Usage¶

Installation¶

With conda:

$ conda install -c conda-forge neo4jsbml

Principles¶

Import data from SBML into the Neo4j database is conducted in several steps:

Define your schema with Arrows and download the schema at the JSON format
Import your data into Neo4j

Define your schema with Arrows¶

Create the schema First of all, the users create a schema defining which entities will be selected from the SBML model with arrows.

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

Download the schema

Configure access to Neo4j¶

The connection to the Neo4j database needs to have several parameters defined:

protocol: neo4j, neo4j+s, neo4j+ssc, bolt, bolt+s, bolt+ssc (default: neo4j)
url (default: localhost)
user name (default: neo4j)
port (default: None)
password (default: None)
database name (default: neo4j)

The user has two options: passing arguments individually by the command line or by an ini file with this structure:

Command line

--input-protocol-str: Protocol to communicate with the database
--input-url-str: Url of Neo4j
--input-port-int: Port number tot communicate with the database
--input-user-str: Username to log with the database
--input-password-txt: Password to log with the database
--input-database-str: Database name

Configuration file Several options, either

--input-config-ini: An ìni file containing all these informations above

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

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

Note

For safety, passing a password through the command line must be given by a file. No extra character must be in the file, otherwise it would be consider as the password.

or either

--input-auradb-txt: A txt 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

Import your data into Neo4j¶

Command line¶

To import your data with neo4jsbml into Neo4j, you will need: 1. the database parameters 2. the SBML file, e.g. the model 3. the JSON file downloaded from arrows

$ neo4jsbml sbml-to-neo4j
    <database parameters>

    --input-model-sbml <file> \
    --input-arrows-json <file>

Note

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 with the argument --parameter-tag-property-str

Plugins compatibility¶

Package	Compatibility
Arrays	No
Hierarchical Model Composition	No
Distributions	No
Dynamic Structures	No
Flux Balance Constraints	Yes
Groups	Yes
Layout	Yes
Extended MathML	No
Multistate, Multicomponent and Multicompartment Species	No
Qualitative models	Yes
Rendering	No
Spatial Processes	No

Export your data into Neo4j¶

Command line¶

To export your data with neo4jsbml into Neo4j, you will need: 1. the database parameters 1. the JSON file downloaded from arrows

$ neo4jsbml sbml-from-neo4j
    <database parameters>

    --input-arrows-json <file> \
    --output-model-sbml <file>

Note

neo4jsbml tries to map your arrows schema to the structure of the SBML document. It’s better to keep the SBML structure in Neo4j and in the Arrows schema, notably to keep a Model entity.

Plugins compatibility¶

Package	Compatibility
Arrays	No
Hierarchical Model Composition	No
Distributions	No
Dynamic Structures	No
Flux Balance Constraints	No
Groups	No
Layout	No
Extended MathML	No
Multistate, Multicomponent and Multicompartment Species	No
Qualitative models	No
Rendering	No
Spatial Processes	No

With python¶

from neo4jsbml import arrows, connect, sbml

# Either you have a configuration file or overwrite individually
path_config = None
con = connect.Connect.from_config(path=path_config)
# Or
path_password = None
con = connect.Connect(
    protocol="neo4j",
    url="localhost",
    port="7687",
    user="neo4j"
    database="neo4j",
    password_path=path_password,
)

# Load model - Define a tag here if needed
tag = None
path_model = ""
sbm = sbml.Sbml.from_sbml(path=path_model, tag=tag)

# Load modelisation
path_modelisation = ""
arr = arrows.Arrows.from_json(path=path_modelisation)

# Mapping
nod = sbm.format_nodes(nodes=arr.nodes)
rel = sbm.format_relationships(relationships=arr.relationships)

# Import into neo4j
con.create_nodes(nodes=nod)
con.create_relationships(relationships=rel)