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Unified Medical Language System® (UMLS®)

2012AB US Extension to SNOMED CT Source Information




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Notes

The RF1 format files were processed for SCTUSX_2012_09_01.  Metathesaurus SCTUSX data is extracted from the following tab-delimited files:

SnomedCT_Release_US1000124_20120901/RF1Release/Terminology/Content:
  • sct1_Concepts_US1000124_20120901.txt
    sct1_Descriptions_en-US_US1000124_20120901.txt
    sct1_Relationships_US1000124_20120901.txt
SnomedCT_Release_US1000124_20120901/RF1Release/Subsets/Language-en-US/
  • der1_SubsetMembers_en-US_US1000124_20120901.txt
    der1_Subsets_en-US_US1000124_20120901.txt
Note:  The SCTUSX hierarchy is designed as an extension to the SNOMEDCT hierarchy.  Due to complications in representing a mixed-source hierarchy, the SCTUSX hierarchy is not represented in MRHIER.RRF, however it is represented in MRREL.RRF as follows: 
  • REL/REL_INVERSE:  PAR/CHD
  • RELA/RELA_INVERSE:  inverse_isa/isa

Summary of Changes

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The directory structure and file names for the SCTUSX release have changed, however there are no changes to processing of files in the Terminology subdirectory.

The SCTUSX_2012_09_01 release includes a "Subsets/Language-en-US" subdirectory which was not present in the previous release.  These files were processed in accordance with the SNOMEDCT RF1 subset file processing.

New ATNs:
    REFINABILITY and CHARACTERISTICTYPE are included in SCTUSX_2012_09_01.  These attributes were omitted from SCTUSX_2012_03_01


Summary of Source-Provided Files

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Documentation and Reference (RF1):

Documentation for the RF1 format can be found in the SNOMEDCT release:

File Name Description
Readme_en_20120731.txt Lists the files included in the release
doc_TechnicalImplementationGuide_Current-en-US_INT_20120731.pdf Technical Implementation Guide
doc_EditorialGuide_Current-en-US_INT_20120731.pdf Editorial Guide
doc_IhtsdoGlossary_Current-en-US_INT_20120731.pdf
Glossary (draft)
doc_RF1Guide_Current-en-US_INT_20120731.pdf
RF1 Guide
doc_NamespaceIdentifierRegistry_Current-en-US_INT_20120731.pdf Namespece Identifier Registry
doc_ScopeMemo_Current-en-US_INT_20120731.pdf Scope Memo
doc_UserGuide_Current-en-US_INT_20120731.pdf User Guide
doc1_CanonicalTableGuide_Current-en-US_INT_20120731.pdf Canonical Table Guide
doc_DeveloperToolkitGuide_Current-en-US_INT_20120731.pdf Developer Toolkit Guide


Data Files

File Name Description
sct1_Concepts_US1000124_20120901.txt Concepts - Tab-Delimited Format
sct1_Descriptions_en-US_US1000124_20120901.txt Descriptions - Tab-Delimited Format
sct1_Relationships_US1000124_20120901.txt Relationships - Tab-Delimited Format
sct1_ComponentHistory_US1000124_20120901.txt Component History - Tab-Delimited Format
sct1_References_US1000124_20120901.txt References for inactive components - Tab-Delimited Format
der1_Subsets_en-US_US1000124_20120901.txt US English dialect subsets - Tab-Delimited Format
der1_SubsetMembers_en-US_US1000124_20120901.txt US English dialect subset members - Tab Delimited Format

* Certain fields and files may not be directly processed because they contain redundant data or are not part of the core SNOMED CT data.

Source-Provided File Details

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Details on format of input files and representation of source data. Consult the SNOMED CT documentation for additional details.

file:sct1_Concepts_US1000124_yyyymmdd.txt

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Concepts

# Field Name Description Representation
1 CONCEPTID SCTSUX concept ID MRSAT.CUI populated by the Metathesaurus CUI corresponding to CONCEPTID.
2 CONCEPTSTATUS Concept Status MRSAT.ATN="CONCEPTSTATUS"
3 FULLYSPECIFIEDNAME Fully-specified concept name with top-level hierarchical location appended in parentheses (Not processed - these names also appear as entries in the Descriptions table having DESCRIPTIONTYPE=3.)
4 CTV3ID Not populated for SCTUSX
Not applicable
5 SNOMEDID Not populated for SCTUSX
Not applicable
6 ISPRIMITIVE Primitive flag - indicates whether concept is primitive or fully defined MRSAT.ATN="ISPRIMITIVE"

file:sct1_Descriptions_en-US_US1000124_yyyymmdd.txt

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Descriptions

# Field Name Description Representation
1 DESCRIPTIONID SCTUSX_Description ID MRCONSO.SAUI
2 DESCRIPTIONSTATUS* Description Status MRSAT.ATN="DESCRIPTIONSTATUS"

A combination of the "DESCRIPTIONSTATUS," "DESCRIPTIONTYPE," and "LANGUAGECODE" values are used to determine MRCONSO.TTY assignment
3 CONCEPTID Concept ID of the associated concept MRCONSO.SCUI and MRCONSO.CODE; for attributes, MRSAT.CUI populated by the Metathesaurus CUI corresponding to CONCEPTID
4 TERM Text of a term used to describe the associated concept MRCONSO.STR
5 INITIALCAPITALSTATUS 1=capitalization status of first character of TERM is significant,
0=capitalization status of first character of TERM is not significant
MRSAT.ATN="INITIALCAPITALSTATUS"
6 DESCRIPTIONTYPE* Indicates whether the term is the Preferred Term (1), a Synonym (2), or the FullySpecifiedName (3) of the associated concept; a value of 0 indicates the type will be assigned by a Subset that includes the term MRSAT.ATN="DESCRIPTIONTYPE"

A combination of the "DESCRIPTIONSTATUS," "DESCRIPTIONTYPE," and "LANGUAGECODE" values are used to determine MRCONSO.TTY assignment
7 LANGUAGECODE* The 2-character ISO639-1 code indicating the language of the term, optionally followed by a hyphen and a subcode string indicating a dialect; if the dialect is general to an entire country, the subcode will be the two-letter ISO 3166 country code MRSAT.ATN="LANGUAGECODE"

A combination of the "DESCRIPTIONSTATUS," "DESCRIPTIONTYPE," and "LANGUAGECODE" values are used to determine MRCONSO.TTY assignment

 *  TTY assignment is based on a combination of fields from sct1_Descriptions_en-US_US1000124_yyyymmdd.txt: DESCRIPTIONSTATUS, DESCRIPTIONTYPE, and LANGUAGECODE.  The assignments are as follows:

DESCRIPTIONSTATUS DESCRIPTIONTYPE LANGUAGECODE TTY
0 1 en-US PT
0 2 en SY
0
2
en-US
SY
0 3 en FN
0
3
en-US
FN
5
1 en OP
5
2 en IS
5
3 en OF
8 1 en OP
8
1
en-US
OP
8 2 en IS
8
2
en-US
IS
8 3 en-US OF

file:sct1_Relationships_US1000124_yyyymmdd.txt


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Relationships

# Field Name Description Representation
1 RELATIONSHIPID SCTUSX Relationship ID MRREL.SRUI
2 CONCEPTID1 SNOMEDCT or SCTUSX Concept ID of relationship's source concept MRREL.CUI2 populated by the Metathesaurus CUI corresponding to CONCEPTID1
3 RELATIONSHIPTYPE SNOMEDCT Concept ID of concept representing the relationship between the related concepts A relationship-name mapping is used to set MRREL.REL and MRREL.RELA based on this value.

These mappings are expressed as attributes with MRSAT.ATN="UMLSREL" and MRSAT.ATN="UMLSRELA", specifying the REL and RELA values used for eacah RELATIONSHIPTYPE.
4 CONCEPTID2 SNOMEDCT or SCTUSX Concept ID of relationship's target concept MRREL.CUI1 populated by the Metathesaurus CUI corresponding to CONCEPTID2
5 CHARACTERISTICTYPE Indicates whether this relationship is a defining (0) or historical (2) MRSAT.ATN="CHARACTERISTICTYPE" where MRSAT.METAUI is the MRREL.RUI assigned where MRREL.SRUI = this relationship's RELATIONSHIPID
6 REFINABILITY Indicates whether the target concept may (1), or may not (0) be refined when using this relationship as a clinical data entry template. MRSAT.ATN="REFINABILITY" where MRSAT.METAUI is the MRREL.RUI assigned where MRREL.SRUI = this relationship's RELATIONSHIPID
7 RELATIONSHIPGROUP An integer indicating whether this relationship is (if non-zero) or is not (if 0) associated with other relationships. When non-zero, all relationships having the same CONCEPTID1 and RELATIONSHIPGROUP values are associated. MRREL.RG

file:sct1_ComponentHistory_US1000124_yyyymmdd.txt

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Component History

# Field Name Description Representation
1 COMPONENTID SCTUSX ID for the changed component MRHIST.SOURCEUI
MRHIST.CHANGEKEY = DESCRIPTIONSTATUS if COMPONENTID is a DESCRIPTIONID
MRHIST.CHANGEKEY = CONCEPTSTATUS if COMPONENTID is a CONCEPTID
2 RELEASEVERSION SCTUSX version in which the change was made MRHIST.SVER
3 CHANGETYPE Indicates the type of change that occurred MRHIST.CHANGETYPE
4 STATUS Indicates the component's status after the change MRHIST.CHANGEVAL
5 REASON Textual description of the reason for the change MRHIST.REASON

file:sct1_References_US1000124_yyyymmdd.txt

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References for inactive components

# Field Name Description Representation
1 COMPONENTID SCTUSX ID for the inactive component MRREL.CUI2 populated by the Metathesaurus CUI corresponding to COMPONENTID
2 REFERENCETYPE Indicates type of relationship between the inactive component and the referenced component MRREL.REL and MRREL.RELA mapped from REFERENCETYPE
3 REFERENCEDID SCTUSX ID for the referenced component MRREL.CUI1 populated by the Metathesaurus CUI corresponding to REFERENCEDID


file:der1_Subsets_en-US_US1000124_.txt

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References for inactive components

# Field Name Description Representation
1 SUBSETID SCTUSX ID for this subset
MRCONSO.SCUI and CODE for an atom with SAB = "SCTUSX", TTY = "SB";
for attributes, MRSAT.SCUI populated by the Metathesaurus CUI corresponding to the SB atom for this SUBSETID
2 SUBSETORIGINALID The SCTUSX ID of the original subset of which this is an updated version
MRSAT.ATN = "SUBSETORIGINALID"
3 SUBSETVERSION The version number of this release of the subset
MRSAT.ATN = "SUBSETVERSION"
4
SUBSETNAME
The name of this subset
MRCONSO.STR for the SCTUSX/SB atom with CODE = SUBSETID
5
SUBSETTYPE
Indicates the type of the subset and what kind of components it includes
MRSAT.ATN = "SUBSETTYPE"
6
LANGUAGECODE
The 2-character ISO639-1 code indicating the language of the subset, optionally followed by a hyphen and a subcode string indicating a dialect;  if the dialect is general to an entire country, the subcode will be the two-letter ISO 3166 country code
MRSAT.ATN = "SUBSETLANGUAGECODE"

file:der1_SubsetMembers_en-US_US1000124_yyyymmdd.txt

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References for inactive components

# Field Name Description Representation
1 SUBSETID SCTUSX ID of the subset containing this member
First ~ - separated component of MRSAT.ATV where MRSAT.ATN = "SUBSETMEMBER"
2 MEMBERID SCTUSX ID of this subset member (may be a description, concept or relationship ID)
MRSAT.METAUI for MRSAT.ATN = "SUBSETMEMBER" populated by the Metathesaurus AUI corresponding to MEMBERID
3 MEMBERSTATUS Integer specifying the type, status or order of this member in this subset
Second ~ - separated component of MRSAT.ATV where MRSAT.ATN = "SUBSETMEMBER"
4
LINKEDID
(valid for Navigation and Duplicate Terms subsets only)
N/A