| 2012 | AMIA | Active Learning-Based Corpus Annotation - The PathoJen Experience. | Udo Hahn, Elena Beisswanger, Ekaterina Buyko, Erik Faessler |
| 2012 | LREC | Iterative Refinement and Quality Checking of Annotation Guidelines - How to Deal Effectively with Semantically Sloppy Named Entity Types, such as Pathological Phenomena. | Udo Hahn, Elena Beisswanger, Ekaterina Buyko, Erik Faessler, Jenny Traumller, Susann Schrder, Kerstin Hornbostel |
| 2012 | PSB | The Extraction of Pharmacogenetic and Pharmacogenomic Relations - A Case Study Using PharmGKB. | Ekaterina Buyko, Elena Beisswanger, Udo Hahn |
| 2010 | LREC | The GeneReg Corpus for Gene Expression Regulation Events - An Overview of the Corpus and its In-Domain and Out-of-Domain Interoperability. | Ekaterina Buyko, Elena Beisswanger, Udo Hahn |
| 2010 | LREC | The CALBC Silver Standard Corpus for Biomedical Named Entities - A Study in Harmonizing the Contributions from Four Independent Named Entity Taggers. | Dietrich Rebholz-Schuhmann, Antonio Jos Jimeno-Yepes, Erik M. van Mulligen, Ning Kang, Jan A. Kors, David Milward, Peter T. Corbett, Ekaterina Buyko, Katrin Tomanek, Elena Beisswanger, Udo Hahn |
| 2008 | ACL | Building a BioWordNet Using WordNet Data Structures and WordNet's Software Infrastructure-A Failure Story. | Michael Poprat, Elena Beisswanger, Udo Hahn |
| 2008 | LREC | Semantic Annotations for Biology: a Corpus Development Initiative at the Jena University Language & Information Engineering (JULIE) Lab. | Udo Hahn, Elena Beisswanger, Ekaterina Buyko, Michael Poprat, Katrin Tomanek, Joachim Wermter |
| 2007 | AMIA | An Ontology for Major Histocompatibility Complex (MHC) Alleles and Molecules. | Elena Beisswanger, David S. DeLuca, Rainer Blasczyk, Udo Hahn |
| 2006 | AMIA | Towards an Upper-Level Ontology for Molecular Biology. | Stefan Schulz, Elena Beisswanger, Joachim Wermter, Udo Hahn |
| 2006 | FOIS | From GENIA to BIOTOP - Towards a Top-Level Ontology for Biology. | Stefan Schulz, Elena Beisswanger, Udo Hahn, Joachim Wermter, Anand Kumar, Holger Stenzhorn |