Papers

2010

• 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.

2009

• 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.

  2008

• 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.

2007

• 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.

  2006

• 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.

  2005

• Situations in the General Formal Ontology. Robert Hoehndorf. Master's thesis. University of Leipzig, 2005.

Poster, Talks and misc

Theses

• Basic considerations for improving interoperability between ontology-based biological information systems. PhD thesis. University of Leipzig, 2009.
• Situations in the General Formal Ontology - Master's thesis. University of Leipzig, 2005.

Posters

• Relating functions and dispositions using non-monotonic reasoning Presented at ICBO, 2009.
• The Ontology of Functions Presented at the GMDS Jahrestagung 2006, Leipzig, Germany, 2006. Poster.
• GFO-Bio: A biomedical core ontology. Robert Hoehndorf, Janet Kelso, Heinrich Herre. ISCB Student Council, 2006. Poster.

Talks

• A formal ontology of sequences. Presented at ICBO, Buffalo, USA.
• Towards Ontological Interpretations. Presented at Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), Turku, Finland, 2008.
• Representing defaults in biomedical ontologies. Presented at Dagstuhl Seminar on Ontologies and Text Mining for Life Sciences : Current Status and Future Perspectives, Dagstuhl, Germany, 2008.
• Towards interoperability between anatomy and phenotype ontologies. Presented at 3rd ISCB Student Council Symposium (ISMB/ECCB). Austria, 2007.
• Ontology-integration and non-monotonic reasoning. Presented at the Dagstuhl Seminar Towards Interoperability of Biomedical Ontologies, Dagstuhl, Germany, 2008.
• Ontology of Functions. Presented at ISMB 2006.
• Design of a wiki-based curation system for the Ontology of Functions.. Presented at The Joint BioOntology and BioLINK Meeting, 2006.
• Situations in the General Formal Ontology. Presented at the Institute for Informatics, University of Vitoria Espirito Santo, 2006.

Program committee, etc.

• ISMB/ECCB 2007, program committee
• ISMB2008, program committee