Difference between revisions of "Building biological models automatically using the Semantic Web"

From Master Projects
Jump to: navigation, search
Line 10: Line 10:
 
|Poster=Posternaam.pdf
 
|Poster=Posternaam.pdf
 
}}
 
}}
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.
+
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.<ref>[http://www.springerlink.com/content/2660p61h7072640l/ Krepska E, et al. 2008] Krepska E, Bonzanni N, Feenstra KA, Fokkink W, Kielmann T, Bal H, Heringa J. '''Design issues for qualitative modelling of biological cells with Petri nets'''. In: '''Proceedings of the Formal Methods in Systems Biology''' 2008 (2008) ''5054''. Cambridge, UK: Springer. 48–62. of LNBI.</ref><ref>[http://www.ncbi.nlm.nih.gov/pubmed/19515963 Bonzanni et al. 2008] Bonzanni N, Krepska E, Feenstra KA, Fokkink W, Kielmann T, Bal H, Heringa J. '''Executing Multicellular Differentiation - Quantitative Predictive Modelling of C elegans Vulval Development''' Bioinformatics. 2009 ''25'':2049-56.</ref>
  
 
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).
 
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).
 +
 +
==Related Projects==
 +
* [[Implementing GPCR signaling network model in Petri-Net|Implementing GPCR signaling network model in Petri-Net (Michiel Vegt)]]
 +
* [[Refining WNT/b-Catenin signalling network in Petri-net model|Refining WNT/b-Catenin signalling network in Petri-net model (Matthias Seenok)]]
 +
 +
==References==
 +
<references />
 +
 +
==Further Reading==
 +
* [http://www.wikipathways.org Wikipathways]
 +
* [http://jena.apache.org/tutorials/sparql.html SPARQL tutorial]

Revision as of 14:25, 19 March 2013


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

Signature supervisor



..................................

Abstract

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.[1][2]

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).

Related Projects

References

  1. Krepska E, et al. 2008 Krepska E, Bonzanni N, Feenstra KA, Fokkink W, Kielmann T, Bal H, Heringa J. Design issues for qualitative modelling of biological cells with Petri nets. In: Proceedings of the Formal Methods in Systems Biology 2008 (2008) 5054. Cambridge, UK: Springer. 48–62. of LNBI.
  2. Bonzanni et al. 2008 Bonzanni N, Krepska E, Feenstra KA, Fokkink W, Kielmann T, Bal H, Heringa J. Executing Multicellular Differentiation - Quantitative Predictive Modelling of C elegans Vulval Development Bioinformatics. 2009 25:2049-56.

Further Reading