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These python scripts connect to the Unified Medical Language System (UMLS) database and translate the ontologies into RDF/OWL files. This is part of the BioPortal project.
Python Shell
Branch: master


This project takes the MYSQL Unified Medical Language System (UMLS) database to convert the ontologies to RDF using OWL and SKOS as main schemas.

To use it:
    (a) Specify your database connection
    (b) Specify the SAB ontologies to export in umls.conf.

The configuration file umls.conf must contain one ontology per line. The lines are comma separated tuples where the elements are:
    (0) SAB
    (1) BioPortal Virtual ID. This is optional, any value works.
    (2) Output file name.
    (3) Conversion strategy. Accepted values (load_on_codes, load_on_cuis). has been designed to be an off-line run-once process, it is a memory intensive process and exports all the default ontologies in umls.conf in 3h 30min. The ontologies listed in umls.conf are the UMLS ontologies accessible at
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