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Unified Medical Language System® (UMLS®)

2012AB SNOMED CT Source Information




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

VSAB: SNOMEDCT_2012_07_31

Summary of Changes

There have been no changes to the SNOMEDCT format or processing of the data, however atoms with DESCRIPTIONSTATUS = 7 (Inappropriate) have been assigned TTYs as follows:

DESCRIPTIONTYPE DESCRIPTIONSTATUS LANG
TTY
SUPPRESS
LAT
2 7
en-GB
IS
O
ENG
1 7
en
OP
O
ENG
1 7
en-GB
OP
O
ENG

In the future, the new SNOMEDCT RF2 format will be processed, and this document will be updated to reflect the changes.

Original Files:


The Metathesaurus SNOMEDCT data is taken from the following tab-delimited SNOMEDCT files, found in the specified folders:
  • SnomedCT_Release_INT_20120731/RF1Release/Terminology/Content:
    • sct1_Concepts_Core_INT_20120731.txt
    • sct1_Descriptions_en_INT_20120731.txt
    • sct1_Relationships_Core_INT_20120731.txt
  • SnomedCT_Release_INT_201207311/RF1Release/Terminology/History:
    • sct1_ComponentHistory_Core_INT_20120731.txt
    • sct1_References_Core_INT_20120731.txt
  • SnomedCT_Release_INT_20120731/RF1Release/CrossMaps/ICD9:
    • der1_CrossMaps_ICD9_INT_20120731.txt
    • der1_CrossMapSets_ICD9_INT_20120731.txt
    • der1_CrossMapTargets_ICD9_INT_20120731.txt
  • SnomedCT_Release_INT_20120731/RF1Release/OtherResources/TextDefinitions:
    • sct1_TextDefinitions_en-US_INT_20120731.txt
  • SnomedCT_Release_INT_20120731/RF1Release/Subsets/Language-en-US:
    • der1_Subsets_en-US_INT_20120731.txt
    • der1_SubsetMembers_en-US_INT_20120731.txt
  • SnomedCT_Release_INT_20120731/RF1Release/Subsets/Language-en-GB:
    • der1_Subsets_en-GB_INT_20120731.txt
    • der1_SubsetMembers_en-GB_INT_20120731.txt

Identifiers


Identifiers are assigned as follows:
  • CODE: CONCEPTID
  • SAUI: DESCRIPTIONID
  • SCUI: Same as CODE
  • SDUI: Not Applicable

Atoms (MRCONSO)

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Term Type Origin
FN An FN (Fully Specified Name) atom is created for each line of sct1_Descriptions_en_INT_yyyymmdd.txt having DESCRIPTIONTYPE=3, DESCRIPTIONSTATUS=0, and a LANGUAGECODE of "en" as follows:
CODE, SCUI = CONCEPTID
SAUI = DESCRIPTIONID
STR = TERM
SUPPRESSIBLE=N
OF An OF (Obsolete Fully specified name) atom is created for each line of sct1_Descriptions_en_INT_yyyymmdd.txt having DESCRIPTIONTYPE=3, a DESCRIPTIONSTATUS other than 0, and a LANGUAGECODE of "en" as follows:
CODE, SCUI = CONCEPTID
SAUI = DESCRIPTIONID
STR = TERM
SUPPRESSIBLE=O
PT A PT (Preferred Term) atom is created for each line of sct1_Descriptions_en_INT_yyyymmdd.txt having DESCRIPTIONTYPE=1, DESCRIPTIONSTATUS=0, and a LANGUAGECODE of "en" or "en-US", as follows:
CODE, SCUI = CONCEPTID
SAUI = DESCRIPTIONID
STR = TERM
SUPPRESSIBLE=N
PT atoms are also created for lines of sct1_Descriptions_en_INT_yyyymmdd.txt having DESCRIPTIONTYPE=0 and DESCRIPTIONSTATUS=0 if, when you look up that line's DESCRIPTIONID in the MEMBERID field of the der1_Subsets_en-US_INT_yyyymmdd.txt file, the value of MEMBERSTATUS is 1. (Note that these atoms are actually preferred only in the US English subset and are synonyms in the GB English subset.)
PTGB A PTGB (Preferred Term in the GB English dialect) atom is created for each line of sct1_Descriptions_en_INT_yyyymmdd.txt having DESCRIPTIONTYPE=1, DESCRIPTIONSTATUS=0, and a LANGUAGECODE of "en-GB", as follows:
CODE, SCUI = CONCEPTID
SAUI = DESCRIPTIONID
STR = TERM
SUPPRESSIBLE=N
OP An OP (Obsolete Preferred term) atom is created for each line of sct1_Descriptions_en_INT_yyyymmdd.txt having DESCRIPTIONTYPE=1 and a DESCRIPTIONSTATUS other than 0, as follows:
CODE, SCUI = CONCEPTID
SAUI = DESCRIPTIONID
STR = TERM
SUPPRESSIBLE=O
SY An SY (Synonym) atom is created for each line of sct1_Descriptions_en_INT_yyyymmdd.txt having DESCRIPTIONTYPE=2, DESCRIPTIONSTATUS=0, and a LANGUAGECODE of "en" or "en-US", as follows:
CODE, SCUI = CONCEPTID
SAUI = DESCRIPTIONID
STR = TERM
SUPPRESSIBLE=N
SY atoms are also created for lines of sct1_Descriptions_en_INT_yyyymmdd.txt having DESCRIPTIONTYPE=0 and DESCRIPTIONSTATUS=0 if, when you look up that line's DESCRIPTIONID in the MEMBERID field of the der1_Subsets_en-US_INT_yyyymmdd.txt file, the value of MEMBERSTATUS is 2. (Note that these atoms are actually synonyms only in the US English subset and are preferred in the GB English subset.)
SYGB An SYGB (Synonym in the GB English dialect) atom is created for each line of sct1_Descriptions_en_INT_yyyymmdd.txt having DESCRIPTIONTYPE=2, DESCRIPTIONSTATUS=0, and a LANGUAGECODE of "en-GB", as follows:
CODE, SCUI = CONCEPTID
SAUI = DESCRIPTIONID
STR = TERM
SUPPRESSIBLE=N
IS An IS (obsolete Synonym) atom is created for each line of sct1_Descriptions_en_INT_yyyymmdd.txt having DESCRIPTIONTYPE=2 and a DESCRIPTIONSTATUS other than 0, as follows:
CODE, SCUI = CONCEPTID
SAUI = DESCRIPTIONID
STR = TERM
SUPPRESSIBLE=O
MTH_FN
MTH_OF
MTH_PT
MTH_PTGB
MTH_OP
MTH_SY
MTH_SYGB
MTH_IS
Special MTH_* forms are algorithmically generated for atoms with the termtypes listed above, in two situations:
(1) If the STR contains one or more non-ASCII UTF-8 characters, an MTH_* form is generated in which these characters are converted to pure ASCII using the -f:q5 flow of the UMLS lvg (lexical variant generation) tool

(2) If the STR contains the markup syntax SNOMEDCT uses to indicate superscripts ("^sup^") and/or subscripts (">sub<"), two MTH_* forms are generated:
1. One in which the markup syntax is removed, e.g., "CO>2<" becomes "CO2"
2. One in which the markup syntax is converted to an xml-style syntax using "<sup> for superscripts and "<sub>" for subscripts, e.g., "CO>2<" becomes "CO<sub>2</sub>".



This data is added during Metathesaurus source processing
SB One SB (Subset) atom is generated for each line of der1_Subsets_en-GB_INT_yyyymmdd.txt and der1_Subsets_en-US_INT_yyyymmdd.txt, as follows:
CODE, SCUI = SUBSETID
STR = SUBSETNAME
XM One XM (cross Mapping set) atom is generated for each line of der1_CrossMapSets_ICD9_INT_yyyymmdd.txt, as follows:
CODE, SCUI = MAPSETID
STR = "SNOMEDCT_yyyy_mm_dd to ICD9CM_vvvv Mappings" (where vvvv is the value of MAPSETSCHEMEVERSION)

Attributes (MRSAT)

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Attribute Name STYPE Origin
AQ SCUI Used for "allowed qualifier" relationships from sct1_Relationships_Core_INT_yyyymmdd.txt, where CHARACTERISTICTYPE=1 (qualifier) and REFINABILITY=2 (mandatory)
CHARACTERISTICTYPE RUI CHARACTERISTICTYPE from sct1_Relationships_Core_INT_yyyymmdd.txt
CONCEPTSTATUS SCUI CONCEPTSTATUS from sct1_Concepts_Core_INT_yyyymmdd.txt
CTV3ID SCUI CTV3ID from sct1_Concepts_Core_INT_yyyymmdd.txt
DESCRIPTIONSTATUS AUI DESCRIPTIONSTATUS from sct1_Descriptions_en_INT_yyyymmdd.txt
DESCRIPTIONTYPE AUI DESCRIPTIONTYPE from sct1_Descriptions_en_INT_yyyymmdd.txt
FROMRSAB CODE "SNOMEDCT", attached to the XM atom for the Cross Map Set
FROMVSAB CODE "SNOMEDCT_yyyy_mm_dd", attached to the XM atom for the Cross Map Set
INITIALCAPITALSTATUS AUI INITIALCAPITALSTATUS from sct1_Descriptions_en_INT_yyyymmdd.txt
ISPRIMITIVE SCUI ISPRIMITIVE from sct1_Concepts_Core_INT_yyyymmdd.txt
LANGUAGECODE AUI LANGUAGECODE from sct1_Descriptions_en_INT_yyyymmdd.txt
MAPSETNAME CODE MAPSETNAME from der1_CrossMapSets_ICD9_INT_yyyymmdd.txt, attached to the XM atom for the Cross Map Set
MAPSETREALMID CODE MAPSETREALMID from der1_CrossMapSets_ICD9_INT_yyyymmdd.txt, attached to the XM atom for the Cross Map Set
MAPSETRSAB CODE "SNOMEDCT", attached to the XM atom for the Cross Map Set
MAPSETRULETYPE CODE MAPSETRULETYPE from der1_CrossMapSets_ICD9_INT_yyyymmdd.txt, attached to the XM atom for the Cross Map Set
MAPSETSCHEMEID CODE MAPSETSCHEMEID from der1_CrossMapSets_ICD9_INT_yyyymmdd.txt, attached to the XM atom for the Cross Map Set
MAPSETSCHEMENAME CODE MAPSETSCHEMENAME from der1_CrossMapSets_ICD9_INT_yyyymmdd.txt, attached to the XM atom for the Cross Map Set
MAPSETSCHEMEVERSION CODE MAPSETSCHEMEVERSION from der1_CrossMapSets_ICD9_INT_yyyymmdd.txt, attached to the XM atom for the Cross Map Set
MAPSETSEPARATORCODE CODE XML character entity for MAPSETSEPARATOR from der1_CrossMapSets_ICD9_INT_yyyymmdd.txt, attached to the XM atom for the Cross Map Set
MAPSETSID CODE MAPSETSID from der1_CrossMapSets_ICD9_INT_yyyymmdd.txt, attached to the XM atom for the Cross Map Set
MAPSETTYPE CODE MAPSETTYPE from der1_CrossMapSets_ICD9_INT_yyyymmdd.txt, attached to the XM atom for the Cross Map Set
MAPSETVERSION CODE MAPSETVERSION from der1_CrossMapSets_ICD9_INT_yyyymmdd.txt, attached to the XM atom for the Cross Map Set
MAPSETVSAB CODE "SNOMEDCT_yyyy_mm_dd", attached to the XM atom for the Cross Map Set
MAPSETXRTARGETID CODE TARGETID from der1_CrossMapTargets_ICD9_INT_yyyymmdd.txt where TARGETCODES is blank, attached to the XM atom for the Cross Map Set
MTH_MAPFROMCOMPLEXITY CODE "SINGLE_SCUI", attached to the XM atom for the Cross Map Set;  this data is added during Metathesaurus Source processing.
MTH_MAPFROMEXHAUSTIVE CODE "N", attached to the XM atom for the Cross Map Set;  this data is added during Metathesaurus Source processing
MTH_MAPSETCOMPLEXITY CODE "N TO ONE", attached to the XM atom for the Cross Map Set;  this data is added during Metathesaurus Source processing
MTH_MAPTOCOMPLEXITY CODE "SINGLE CODE, MULTIPLE CODE", attached to the XM atom for the Cross Map Set;  this data is added during Metathesaurus Source processing
MTH_MAPTOEXHAUSTIVE CODE "N", attached to the XM atom for the Cross Map Set;  this data is added during Metathesaurus Source processing
MTH_UMLSMAPSETSEPARATOR CODE "AND", attached to the XM atom for the Cross Map Set;  this data is added during Metathesaurus Source processing
REFINABILITY RUI REFINABILITY from sct1_Relationships_Core_INT_yyyymmdd.txt
SNOMEDID SCUI SNOMEDID from sct1_Concepts_Core_INT_yyyymmdd.txt
SOS CODE "This set maps SNOMEDCT concept identifiers to ICD-9-Cm codes; a single SNOMEDCT conce pt id may be mapped to one or more ICD-9-CM codes", attached to the XM atom for the Cross Map Set
SUBSETCONTEXTID AUI CONTEXTID from der1_Subsets_en-GB_INT_yyyymmdd.txt and der1_Subsets_en-US_INT_yyyymmdd.txt
SUBSETLANGUAGECODE AUI LANGUAGECODE from der1_Subsets_en-GB_INT_yyyymmdd.txt and der1_Subsets_en-US_INT_yyyymmdd.txt
SUBSETMEMBER AUI Has 3 components, separated by "~" characters: SUBSETID, MEMBERSTATUS, and LINKEDID, from der1_SubsetMembers_en-GB_INT_yyyymmdd.txt and der1_SubsetMembers_en-US_INT_yyyymmdd.txt
SUBSETORIGINALID AUI SUBSETORIGINALID from der1_Subsets_en-GB_INT_yyyymmdd.txt and der1_Subsets_en-US_INT_yyyymmdd.txt
SUBSETREALMID AUI REALMID from der1_Subsets_en-GB_INT_yyyymmdd.txt and der1_Subsets_en-US_INT_yyyymmdd.txt
SUBSETTYPE AUI SUBSETTYPE from der1_Subsets_en-GB_INT_yyyymmdd.txt and der1_Subsets_en-US_INT_yyyymmdd.txt
SUBSETVERSION AUI SUBSETVERSION from der1_Subsets_en-GB_INT_yyyymmdd.txt and der1_Subsets_en-US_INT_yyyymmdd.txt
TARGETSCHEMEID CODE TARGETSCHEMEID from der1_CrossMapTargets_ICD9_INT_yyyymmdd.txt (which is the same for all cross map targets), attached to the XM atom for the Cross Map Set
TORSAB CODE The RSAB ("ICD9CM") corresponding to the MAPSETSCHEMENAME from der1_CrossMapSets_ICD9_INT_yyyymmdd.txt
TOVSAB CODE The VSAB ("ICD9CM_yyyy") corresponding to the MAPSETSCHEMENAME and MAPSETSCHEMEVERSION from der1_CrossMapSets_ICD9_INT_yyyymmdd.txt
UMLSREL SCUI The relationship type for MRREL.RRF, attached to the atoms for each RELATIONSHIPTYPE value used in sct1_Relationships_Core_INT_yyyymmdd.txt. Note that this will normally be the same as the REL value used in MRREL.RRF for this relationship, except that when the UMLSREL value is given as "RT" or "NT", the REL value in MRREL.RRF will be "RO" or "RN", respectively.
UMLSRELA SCUI The RELA value used in MRREL.RRF, attached to the atoms for each RELATIONSHIPTYPE value used in sct1_Relationships_Core_INT_yyyymmdd.txt.

Definitions (MRDEF)

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ORIGIN
Taken from the sct1_TextDefinitions_en-US_INT_yyyymmdd.txt file

Relationships (MRREL)

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REL RELA/Inverse RELA ORIGIN
CHD
PAR
(blank) Hierarchical relationships are derived from rows of sct1_Relationships_Core_INT_yyyymmdd.txt where RELATIONSHIPTYPE is 116680003 ("Is a").
RB
RN
RO
SY
 (many RELA values) These are derived from rows of sct1_Relationships_Core_INT_yyyymmdd.txt where RELATIONSHIPTYPE is not 116680003 ("Is a"). The REL and RELA values used for each RELATIONSHIPTYPE are specified by UMLSREL and UMLSRELA attributes, respectively (see above).
RQ mapped_from, mapped_to These are a representation of the simple cross maps in der1_CrossMaps_ICD9_INT_yyyymmdd.txt where there is only one ICD9CM code in the TARGETCODES field.

Mappings (MRMAP)

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The Metathesaurus includes SNOMEDCT's mappings (an XM atom, along with associated attributes and mappings) to ICD9CM. These are taken from the der1_CrossMapSets_ICD9_INT_yyyymmdd.txt, der1_CrossMapTargets_ICD9_INT_yyyymmdd.txt, and der1_CrossMaps_ICD9_INT_yyyymmdd.txt files.


History (MRHIST)

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All SNOMEDCT data is extracted from sct1_ComponentHistory_Core_INT_yyyymmdd.txt:

COLUMN
ORIGIN
SOURCEUI COMPONENTID
SVER
RELEASEVERSION
CHANGETYPE
CHANGETYPE
CHANGEKEY
DESCRIPTIONSTATUS if COMPONENTID is a DESCRIPTIONID
CONCEPTSTATUS if COMPONENTID is a CONCEPTID
CHANGEVAL
STATUS
REASON
REASON