Robert Hoehndorf

According to our database1, Robert Hoehndorf authored at least 107 papers between 2006 and 2023.

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Bibliography

2023
Semantic Units: Organizing knowledge graphs into semantically meaningful units of representation.
CoRR, 2023

2022
Evaluating semantic similarity methods for comparison of text-derived phenotype profiles.
BMC Medical Informatics Decis. Mak., 2022

FALCON: Sound and Complete Neural Semantic Entailment over ALC Ontologies.
CoRR, 2022

Joint Abductive and Inductive Neural Logical Reasoning.
CoRR, 2022

Description Logic EL++ Embeddings with Intersectional Closure.
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

2021
DeepGOWeb: fast and accurate protein function prediction on the (Semantic) Web.
Nucleic Acids Res., 2021

Effects of Negation and Uncertainty Stratification on Text-Derived Patient Profile Similarity.
Frontiers Digit. Health, 2021

Multi-faceted semantic clustering with text-derived phenotypes.
Comput. Biol. Medicine, 2021

Towards similarity-based differential diagnostics for common diseases.
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

DeepGOPlus: improved protein function prediction from sequence.
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

Semantic similarity and machine learning with ontologies.
Briefings 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

Efficient long-distance relation extraction with DG-SpanBERT.
CoRR, 2020

Combining lexical and context features for automatic ontology extension.
J. Biomed. Semant., 2020

Formal axioms in biomedical ontologies improve analysis and interpretation of associated data.
Bioinform., 2020

2019
Ontology based mining of pathogen-disease associations from literature.
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

EL Embeddings: Geometric Construction of Models for the Description Logic EL++.
Proceedings of the Twenty-Eighth International Joint Conference on Artificial Intelligence, 2019

2018
The Flora Phenotype Ontology (FLOPO) and the FLOPO Knowledgebase.
Proceedings of the Application of Semantic Technology in Biodiversity Science, 2018

Inferring ontology graph structures using OWL reasoning.
BMC Bioinform., 2018

Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations.
Bioinform., 2018

Ontology-based validation and identification of regulatory phenotypes.
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

Notions of similarity for systems biology models.
Briefings Bioinform., 2018

The anatomy of phenotype ontologies: principles, properties and applications.
Briefings Bioinform., 2018

Vec2SPARQL: integrating SPARQL queries and knowledge graph embeddings.
Proceedings of the 11th International Conference Semantic Web Applications and Tools for Life Sciences, 2018

2017
Semantic prioritization of novel causative genomic variants.
PLoS Comput. Biol., 2017

Data Science and symbolic AI: Synergies, challenges and opportunities.
Data Sci., 2017

Usage of cell nomenclature in biomedical literature.
BMC Bioinform., 2017

Integrating phenotype ontologies with PhenomeNET.
J. Biomed. Semant., 2017

Evaluating the effect of annotation size on measures of semantic similarity.
J. Biomed. Semant., 2017

Neuro-symbolic representation learning on biological knowledge graphs.
Bioinform., 2017

2016
DESM: portal for microbial knowledge exploration systems.
Nucleic Acids Res., 2016

Using AberOWL for fast and scalable reasoning over BioPortal ontologies.
J. Biomed. Semant., 2016

The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants.
J. Biomed. Semant., 2016

DermO; an ontology for the description of dermatologic disease.
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

Updates to the AberOWL Ontology Repository.
Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016

FoodON: A Global Farm-to-Fork Food Ontology.
Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016

SPARQL2OWL: Towards Bridging the Semantic Gap Between RDF and OWL.
Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016

Large-Scale Reasoning over Functions in Biomedical Ontologies.
Proceedings of the Formal Ontology in Information Systems, 2016

2015
Aber-OWL: a framework for ontology-based data access in biology.
BMC Bioinform., 2015

Similarity-based search of model organism, disease and drug effect phenotypes.
J. Biomed. Semant., 2015

The role of ontologies in biological and biomedical research: a functional perspective.
Briefings Bioinform., 2015

Visualising Ontologies with AberOWL.
Proceedings of the 8th Semantic Web Applications and Tools for Life Sciences International Conference, 2015

Experiences with Aber-OWL, an Ontology Repository with OWL EL Reasoning.
Proceedings of the Ontology Engineering, 2015

AberOWL: an ontology portal with OWL EL reasoning.
Proceedings of the International Conference on Biomedical Ontology, 2015

Using Aber-OWL for fast and scalable reasoning over BioPortal ontologies.
Proceedings of the International Conference on Biomedical Ontology, 2015

2014
Thematic series on biomedical ontologies in JBMS: challenges and new directions.
J. Biomed. Semant., 2014

The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery.
J. Biomed. Semant., 2014

Mouse model phenotypes provide information about human drug targets.
Bioinform., 2014

2013
Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources.
J. Biomed. Semant., 2013

Representing physiological processes and their participants with PhysioMaps.
J. Biomed. Semant., 2013

Evaluation of research in biomedical ontologies.
Briefings Bioinform., 2013

2012
Towards quantitative measures in applied ontology
CoRR, 2012

Quantitative comparison of mapping methods between Human and Mammalian Phenotype Ontology.
J. Biomed. Semant., 2012

Towards improving phenotype representation in OWL.
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

The Units Ontology: a tool for integrating units of measurement in science.
Database J. Biol. Databases Curation, 2012

Profiling of Semantically Annotated Proteins.
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

Argumentation to Represent and Reason over Biological Systems.
Proceedings of the Information Technology in Bio- and Medical Informatics, 2012

2011
Integrating systems biology models and biomedical ontologies.
BMC Syst. Biol., 2011

Ontology design patterns to disambiguate relations between genes and gene products in GENIA.
J. Biomed. Semant., 2011

OBML - Ontologies in Biomedicine and Life Sciences.
J. Biomed. Semant., 2011

A common layer of interoperability for biomedical ontologies based on OWL EL.
Bioinform., 2011

PIDO: the primary immunodeficiency disease ontology.
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

An Advanced Strategy for Integration of Biological Measurement Data.
Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

2010
Relations as patterns: bridging the gap between OBO and OWL.
BMC Bioinform., 2010

Applying the functional abnormality ontology pattern to anatomical functions.
J. Biomed. Semant., 2010

Interoperability between phenotype and anatomy ontologies.
Bioinform., 2010

Applying ontology design patterns to the implementation of relations in GENIA.
Proceedings of the Fourth International Symposium for Semantic Mining in Biomedicine, 2010

Relational Patterns in OWL and Their Application to OBO.
Proceedings of the 7th International Workshop on OWL: Experiences and Directions (OWLED 2010), 2010

Realism for scientific ontologies.
Proceedings of the Formal Ontology in Information Systems, 2010

2009
Basic considerations for improving interoperability between ontology based biological information systems.
PhD thesis, 2009

The ontology of biological sequences.
BMC Bioinform., 2009

BOWiki: an ontology-based wiki for annotation of data and integration of knowledge in biology.
BMC Bioinform., 2009

Developing Consistent and Modular Software Models with Ontologies.
Proceedings of the New Trends in Software Methodologies, Tools and Techniques, 2009

2008
GFO-Bio: A biological core ontology.
Appl. Ontology, 2008

BOWiki: Ontology-based Semantic Wiki with ABox Reasoning.
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

BOWiki - a Collaborative Annotation and Ontology Curation Framework.
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
A Proposal for a Gene Functions Wiki.
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


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