edsnlp.pipes.ner.umls.patterns
get_patterns [source]
Load the UMLS terminology patterns.
Parameters
| PARAMETER | DESCRIPTION |
|---|---|
config | Languages and sources to select from the whole terminology. For both keys, None will select all values. TYPE: |
Return
patterns : dict[list] The mapping between CUI codes and their synonyms.
Notes
When run for the first time, this method will download the entire UMLS file and store it at ~/.data/bio/umls/2022AA/. Therefore the second run will be significantly faster than the first one.
get_path [source]
Get the path, module and filename of the UMLS file.
Parameters
| PARAMETER | DESCRIPTION |
|---|---|
config | Languages and sources to select from the whole terminology. For both keys, None will select all values. TYPE: |
Return
path, module, filename : pathlib.Path, pystow.module, str
Notes
get_path will convert the config dict into a pretty filename.
Examples
config = {"languages": ["FRE", "ENG"], "sources": None} print(get_path(config)) .data/bio/umls/2022AA/languagesFRE-ENG_sourcesNone.pkl"
download_and_agg_umls [source]
Download the UMLS if not exist and create a mapping between CUI code and synonyms.
Parameters
| PARAMETER | DESCRIPTION |
|---|---|
config | Languages and sources to select from the whole terminology. For both keys, None will select all values. TYPE: |
Return
patterns : dict[list] The mapping between CUI codes and their synonyms.
Notes
Performs filtering on the returned mapping only, not the downloaded resource.