https://github.com/biocypher/omnipath-secondary-adapter
BioCypher adapter to retrieve data from Omnipath database (Networks, Intercell, Complexes, EnzymePTM and Annotations).
https://github.com/biocypher/omnipath-secondary-adapter
biocypher biological-networks knowledge-graph neo4j ontoweaver
Last synced: 4 months ago
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BioCypher adapter to retrieve data from Omnipath database (Networks, Intercell, Complexes, EnzymePTM and Annotations).
- Host: GitHub
- URL: https://github.com/biocypher/omnipath-secondary-adapter
- Owner: biocypher
- License: mit
- Created: 2024-10-01T13:26:31.000Z (about 1 year ago)
- Default Branch: main
- Last Pushed: 2025-05-21T09:28:31.000Z (5 months ago)
- Last Synced: 2025-05-21T09:29:28.195Z (5 months ago)
- Topics: biocypher, biological-networks, knowledge-graph, neo4j, ontoweaver
- Language: Jupyter Notebook
- Homepage:
- Size: 1.58 MB
- Stars: 0
- Watchers: 1
- Forks: 3
- Open Issues: 6
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Omnipath Secondary Adapter
## About OmniPath
[Omnipath](https://omnipathdb.org/) is a database of molecular biology prior knowledge developed in [Saez Lab](https://saezlab.org/) and [Korcsmaros Lab](https://www.earlham.ac.uk/korcsmaros-group). 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](https://biocypher.org/):it is a framework for building biomedical knowledge graphs by integrating heterogeneous data into a structured, ontology-aligned graph representation.
- [OntoWeaver](https://github.com/oncodash/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](https://python-poetry.org/docs/#installation)
- *git*: version control manager
- [Install git](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git)
| Prerequisite | Version | Verify installation | How to install? |
| --------------- | --------- | ------------------------ | --------------------------------------------------------------------- |
| *Python 3* | >=3.12 | ```$ python --version``` | [link](https://docs.python.org/3/using/index.html) |
| *Poetry* | 1.8 | ```$ poetry about``` | [link](https://python-poetry.org/docs/1.8/#installation) |
| *git* | >= 2.0 | ```$ git --version``` | [link](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git) |
| *Neo4j desktop* | 2025.04.0 | ```$ neo4j --version``` | [link](https://neo4j.com/download) |
## 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 |
We have built a ready-to-use script that downloads the resources from Omnipath, and generate the scripts to export a Neo4j graph.
### *Networks*
```bash
poetry run python weave_knowledge_graph.py -net download
```
### *Enzyme-PTM*
```bash
poetry run python weave_knowledge_graph.py -enz download
```
4. Once the script has processed the data, you can verify a folder has been generated in `biocypher-out`. It contains the following:
- `neo4j-admin-import-call.sh`
- 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.
5. Populate the neo4j database, adapt the script path:
```bash
sudo neo4j stop
sudo bash biocypher-out/20250430155445/neo4j-admin-import-call.sh
sudo neo4j start
```
6. Open the Neo4j platform on http://localhost:7474
7. At the end, you have you Knowledge Graph! 🎉 Congratulations!
