Curriculum Vitae

Robert Hoehndorf

Department of Genetics
University of Cambridge
Downing Street
Cambridge CB2 3EH, UK
leechuck@leechuck.de

Date of birth: 30/05/1980
Place of birth: Leipzig, Germany

Education

• 30/06/2010-present: Postdoctoral researcher with the Department of Genetics at the University of Cambridge.
• 01/12/2009-31/05/2010: Postdoctoral researcher with the Text Mining Group at the European Bioinformatics Institute
• 25/06/2009-30/09/2009: Postdoctoral researcher at Research Group "Ontologies in Medicine", University of Leipzig and Max Planck Institute for Evolutionary Anthropology.
• 01/06/2005-24/06/2009: PhD student Research Group "Ontologies in Medicine", University of Leipzig and Max Planck Institute for Evolutionary Anthropology. Thesis title Basic considerations for improving interoperability between ontology-based biological information systems.
• 27/03/2005: Diplom (Master of Science) in Computer Science from University of Leipzig in Leipzig, Germany; Master thesis titled "Ontology of Situations in the framework of the GOL ontology".

Publications

• Statistical Tests for Associations between Two Directed Acyclic Graphs. Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Michael Dannemann, Janet Kelso. PLoS ONE, 2010.
• Relational patterns in OWL and their application to OBO. Robert Hoehndorf, Anika Oellrich, Michel Dumontier, Janet Kelso, Heinrich Herre, Dietrich Rebholz-Schuhmann. OWL: Experiences and Directions (OWLED), 2010.
• OWLDEF: Integrating OBO and OWL. Robert Hoehndorf, Anika Oellrich, Michel Dumontier, Janet Kelso, Heinrich Herre, Dietrich Rebholz-Schuhmann. Bio-Ontologies, 2010.
• What is an upper level ontology? Robert Hoehndorf. Ontogenesis, 2010. (Blog article)
• Applying the functional abnormality ontology pattern to anatomical functions. Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo and Janet Kelso. Journal of Biomedical Semantics, 2010, 1:4.
• Realism for scientific ontologies. Michel Dumontier and Robert Hoehndorf. In Proceedings of the 6th International Conference on Formal Ontology in Information Systems (FOIS), 2010.
• Ontologies in Biology. Janet Kelso, Robert Hoehndorf and Kay Pruefer. In Theory and Application of Ontologies. Volume II: Computer Applications. Editors: Roberto Poli, Michael Healy and Achilles Kameas. Springer Netherlands, May 2010.
• The ontology of biological sequences. Robert Hoehndorf, Janet Kelso and Heinrich Herre. BMC Bioinformatics, 2009, 10:377.
• The application of an ontology design pattern for functional abnormalities to phenotype ontologies and the extraction of an ontology of anatomical functions. Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo and Janet Kelso. Proceedings of the The 3rd International Symposium on Languages in Biology and Medicine, 2009.
• Developing Consistent and Modular Software Models with Ontologies. Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo and Heinrich Herre. SOMET, 2009.
• Contributions to the formal ontology of functions and dispositions: an application of non-monotonic reasoning. Robert Hoehndorf, Janet Kelso and Heinrich Herre. Bio-Ontology Meeting, 2009.
• A formal ontology of sequences. Robert Hoehndorf, Janet Kelso and Heinrich Herre. First International Conference of Biomedical Ontologies, 2009.
• BOWiki: an ontology-based wiki for annotation of data and integration of knowledge in biology. Robert Hoehndorf, Joshua Bacher, Michael Backhaus, Sergio E. Gregorio, Frank Loebe, Kay Pruefer, Alexandr Uciteli, Heinrich Herre, Janet Kelso. BMC Bioinformatics, 2009, 10(Suppl. 5):S5.
• Towards Ontological Interpretations for Improved Text Mining. Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo and Michael Dannemann. Proceedings of 3rd International Symposium on Semantic Mining in Biomedicine, 2008.
• From Terms to Categories: Testing the Significance of Co-occurrences between Ontological Categories. Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Michael Dannemann and Janet Kelso. Proceedings of 3rd International Symposium on Semantic Mining in Biomedicine, 2008.
• BOWiki: An ontology-based wiki for annotation of data and integration of knowledge in biology. Robert Hoehndorf, Joshua Bacher, Michael Backhaus, Sergio E. Gregorio, Jr., Frank Loebe, Kay Prufer, Alexandr Uciteli, Johann Visagie, Heinrich Herre and Janet Kelso. The 11th Annual Bio-Ontologies Meeting, 2008.
• GFO-Bio: A biological core ontology. Robert Hoehndorf, Frank Loebe, Roberto Poli, Heinrich Herre, Janet Kelso. Applied Ontology, 2008.
• Representing default knowledge in biomedical ontologies: Application to the integration of Anatomy and Phenotype Ontologies. Robert Hoehndorf, Frank Loebe, Janet Kelso, Heinrich Herre. BMC Bioinformatics, 2007.
• BOWiki: A collaborative annotation and ontology curation framework. Michael Backhaus, Janet Kelso, Heinrich Herre, Robert Hoehndorf, Frank Loebe, Kay Pruefer, Johann Visagie. Proceedings of Workshop on Social and Collaborative Construction of Structured Knowledge, 2007.
• A proposal for a gene function wiki. Robert Hoehndorf, Kay Pruefer, Michael Backhaus, Heinrich Herre, Janet Kelso, Frank Loebe, Johann Visagie. OTM Workshop Proceedings, 2006.
• A top-level ontology of functions and its application in the Open Biomedical Ontologies. Patryk Burek, Robert Hoehndorf, Frank Loebe, Johann Visagie, Janet Kelso, Heinrich Herre. Bioinformatics, 2006.
• The design of a wiki-based curation system for the Ontology of Functions. Robert Hoehndorf, Kay Pruefer, Michael Backhaus, Johann Visagie, Janet Kelso. Proceedings of the Joint BioLINK and 9th Bio-Ontologies Meeting, 2006.
• General Formal Ontology (GFO): A Foundational Ontology Integrating Objects and Processes. Part I: Basic Principles (Version 1.0).Heinrich Herre, Barbara Heller, Patryk Burek, Robert Hoehndorf, Frank Loebe and Hannes Michalek. Onto-Med Report Nr. 8. Research Group Ontologies in Medicine (Onto-Med), University of Leipzig, 2006.

Scientific Activities

Professional memberships

• International Association for Ontology and its Applications
• Association for Computing Machinery
• Nicolai Hartmann Society

Review activity

• PC-Member of ESWC 2010
• Reviewer for EMBC09.
• PC-Member of ISMB/ECCB 2007.
• PC-Member of ISMB 2008 and ISMB 2010.
• Reviewer for MIE 2008 and MIE 2009.
• Reviewer for Bioinformatics, Journal of Biomedical Informatics, PLoS ONE and others.

Additional Work Experience

• 1998-2000: IT-Netservice GmbH, Part-time programmer
• 2001-2004: Teaching assistant, University of Leipzig; C and Java programming courses
• March 2003-June 2003: Systems analyst, National Planning Commission of Namibia