open_umls_hierarchy

open_umls_hierarchy(version=None, *, api_key=None, force=False)[source]

Ensure and open a UMLS file from the given version.

Parameters:

version (Optional[str]) – The version of UMLS to ensure. If not given, is looked up with bioversions.
api_key (Optional[str]) – An API key. If not given, is looked up using pystow.get_config() with the umls module and api_key key.
force (bool) – Should the file be re-downloaded, even if it already exists?

Yields:

The file, which is used in the context manager.

This file contains the following columns:

CUI	Unique identifier of concept
AUI	Unique identifier of atom - variable length field, 8 or 9 characters
CXN	Context number (e.g., 1, 2, 3)
PAUI	Unique identifier of atom’s immediate parent within this context
SAB	Abbreviated source name (SAB) of the source of atom
RELA	Relationship of atom to its immediate parent
PTR	Path to the top or root of the hierarchical context from this atom.
HCD	Source asserted hierarchical number or code for this atom in this context.
CVF	Content View Flag. Bit field used to flag rows included in Content View.