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Unified Medical Language System® (UMLS®)

2014AB UMLS NCBI Taxonomy Source Information

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


Skip to: Atoms, Attributes, Definitions, Relationships, Mappings

VSAB: NCBI2014_04_01

Summary of Changes

None

Notes:

Many concepts and terms from the NCBI Taxonomy are excluded during Metathesarus source processing.  The criteria for determining which concepts and terms are excluded or retained are outlined below.  See term type descriptions for additional information.

1.  Exclude all names that do not have one of the following name classes:
    scientific name
    synonym
    equivalent name
    common name
    authority

2.  Exclude all concepts below the "species" level in the hierarchy.  Selected concepts with a rank of "no rank" may be retained, depending on their hierarchical level.

3.  Exclude all concepts that have a "division id" value of 11 (environmental samples) and exclude their descendents.

4.  Exclude concepts and terms based on certain patterns, e.g. remove concepts with rank = "species" and the following words in the scientific name "uncultured," "clone," "unidentified," "uncultivated."

5.   Exclude concepts with ugly names (e.g., "xxxx", "4").

6.   Exclude concepts and their children if the information is enclosed in single or double quotes

7.   Exclude concepts starting with "other", "unclassified", "unclassified sequences", "artificial sequences", "insertion sequences", "midivariant sequence", "transposons" and all their children.

8.   Exclude concepts containing "?" and their children

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):

  (return to top)
Term Type Description
Origin
AUN
Authority name
CODE = names.dmp.tax_id
STRING = names.dmp.name_txt
SCUI = names.dmp.tax_id
 TTY = "AUN" is assigned where "name class" = "authority"
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"
UAUN
Unique authority name
CODE = names.dmp.tax_id
STRING = names.dmp.unique_name
SCUI = names.dmp.tax_id
 TTY = "UAUN" is assigned where "name class" = "authority"
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"
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"

Note on suppressibility:  For term types "AUN" and "UAUN," MRCONSO.SUPPRESS is set to "Y" 

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):

  (return to top)
Attribute Name Description
Origin
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):

  (return to top)

No definitions are included in the NCBI data.


Relationships (MRREL):

  (return to top)
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):

  (return to top)

No mappings are included in the NCBI data.
http://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NCBI/metarepresentation.html
www.nlm.nih.gov
crawl=CC-MAIN-2015-35
20131
application/http; msgtype=response
sha1:HW3GZQMM2WLTQYQQC6FPSCNEJYCZ6IQL
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2015-09-01T03:56:27Z
130.14.16.110
sha1:3EGOZD46ORQRLONLGWRFYVOJDW6HEDUG
<urn:uuid:237f99a7-d14a-4e60-8cb6-afb3421f6abe>
http://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NCBI/metarepresentation.html
response
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robots: classic
hostname: ip-10-171-96-226.ec2.internal
software: Nutch 1.6 (CC)/CC WarcExport 1.0
isPartOf: CC-MAIN-2015-35
operator: CommonCrawl Admin
description: Wide crawl of the web for August 2015
publisher: CommonCrawl
format: WARC File Format 1.0
conformsTo: http://bibnum.bnf.fr/WARC/WARC_ISO_28500_version1_latestdraft.pdf