Designed by macrovector / Freepik
This package sets up an instance of the UMLS Metathesaurus in either the native MySQL5.5 or Postgres DBMS sourced from the RRF files downloaded and from https://www.nlm.nih.gov/research/umls/licensedcontent/umlsknowledgesources.html. The list of instantiated tables can be customized depending on user needs. These options include
All SQL scripts used in this package can be accessed at inst/sql to run directly in the client instead. If you'd like to run Metamorphosys to set configurations prior to installation, jump to Metamorphosys
This package requires a connection by RMySQL::dbConnect
or DatabaseConnector::dbConnect
for MySQL and Postgres, respectively.
devtools::install_github("meerapatelmd/setupMetathesaurus")
Example of creating a database named umls
using root
as user:
```
-mysql -u root -p
-mysql> CREATE DATABASE umls;
-mysql -u root -p --local-infile umls
-mysql> SHOW PROCESSLIST
```
MetamorphoSys is the UMLS installation and customization java application for local installation of all of the UMLS Knowledge Sources (MTH, Semantic Network, and SPECIALIST Lexicon). Metamorphosys also supports the creation of custom subsets of the Metathesaurus to meet specific use cases.
A Full Release download at https://www.nlm.nih.gov/research/umls/licensedcontent/umlsknowledgesources.html is required to run Metamorphosys, at which point the user can select various specialized configurations desired in the MySQL or Postgres Tables, such as a specific set of source vocabularies. The total time estimations of downloading, configuring, and processing the Metathesaurus tables in this way is approximately 2-3 hours. To save time, the Metamorphosys step may be skipped if the user does not desire this type of customizability and the UMLS Metathesaurus Files
can be downloaded directly at the link and used as the source files in lieu of the Full Release.
Setup and Run Metamorphosys
openMetamorphysis()
with path to run_mac.sh
as the argument Please note that the setupMetathesaurus project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.