Progress and Prospects in Parkinson's Research/Magazine Section/PD pathogenesis map
Mapping Parkinson's pathogenesis - all of it!Edit
The pathogenesis of Parkinson's is so complex, how can you understand it? So many complex molecular pathways are involved - synaptic and mitochondrial dysfunction, impaired protein degradation, alpha-synuclein pathobiology, neuroinflammation and so on. A map would be handy.
But a map is exactly what a joint Luxembourgian/Japanese team has come up with. It is simply called the PD Map and it shows in one, very large interactive diagram all the molecular pathways that have been found to be involved in Parkinson's pathogenesis. By clicking a button you can see how the pathways are perturbed in the Parkinsonian condition; the expression of some proteins and other entities are suppressed and others are overexpressed and this is shown by the symbols that represent them on the map turning red or green.
Enabling a better understanding of the processes underlying Parkinson's by presenting them in a graphical form is the aim of this relatively new project which is impressive already. To complete it, the team are relying on 'crowd sourcing' where experts from anywhere in the world can add new material and fill in the gaps.
Unless you are an expert molecular biologist with a good grasp of bioinformatics, don't go straight to the PD map itself but read the recent paper on it first. The paper describes the power of this concept - which links 'objects' on the map to external references, such as PubMed, and databases. It consolidates into one, overall, comprehensive scheme all those areas of research conducted in the silos that tend to be insulated from each other. The potential is clear. The links between different areas of interest are laid out. This picture - and it is a complex one - is worth a few thousand words.
Understanding the map is not easy at first because it uses the Systems Biology Graphical Notation (SBGN). You need to understand what all the various symbols and labels mean to make sense of it. The PD map is a Process Description diagram created with graphical symbols from the Process Description language. This is just one of the three SBGN graphical languages used for creating three different types of diagram: Process Description, Entity-Relationship and Activity Flow. 
The map itself is very much work in progress. And so it should be while the puzzle of Parkinson's itself remains work in progress. Yet an impressive start has been made to gathering together the wealth of detailed progress that has been made in teasing out the perturbations that Parkinson's wreaks on the biochemical functioning in and between cells.
A brief note on the PD Map project is in Progress and Prospects: A pathogenesis Map
- 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.