Unified Medical Language System® (UMLS®)
2012AB SNOMED CT Source Information
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)
)| 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
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.)SAUI = DESCRIPTIONID STR = TERM SUPPRESSIBLE=N |
| 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
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.)SAUI = DESCRIPTIONID STR = TERM SUPPRESSIBLE=N |
| 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)
)| 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. |
Relationships (MRREL)
)| 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)
)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)
)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 |
