VaxKG

This project provides Python scripts to import and map the Vaccine Ontology (VO) into a Neo4j graph database. It leverages the Neosemantics (n10s) library for RDF import and performs subsequent mapping to align the ontology with domain-specific nodes and relationships.

Table of Contents

• Prerequisites
• Installation
• Configuration
  • .env File Configuration
  • Neosemantics (n10s) Configuration
• Usage
• Code Overview
• Environment Setup
• Contributing

Prerequisites

Before you begin, ensure you have the following installed:

• Python 3.6 or higher: Required to run the Python scripts.
• Neo4j Graph Database: You need a running instance of Neo4j.
• Neo4j Python Driver: This project uses the official Neo4j Python driver. You can install it using pip:

  pip install neo4j

• dotenv: For managing environment variables. Install using pip:

  pip install python-dotenv

• Neosemantics (n10s): This Neo4j extension is used for importing the OWL ontology.

Installation

1. Clone the repository (if you have the code in a repository):

   git clone <repository_url>
   cd <repository_directory>

Configuration

.env File Configuration

This project uses a .env file to store sensitive information like your Neo4j connection URI, username, and password.

1. Create a .env file in the root directory of your project.
2. Add your Neo4j connection details to the .env file. Replace the placeholders with your actual credentials:

   URI=bolt://localhost:7687  # Replace with your Neo4j URI
   USERNAME=neo4j             # Replace with your Neo4j username
   PASSWORD=your_password     # Replace with your Neo4j password

Neosemantics (n10s) Configuration

To enable the import of the OWL ontology, you need to configure Neosemantics in your Neo4j instance. Follow these steps:

1. Download Neosemantics: Download the latest stable release JAR file of Neosemantics from the official GitHub releases page: https://github.com/neo4j-labs/neosemantics/releases. Look for a file named something like neosemantics-{version}.jar.

2. Place the JAR file in the plugins directory: Locate your Neo4j installation directory. Inside it, you will find a plugins directory. Copy the downloaded Neosemantics JAR file into this directory.

3. Configure neo4j.conf: Open the neo4j.conf file located in the conf directory of your Neo4j installation.

4. Add the following lines to the neo4j.conf file:

   • Enable unmanaged extensions for Neosemantics:

     dbms.unmanaged_extension_classes=n10s.extension=/rdf
     

   • Set the import directory: This allows Neo4j to access files in the specified import directory. While this project imports from a remote URL, it's a good practice to configure it.

     dbms.directories.import=import
     

     Note: Ensure that the import directory exists within your Neo4j installation directory. You might need to create it if it doesn't exist.

5. Restart Neo4j: After making these changes, you need to restart your Neo4j server for the configuration to take effect.

Usage

1. Activate your Python environment (if applicable): If you are working within a virtual environment, make sure to activate it. For example, if you used venv:

   source neo4j-env/Scripts/activate  # On Windows
   source neo4j-env/bin/activate    # On macOS and Linux

   (This step is also mentioned in the code comments).

2. Run the main script (__main__.py if you structure your project that way, or directly run the provided script): Execute the 2 Python scripts to start the import and mapping process.

   python import_to_neo4j.py

   and then

   python ontology_mapping.py

The script will perform the following actions:

• Import Ontology: Downloads the Vaccine Ontology (VO) from the specified GitHub URL and imports it into Neo4j using Neosemantics.
• Map Ontology: Maps the imported ontology nodes to domain-specific nodes (like Vaccine and Pathogen) and creates VO_REPRESENTATION relationships.
• Update Resource Properties: Transforms complex IAO and UBPROP codes on Resource nodes into more human-readable properties.

You can observe the progress and any potential errors in the console output.

Code Overview

The provided Python code contains the following key functions:

• import_ontology_complete(driver): Imports the complete Vaccine Ontology (VO) from a remote GitHub URL into Neo4j using Neosemantics. It handles constraint creation, graph configuration, and error handling.
• map_ontology(driver): Orchestrates the mapping of imported ontology nodes to domain-specific nodes (Vaccine, Pathogen, etc.) by calling individual mapping functions.
• map_vaccine_nodes_gemini_way(session): Maps Vaccine nodes using their c_vo_id property and also links them to the general VO_0000001 Resource node.
• update_resource_properties(session): Updates the properties of Resource nodes by converting IAO and UBPROP codes to more readable names.
• map_vaccine_nodes(session): Maps Vaccine nodes to their corresponding VO Resource representations, remapping properties and creating VO_REPRESENTATION relationships.
• map_pathogen_nodes(session): Maps Pathogen nodes to their corresponding Taxonomy Resource representations based on their c_taxon_id.
• map_relationships_vo_aligned(session, relationship_queries): Executes Cypher queries to create relationships aligned with VO concepts (this function is defined but not actively used with specific queries in the provided code).
• import_data(): The main function that establishes the Neo4j connection, calls the ontology import and mapping functions, and handles overall execution.
• execute_queries(driver, queries): A helper function to execute a dictionary of Cypher queries (used in the import_data() function defined at the end of the script, which seems to be a different version focusing on CSV import - the main execution calls the earlier import_data() function).

The script loads Neo4j connection details from a .env file for security and ease of configuration.

Environment Setup

As mentioned in the code comments, if you are working in a Python virtual environment, you might need to activate it before running the script. The comment provides examples for both Windows and macOS/Linux.

Contributing

Contributions to this project are welcome. If you find any issues or have suggestions for improvements, please feel free to open an issue or submit a pull request.