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Research Scientist @ Foundation AI
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UMLS

The Unified Medical Language System (UMLS) is a compendium of many controlled vocabularies in the biomedical sciences (created 1986). It provides a mapping structure among these vocabularies and thus allows one to translate among the various terminology systems. It may also be viewed as a comprehensive thesaurus and ontology of biomedical concepts. UMLS further provides facilities for natural language processing. It is intended to be used mainly by developers of systems in medical informatics.

UMLS consists of Knowledge Sources (databases) and a set of software tools.

UMLS Knowledge Sources

  • Metathesaurus: The Metathesaurus forms the base of the UMLS and comprises over 1 million biomedical concepts and 5 million concept names, all of which stem from the over 100 incorporated controlled vocabularies and classification systems. Some examples of the incorporated controlled vocabularies are ICD-10, MeSH, SNOMED CT, DSM-IV, LOINC, WHO Adverse Drug Reaction Terminology, UK Clinical Terms, RxNorm, Gene Ontology, and OMIM etc.

  • Semantic Network: Each concept in the Metathesaurus is assigned one or more semantic types (categories), which are linked with one another through semantic relationships. The semantic network is a catalog of these semantic types and relationships. This is a rather broad classification; there are 127 semantic types and 54 relationships in total.

  • Specialist Lexicon: The SPECIALIST Lexicon contains information about common English vocabulary, biomedical terms, terms found in MEDLINE and terms found in the UMLS Metathesaurus. Each entry contains syntactic (how words are put together to create meaning), morphological (form and structure) and orthographic (spelling) information. A set of Java programs use the lexicon to work through the variations in biomedical texts by relating words by their parts of speech, which can be helpful in web searches or searches through an electronic medical record.

UMLS Metathesaurus to MySQL

The setup procedure can be broken down into two steps mainly:

  1. Creating the MySQL Script
  2. Loading the MySQL Script to SQL Server.
  • Creating MySQL Script (Current Version - 2017AA):
    • Download the Full Release from UMLS Knowledge Sources which would be over 4.5GB in size and requires licence to login and download.
    • Extract umls-2017AA-full.zip which requires over 30GB free space
    • cd 2017AA-full
    • Extract mmsys.zip
    • Copy contents of folder mmsys to parent folder 2017AA-full
    • Go to Terminal and run .\run_linux.sh or .\run_mac.command based on platform
    • After MetaMorphosys starts click Install UMLS
    • Select Source : <path_to_folder>/2017AA-full, Destination, and Metathesaurus only from Knowledge Source List.
    • Click New Configuration and Accept Licence Agreement Notice
    • Select Level 0 among options in Default Subset Configuration
    • Input Data Format should be NLM Data File Format in Input Options tab
    • Select Database to MySQL in Write Database Load Script section of Output Options tab
    • Select all ENG souces from Source List after selecting INCLUDE in subset option
    • Click Done in the Action Bar and let the process finish.
  • Shortcut: Can skip the above step by downloading the 2017AA.tar.gz directly

  • Loading From MySQL Script:
    • Go to Destination folder provided in previous section
    • cd 2017AA/META
    • Edit populate_mysql_db.sh to provide details of MYSQL_HOME, user, password and db_name
    • Save and run .\populate_mysql_db.sh
    • Run tail -f mysql.log to follow the logs.

REFERENCES:

Unified Medical Language System
Unified Medical Language System - Knowledge Sources Downloads

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