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2020 – today
- 2024
[j80]Lars Vogt
, Tobias Kuhn, Robert Hoehndorf:
Semantic units: organizing knowledge graphs into semantically meaningful units of representation. J. Biomed. Semant. 15(1): 7 (2024)- [j79]Lars Vogt, Tobias Kuhn, Robert Hoehndorf:
Correction to: Semantic units: organizing knowledge graphs into semantically meaningful units of representation. J. Biomed. Semant. 15(1): 10 (2024) - [j78]Maxat Kulmanov, Francisco J. Guzmán-Vega, Paula Duek Roggli, Lydie Lane, Stefan T. Arold, Robert Hoehndorf:
Protein function prediction as approximate semantic entailment. Nat. Mac. Intell. 6(2): 220-228 (2024) - [c41]Yasir Ghunaim, Robert Hoehndorf:
Large-Scale Knowledge Integration for Enhanced Molecular Property Prediction. NeSy (2) 2024: 89-97 - [c40]Olga Mashkova, Fernando Zhapa-Camacho, Robert Hoehndorf:
Enhancing Geometric Ontology Embeddings for Eℒ++ with Negative Sampling and Deductive Closure Filtering. NeSy (1) 2024: 331-354 - [c39]Fernando Zhapa-Camacho, Robert Hoehndorf:
Lattice-Preserving ALC Ontology Embeddings. NeSy (1) 2024: 355-369 - [i23]Olga Mashkova, Fernando Zhapa-Camacho, Robert Hoehndorf:
Enhancing Geometric Ontology Embeddings for ℰℒ++ with Negative Sampling and Deductive Closure Filtering. CoRR abs/2405.04868 (2024) - [i22]Jiaoyan Chen, Olga Mashkova, Fernando Zhapa-Camacho, Robert Hoehndorf, Yuan He, Ian Horrocks:
Ontology Embedding: A Survey of Methods, Applications and Resources. CoRR abs/2406.10964 (2024) - [i21]Mahdi Buali, Robert Hoehndorf:
Towards Automated Functional Equation Proving: A Benchmark Dataset and A Domain-Specific In-Context Agent. CoRR abs/2407.14521 (2024) - [i20]Yasir Ghunaim, Robert Hoehndorf:
Large-Scale Knowledge Integration for Enhanced Molecular Property Prediction. CoRR abs/2410.11914 (2024) - 2023
- [j77]Fernando Zhapa-Camacho, Maxat Kulmanov, Robert Hoehndorf:
mOWL: Python library for machine learning with biomedical ontologies. Bioinform. 39(1) (2023) - [j76]Sarah M. Alghamdi, Robert Hoehndorf:
Improving the classification of cardinality phenotypes using collections. J. Biomed. Semant. 14(1): 9 (2023) - [j75]Senay Kafkas, Marwa Abdelhakim, Mahmut Uludag, Azza Althagafi, Malak Alghamdi, Robert Hoehndorf:
Starvar: symptom-based tool for automatic ranking of variants using evidence from literature and genomes. BMC Bioinform. 24(1): 294 (2023) - [j74]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:
Klarigi: Characteristic explanations for semantic biomedical data. Comput. Biol. Medicine 153: 106425 (2023) - [c38]Sumyyah Toonsi, Senay Kafkas, Robert Hoehndorf:
Exploring the Use of Ontology Components for Distantly-Supervised Disease and Phenotype Named Entity Recognition. ICBO 2023: 13-24 - [c37]Fernando Zhapa-Camacho, Robert Hoehndorf:
From Axioms over Graphs to Vectors, and Back Again: Evaluating the Properties of Graph-based Ontology Embeddings. NeSy 2023: 85-102 - [c36]Zhenwei Tang, Shichao Pei, Xi Peng, Fuzhen Zhuang, Xiangliang Zhang, Robert Hoehndorf:
Neural Multi-hop Logical Query Answering with Concept-Level Answers. ISWC 2023: 522-540 - [c35]Fernando Zhapa-Camacho, Robert Hoehndorf:
Evaluating Different Methods for Semantic Reasoning Over Ontologies. QALD/SemREC@ISWC 2023 - [c34]Núria Queralt-Rosinach, Paul N. Schofield, Marco Roos, Robert Hoehndorf:
Updating the CEMO ontology for future epidemiological challenges. SWAT4HCLS 2023: 151-152 - [i19]Lars Vogt, Tobias Kuhn, Robert Hoehndorf:
Semantic Units: Organizing knowledge graphs into semantically meaningful units of representation. CoRR abs/2301.01227 (2023) - [i18]Fernando Zhapa-Camacho, Robert Hoehndorf:
From axioms over graphs to vectors, and back again: evaluating the properties of graph-based ontology embeddings. CoRR abs/2303.16519 (2023) - [i17]Fernando Zhapa-Camacho, Robert Hoehndorf:
CatE: Embedding ALC ontologies using category-theoretical semantics. CoRR abs/2305.07163 (2023) - [i16]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:
An Open-Source Knowledge Graph Ecosystem for the Life Sciences. CoRR abs/2307.05727 (2023) - [i15]Md Nurul Muttakin, Malik Shahid Sultan, Robert Hoehndorf, Hernando Ombao:
Stylized Projected GAN: A Novel Architecture for Fast and Realistic Image Generation. CoRR abs/2307.16275 (2023) - 2022
- [j73]Azza Althagafi, Lamia Alsubaie, Nagarajan Kathiresan, Katsuhiko Mineta, Taghrid Aloraini, Fuad Al Mutairi, Majid Alfadhel, Takashi Gojobori, Ahmad Alfares, Robert Hoehndorf:
DeepSVP: integration of genotype and phenotype for structural variant prioritization using deep learning. Bioinform. 38(6): 1677-1684 (2022) - [j72]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:
A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology. J. Biomed. Semant. 13(1): 25 (2022) - [j71]Luke T. Slater, Sophie Russell, Silver Makepeace, Alexander Carberry, Andreas Karwath, John A. Williams, Hilary Fanning, Simon Ball, Robert Hoehndorf, Georgios V. Gkoutos:
Evaluating semantic similarity methods for comparison of text-derived phenotype profiles. BMC Medical Informatics Decis. Mak. 22(1): 33 (2022) - [c33]Sarah M. Alghamdi, Robert Hoehndorf:
Ontological Analysis of Collection Improves Classification of Cardinality Phenotypes. ICBO 2022: 1-2 - [c32]Robert Hoehndorf:
The Coevolution of Ontologies and Knowledge-based Analytics in Bioinformatics. ICBO 2022: 1-4 - [c31]Zhenwei Tang, Shichao Pei, Zhao Zhang, Yongchun Zhu, Fuzhen Zhuang, Robert Hoehndorf, Xiangliang Zhang:
Positive-Unlabeled Learning with Adversarial Data Augmentation for Knowledge Graph Completion. IJCAI 2022: 2248-2254 - [c30]Sarah M. Alghamdi, Fernando Zhapa-Camacho, Robert Hoehndorf:
A-LIOn - alignment learning through inconsistency negatives of the aligned ontologies. OM@ISWC 2022: 137-144 - [c29]Ali Syed, Senay Kafkas, Maxat Kulmanov, Robert Hoehndorf:
Using SPARQL to Unify Queries over Data, Ontologies, and Machine Learning Models in the PhenomeBrowser Knowledgebase. SWAT4HCLS 2022: 97-102 - [i14]Xi Peng, Zhenwei Tang, Maxat Kulmanov, Kexin Niu, Robert Hoehndorf:
Description Logic EL++ Embeddings with Intersectional Closure. CoRR abs/2202.14018 (2022) - [i13]Zhenwei Tang, Shichao Pei, Zhao Zhang, Yongchun Zhu, Fuzhen Zhuang, Robert Hoehndorf, Xiangliang Zhang:
Positive-Unlabeled Learning with Adversarial Data Augmentation for Knowledge Graph Completion. CoRR abs/2205.00904 (2022) - [i12]Zhenwei Tang, Shichao Pei, Xi Peng, Fuzhen Zhuang, Xiangliang Zhang, Robert Hoehndorf:
Joint Abductive and Inductive Neural Logical Reasoning. CoRR abs/2205.14591 (2022) - [i11]Zhenwei Tang, Tilman Hinnerichs, Xi Peng, Xiangliang Zhang, Robert Hoehndorf:
FALCON: Sound and Complete Neural Semantic Entailment over ALC Ontologies. CoRR abs/2208.07628 (2022) - 2021
- [j70]Maxat Kulmanov, Fatima Zohra Smaili, Xin Gao, Robert Hoehndorf:
Semantic similarity and machine learning with ontologies. Briefings Bioinform. 22(4) (2021) - [j69]Jun Chen, Azza Althagafi, Robert Hoehndorf:
Predicting candidate genes from phenotypes, functions and anatomical site of expression. Bioinform. 37(6): 853-860 (2021) - [j68]Maxat Kulmanov, Robert Hoehndorf:
DeepGOPlus: improved protein function prediction from sequence. Bioinform. 37(8): 1187 (2021) - [j67]Wang Liu-Wei, Senay Kafkas, Jun Chen, Nicholas J. Dimonaco, Jesper Tegnér, Robert Hoehndorf:
DeepViral: prediction of novel virus-host interactions from protein sequences and infectious disease phenotypes. Bioinform. 37(17): 2722-2729 (2021) - [j66]Tilman Hinnerichs, Robert Hoehndorf:
DTI-Voodoo: machine learning over interaction networks and ontology-based background knowledge predicts drug-target interactions. Bioinform. 37(24): 4835-4843 (2021) - [j65]Luke T. Slater, William Bradlow, Simon Ball, Robert Hoehndorf, Georgios V. Gkoutos:
Improved characterisation of clinical text through ontology-based vocabulary expansion. J. Biomed. Semant. 12(1): 7 (2021) - [j64]Senay Kafkas, Sara Althubaiti, Georgios V. Gkoutos, Robert Hoehndorf, Paul N. Schofield:
Linking common human diseases to their phenotypes; development of a resource for human phenomics. J. Biomed. Semant. 12(1): 17 (2021) - [j63]Luke T. Slater, William Bradlow, Dino FA. Motti, Robert Hoehndorf, Simon Ball, Georgios V. Gkoutos:
A fast, accurate, and generalisable heuristic-based negation detection algorithm for clinical text. Comput. Biol. Medicine 130: 104216 (2021) - [j62]Luke T. Slater, Andreas Karwath, John A. Williams, Sophie Russell, Silver Makepeace, Alexander Carberry, Robert Hoehndorf, Georgios V. Gkoutos:
Towards similarity-based differential diagnostics for common diseases. Comput. Biol. Medicine 133: 104360 (2021) - [j61]Luke T. Slater, John A. Williams, Andreas Karwath, Hilary Fanning, Simon Ball, Paul N. Schofield, Robert Hoehndorf, Georgios V. Gkoutos:
Multi-faceted semantic clustering with text-derived phenotypes. Comput. Biol. Medicine 138: 104904 (2021) - [j60]Luke T. Slater, Andreas Karwath, Robert Hoehndorf, Georgios V. Gkoutos:
Effects of Negation and Uncertainty Stratification on Text-Derived Patient Profile Similarity. Frontiers Digit. Health 3: 781227 (2021) - [j59]Maxat Kulmanov, Fernando Zhapa-Camacho, Robert Hoehndorf:
DeepGOWeb: fast and accurate protein function prediction on the (Semantic) Web. Nucleic Acids Res. 49(Webserver-Issue): 140-146 (2021) - [e4]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:
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. CEUR Workshop Proceedings 2969, CEUR-WS.org 2021 [contents] - 2020
- [j58]Maxat Kulmanov, Robert Hoehndorf:
DeepGOPlus: improved protein function prediction from sequence. Bioinform. 36(2): 422-429 (2020) - [j57]Fatima Zohra Smaili, Xin Gao, Robert Hoehndorf:
Formal axioms in biomedical ontologies improve analysis and interpretation of associated data. Bioinform. 36(7): 2229-2236 (2020) - [j56]Sara Althubaiti, Senay Kafkas, Marwa Abdelhakim, Robert Hoehndorf:
Combining lexical and context features for automatic ontology extension. J. Biomed. Semant. 11(1): 1 (2020) - [j55]Luke T. Slater, Georgios V. Gkoutos, Robert Hoehndorf:
Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies. BMC Medical Informatics Decis. Mak. 20-S(10): 311 (2020) - [j54]Maxat Kulmanov, Robert Hoehndorf:
DeepPheno: Predicting single gene loss-of-function phenotypes using an ontology-aware hierarchical classifier. PLoS Comput. Biol. 16(11) (2020) - [e3]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:
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. CEUR Workshop Proceedings 2708, CEUR-WS.org 2020 [contents] - [i10]Jun Chen, Robert Hoehndorf, Mohamed Elhoseiny, Xiangliang Zhang:
Efficient long-distance relation extraction with DG-SpanBERT. CoRR abs/2004.03636 (2020) - [i9]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:
BioHackathon 2015: Semantics of data for life sciences and reproducible research. F1000Research 9: 136 (2020)
2010 – 2019
- 2019
- [j53]Senay Kafkas, Robert Hoehndorf:
Ontology based text mining of gene-phenotype associations: application to candidate gene prediction. Database J. Biol. Databases Curation 2019: baz019 (2019) - [j52]Fatima Zohra Smaili, Xin Gao, Robert Hoehndorf:
OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction. Bioinform. 35(12): 2133-2140 (2019) - [j51]Senay Kafkas, Robert Hoehndorf:
Ontology based mining of pathogen-disease associations from literature. J. Biomed. Semant. 10(1): 15:1-15:5 (2019) - [j50]Imane Boudellioua, Maxat Kulmanov, Paul N. Schofield, Georgios V. Gkoutos, Robert Hoehndorf:
DeepPVP: phenotype-based prioritization of causative variants using deep learning. BMC Bioinform. 20(1): 65 (2019) - [c28]Maxat Kulmanov, Wang Liu-Wei, Yuan Yan, Robert Hoehndorf:
EL Embeddings: Geometric Construction of Models for the Description Logic EL++. IJCAI 2019: 6103-6109 - [c27]Shichao Pei, Lu Yu, Robert Hoehndorf, Xiangliang Zhang:
Semi-Supervised Entity Alignment via Knowledge Graph Embedding with Awareness of Degree Difference. WWW 2019: 3130-3136 - [i8]Maxat Kulmanov, Wang Liu-Wei, Yuan Yan, Robert Hoehndorf:
EL Embeddings: Geometric construction of models for the Description Logic EL ++. CoRR abs/1902.10499 (2019) - [i7]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:
BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services. F1000Research 8: 1677 (2019) - 2018
- [j49]Ron Henkel, Robert Hoehndorf, Tim Kacprowski, Christian Knüpfer, Wolfram Liebermeister, Dagmar Waltemath:
Notions of similarity for systems biology models. Briefings Bioinform. 19(1): 77-88 (2018) - [j48]Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf:
The anatomy of phenotype ontologies: principles, properties and applications. Briefings Bioinform. 19(5): 1008-1021 (2018) - [j47]Maxat Kulmanov, Mohammad Asif Khan, Robert Hoehndorf:
DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier. Bioinform. 34(4): 660-668 (2018) - [j46]Fatima Zohra Smaili, Xin Gao, Robert Hoehndorf:
Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations. Bioinform. 34(13): i52-i60 (2018) - [j45]Maxat Kulmanov, Paul N. Schofield, Georgios V. Gkoutos, Robert Hoehndorf:
Ontology-based validation and identification of regulatory phenotypes. Bioinform. 34(17): i857-i865 (2018) - [j44]Mona Alshahrani, Robert Hoehndorf:
Semantic Disease Gene Embeddings (SmuDGE): phenotype-based disease gene prioritization without phenotypes. Bioinform. 34(17): i901-i907 (2018) - [j43]Miguel Ángel Rodríguez-García, Robert Hoehndorf:
Inferring ontology graph structures using OWL reasoning. BMC Bioinform. 19(1): 7:1-7:9 (2018) - [c26]Maxat Kulmanov, Senay Kafkas, Andreas Karwath, Alexander Malic, Georgios V. Gkoutos, Michel Dumontier, Robert Hoehndorf:
Vec2SPARQL: integrating SPARQL queries and knowledge graph embeddings. SWAT4LS 2018 - [p1]Robert Hoehndorf, Claus Weiland, Marco Schmidt, Quentin Groom, George Gosline, Stefan Dressler, Thomas Hamann:
The Flora Phenotype Ontology (FLOPO) and the FLOPO Knowledgebase. Application of Semantic Technology in Biodiversity Science 2018: 107-119 - [i6]Fatima Zohra Smaili, Xin Gao, Robert Hoehndorf:
Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations. CoRR abs/1802.00864 (2018) - [i5]Fatima Zohra Smaili, Xin Gao, Robert Hoehndorf:
OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction. CoRR abs/1804.10922 (2018) - 2017
- [j42]Ron Henkel, Robert Hoehndorf, Tim Kacprowski, Christian Knüpfer, Wolfram Liebermeister, Dagmar Waltemath:
Notions of similarity for systems biology models. Briefings Bioinform. 18(5): 902 (2017) - [j41]Mona Alshahrani, Mohammad Asif Khan, Omar Maddouri, Akira R. Kinjo, Núria Queralt-Rosinach, Robert Hoehndorf:
Neuro-symbolic representation learning on biological knowledge graphs. Bioinform. 33(17): 2723-2730 (2017) - [j40]Maxat Kulmanov, Robert Hoehndorf:
Evaluating the effect of annotation size on measures of semantic similarity. J. Biomed. Semant. 8(1): 7:1-7:10 (2017) - [j39]Miguel Ángel Rodríguez-García, Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf:
Integrating phenotype ontologies with PhenomeNET. J. Biomed. Semant. 8(1): 58:1-58:11 (2017) - [j38]Senay Kafkas, Sirarat Sarntivijai, Robert Hoehndorf:
Usage of cell nomenclature in biomedical literature. BMC Bioinform. 18(S-17): 17-24 (2017) - [j37]Robert Hoehndorf, Núria Queralt-Rosinach:
Data Science and symbolic AI: Synergies, challenges and opportunities. Data Sci. 1(1-2): 27-38 (2017) - [j36]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:
Semantic prioritization of novel causative genomic variants. PLoS Comput. Biol. 13(4) (2017) - [i4]Maxat Kulmanov, Mohammad Asif Khan, Robert Hoehndorf:
DeepGO: Predicting protein functions from sequence and interactions using a deep ontology-aware classifier. CoRR abs/1705.05919 (2017) - 2016
- [j35]Hannah M. Fisher, Robert Hoehndorf, Bruno S. Bazelato, Soheil S. Dadras, Lloyd E. King, Georgios V. Gkoutos, John P. Sundberg, Paul N. Schofield:
DermO; an ontology for the description of dermatologic disease. J. Biomed. Semant. 7: 38 (2016) - [j34]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:
FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation. J. Biomed. Semant. 7: 39 (2016) - [j33]Luke T. Slater, Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf:
Using AberOWL for fast and scalable reasoning over BioPortal ontologies. J. Biomed. Semant. 7: 49 (2016) - [j32]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:
The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants. J. Biomed. Semant. 7: 65:1-65:11 (2016) - [j31]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:
DESM: portal for microbial knowledge exploration systems. Nucleic Acids Res. 44(Database-Issue): 624-633 (2016) - [c25]Robert Hoehndorf, Liam Mencel, Georgios V. Gkoutos, Paul N. Schofield:
Large-Scale Reasoning over Functions in Biomedical Ontologies. FOIS 2016: 299-312 - [c24]Mona Alshahrani, Hussein Almashouq, Robert Hoehndorf:
SPARQL2OWL: Towards Bridging the Semantic Gap Between RDF and OWL. ICBO/BioCreative 2016 - [c23]Emma J. Griffiths, Damion M. Dooley, Pier Luigi Buttigieg, Robert Hoehndorf, Fiona S. L. Brinkman, William W. L. Hsiao:
FoodON: A Global Farm-to-Fork Food Ontology. ICBO/BioCreative 2016 - [c22]Miguel Ángel Rodríguez-García, Luke T. Slater, Imane Boudellioua, Paul N. Schofield, Georgios V. Gkoutos, Robert Hoehndorf:
Updates to the AberOWL Ontology Repository. ICBO/BioCreative 2016 - [c21]Luke T. 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). ICBO/BioCreative 2016 - [c20]Miguel Ángel Rodríguez-García, Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf:
Integrating phenotype ontologies with PhenomeNET. OM@ISWC 2016: 201-209 - [c19]Claus Weiland, Robert Hoehndorf, George Gosline, Quentin Groom, Thomas Hamann, Marco Schmidt:
FLOPO - An Ontology for the Integration of Trait Data from Digitized Floras and Plant Image Collections. SWAT4LS 2016 - [e2]Pankaj Jaiswal, Robert Hoehndorf, Cecilia N. Arighi, Austin Meier:
Proceedings of the Joint International Conference on Biological Ontology and BioCreative, Corvallis, Oregon, United States, August 1-4, 2016. CEUR Workshop Proceedings 1747, CEUR-WS.org 2016 [contents] - [i3]Mona Alshahrani, Mohammad Asif Khan, Omar Maddouri, Akira R. Kinjo, Núria Queralt-Rosinach, Robert Hoehndorf:
Neuro-symbolic representation learning on biological knowledge graphs. CoRR abs/1612.04256 (2016) - 2015
- [j30]Robert Hoehndorf, Paul N. Schofield, Georgios V. Gkoutos:
The role of ontologies in biological and biomedical research: a functional perspective. Briefings Bioinform. 16(6): 1069-1080 (2015) - [j29]Robert Hoehndorf, Michael Gruenberger, Georgios V. Gkoutos, Paul N. Schofield:
Similarity-based search of model organism, disease and drug effect phenotypes. J. Biomed. Semant. 6: 6 (2015) - [j28]Robert Hoehndorf, Luke T. Slater, Paul N. Schofield, Georgios V. Gkoutos:
Aber-OWL: a framework for ontology-based data access in biology. BMC Bioinform. 16: 26:1-26:9 (2015) - [c18]Luke T. Slater, Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf:
Using Aber-OWL for fast and scalable reasoning over BioPortal ontologies. ICBO 2015 - [c17]Luke T. Slater, Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf:
AberOWL: an ontology portal with OWL EL reasoning. ICBO 2015 - [c16]Luke T. Slater, Miguel Ángel Rodríguez-García, Keiron O'Shea, Paul N. Schofield, Georgios V. Gkoutos, Robert Hoehndorf:
Experiences with Aber-OWL, an Ontology Repository with OWL EL Reasoning. OWLED 2015: 81-86 - [c15]Miguel Ángel Rodríguez-García, Luke T. Slater, Keiron O'Shea, Paul N. Schofield, Georgios V. Gkoutos, Robert Hoehndorf:
Visualising Ontologies with AberOWL. SWAT4LS 2015: 183-192 - 2014
- [j27]Robert Hoehndorf, Tanya Hiebert, Nigel W. Hardy, Paul N. Schofield, Georgios V. Gkoutos, Michel Dumontier:
Mouse model phenotypes provide information about human drug targets. Bioinform. 30(5): 719-725 (2014) - [j26]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:
The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery. J. Biomed. Semant. 5: 14 (2014) - [j25]Robert Hoehndorf, Dietrich Rebholz-Schuhmann, Melissa A. Haendel, Robert Stevens:
Thematic series on biomedical ontologies in JBMS: challenges and new directions. J. Biomed. Semant. 5: 15 (2014) - [c14]Robert Hoehndorf, Luke T. Slater, Paul N. Schofield, Georgios V. Gkoutos:
Aber-OWL: A Framework for Ontology-based Data Access in Biology. SWAT4LS 2014 - [i2]Robert Hoehndorf, Luke T. Slater, Paul N. Schofield, Georgios V. Gkoutos:
Aber-OWL: a framework for ontology-based data access in biology. CoRR abs/1407.6812 (2014) - 2013
- [j24]Robert Hoehndorf, Michel Dumontier, Georgios V. Gkoutos:
Evaluation of research in biomedical ontologies. Briefings Bioinform. 14(6): 696-712 (2013) - [j23]Dietrich Rebholz-Schuhmann, Senay Kafkas, Jee-Hyub Kim, Chen Li, Antonio Jimeno-Yepes, Robert Hoehndorf, Rolf Backofen, Ian Lewin:
Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources. J. Biomed. Semant. 4: 28 (2013) - [j22]Daniel L. Cook, Maxwell Lewis Neal, Robert Hoehndorf, Georgios V. Gkoutos, John H. Gennari:
Representing physiological processes and their participants with PhysioMaps. J. Biomed. Semant. 4(S-1): S2 (2013) - [e1]Michel Dumontier, Robert Hoehndorf, Christopher J. O. Baker:
Proceedings of the 4th International Conference on Biomedical Ontology, ICBO 2013, Montreal, Canada, July 7-12, 2013. CEUR Workshop Proceedings 1060, CEUR-WS.org 2013 [contents] - 2012
- [j21]Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf:
The Units Ontology: a tool for integrating units of measurement in science. Database J. Biol. Databases Curation 2012 (2012) - [j20]Sarala M. Wimalaratne, Pierre Grenon, Robert Hoehndorf, Georgios V. Gkoutos, Bernard de Bono:
An infrastructure for ontology-based information systems in biomedicine: RICORDO case study. Bioinform. 28(3): 448-450 (2012) - [j19]Robert Hoehndorf, Midori A. Harris, Heinrich Herre, Gabriella Rustici, Georgios V. Gkoutos:
Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology. Bioinform. 28(13): 1783-1789 (2012) - [j18]Robert Hoehndorf, Michel Dumontier, Georgios V. Gkoutos:
Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics. Bioinform. 28(16): 2169-2175 (2012) - [j17]Simon Jupp, Robert Stevens, Robert Hoehndorf:
Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL. J. Biomed. Semant. 3(S-1): S3 (2012) - [j16]Anika Oellrich, Georgios V. Gkoutos, Robert Hoehndorf, Dietrich Rebholz-Schuhmann:
Quantitative comparison of mapping methods between Human and Mammalian Phenotype Ontology. J. Biomed. Semant. 3(S-2): S1 (2012) - [j15]Frank Loebe, Frank Stumpf, Robert Hoehndorf, Heinrich Herre:
Towards improving phenotype representation in OWL. J. Biomed. Semant. 3(S-2): S5 (2012) - [j14]Georgios V. Gkoutos, Robert Hoehndorf:
Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes. J. Biomed. Semant. 3(S-2): S6 (2012) - [c13]Adam Z. Wyner, Luke Riley, Robert Hoehndorf, Samuel Croset:
Argumentation to Represent and Reason over Biological Systems. ITBAM 2012: 124-138 - [c12]Robert Hoehndorf, Anika Oellrich, Dietrich Rebholz-Schuhmann, Paul N. Schofield, Georgios V. Gkoutos:
Linking PharmGKB to Phenotype Studies and Animal Models of Disease for Drug Repurposing. Pacific Symposium on Biocomputing 2012: 388-399 - [c11]Jens Hollunder, Vladimir Mironov, Erick Antezana, Robert Hoehndorf, Martin Kuiper:
Profiling of Semantically Annotated Proteins. SWAT4LS 2012 - [i1]Robert Hoehndorf, Michel Dumontier, Georgios V. Gkoutos:
Towards quantitative measures in applied ontology. CoRR abs/1202.3602 (2012) - 2011
- [j13]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:
The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data. Appl. Ontology 6(1): 53-89 (2011) - [j12]Robert Hoehndorf, Michel Dumontier, Anika Oellrich, Sarala M. Wimalaratne, Dietrich Rebholz-Schuhmann, Paul N. Schofield, Georgios V. Gkoutos:
A common layer of interoperability for biomedical ontologies based on OWL EL. Bioinform. 27(7): 1001-1008 (2011) - [j11]Nico Adams, Robert Hoehndorf, Georgios V. Gkoutos, Gesine Hansen, Christian Hennig:
PIDO: the primary immunodeficiency disease ontology. Bioinform. 27(22): 3193-3199 (2011) - [j10]Heinrich Herre, Robert Hoehndorf, Janet Kelso, Frank Loebe, Stefan Schulz:
OBML - Ontologies in Biomedicine and Life Sciences. J. Biomed. Semant. 2(S-4): I1 (2011) - [j9]Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Sampo Pyysalo, Tomoko Ohta, Anika Oellrich, Dietrich Rebholz-Schuhmann:
Ontology design patterns to disambiguate relations between genes and gene products in GENIA. J. Biomed. Semant. 2(S-5): S1 (2011) - [j8]Robert Hoehndorf, Michel Dumontier, John H. Gennari, Sarala M. Wimalaratne, Bernard de Bono, Daniel L. Cook, Georgios V. Gkoutos:
Integrating systems biology models and biomedical ontologies. BMC Syst. Biol. 5: 124 (2011) - [c10]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:
An Advanced Strategy for Integration of Biological Measurement Data. ICBO 2011 - [c9]Stefan Schulz, Mathias Brochhausen, Robert Hoehndorf:
Higgs Bosons, Mars Missions, and Unicorn Delusions: How to Deal with Terms of Dubious Reference in Scientific Ontologies. ICBO 2011 - 2010
- [j7]Robert Hoehndorf, Anika Oellrich, Dietrich Rebholz-Schuhmann:
Interoperability between phenotype and anatomy ontologies. Bioinform. 26(24): 3112-3118 (2010) - [j6]Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Janet Kelso:
Applying the functional abnormality ontology pattern to anatomical functions. J. Biomed. Semant. 1: 4 (2010) - [j5]Robert Hoehndorf, Anika Oellrich, Michel Dumontier, Janet Kelso, Dietrich Rebholz-Schuhmann, Heinrich Herre:
Relations as patterns: bridging the gap between OBO and OWL. BMC Bioinform. 11: 441 (2010) - [c8]Michel Dumontier, Robert Hoehndorf:
Realism for scientific ontologies. FOIS 2010: 387-399 - [c7]Robert Hoehndorf, Anika Oellrich, Michel Dumontier, Heinrich Herre, Dietrich Rebholz-Schuhmann:
Relational Patterns in OWL and Their Application to OBO. OWLED 2010 - [c6]Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Sampo Pyysalo, Tomoko Ohta, Anika Oellrich, Dietrich Rebholz-Schuhmann:
Applying ontology design patterns to the implementation of relations in GENIA. Semantic Mining in Biomedicine 2010
2000 – 2009
- 2009
- [b1]Robert Hoehndorf:
Basic considerations for improving interoperability between ontology based biological information systems. University of Leipzig, 2009, pp. 1-242 - [j4]Robert Hoehndorf, Joshua Bacher, Michael Backhaus, Sergio E. Gregorio Jr., Frank Loebe, Kay Prüfer, Alexandr Uciteli, Johann Visagie, Heinrich Herre, Janet Kelso:
BOWiki: an ontology-based wiki for annotation of data and integration of knowledge in biology. BMC Bioinform. 10(S-5) (2009) - [j3]Robert Hoehndorf, Janet Kelso, Heinrich Herre:
The ontology of biological sequences. BMC Bioinform. 10: 377 (2009) - [c5]Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Heinrich Herre:
Developing Consistent and Modular Software Models with Ontologies. SoMeT 2009: 399-412 - 2008
- [j2]Robert Hoehndorf, Frank Loebe, Roberto Poli, Heinrich Herre, Janet Kelso:
GFO-Bio: A biological core ontology. Appl. Ontology 3(4): 219-227 (2008) - [c4]Joshua Bacher, Robert Hoehndorf, Janet Kelso:
BOWiki: Ontology-based Semantic Wiki with ABox Reasoning. SemWiki 2008 - 2007
- [j1]Robert Hoehndorf, Frank Loebe, Janet Kelso, Heinrich Herre:
Representing default knowledge in biomedical ontologies: application to the integration of anatomy and phenotype ontologies. BMC Bioinform. 8 (2007) - [c3]Michael Backhaus, Janet Kelso, Joshua Bacher, Heinrich Herre, Robert Hoehndorf, Frank Loebe, Johann Visagie:
BOWiki - a Collaborative Annotation and Ontology Curation Framework. CKC 2007 - 2006
- [c2]Patryk Burek, Robert Hoehndorf, Frank Loebe, Johann Visagie, Heinrich Herre, Janet Kelso:
A top-level ontology of functions and its application in the Open Biomedical Ontologies. ISMB (Supplement of Bioinformatics) 2006: 66-73 - [c1]Robert Hoehndorf, Kay Prüfer, Michael Backhaus, Heinrich Herre, Janet Kelso, Frank Loebe, Johann Visagie:
A Proposal for a Gene Functions Wiki. OTM Workshops (1) 2006: 669-678
Coauthor Index
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