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Unified Medical Language System® (UMLS®)

New and Updated Sources (Expanded Representation Information) - 2013AB Release

General Information:

What's New to the Metathesaurus

For 2013AB, there are 4 new sources (ATC, CDT, CVX, SNOMEDCT_US) and 47 updated sources (including subsources and translation sources).

ATC represents the Anatomical Therapeutic Chemical Classification System, maintained by the WHO Collaborating Centre for Drug Statistics Methodology (WHOCC). The ATC divides drugs into different groups according to the organ or system on which they act and their chemical, pharmacological and therapeutic properties. The purpose is to serve as a tool for drug utilization research in order to improve quality of drug use.

CDT represents the Code on Dental Procedures and Nomenclature as received from the American Dental Association (ADA). The purpose of the CDT is to achieve uniformity, consistency and specificity in accurately reporting dental treatment and to provide for the efficient processing of dental claims. CDT is the same as the HCPCS version of CDT (SAB = HCDT) except for the hierarchy and a few different attributes.

CVX represents the Vaccines Administered code set which is developed and maintained by the National Center of Immunization and Respiratory Diseases (NCIRD). It includes codes and notes for active and inactive vaccines available in the U.S.

SNOMEDCT_US represents The US Edition of SNOMED CT which is the official source of SNOMED CT for use in US healthcare systems. It is composed of 1) the International Release of SNOMED CT and 2) the US Extension to SNOMED CT. SNOMEDCT_US replaces the 2 individual sources of SNOMEDCT (International Release) and SNOMED_USX (US Extension) which have been deprecated.

Also, starting with this release, the NLM will no longer create "plain ASCII" versions of atoms when the original STR value includes non-ASCII characters. Existing terms and sources created for this purpose have been removed and the indexes have been restructured to maintain existing search and retrieval capabilities. The 2 sources that have been deprecated as a result of this new policy are: 1) MTHHL7V2.5 (HL7 Vocabulary Version 2.5, 7-bit Equivalents) and 2) MTHICPC2ICD107B (International Classification of Primary Care 2nd Edition, 7-bit Equivalents)/

For detailed information about sources that are new or have had changes made (e.g. new term types, new attribute names, etc.):

Code on Dental Procedures and Nomenclature, CDT2013
Vaccines Administered, CVX2013_05_01
GO Ontology, GO2013_04_06
HUGO Gene Nomenclature Committee, HGNC2013_04
International Classification for Nursing Practice, ICNP_2013
Logical Observation Identifiers Names and Codes (LOINC), LNC244
Medical Dictionary for Regulatory Activities Terminology (MedDRA), MDR16_0
Medicomp Systems, MEDCIN [terminology files], MEDCIN3_2013_07_15
NCI Thesaurus, NCI2013_03D
NeuroNames Brain Hierarchy, NEU2013_06_09
RXNORM Vocabulary, RXNORM_13AA_130903F
SNOMED Clinical Terms, Spanish Language Edition, SCTSPA_2013_04_30
SNOMED CT US Edition, SNOMEDCT_US_2013_09_01


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What's New to the Metathesaurus:

Attribute name (ATN):
      ATC_LEVEL
      CHANGE_CLASS
      HGNC_ID
      IS_DRUG_CLASS
      TRANSLATION
      VACCINE_STATUS
     
Relationship attribute(RELA)| RELA inverse:
      has_access_instrument|access_instrument_of
      has_alternative|alternative_of
      has_approach|approach_of
      has_associated_etiologic_finding|associated_etiologic_finding_of
      has_associated_function|associated_function_of
      has_communication_with_wound|wound_has_communication_with
      has_course|course_of
      has_data_element|data_element_of
      has_dependent|dependent_of
      has_extent|extent_of
      has_instrumentation|instrumentation_of
      has_measured_component|measured_component_of
      has_multipart|multipart_of
      has_onset|onset_of
      has_quotient|quotient_of
      has_stage|stage_of
      has_subject_of_information|subject_of_information_of
      member_of|has_member
           (RELA = member_of was changed from the RELA = member_of_cluster for purposes of clarity. The inverse remains the same 'has_member')
      possibly_equivalent_to|possibly_equivalent_to
      temporally_follows|temporally_followed_by

Term type (TTY):
      CTEP-SDCPT
      CTEP-SDCSY
      MTH_OAF
      MTH_OAP
      MTH_OAS
      MTH_OET
      OAF
      OAP
      OAS
      RXN_IN
      RXN_PT

------------------------------------------
Source: Code on Dental Procedures and Nomenclature
VSAB: CDT2013

1. New term type (TTY) | Suppressible value:
      HT|N
      PT|N

2. New attribute name (ATN):
      CHANGE_CLASS

Discussion:

1. New source.

2. CDT is extracted from a file provided by the American Dental Association (ADA). It is the same as the HCPCS version of CDT (SAB = HCDT) except for the hierarchy and a few different attributes. The CDT hierarchy is created from an ASCII data file while the HCDT hierarchy is created during Metathesaurus production.

HCDT remains as a UMLS source. It is not being removed.

3. ATN = CHANGE_CLASS identifies the type of change made to this version of the code. Valid values: 30 (no change), 31 (new code), 35 (revision).

------------------------------------------
Source: Vaccines Administered
VSAB: CVX2013_05_01

1. New term type (TTY) | Suppressible value:
      AB|Y
      OA|O
      OP|O
      PT|O

2. New relationship | relationship attribute(RELA) | RELA inverse:
      SY|has_expanded_form|expanded_form_of

3. New attribute name (ATN):
      DATE_LAST_MODIFIED
      SOS
      VACCINE_STATUS

Discussion:

1. New source.

2. TTY = AB or PT indicates an active or pending vaccine.

3. TTY = OA or OP indicates an inactive or never active vaccine.

4. RELA = has_expanded_form/expanded_form_of connects abbreviations (TTY = AB) with their long forms (TTY = PT or OP).

5. ATN = SOS represents information held in the notes field of the source.

6. ATN = VACCINE_STATUS has the valid values of: Active, Inactive, Never Active, Pending.

------------------------------------------
Source: Gene Ontology
VSAB: GO2013_04_06

New term type (TTY) | Suppressible value:
      MTH_OET|O

Discussion:

For the GO Cellular Component Ontology, TTY = MTH_OET atoms are created for selected strings by including the word "location" in the string for additional clarification.

------------------------------------------
Source: HUGO Gene Nomenclature Committee
VSAB: HGNC2013_04

Dropped attribute name (ATN):
      MAPPED_GDB_ID
      MTH_LOCUS_SPECIFIC_DB_XR

Discussion:

1. Source deprecated field 33, the GDB_ID (mapped data) field.

2. Metathesaurus created attributes(e.g., MTH_LOCUS_SPECIFIC_DB_XR) that were created as a result of needing plain text versions of UTF-8 strings have been deprecated.

------------------------------------------
Source: International Classification for Nursing Practice
VSAB: ICNP_2013

1. New relationship | relationship attribute(RELA) | RELA inverse:
      RB|mapped_from|mapped_to
      RN|mapped_from|mapped_to
      SY|mapped_from|mapped_to

2. Dropped relationship | relationship attribute (RELA):
      RQ|mapped_from

3. New attribute name (ATN):
      MAPSETXRTARGETID

4. Dropped attribute name (ATN):
      MAPSETTYPE

Discussion:

1. All mappings are to SNOMEDCT_US_2013_03_01.

2. REL/RELA = SY|mapped_from|mapped_to represent one-to-one relationships with SNOMEDCT.

3. ATN = MAPSETXRTARGETID is added during Metathesaurus construction and represents the map set target identifier used for XR mappings.

------------------------------------------
Source: Logical Observation Identifiers Names and Codes (LOINC)
VSAB: LNC244

This version includes:
      LNC244_ASQ_3_2009
      LNC244_BRADEN_1988
      LNC244_CAM_2003
      LNC244_FACIT
      LNC244_FLACC_1997
      LNC244_MDS20
      LNC244_MLHFQ_1986
      LNC244_NEUROQOL_2010
      LNC244_NPUAP_2012
      LNC244_OASIS_2002
      LNC244_OPTIMAL_2005
      LNC244_PHQ_9_1999
      LNC244_RHO_2008
      LNC244_SPERTUS_2005
      LNC244_VR_12_2004
      LNC244_WHO_2006

1. New term type (TTY) | Suppressible value | Source(s):
      LO|O|LNC244_FACIT, LNC244_NEUROQOL_2010
      MTH_LO|O|LNC244_FACIT, LNC244_NEUROQOL_2010
      OLC|O|LNC244_FACIT, LNC244_NEUROQOL_2010

2. Dropped term type (TTY):
      MTH_LPN

3. New relationship | relationship attribute (RELA) | RELA inverse | Source(s):
      RQ|mapped_from|mapped_to|LNC244
      RO|has_multipart|multipart_of|LNC244
      RO|has_quotient|quotient_of|LNC244

4. Dropped relationship | relationship attribute (RELA):
      SY|mth_has_plain_text_form

5. New attribute name (ATN) | Source(s):
      LMP|LNC244

6. Dropped attribute name (ATN):
      MAPSETTYPE
      MTH_COPYRIGHT
      MTH_LEA
      MTH_LFO
      MTH_LQT
      MTH_LRN2
      MTH_LSU
      MTH_SOS

Discussion:

1. Subsources within the LNC source data that are not included in the Metathesaurus:
      Blessed Orientation-Memory-Concentration Test
      Borderline Symptom List - 23 Item
      Borderline Symptom List - Supplement
      Edinburgh Postnatal Depression Scale
      Edinburgh Postnatal Depression Scaletient Reported Outcomes Measurement (PROMIS)
      Test of Infant Motor Performance (TIMP)

2. The process for identifying subsources has changed. Subsources are now created based on the external copyright field (field 33) only. Previously, they were created based on a combination of fields. Due to this new process, two subsources have been deprecated, MDS30 and AD8, however, the content from these subsources is still included in the Metathesaurus under the SAB = LNC.

3. ATN = LMP identifies the superceding code of that term.

4. Metathesaurus created attributes, relationships, and term types (e.g., MTH_LEA, mth_has_plain_text_form, MTH_LPN, etc.) that were created as a result of needing plain text versions of UTF-8 strings have been deprecated.

-----------------------------------------------
Source: Medical Dictionary for Regulatory Activities Terminology (MedDRA)
VSAB: MDR16_0

1. New relationship | relationship attribute(RELA) | RELA inverse:
      RO|member_of|has_member

2. Dropped relationships | relationship attribute (RELA):
      RO|member_of_cluster|has_member

Discussion:

RELA = member_of_cluster was changed to 'member_of' for purposes of clarity. The inverse remains the same, 'has_member'.

-----------------------------------------------
Source: Medicomp Systems, MEDCIN [terminology files]
VSAB: MEDCIN3_2013_07_15

1. Dropped term type (TTY):
      MTH_FN
      MTH_PT
      MTH_SY

2. New relationship | relationship attribute(RELA) | RELA inverse:
      RO|has_finding_context|finding_context_of
      RO|has_procedure_context|procedure_context_of
      RO|has_specimen_source_topography|specimen_source_topography_of

3. Dropped relationship | relationship attribute (RELA):
      RO|has_specimen_procedure
      SY|mth_plain_text_form_of

Discussion:

Metathesaurus created term types and relationships (e.g., MTH_FN, etc.) that were created as a result of needing plain text versions of UTF-8 strings have been deprecated.

------------------------------------------------
Source: NCI Thesaurus
VSAB: NCI2013_03D

1. New term type (TTY) | Suppressible value:
      CTEP-SDCPT|N
      CTEP-SDCSY|N

2. New relationship | relationship attribute(RELA) | RELA inverse:
      RO|has_data_element|data_element_of

3. Dropped relationship | relationship attribute(RELA):
      RO|allele_associated_with_disease
      RO|allele_not_associated_with_disease
      RO|gene_product_has_malfunction_type

4. New attribute name (ATN):
      HGNC_ID

Discussion:

New subsource CTEP-SDC: Cancer Therapy Evaluation Program - Simple Disease Classification.

----------------------------------------------
Source: NeuroNames Brain Hierarchy
VSAB: NEU2013_06_09

1. New term type (TTY) | Suppressible value:
      IS|N
      OP|N

2. Dropped term type (TTY):
      CHISY
      FRESY
      GERSY
      INDSY
      ITASY
      KORSY
      LATSY
      RUSSY
      SPASY
      TURSY

3. New attribute name (ATN):
      TRANSLATION

Discussion:

1. Non-English synonyms (except for Latin) are mapped to ATN = TRANSLATION. The ATV has the format "language: string" (e.g., TRANSLATION|Italian: encefalo).

In previous inversions the non-English synonyms were assigned specific TTYs such as CHISY, RUSSY, etc. All of these TTYs have been deprecated.

Latin synonyms are considered scientific names so they are treated as English strings and assigned the TTY=SY. The previous TTY=LATSY has been deprecated.

2. TTY = OP (obsolete preferred term) and TTY = IS (obsolete synonym). If the preferred term is obsolete, it is assumed that all associated synonyms are also obsolete regardless if they are marked obsolete or not.

----------------------------------------------
Source: RXNORM Vocabulary
VSAB: RXNORM_13AA_130903F

This version includes:
      ATC_2013 (Anatomical Therapeutic Chemical Classification System)
      GS_2013_08_05 (Gold Standard Drug Database)
      MDDB_2013_08_07 (Master Drug Data Base. Medi-Span, a division of Wolters Kluwer Health)
      MMSL_2013_08_01 (Multum MediSource Lexicon)
      MMX_2013_08_05 (Micromedex RED BOOK)
      MTHFDA_2011_06_01_13_05_06 (FDA National Drug Code Directory)
      MTHSPL_2013_08_26 (FDA Structured Product Labels)
      NDDF_2013_08_07 (FDB MedKnowledge)
      NDFRT_2013_09_03 (National Drug File)
      VANDF_2013_07_19 (Veterans Health Administration National Drug File)

1. New term type (TTY) | Suppressible value | Source(s):
      IN|N|ATC_2013
      PT|N|ATC_2013
      RXN_IN|N|ATC_2013
      RXN_PT|N|ATC_2013

2. New attribute name (ATN) | Source(s):
      ATC_LEVEL|ATC_2013
      IS_DRUG_CLASS|ATC_2013

3. Dropped attribute name (ATN) | Source(s):
      NST (Normalized strength and units for drugs with one active ingredient)|MTHFDA_2011_06_01_13_05_06
      RXO (Drug Description from NDF)|MTHFDA_2011_06_01_13_05_06
      TRN (Trade name of product)|MTHFDA_2011_06_01_13_05_06

Discussion:

1. New subsource = ATC is included in this Metathesaurus release as part of RxNorm, however, it was not updated in this version. Per RxNorm, ATC is updated yearly in the July or August version.

2. TTY = IN (ingredient name) and TTY = RXN_IN (RxNorm preferred ingredient).

3. ATN = ATC_LEVEL indicates drug classification level. Valid levels: 1-5.

4. ATN = IS_DRUG_CLASS has valid value of Y.

5. MTHFDA is included in each Metathesaurus release as part of RxNorm, however, it was not updated in this version. MTHFDA was last updated in 2011.

6. Selected portions of MSH and SNOMEDCT_US are included in the RxNorm release files, however, they are not processed as part of RxNorm for the Metathesaurus except in assigning RXCUI and RXAUI attributes.

------------------------------------------------------------
Source: SNOMED Clinical Terms, Spanish Language Edition
VSAB: SCTSPA_2013_04_30

1. Dropped term type (TTY):
      SCTSPA_2013_04_30/MTH_FN
      SCTSPA_2013_04_30/MTH_IS
      SCTSPA_2013_04_30/MTH_OF
      SCTSPA_2013_04_30/MTH_OP
      SCTSPA_2013_04_30/MTH_PT
      SCTSPA_2013_04_30/MTH_SY

2. New relationship | relationship attribute(RELA) | RELA inverse:
      RO|has_access_instrument|access_instrument_of
      RO|has_approach|approach_of
      RO|has_associated_etiologic_finding|associated_etiologic_finding_of
      RO|has_associated_function|associated_function_of
      RO|has_communication_with_wound|wound_has_communication_with
      RO|has_course|course_of
      RO|has_dependent|dependent_of
      RO|has_extent|extent_of
      RO|has_instrumentation|instrumentation_of
      RO|has_location|location_of
      RO|has_measured_component|measured_component_of
      RO|has_onset|onset_of
      RO|has_stage|stage_of
      RO|has_subject_of_information|subject_of_information_of
      RO|has_time_aspect|time_aspect_of
      RO|measures|measured_by
      RO|temporally_follows|temporally_followed_by
      RO|uses|used_by

3. Dropped relationship | relationship attribute (RELA):
      RN|as_a
      RO|may_be_a
      RO|moved_to
      RO|replaced_by
      SY|same_as

4. New RF2 attribute name (ATN) | former RF1 attribute name (ATN), if applicable:
      ACTIVE | CONCEPTSTATUS or DESCRIPTIONSTATUS
      CASE_SIGNIFICANCE_ID | INITIALCAPITALSTATUS
      CHARACTERISTIC_TYPE_ID | CHARACTERISTICTYPE
      DEFAULT_MODULE_ID
      DEFINITION_STATUS_ID | ISPRIMITIVE
      INACTIVATION_INDICATOR | CONCEPTSTATUS or DESCRIPTIONSTATUS
      MODIFIER_ID
      MODULE_ID
      SOURCE_EFFECTIVE_TIME
      SUBSET_MEMBER
      TARGET_EFFECTIVE_TIME
      TYPE_ID | DESCRIPTIONTYPE

5. Dropped attribute name (ATN):
      AQ
      CHARACTERISTICTYPE
      CONCEPTSTATUS
      CTV3ID
      DESCRIPTIONSTATUS
      DESCRIPTIONTYPE
      INITIALCAPITALSTATUS
      ISPRIMITIVE
      REFINABILITY
      SNOMEDID
      SUBSETCONTEXTID
      SUBSETLANGUAGECODE
      SUBSETMEMBER
      SUBSETORIGINALID
      SUBSETREALMID
      SUBSETTYPE
      SUBSETVERSION

Discussion:

1. This version of SCTSPA is in the new RF2 format so elements unique to RF2 are now included while elements unique to the RF1 format have been deprecated.

2. Metathesaurus created term types (e.g., MTH_FN, etc.) that were created as a result of needing plain text versions of UTF-8 strings have been deprecated.

------------------------------------------------------------
Source: SNOMED CT US Edition
VSAB: SNOMEDCT_US_2013_09_01

1. New term type (TTY) | Suppressible value:
      MTH_OAF|O
      MTH_OAP|O
      MTH_OAS|O
      OAF|O
      OAP|O
      OAS|O

2. Dropped term type (TTY):
      MTH_OP

3. New relationship | relationship attribute(RELA) | RELA inverse:
      RN|has_alternative|alternative_of
      RN|refers_to|referred_to_by
      RO|has_access_instrument|access_instrument_of
      RO|has_approach|approach_of
      RO|has_associated_etiologic_finding|associated_etiologic_finding_of
      RO|has_associated_function|associated_function_of
      RO|has_communication_with_wound|wound_has_communication_with
      RO|has_course|course_of
      RO|has_dependent|dependent_of
      RO|has_extent|extent_of
      RO|has_instrumentation|instrumentation_of
      RO|has_location|location_of
      RO|has_measured_component|measured_component_of
      RO|has_onset|onset_of
      RO|has_stage|stage_of
      RO|has_subject_of_information|subject_of_information_of
      RO|has_time_aspect|time_aspect_of
      RO|measures|measured_by
      RO|moved_from|moved_to
      RO|possibly_equivalent_to|possibly_equivalent_to
      RO|temporally_follows|temporally_followed_by
      RO|uses|used_by

4. Dropped relationship | relationship attribute (RELA):
      RO|is_alternative_use
      RO|may_be_a
      RO|refers_to
      RO|replaces

5. New RF2 attribute name (ATN) | former RF1 attribute name (ATN), if applicable:
      ACTIVE | CONCEPTSTATUS or DESCRIPTIONSTATUS
      CASE_SIGNIFICANCE_ID | INITIALCAPITALSTATUS
      CHARACTERISTIC_TYPE_ID | CHARACTERISTICTYPE
      DEFAULT_MODULE_ID
      DEFINITION_STATUS_ID | ISPRIMITIVE
      DESCRIPTION_FORMAT
      DESCRIPTION_LENGTH
      ICD-O-3_CODE
      INACTIVATION_INDICATOR | CONCEPTSTATUS or DESCRIPTIONSTATUS
      MODIFIER_ID
      MODULE_ID
      REFSET_PATTERN
      SOURCE_EFFECTIVE_TIME
      SUBSET_MEMBER
      TARGET_EFFECTIVE_TIME
      TYPE_ID | DESCRIPTIONTYPE

6. Dropped attribute name (ATN):
      AQ
      CHARACTERISTICTYPE
      COMPONENTHISTORY
      CONCEPTSTATUS
      DESCRIPTIONSTATUS
      DESCRIPTIONTYPE
      INITIALCAPITALSTATUS
      ISPRIMITIVE
      MAPSETREALMID
      MAPSETRULETYPE
      MAPSETSCHEMEID
      MAPSETSCHEMENAME
      MAPSETSCHEMEVERSION
      MAPSETSEPARATORCODE
      MAPSETTYPE
      REFINABILITY
      SUBSETCONTEXTID
      SUBSETLANGUAGECODE
      SUBSETMEMBER
      SUBSETORIGINALID
      SUBSETREALMID
      SUBSETTYPE
      SUBSETVERSION
      TARGETSCHEMEID

Discussion:

A new set of SNOMEDCT-to-ICD10 mappings is included in this release.