UMLS Downloader 0.1.4-dev Documentation

Reference

umls_downloader Package

Automate downloading content from the UMLS Terminology Services (UTS).

Functions

download_rxnorm([version, api_key, force])

Ensure the given version of the RxNorm monthly file.

download_rxnorm_prescribable([version, force])

Ensure the given version of the RxNorm prescribable content file.

download_semmeddb_citations(**kwargs)

Download the SemMedDB citations file.

download_semmeddb_concept(**kwargs)

Download the SemMedDB generic concepts file.

download_semmeddb_entity(**kwargs)

Download the SemMedDB entities file.

download_semmeddb_predication(**kwargs)

Download the SemMedDB predication file.

download_semmeddb_predication_aux(**kwargs)

Download the SemMedDB predication (aux) file.

download_semmeddb_sentence(**kwargs)

Download the SemMedDB sentence file.

download_snomed_international(**kwargs)

Download the SNOMED-CT international version.

download_snomed_us(**kwargs)

Download the SNOMED-CT United States version.

download_tgt(url, path, *[, api_key, force])

Download a file via the UMLS ticket granting system.

download_tgt_versioned(url_fmt[, version, ...])

Download a file via the UMLS ticket granting system.

download_umls([version, api_key, force])

Ensure the given version of the UMLS MRCONSO.RRF file.

download_umls_full([version, api_key, force])

Ensure the given version of the UMLS MRSTY.RRF file.

download_umls_metathesaurus([version, ...])

Ensure the given version of the UMLS metathesaurus zip archive.

open_umls([version, api_key, force])

Ensure and open the UMLS MRCONSO.RRF file from the given version.

open_umls_full(name[, version, api_key, force])

Ensure and open a UMLS file from the given version.

open_umls_hierarchy([version, api_key, force])

Ensure and open a UMLS file from the given version.

open_umls_semantic_types([version, api_key, ...])

Ensure and open a UMLS file from the given version.

Command Line Interface

The UMLS Downloader automatically installs the command umls_downloader. See umls_downloader --help for usage details.

umls_downloader

Download files from the UMLS Terminology Service.

umls_downloader [OPTIONS] COMMAND [ARGS]...

custom

Download a file via a custom URL.

umls_downloader custom [OPTIONS]

Options

-v, --verbose

Enable verbose mode. More -v’s means more verbose.

--api-key <api_key>

The API key for the UMLS ticket granting system. If not given, uses pystow to load. Get one at https://uts.nlm.nih.gov/uts/edit-profile.

-f, --force
--url <url>

Required The URL for a file to be downloaded through the UMLS ticket granting system.

-o, --output <output>

Required The local file path to download a file to

rxnorm

Download the RxNorm data and print the path to stdout.

umls_downloader rxnorm [OPTIONS]

Options

-v, --verbose

Enable verbose mode. More -v’s means more verbose.

--version <version>

The version to download. If none specified, looks up the latest with bioversions

-f, --force
--api-key <api_key>

The API key for the UMLS ticket granting system. If not given, uses pystow to load. Get one at https://uts.nlm.nih.gov/uts/edit-profile.

umls

Download the UMLS data and print the path to stdout.

umls_downloader umls [OPTIONS]

Options

-v, --verbose

Enable verbose mode. More -v’s means more verbose.

--version <version>

The version to download. If none specified, looks up the latest with bioversions

-f, --force
--api-key <api_key>

The API key for the UMLS ticket granting system. If not given, uses pystow to load. Get one at https://uts.nlm.nih.gov/uts/edit-profile.

Indices and Tables