Reaction exporter

Creates diagram files out of single reactions, using the graph database as resource.

Taking a single reaction, this library performs 3 steps:

1. queries the graph database to retrieve the reaction, its participants and the compartments containing them.
2. applies an automatic layout to show a left to right view of the reaction, while keeping every participant in its compartment.
3. generates a diagram (.json) and a graph (.graph.json) files following Reactome specifications.

Usage:

This project can be used as a standalone compiled tool through the provided reaction-exporter.jar file.

java -jar reaction-exporter-exec.jar [--help] [(-h|--host) <host>] [(-p|--port) <port>] [(-u|--user) <user>] (-d|--password) <password> (-s|--stId) <stId> (-o|--path) <path> [(-f|--format) <format>]
  [--help]
        Prints this help message.

  [(-h|--host) <host>]
        The neo4j host (default: bolt://localhost:7687)
  [(-u|--user) <user>]
        The neo4j user (default: neo4j)
  (-d|--password) <password>
        The neo4j password (default: neo4j)

  (-t|--target) <target>
        Reaction stable identifier

  (-o|--path) <path>
        Output path. File will be named 'path'/'target'.'format'

  [(-f|--format) <format>]
        Output format (default: png)

Or as a maven dependency:

<dependency>
    <groupId>org.reactome.server.tools</groupId>
    <artifactId>reaction-exporter</artifactId>
    <version>1.1.2</version>
</dependency>

<repository>
    <id>pst-release</id>
    <name>EBI Nexus Repository</name>
    <url>https://www.ebi.ac.uk/Tools/maven/repos/content/repositories/pst-release</url>
</repository>

Update GO ontology

If some recent GO term has been added to reactome database after the last update of /src/main/resources/ontologies/go-basic.obo

Last update: 15/11/2023

We should update the resource file from Gene Ontology at https://purl.obolibrary.org/obo/go.obo