Robert Hoehndorf

162 papers A* 3C 4Misc 2Journal 115Unranked 32

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Causal knowledge graph analysis identifies adverse drug effects. Bioinform. Sumyyah Toonsi, Paul N. Schofield, Robert Hoehndorf
2026	J	`jnl`	GRAFT: Decoupling Ranking and Calibration for Survival Analysis. CoRR Mohammad Ashhad, Robert Hoehndorf, Ricardo Henao
2026	J	`jnl`	SIDEKICK: A Semantically Integrated Resource for Drug Effects, Indications, and Contraindications. CoRR Mohammad Ashhad, Olga Mashkova, Ricardo Henao, Robert Hoehndorf
2025	J	`jnl`	Causal knowledge graph analysis identifies adverse drug effects. CoRR Sumyyah Toonsi, Paul N. Schofield, Robert Hoehndorf
2025	J	`jnl`	Fully Geometric Multi-Hop Reasoning on Knowledge Graphs with Transitive Relations. CoRR Fernando Zhapa-Camacho, Robert Hoehndorf
2025	J	`jnl`	Nanodesigner: resolving the complex-CDR interdependency with iterative refinement. J. Cheminformatics Melissa Maria Rios Zertuche, Senay Kafkas, Dominik Renn, Magnus Rueping, Robert Hoehndorf
2025	J	`jnl`	Ontology Embedding: A Survey of Methods, Applications and Resources. IEEE Trans. Knowl. Data Eng. Jiaoyan Chen, Olga Mashkova, Fernando Zhapa-Camacho, Robert Hoehndorf, Yuan He, Ian Horrocks
2024	J	`jnl`	Causal relationships between diseases mined from the literature improve the use of polygenic risk scores. Bioinform. Sumyyah Toonsi, Iris Ivy M. Gauran, Hernando Ombao, Paul N. Schofield, Robert Hoehndorf
2024	J	`jnl`	Correction to: Semantic units: organizing knowledge graphs into semantically meaningful units of representation. J. Biomed. Semant. Lars Vogt, Tobias Kuhn, Robert Hoehndorf
2024	J	`jnl`	DELE: Deductive ℰℒ CoRR Olga Mashkova, Fernando Zhapa-Camacho, Robert Hoehndorf
2024	—	`conf`	Enhancing Geometric Ontology Embeddings for NeSy (1) Olga Mashkova, Fernando Zhapa-Camacho, Robert Hoehndorf
2024	J	`jnl`	Enhancing Geometric Ontology Embeddings for ℰℒ CoRR Olga Mashkova, Fernando Zhapa-Camacho, Robert Hoehndorf
2024	—	`conf`	Large-Scale Knowledge Integration for Enhanced Molecular Property Prediction. NeSy (2) Yasir Ghunaim, Robert Hoehndorf
2024	J	`jnl`	Large-Scale Knowledge Integration for Enhanced Molecular Property Prediction. CoRR Yasir Ghunaim, Robert Hoehndorf
2024	—	`conf`	Lattice-Preserving NeSy (1) Fernando Zhapa-Camacho, Robert Hoehndorf
2024	J	`jnl`	Ontology Embedding: A Survey of Methods, Applications and Resources. CoRR Jiaoyan Chen, Olga Mashkova, Fernando Zhapa-Camacho, Robert Hoehndorf, Yuan He, Ian Horrocks
2024	J	`jnl`	Predicting protein functions using positive-unlabeled ranking with ontology-based priors. Bioinform. Fernando Zhapa-Camacho, Zhenwei Tang, Maxat Kulmanov, Robert Hoehndorf
2024	J	`jnl`	Prioritizing genomic variants through neuro-symbolic, knowledge-enhanced learning. Bioinform. Azza Althagafi, Fernando Zhapa-Camacho, Robert Hoehndorf
2024	J	`jnl`	Protein function prediction as approximate semantic entailment. Nat. Mac. Intell. Maxat Kulmanov, Francisco J. Guzmán-Vega, Paula Duek Roggli, Lydie Lane, Stefan T. Arold, Robert Hoehndorf
2024	J	`jnl`	Semantic units: organizing knowledge graphs into semantically meaningful units of representation. J. Biomed. Semant. Lars Vogt, Tobias Kuhn, Robert Hoehndorf
2024	J	`jnl`	Towards Automated Functional Equation Proving: A Benchmark Dataset and A Domain-Specific In-Context Agent. CoRR Mahdi Buali, Robert Hoehndorf
2023	J	`jnl`	An Open-Source Knowledge Graph Ecosystem for the Life Sciences. CoRR Tiffany J. Callahan, Ignacio J. Tripodi, Adrianne L. Stefanski, Luca Cappelletti, Sanya Bathla Taneja, Jordan M. Wyrwa, Elena Casiraghi, Nicolas A. Matentzoglu, Justin T. Reese, Jonathan C. Silverstein, Charles Tapley Hoyt, Richard D. Boyce, Scott A. Malec, Deepak R. Unni, Marcin P. Joachimiak, Peter N. Robinson, Christopher J. Mungall, Emanuele Cavalleri, Tommaso Fontana, Giorgio Valentini, Marco Mesiti, Lucas A. Gillenwater, Brook E. Santangelo, Nicole A. Vasilevsky, Robert Hoehndorf, Tellen D. Bennett, Patrick B. Ryan, George Hripcsak, Michael G. Kahn, Michael Bada, William A. Baumgartner Jr., Lawrence E. Hunter
2023	J	`jnl`	CatE: Embedding ALC ontologies using category-theoretical semantics. CoRR Fernando Zhapa-Camacho, Robert Hoehndorf
2023	—	`conf`	Evaluating Different Methods for Semantic Reasoning Over Ontologies. QALD/SemREC@ISWC Fernando Zhapa-Camacho, Robert Hoehndorf
2023	—	`conf`	Exploring the Use of Ontology Components for Distantly-Supervised Disease and Phenotype Named Entity Recognition. ICBO Sumyyah Toonsi, Senay Kafkas, Robert Hoehndorf
2023	C	`conf`	From Axioms over Graphs to Vectors, and Back Again: Evaluating the Properties of Graph-based Ontology Embeddings. NeSy Fernando Zhapa-Camacho, Robert Hoehndorf
2023	J	`jnl`	From axioms over graphs to vectors, and back again: evaluating the properties of graph-based ontology embeddings. CoRR Fernando Zhapa-Camacho, Robert Hoehndorf
2023	J	`jnl`	Improving the classification of cardinality phenotypes using collections. J. Biomed. Semant. Sarah M. Alghamdi, Robert Hoehndorf
2023	J	`jnl`	Klarigi: Characteristic explanations for semantic biomedical data. Comput. Biol. Medicine Luke T. Slater, John A. Williams, Paul N. Schofield, Sophie Russell, Samantha C. Pendleton, Andreas Karwath, Hilary Fanning, Simon Ball, Robert Hoehndorf, Georgios V. Gkoutos
2023	Misc	`conf`	Neural Multi-hop Logical Query Answering with Concept-Level Answers. ISWC Zhenwei Tang, Shichao Pei, Xi Peng, Fuzhen Zhuang, Xiangliang Zhang, Robert Hoehndorf
2023	J	`jnl`	Semantic Units: Organizing knowledge graphs into semantically meaningful units of representation. CoRR Lars Vogt, Tobias Kuhn, Robert Hoehndorf
2023	J	`jnl`	Starvar: symptom-based tool for automatic ranking of variants using evidence from literature and genomes. BMC Bioinform. Senay Kafkas, Marwa Abdelhakim, Mahmut Uludag, Azza Althagafi, Malak Alghamdi, Robert Hoehndorf
2023	J	`jnl`	Stylized Projected GAN: A Novel Architecture for Fast and Realistic Image Generation. CoRR Md Nurul Muttakin, Malik Shahid Sultan, Robert Hoehndorf, Hernando Ombao
2023	—	`conf`	Updating the CEMO ontology for future epidemiological challenges. SWAT4HCLS Núria Queralt-Rosinach, Paul N. Schofield, Marco Roos, Robert Hoehndorf
2023	J	`jnl`	mOWL: Python library for machine learning with biomedical ontologies. Bioinform. Fernando Zhapa-Camacho, Maxat Kulmanov, Robert Hoehndorf
2022	J	`jnl`	A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology. J. Biomed. Semant. Yongqun He, Hong Yu, Anthony Huffman, Asiyah Yu Lin, Darren A. Natale, John Beverley, Ling Zheng, Yehoshua Perl, Zhigang Wang, Yingtong Liu, Edison Ong, Yang Wang, Philip Huang, Long Tran, Jinyang Du, Zalan Shah, Easheta Shah, Roshan Desai, Hsin-Hui Huang, Yujia Tian, Eric Merrell, William D. Duncan, Sivaram Arabandi, Lynn M. Schriml, Jie Zheng, Anna Maria Masci, Liwei Wang, Hongfang Liu, Fatima Zohra Smaili, Robert Hoehndorf, Zoë May Pendlington, Paola Roncaglia, Xianwei Ye, Jiangan Xie, Yi-Wei Tang, Xiaolin Yang, Suyuan Peng, Luxia Zhang, Luonan Chen, Junguk Hur, Gilbert S. Omenn, Brian D. Athey, Barry Smith
2022	—	`conf`	A-LIOn - alignment learning through inconsistency negatives of the aligned ontologies. OM@ISWC Sarah M. Alghamdi, Fernando Zhapa-Camacho, Robert Hoehndorf
2022	J	`jnl`	DeepGOZero: improving protein function prediction from sequence and zero-shot learning based on ontology axioms. Bioinform. Maxat Kulmanov, Robert Hoehndorf
2022	J	`jnl`	DeepSVP: integration of genotype and phenotype for structural variant prioritization using deep learning. Bioinform. Azza Althagafi, Lamia Alsubaie, Nagarajan Kathiresan, Katsuhiko Mineta, Taghrid Aloraini, Fuad Al Mutairi, Majid Alfadhel, Takashi Gojobori, Ahmad Alfares, Robert Hoehndorf
2022	J	`jnl`	Description Logic EL++ Embeddings with Intersectional Closure. CoRR Xi Peng, Zhenwei Tang, Maxat Kulmanov, Kexin Niu, Robert Hoehndorf
2022	J	`jnl`	Evaluating semantic similarity methods for comparison of text-derived phenotype profiles. BMC Medical Informatics Decis. Mak. Luke T. Slater, Sophie Russell, Silver Makepeace, Alexander Carberry, Andreas Karwath, John A. Williams, Hilary Fanning, Simon Ball, Robert Hoehndorf, Georgios V. Gkoutos
2022	J	`jnl`	FALCON: Sound and Complete Neural Semantic Entailment over ALC Ontologies. CoRR Zhenwei Tang, Tilman Hinnerichs, Xi Peng, Xiangliang Zhang, Robert Hoehndorf
2022	J	`jnl`	Joint Abductive and Inductive Neural Logical Reasoning. CoRR Zhenwei Tang, Shichao Pei, Xi Peng, Fuzhen Zhuang, Xiangliang Zhang, Robert Hoehndorf
2022	—	`conf`	Ontological Analysis of Collection Improves Classification of Cardinality Phenotypes. ICBO Sarah M. Alghamdi, Robert Hoehndorf
2022	A*	`conf`	Positive-Unlabeled Learning with Adversarial Data Augmentation for Knowledge Graph Completion. IJCAI Zhenwei Tang, Shichao Pei, Zhao Zhang, Yongchun Zhu, Fuzhen Zhuang, Robert Hoehndorf, Xiangliang Zhang
2022	J	`jnl`	Positive-Unlabeled Learning with Adversarial Data Augmentation for Knowledge Graph Completion. CoRR Zhenwei Tang, Shichao Pei, Zhao Zhang, Yongchun Zhu, Fuzhen Zhuang, Robert Hoehndorf, Xiangliang Zhang
2022	—	`conf`	The Coevolution of Ontologies and Knowledge-based Analytics in Bioinformatics. ICBO Robert Hoehndorf
2022	—	`conf`	Using SPARQL to Unify Queries over Data, Ontologies, and Machine Learning Models in the PhenomeBrowser Knowledgebase. SWAT4HCLS Ali Syed, Senay Kafkas, Maxat Kulmanov, Robert Hoehndorf
2021	J	`jnl`	A fast, accurate, and generalisable heuristic-based negation detection algorithm for clinical text. Comput. Biol. Medicine Luke T. Slater, William Bradlow, Dino FA. Motti, Robert Hoehndorf, Simon Ball, Georgios V. Gkoutos
2021	J	`jnl`	DTI-Voodoo: machine learning over interaction networks and ontology-based background knowledge predicts drug-target interactions. Bioinform. Tilman Hinnerichs, Robert Hoehndorf
2021	J	`jnl`	DeepGOPlus: improved protein function prediction from sequence. Bioinform. Maxat Kulmanov, Robert Hoehndorf
2021	J	`jnl`	DeepGOWeb: fast and accurate protein function prediction on the (Semantic) Web. Nucleic Acids Res. Maxat Kulmanov, Fernando Zhapa-Camacho, Robert Hoehndorf
2021	J	`jnl`	DeepViral: prediction of novel virus-host interactions from protein sequences and infectious disease phenotypes. Bioinform. Wang Liu-Wei, Senay Kafkas, Jun Chen, Nicholas J. Dimonaco, Jesper Tegnér, Robert Hoehndorf
2021	J	`jnl`	Effects of Negation and Uncertainty Stratification on Text-Derived Patient Profile Similarity. Frontiers Digit. Health Luke T. Slater, Andreas Karwath, Robert Hoehndorf, Georgios V. Gkoutos
2021	J	`jnl`	Improved characterisation of clinical text through ontology-based vocabulary expansion. J. Biomed. Semant. Luke T. Slater, William Bradlow, Simon Ball, Robert Hoehndorf, Georgios V. Gkoutos
2021	J	`jnl`	Linking common human diseases to their phenotypes; development of a resource for human phenomics. J. Biomed. Semant. Senay Kafkas, Sara Althubaiti, Georgios V. Gkoutos, Robert Hoehndorf, Paul N. Schofield
2021	J	`jnl`	Multi-faceted semantic clustering with text-derived phenotypes. Comput. Biol. Medicine Luke T. Slater, John A. Williams, Andreas Karwath, Hilary Fanning, Simon Ball, Paul N. Schofield, Robert Hoehndorf, Georgios V. Gkoutos
2021	J	`jnl`	Predicting candidate genes from phenotypes, functions and anatomical site of expression. Bioinform. Jun Chen, Azza Althagafi, Robert Hoehndorf
2021	—	`ed.`	Proceedings of the Joint Ontology Workshops 2021 Episode VII: The Bolzano Summer of Knowledge co-located with the 12th International Conference on Formal Ontology in Information Systems (FOIS 2021), and the 12th International Conference on Biomedical Ontologies (ICBO 2021), Bolzano, Italy, September 11-18, 2021. JOWO Emilio M. Sanfilippo, Oliver Kutz, Nicolas Troquard, Torsten Hahmann, Claudio Masolo, Robert Hoehndorf, Randi Vita, Maria M. Hedblom, Guendalina Righetti, Dusan Sormaz, Walter Terkaj, Tiago Prince Sales, Sergio de Cesare, Frederik Gailly, Giancarlo Guizzardi, Mark Lycett, Chris Partridge, Oscar Pastor, Daniel Beßler, Stefano Borgo, Mohammed Diab, Aldo Gangemi, Alberto Olivares Alarcos, Mihai Pomarlan, Robert Porzel, Ludger Jansen, Mathias Brochhausen, Daniele Porello, Pawel Garbacz, Selja Seppälä, Michael Grüninger, Amanda Vizedom, Damion M. Dooley, Robert Warren, Hande Küçük-McGinty, Matthew Lange, Alsayed Algergawy, Naouel Karam, Friederike Klan, Franck Michel, Ilaria Rosati
2021	J	`jnl`	Semantic similarity and machine learning with ontologies. Briefings Bioinform. Maxat Kulmanov, Fatima Zohra Smaili, Xin Gao, Robert Hoehndorf
2021	J	`jnl`	Towards similarity-based differential diagnostics for common diseases. Comput. Biol. Medicine Luke T. Slater, Andreas Karwath, John A. Williams, Sophie Russell, Silver Makepeace, Alexander Carberry, Robert Hoehndorf, Georgios V. Gkoutos
2020	J	`jnl`	BioHackathon 2015: Semantics of data for life sciences and reproducible research. F1000Research Rutger A. Vos, Toshiaki Katayama, Hiroyuki Mishima, Shin Kawano, Shuichi Kawashima, Jin-Dong Kim, Yuki Moriya, Toshiaki Tokimatsu, Atsuko Yamaguchi, Yasunori Yamamoto, Hongyan Wu, Peter Amstutz, Erick Antezana, Nobuyuki P. Aoki, Kazuharu Arakawa, Jerven T. Bolleman, Evan E. Bolton, Raoul Jean Pierre Bonnal, Hidemasa Bono, Kees Burger, Hirokazu Chiba, Kevin Bretonnel Cohen, Eric W. Deutsch, Jesualdo Tomás Fernández-Breis, Gang Fu, Takatomo Fujisawa, Atsushi Fukushima, Alexander García Castro, Naohisa Goto, Tudor Groza, Colin Hercus, Robert Hoehndorf, Kotone Itaya, Nick S. Juty, Takeshi Kawashima, Jee-Hyub Kim, Akira R. Kinjo, Masaaki Kotera, Kouji Kozaki, Sadahiro Kumagai, Tatsuya Kushida, Thomas Lütteke, Masaaki Matsubara, Joe Miyamoto, Attayeb Mohsen, Hiroshi Mori, Yuki Naito, Takeru Nakazato, Jeremy NguyenXuan, Kozo Nishida, Naoki Nishida, Hiroyo Nishide, Soichi Ogishima, Tazro Ohta, Shujiro Okuda, Benedict Paten, Jean-Luc Perret, Philip Prathipati, Pjotr Prins, Núria Queralt-Rosinach, Daisuke Shinmachi, Shinya Suzuki, Tsuyosi Tabata, Terue Takatsuki, Kieron R. Taylor, Mark Thompson, Ikuo Uchiyama, Bruno Vieira, Chih-Hsuan Wei, Mark D. Wilkinson, Issaku Yamada, Ryota Yamanaka, Kazutoshi Yoshitake, Akiyasu C. Yoshizawa, Michel Dumontier, Kenjiro Kosaki, Toshihisa Takagi
2020	J	`jnl`	Combining lexical and context features for automatic ontology extension. J. Biomed. Semant. Sara Althubaiti, Senay Kafkas, Marwa Abdelhakim, Robert Hoehndorf
2020	J	`jnl`	DeepGOPlus: improved protein function prediction from sequence. Bioinform. Maxat Kulmanov, Robert Hoehndorf
2020	J	`jnl`	DeepPheno: Predicting single gene loss-of-function phenotypes using an ontology-aware hierarchical classifier. PLoS Comput. Biol. Maxat Kulmanov, Robert Hoehndorf
2020	J	`jnl`	Efficient long-distance relation extraction with DG-SpanBERT. CoRR Jun Chen, Robert Hoehndorf, Mohamed Elhoseiny, Xiangliang Zhang
2020	J	`jnl`	Formal axioms in biomedical ontologies improve analysis and interpretation of associated data. Bioinform. Fatima Zohra Smaili, Xin Gao, Robert Hoehndorf
2020	—	`ed.`	Proceedings of the Joint Ontology Workshops co-located with the Bolzano Summer of Knowledge (BOSK 2020), Virtual & Bozen-Bolzano, Italy, August 31st to October 7th, 2020. JOWO Karl Hammar, Oliver Kutz, Anastasia Dimou, Torsten Hahmann, Robert Hoehndorf, Claudio Masolo, Randi Vita, Sarra Ben Abbès, Rim Hantach, Philippe Calvez, Tiago Prince Sales, Daniele Porello, Daniel Beßler, Stefano Borgo, Mohammed Diab, Aldo Gangemi, Alberto Olivares Alarcos, Mihai Pomarlan, Robert Porzel, Martin G. Skjæveland, Daniel P. Lupp, Ian Horrocks, Johan W. Klüwer, Christian Kindermann, Loris Bozzato, Till Mossakowski, Luciano Serafini
2020	J	`jnl`	Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies. BMC Medical Informatics Decis. Mak. Luke T. Slater, Georgios V. Gkoutos, Robert Hoehndorf
2019	J	`jnl`	BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services. F1000Research Toshiaki Katayama, Shuichi Kawashima, Gos Micklem, Shin Kawano, Jin-Dong Kim, Simon Kocbek, Shinobu Okamoto, Yue Wang, Hongyan Wu, Atsuko Yamaguchi, Yasunori Yamamoto, Erick Antezana, Kiyoko F. Aoki-Kinoshita, Kazuharu Arakawa, Masaki Banno, Joachim Baran, Jerven T. Bolleman, Raoul Jean Pierre Bonnal, Hidemasa Bono, Jesualdo Tomás Fernández-Breis, Robert M. Buels, Matthew P. Campbell, Hirokazu Chiba, Peter J. A. Cock, Kevin Bretonnel Cohen, Michel Dumontier, Takatomo Fujisawa, Toyofumi Fujiwara, Leyla J. García, Pascale Gaudet, Emi Hattori, Robert Hoehndorf, Kotone Itaya, Maori Ito, Daniel Jamieson, Simon Jupp, Nick S. Juty, Alex Kalderimis, Fumihiro Kato, Hideya Kawaji, Takeshi Kawashima, Akira R. Kinjo, Yusuke Komiyama, Masaaki Kotera, Tatsuya Kushida, James Malone, Masaaki Matsubara, Satoshi Mizuno, Sayaka Mizutani, Hiroshi Mori, Yuki Moriya, Katsuhiko Murakami, Takeru Nakazato, Hiroyo Nishide, Yosuke Nishimura, Soichi Ogishima, Tazro Ohta, Shujiro Okuda, Hiromasa Ono, Yasset Pérez-Riverol, Daisuke Shinmachi, Andrea Splendiani, Francesco Strozzi, Shinya Suzuki, Junichi Takehara, Mark Thompson, Toshiaki Tokimatsu, Ikuo Uchiyama, Karin Verspoor, Mark D. Wilkinson, Sarala M. Wimalaratne, Issaku Yamada, Nozomi Yamamoto, Masayuki Yarimizu, Shoko Kawamoto, Toshihisa Takagi
2019	J	`jnl`	DeepPVP: phenotype-based prioritization of causative variants using deep learning. BMC Bioinform. Imane Boudellioua, Maxat Kulmanov, Paul N. Schofield, Georgios V. Gkoutos, Robert Hoehndorf
2019	A*	`conf`	EL Embeddings: Geometric Construction of Models for the Description Logic EL++. IJCAI Maxat Kulmanov, Wang Liu-Wei, Yuan Yan, Robert Hoehndorf
2019	J	`jnl`	EL Embeddings: Geometric construction of models for the Description Logic EL ++. CoRR Maxat Kulmanov, Wang Liu-Wei, Yuan Yan, Robert Hoehndorf
2019	J	`jnl`	OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction. Bioinform. Fatima Zohra Smaili, Xin Gao, Robert Hoehndorf
2019	J	`jnl`	Ontology based mining of pathogen-disease associations from literature. J. Biomed. Semant. Senay Kafkas, Robert Hoehndorf
2019	J	`jnl`	Ontology based text mining of gene-phenotype associations: application to candidate gene prediction. Database J. Biol. Databases Curation Senay Kafkas, Robert Hoehndorf
2019	A*	`conf`	Semi-Supervised Entity Alignment via Knowledge Graph Embedding with Awareness of Degree Difference. WWW Shichao Pei, Lu Yu, Robert Hoehndorf, Xiangliang Zhang
2018	J	`jnl`	DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier. Bioinform. Maxat Kulmanov, Mohammad Asif Khan, Robert Hoehndorf
2018	J	`jnl`	Inferring ontology graph structures using OWL reasoning. BMC Bioinform. Miguel Ángel Rodríguez-García, Robert Hoehndorf
2018	J	`jnl`	Notions of similarity for systems biology models. Briefings Bioinform. Ron Henkel, Robert Hoehndorf, Tim Kacprowski, Christian Knüpfer, Wolfram Liebermeister, Dagmar Waltemath
2018	J	`jnl`	OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction. CoRR Fatima Zohra Smaili, Xin Gao, Robert Hoehndorf
2018	J	`jnl`	Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations. Bioinform. Fatima Zohra Smaili, Xin Gao, Robert Hoehndorf
2018	J	`jnl`	Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations. CoRR Fatima Zohra Smaili, Xin Gao, Robert Hoehndorf
2018	J	`jnl`	Ontology-based validation and identification of regulatory phenotypes. Bioinform. Maxat Kulmanov, Paul N. Schofield, Georgios V. Gkoutos, Robert Hoehndorf
2018	J	`jnl`	Semantic Disease Gene Embeddings (SmuDGE): phenotype-based disease gene prioritization without phenotypes. Bioinform. Mona Alshahrani, Robert Hoehndorf
2018	—	`ch.`	The Flora Phenotype Ontology (FLOPO) and the FLOPO Knowledgebase. Application of Semantic Technology in Biodiversity Science Robert Hoehndorf, Claus Weiland, Marco Schmidt, Quentin Groom, George Gosline, Stefan Dressler, Thomas Hamann
2018	J	`jnl`	The anatomy of phenotype ontologies: principles, properties and applications. Briefings Bioinform. Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf
2018	—	`conf`	Vec2SPARQL: integrating SPARQL queries and knowledge graph embeddings. SWAT4LS Maxat Kulmanov, Senay Kafkas, Andreas Karwath, Alexander Malic, Georgios V. Gkoutos, Michel Dumontier, Robert Hoehndorf
2017	J	`jnl`	Data Science and symbolic AI: Synergies, challenges and opportunities. Data Sci. Robert Hoehndorf, Núria Queralt-Rosinach
2017	J	`jnl`	DeepGO: Predicting protein functions from sequence and interactions using a deep ontology-aware classifier. CoRR Maxat Kulmanov, Mohammad Asif Khan, Robert Hoehndorf
2017	J	`jnl`	Evaluating the effect of annotation size on measures of semantic similarity. J. Biomed. Semant. Maxat Kulmanov, Robert Hoehndorf
2017	J	`jnl`	Integrating phenotype ontologies with PhenomeNET. J. Biomed. Semant. Miguel Ángel Rodríguez-García, Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf
2017	J	`jnl`	Neuro-symbolic representation learning on biological knowledge graphs. Bioinform. Mona Alshahrani, Mohammad Asif Khan, Omar Maddouri, Akira R. Kinjo, Núria Queralt-Rosinach, Robert Hoehndorf
2017	J	`jnl`	Notions of similarity for systems biology models. Briefings Bioinform. Ron Henkel, Robert Hoehndorf, Tim Kacprowski, Christian Knüpfer, Wolfram Liebermeister, Dagmar Waltemath
2017	J	`jnl`	Semantic prioritization of novel causative genomic variants. PLoS Comput. Biol. Imane Boudellioua, Rozaimi B. Mahamad Razali, Maxat Kulmanov, Yasmeen Hashish, Vladimir B. Bajic, Eva Goncalves-Serra, Nadia Schoenmakers, Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf
2017	J	`jnl`	Usage of cell nomenclature in biomedical literature. BMC Bioinform. Senay Kafkas, Sirarat Sarntivijai, Robert Hoehndorf
2016	J	`jnl`	DESM: portal for microbial knowledge exploration systems. Nucleic Acids Res. Adil Salhi, Magbubah Essack, Aleksandar Radovanovic, Benoit Marchand, Salim Bougouffa, André Antunes, Marta Filipa Simões, Feras F. Lafi, Olaa A. Motwalli, Ameerah Bokhari, Tariq Malas, Soha Al Amoudi, Ghofran Othum, Intikhab Alam, Katsuhiko Mineta, Xin Gao, Robert Hoehndorf, John A. C. Archer, Takashi Gojobori, Vladimir B. Bajic
2016	J	`jnl`	DermO; an ontology for the description of dermatologic disease. J. Biomed. Semant. Hannah M. Fisher, Robert Hoehndorf, Bruno S. Bazelato, Soheil S. Dadras, Lloyd E. King, Georgios V. Gkoutos, John P. Sundberg, Paul N. Schofield
2016	J	`jnl`	FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation. J. Biomed. Semant. Jerven T. Bolleman, Christopher J. Mungall, Francesco Strozzi, Joachim Baran, Michel Dumontier, Raoul Jean Pierre Bonnal, Robert M. Buels, Robert Hoehndorf, Takatomo Fujisawa, Toshiaki Katayama, Peter J. A. Cock
2016	—	`conf`	FLOPO - An Ontology for the Integration of Trait Data from Digitized Floras and Plant Image Collections. SWAT4LS Claus Weiland, Robert Hoehndorf, George Gosline, Quentin Groom, Thomas Hamann, Marco Schmidt
2016	—	`conf`	FoodON: A Global Farm-to-Fork Food Ontology. ICBO/BioCreative Emma J. Griffiths, Damion M. Dooley, Pier Luigi Buttigieg, Robert Hoehndorf, Fiona S. L. Brinkman, William W. L. Hsiao
2016	—	`conf`	Integrating phenotype ontologies with PhenomeNET. OM@ISWC Miguel Ángel Rodríguez-García, Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf
2016	C	`conf`	Large-Scale Reasoning over Functions in Biomedical Ontologies. FOIS Robert Hoehndorf, Liam Mencel, Georgios V. Gkoutos, Paul N. Schofield
2016	J	`jnl`	Neuro-symbolic representation learning on biological knowledge graphs. CoRR Mona Alshahrani, Mohammad Asif Khan, Omar Maddouri, Akira R. Kinjo, Núria Queralt-Rosinach, Robert Hoehndorf
2016	—	`ed.`	Proceedings of the Joint International Conference on Biological Ontology and BioCreative, Corvallis, Oregon, United States, August 1-4, 2016. ICBO/BioCreative Pankaj Jaiswal, Robert Hoehndorf, Cecilia N. Arighi, Austin Meier
2016	—	`conf`	SPARQL2OWL: Towards Bridging the Semantic Gap Between RDF and OWL. ICBO/BioCreative Mona Alshahrani, Hussein Almashouq, Robert Hoehndorf
2016	J	`jnl`	The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants. J. Biomed. Semant. Robert Hoehndorf, Mona Alshahrani, Georgios V. Gkoutos, George Gosline, Quentin Groom, Thomas Hamann, Jens Kattge, Sylvia Mota de Oliveira, Marco Schmidt, Soraya Sierra, Erik Smets, Rutger A. Vos, Claus Weiland
2016	—	`conf`	To MIREOT or not to MIREOT? A Case Study of the Impact of Using MIREOT in the Experimental Factor Ontology (EFO). ICBO/BioCreative Luke T. Slater, Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf
2016	—	`conf`	Updates to the AberOWL Ontology Repository. ICBO/BioCreative Miguel Ángel Rodríguez-García, Luke T. Slater, Imane Boudellioua, Paul N. Schofield, Georgios V. Gkoutos, Robert Hoehndorf
2016	J	`jnl`	Using AberOWL for fast and scalable reasoning over BioPortal ontologies. J. Biomed. Semant. Luke T. Slater, Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf
2015	J	`jnl`	Aber-OWL: a framework for ontology-based data access in biology. BMC Bioinform. Robert Hoehndorf, Luke T. Slater, Paul N. Schofield, Georgios V. Gkoutos
2015	—	`conf`	AberOWL: an ontology portal with OWL EL reasoning. ICBO Luke T. Slater, Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf
2015	—	`conf`	Experiences with Aber-OWL, an Ontology Repository with OWL EL Reasoning. OWLED Luke T. Slater, Miguel Ángel Rodríguez-García, Keiron O'Shea, Paul N. Schofield, Georgios V. Gkoutos, Robert Hoehndorf
2015	J	`jnl`	Similarity-based search of model organism, disease and drug effect phenotypes. J. Biomed. Semant. Robert Hoehndorf, Michael Gruenberger, Georgios V. Gkoutos, Paul N. Schofield
2015	J	`jnl`	The role of ontologies in biological and biomedical research: a functional perspective. Briefings Bioinform. Robert Hoehndorf, Paul N. Schofield, Georgios V. Gkoutos
2015	—	`conf`	Using Aber-OWL for fast and scalable reasoning over BioPortal ontologies. ICBO Luke T. Slater, Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf
2015	—	`conf`	Visualising Ontologies with AberOWL. SWAT4LS Miguel Ángel Rodríguez-García, Luke T. Slater, Keiron O'Shea, Paul N. Schofield, Georgios V. Gkoutos, Robert Hoehndorf
2014	—	`conf`	Aber-OWL: A Framework for Ontology-based Data Access in Biology. SWAT4LS Robert Hoehndorf, Luke T. Slater, Paul N. Schofield, Georgios V. Gkoutos
2014	J	`jnl`	Aber-OWL: a framework for ontology-based data access in biology. CoRR Robert Hoehndorf, Luke T. Slater, Paul N. Schofield, Georgios V. Gkoutos
2014	J	`jnl`	Mouse model phenotypes provide information about human drug targets. Bioinform. Robert Hoehndorf, Tanya Hiebert, Nigel W. Hardy, Paul N. Schofield, Georgios V. Gkoutos, Michel Dumontier
2014	J	`jnl`	The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery. J. Biomed. Semant. Michel Dumontier, Christopher J. O. Baker, Joachim Baran, Alison Callahan, Leonid L. Chepelev, Jose Cruz-Toledo, Nicholas R. Del Rio, Geraint Duck, Laura Inés Furlong, Nichealla Keath, Dana Klassen, Jamie P. McCusker, Núria Queralt-Rosinach, Matthias Samwald, Natalia Villanueva-Rosales, Mark D. Wilkinson, Robert Hoehndorf
2014	J	`jnl`	Thematic series on biomedical ontologies in JBMS: challenges and new directions. J. Biomed. Semant. Robert Hoehndorf, Dietrich Rebholz-Schuhmann, Melissa A. Haendel, Robert Stevens
2013	J	`jnl`	Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources. J. Biomed. Semant. Dietrich Rebholz-Schuhmann, Senay Kafkas, Jee-Hyub Kim, Chen Li, Antonio Jimeno-Yepes, Robert Hoehndorf, Rolf Backofen, Ian Lewin
2013	J	`jnl`	Evaluation of research in biomedical ontologies. Briefings Bioinform. Robert Hoehndorf, Michel Dumontier, Georgios V. Gkoutos
2013	—	`ed.`	Proceedings of the 4th International Conference on Biomedical Ontology, ICBO 2013, Montreal, Canada, July 7-12, 2013. ICBO Michel Dumontier, Robert Hoehndorf, Christopher J. O. Baker
2013	J	`jnl`	Representing physiological processes and their participants with PhysioMaps. J. Biomed. Semant. Daniel L. Cook, Maxwell Lewis Neal, Robert Hoehndorf, Georgios V. Gkoutos, John H. Gennari
2012	J	`jnl`	An infrastructure for ontology-based information systems in biomedicine: RICORDO case study. Bioinform. Sarala M. Wimalaratne, Pierre Grenon, Robert Hoehndorf, Georgios V. Gkoutos, Bernard de Bono
2012	—	`conf`	Argumentation to Represent and Reason over Biological Systems. ITBAM Adam Z. Wyner, Luke Riley, Robert Hoehndorf, Samuel Croset
2012	J	`jnl`	Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics. Bioinform. Robert Hoehndorf, Michel Dumontier, Georgios V. Gkoutos
2012	Misc	`conf`	Linking PharmGKB to Phenotype Studies and Animal Models of Disease for Drug Repurposing. Pacific Symposium on Biocomputing Robert Hoehndorf, Anika Oellrich, Dietrich Rebholz-Schuhmann, Paul N. Schofield, Georgios V. Gkoutos
2012	J	`jnl`	Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL. J. Biomed. Semant. Simon Jupp, Robert Stevens, Robert Hoehndorf
2012	J	`jnl`	Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes. J. Biomed. Semant. Georgios V. Gkoutos, Robert Hoehndorf
2012	—	`conf`	Profiling of Semantically Annotated Proteins. SWAT4LS Jens Hollunder, Vladimir Mironov, Erick Antezana, Robert Hoehndorf, Martin Kuiper
2012	J	`jnl`	Quantitative comparison of mapping methods between Human and Mammalian Phenotype Ontology. J. Biomed. Semant. Anika Oellrich, Georgios V. Gkoutos, Robert Hoehndorf, Dietrich Rebholz-Schuhmann
2012	J	`jnl`	Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology. Bioinform. Robert Hoehndorf, Midori A. Harris, Heinrich Herre, Gabriella Rustici, Georgios V. Gkoutos
2012	J	`jnl`	The Units Ontology: a tool for integrating units of measurement in science. Database J. Biol. Databases Curation Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf
2012	J	`jnl`	Towards improving phenotype representation in OWL. J. Biomed. Semant. Frank Loebe, Frank Stumpf, Robert Hoehndorf, Heinrich Herre
2012	J	`jnl`	Towards quantitative measures in applied ontology CoRR Robert Hoehndorf, Michel Dumontier, Georgios V. Gkoutos
2011	J	`jnl`	A common layer of interoperability for biomedical ontologies based on OWL EL. Bioinform. Robert Hoehndorf, Michel Dumontier, Anika Oellrich, Sarala M. Wimalaratne, Dietrich Rebholz-Schuhmann, Paul N. Schofield, Georgios V. Gkoutos
2011	—	`conf`	An Advanced Strategy for Integration of Biological Measurement Data. ICBO Hiroshi Masuya, Georgios V. Gkoutos, Nobuhiko Tanaka, Kazunori Waki, Yoshihiro Okuda, Tatsuya Kushida, Norio Kobayashi, Koji Doi, Kouji Kozaki, Robert Hoehndorf, Shigeharu Wakana, Tetsuro Toyoda, Riichiro Mizoguchi
2011	—	`conf`	Higgs Bosons, Mars Missions, and Unicorn Delusions: How to Deal with Terms of Dubious Reference in Scientific Ontologies. ICBO Stefan Schulz, Mathias Brochhausen, Robert Hoehndorf
2011	J	`jnl`	Integrating systems biology models and biomedical ontologies. BMC Syst. Biol. Robert Hoehndorf, Michel Dumontier, John H. Gennari, Sarala M. Wimalaratne, Bernard de Bono, Daniel L. Cook, Georgios V. Gkoutos
2011	J	`jnl`	OBML - Ontologies in Biomedicine and Life Sciences. J. Biomed. Semant. Heinrich Herre, Robert Hoehndorf, Janet Kelso, Frank Loebe, Stefan Schulz
2011	J	`jnl`	Ontology design patterns to disambiguate relations between genes and gene products in GENIA. J. Biomed. Semant. Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Sampo Pyysalo, Tomoko Ohta, Anika Oellrich, Dietrich Rebholz-Schuhmann
2011	J	`jnl`	PIDO: the primary immunodeficiency disease ontology. Bioinform. Nico Adams, Robert Hoehndorf, Georgios V. Gkoutos, Gesine Hansen, Christian Hennig
2011	J	`jnl`	The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data. Appl. Ontology Robert Hoehndorf, Colin R. Batchelor, Thomas Bittner, Michel Dumontier, Karen Eilbeck, Rob Knight, Chris Mungall, Jane S. Richardson, Jesse Stombaugh, Eric Westhof, Craig L. Zirbel, Neocles Leontis
2010	—	`conf`	Applying ontology design patterns to the implementation of relations in GENIA. Semantic Mining in Biomedicine Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Sampo Pyysalo, Tomoko Ohta, Anika Oellrich, Dietrich Rebholz-Schuhmann
2010	J	`jnl`	Applying the functional abnormality ontology pattern to anatomical functions. J. Biomed. Semant. Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Janet Kelso
2010	J	`jnl`	Interoperability between phenotype and anatomy ontologies. Bioinform. Robert Hoehndorf, Anika Oellrich, Dietrich Rebholz-Schuhmann
2010	C	`conf`	Realism for scientific ontologies. FOIS Michel Dumontier, Robert Hoehndorf
2010	—	`conf`	Relational Patterns in OWL and Their Application to OBO. OWLED Robert Hoehndorf, Anika Oellrich, Michel Dumontier, Heinrich Herre, Dietrich Rebholz-Schuhmann
2010	J	`jnl`	Relations as patterns: bridging the gap between OBO and OWL. BMC Bioinform. Robert Hoehndorf, Anika Oellrich, Michel Dumontier, Janet Kelso, Dietrich Rebholz-Schuhmann, Heinrich Herre
2009	J	`jnl`	BOWiki: an ontology-based wiki for annotation of data and integration of knowledge in biology. BMC Bioinform. Robert Hoehndorf, Joshua Bacher, Michael Backhaus, Sergio E. Gregorio Jr., Frank Loebe, Kay Prüfer, Alexandr Uciteli, Johann Visagie, Heinrich Herre, Janet Kelso
2009	—	`—`	Basic considerations for improving interoperability between ontology based biological information systems. Robert Hoehndorf
2009	C	`conf`	Developing Consistent and Modular Software Models with Ontologies. SoMeT Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Heinrich Herre
2009	J	`jnl`	The ontology of biological sequences. BMC Bioinform. Robert Hoehndorf, Janet Kelso, Heinrich Herre
2008	—	`conf`	BOWiki: Ontology-based Semantic Wiki with ABox Reasoning. SemWiki Joshua Bacher, Robert Hoehndorf, Janet Kelso
2008	J	`jnl`	GFO-Bio: A biological core ontology. Appl. Ontology Robert Hoehndorf, Frank Loebe, Roberto Poli, Heinrich Herre, Janet Kelso
2007	—	`conf`	BOWiki - a Collaborative Annotation and Ontology Curation Framework. CKC Michael Backhaus, Janet Kelso, Joshua Bacher, Heinrich Herre, Robert Hoehndorf, Frank Loebe, Johann Visagie
2007	J	`jnl`	Representing default knowledge in biomedical ontologies: application to the integration of anatomy and phenotype ontologies. BMC Bioinform. Robert Hoehndorf, Frank Loebe, Janet Kelso, Heinrich Herre
2006	—	`conf`	A Proposal for a Gene Functions Wiki. OTM Workshops (1) Robert Hoehndorf, Kay Prüfer, Michael Backhaus, Heinrich Herre, Janet Kelso, Frank Loebe, Johann Visagie
2006	—	`conf`	A top-level ontology of functions and its application in the Open Biomedical Ontologies. ISMB (Supplement of Bioinformatics) Patryk Burek, Robert Hoehndorf, Frank Loebe, Johann Visagie, Heinrich Herre, Janet Kelso