Abstract
Within the last years the Web dramatically influenced biomedical research. Although it allows for almost instantaneous access to a huge amount of distributed information the problem how to retrieve useful information still persist. With semantic technologies (especially Topic Maps) the solution becomes tangible. We will discuss in this paper concepts and a technical realization for knowledge representation within the biomedical domain. This includes not only the semantic access of distributed and heterogeneous resources based on state-of-the-art enterprise integration technologies (J2EE, Web Services) but also an approach for Topic Map based views on unstructured information from scientific publications. We will furthermore present the implementation of an information portal based on the seamless semantic integration of ~ 500 genome databases and ~16.000.000 abstracts.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
Jensen, L.J., Saric, J., Bork, P.: Literature mining for the biologist: From information retrieval to biological discovery. Nat. Rev. Genet. 7, 119–129 (2006)
Clegg, A.B., Shepherd, A.J.: Benchmarking natural-language parsers for biological applications using dependency graphs. BMC Bioinformatics 8(24) (2007)
Kogan, Y., Collier, N., Pakhomov, S., Krauthammer, M.: Towards semantic role labeling & IE in the medical literature. In: AMIA Annu. Symp. Proc., pp. 410–414 (2005)
Pruitt, K.D., Tatusova, T., Maglott, D.R.: NCBI Reference Sequence (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res., D501–D504 (2005)
Kanehisa, M., Goto, S., Hattori, M., Aoki-Kinoshita, K.F., Itoh, M., Kawashima, S., Katayama, T., Araki, M., Hirakawa, M.: From genomics to chemical genomics: New developments in KEGG. Nucleic Acids Res., D354–D357 (2006)
McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University (Baltimore, MD) and National Center for Biotechnology Information, National Library of Medicine (Bethesda, MD): Online Mendelian Inheritance in Man, OMIM (TM). Dez (2006), http://www.ncbi.nlm.nih.gov/omim/
Schomburg, I., Chang, A., Ebeling, C., Gremse, M., Heldt, C., Huhn, G., Schomburg, D.: BRENDA, the enzyme database: Updates and major new developments. Nucleic Acids Res., D431–D433 (2004)
Pradhan, S., Ward, W., Hacioglu, K., Martin, J., Jurafsky, D.: Shallow Semantic Parsing using Support Vector Machines. In: Proc. of the Human Language Technology Conference/North American chapter of the Association for Computational Linguistics annual meeting (HLT/NAACL-2004), Boston, MA (2004)
Stein, L.D.: Integrating biological databases. Nat. Rev. Genet. 4, 337–345 (2003)
Cheung, K.H., Yip, K.Y., Smith, A., Deknikker, R., Masiar, A., Gerstein, M.: YeastHub: A semantic web use case for integrating data in the life sciences domain. Bioinformatics 21(suppl 1), 85–96 (2005)
Merali, Z., Giles, J.: Databases in peril. Nature 435, 1010-1011 (2005)
Topicmaps.Org Authoring Group. XTM Specification (2001)
Biezunski, M., Bryan, M., Newcomb, S.R.: ISO/IEC 13250:2000 Topic Maps: Information Technology – Document Description and Markup Languages (2004), http://www.y12.doe.gov/sgml/sc34/document/0129.pdf
MEDLINE® (Medical Literature Analysis and Retrieval System Online): NLM’s premier bibliographic database. U.S. National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2008 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Stümpflen, V., Barnickel, T., Nenova, K. (2008). Large Scale Knowledge Representation of Distributed Biomedical Information. In: Maicher, L., Garshol, L.M. (eds) Scaling Topic Maps. TMRA 2007. Lecture Notes in Computer Science(), vol 4999. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-70874-2_12
Download citation
DOI: https://doi.org/10.1007/978-3-540-70874-2_12
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-70873-5
Online ISBN: 978-3-540-70874-2
eBook Packages: Computer ScienceComputer Science (R0)