| Name | cumulus-library-umls JSON |
| Version |
0.3.2
JSON |
| download |
| home_page | None |
| Summary | A Unified Medical Language System® Metathesaurus study for the Cumulus project |
| upload_time | 2025-07-10 14:31:49 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.11 |
| license | None |
| keywords |
fhir
sql
health informatics
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# Cumulus Library UMLS
An installation of the Unified Medical Language System® Metathesaurus®. Part of the [SMART on FHIR Cumulus Project](https://smarthealthit.org/cumulus)
For more information, [browse the documentation](https://docs.smarthealthit.org/cumulus/library).
## 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](https://uts.nlm.nih.gov/uts/signup-login).
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®](https://uts.nlm.nih.gov/uts/assets/LicenseAgreement.pdf)
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.
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"description": "# Cumulus Library UMLS\n\nAn installation of the Unified Medical Language System\u00ae Metathesaurus\u00ae. Part of the [SMART on FHIR Cumulus Project](https://smarthealthit.org/cumulus)\n\nFor more information, [browse the documentation](https://docs.smarthealthit.org/cumulus/library).\n## Usage\n\nIn 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](https://uts.nlm.nih.gov/uts/signup-login).\n\nYou can then install this module by running `pip install cumulus-library-umls`.\n\nThis will add a `umls` target to `cumulus-library`. You'll need to pass your\nAPI key via the `--umls-key` CLI flag, or set the `UMLS_API_KEY` environment variable\nto the key you received from NIH.\n\nThis ends up being a fairly intensive operation - we download a large file,\nextract it, create parquet files from Athena, and then upload it. It usually\ntakes a half hour to run. We try to preserve some of those artifacts along\nthe way to make rebuilds faster. If you need to force recreation from scratch, the\n`--force-upload` CLI flag will handle this.\n\nNote: This study is explicitly namespaced in its own schema, `umls`. Make sure your\ndatabase is not using this schema for another use. Do not create tables inside this\nschema by another means.\n\n## Additional custom tables\n\nThe following tables are a derived from the primary tables, and are included here as a \nconvenience to avoid having to compute these on a repeated basis\n\n- **mrrel_drug_is_a** a subset of the relationships in mrrel, including only those that define\nthat concept A is a member of concept B (i.e. is a child, or is explicitly marked as\nbeing a tradename/member belonging to the parent concept), for drugs and drug-related topics.\n- **mrconso_drugs** a subset of the entity list in mrconso, limited to vocabularies\nspecifically dealing with drug identifiers (i.e. SNOMED, RxNorm, etc.)\n- **mrconso_icd10cm**/**mrrel__icd10cm** are slices of the respective main tables,\nonly containing records from the ICD10 coding system\n- **icd10_(type)** are slices of a given coding system at the relevant level of the\nICD10 hierarchy (category,block,chapter,subcategory[1-3], extension)\n- **icd10_tree** provides a relation-navigable code hierarchy of the individual levels\nin the ICD10 hierarchy\n- **icd10_hierarchy** provides a extracted tablular representation of the full ICD10\ncode system\n\n## Licensing details\n\nThe `cumulus-library-umls` study is provided as a convenience to install the\nUMLS Metathesaurus, but is not shipped with the Metathesaurus dataset. It will\nrequire an API key to download the data from NIH directly.\n\nAs a reminder, the \n[License Agreement for Use of the UMLS\u00ae Metathesaurus\u00ae](https://uts.nlm.nih.gov/uts/assets/LicenseAgreement.pdf)\nprovides several restrictions on this usage of this data (including distributing\nthe dataset). When you sign up for a UMLS key, you are assuming responsibility\nfor complying with these terms, or an alternate licensing agreement with the\nowner of the Metathesaus data if you are provided with one.\n\n\n## Citations\n\nBodenreider 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.\n",
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