Omnipath Secondary Adapter

About OmniPath

Omnipath is a database of molecular biology prior knowledge developed in Saez Lab and Korcsmaros Lab. It combines data from more than 100 resources and contains:

• protein-protein and gene regulatory interactions
• Enzyme and Post-Translational-Modifications(PTM) relationships
• Protein complexes
• Protein annotations
• intercellular communication.

Omnipath database stores the information in five different tables containing the aforementioned data. - Networks - Enzyme-PTM - Complexes - Annotations - Intercell

> [!WARNING]

> This BioCypher adapter relies on the Ontoweaver library that works with Python 3.12. Ensure the #Python version is 3.12 in your virtual environment.

About this adapter

The main goal of this adapter is to enable users to retrieve data from the Omnipath database and use that information to generate a knowledge graph. For achieving this goal, we are going use BioCypher and OntoWeaver.

• BioCypher:it is a framework for building biomedical knowledge graphs by integrating heterogeneous data into a structured, ontology-aligned graph representation.

• OntoWeaver: it is a visual and declarative ontology-based tool for designing and managing data integration systems, enabling intuitive schema mapping and semantic consistency. OntoWeaver has been built built on top of Biocypher.

Prerequisites

• Python 3
• Poetry [recommended]: Python packaging and dependency manager.
  • Install Poetry
• git: version control manager
  • Install git

| Prerequisite | Version | Verify installation | How to install? | | --------------- | --------- | ------------------------ | --------------------------------------------------------------------- | | Python 3 | >=3.12 | $ python --version | link | | Poetry | 1.8 | $ poetry about | link | | git | >= 2.0 | $ git --version | link | | Neo4j server | 2025.04.0 | $ neo4j --version | link |

Usage

1. Clone this repository and change to the directory: bash git clone https://github.com/biocypher/omnipath-secondary-adapter cd omnipath-secondary-adapter

2. Install all the dependencies (pre-configured in the pyproject.toml file): bash poetry lock poetry install --no-root

3. This current implementation generates Neo4j scripts for each table in the Omnipath database

| Omnipath table | Script parameter | Neo4j script generation | | ------------------ | :-------------------------------- | :-------------------------: | | Networks | -net or --networks | ✅ Done | | Enzyme-PTM | -enz or --enzyme-PTM | ✅ Done | | Complexes | -co or --complexes | ✅ Done | | Annotations | -an or --annotations | ✅ Done | | Intercell | -inter or --intercell | ✅ Done |

Use the following commands to generate import scripts for each Omnipath table:

Networks

bash poetry run python weave_knowledge_graph.py -net download

Enzyme-PTM

bash poetry run python weave_knowledge_graph.py -enz download

Complexess

bash poetry run python weave_knowledge_graph.py -co download

Annotations

bash poetry run python weave_knowledge_graph.py -an download

Intercell

bash poetry run python weave_knowledge_graph.py -inter download

4. Once the script has processed the data, you can verify a folder has been generated under biocypher-out. The folder is named after the created date (e.g., 20250610172616). This folder contains the following:

• neo4j-admin-import-call.sh: script to import the the data in Neo4j.
• CSV files:
  • *-header.csv: indicate the node/edge properties fields
  • *-part000.csv, *-part001.csv,...: store nodes/edges data based on the structure indicated in the *-header.csv files.

1. Stop the running instances of Neo4j by running: bash sudo neo4j stop

2. Run the import script generated by step 4. bash sudo bash biocypher-out/<datetime>/neo4j-admin-import-call.sh

3. Start again Neo4j by running: bash sudo neo4j start

4. Open the Neo4j platform on http://localhost:7474. You will be ask for credentials. By default the Neo4j credentials are:

• Database User: neo4j
• Password: neo4j

Note: change the password as requested.

1. At the end, you have you Knowledge Graph! 🎉 Congratulations!