Knowledge environments representing molecular entities for the virtual physiological human.

Full Abstract

In essence, the virtual physiological human (VPH) is a multiscale representation of human physiology spanning from the molecular level via cellular processes and multicellular organization of tissues to complex organ function. The different scales of the VPH deal with different entities, relationships and processes, and in consequence the models used to describe and simulate biological functions vary significantly. Here, we describe methods and strategies to generate knowledge environments representing molecular entities that can be used for modelling the molecular scale of the VPH. Our strategy to generate knowledge environments representing molecular entities is based on the combination of information extraction from scientific text and the integration of information from biomolecular databases. We introduce @neuLink, a first prototype of an automatically generated, disease-specific knowledge environment combining biomolecular, chemical, genetic and medical information. Finally, we provide a perspective for the future implementation and use of knowledge environments representing molecular entities for the VPH.

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Author information

Author/s: Hofmann-Apitius, Martin (M); Fluck, Juliane (J); Furlong, Laura (L); Fornes, Oriol (O); Kolárik, Corinna (C); Hanser, Susanne (S); Boeker, Martin (M); Schulz, Stefan (S); Sanz, Ferran (F); Klinger, Roman (R); Mevissen, Theo (T); Gattermayer, Tobias (T); Oliva, Baldo (B); Friedrich, Christoph M (CM);

Affiliation: Bonn-Aachen International Center for Information Technology, University of Bonn, Dahlmannstrasse 2, 53113 Bonn, Germany. martin.hofmann-apitius(-atsign-)scai.fraunhofer.de

Journal and publication information

Publication Type: Journal Article

Journal: Philosophical transactions. Series A, Mathematical, physical, and engineering sciences (Philos Transact A Math Phys Eng Sci), published in England. (Language: eng)

Reference: 2008-Sep; vol 366 (issue 1878) : pp 3091-110

Dates: Created 2008/07/28; Completed 2008/09/30;

PMID: 18559317, status: MEDLINE (last retrieval date: 11/6/2008)

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