Publications

A complete list of publications by members of the Bio-Ontology Research Group, drawn from our local research knowledge graph (223 entries).

Quick filters: Neuro-symbolic AI Ontology engineering Applied Ontology Protein function Rare disease Drug mechanisms Genomics Biomedical informatics Semantic similarity Microbial communities Phenotype informatics Bioengineering

Publications by topic

Neuro-symbolic AI (29)

(2025) Ontology Embedding: A Survey of Methods, Applications and Resources
(2025) Neuro-Symbolic AI in Life Sciences
(2024) Predicting protein functions using positive-unlabeled ranking with ontology-based priors
(2024) Prioritizing genomic variants through neuro-symbolic, knowledge-enhanced learning
(2024) Large-Scale Knowledge Integration for Enhanced Molecular Property Prediction
(2024) Enhancing Geometric Ontology Embeddings for $\mathcalE\mathcalL^++$ with Negative Sampling and Deductive Closure Filtering
(2024) Lattice-Preserving $\mathcal ALC$ Ontology Embeddings
(2023) mOWL: Python library for machine learning with biomedical ontologies
(2023) From Axioms over Graphs to Vectors, and Back Again: Evaluating the Properties of Graph-based Ontology Embeddings
(2022) Combining biomedical knowledge graphs and text to improve predictions for drug-target interactions and drug-indications
(2022) DeepGOZero: improving protein function prediction from sequence and zero-shot learning based on ontology axioms
(2022) Positive-Unlabeled Learning with Adversarial Data Augmentation for Knowledge Graph Completion
(2021) DTI-Voodoo: machine learning over interaction networks and ontology-based background knowledge predicts drug\textendashtarget interactions
(2020) Semantic similarity and machine learning with ontologies
(2020) DeepGOPlus: improved protein function prediction from sequence
(2020) DeepPheno: Predicting single gene loss-of-function phenotypes using an ontology-aware hierarchical classifier
(2019) A Machine Learning Based Approach for Similarity Search on Biodiversity Knowledge Graphs
(2019) DeepPVP: phenotype-based prioritization of causative variants using deep learning
(2019) EL Embeddings: Geometric construction of models for the Description Logic EL++
(2019) Semi-Supervised Entity Alignment via Knowledge Graph Embedding with Awareness of Degree Difference
(2018) Vec2SPARQL: integrating SPARQL queries and knowledge graph embeddings
(2018) Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations
(2018) OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction
(2018) Semantic Disease Gene Embeddings (SmuDGE): phenotype-based disease gene prioritization without phenotypes
(2018) Ontology-Based Concept Recognition by Using Word Embeddings
(2017) Neuro-symbolic representation learning on biological knowledge graphs
(2017) Data science and symbolic AI: Synergies, challenges and opportunities
(2017) DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier
() Neural Multi-hop Logical Query Answering with Concept-Level Answers

Ontology engineering (42)

Applied Ontology (63)

Protein function (13)

Rare disease (32)

Drug mechanisms (15)

Genomics (16)

Biomedical informatics (46)

Semantic similarity (15)

Microbial communities (4)

Phenotype informatics (31)

Bioengineering (7)

Publications by year

2023

DeepGOMeta: Functional Insights into Microbial Communities with Deep Learning-Based Protein Function Prediction.
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\'\ilia, 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.
Sarah M. Alghamdi, Robert Hoehndorf. Improving the classification of cardinality phenotypes using collections Journal of Biomedical Semantics.
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.
Fernando Zhapa-Camacho, Maxat Kulmanov, Robert Hoehndorf. mOWL: Python library for machine learning with biomedical ontologies Bioinformatics.
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.
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.
N\'uria 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.
Causal Knowledge Graphs: Leveraging Background Knowledge for Causal Inference at Scale.
Causal Knowledge Graphs: Leveraging Background Knowledge for Causal Inference at Scale.
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.
Context-based protein function prediction in bacterial genomes.
Sarah Alghamdi, Paul N. Schofield, Robert Hoehndorf. Contribution of model organism phenotypes to the computational identification of human disease genes Disease Models \& Mechanisms.
Maxat Kulmanov, Robert Hoehndorf. DeepGOZero: improving protein function prediction from sequence and zero-shot learning based on ontology axioms Bioinformatics.
Azza Althagafi, Lamia Alsubaie, Nagarajan Kathiresan, Katsuhiko Mineta et al.. DeepSVP: integration of genotype and phenotype for structural variant prioritization using deep learning Bioinformatics.
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.
Exploring the Use of Ontology Components for Distantly-Supervised Disease and Phenotype Named Entity Recognition.
INDIGENA: inductive prediction of disease--gene associations using phenotype ontologies Supplementary Material.
Large-Scale Knowledge Integration for Enhanced Molecular Property Prediction.
mOWL: revision document.
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.
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.
Liu-Wei, Kafkas, Chen, Dimonaco et al.. DeepViral: prediction of novel virus–host interactions from protein sequences and infectious disease phenotypes Bioinformatics.
Tilman Hinnerichs, Robert Hoehndorf. DTI-Voodoo: machine learning over interaction networks and ontology-based background knowledge predicts drug\textendashtarget interactions Bioinformatics.
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.
How much do model organism phenotypes contribute to the computational identification of human disease genes?.
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.
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.
Jun Chen, Azza Althagafi, Robert Hoehndorf. Predicting candidate genes from phenotypes, functions and anatomical site of expression Bioinformatics.

2020

Rutger A. Vos, Toshiaki Katayama, Hiroyuki Mishima, Shin Kawano et al.. BioHackathon 2015: Semantics of data for life sciences and reproducible research F1000Research.
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.
Kulmanov, Hoehndorf. DeepGOPlus: improved protein function prediction from sequence Bioinformatics.
DeepGOWeb: Fast and accurate protein function prediction on the (Semantic) Web.
Kulmanov, Hoehndorf. DeepPheno: Predicting single gene loss-of-function phenotypes using an ontology-aware hierarchical classifier PLOS Computational Biology.
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.
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.
PAVS: A database of phenotype-associated variants in Saudi Arabia.
Semantic similarity and machine learning with biomedical ontologies.
Kulmanov, Smaili, Gao, Hoehndorf. Semantic similarity and machine learning with ontologies Briefings in Bioinformatics.
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.
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.

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.
DeepGOPlus: Improved protein function prediction from sequence.
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.
Formal axioms in biomedical ontologies improve analysis and interpretation of associated data.
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.
Linn, Mustonen, Silva, Kennedy et al.. Nail abnormalities identified in an ageing study of 30 inbred mouse strains Experimental Dermatology.
Senay Kafkas, Robert Hoehndorf. Ontology based mining of pathogen--disease associations from literature Journal of Biomedical Semantics.
Ontology based text mining of gene--phenotype associations: application to candidate gene prediction.
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.
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.
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.
Formal axioms in biomedical ontologies improve analysis and interpretation of associated data.
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.
Ontology Embedding: A Survey of Methods, Applications and Resources.
Sara Althubaiti, Senay Kafkas, Robert Hoehndorf. Ontology-Based Concept Recognition by Using Word Embeddings Bio-Ontologies COSI.
Ontology-based prediction of cancer driver genes.
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.
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.
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.
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.
Motwalli, Essack, Jankovic, Ji et al.. In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria BMC Genomics.
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.
Kafkas, Sarntivijai, Hoehndorf. Usage of cell nomenclature in biomedical literature BMC Bioinformatics.

2016

Hoehndorf, Gkoutos, Schofield. Datamining with Ontologies Data Mining Techniques for the Life Sciences.
DeepPVP: Phenotype-based prioritization of causative variants using deep learning.
Fisher, Hoehndorf, Bazelato, Dadras et al.. DermO; an ontology for the description of dermatologic disease Journal of Biomedical Semantics.
Salhi, Essack, Radovanovic, Marchand et al.. DESM: portal for microbial knowledge exploration systems Nucleic Acids Research.
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.
Bolleman, Mungall, Strozzi, Baran et al.. FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation Journal of Biomedical Semantics.
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.
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Self-normalizing learning on biomedical ontologies.
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.
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.
Martin Hrab\ve 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.
Baran, Durgahee, Eilbeck, Antezana et al.. GFVO: the Genomic Feature and Variation Ontology PeerJ.
Klarigi: Explanations for Semantic Groupings Supplementary Material.
Ontology-based prediction of cancer driver genes.
Predicting protein functions from sequence by a neuro-symbolic deep learning model.
Gottlieb, Hoehndorf, Dumontier, Altman. Ranking Adverse Drug Reactions With Crowdsourcing J Med Internet Res.
Hoehndorf, Gruenberger, Gkoutos, Schofield. Similarity-based search of model organism, disease and drug effect phenotypes Journal of Biomedical Semantics.
The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients.
The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients.
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

A-PATH: Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics.
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.
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.
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.
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.
Combining lexical and context features for automatic ontology extension.
Combining lexical and context features for automatic ontology extension.
DDIEM: Drug Database for Inborn Errors of Metabolism.
DeepPVP: phenotype-based prioritization of causative variants using deep learning.
Hoehndorf, Dumontier, Gkoutos. Evaluation of research in biomedical ontologies Briefings in Bioinformatics.
Exploring the Use of Ontology Components for Distantly-Supervised Disease and Phenotype Named Entity Recognition.
Hoehndorf, Dumontier, Gkoutos. Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics Bioinformatics.
Improved characterisation of clinical text through ontology-based vocabulary expansion.
Improving the classification of cardinality phenotypes using collections.
Integrating phenotype ontologies with PhenomeNET.
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).
Komenti: A Semantic Text-mining Framework.
Linking common human diseases to their phenotypes; development of a resource for human phenomics.
Ontology based mining of pathogen--disease associations from literature.
Ontology based mining of pathogen-disease associations from literature.
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.
STARVar: Symptom-based Tool for Automatic Ranking of Variants using evidence from literature and genomes.
Dietrich Rebholz-Schuhmann, Anika Oellrich, Robert Hoehndorf. Text-mining solutions for biomedical research: enabling integrative biology Nature Reviews Genetics.
The Flora Phenotype Ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants.
The Flora Phenotype Ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants.
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.
Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies.
VSIM: Visualization and simulation of variants in personal genomes with an application to premarital testing.

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.
Applying GWAS on UK Biobank by using enhanced phenotype information based on Ontology-Wide Association Study.
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.
Klarigi: Characteristic Explanations for Semantic Data.
Klarigi: Characteristic Explanations for Semantic Data.
Lattice-based $\mathcalALC$ ontology embeddings with saturation.
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.
Hoehndorf, Ngonga Ngomo, Pyysalo, Ohta et al.. Ontology design patterns to disambiguate relations between genes and gene products in GENIA Journal of Biomedical Semantics.
PhenomeBrowser: Integrating phenotypes, their semantics, and phenotype-based machine learning across domains, organisms, and applications.
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.
Using SPARQL to unify queries over data, ontologies, and machine learning models in the PhenomeBrowser knowledgebase.

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