UMLS Vocabularies

A

B

C

D

F

G

H

I

J

JABL

K

KCD5

M

N

O

P

Q

R

S

T

TKMT

U

V

VANDF

W

NCBI (NCBI Taxonomy) - Metathesaurus Representation

This page lists UMLS Metathesaurus data elements and traces them back to the specific source data that populates them.

VSAB: NCBI2023_04_13

Summary of Changes

No changes were made to the source data format or to Metathesaurus source processing

Notes:

The UMLS includes concepts where the "specified_species" value in nodes.dmp = 1, indicating that a species in the node's lineage has a formal name. All higher level concepts needed to make a complete hierarchy are also included. Other concepts are excluded.

Source file: taxdmp.zip.
Files included in taxdmp.zip are:

File	Description
citations.dmp	Citations (not directly processed)
delnodes.dmp	Deleted nodes (not directly processed)
division.dmp	Divisions
gc.prt	Genetic code table (not directly processed)
gencode.dmp	Genetic codes (not directly processed)
merged.dmp	Merged nodes (not directly processed)
names.dmp	Taxonomy names
nodes.dmp	Taxonomy nodes (hierarchy)
readme.txt	README file

Identifiers:

Identifiers are assigned as follows:

CODE: names.dmp.tax_id
SAUI: not applicable
SCUI: names.dmp.tax_id
SDUI: not applicable

Atoms (MRCONSO):

Term Type	Description	Origin
CMN	Common name	CODE = names.dmp.tax_id STRING = names.dmp.name_txt SCUI = names.dmp.tax_id TTY = "CMN" is assigned where "name class" = "common name"
EQ	Equivalent name	CODE = names.dmp.tax_id STRING = names.dmp.name_txt SCUI = names.dmp.tax_id TTY = "EQ" is assigned where "name class" = "equivalent name"
SCN	Scientific name	CODE = names.dmp.tax_id STRING = names.dmp.name_txt SCUI = names.dmp.tax_id TTY = "SCN" is assigned where "name class" = "scientific name"
SY	Designated synonym	CODE = names.dmp.tax_id STRING = names.dmp.name_txt SCUI = names.dmp.tax_id TTY = "SY" is assigned where "name class" = "synonym"
UCN	Unique common name	CODE = names.dmp.tax_id STRING = names.dmp.unique_name SCUI = names.dmp.tax_id TTY = "UCN" is assigned where "name class" = "common name"
UE	Unique equivalent name	CODE = names.dmp.tax_id STRING = names.dump.unique_name SCUI = namese.dmp.tax_id TTY = "UE" is assigned where "name class" = "equivalent name"
USN	Unique scientific name	CODE = names.dmp.tax_id STRING = names.dmp.unique_name SCUI = names.dmp.tax_id TTY = "USN" is assigned where "name class" = "scientific name"
USY	Unique synonym	CODE = names.dmp.tax_id STRING = names.dmp.unique_name SCUI = names.dmp.tax_id TTY = "USY" is assigned where "name class" = "synonym"

Atoms with other term types may systematically be set to "E" based on certain string patterns which indicate ambiguity or are not terminologically useful. In addition, for term types other than "SCN," if names.dmp contains a "unique_name," the atom created from "name_txt" will have SUPPRESS set to "E."

Attributes (MRSAT):

Attribute Name	Description	Origin
AUTHORITY_NAME	Authority name	names.dmp.name	Created where class = "authority"
DIV	Division/phyla	nodes.dmp.division id The ATV is the textual value of the "division id" from division.dmp
RANK	Taxonomic rank (e.g. kingdom, species, etc.)	nodes.dmp.rank

Definitions (MRDEF):

No definitions are included in the NCBI data.

Relationships (MRREL):

REL	RELA Inverse RELA	ORIGIN
PAR CHD	(no RELA)	nodes.dmp.parent tax_id
SY	expanded_form_of has_expanded_form	Connects names.dmp.name_txt to names.dmp.unique_name

Mappings (MRMAP):

No mappings are included in the NCBI data.

Unified Medical Language System (UMLS)