cumulus-library-umls 0.3.1

A Unified Medical Language System® Metathesaurus study for the Cumulus project

Cumulus Library UMLS

An installation of the Unified Medical Language System® Metathesaurus®. Part of the SMART on FHIR Cumulus Project

For more information, browse the documentation.

Usage

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.

Additional custom tables

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_drug_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), for drugs and drug-related topics.
• mrconso_drugs a subset of the entity list in mrconso, limited to vocabularies specifically dealing with drug identifiers (i.e. SNOMED, RxNorm, etc.)
• mrconso_icd10cm/mrrel__icd10cm are slices of the respective main tables, only containing records from the ICD10 coding system
• icd10_(type) are slices of a given coding system at the relevant level of the ICD10 hierarchy (category,block,chapter,subcategory[1-3], extension)
• icd10_tree provides a relation-navigable code hierarchy of the individual levels in the ICD10 hierarchy
• icd10_hierarchy provides a extracted tablular representation of the full ICD10 code system

Licensing details

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.

Citations

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.