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Unified Medical Language System® (UMLS®)


Insertion of SNOMED CT® into the UMLS® Metathesaurus®: Explanatory Notes

Introduction

SNOMED CT was first available from the UMLS Metathesaurus in the 2004AA release. Until the 2005AB release, only the active core SNOMED CT content (i.e., concepts and concept names with status of 0 – 'current' or 6 – 'limited') was included. From 2005AC onwards, the obsolete SNOMED CT content has also been incorporated. Apart from the core English content, the Spanish SNOMED CT and a set of mappings from SNOMED CT to ICD-9-CM are also available from the UMLS.

Intentional Differences between SNOMED CT and UMLS Concept Structures

There are cases in which concept names assigned different meanings in SNOMED CT are viewed as synonyms in the UMLS Metathesaurus and vice versa. Although the Metathesaurus concept structure differs from that of SNOMED CT for about 14% of SNOMED CT concepts, by the principle of source transparency, the original SNOMED CT representation is always preserved and can be retrieved or reconstructed from the Metathesaurus.

The great majority of the differences between the concept structures of SNOMED CT and the UMLS Metathesaurus are due to a few differences in their concept models. In several cases, SNOMED CT's description logic defines as distinct concepts what the Metathesaurus sees as different perspectives on a single concept. Some of the principal cases are outlined below:

1. substance / product

SNOMED CT has distinct concepts for drug classes and ingredients . The UMLS Metathesaurus does not. For example, the UMLS Metathesaurus views the following as synonymous:

Aspirin (substance)
Aspirin (product)

In SNOMED CT, the above concepts are linked by the attribute "has active ingredient". This relationship is represented in the Metathesaurus as a SNOMED-asserted relationship between two SNOMED CT concept names within the same UMLS concept.

2. morphologic abnormality / clinical finding

SNOMED CT makes distinction between some morphologic abnormality and clinical finding concepts which the UMLS Metathesaurus sees as synonymous e.g.

Glomus tumor (morphologic abnormality)
Glomus tumor (disorder)

In SNOMED CT, the above concepts are linked by the "associated morphology"attribute. This relationship is represented in the Metathesaurus as a SNOMED-asserted relationship between two SNOMED CT concept names within the same UMLS concept.

3. clinical finding / {observable entity, situation with explicit context}

SNOMED CT makes distinction between some clinical finding, observable entity and situation with explicit context concepts which the UMLS Metathesaurus does not. For example, the UMLS Metathesaurus views each of the following pairs as synonymous concepts:

Crying (finding)
Crying (observable entity)

Nasal obstruction (finding)
Nasal obstruction present (situation)

Possibly Unintentional Differences, including Missed Synonymy

In inserting any source vocabulary into the UMLS Metathesaurus, NLM employs a rigorous protocol of lexical normalization and matching in addition to manual review. This process uncovered a relatively few cases of apparent missed synonymy within SNOMED CT. The synonymous SNOMED CT concepts are merged in the same UMLS concept. There are also a small number of cases where terms labeled as synonyms in SNOMED CT were split into different concepts in the Metathesaurus. One example is the splitting of the SNOMED CT synonym ‘Motor vehicle accident’ from the SNOMED CT concept ‘Motor vehicle accident victim (finding)’. All these cases have been communicated to the College of American Pathologists for possible revision in future versions of SNOMED CT.

Location of SNOMED CT Fields within the UMLS Metathesaurus Files

For users who are familiar with the file formats of SNOMED CT, the following tables will help to navigate the Metathesaurus files to retrieve the fields from the three main SNOMED CT tables. To retrieve preferred names and synonyms of a concept, it is easier to make use of the TTY field in MRCONSO.RRF (or MRSO in the UMLS Original Release Format (ORF)) than going through the DescriptionType value from MRSAT.RRF (or MRSAT). The TTYs FN, PT and SY correspond to Fully Specified Name, Preferred and Synonym description types in SNOMED CT. In cases where the British spelling differs from the American spelling, the British preferred names and synonyms are given the TTYs PTGB and SYGB respectively. For details, see the FullySpecifiedName rows in the following tables. For the sake of conciseness, relations and attributes of a SNOMED CT concept are only represented once using the PT atom as the proxy for the concept, instead of being repeated for every atom of the concept.

For the new UMLS Rich Release Format (RRF):

SNOMED CT tables and fields UMLS Metathesaurus tables and fields
Corresponding field and table in Metathesaurus Sample SQL statements
( SAB = 'SNOMEDCT' is used to label data from SNOMED CT in all tables)
CONCEPTS
ConceptId SCUI or CODE in MRCONSO.RRF SELECT SCUI FROM MRCONSO.RRF will get all ConceptIds
ConceptStatus ATV in MRSAT.RRF SELECT ATV FROM MRSAT.RRF WHERE CODE = ConceptId AND ATN = 'CONCEPTSTATUS' will get the ConceptStatus for a ConceptId
FullySpecifiedName STR in MRCONSO.RRF SELECT STR FROM MRCONSO.RRF WHERE SCUI = ConceptId AND TTY = 'FN' will get the FullySpecifiedName for a ConceptId
CTV3ID ATV in MRSAT.RRF Same as ConceptStatus except ATN = 'CTV3ID'
SNOMEDID ATV in MRSAT.RRF Same as ConceptStatus except ATN = 'SNOMEDID'
IsPrimitive ATV in MRSAT.RRF Same as ConceptStatus except ATN = 'ISPRIMITIVE'
DESCRIPTIONS
DescriptionId SAUI in MRCONSO.RRF SELECT SAUI FROM MRCONSO.RRF will get all DescriptionIds
DescriptionStatus ATV in MRSAT.RRF SELECT MRSAT.RRF.ATV FROM (JOIN MRCONSO.RRF, MRSAT.RRF ON MRCONSO.RRF.AUI = MRSAT.RRF.METAUI) WHERE MRCONSO.RRF. SAUI = DescriptionId AND MRSAT.RRF.ATN = 'DESCRIPTIONSTATUS' will get the DescriptionStatus for a DescriptionId
ConceptId SCUI or CODE in MRCONSO.RRF SELECT SCUI FROM MRCONSO.RRF WHERE SAUI = 'DescriptionId' will get the ConceptId for a DescriptionId
Term STR in MRCONSO.RRF SELECT STR FROM MRCONSO.RRF WHERE SAUI = 'DescriptionId' will get the Term for a DescriptionId
InitialCapitalStatus ATV in MRSAT.RRF Same as DescriptionStatus except MRSAT.RRF.ATN = 'INITIALCAPITALSTATUS'
DescriptionType ATV in MRSAT.RRF Same as DescriptionStatus except MRSAT.RRF.ATN = 'DESCRIPTIONTYPE'
LanguageCode ATV in MRSAT.RRF Same as DescriptionStatus except MRSAT.RRF.ATN = 'LANGUAGECODE'
RELATIONSHIPS (See footnote 1)
RelationshipId SRUI in MRREL.RRF SELECT SRUI FROM MRREL.RRF WHERE DIR = 'Y' will get all RelationshipIds
ConceptId1 SCUI or CODE in MRCONSO.RRF SELECT MRCONSO.RRF.SCUI FROM (JOIN MRCONSO.RRF, MRREL.RRF ON MRCONSO.RRF.AUI = MRREL.RRF.AUI2) WHERE MRREL.RRF.SRUI = RelationshipId AND MRREL.RRF.DIR = 'Y' will get the ConceptId1 for a RelationshipId (See footnote 2)
RelationshipType RELA in MRREL.RRF (See footnote 3) SELECT RELA FROM MRREL.RRF WHERE SRUI = RelationshipId AND MRREL.RRF.DIR = 'Y' will get the name of the relationship for a RelationshipId
ConceptId2 SCUI or CODE in MRCONSO.RRF Same as ConceptId1 except AUI2 becomes AUI1 (See footnote 2)
CharacteristicType ATV in MRSAT.RRF SELECT MRSAT.RRF.ATV FROM (JOIN MRREL.RRF, MRSAT.RRF ON MRREL.RRF.RUI = MRSAT.RRF.METAUI) WHERE MRREL.RRF.SRUI = RelationshipId AND MRREL.RRF.DIR = 'Y' AND MRSAT.RRF.ATN = 'CHARACTERISTICTYPE' will get the CharacteristicType for a RelationshipId
Refinability ATV in MRSAT.RRF Same as CharacteristicType except MRSAT.RRF.ATN = 'REFINABILITY'
RelationshipGroup RG in MRREL.RRF SELECT MRREL.RRF.RG FROM (JOIN MRCONSO.RRF, MRREL.RRF ON MRCONSO.RRF.AUI = MRREL.RRF.AUI2) WHERE MRCONSO.RRF.SCUI = ConceptId1 AND MRREL.RRF.DIR = 'Y' will get the RelationshipGroup for a ConceptId1

In the old UMLS Original Release Format (ORF):

SNOMED CT tables and fields UMLS Metathesaurus tables and fields
Corresponding field and table in Metathesaurus Sample SQL statements
(SAB = 'SNOMEDCT' is used to label data from SNOMED CT in all tables, except MRCON, which must be joined with MRSO to identify concept names from SNOMED CT)
CONCEPTS
ConceptId CODE in MRSO SELECT CODE FROM MRSO will get all ConceptIds
ConceptStatus ATV in MRSAT SELECT ATV FROM MRSAT WHERE CODE = ConceptId AND ATN = 'CONCEPTSTATUS' will get the ConceptStatus for a ConceptId
FullySpecifiedName STR in MRCON SELECT MRCON.STR FROM (JOIN MRCON, MRSO ON CUI, SUI) WHERE MRSO.CODE = ConceptId AND MRSO.TTY = 'FN' will get the FullySpecifiedName for a ConceptId
CTV3ID ATV in MRSAT Same as ConceptStatus except ATN = 'CTV3ID'
SNOMEDID ATV in MRSAT Same as ConceptStatus except ATN = 'SNOMEDID'
IsPrimitive ATV in MRSAT Same as ConceptStatus except ATN = 'ISPRIMITIVE'
DESCRIPTIONS
DescriptionId Not stored in ORF
DescriptionStatus ATV in MRSAT SELECT MRSAT.ATV FROM (JOIN MRCON, MRSO, MRSAT ON CUI, SUI) WHERE MRCON.STR = Term AND MRSO.CODE = ConceptId AND MRSAT.ATN = 'DESCRIPTIONSTATUS' will get the DescriptionStatus for a ConceptId/Term combination
ConceptId CODE in MRSO SELECT MRSO.CODE FROM (JOIN MRCON, MRSO ON CUI, SUI) WHERE MRCON.STR = Term will get the ConceptId(s) for a Term
Term STR in MRCON SELECT MRCON.STR FROM (JOIN MRCON, MRSO ON CUI, SUI) WHERE MRSO.CODE = ConceptId will get the Term(s) for a ConceptId
InitialCapitalStatus ATV in MRSAT Same as DescriptionStatus except MRSAT.ATN = 'INITIALCAPITALSTATUS'
DescriptionType ATV in MRSAT Same as DescriptionStatus except MRSAT.ATN = 'DESCRIPTIONTYPE'
LanguageCode ATV in MRSAT Same as DescriptionStatus except MRSAT.ATN = 'LANGUAGECODE'
RELATIONSHIPS
RelationshipId Not stored in ORF
ConceptId1 CODE in MRSO SELECT MRREL.* FROM (JOIN MRSO, MRREL ON MRSO.CUI = MRREL.CUI2) WHERE MRSO.CODE = ConceptId1 will get the MRREL rows with ConceptId1 as the first component of the relationship (See footnote 1)
RelationshipType RELA in MRREL (See footnote 2) In the MRREL rows retrieved for specific ConceptIds, the RELA field will give the name(s) of the relationship
ConceptId2 CODE in MRSO SELECT MRREL.* FROM (JOIN MRSO, MRREL ON MRSO.CUI = MRREL.CUI1) WHERE MRSO.CODE = ConceptId2 will get the MRREL rows with ConceptId2 as the second component of the relationship (See footnote 1)
CharacteristicType These fields are not available in the ORF because of limitation in its data structure. Refer to the RRF section above.
Refinability
RelationshipGroup

Footnotes:
1. In UMLS, every source relationship is represented in two directions (e.g. is-a and inverse-is-a) in separate rows. In MRREL.RRF, those rows with DIR = 'Y' are those with the same directionality as in the source.
2. The directionality of a relationship row is interpreted left-to-right in SNOMED CT but right-to-left in the Metathesaurus. This means that ConceptId1 in the RELATIONSHIPS table will correspond to AUI2/CUI2 in MRREL.RRF (or MRREL).
3. In SNOMED CT the RelationshipType field contains a ConceptId pointing to a linkage concept in the 'Attribute' hierarchy. In UMLS, the RELA field stores directly the name of the linkage concept (e.g. 'is a') instead of its ConceptId ('116680003') to enhance readability. The mapping between a RELA label and its corresponding SNOMED CT ConceptId can be found in MRDOC.RRF (look for all entries with TYPE='snomedct_rela_mapping').