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ComPath Template Package

A template package for integrating new pathway databases to ComPath.

Package Structure

The template contains the following modules:

  • manager.py: Implements the database manager. All methods used in ComPath and inherited from the ComPathManager class, as well as useful commands for querying and populating. Here, it needs to be implemented a parser adapting the new pathway-protein association file. The parser should process the file to an iterator where each iteration contains the gene as well as the pathway level linkage.

  • models.py: Defines the database model. By default, each ComPath pathway package (following the Bio2BEL. structure) should contain at least the following two models:

    1. Pathway model: containing the name of the pathway and the link with the Protein model.
    2. Protein model: containing the HGNC symbol of the gene coding for the protein.

  • cli.py: Defines all commands to manage the package. Among them, there are defined the 'populate' and drop' commands that correspondingly load and erase the database.

  • constants.py: Contains the constants used by the package such as name, base URLs from RESTful APis, etc.

All modules described above contain the minimum methods for their compatibility with ComPath. A list of 'TODOs' is included within each package stating what needs to be added. Furthermore, the 'example' module outlines a parser example. A mature example of a ComPath template would be ComPath HGNC.