SCRIPT TO ANNOTATE SBML MODELS AUTOMATICALLY

Files

• add_annotations.sh, the main runnable file coded in Bash.
• add_annotations.py, the main script written in Python 3.
• updated_annotations_samples.(xlsx, csv): structured data files containing annotations that you want to add to your models. The excel file facilitates for editing, then save as... as csv to make it as an input of the script.
• *.xml are your SBML models.

How to install required packages/libraries

I strongly recommend you making use a virtual environment in Python to install and operate the script. To create a new virtual environment, there are some approaches, but I often use the following command:

python3 -m venv venv

where python3 -m venv is required part of that command and venv is the directory name to contain Python.

This script requires libsbml installed. To install it, the easiest way is to run the following command to install the required packages for the project which were defined in the requirements.txt file.

pip install -r requirements.txt

How to run the script to add annotations

From the terminal pointing to the folder containing these scripts, type:

sh add_annotations.sh model.xml annotations_added.csv updated_model.xml

Or

./add_annotations.sh model.xml annotations_added.csv updated_model.xml

How to run the script to extract annotations

To contribute to the building the input file for the script of adding annotations, we also provide with you the script to extract annotations being used in your SBML file.

The script will return data in CSV format but you need to pipe the output into a file.

To run the script, just hit Enter after the following command:

sh extract_elements.sh your_SBML_file.xml

To save the output into a file, run as below:

sh extract_elements.sh your_SBML_file.xml > elements.csv

Enjoy your work!