BioPAX to GO-CAM Converter in Python

The primary objective of this project is to convert BioPAX files into the GO-CAM format using Python. This serves as a modernized and optimized rewrite of the existing BioPAX to GO-CAM conversion code, which was originally implemented in Java. The goal is to produce code that is more readable, maintainable, and efficient.

Features

• Parsing: Utilize the PyBioPAX library to parse BioPAX data.

  • inferTransportProcess
  • inferMolecularFunctionFromEnablers
  • inferOccursInFromEntityLocations
  • inferRegulatesViaOutputRegulates
  • inferRegulatesViaOutputEnables
  • inferProvidesInput
  • inferSmallMoleculeRegulators

• Transformation/Derivation Stage: Implement various inference steps to transform and derive new data values.

• Transformer Classes: Create transformer classes, such as ReactomeTransformer, potentially using the Factory pattern if multiple transformers are needed.

Languages and Frameworks

The project is primarily developed in Python. Key libraries and frameworks include:

• PyBioPAX: For parsing and processing BioPAX files.
• rdflib: For working with RDF data, aiding in generating the GO-CAM models in .ttl format.
• Ontobio: Contains GO-CAM specific functions using rdflib for quick generation of GO-CAM TTL.
• OAK: Provides ontology parsing and traversal utilities for tasks requiring GO, CHEBI, and other ontologies.

Installation

1. Clone the repository:

git clone https://github.com/geneontology/pybiopax2gocam.git
cd pybiopax2gocam

3. Install the required packages:

pip install -r requirements.txt

Usage

To run the converter, use the following command:

python3 -m src.controllers.biopax_controller -t [parser_type] -v [view_type] -i [path_to_biopax]

Arguments:

• -t, --parser_type: Specifies the parser type. Choices are yeast or reactome.
• -v, --view_type: Specifies the view type. Choices are gocamgen, json, yaml, or vis.
• -i, --biopax_path: Path to the BioPAX file or folder containing BioPAX files.

Example:

python3 -m src.controllers.biopax_controller -t reactome -v json -i resources/test_biopax/reactome/R-HSA-204174_level3.owl

Data Flow

Deliverables

By the end of the project, the following deliverables are expected:

1. A rewritten BioPAX to GO-CAM converter tool in Python.
2. Comprehensive documentation detailing the usage of the converter tool.
3. Validation and testing mechanisms for the converter tool.
4. Integration with existing systems.
5. A final project report detailing the development process, challenges, and outcomes.