Guide to Pharmacology (GtoP) Cross-Referencer to ChEBI

This tool will perform an update to ReferenceTherapeutic instances (representing Guide to Pharmacology identifiers) by adding and removing cross-references to ChEBI identifiers as needed.

It will:

• Download mapping files for Guide to Pharmacology ligands (GtoP to PubChem mapping) and PubChem synonyms (PubChem to ChEBI mapping)
• Process the mapping files to build a GtoP to ChEBI mapping
• Add ChEBI cross-references to the ReferenceTherapeutics that have a GtoP identifier in the mapping
• Remove any existing ChEBI cross-references to the ReferenceTherapeutics that do not have a GtoP identifier in the mapping

Configuration

This application requires a properties file at src/main/resources/config.properties that looks like this (with the appropriate values filled in place of the placeholders):

curator.database.user=username
curator.database.password=password
curator.database.host=localhost
curator.database.name=gk_central
personId=person_db_id

Compiling & Running

This is a Java application which requires a Java 8+ environment. You will need maven and a full JDK to compile.

To compile the application, run this command:

$ mvn clean package

To run the program, execute this command:

$ java -jar target/gtp_chebi_mapping-jar-with-dependencies.jar -c /path/to/config.properties -o /path/to/output.txt