Science Score: 41.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
-
○DOI references
-
✓Academic publication links
Links to: zenodo.org -
○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.9%) to scientific vocabulary
Keywords
Repository
Bridge the gap between SBML data and Neo4j
Basic Info
- Host: GitHub
- Owner: brsynth
- License: mit
- Language: Python
- Default Branch: main
- Homepage: https://neo4jsbml.readthedocs.io/
- Size: 27.8 MB
Statistics
- Stars: 4
- Watchers: 1
- Forks: 0
- Open Issues: 1
- Releases: 12
Topics
Metadata Files
README.md
Neo4jSbml
Install
sh
conda install -c conda-forge neo4jsbml
Usage
Step 1
Create a schema with arrows like:
Rules:
* Nodes are labelled based on SBML object name as defined in the SBML specification
* Properties are labelled based on SBML object properties as defined the SBML specification
Step 2
Export your schema at the JSON format.
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
--input-file-sbml <file> \
--input-modelisation-json <file> \
# 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
NEO4JURI=neo4j+s://test.neo4j.io NEO4JUSERNAME=neo4j NEO4J_PASSWORD=thepassword
second comment
AURAINSTANCEID=422DEf4 AURAINSTANCENAME=Instance01 ```
Owner
- Name: BioRetroSynth
- Login: brsynth
- Kind: organization
- Website: http://www.jfaulon.com
- Repositories: 33
- Profile: https://github.com/brsynth
Our group is interested in synthetic biology and systems metabolic engineering in whole-cell and cell-free systems.
Citation (CITATION.bib)
@article{gricourtNeo4jsbmlImportSystems2024,
title = {Neo4jsbml: Import Systems Biology Markup Language Data into the Graph Database {{Neo4j}}},
shorttitle = {Neo4jsbml},
author = {Gricourt, Guillaume and Duigou, Thomas and Dérozier, Sandra and Faulon, Jean-Loup},
date = {2024-01-16},
journaltitle = {PeerJ},
volume = {12},
pages = {e16726},
issn = {2167-8359},
doi = {10.7717/peerj.16726},
url = {https://peerj.com/articles/16726},
urldate = {2024-01-22},
langid = {english},
}
GitHub Events
Total
Last Year
Dependencies
- actions/checkout v4 composite
- actions/download-artifact v3 composite
- actions/upload-artifact v3 composite
- ad-m/github-push-action master composite
- conda-incubator/setup-miniconda v2 composite
- docker://pandoc/core 2.9 composite
- mathieudutour/github-tag-action v6.1 composite
- ruby/setup-ruby v1 composite
- softprops/action-gh-release v1 composite
- actions/checkout v4 composite
- github/super-linter v5 composite
- actions/checkout v4 composite
- conda-incubator/setup-miniconda v2 composite
- mdanics/Setup-Neo4j 1.0.0 composite
- neo4j 5.3.0-community
- org.dom4j:dom4j 2.0.3 compile
- org.neo4j.procedure:apoc-common 5.12.0 compile
- org.neo4j:neo4j 5.12.0 provided
- ch.javasoft:metabolic-efm 4.7.1
- org.assertj:assertj-core 3.24.2 test
- org.junit.jupiter:junit-jupiter-engine 5.10.0 test
- org.neo4j.driver:neo4j-java-driver 5.12.0 test
- org.neo4j.test:neo4j-harness 5.12.0 test