GUS Wiki - GOOntology Tables

Download GO ontology data from NCBI site. The files needed are:

process.ontology
component.ontology
function.ontology

Save files in /usr/local/src/gus-related/ontology/. Register the LoadGoOntology plugin;

$ ga +create GUS::GOPredict::Plugin::LoadGoOntology --commit

Add data to the SRes::GORelationshipType table using the SubmitRow plugin. See Section Inserting Initial Rows into SRes::GORelationshipType for the commands used. Finally, upload the ontology data with command:

ga GUS::GOPredict::Plugin::LoadGoOntology --file_path=/usr/local/src/gus-related/ontology/ \
                                          --id_file=/home/apps/GUS/dev/uploads/go-ids \
                                          --process_db_id=3 \
                                          --process_ext_db_rel=3 \
                                          --function_db_id=1 \
                                          --function_ext_db_rel=1 \
                                          --component_db_id=2 \
                                          --component_ext_db_rel=2 \
                                          --commit \
                                          >& /home/apps/GUS/dev/uploads/go-ontology-upload.out

NOTE: IF YOU –COMMIT AT THE FIRST INSTANCE IT WORKS. OTHERWISE IF YOU WANT TO MAKE IT TWICE, CHOOSE ANOTHER NAME FOR THE ID FILE PARAMETER e.g., IF YOU CHOSE id go FIRST TIME THEN CHOOSE id go1.

GOOntologyTables