Owl2Obo

Owl2Obo is a Python-based toolkit for working with ontologies, specifically designed to convert ontologies from the OWL format to the OBO format, createa network from OBO file and then examine the robustness of the network. It includes three main programs: owl-obo.py, cross-ontology_parser.py, and Perturbation.py.

Table of Contents

• Setup
• Requirements
• Running programs
  • owl-obo.py
  • cross_ontology_parser.py
  • Perturbation.py
• Output
• Contact

Setup

Clone the repository:

git clone git@github.com:samanehsalehi/owl2obo.git

Requirements

Install requirements:

pip install -r requirements.txt

Running programs

1. owl-obo.py

Converts ontologies from OWL format to OBO format. Command:

python owl-obo.py -i input_file.owl -o output_file.obo

2. cross_ontology_parser.py

Extracts terms, term IDs, is-a relationships, and xref relations from an OBO file. Command:

python cross_ontology_parser.py -i input_file.obo -o output_file.txt

3. Perturbation.py

Checks the robustness of a network created from the file generated by cross-ontology_parser.py. Command:

python Perturbation.py -i input_file.txt

Output

1. owl-obo.py

• obo file

2. cross_ontology_parser.py

• text file

3. Perturbation.py

• csv file

Contact

• Samaneh Salehi Nasab
• Email: samaneh.s@aol.com