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Loading a dictionary

For loading the dictionaries the ETL tool transmart-data is used. Make use of the following commands for importing the data:

// CHANGE TO YOUR INSTALLATION PATH OF TRANSMART-DATA
cd transmart-data	

// SOURCE THE VARS-FILE
. ./vars

// LOAD THE DICTIONARIES
make -C data/postgres/ load_mirna_dictionary
make -C data/postgres/ load_proteomics_dictionary
make -C data/postgres/ load_metabolomics_dictionary

The gene dictionary is loaded when creating the database.

Overview of existing dictionaries

An overview of the existing dictionaries can be found here: http://library.transmartfoundation.org/dictionaries/

Storage of dictionaries

Data for each dictionary is loaded in tables that can be queried using the following queries.
Replace MIRNA with any of {GENE, MIRNA, PROTEIN, METABOLITE}.
Replace 'select *' with 'delete' to delete the entries (start from the bottom).

select * from biomart.bio_marker where bio_marker_type = 'MIRNA';
select * from biomart.bio_data_ext_code where bio_data_type = 'BIO_MARKER.MIRNA';
select * from biomart.bio_data_correlation where bio_data_id in (select bio_marker_id from biomart.bio_marker where bio_marker_type = 'MIRNA');
select * from biomart.bio_data_correlation where asso_bio_data_id in (select bio_marker_id from biomart.bio_marker where bio_marker_type = 'MIRNA');
select * from SEARCHAPP.search_keyword where data_category = 'MIRNA'; 
select * from SEARCHAPP.search_keyword_term where search_keyword_id in (select search_keyword_id from SEARCHAPP.search_keyword where data_category = 'MIRNA');
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