Biosemantics: a concept-driven approach to literature based discovery

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Biosemantics: A concept-driven approach to literature based discovery.
Barend Mons PhD.
This seminar is meant as an introduction of the work that Barend Mons and his team have done for the past three years at the department of Medical Informatics of the Erasmus Medical Centre. The so-called Biosemantics group of that department is developing tools to assist in post high-throughput literature and database studies aimed at elucidating functional relationships between long lists of potentially interesting molecules. The approach is fundamentally different form classical pathway-based or text mining tools.

After a period of formal evaluation of the basic technology (see list of publications and ) , the time has come to test the set of tools in ‘real life’ situations and to collect feed back of day-to-day research dealing with complex systems biology issues.

To that end, Barend was recently appointed for two days per week at the department of Human Genetics. During the first few months, he will mainly assist interested LUMC people with the analysis of their gene or protein lists in order to evaluate the value of the tools in practice, and hopefully speeding up the discovery process of the researchers.
During the first part of the seminar, Barend will explain the basics of the Biosemantics approach and their will be ample time for detailed technical questions and discussion. The systems designers from Rotterdam will also be present to answer specific technical questions.
Interested colleagues can stay on after the meeting to test some of the tools in practice, possibly already with their gene or protein lists of interest. In that case it is advisable to bring a list EntrezGene (former LocusLink) or SwissProt ID’s on a memory stick.
Van der Eijk, E.M. van Mulligen, J.A. Kors, B. Mons and J. van den Berg (2004) "Constructing an associative concept space for literature-based discovery", JASIST 55(5): 436-444.
Schuemie MJ, Weeber M, Schijvenaars BJ, van Mulligen EM, van der Eijk CC, Jelier R, Mons B, Kors J.. Distribution of information in biomedical abstracts and full-text publications. Bioinformatics 2004;20(16):2597-604.

Stuckenschmidt, H. van Harmelen, F. de Waard, A. Scerri, T. Bhogal, R. van Buel, J. Crowlesmith, I. Fluit, C. Kampman, A. Broekstra, J. van Mulligen, EM. Exploring large document repositories with RDF technology: the DOPE project. Intelligent Systems, IEEE; 2004;19(3):34-40

R. Jelier1, G. Jenster2, L.C.J. Dorssers3, C.C. van der Eijk1, E.M. van Mulligen1, B. Mons1, J.A. Kors1

Co-occurrence based meta-analysis of scientific texts: retrieving biological relationships between genes Bioinformatics (accepted for publication)

Schuemie MJ, Kors J, Mons, B.

Word sense disambiguation in the biomedical domain: an overview

Journal of Computational Biology ((accepted for publication)

Bob J.A. Schijvenaars,1 Barend Mons,1 Marc Weeber,1 Martijn J. Schuemie,1 Erik M. van Mulligen,1 Hester M. Wain,2 Johan van der Lei,1 and Jan A. Kors1*

Thesaurus-based disambiguation of gene symbols in large text corpora, BMC Bioinformatics, (conditionally accepted for publication)

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