medkit.text.ner.umls_utils#

Classes:

UMLSEntry(cui, term)

Entry in MRCONSO.RRF file of a UMLS dictionary

Functions:

`guess_umls_version`(path)	Try to infer UMLS version (ex: "2021AB") from any UMLS-related path
`load_umls`(mrconso_file[, sources, ...])	Load all terms and associated CUIs found in a UMLS MRCONSO.RRF file
`preprocess_term_to_match`(term, lowercase, ...)	Preprocess a UMLS term for matching purposes

class UMLSEntry(cui, term)[source]#

Entry in MRCONSO.RRF file of a UMLS dictionary

Variables

load_umls(mrconso_file, sources=None, languages=None, show_progress=False)[source]#

Load all terms and associated CUIs found in a UMLS MRCONSO.RRF file

Parameters

mrconso_file (Union[str, Path]) – Path to the UMLS MRCONSO.RRF file
sources (Optional[List[str]]) – Sources to consider (ex: ICD10, CCS) If none provided, CUIs and terms of all sources will be taken into account.
languages (Optional[List[str]]) – Languages to consider. If none provided, CUIs and terms of all languages will be taken into account
show_progress (bool) – Whether to show a progressbar

Return type

Iterator[UMLSEntry]

Returns

Iterator[UMLSEntry] – Iterator over all term entries found in UMLS install

preprocess_term_to_match(term, lowercase, normalize_unicode, clean_nos=True, clean_brackets=True, clean_dashes=True)[source]#

Preprocess a UMLS term for matching purposes

Parameters

term (str) – Term to preprocess
lowercase (bool) – Whether term should be lowercased
normalize_unicode (bool) – Whether term_to_match should be ASCII-only (non-ASCII chars replaced by closest ASCII chars)
clean_nos (bool) – Whether to remove “NOS”
clean_brackets (bool) – Whether to remove brackets
clean_dashes (bool) – Wehther to remove dashes

guess_umls_version(path)[source]#

Try to infer UMLS version (ex: “2021AB”) from any UMLS-related path

Parameters

path (Union[str, Path]) – Path to the root directory of the UMLS install or any file inside that directory

Return type

str

Returns