UMLS

UMLS (Unified Medical Language system)

The UMLS was designed by the US National Library of Medicine(NLM) in the year 1986. The main purpose of UMLS is to connect different national and international terminologies, thesaurus, data bases, classifications and vocabularies through Mapping. It provides such a mapping structure among these vocabularies and thus allows one to translate among the various terminology systems. It can also be looked upon as a comprehensive thesaurus and ontology of biomedical concepts. UMLS further provides facilities for natural language processing. It is also intended to be used mainly by developers of systems in medical informatics.

UMLS consists of the following components:

  • UMLS Metathesaurus, the core database of the UMLS, a collection of concepts and terms from the various controlled vocabularies, and their relationships;
  • Semantic Network, a set of categories and relationships that are being used to classify and relate the entries in the Metathesaurus;
  • SPECIALIST Lexicon, a database of lexicographic information for use in natural language processing;
  • a number of supporting software tools(example: MetamorphoSys).

Purpose of UMLS:

The UMLS is not an end-user application. The purpose of UMLS is to facilitate the development of computer systems that behave as if they understand the meaning of the language of biomedicine and health. The US National Library of Medicine produces and distributes the UMLS Knowledge Sources (databases) and associated software tools (programs) for use by system developers in building or enhancing electronic information systems that create, process, retrieve, integrate, and/or aggregate biomedical and health data and information, as well as in informatics research.

Acessing UMLS:

UMLS offers several powerful tools to navigate and to view the Subsets. They are:
1. Navigation by means of RFF browsers
2. Database queries (after generating database by means of load file)
3. Text editor

The Rich Release Format (RRF) Subset Browser

The RRF Subset browser provides users with an easy way to search local subsets, print concept reports, and view raw file information for a specific concept. It is included in MetamorphoSys on the UMLS DVD or available for download from the UMLSKS. The RRF Subset browser can only access Rich Release Format subsets.

Users can search for a concept by:

  • Concept number, for example (C0027051)
  • String (with right truncation), for example (heart att*)
  • By code, for example (D003924, the MeSH code for Diabetes Mellitus, Non-Insulin-Dependent)
  • Using a tree browser to search the hierarchy

Clicking on an item from the search results list will display the concept information. Users can view concept date in the easily printed report view or the raw records view.

Users can filter the results of their searches by semantic type, content view flag, or source and change the display of the data using the 'Restrict Searches and Views' option from the options drop down menu. Other options include limiting the maximum number of child terms displayed and restricting a search string and the results to a specific language.

Table Structure, Data and their Relations:

MRFILES
This table contains information about the entities and the number of its entries.

MRFILES Description
FIL varchar(50) Physical FILENAME
DES varchar(200) Descriptive Name
FMT text Comma separated list of column names (COL), in order
CLS int unsigned Number of COLUMNS
RWS int unsigned Number of ROWS
BTS bigint Size in bytes in this format (ISO/PC or Unix)

Sample Records
MRCOC.RRF|Co-occurringConcepts|CUI1,AUI1,CUI2,AUI2,SAB,COT,COF,COA,CVF|9|13939548|786509996|
MRSTY.RRF|Semantic Types|CUI,TUI,STN,STY,ATUI,CVF|6|1146352|64528811|

How to retrieve data from Database:

To retrieve Details about a concept the following sql query is used:

select LUI,SUI,AUI,SAB,STR from MRCONSO where cui='<CUI>'

To retrieve Definitions about a concept the following sql query is used:

select a.AUI as AUI,b.STR as STR,a.DEF as DEF from MRDEF a,MRCONSO b where a.CUI= '<CUI>' AND a.AUI=b.AUI

To retrieve Semantics about a concept the following sql query is used:

select sty from MRSTY where cui='<CUI>'

To retrieve Relations about a concept the following sql query is used:

select a.CUI1 as CUI1,b.STR as STR,a.CUI2 as CUI2,a.REL as REL,a.RELA as RELA from MRREL a,MRCONSO b where a.cui2='<CUI>' AND a.CUI1=b.CUI

How are Relations Stored?

The Metathesaurus includes many relationships between different concepts. Most of these relationships come from individual source vocabularies. Some are added by NLM during Metathesaurus construction. Some have been contributed by Metathesaurus users to support certain types of applications.

Relationships are expressed in terms of CUIs and AUIs. Metathesaurus relationship files do not include concept names.

Relations are stored like Child, Parent, Sibling, Related narrow, Related broad, Alike terms, Related other, Co-occuring, Synonym, Is-a, Allowed qualifier.

Every relationship present in the Metathesaurus has a unique relationship identifier (RUI). The primary purpose of these identifiers is to enable easy detection of changes in relationships across versions of the Metathesaurus.

References:

  1. New Users' Guide to the UMLS, http://www.nlm.nih.gov/research/umls/new_users.html
  2. UMLS Load Scripts, http://www.nlm.nih.gov/research/umls/load_scripts.html
  3. Unified Medical Language System (UMLS) Documentation, http://www.nlm.nih.gov/research/umls/documentation.html
  4. Unified Medical Language System (UMLS) Teil I (Reference: http://www.people.imise.uni-leipzig.de/barbara.heller/Folien/Folien-Vorlesung-UMLS-Teil-I.pdf)
  5. Unified Medical Language System (UMLS) Teil II (Reference: http://www.people.imise.uni-leipzig.de/barbara.heller/Folien/Folien-Vorlesung-UMLS-Teil-II.pdf)
  6. Using JDBC with MySQL, Getting Started, http://www.developer.com/java/data/article.php/3417381#Installation_and_Preparation_of_MySQL1

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