Robert Hoehndorf
Orcid: 0000-0001-8149-5890
According to our database1,
Robert Hoehndorf
authored at least 132 papers
between 2006 and 2024.
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Bibliography
2024
Correction to: Semantic units: organizing knowledge graphs into semantically meaningful units of representation.
J. Biomed. Semant., December, 2024
Semantic units: organizing knowledge graphs into semantically meaningful units of representation.
J. Biomed. Semant., December, 2024
Nat. Mac. Intell., 2024
Towards Automated Functional Equation Proving: A Benchmark Dataset and A Domain-Specific In-Context Agent.
CoRR, 2024
Enhancing Geometric Ontology Embeddings for ℰℒ<sup>++</sup> with Negative Sampling and Deductive Closure Filtering.
CoRR, 2024
Proceedings of the Neural-Symbolic Learning and Reasoning - 18th International Conference, 2024
Enhancing Geometric Ontology Embeddings for <i>E</i>ℒ<sup>++</sup> with Negative Sampling and Deductive Closure Filtering.
Proceedings of the Neural-Symbolic Learning and Reasoning - 18th International Conference, 2024
Proceedings of the Neural-Symbolic Learning and Reasoning - 18th International Conference, 2024
2023
Starvar: symptom-based tool for automatic ranking of variants using evidence from literature and genomes.
BMC Bioinform., December, 2023
J. Biomed. Semant., December, 2023
Comput. Biol. Medicine, February, 2023
Bioinform., January, 2023
Stylized Projected GAN: A Novel Architecture for Fast and Realistic Image Generation.
CoRR, 2023
Proceedings of the 14th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4HCLS 2023), 2023
Proceedings of the Joint Proceedings of Scholarly QALD 2023 and SemREC 2023 co-located with 22nd International Semantic Web Conference ISWC 2023, 2023
Proceedings of the Semantic Web - ISWC 2023, 2023
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, 2023
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), Brasília, Brazil, August 28, 2023
2022
Evaluating semantic similarity methods for comparison of text-derived phenotype profiles.
BMC Medical Informatics Decis. Mak., 2022
CoRR, 2022
A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology.
J. Biomed. Semant., 2022
DeepSVP: integration of genotype and phenotype for structural variant prioritization using deep learning.
Bioinform., 2022
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, 2022
A-LIOn - alignment learning through inconsistency negatives of the aligned ontologies.
Proceedings of the 17th International Workshop on Ontology Matching (OM 2022) co-located with the 21th International Semantic Web Conference (ISWC 2022), 2022
Positive-Unlabeled Learning with Adversarial Data Augmentation for Knowledge Graph Completion.
Proceedings of the Thirty-First International Joint Conference on Artificial Intelligence, 2022
Proceedings of the International Conference on Biomedical Ontology 2022 (ICBO), Ann Arbor, Michigan, USA, September 25, 2022
Ontological Analysis of Collection Improves Classification of Cardinality Phenotypes.
Proceedings of the International Conference on Biomedical Ontology 2022 (ICBO), Ann Arbor, Michigan, USA, September 25, 2022
2021
Nucleic Acids Res., 2021
Effects of Negation and Uncertainty Stratification on Text-Derived Patient Profile Similarity.
Frontiers Digit. Health, 2021
Comput. Biol. Medicine, 2021
Comput. Biol. Medicine, 2021
A fast, accurate, and generalisable heuristic-based negation detection algorithm for clinical text.
Comput. Biol. Medicine, 2021
Improved characterisation of clinical text through ontology-based vocabulary expansion.
J. Biomed. Semant., 2021
Linking common human diseases to their phenotypes; development of a resource for human phenomics.
J. Biomed. Semant., 2021
DeepViral: prediction of novel virus-host interactions from protein sequences and infectious disease phenotypes.
Bioinform., 2021
DTI-Voodoo: machine learning over interaction networks and ontology-based background knowledge predicts drug-target interactions.
Bioinform., 2021
Predicting candidate genes from phenotypes, functions and anatomical site of expression.
Bioinform., 2021
2020
DeepPheno: Predicting single gene loss-of-function phenotypes using an ontology-aware hierarchical classifier.
PLoS Comput. Biol., 2020
Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies.
BMC Medical Informatics Decis. Mak., 2020
F1000Research, 2020
J. Biomed. Semant., 2020
Formal axioms in biomedical ontologies improve analysis and interpretation of associated data.
Bioinform., 2020
2019
BMC Bioinform., December, 2019
BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services.
F1000Research, 2019
J. Biomed. Semant., 2019
OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction.
Bioinform., 2019
Ontology based text mining of gene-phenotype associations: application to candidate gene prediction.
Database J. Biol. Databases Curation, 2019
Semi-Supervised Entity Alignment via Knowledge Graph Embedding with Awareness of Degree Difference.
Proceedings of the World Wide Web Conference, 2019
Proceedings of the Twenty-Eighth International Joint Conference on Artificial Intelligence, 2019
2018
Proceedings of the Application of Semantic Technology in Biodiversity Science, 2018
Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations.
Bioinform., 2018
Bioinform., 2018
DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier.
Bioinform., 2018
Semantic Disease Gene Embeddings (SmuDGE): phenotype-based disease gene prioritization without phenotypes.
Bioinform., 2018
Briefings Bioinform., 2018
Proceedings of the 11th International Conference Semantic Web Applications and Tools for Life Sciences, 2018
2017
PLoS Comput. Biol., 2017
Data Sci., 2017
J. Biomed. Semant., 2017
Bioinform., 2017
2016
J. Biomed. Semant., 2016
The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants.
J. Biomed. Semant., 2016
J. Biomed. Semant., 2016
FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation.
J. Biomed. Semant., 2016
FLOPO - An Ontology for the Integration of Trait Data from Digitized Floras and Plant Image Collections.
Proceedings of the 9th International Conference Semantic Web Applications and Tools for Life Sciences, 2016
To MIREOT or not to MIREOT? A Case Study of the Impact of Using MIREOT in the Experimental Factor Ontology (EFO).
Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016
Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016
Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016
Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016
Proceedings of the Formal Ontology in Information Systems, 2016
2015
BMC Bioinform., 2015
J. Biomed. Semant., 2015
The role of ontologies in biological and biomedical research: a functional perspective.
Briefings Bioinform., 2015
Proceedings of the 8th Semantic Web Applications and Tools for Life Sciences International Conference, 2015
Proceedings of the Ontology Engineering, 2015
Proceedings of the International Conference on Biomedical Ontology, 2015
Proceedings of the International Conference on Biomedical Ontology, 2015
2014
J. Biomed. Semant., 2014
The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery.
J. Biomed. Semant., 2014
Bioinform., 2014
2013
Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources.
J. Biomed. Semant., 2013
J. Biomed. Semant., 2013
2012
Quantitative comparison of mapping methods between Human and Mammalian Phenotype Ontology.
J. Biomed. Semant., 2012
Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL.
J. Biomed. Semant., 2012
Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes.
J. Biomed. Semant., 2012
An infrastructure for ontology-based information systems in biomedicine: RICORDO case study.
Bioinform., 2012
Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology.
Bioinform., 2012
Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics.
Bioinform., 2012
Database J. Biol. Databases Curation, 2012
Proceedings of the 5th International Workshop on Semantic Web Applications and Tools for Life Sciences, 2012
Linking PharmGKB to Phenotype Studies and Animal Models of Disease for Drug Repurposing.
Proceedings of the Biocomputing 2012: Proceedings of the Pacific Symposium, 2012
Proceedings of the Information Technology in Bio- and Medical Informatics, 2012
2011
Ontology design patterns to disambiguate relations between genes and gene products in GENIA.
J. Biomed. Semant., 2011
Bioinform., 2011
The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data.
Appl. Ontology, 2011
Higgs Bosons, Mars Missions, and Unicorn Delusions: How to Deal with Terms of Dubious Reference in Scientific Ontologies.
Proceedings of the 2nd International Conference on Biomedical Ontology, 2011
Proceedings of the 2nd International Conference on Biomedical Ontology, 2011
2010
J. Biomed. Semant., 2010
Proceedings of the Fourth International Symposium for Semantic Mining in Biomedicine, 2010
Proceedings of the 7th International Workshop on OWL: Experiences and Directions (OWLED 2010), 2010
Proceedings of the Formal Ontology in Information Systems, 2010
2009
Basic considerations for improving interoperability between ontology based biological information systems.
PhD thesis, 2009
BOWiki: an ontology-based wiki for annotation of data and integration of knowledge in biology.
BMC Bioinform., 2009
Proceedings of the New Trends in Software Methodologies, Tools and Techniques, 2009
2008
Proceedings of the 3rd Semantic Wiki Workshop (SemWiki 2008) at the 5th European Semantic Web Conference (ESWC 2008), 2008
2007
Representing default knowledge in biomedical ontologies: application to the integration of anatomy and phenotype ontologies.
BMC Bioinform., 2007
Proceedings of the Workshop on Social and Collaborative Construction of Structured Knowledge (CKC 2007) at the 16th International World Wide Web Conference (WWW2007) Banff, 2007
2006
Proceedings of the On the Move to Meaningful Internet Systems 2006: OTM 2006 Workshops, 2006
A top-level ontology of functions and its application in the Open Biomedical Ontologies.
Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006