ImmunoGIT: A Repository of Models and Metadata for Human Immune System Responses

Description

ImmunoGIT is a project focused on extracting, enriching, and organizing computational models related to immune system responses. The project interacts with the BioModels platform to retrieve SBML and SBML-QUAL models, enriches their metadata with relevant biological descriptions, and centralizes them in a public GitHub repository with a user-friendly interface via GitHub Pages.

Table of Contents

• Installation and Quick Startup
• Key Features
• Folder Structure
• Model Verification
• Contributing
• GitHub Pages
• Documentation and User Guide
• License
• Acknowledgments
• References

Installation and Quick Startup

To set up the project locally, follow these steps:

Running Python Notebooks

1. Launch Jupyter notebook:

   jupyter notebook

2. Open GetModelsAndMetadata.ipynb and run the cells to interact with the BioModels API.

Browsing and Downloading Models

• Access the GitHub Pages interface for viewing and downloading models.
• Browse through the organized models by source and format.
• Download metadata in JSON or CSV format.

Key Features

Development of Python3 Notebooks

• Objective: Interface with BioModels API using Python notebooks.
• Tools: bioservices library.
• Steps:
  • Use GetModelsAndMetadata.ipynb to search for and download SBML/SBML-QUAL models.
  • Filter models based on keywords like "immune response," "cytokines," etc.
  • Retrieve metadata (ID, name, authors, description) in JSON format.

Metadata Extraction and Enrichment

• Objective: Enrich metadata of models that are not manually curated.
• Steps:
  • Add tags and annotations compliant with international standards (e.g., Gene Ontology, MeSH).
  • Enrich SBML-QUAL metadata with both biological and relevant descriptions.
  • Use GUI tools for tagging, and apply FAIR principles.

Result Centralization

• Objective: Host models and enriched metadata in this GitHub repository.
• Steps:
  • Organize models into subdirectories based on source (e.g., BioModels, Reactome).
  • Centralize metadata in JSON and CSV formats.
  • Provide a web interface using GitHub Pages for browsing and downloading models.

Model Verification and Testing

• Objective: Verify the format of models (SBML/SBML-QUAL).
• Steps:
  • Use scripts to check if the models conform to expected formats.

Folder Structure

Here’s the structure of the repository:

/models/
    /BioModels/        # Models from BioModels
    /Reactome/         # Models from Reactome
    /SBGN/             # Models in SBGN format
/metadata/
    models_metadata.json  # Global metadata
    metadata_BioModels.json  # BioModels-specific metadata
/notebooks/
    GetModelsAndMetadata.ipynb  # Python scripts for interacting with BioModels
/docs/
    README.md             # Project overview and instructions
    UserGuide.md          # Detailed usage instructions
    ContributionGuide.md  # How to contribute to the project

Model Verification

Before integrating models into the GitHub repository, we ensure they meet the following criteria:

• Format: Check that models are in SBML or SBML-QUAL format.
• Metadata: Ensure that metadata is enriched and complies with FAIR principles.
• Test models for compatibility with existing tools.

Contributing

If you’d like to contribute :

For detailed instructions, refer to the Contribution Guide.

GitHub Pages

Visit the GitHub Pages site to:

• Browse models and metadata.
• Download models and metadata files.
• Access interactive visualizations or results.

Documentation and User Guide

A detailed user guide will be available in the docs/ folder. The guide will include:

• How to use the notebooks.
• Step-by-step instructions for interacting with models and metadata.
• Troubleshooting and common errors.

License

This project is licensed. See the LICENSE file for more details.

Additional assistance

• To view the technical specifications, see Specifications.md.

---

Credits

Supervisors

• Anna Niarakis – PU, CoSysBio, MCD-CBI
• Nicolas Ricort - Teixidor – IE, CoSysBio, MCD-CBI

Students

• Guillaume Souède
• Issa Kerima Khalil
• Mamadou Hawa Bakle
• Yasmine Boukakida

Affiliations

• University of Toulouse
  M1 Bioinformatics and Systems Biology (M1-BBS)

• Building Immune Digital Twins WG (BIDT-WG)
  Research Data Alliance (RDA)

• Centre de Biologie Intégrative Toulouse (CBI)
  Molecular, Cellular and Developmental biology unit (MCD)
  Computational Systems Biology for complex human diseases (CoSysBio)

References

1. Research Data Alliance (RDA)
2. Building Immune Digital Twins WG Feed
3. RDA Working Group: Building Immune Digital Twins - Case Statement