Knowledge environments representing molecular entities for the virtual physiological human.
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.
Bonn-Aachen International Center for Information Technology, University of Bonn, Dahlmannstrasse 2, 53113 Bonn, Germany. martin.hofmann-apitius@scai.fraunhofer.de
Martin
M
Hofmann-Apitius
Juliane
J
Fluck
Laura
L
Furlong
Oriol
O
Fornes
Corinna
C
Kolárik
Susanne
S
Hanser
Martin
M
Boeker
Stefan
S
Schulz
Ferran
F
Sanz
Roman
R
Klinger
Theo
T
Mevissen
Tobias
T
Gattermayer
Baldo
B
Oliva
Christoph M
CM
Friedrich
D000483:Alleles; D001185:Artificial Intelligence; D003198:Computer Simulation; D006801:Humans; D051188:Knowledge Bases; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D010827:Physiology; D020641:Polymorphism, Single Nucleotide; D014584:User-Computer Interface