MODGet

This is a java class to get the list of proteins that can have a specific modification. The PTMs are identified using the PSIMOD Ontology.

INPUT

• PSIMOD id: A 5 digit number.
• OUTPUT file: [Path] + file name.

OUTPUT

A file containing a list of proteins that can have the specified modification or sub types of that modification in the ontology hierarchy. Only following the "protein modifications by chemical process".

Command line

Parameter names	Type	Required	Description
-m,--mod	Integer	Yes	The PSIMOD id for the Post Translational Modification that will be used to select the proteins that can have that modification.
-o,--output	String	Yes	Output file path and name
-c,--confPath	String	No	config.txt file path and name
-h,--host	String	No	Url of the Neo4j database with Reactome
-u,--username	String	No	Username to access the database with Reactome
-p,--password	String	No	Password related to the username provided to access the database with Reactome

Example:

java -cp PathwayQuery-0.3.jar no.uib.tools.MODGet -m 00861 -o ./output.txt

Example 2:

java -cp PathwayQuery-0.3.jar no.uib.tools.MODGet -m 00861 -o ../../../anotherName.csv -h bolt://localhost -u someUser -p somePassword