https://github.com/brsynth/neo4jsbml

Bridge the gap between SBML data and Neo4j
https://github.com/brsynth/neo4jsbml

bioinformatics neo4j sbml

Last synced: 10 days ago
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Bridge the gap between SBML data and Neo4j

• Host: GitHub
• URL: https://github.com/brsynth/neo4jsbml
• Owner: brsynth
• License: mit
• Created: 2023-01-06T09:17:36.000Z (about 3 years ago)
• Default Branch: main
• Last Pushed: 2024-09-02T11:52:54.000Z (over 1 year ago)
• Last Synced: 2025-12-09T03:14:49.187Z (about 2 months ago)
• Topics: bioinformatics, neo4j, sbml
• Language: Python
• Homepage: https://neo4jsbml.readthedocs.io/
• Size: 27.8 MB
• Stars: 4
• Watchers: 1
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • Contributing: .github/CONTRIBUTING.rst
  • License: LICENSE
  • Code of conduct: .github/CODE_OF_CONDUCT.rst
  • Citation: CITATION.bib

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README

          
# Neo4jSbml

[![Github Version](https://img.shields.io/github/v/release/brsynth/neo4jsbml?display_name=tag&sort=semver)](version) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)  

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[![DOI](https://zenodo.org/badge/585859244.svg)](https://zenodo.org/badge/latestdoi/585859244)  

## Install

```sh

conda install -c conda-forge neo4jsbml

```

## Usage

### Step 1

Create a schema with [arrows](https://arrows.app) like:  

![schema](docs/_static/usage/PathwayModelisation-1.0.0.png "Schema SBML")  

Rules:

* Nodes are labelled based on SBML object name as defined in the [SBML specification](https://sbml.org)

* Properties are labelled based on SBML object properties as defined the [SBML specification](https://sbml.org)

### Step 2

Export your schema at the JSON format.  

![schema](docs/_static/usage/arrows.dwl.png "Download JSON")

### Step 3

Import your data with `neo4jsbml` into Neo4j.  

* Use either a configuration file `ini` or individual parameters

* Password needs to be store in a file for safety security

* If you have multiple model in the database, pass a `tag` to identify the model loaded into the database if you want to avoid collision

```sh

neo4jsbml sbml-to-neo4j \

    # Database parameters

    --input-protocol-str ["neo4j", "neo4j+s", "neo4j+ssc", "bolt", "bolt+s", "bolt+ssc"] \

    --input-url-str "localhost" \

    --input-user-str "neo4j" \

    --input-port-int  \

    --input-password-file  \

    --input-database-str  \

    # Config file

    --input-config-file  \

    # AuraDB file

    --input-auradb-file  \

    # Input

    --input-file-sbml  \

    --input-modelisation-json  \

    # Parameter

    --input-tag-str ""

```

## Config file

### Neo4jsbml

A config file is expected `.ini`

```ini

[connection]

protocol = neo4j

url = localhost

port = 7687

[database]

user = neo4j

password = abc

name = neo4j

```

### AuraDB

A file provided by AuraDB

```bash

# one comment

NEO4J_URI=neo4j+s://test.neo4j.io

NEO4J_USERNAME=neo4j

NEO4J_PASSWORD=thepassword

# second comment

AURA_INSTANCEID=422DEf4

AURA_INSTANCENAME=Instance01

```