Beisswanger, Elena and Hahn, Udo. "Towards valid and reusable reference alignments - Ten basic quality checks for ontology alignments and their application to three different reference data sets", in: Journal of Biomedical Semantics (accepted)
Buyko, Ekaterina, Beisswanger, Elena and Hahn, Udo. Extraction of Pharmacogenetic and Pharmacogenomic Relations - A Case Study Using PharmGKB, in: Proceedings of the Pacific Symposium on Biocomputing (PSB) 2012.
2011
Beisswanger, Elena and Hahn, Udo. "Of Mice and Men" Revisited - Basic Quality Checks for Reference Alignments Applied to the Human-Mouse Anatomy Alignment, in: Proceedings of the 11th Bio-Ontologies Special Interest Group Meeting at ISMB 2011, 2011.
Rebholz-Schuhmann, D, Yepes, AJ, Li, C, Kafkas, S, Lewin, I, Kang, N, Corbett, P, Milward, D, Buyko, E, Beisswanger, E, Hornbostel, K, Kouznetsov, A, Witte, R, Laurila, JB, Baker, CJ, Kuo, CJ, Clematide, S, Rinaldi, F, Farkas, R, Móra, G, Hara, K, Furlong, LI, Rautschka, M, Neves, ML, Pascual-Montano, A, Wei, Q, Collier, N, Chowdhury, MF, Lavelli, A, Berlanga, R, Morante, R, Van Asch, V, Daelemans, W, Marina, JL, van Mulligen, E, Kors, J, Hahn, U. Assessment of NER solutions against the first and second CALBC Silver Standard Corpus, in: Journal of Biomedical Semantics, Vol. 2, Suppl 5, S11, 2011.
2010
Beisswanger, Elena, Exploiting Relation Extraction for Ontology Alignment, in: Proceedings of the 9th International Semantic Web Conference (ISWC 2010) Doctoral Consortium, Lecture Notes in Computer Science (LNCS), 6414, Springer, 2010.
Beisswanger, Elena, Wermter, Joachim and Hahn, Udo,Linking UniProt and MeSH: A Case Study on Human Protein Terms, in: Proceedings of the 13th International Congress on Medical Informatics (MedInfo 2010), 2010.
Hahn, Udo, Tomanek, Katrin, Beisswanger, Elena and Faessler, Erik, A Proposal for a Configurable Silver Standard, in: Proceedings of the Fourth Linguistic Annotation Workshop (LAW 2010) at ACL 2010, pages 235-242, 2010.
Beisswanger, Elena and Hahn, Udo, JULIE Lab's UIMA Collection Reader for WIKIPEDIA, in: Proceedings of the LREC 2010 Workshop on New Challenges for NLP Frameworks, pages 15--19, 2010.
Buyko, Ekaterina, Beisswanger,Elena and Hahn, Udo, The GeneReg Corpus for Gene Expression Regulation Events - An Overview of the Corpus and its In-Domain and Out-of-Domain Interoperability, in: Proceedings of the 7th International Conference on Language Resources and Evaluation (LREC 2010), 2010.
Rebholz-Schuhmann, Dietrich, Jimeno-Yepes, Antonio José, van Mulligen, Erik M., Kang, Ning, Kors, Jan, Milward, David, Corbett, Peter, Buyko, Ekaterina, Tomanek, Katrin, Beisswanger, Elena and Hahn, Udo, The CALBC Silver Standard Corpus for Biomedical Named Entities ― A Study in Harmonizing the Contributions from Four Independent Named Entity Taggers, in: Proceedings of the 7th International Conference on Language Resources and Evaluation (LREC 2010), 2010.
Rebholz-Schuhmann, Dietrich, Jimeno-Yepes, Antonio José, van Mulligen, Erik M., Kang, Ning, Kors, Jan, Milward, David, Corbett, Peter, Buyko, Ekaterina, Beisswanger, Elena and Hahn, Udo, The CALBC Silver Standard Corpus - Harmonizing Multiple Semantic Annotations in a Large Biomedical Corpus. Journal of Bioinformatics and Computational Biology, Vol. 8, No. 1, 2010.
2009
Schulz, Stefan, Beisswanger, Elena, van den Hoek, Laszlo, Bodenreider, Olivier and van Mulligen, Erik M., Alignment of the UMLS semantic network with BioTop: methodology and assessment, in: Bioinformatics, volume 25, number 12, pages i69-76, 2009.
DeLuca, David S., Beisswanger, Elena, Wermter, Joachim, Horn, Peter A., Hahn, Udo and Blasczyk, Rainer, MaHCO: An Ontology of the Major Histocompatibility Complex for Immunoinformatic Applications and Text Mining, in: Bioinformatics, ISSN 1460-2059, 2009.
2008
Beisswanger, Elena, Poprat, Michael and Hahn, Udo, Lexical Properties of OBO Ontology Class Names and Synonyms , in: Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), pages 13-20, 2008.
Buyko, Ekaterina, Beisswanger, Elena and Hahn, Udo, Testing Different ACE-Style Feature Sets for the Extraction of Gene Regulation Relations from MEDLINE Abstracts , in: Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), pages 21-28, 2008.
Poprat, Michael, Beisswanger, Elena and Hahn, Udo, Building a BioWordNet Using WordNet Data Structures and WordNet's Software Infrastructure - A Failure Story , in: Proceedings of the ACL 2008 workshop on Software Engineering, Testing, and Quality Assurance for Natural Language Processing, pages 31-39, 2008.
Hahn, Udo, Beisswanger, Elena, Buyko, Ekaterina, Poprat, Michael, Tomanek, Katrin and Wermter, Joachim, Semantic Annotations for Biology -- A Corpus Development Initiative at the Jena University Language & Information Engineering (JULIE) Lab, in: Proceedings of the Sixth International Language Resources and Evaluation Conference(LREC 2008), 2008.
Beisswanger, Elena, Lee, Vivian, Kim, Jung Jae, Rebholz-Schuhmann, Dietrich, Splendiani, Andrea, Dameron, Olivier, Schulz, Stefan and Hahn, Udo, Gene Regulation Ontology (GRO): Design Principles and Use Cases , in: Proceedings of the 21st International Congress of the European Federation for Medical Informatics(MIE 2008), pages 9-14, 2008.
Beisswanger, Elena, Schulz, Stefan, Stenzhorn, Holger and Hahn, Udo, BioTop: An upper domain ontology for the life sciences. A description of its current structure, contents and interfaces to OBO ontologies, in: Applied Ontology, volume 3, number 4, pages 205-212, 2008.
2007
Stenzhorn, Holger, Beisswanger, Elena and Schulz, Stefan, Towards a top-domain ontology for linking biomedical ontologies , in: Proceedings of the 12th Conference on Medical Informatics(MedInfo 2007), pages 1225-1229, IOS Press, 2007.
Beisswanger, Elena, DeLuca, David S., Blasczyk, Rainer and Hahn, Udo, An Ontology for Major Histocompatibility Complex (MHC) Alleles and Molecules , in: Proceedings of the Annual Symposium of the American Medical Informatics Association (AMIA 2007), 2007.
2006
Schulz, Stefan, Beisswanger, Elena, Hahn, Udo, Wermter, Joachim, Kumar, Amand and Stenzhorn, Holger, From Genia to BioTop: towards a top-level ontology for biology , in: Proceedings of the 4th International Conference on Formal Ontology in Information Systems (FOIS 2006), pages 103-114, IOS Press, 2006.
Schulz, Stefan, Beisswanger, Elena, Wermter, Joachim and Hahn, Udo, Towards an Upper-Level Ontology for Molecular Biology , in: Proceedings of the Annual Symposium of the American Medical Informatics Association (AMIA 2006), pages 694-698, 2006.
Redaktion 