Robert Hoehndorf

Summary

Affiliation: University of Cambridge
Country: UK

Publications

  1. pmc Interoperability between biomedical ontologies through relation expansion, upper-level ontologies and automatic reasoning
    Robert Hoehndorf
    Department of Genetics, University of Cambridge, Cambridge, United Kingdom
    PLoS ONE 6:e22006. 2011
  2. pmc Towards improving phenotype representation in OWL
    Frank Loebe
    Department of Computer Science, University of Leipzig, 04103 Leipzig, Germany
    J Biomed Semantics 3:S5. 2012
  3. pmc Systematic analysis of experimental phenotype data reveals gene functions
    Robert Hoehndorf
    Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
    PLoS ONE 8:e60847. 2013
  4. pmc Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics
    Robert Hoehndorf
    Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
    Bioinformatics 28:2169-75. 2012
  5. pmc Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology
    Robert Hoehndorf
    Department of Genetics, University of Cambridge, Downing Street, Cambridge, Cambridge CB2 3EH, UK
    Bioinformatics 28:1783-9. 2012
  6. pmc Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL
    Simon Jupp
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK
    J Biomed Semantics 3:S3. 2012
  7. pmc OBML - Ontologies in Biomedicine and Life Sciences
    Heinrich Herre
    Institute for Medical Informatics, Statistics and Epidemiology IMISE, University of Leipzig, Haertelstrasse 16 18, 04107 Leipzig, Germany
    J Biomed Semantics 2:I1. 2011
  8. pmc Relations as patterns: bridging the gap between OBO and OWL
    Robert Hoehndorf
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    BMC Bioinformatics 11:441. 2010
  9. pmc Ontology design patterns to disambiguate relations between genes and gene products in GENIA
    Robert Hoehndorf
    European Bioinformatics Institute, Hinxton, Cambridge, UK
    J Biomed Semantics 2:S1. 2011
  10. pmc Interoperability between phenotype and anatomy ontologies
    Robert Hoehndorf
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Bioinformatics 26:3112-8. 2010

Collaborators

Detail Information

Publications27

  1. pmc Interoperability between biomedical ontologies through relation expansion, upper-level ontologies and automatic reasoning
    Robert Hoehndorf
    Department of Genetics, University of Cambridge, Cambridge, United Kingdom
    PLoS ONE 6:e22006. 2011
    ..Our results and analysis software are available at http://bioonto.de/pmwiki.php/Main/ReasonableOntologies...
  2. pmc Towards improving phenotype representation in OWL
    Frank Loebe
    Department of Computer Science, University of Leipzig, 04103 Leipzig, Germany
    J Biomed Semantics 3:S5. 2012
    ..EQ-based definitions have been developed for many phenotype ontologies, including the Human and Mammalian Phenotype ontologies...
  3. pmc Systematic analysis of experimental phenotype data reveals gene functions
    Robert Hoehndorf
    Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
    PLoS ONE 8:e60847. 2013
    ....
  4. pmc Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics
    Robert Hoehndorf
    Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
    Bioinformatics 28:2169-75. 2012
    ..This information is currently distributed over several pharmacogenomics databases. An integrated analysis of the information in these databases can reveal disease pathways and facilitate novel biomedical analyses...
  5. pmc Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology
    Robert Hoehndorf
    Department of Genetics, University of Cambridge, Downing Street, Cambridge, Cambridge CB2 3EH, UK
    Bioinformatics 28:1783-9. 2012
    ..Applying ontologies to unify phenotype descriptions in the domain of physiology has been a particular challenge due to the high complexity of the underlying domain...
  6. pmc Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL
    Simon Jupp
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK
    J Biomed Semantics 3:S3. 2012
    ..In addition, the semantics of these ontology's representations should be able to, through automated reasoning, afford richer query opportunities of the gene product annotations than is currently possible...
  7. pmc OBML - Ontologies in Biomedicine and Life Sciences
    Heinrich Herre
    Institute for Medical Informatics, Statistics and Epidemiology IMISE, University of Leipzig, Haertelstrasse 16 18, 04107 Leipzig, Germany
    J Biomed Semantics 2:I1. 2011
    ..The next event emphasizes the special topic of the ontology of phenotypes, in Berlin, Germany on October 6-7, 2011...
  8. pmc Relations as patterns: bridging the gap between OBO and OWL
    Robert Hoehndorf
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    BMC Bioinformatics 11:441. 2010
    ..Since the Web Ontology Language (OWL) is an expressive language with a formal semantics, it is suitable to de ne the meaning of relations accurately...
  9. pmc Ontology design patterns to disambiguate relations between genes and gene products in GENIA
    Robert Hoehndorf
    European Bioinformatics Institute, Hinxton, Cambridge, UK
    J Biomed Semantics 2:S1. 2011
    ..Consistent semantic annotations facilitate the automatic discovery of new information through deductive inferences...
  10. pmc Interoperability between phenotype and anatomy ontologies
    Robert Hoehndorf
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Bioinformatics 26:3112-8. 2010
    ..Therefore, valuable resources for the analysis of phenotype studies remain unconnected and inaccessible to automated analysis and reasoning...
  11. pmc A common layer of interoperability for biomedical ontologies based on OWL EL
    Robert Hoehndorf
    Department of Genetics, University of Cambridge, Cambridge, UK
    Bioinformatics 27:1001-8. 2011
    ..We propose the use of less expressive subsets of ontology representation languages to enable efficient reasoning and achieve the goal of genuine interoperability between ontologies...
  12. pmc PhenomeNET: a whole-phenome approach to disease gene discovery
    Robert Hoehndorf
    Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
    Nucleic Acids Res 39:e119. 2011
    ..Our method implements a whole-phenome approach toward disease gene discovery and can be applied to prioritize genes for rare and orphan diseases for which the molecular basis is unknown...
  13. pmc Integrating systems biology models and biomedical ontologies
    Robert Hoehndorf
    Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
    BMC Syst Biol 5:124. 2011
    ..Biomedical ontologies were developed to facilitate such an integration of data and are often used to annotate biosimulation models in systems biology...
  14. pmc Mouse model phenotypes provide information about human drug targets
    Robert Hoehndorf
    Department of Computer Science, University of Aberystwyth, Old College, King Street, Aberystwyth SY23 2AX, Department of Biology, Institute of Biochemistry and School of Computer Science, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada and Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
    Bioinformatics 30:719-25. 2014
    ..One set of resources that has been relatively neglected for drug repurposing is animal model phenotype...
  15. doi request reprint Text-mining solutions for biomedical research: enabling integrative biology
    Dietrich Rebholz-Schuhmann
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nat Rev Genet 13:829-39. 2012
    ..Here we explore the latest advancements in automated literature analysis and its contribution to innovative research approaches...
  16. doi request reprint An infrastructure for ontology-based information systems in biomedicine: RICORDO case study
    Sarala M Wimalaratne
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
    Bioinformatics 28:448-50. 2012
    ..The infrastructure is being prototyped and developed and evaluated by the RICORDO project in support of the knowledge management of biomedical resources, including physiology and pharmacology models and associated clinical data...
  17. pmc New approaches to the representation and analysis of phenotype knowledge in human diseases and their animal models
    Paul N Schofield
    University of Cambridge, Department of Genetics, UK
    Brief Funct Genomics 10:258-65. 2011
    ..In particular, we discuss how the use of ontologies and automated reasoning can significantly contribute to the analysis of phenotypes and demonstrate their potential for enabling translational research...
  18. doi request reprint The neurobehavior ontology: an ontology for annotation and integration of behavior and behavioral phenotypes
    Georgios V Gkoutos
    Department of Genetics, University of Cambridge, Cambridge, UK
    Int Rev Neurobiol 103:69-87. 2012
    ..The neurobehavior ontology facilitates the systematic representation of behavior and behavioral phenotypes, thereby improving the unification and integration behavioral data in neuroscience research...
  19. pmc Computational tools for comparative phenomics: the role and promise of ontologies
    Georgios V Gkoutos
    Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
    Mamm Genome 23:669-79. 2012
    ....
  20. pmc Improving disease gene prioritization by comparing the semantic similarity of phenotypes in mice with those of human diseases
    Anika Oellrich
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
    PLoS ONE 7:e38937. 2012
    ..google.com/p/phenomeblast/wiki/CAMP. Furthermore, our method has been integrated in PhenomeNET and the results can be explored using the PhenomeBrowser at http://phenomebrowser.net...
  21. pmc Quantitative comparison of mapping methods between Human and Mammalian Phenotype Ontology
    Anika Oellrich
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
    J Biomed Semantics 3:S1. 2012
    ..Our results suggest that combining both approaches will yield a better mappings in terms of completeness, specificity and application purposes...
  22. pmc Mouse genetic and phenotypic resources for human genetics
    Paul N Schofield
    Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
    Hum Mutat 33:826-36. 2012
    ....
  23. doi request reprint PIDO: the primary immunodeficiency disease ontology
    Nico Adams
    Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
    Bioinformatics 27:3193-9. 2011
    ..The development of an ontology of PIDs is therefore a central step toward developing informatics tools, which can support the clinician in the diagnosis and treatment of these diseases...
  24. pmc Evaluation and cross-comparison of lexical entities of biological interest (LexEBI)
    Dietrich Rebholz-Schuhmann
    Department of Computational Linguistics, University of Zurich, Zurich, Switzerland European Molecular Biology Laboratory, European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    PLoS ONE 8:e75185. 2013
    ..This goal does not only require that we are aware of all existing terms, but would also profit from knowing all their senses and their semantic interpretation (ambiguities, nestedness)...
  25. pmc The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions
    Bernard de Bono
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
    BMC Res Notes 4:313. 2011
    ..abstract:..
  26. pmc Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes
    Georgios V Gkoutos
    Department of Genetics, University of Cambridge, Downing Street, Cambridge, Cambridge CB2 3EH, UK
    J Biomed Semantics 3:S6. 2012
    ..Furthermore, we utilize our definitions and the yeast phenotype annotations to suggest novel functional annotations of gene products in yeast...