Installation

Package installation

Python 3.10 recommended

PyPI

pip install ontosunburst

Local

Requirements

• numpy>=1.26.1
• plotly>=5.17.0
• scipy>=1.11.3
• SPARQLWrapper>=2.0.0
• pandas>=1.5.3

Inside the cloned repository :

pip install -r requirements.txt
pip install -e .

Set up Jena SPARQL server (optional : for ChEBI and GO)

Requirements

Need Apache Jena Fuseki SPARQL server for ChEBI and GO requests and their OWL files.

• Download Apache Jena Fuseki : https://jena.apache.org/download/index.cgi
• Download ChEBI ontology : https://ftp.ebi.ac.uk/pub/databases/chebi/ontology/ (chebi.owl or chebi_lite.owl)
• Download GO ontology : https://geneontology.org/docs/download-ontology/ (go.owl)

Utilisation

Execute followed bash script to launch server.

ChEBI

#!/bin/bash

FUSEKI_PATH=/path/to/apache-jena-fuseki-x.x.x
CHEBI_PATH=/path/to//chebi_lite.owl

${FUSEKI_PATH}/fuseki-server --file=${CHEBI_PATH} /chebi

GO

#!/bin/bash

FUSEKI_PATH=/path/to/apache-jena-fuseki-x.x.x
GO_PATH=/path/to/go.owl

${FUSEKI_PATH}/fuseki-server --file=${GO_PATH} /go