Building biological models automatically using the Semantic Web

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Building biological models automatically using the Semantic Web
status: ongoing
Student name: student name::Timo Willemsen
Start start date:=2013/04/11
End end date:=2013/08/11
Supervisor: Anton Feenstra
Second supervisor: Paul Groth
Thesis: has thesis::Media:Thesis.pdf
Poster: has poster::Media:Posternaam.pdf

Signature supervisor



The Semantic Web offers us a powerful mechanism for data integration. One (very) complex source of data are biological pathways and networks, e.g. for signalling and regulation. These networks are often used to model the biological system, e.g. using Petri nets.

This project will explore the possibilities of a system for retrieval of pathway and network information using RDF queries and the automatic construction of Petri net models for the biological system. We will evaluate the feasibility of this approach based on two case studies for which we previously constructed working Petri net models. These are the MapK/Notch signalling pathway for cellular differentiation in C. elegans, and the beta-Catenin pathway involved in regulation of development in Humans (and many other species).