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Reactome Files Export Module

What is the Reactome Files Export Module

The Files export module is used to create the exporting files based on queries to the Reactome Graph Database. The module acts as a collection of tasks run against the database using the graph core library.

Project components used:

Project usage:

The data-export can be executed by running the executable jar file. Please ensure that Neo4j database is running and correct properties are specified.

Properties

When executing the jar file the following properties have to be set.

-h  Reactome Neo4j host. DEFAULT: bolt://localhost:7687
-u  Reactome Neo4j user. DEFAULT: neo4j
-p  Reactome Neo4j password. DEFAULT: neo4j
-o  Output directory. DEFAULT: ./export
-v  Verbose output

java -Xmx10G -jar target/data-exporter-exec.jar <arguments>

Recommendations

Ensembl mapping file may cause java.lang.OutOfMemoryError: GC overhead limit exceeded due to excessive data returned in its query. Before you experience that, we recommend that you adjust memory setting to -Xmx10G

Extras

Open Targets Schema Validator validator

export OBJC_DISABLE_INITIALIZE_FORK_SAFETY=YES; cat file.json | opentargets_validator --schema https://raw.githubusercontent.com/opentargets/json_schema/1.6.2/opentargets.json