Neo4jSbml

Install

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

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 <port> \
    --input-password-file <file> \
    --input-database-str <str> \
    # Config file
    --input-config-file <file> \
    # AuraDB file
    --input-auradb-file <file> \

    # Input
    --input-file-sbml <file> \
    --input-modelisation-json <file> \

    # Parameter
    --input-tag-str ""

Config file

Neo4jsbml

A config file is expected .ini

[connection]
protocol = neo4j
url = localhost
port = 7687

[database]
user = neo4j
password = abc
name = neo4j

AuraDB

A file provided by AuraDB

# one comment
NEO4J_URI=neo4j+s://test.neo4j.io
NEO4J_USERNAME=neo4j
NEO4J_PASSWORD=thepassword
# second comment
AURA_INSTANCEID=422DEf4
AURA_INSTANCENAME=Instance01