Others titles

  • Metathesaurus Concepts and Their Semantic Types
  • Processes Biologic Function Concepts and Types
  • MRCONSO & MRSTY

Keywords

  • UMLS
  • Metathesaurus
  • UMLS concepts
  • Semantic Type
  • RRF
  • NLM

Biologic Function Concepts and Types

This dataset contains the entire concept structure of UMLS Metathesaurus for the semantic type “Biologic Function”. One of the primary purposes of this dataset is to connect different names for all the concepts for a specific Semantic Type. There are 125 semantic types in the Semantic Network. Every Metathesaurus concept is assigned at least one semantic type; very few terms are assigned as many as five semantic types.

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Description

The UMLS, or Unified Medical Language System, is a set of files and software that brings together many health and biomedical vocabularies and standards to enable interoperability between computer systems. One powerful use of the UMLS is linking health information, medical terms, drug names, and billing codes across different computer systems. Some examples of this are:
– Linking terms and codes between your doctor, your pharmacy, and your insurance company
– Patient care coordination among several departments within a hospital
The UMLS has many other uses, including search engine retrieval, data mining, public health statistics reporting, and terminology research.
The UMLS has three tools (Knowledge Sources):
– Metathesaurus: Terms and codes from many vocabularies, including CPT, ICD-10-CM, LOINC, MeSH, RxNorm, and SNOMED CT
– Semantic Network: Broad categories (semantic types) and their relationships (semantic relations)
– SPECIALIST Lexicon and Lexical Tools: Natural language processing tools

The 2018AB Metathesaurus contains approximately 3.44 million concepts and 13.7 million unique concept names from 199 source vocabularies. The Metathesaurus is a very large, multi-purpose, and multi-lingual vocabulary database that contains information about biomedical and health related concepts, their various names, and the relationships among them. It is built from the electronic versions of many different thesauri, classifications, code sets, and lists of controlled terms used in patient care, health services billing, public health statistics, indexing and cataloging biomedical literature, and /or basic, clinical, and health services research. In this documentation, these are referred to as the “source vocabularies” of the Metathesaurus. In the Metathesaurus, all the source vocabularies are available in a single, fully-specified database format.

The Metathesaurus is organized by concept or meaning. In essence, its purpose is to link alternative names and views of the same concept together and to identify useful relationships between different concepts. All concepts in the Metathesaurus are assigned to at least one semantic type from the Semantic Network. This provides consistent categorization of all concepts in the Metathesaurus at the relatively general level represented in the Semantic Network.
The purpose of the Semantic Network is to provide a consistent categorization of all concepts represented in the UMLS Metathesaurus and to provide a set of useful relationships between these concepts. All information about specific concepts is found in the Metathesaurus; the Network provides information about the set of basic semantic types, or categories, which may be assigned to these concepts, and it defines the set of relationships that may hold between the semantic types. The current release of the Semantic Network contains 125 semantic types and 54 relationships. The Semantic Network serves as an authority for the semantic types that are assigned to concepts in the Metathesaurus. The Network defines these types, both with textual descriptions and by means of the information inherent in its hierarchies.

About this Dataset

Data Info

Date Created

2009-07-29

Last Modified

2021-05-05

Version

2021AA

Update Frequency

Semiannual

Temporal Coverage

N/A

Spatial Coverage

N/A

Source

John Snow Labs; U.S. National Library of Medicine (NLM);

Source License URL

Source License Requirements

Reporting Requirements

Source Citation

N/A

Keywords

UMLS, Metathesaurus, UMLS concepts, Semantic Type, RRF, NLM

Other Titles

Metathesaurus Concepts and Their Semantic Types, Processes Biologic Function Concepts and Types, MRCONSO & MRSTY

Data Fields

Name Description Type Constraints
Concept_Unique_IdentifierConcept Unique Identifier (CUI) is the unique identifier for a Metathesaurus concept to which strings with the same meaning are linked. CUI starts with C followed by 7 digits.stringrequired : 1
Language_of_TermsLanguage of terms in the source vocabularystringrequired : 1
Term_StatusStatus of the term. P= Preferred LUI of the CUI, S= Non-Preferred LUI of the CUIstringrequired : 1
Lexical_Unique_IdentifierLexical Unique Identifier (LUI) is the unique identifier of a term in the Metathesaurus. Terms are different from strings in that they group together strings that are lexical variants of one another. LUI starts with L followed by 7 digits.stringrequired : 1
String_TypeType of string. PF= Preferred form of the term, VCW=Case and word-order variant of the preferred form, VC=Case variant of the preferred form, VO=Variant of the preferred form, VW=Word-order variant of the preferred form.stringrequired : 1
String_Unique_IdentifierString Unique Identifier (SUI) is a unique identifier for each unique string in the Metathesaurus. Strings that differ in any way, e.g., by upper or lower case, will have different SUIs. SUI starts with S followed by 7 digits.stringrequired : 1
Is_PreferredIndicates if the atom status is preferred (true) or not (false) for this string within this concept.booleanrequired : 1
Atom_Unique_IdentifierAtom Unique Identifier (AUI) is an identifier for the atom in the UMLS. It is the primary key to the concepts table. AUI starts with A followed by 7 digits. They are the concept names or strings from each of the source vocabulariesstringrequired : 1
Source_Asserted_Atom_IdentifierSource asserted identifier for an atomstring-
Source_Asserted_Concept_IdentifierSource asserted identifier for a conceptstring-
Source_Asserted_Descriptor_IdentifierSource asserted identifier for descriptor in the metathesaurusstring-
Source_AbbreviationAbbreviation of the source vocabularystringrequired : 1
Term_TypeType of term within the source vocabulary. A value indicating the kind of role an atom plays in its source. Examples include PT for "preferred term," SY for "synonym," and MH for "main heading."string-
Source_String_CodeSource string code (CODE) is the Unique Identifier or code for string in sourcestring-
String_NameName of string in the Metathesaurusstring-
Source_Restriction_Levelintegerlevel : Nominalrequired : 1
Suppressible_FlagIn the UMLS Metathesaurus terms can be marked as "suppressible", these terms can then be removed from the subset. These terms are most often identified as suppressible because of ambiguity in meaning or lack of face validity. Suppressible flag. Values = E: Suppressible due to editor decision, N: Not suppressible, O: Obsolete, Y: Suppressible due to SABstringrequired : 1
Content_View_Flag_1Content View Flag. Bit field used to flag rows included in Content View. This field is a varchar field to maximize the number of bits available for use.integerlevel : Nominal
Semantic_Type_Unique_IdentifierUnique id assigned to semantic type e.g., T004=Fungus, T005=Virusstringrequired : 1
Semantic_Type_Tree_IdentifierSemantic type tree numberstringrequired : 1
Semantic_Type_NameName of semantic typestringrequired : 1
Attribute_Type_IdentifierEach concept has specific attributes defining its meaning and is linked to the corresponding concept names in the various source vocabulariesstringrequired : 1
Content_View_Flag_2A bit field used to flag rows included in Content View. This field is a varchar field to maximize the number of bits available for use.integerlevel : Nominal

Data Preview

Concept Unique IdentifierLanguage of TermsTerm StatusLexical Unique IdentifierString TypeString Unique IdentifierIs PreferredAtom Unique IdentifierSource Asserted Atom IdentifierSource Asserted Concept IdentifierSource Asserted Descriptor IdentifierSource AbbreviationTerm TypeSource String CodeString NameSource Restriction LevelSuppressible FlagContent View Flag 1Semantic Type Unique IdentifierSemantic Type Tree IdentifierSemantic Type NameAttribute Type IdentifierContent View Flag 2
C0003261ENGPL0003261PFS0014564FalseA0024784M0001366D000917MSHMHD000917Antibody Formation0N256.0T038B2.2.1Biologic FunctionAT67893814256
C0003261ENGPL0003261PFS0014564TrueA19655824MTHPNNOCODEAntibody Formation0N256.0T038B2.2.1Biologic FunctionAT67893814256
C0003261ENGPL0003261VOS0042554TrueA0060606M0001366D000917MSHPMD000917Formation, Antibody0N256.0T038B2.2.1Biologic FunctionAT67893814256
C0003261ENGPL0003261VOS0414962FalseA186457052840.00000001272CHVSY0000001272antibody formation0N256.0T038B2.2.1Biologic FunctionAT67893814256
C0003261ENGPL0003261VOS0414962TrueA04737391556-2459CSPPT1556-2459antibody formation0N256.0T038B2.2.1Biologic FunctionAT67893814256
C0003261ENGSL0709410PFS0806321TrueA26600572M0001366D000917MSHETD000917Antibody Production0NT038B2.2.1Biologic FunctionAT67893814256
C0003261ENGSL0709410VOS0998419TrueA1056806M0001366D000917MSHPMD000917Production, Antibody0N256.0T038B2.2.1Biologic FunctionAT67893814256
C0003261ENGSL0709410VOS11850286TrueA186826912838.00000001272CHVSY0000001272antibodies production0N256.0T038B2.2.1Biologic FunctionAT67893814256
C0003261ENGSL0709410VOS7269772FalseA11581945GO:0002377GOSYGO:0002377antibody production0N256.0T038B2.2.1Biologic FunctionAT67893814256
C0003261ENGSL0709410VOS7269772TrueA186826922841.00000001272CHVPT0000001272antibody production0N256.0T038B2.2.1Biologic FunctionAT67893814256