This project takes a MySQL Unified Medical Language System (UMLS) database and converts the ontologies to RDF using OWL and SKOS as the main schemas.
Virtual Appliance users can review the [documentation in the OntoPortal Administration Guide}(https://ontoportal.github.io/documentation/administration/ontologies/handling_umls).
To use it:
- Specify your database connection conf.py
- Specify the SAB ontologies to export in umls.conf
The umls.conf configuration file must contain one ontology per line. The lines are comma separated tuples where the elements are:
The following list needs updating.
(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).
Note 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 is designed to be an offline, run-once process. It's memory intensive and exports all of the default ontologies in umls.conf in 3h 30min. The ontologies listed in umls.conf are the UMLS ontologies accessible in BioPortal.
If you get an error when installing the MySQL-python python library, https://stackoverflow.com/questions/12218229/my-config-h-file-not-found-when-intall-mysql-python-on-osx-10-8 may be of help.
If running a Windows 10 OS with MySQL, the following tips may be of help.
- Install MySQL 5.5 to avoid the InnoDB space disclaimer by NLM.
- Python 2.7.x should be used to avoid syntax errors on 'raise Attribute'
- For installtion of the MySQLdb module
python -m pip install MySQLdb
is error prone. Install with executable MySQL-python-1.2.3.win-amd64-py2.7 (last known location). - Create your RRF subset(s) using mmsys with the MySQL load option, load your database, edit conf.py and umls.py to specifications, run umsl2rdf.py