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Robert Hoehndorf
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DeepGO: Predicting protein functions from sequence and interactions using a deep ontology-aware classifier
M Kulmanov, MA Khan, R Hoehndorf
Bioinformatics 34 (4), 660-668, 2017
4282017
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
N Zhou, Y Jiang, TR Bergquist, AJ Lee, BZ Kacsoh, AW Crocker, ...
Genome biology 20, 1-23, 2019
3582019
DeepGOPlus: Improved protein function prediction from sequence
M Kulmanov, R Hoehndorf
Bioinformatics 36 (2), 422–429, 2020
3552020
The role of ontologies in biological and biomedical research: a functional perspective
R Hoehndorf, PN Schofield, GV Gkoutos
Briefings in bioinformatics 16 (6), 1069-1080, 2015
3222015
Text-mining solutions for biomedical research: enabling integrative biology
D Rebholz-Schuhmann, A Oellrich, R Hoehndorf
Nature Reviews Genetics 13 (12), 829-839, 2012
2752012
FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration
DM Dooley, EJ Griffiths, GS Gosal, PL Buttigieg, R Hoehndorf, MC Lange, ...
npj Science of Food 2 (1), 23, 2018
2602018
The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery
M Dumontier, CJO Baker, J Baran, A Callahan, L Chepelev, ...
Journal of biomedical semantics 5, 1-11, 2014
2522014
PhenomeNET: a whole-phenome approach to disease gene discovery
R Hoehndorf, PN Schofield, GV Gkoutos
Nucleic acids research 39 (18), e119-e119, 2011
2432011
Semantic similarity and machine learning with ontologies.
M Kulmanov, FZ Smaili, X Gao, R Hoehndorf
Briefings in Bioinformatics, 2020
180*2020
Neuro-symbolic representation learning on biological knowledge graphs
M Alshahrani, MA Khan, O Maddouri, AR Kinjo, N Queralt-Rosinach, ...
Bioinformatics 33 (17), 2723-2730, 2017
1682017
Opa2vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction
FZ Smaili, X Gao, R Hoehndorf
Bioinformatics 35 (12), 2133-2140, 2018
1532018
Semi-supervised entity alignment via knowledge graph embedding with awareness of degree difference
S Pei, L Yu, R Hoehndorf, X Zhang
The world wide web conference, 3130-3136, 2019
1452019
Analysis of mammalian gene function through broad-based phenotypic screens across a consortium of mouse clinics
M Hrabě de Angelis, G Nicholson, M Selloum, JK White, H Morgan, ...
Nature genetics 47 (9), 969-978, 2015
1452015
General Formal Ontology (GFO): A foundational ontology integrating objects and processes
H Herre, B Heller, P Burek, R Hoehndorf, F Loebe, H Michalek
Onto-Med Report 8, 53, 2006
1302006
Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations
FZ Smaili, X Gao, R Hoehndorf
Bioinformatics 34 (13), i52–i60, 2018
1292018
The Units Ontology: a tool for integrating units of measurement in science
GV Gkoutos, PN Schofield, R Hoehndorf
Database 2012, bas033, 2012
1252012
Analysis of the human diseasome using phenotype similarity between common, genetic and infectious diseases
R Hoehndorf, PN Schofield, GV Gkoutos
Scientific reports 5 (1), 1-14, 2015
1132015
Evaluation of research in biomedical ontologies
R Hoehndorf, M Dumontier, GV Gkoutos
Briefings in bioinformatics 14 (6), 696-712, 2013
1132013
Aber-OWL: a framework for ontology-based data access in biology
R Hoehndorf, L Slater, PN Schofield, GV Gkoutos
BMC bioinformatics 16, 1-9, 2015
1102015
EL Embeddings: Geometric construction of models for the Description Logic EL++
M Kulmanov, W Liu-Wei, Y Yan, R Hoehndorf
Proceedings of the Twenty-Eighth International Joint Conference on …, 2019
1092019
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