Unified Medical Language System® (UMLS®)
2012AB NCBI Taxonomy Source Information
VSAB: NCBI2012_04_16
Summary of Changes
1) Dropped term type (TTY):- UE
- UNIQ_UNPUBL_NAME
- UNPUBL_NAME
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 information1. 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."
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 |
|---|---|---|
| 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):
)| 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 |
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.
