation size on measures of semantic similarity Proceedings of Bio-Ontologies SIG. (2016) Hoehndorf, Gkoutos, Schofield. Datamining with Ontologies Data Mining Techniques for the Life Sciences. [live] (2015) Baran, Durgahee, Eilbeck, Antezana et al.. GFVO: the Genomic Feature and Variation Ontology PeerJ. [live] (2015) Gkoutos, Hoehndorf, Tsaprouni, Schofield. Best behaviour? Ontologies and the formal description of animal behaviour Mammalian Genome. [live] (2015) Hoehndorf, Schofield, Gkoutos. The role of ontologies in biological and biomedical research: a functional perspective Briefings in Bioinformatics. (2015) Oellrich, Walls, Cannon, Cannon et al.. An ontology approach to comparative phenomics in plants Plant Methods. [live] (2014) Dumontier, Baker, Baran, Callahan et al.. The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery Journal of Biomedical Semantics. (2014) Hoehndorf, Haendel, Stevens, Rebholz-Schuhmann. Thematic series on biomedical ontologies in JBMS: challenges and new directions Journal of Biomedical Semantics. (2014) Hoehndorf, Hancock, Hardy, Mallon et al.. Analyzing gene expression data in mice with the Neuro Behavior Ontology Mamm Genome. (2014) Rutger Vos, Jordan Biserkov, Bachir Balech, Niall Beard et al.. Enriched biodiversity data as a resource and service Biodiversity Data Journal. [live] (2013) Cook, Neal, Hoehndorf, Gkoutos et al.. Representing physiological processes and their participants with PhysioMaps Journal of Biomedical Semantics. [live] (2013) Dietrich Rebholz-Schuhmann, Jee-Hyub Kim, Ying Yan, Abhishek Dixit et al.. Evaluation and Cross-Comparison of Lexical Entities of Biological Interest (LexEBI) PLoS ONE. (2013) Dumontier, Chepelev, Hoehndorf. Semantic Systems Biology: Formal Knowledge Representation in Systems Biology for Model Construction, Retrieval, Validation and Discovery Systems Biology. (2012) Hoehndorf, Harris, Herre, Rustici et al.. Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology Bioinformatics. [live] (2012) Oellrich, Gkoutos, Hoehndorf, Rebholz-Schuhmann. Quantitative comparison of mapping methods between Human and Mammalian Phenotype Ontology Journal of Biomedical Semantics. (2012) Loebe, Stumpf, Hoehndorf, Herre. Towards improving phenotype representation in OWL Journal of Biomedical Semantics. (2012) Gkoutos, Hoehndorf. Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes Journal of Biomedical Semantics. (2012) Hoehndorf, Dumontier, Gkoutos. Evaluation of research in biomedical ontologies Briefings in Bioinformatics. (2012) Gkoutos, Schofield, Hoehndorf. The Units Ontology: a tool for integrating units of measurement in science Database. (2012) Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf. Chapter Four - The Neurobehavior Ontology: An Ontology for Annotation and Integration of Behavior and Behavioral Phenotypes Bioinformatics of Behavior: Part 1. [live] (2012) Adam Wyner, Luke Riley, Robert Hoehndorf, Samuel Croset. Argumentation to Represent and Reason over Biological Systems Proceedings of the 3rd International Conference on Information Technology in Bio- and Medical Informatics (ITBAM 2012). (2011) Stefan Schulz, Mathias Brochhausen, Robert Hoehndorf. Higgs bosons, mars missions, and unicorn delusions: How to deal with terms of dubious reference in scientific ontologies Proceedings of the Second International Conference on Biomedical Ontology. (2011) Hiroshi Masuya, Georgios V. Gkoutos, Nobuhiko Tanaka, Kazunori Waki et al.. Investigation of the fundamental strategy for interoperability of description of biological measurements Proceedings of the Second International Conference on Biomedical Ontology. (2011) Simon Jupp, Robert Stevens, Robert Hoehndorf. Exploring Gene Ontology Annotations with OWL Proceedings of the 13th Bio-Ontology Meeting. (2011) Georgios V. Gkoutos, Robert Hoehndorf. Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes Proceedings of the 3rd Workshop for Ontologies in Biomedicine and Life sciences (OBML). (2011) Frank Loebe, Frank Stumpf, Robert Hoehndorf, Heinrich Herre. Towards Improving Phenotype Representation in OWL Proceedings of the 3rd Workshop for Ontologies in Biomedicine and Life sciences (OBML). Hoehndorf, Oellrich, Rebholz-Schuhmann. Interoperability between phenotype and anatomy ontologies Bioinformatics. Robert Hoehndorf, Michel Dumontier, Anika Oellrich, Sarala Wimalaratne et al.. A common layer of interoperability for biomedical ontologies based on OWL EL Bioinformatics. Robert Hoehndorf, Colin Batchelor, Thomas Bittner, Michel Dumontier et al.. The RNA Ontology (RNAO): An Ontology for Integrating RNA Sequence and Structure Data Applied Ontology. Robert Hoehndorf, Michel Dumontier, Anika Oellrich, Dietrich Rebholz-Schuhmann et al.. Interoperability between biomedical ontologies through relation expansion, upper-level ontologies and automatic reasoning PLOS ONE. Adams, Hoehndorf, Gkoutos, Hansen et al.. PIDO: The Primary Immunodeficiency Disease Ontology Bioinformatics. Hoehndorf, Ngonga Ngomo, Pyysalo, Ohta et al.. Ontology design patterns to disambiguate relations between genes and gene products in GENIA Journal of Biomedical Semantics. [live] Schofield, Sundberg, Hoehndorf, Gkoutos. New approaches to the representation and analysis of phenotype knowledge in human diseases and their animal models Briefings in Functional Genomics. Herre, Hoehndorf, Kelso, Loebe et al.. OBML - Ontologies in Biomedicine and Life Sciences Journal of Biomedical Semantics. [live] Robert Hoehndorf, Anika Oellrich, Dietrich Rebholz-Schuhmann, Paul N. Schofield et al.. Linking PharmGKB to phenotype studies and animal models of disease for drug repurposing Pacific Symposium on Biocomputing (PSB). Jupp, Stevens, Hoehndorf. Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL Journal of Biomedical Semantics. Protein function (13) (2025) Zhapa-Camacho, Mashkova, Hoehndorf, Kulmanov. LLM Agent Based Protein Function Prediction Biocomputing 2026. [live] (2025) Kulmanov, Hoehndorf. Computational prediction of protein functional annotations Protein Function Prediction. [live] (2025) Tawfiq, Niu, Kulmanov, Hoehndorf. Annotating genomes with DeepGO protein function prediction tools Protein Function Prediction. [live] (2024) Zhapa-Camacho, Tang, Kulmanov, Hoehndorf. Predicting protein functions using positive-unlabeled ranking with ontology-based priors Bioinformatics. [live] (2024) Tawfiq, Niu, Hoehndorf, Kulmanov. DeepGOMeta for functional insights into microbial communities using deep learning-based protein function prediction Scientific Reports. [live] (2022) Maxat Kulmanov, Robert Hoehndorf. DeepGOZero: improving protein function prediction from sequence and zero-shot learning based on ontology axioms Bioinformatics. [live] (2021) Maxat Kulmanov, Fernando Zhapa-Camacho, Robert Hoehndorf. DeepGOWeb: fast and accurate protein function prediction on the (Semantic) Web Nucleic Acids Research. [live] (2020) Kulmanov, Hoehndorf. DeepGOPlus: improved protein function prediction from sequence Bioinformatics. (2019) Zhou, Jiang, Bergquist, Lee et al.. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens Genome Biology. (2017) Kulmanov, Khan, Hoehndorf. DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier Bioinformatics. (2016) Boudellioua, Saidi, Hoehndorf, Martin et al.. Prediction of Metabolic Pathway Involvement in Prokaryotic UniProtKB Data by Association Rule Mining PLoS ONE. [live] (2011) Simon Jupp, Robert Stevens, Robert Hoehndorf. Exploring Gene Ontology Annotations with OWL Proceedings of the 13th Bio-Ontology Meeting. Jupp, Stevens, Hoehndorf. Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL Journal of Biomedical Semantics. Rare disease (32) (2025) Kafkas, Abdelhakim, Althagafi, Toonsi et al.. The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients Scientific Reports. [live] (2025) Aspromonte, Del Conte, Zhu, Tan et al.. CAGI6 ID panel challenge: assessment of phenotype and variant predictions in 415 children with neurodevelopmental disorders (NDDs) Human Genetics. [live] (2025) Maktabi, Liu, Almesfer, Abdelhakim et al.. Genomic landscape of retinoblastoma: Insights into risk stratification and precision pediatric Neuro-Oncology Neuro-Oncology Pediatrics. [live] (2024) Althagafi, Zhapa-Camacho, Hoehndorf. Prioritizing genomic variants through neuro-symbolic, knowledge-enhanced learning Bioinformatics. [live] (2024) Stenton, O’Leary, Lemire, VanNoy et al.. Critical assessment of variant prioritization methods for rare disease diagnosis within the rare genomes project Human Genomics. [live] (2024) Toonsi, Gauran, Ombao, Schofield et al.. Causal relationships between diseases mined from the literature improve the use of polygenic risk scores Bioinformatics. [live] (2023) Senay Kafkas, Marwa Abdelhakim, Mahmut Uludag, Azza Althagafi et al.. Starvar: symptom-based tool for automatic ranking of variants using evidence from literature and genomes BMC Bioinformatics. [live] (2022) Sarah Alghamdi, Paul N. Schofield, Robert Hoehndorf. Contribution of model organism phenotypes to the computational identification of human disease genes Disease Models & Mechanisms. [live] (2022) Azza Althagafi, Lamia Alsubaie, Nagarajan Kathiresan, Katsuhiko Mineta et al.. DeepSVP: integration of genotype and phenotype for structural variant prioritization using deep learning Bioinformatics. [live] (2021) Jun Chen, Azza Althagafi, Robert Hoehndorf. Predicting candidate genes from phenotypes, functions and anatomical site of expression Bioinformatics. [live] (2020) Marwa Abdelhakim, Eunice McMurray, Ali Raza Syed, Senay Kafkas et al.. DDIEM: drug database for inborn errors of metabolism Orphanet Journal of Rare Diseases. [live] (2020) Kulmanov, Hoehndorf. DeepPheno: Predicting single gene loss-of-function phenotypes using an ontology-aware hierarchical classifier PLOS Computational Biology. [live] (2020) Ahmed Alfares, Lamia Alsubaie, Taghrid Aloraini, Aljoharah Alaskar et al.. What is the right sequencing approach? Solo VS extended family analysis in consanguineous populations BMC Medical Genomics. [live] (2020) Muhammad Umair, Mariam Ballow, Abdulaziz Asiri, Yusra Alyafee et al.. EMC10 homozygous variant identified in a family with global developmental delay, mild intellectual disability, and speech delay Clinical Genetics. [live] (2019) Boudellioua, Kulmanov, Schofield, Gkoutos et al.. DeepPVP: phenotype-based prioritization of causative variants using deep learning BMC Bioinformatics. (2019) Kafkas, Abdelhakim, Hashish, Kulmanov et al.. PathoPhenoDB: linking human pathogens to their disease phenotypes in support of infectious disease research Scientific Data. [live] (2019) Kafkas, Hoehndorf. Ontology based text mining of gene-phenotype associations: application to candidate gene prediction Database. (2018) Boudellioua, Kulmanov, Schofield, Gkoutos et al.. OligoPVP: Phenotype-driven analysis of individual genomic information to prioritize oligogenic disease variants Scientific Reports. (2018) Alshahrani, Hoehndorf. Semantic Disease Gene Embeddings (SmuDGE): phenotype-based disease gene prioritization without phenotypes Bioinformatics. (2017) Boudellioua, Mahamad Razali, Kulmanov, Hashish et al.. Semantic prioritization of novel causative genomic variants PLOS Computational Biology. [live] (2017) Imane Boudellioua, Maxat Kulmanov, Paul N Schofield, Georgios V Gkoutos et al.. Phenotype-driven discovery of digenic variants in personal genome sequences Proceedings of VarI-SIG. (2016) Miguel Rodriguez-Garcia, Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf. Integrating phenotype ontologies with PhenomeNET Proceedings of Ontology Matching Workshop 2016. (2015) Hoehndorf, Gruenberger, Gkoutos, Schofield. Similarity-based search of model organism, disease and drug effect phenotypes Journal of Biomedical Semantics. [live] (2015) Robert Hoehndorf, Paul N Schofield, Georgios V Gkoutos. Analysis of the human diseasome using phenotype similarity between common, genetic, and infectious diseases Scientific Reports. (2013) Hoehndorf, Schofield, Gkoutos. An integrative, translational approach to understanding rare and orphan genetically based diseases Interface Focus. [live] (2013) Hoehndorf, Hiebert, Hardy, Schofield et al.. Mouse model phenotypes provide information about human drug targets Bioinformatics. (2012) Robert Hoehndorf, Georgios V. Gkoutos. A translational medicine approach to orphan diseases Proceedings of the Virtual Physiological Human Conference 2012 (VPH2012). Hoehndorf, Schofield, Gkoutos. PhenomeNET: a whole-phenome approach to disease gene discovery Nucleic Acids Research. Adams, Hoehndorf, Gkoutos, Hansen et al.. PIDO: The Primary Immunodeficiency Disease Ontology Bioinformatics. Schofield, Sundberg, Hoehndorf, Gkoutos. New approaches to the representation and analysis of phenotype knowledge in human diseases and their animal models Briefings in Functional Genomics. Robert Hoehndorf, Anika Oellrich, Dietrich Rebholz-Schuhmann, Paul N. Schofield et al.. Linking PharmGKB to phenotype studies and animal models of disease for drug repurposing Pacific Symposium on Biocomputing (PSB). Schofield, Hoehndorf, Gkoutos. Mouse genetic and phenotypic resources for human genetics Human Mutation. Drug mechanisms (17) (2026) Alsulami, Lehmann, Daga, Khan et al.. LEP-AD: language embedding of proteins and attention to drugs predicts drug-target interactions Journal of Cheminformatics. [live] (2026) Colombo, Salem, Szczepski, Yu et al.. Molecular basis and cellular effects of Janus-class–driven cytoplasmic PYK2 coacervates Communications Biology. [live] (2026) Ashhad, Mashkova, Henao, Hoehndorf. SIDEKICK: A Semantically Integrated Resource for Drug Effects, Indications, and Contraindications The Semantic Web -- ESWC 2026. [live] (2025) Rios Zertuche, Kafkas, Renn, Rueping et al.. Nanodesigner: resolving the complex-CDR interdependency with iterative refinement Journal of Cheminformatics. [live] (2025) Toonsi, Schofield, Hoehndorf. Causal knowledge graph analysis identifies adverse drug effects Bioinformatics. [live] (2025) Alhattab, Barakeh, Khoja, Elhadi et al.. Su1295: Chemically defined peptide-based matrices enabling the development of colorectal organoid models for therapeutic applications and disease modeling Gastroenterology. [live] (2022) Mona Alshahrani, Abdullah Almansour, Asma Alkhaldi, Maha A. Thafar et al.. Combining biomedical knowledge graphs and text to improve predictions for drug-target interactions and drug-indications PeerJ. [live] (2021) Liu-Wei, Kafkas, Chen, Dimonaco et al.. DeepViral: prediction of novel virus–host interactions from protein sequences and infectious disease phenotypes Bioinformatics. [live] (2021) Tilman Hinnerichs, Robert Hoehndorf. DTI-Voodoo: machine learning over interaction networks and ontology-based background knowledge predicts drug interactions Bioinformatics. [live] (2020) Marwa Abdelhakim, Eunice McMurray, Ali Raza Syed, Senay Kafkas et al.. DDIEM: drug database for inborn errors of metabolism Orphanet Journal of Rare Diseases. [live] (2015) Gottlieb, Hoehndorf, Dumontier, Altman. Ranking Adverse Drug Reactions With Crowdsourcing J Med Internet Res. [live] (2015) Hoehndorf, Gruenberger, Gkoutos, Schofield. Similarity-based search of model organism, disease and drug effect phenotypes Journal of Biomedical Semantics. [live] (2013) Dumontier, Chepelev, Hoehndorf. Semantic Systems Biology: Formal Knowledge Representation in Systems Biology for Model Construction, Retrieval, Validation and Discovery Systems Biology. (2013) Hoehndorf, Hiebert, Hardy, Schofield et al.. Mouse model phenotypes provide information about human drug targets Bioinformatics. (2012) Hoehndorf, Dumontier, Gkoutos. Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics Bioinformatics. (2012) Robert Hoehndorf, Michel Dumontier, Georgios V. Gkoutos. Integration of knowledge for personalized medicine: a pharmacogenomics case-study Proceedings of the Virtual Physiological Human Conference 2012 (VPH2012). Robert Hoehndorf, Anika Oellrich, Dietrich Rebholz-Schuhmann, Paul N. Schofield et al.. Linking PharmGKB to phenotype studies and animal models of disease for drug repurposing Pacific Symposium on Biocomputing (PSB). Genomics (16) (2026) Guzman-Vega, Cardona-Londono, Gonzalez-Alvarez, Pena-Guerra et al.. VarLand: A pipeline to map the structural landscape of missense variants at the proteome scale Journal of Biological Chemistry. [live] (2025) Alarawi, Altammami, Abutarboush, Kulmanov et al.. Genomic diversity and antimicrobial resistance of Staphylococcus aureus in Saudi Arabia: a nationwide study using whole-genome sequencing Microbial Genomics. [live] (2025) Bouchama, Gomez, Abdullah, Al Mahri et al.. Whole genome transcriptomic profiling reveals distinct sex-specific responses to heat stroke Journal of Applied Physiology. [live] (2025) Kulmanov, Ashouri, Liu, Abdelhakim et al.. Phased genome assemblies and pangenome graphs of human populations of Japan and Saudi Arabia Scientific Data. [live] (2025) Maktabi, Liu, Almesfer, Abdelhakim et al.. Genomic landscape of retinoblastoma: Insights into risk stratification and precision pediatric Neuro-Oncology Neuro-Oncology Pediatrics. [live] (2025) Tawfiq, Niu, Kulmanov, Hoehndorf. Annotating genomes with DeepGO protein function prediction tools Protein Function Prediction. [live] (2024) Kulmanov, Tawfiq, Liu, Al Ali et al.. A reference quality, fully annotated diploid genome from a Saudi individual Scientific Data. [live] (2024) Stenton, O’Leary, Lemire, VanNoy et al.. Critical assessment of variant prioritization methods for rare disease diagnosis within the rare genomes project Human Genomics. [live] (2023) Sherin Abdelrahman, Rui Ge, Hepi H. Susapto, Yang Liu et al.. The Impact of Mechanical Cues on the Metabolomic and Transcriptomic Profiles of Human Dermal Fibroblasts Cultured in Ultrashort Self-Assembling Peptide 3D Scaffolds ACS Nano. [live] (2023) Mazen Hassanain, Yang Liu, Weam Hussain, Albandri Binowayn et al.. Genomic landscape in Saudi patients with hepatocellular carcinoma using whole-genome sequencing: a pilot study Frontiers in Gastroenterology. [live] (2022) Azza Althagafi, Lamia Alsubaie, Nagarajan Kathiresan, Katsuhiko Mineta et al.. DeepSVP: integration of genotype and phenotype for structural variant prioritization using deep learning Bioinformatics. [live] (2020) Ahmed Alfares, Lamia Alsubaie, Taghrid Aloraini, Aljoharah Alaskar et al.. What is the right sequencing approach? Solo VS extended family analysis in consanguineous populations BMC Medical Genomics. [live] (2020) Muhammad Umair, Mariam Ballow, Abdulaziz Asiri, Yusra Alyafee et al.. EMC10 homozygous variant identified in a family with global developmental delay, mild intellectual disability, and speech delay Clinical Genetics. [live] (2018) Boudellioua, Kulmanov, Schofield, Gkoutos et al.. OligoPVP: Phenotype-driven analysis of individual genomic information to prioritize oligogenic disease variants Scientific Reports. (2017) Imane Boudellioua, Maxat Kulmanov, Paul N Schofield, Georgios V Gkoutos et al.. Phenotype-driven discovery of digenic variants in personal genome sequences Proceedings of VarI-SIG. (2015) Baran, Durgahee, Eilbeck, Antezana et al.. GFVO: the Genomic Feature and Variation Ontology PeerJ. [live] Biomedical informatics (46) (2026) Guzman-Vega, Cardona-Londono, Gonzalez-Alvarez, Pena-Guerra et al.. VarLand: A pipeline to map the structural landscape of missense variants at the proteome scale Journal of Biological Chemistry. [live] (2025) Kafkas, Abdelhakim, Althagafi, Toonsi et al.. The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients Scientific Reports. [live] (2025) Alarawi, Altammami, Abutarboush, Kulmanov et al.. Genomic diversity and antimicrobial resistance of Staphylococcus aureus in Saudi Arabia: a nationwide study using whole-genome sequencing Microbial Genomics. [live] (2025) Gomez, Al Mahri, Abdullah, Malik et al.. Age-related differences in gene expression and pathway activation following heatstroke Physiological Genomics. [live] (2025) Alhattab, Barakeh, Khoja, Elhadi et al.. Sa1216: Development of colorectal cancer and matched healthy organoids from Saudi patients: a case study Gastroenterology. [live] (2025) Schofield, Hoehndorf, Gkoutos, Smith. The informatics of developmental phenotypes Kaufman’s Atlas of Mouse Development Supplement. [live] (2024) Toonsi, Gauran, Ombao, Schofield et al.. Causal relationships between diseases mined from the literature improve the use of polygenic risk scores Bioinformatics. [live] (2023) Senay Kafkas, Marwa Abdelhakim, Mahmut Uludag, Azza Althagafi et al.. Starvar: symptom-based tool for automatic ranking of variants using evidence from literature and genomes BMC Bioinformatics. [live] (2023) Mazen Hassanain, Yang Liu, Weam Hussain, Albandri Binowayn et al.. Genomic landscape in Saudi patients with hepatocellular carcinoma using whole-genome sequencing: a pilot study Frontiers in Gastroenterology. [live] (2021) Luke T. Slater, William Bradlow, Simon Ball, Robert Hoehndorf et al.. Improved characterisation of clinical text through ontology-based vocabulary expansion Journal of Biomedical Semantics. [live] (2021) Liu-Wei, Kafkas, Chen, Dimonaco et al.. DeepViral: prediction of novel virus–host interactions from protein sequences and infectious disease phenotypes Bioinformatics. [live] (2021) Jun Chen, Azza Althagafi, Robert Hoehndorf. Predicting candidate genes from phenotypes, functions and anatomical site of expression Bioinformatics. [live] (2021) Luke T. Slater, John A. Williams, Andreas Karwath, Hilary Fanning et al.. Multi-faceted semantic clustering with text-derived phenotypes Computers in Biology and Medicine. [live] (2021) Luke T. Slater, Andreas Karwath, Robert Hoehndorf, Georgios V. Gkoutos. Effects of Negation and Uncertainty Stratification on Text-Derived Patient Profile Similarity Frontiers in Digital Health. [live] (2020) Sara Althubaiti, Senay Kafkas, Marwa Abdelhakim, Robert Hoehndorf. Combining lexical and context features for automatic ontology extension Journal of Biomedical Semantics. (2020) Rutger A. Vos, Toshiaki Katayama, Hiroyuki Mishima, Shin Kawano et al.. BioHackathon 2015: Semantics of data for life sciences and reproducible research F1000Research. [live] (2019) Althubaiti, Karwath, Dallol, Noor et al.. Ontology-based prediction of cancer driver genes Scientific Reports. (2019) Senay Kafkas, Robert Hoehndorf. Ontology based mining of pathogen--disease associations from literature Journal of Biomedical Semantics. (2019) Kafkas, Abdelhakim, Hashish, Kulmanov et al.. PathoPhenoDB: linking human pathogens to their disease phenotypes in support of infectious disease research Scientific Data. [live] (2019) Kafkas, Hoehndorf. Ontology based text mining of gene-phenotype associations: application to candidate gene prediction Database. (2019) Katayama, Kawashima, Micklem, Kawano et al.. BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services F1000Research. (2019) Timothy K. Cooper, Kathleen A. Silva, Victoria E. Kennedy, Sarah M. Alghamdi et al.. Hyaline Arteriolosclerosis in 30 Strains of Aged Inbred Mice Veterinary Pathology. [live] (2018) Sohaib Younis, Claus Weiland, Robert Hoehndorf, Stefan Dressler et al.. Taxon and trait recognition from digitized herbarium specimens using deep convolutional neural networks Botany Letters. (2018) Senay Kafkas, Robert Hoehndorf. Ontology based mining of pathogen-disease associations from literature Bio-Ontologies COSI. (2018) Sara Althubaiti, Senay Kafkas, Robert Hoehndorf. Ontology-Based Concept Recognition by Using Word Embeddings Bio-Ontologies COSI. (2017) Kafkas, Sarntivijai, Hoehndorf. Usage of cell nomenclature in biomedical literature BMC Bioinformatics. [live] (2016) Boudellioua, Saidi, Hoehndorf, Martin et al.. Prediction of Metabolic Pathway Involvement in Prokaryotic UniProtKB Data by Association Rule Mining PLoS ONE. [live] (2016) Hoehndorf, Gkoutos, Schofield. Datamining with Ontologies Data Mining Techniques for the Life Sciences. [live] (2015) Robert Hoehndorf, Luke Slater, Paul N Schofield, Georgios V Gkoutos. Aber-OWL: a framework for ontology-based data access in biology BMC Bioinformatics. (2015) Martin Hrabe de Angelis, George Nicholson, Mohammed Selloum, Jacqueline K White et al.. Analysis of mammalian gene function through broad-based phenotypic screens across a consortium of mouse clinics Nature Genetics. (2015) Gottlieb, Hoehndorf, Dumontier, Altman. Ranking Adverse Drug Reactions With Crowdsourcing J Med Internet Res. [live] (2015) Hoehndorf, Schofield, Gkoutos. The role of ontologies in biological and biomedical research: a functional perspective Briefings in Bioinformatics. (2014) Hoehndorf, Hancock, Hardy, Mallon et al.. Analyzing gene expression data in mice with the Neuro Behavior Ontology Mamm Genome. (2014) Rutger Vos, Jordan Biserkov, Bachir Balech, Niall Beard et al.. Enriched biodiversity data as a resource and service Biodiversity Data Journal. [live] (2013) Hoehndorf, Hardy, Osumi-Sutherland, Tweedie et al.. Systematic Analysis of Experimental Phenotype Data Reveals Gene Functions PLoS ONE. (2013) Rebholz-Schuhmann, Kafkas, Kim, Li et al.. Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources Journal of Biomedical Semantics. (2013) Dietrich Rebholz-Schuhmann, Jee-Hyub Kim, Ying Yan, Abhishek Dixit et al.. Evaluation and Cross-Comparison of Lexical Entities of Biological Interest (LexEBI) PLoS ONE. (2012) Hoehndorf, Dumontier, Gkoutos. Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics Bioinformatics. (2012) Hoehndorf, Dumontier, Gkoutos. Evaluation of research in biomedical ontologies Briefings in Bioinformatics. (2012) Dietrich Rebholz-Schuhmann, Anika Oellrich, Robert Hoehndorf. Text-mining solutions for biomedical research: enabling integrative biology Nature Reviews Genetics. (2012) Robert Hoehndorf, Georgios V. Gkoutos. A translational medicine approach to orphan diseases Proceedings of the Virtual Physiological Human Conference 2012 (VPH2012). Robert Hoehndorf, Colin Batchelor, Thomas Bittner, Michel Dumontier et al.. The RNA Ontology (RNAO): An Ontology for Integrating RNA Sequence and Structure Data Applied Ontology. de Bono, Hoehndorf, Wimalaratne, Gkoutos et al.. The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions. BMC Research Notes. Hoehndorf, Ngonga Ngomo, Pyysalo, Ohta et al.. Ontology design patterns to disambiguate relations between genes and gene products in GENIA Journal of Biomedical Semantics. [live] Herre, Hoehndorf, Kelso, Loebe et al.. OBML - Ontologies in Biomedicine and Life Sciences Journal of Biomedical Semantics. [live] Wimalaratne, Grenon, Hoehndorf, Gkoutos et al.. An infrastructure for ontology-based information systems in biomedicine: RICORDO case study Bioinformatics. Semantic similarity (15) (2022) Sarah Alghamdi, Paul N. Schofield, Robert Hoehndorf. Contribution of model organism phenotypes to the computational identification of human disease genes Disease Models & Mechanisms. [live] (2022) Luke T. Slater, Sophie Russell, Silver Makepeace, Alexander Carberry et al.. Evaluating semantic similarity methods for comparison of text-derived phenotype profiles BMC Medical Informatics and Decision Making. [live] (2021) Luke T. Slater, Andreas Karwath, Robert Hoehndorf, Georgios V. Gkoutos. Effects of Negation and Uncertainty Stratification on Text-Derived Patient Profile Similarity Frontiers in Digital Health. [live] (2020) Kulmanov, Smaili, Gao, Hoehndorf. Semantic similarity and machine learning with ontologies Briefings in Bioinformatics. [live] (2019) Claus Weiland, Maxat Kulmanov, Marco Schmidt, Robert Hoehndorf. A Machine Learning Based Approach for Similarity Search on Biodiversity Knowledge Graphs Biodiversity Information Science and Standards. (2018) Ron Henkel, Robert Hoehndorf, Tim Kacprowski, Christian Knupfer et al.. Notions of similarity for systems biology models Briefings in Bioinformatics. (2018) Smaili, Gao, Hoehndorf. OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction Bioinformatics. [live] (2017) Kulmanov, Hoehndorf. Evaluating the effect of annotation size on measures of semantic similarity Journal of Biomedical Semantics. [live] (2017) Boudellioua, Mahamad Razali, Kulmanov, Hashish et al.. Semantic prioritization of novel causative genomic variants PLOS Computational Biology. [live] (2016) Maxat Kulmanov, Robert Hoehndorf. Evaluating the effect of annotation size on measures of semantic similarity Proceedings of Bio-Ontologies SIG. (2015) Hoehndorf, Gruenberger, Gkoutos, Schofield. Similarity-based search of model organism, disease and drug effect phenotypes Journal of Biomedical Semantics. [live] (2015) Robert Hoehndorf, Paul N Schofield, Georgios V Gkoutos. Analysis of the human diseasome using phenotype similarity between common, genetic, and infectious diseases Scientific Reports. (2012) Oellrich, Gkoutos, Hoehndorf, Rebholz-Schuhmann. Quantitative comparison of mapping methods between Human and Mammalian Phenotype Ontology Journal of Biomedical Semantics. (2011) Anika Oellrich, Robert Hoehndorf, Georgios V. Gkoutos, Dietrich Rebholz-Schuhmann. Quantitative comparison of mapping methods between Human and Mammalian Phenotype Ontology Proceedings of the 3rd Workshop for Ontologies in Biomedicine and Life sciences (OBML). Hoehndorf, Schofield, Gkoutos. PhenomeNET: a whole-phenome approach to disease gene discovery Nucleic Acids Research. Microbial communities (4) (2024) Tawfiq, Niu, Hoehndorf, Kulmanov. DeepGOMeta for functional insights into microbial communities using deep learning-based protein function prediction Scientific Reports. [live] (2018) Othoum, Bougouffa, Razali, Bokhari et al.. In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters BMC Genomics. (2017) Motwalli, Essack, Jankovic, Ji et al.. In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria BMC Genomics. [live] (2016) Salhi, Essack, Radovanovic, Marchand et al.. DESM: portal for microbial knowledge exploration systems Nucleic Acids Research. [live] Phenotype informatics (31) (2025) Aspromonte, Del Conte, Zhu, Tan et al.. CAGI6 ID panel challenge: assessment of phenotype and variant predictions in 415 children with neurodevelopmental disorders (NDDs) Human Genetics. [live] (2025) Schofield, Hoehndorf, Gkoutos, Smith. The informatics of developmental phenotypes Kaufman’s Atlas of Mouse Development Supplement. [live] (2022) Sarah Alghamdi, Paul N. Schofield, Robert Hoehndorf. Contribution of model organism phenotypes to the computational identification of human disease genes Disease Models & Mechanisms. [live] (2021) Luke T. Slater, William Bradlow, Simon Ball, Robert Hoehndorf et al.. Improved characterisation of clinical text through ontology-based vocabulary expansion Journal of Biomedical Semantics. [live] (2021) Luke T. Slater, John A. Williams, Andreas Karwath, Hilary Fanning et al.. Multi-faceted semantic clustering with text-derived phenotypes Computers in Biology and Medicine. [live] (2020) Kulmanov, Hoehndorf. DeepPheno: Predicting single gene loss-of-function phenotypes using an ontology-aware hierarchical classifier PLOS Computational Biology. [live] (2019) Timothy K. Cooper, Kathleen A. Silva, Victoria E. Kennedy, Sarah M. Alghamdi et al.. Hyaline Arteriolosclerosis in 30 Strains of Aged Inbred Mice Veterinary Pathology. [live] (2019) Linn, Mustonen, Silva, Kennedy et al.. Nail abnormalities identified in an ageing study of 30 inbred mouse strains Experimental Dermatology. [live] (2018) Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf. The anatomy of phenotype ontologies: principles, properties and applications Briefings in Bioinformatics. [live] (2018) Kulmanov, Schofield, Gkoutos, Hoehndorf. Ontology-based validation and identification of regulatory phenotypes Bioinformatics. (2018) Sohaib Younis, Claus Weiland, Robert Hoehndorf, Stefan Dressler et al.. Taxon and trait recognition from digitized herbarium specimens using deep convolutional neural networks Botany Letters. (2017) Imane Boudellioua, Maxat Kulmanov, Paul N Schofield, Georgios V Gkoutos et al.. Phenotype-driven discovery of digenic variants in personal genome sequences Proceedings of VarI-SIG. (2016) Hoehndorf, Alshahrani, Gkoutos, Gosline et al.. The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants Journal of Biomedical Semantics. [live] (2016) Miguel Rodriguez-Garcia, Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf. Integrating phenotype ontologies with PhenomeNET Proceedings of Ontology Matching Workshop 2016. (2016) Fisher, Hoehndorf, Bazelato, Dadras et al.. DermO; an ontology for the description of dermatologic disease Journal of Biomedical Semantics. [live] (2015) Gkoutos, Hoehndorf, Tsaprouni, Schofield. Best behaviour? Ontologies and the formal description of animal behaviour Mammalian Genome. [live] (2015) Martin Hrabe de Angelis, George Nicholson, Mohammed Selloum, Jacqueline K White et al.. Analysis of mammalian gene function through broad-based phenotypic screens across a consortium of mouse clinics Nature Genetics. (2015) Oellrich, Walls, Cannon, Cannon et al.. An ontology approach to comparative phenomics in plants Plant Methods. [live] (2013) Hoehndorf, Hardy, Osumi-Sutherland, Tweedie et al.. Systematic Analysis of Experimental Phenotype Data Reveals Gene Functions PLoS ONE. (2012) Hoehndorf, Harris, Herre, Rustici et al.. Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology Bioinformatics. [live] (2012) Oellrich, Gkoutos, Hoehndorf, Rebholz-Schuhmann. Quantitative comparison of mapping methods between Human and Mammalian Phenotype Ontology Journal of Biomedical Semantics. (2012) Loebe, Stumpf, Hoehndorf, Herre. Towards improving phenotype representation in OWL Journal of Biomedical Semantics. (2012) Gkoutos, Hoehndorf. Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes Journal of Biomedical Semantics. (2012) Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf. Chapter Four - The Neurobehavior Ontology: An Ontology for Annotation and Integration of Behavior and Behavioral Phenotypes Bioinformatics of Behavior: Part 1. [live] (2011) Georgios V. Gkoutos, Robert Hoehndorf. Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes Proceedings of the 3rd Workshop for Ontologies in Biomedicine and Life sciences (OBML). (2011) Anika Oellrich, Robert Hoehndorf, Georgios V. Gkoutos, Dietrich Rebholz-Schuhmann. Quantitative comparison of mapping methods between Human and Mammalian Phenotype Ontology Proceedings of the 3rd Workshop for Ontologies in Biomedicine and Life sciences (OBML). (2011) Frank Loebe, Frank Stumpf, Robert Hoehndorf, Heinrich Herre. Towards Improving Phenotype Representation in OWL Proceedings of the 3rd Workshop for Ontologies in Biomedicine and Life sciences (OBML). Hoehndorf, Oellrich, Rebholz-Schuhmann. Interoperability between phenotype and anatomy ontologies Bioinformatics. Hoehndorf, Schofield, Gkoutos. PhenomeNET: a whole-phenome approach to disease gene discovery Nucleic Acids Research. Schofield, Sundberg, Hoehndorf, Gkoutos. New approaches to the representation and analysis of phenotype knowledge in human diseases and their animal models Briefings in Functional Genomics. Schofield, Hoehndorf, Gkoutos. Mouse genetic and phenotypic resources for human genetics Human Mutation. Bioengineering (7) (2026) Colombo, Salem, Szczepski, Yu et al.. Molecular basis and cellular effects of Janus-class–driven cytoplasmic PYK2 coacervates Communications Biology. [live] (2025) Bouchama, Gomez, Abdullah, Al Mahri et al.. Whole genome transcriptomic profiling reveals distinct sex-specific responses to heat stroke Journal of Applied Physiology. [live] (2025) Gomez, Al Mahri, Abdullah, Malik et al.. Age-related differences in gene expression and pathway activation following heatstroke Physiological Genomics. [live] (2025) Rios Zertuche, Kafkas, Renn, Rueping et al.. Nanodesigner: resolving the complex-CDR interdependency with iterative refinement Journal of Cheminformatics. [live] (2025) Alhattab, Barakeh, Khoja, Elhadi et al.. Sa1216: Development of colorectal cancer and matched healthy organoids from Saudi patients: a case study Gastroenterology. [live] (2025) Alhattab, Barakeh, Khoja, Elhadi et al.. Su1295: Chemically defined peptide-based matrices enabling the development of colorectal organoid models for therapeutic applications and disease modeling Gastroenterology. [live] (2023) Sherin Abdelrahman, Rui Ge, Hepi H. Susapto, Yang Liu et al.. The Impact of Mechanical Cues on the Metabolomic and Transcriptomic Profiles of Human Dermal Fibroblasts Cultured in Ultrashort Self-Assembling Peptide 3D Scaffolds ACS Nano. [live]
