An installation of the Unified Medical Language System® Metathesaurus®. Part of the SMART on FHIR Cumulus Project
For more information, browse the documentation.
In order to use the Metathesaurus, you'll need to get an API key for access from the National Library of Medicine, which you can sign up for here.
You can then install this module by running pip install cumulus-library-umls.
This will add a umls target to cumulus-library. You'll need to pass your
API key via the --umls-key CLI flag, or set the UMLS_API_KEY environment variable
to the key you received from NIH.
This ends up being a fairly intensive operation - we download a large file,
extract it, create parquet files from Athena, and then upload it. It usually
takes a half hour to run. We try to preserve some of those artifacts along
the way to make rebuilds faster. If you need to force recreation from scratch, the
--force-upload CLI flag will handle this.
Note: This study is explicitly namespaced in its own schema, umls. Make sure your
database is not using this schema for another use. Do not create tables inside this
schema by another means.
The following tables are a derived from the primary tables, and are included here as a convenience to avoid having to compute these on a repeated basis
- mrrel_is_a a subset of the relationships in mrrel, including only those that define that concept A is a member of concept B (i.e. is a child, or is explicitly marked as being a tradename/member belonging to the parent concept).
- mrconso_drugs a subset of the entity list in mrconso, limited to vocabularies specifically dealing with drug identifiers (i.e. SNOMED, RxNorm, etc.)
The cumulus-library-umls study is provided as a convenience to install the
UMLS Metathesaurus, but is not shipped with the Metathesaurus dataset. It will
require an API key to download the data from NIH directly.
As a reminder, the License Agreement for Use of the UMLS® Metathesaurus® provides several restrictions on this usage of this data (including distributing the dataset). When you sign up for a UMLS key, you are assuming responsibility for complying with these terms, or an alternate licensing agreement with the owner of the Metathesaus data if you are provided with one.
Bodenreider O. The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D267-70. doi: 10.1093/nar/gkh061. PubMed PMID: 14681409; PubMed Central PMCID: PMC308795.