Parkinson's Pathogenesis/PD Map

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Needs to be expanded in accessible language with full explanation of the PD Map project and how to get around the map.

See also: Magazine Section - Mapping Parkinson's pathogenesis - all of it!

A Parkinson's Pathogenesis Map

The Luxembourg Centre for Systems Biomedicine (LCSB) in collaboration with the team of Hiroaki Kitano from the Systems Biology Institute (SBI), Tokyo, are developing a disease map of Parkinson’s disease – the so-called PD map.

The PD map is a knowledge repository established to describe the various possible mechanisms of PD by demonstrating the complex relationships between the genetic and environmental risk factors. It also serves as an interface to bioinformatics tools allowing exploration and updating of the contents of the map using standardized annotations. Another functionality of the map is visualization of large experimental datasets, allowing their analysis in the context of disease mechanisms. The map has reached substantial size and complexity. Keeping it up-to-date and refining it with limited resources is recognised by the authors to be a challenge. The PD map is seen as a crowd-sourcing project, where an interested and knowledgeable research community is engaged in solving a problem, similar to WikiPathways or Payao, but focused on disease-related mechanisms. The functionality already implemented allows users directly to send their feedback on the map contents.

The PD map is accessible through a web link [1] and the results to date have been published in an open-access on-line article [2].

The PD map uses the Systems Biology Graphical Notation (SBGN). The SBGN has three types of graphical language for creating three types of diagram: Process Description, Entity-Relationship and Activity Flow. The PD map is a Process Description diagram created with graphical symbols from the Process Description Language. [3]

References[edit]

  1. : http://minerva.uni.lu/MapViewer/map?id=pdmap
  2. Kazahiro A et al, Integrating Pathways of Parkinson's Disease in a Molecular Interaction Map, http://link.springer.com/article/10.1007%2Fs12035-013-8489-4/fulltext.html Molecular Neurobiology July 2013
  3. Some familiarity with the SBGN Process Description language is necessary for understanding the PD map. The user guide can be downloaded from: http://sourceforge.net/projects/sbgn/ - to save confusion, just look at the Process Description user guide file to find the explanations for the symbols used in the PD map.