Pathterpreter Project

On 2011年一月16日, in 個人作品, by markpeng

System Architecture of Pathterpreter


Motivation and System Requirements:


The original initiative of Pathterpreter Project came from the Institute of Chemistry, Academia Sinica, Taiwan. Since the past decades of biological pathway research, a huge amount of pathway data has been generated and stored in different format of pathway databases built by different biological research institutions, for example, KEGG, Panther, BioCarta and GenMapp. Although the Website of those databases provide the access to search for pathway data, the pathway researchers still suffer from having to map the experiment data they generated with pathway data stored in heterogeneous databases manually in order to find out any possible proteins that causes the diseases. It leads to a lot of time and labor costs.

Therefore, motivated by those problems, researchers of the Institute of Chemistry brought up the requirement of having a system that integrates all the pathway databases in common use (KEGG, Panther and BioCarta), and produce the detail information of proteins matched with the variant experiment proteins in specific pathways automatically. The system could also show some statistic information and rankings based some sort of criteria.

Here are the concrete system requirements:

  1. Find out all matched proteins in the pathways and mark them.
  2. Show that of all matched proteins, which belong to main or isolated groups?
  3. Provide a list to tell which pathways are those protein nodes of main groups come from.
  4. If possible, the system should have the ability to show all useful and meaningful information about matched protein in the pathways.
    • Expression labeling (ratio information)
    • Occurrence ranking
    • Connectivity ranking
    • Association analysis
    • Statistical analysis
  5. Visualization of Pathway graphs. Provide multiple sorts of display.


  • Java, JDBC, MySQL, GraphViz, Grappa

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