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 conf.py (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).

Notice that 'CCS COSTAR DSM3R DSM4 DXP ICPC2ICD10ENG MCM MMSL MMX MTHCMSFRF MTHMST MTHSPL MTH NDFRT SNM' have no code and should not be loaded on loads_on_codes

umls2rdf.py 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 bioportal.bioontology.org.