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0.1 Purpose of this Documentation

The Unified Medical Language System^® (UMLS) documentation describes the UMLS Knowledge Sources and related tools that are produced and distributed by the National Library of Medicine, a part of the National Institutes of Health in the U.S. Department of Health and Human Services. This documentation explains the following procedures and concepts:

• The purpose, content, and file structure of the three UMLS Knowledge Sources: the Metathesaurus^®, the Semantic Network, and the SPECIALIST Lexicon
• The way to use associated UMLS programs:
  • MetamorphoSys, the installation program for the three UMLS Knowledge Sources. MetamorphoSys is also the customization program for the Metathesaurus, providing several output options, including Rich Release and Original Release Formats, and a choice of preferred character sets to produce custom subsets of the Metathesaurus.
  • Lexical Programs, which help to deal with inflectional variation (e.g., treat, treats, treating, treatment) in the English language, convert American English to British English and vice versa, and map text to concepts in the Metathesaurus
• The way to access the UMLS resources using the UMLS Knowledge Source Server, i.e., download, application programming interface (API), or Web browser
• The DVD-ROM distribution format for the UMLS Knowledge Sources and associated UMLS programs. The DVD is available upon request.

0.2 Release Schedule

This documentation is updated for each release of the UMLS. It may be updated between releases if errors or omissions are found. The current document refers to the 2008AB version, released in November 2008. The next UMLS version will be 2009AA, scheduled for release in April 2009.

0.3 Audience

This documentation and the UMLS resources it describes are intended for system developers, informatics researchers, librarians, and other information professionals. The documentation assumes that you are familiar with database concepts and the Internet. If you intend to use the UMLS Knowledge Sources in software applications, it assumes that you have experience with building and using complex databases. If you intend to use any of the UMLS programs, it assumes basic familiarity with Java.

Neither the UMLS resources nor this documentation are intended for end users such as individual health professionals or members of the general public, unless they are also software developers.

0.4 Using this Documentation

0.4.0 Experienced UMLS Users

If you have done substantive work with preceding versions of the UMLS resources, go directly to Section 0.5, which describes any changes in the documentation and in the UMLS resources. Section 0.5 will direct you to the parts of the documentation that describe any changes to data files, content, or format introduced in this release.

0.4.1 Novice UMLS Users

If you are new to the UMLS, Section 0.5 may not be relevant, but you should read the rest of Section 0 and all of Section 1 before moving on to other parts of the documentation. The following brief overview describes what you will find in each section of the documentation.

Section 1. Introduction to the UMLS

This section explains the purpose of the UMLS, the conditions under which you may use the different UMLS components, and how these conditions relate to Open Access/Open Source principles. It also briefly describes each of the UMLS components and the relationships between them, suggests ways to build your understanding of UMLS features and capabilities, and provides a list of additional UMLS reference materials.

Section 2. Metathesaurus

This section describes the content and structure of the Metathesaurus, a large concept-oriented database that incorporates numerous biomedical and health-related vocabularies, classifications, and coding systems. The Metathesaurus categorizes these concepts by assigned basic Semantic Types and makes all information from these terminologies accessible in common, fully-specified file formats. The Metathesaurus includes coding systems and vocabularies designated as U.S. standards under the Administrative Simplification provisions of the Health Insurance Portability and Accountability Act of 1996 (HIPPA) and as target U.S. government-wide standards by the Consolidated Health Informatics eGov initiative.

Section 3. Semantic Network

This section describes the content and structure of the Semantic Network, a small database that includes information about the set of basic Semantic Types, or categories, to which Metathesaurus concepts may be assigned. The Semantic Network defines the relationships that may hold between these Semantic Types and between broad groupings of Semantic Types, such as all types that denote disorders (Disease or Syndrome, Acquired Abnormality, Neoplastic Process, etc.).

Section 4. SPECIALIST Lexicon and Lexical Programs

This section describes the content and structure of the following programs:

• The SPECIALIST Lexicon, a database of syntactic, morphological and orthographic information for commonly occurring English language words and biomedical vocabulary. The SPECIALIST Lexicon is useful for natural language processing applications.
• The Lexical Programs, which detect and abstract away from the inflectional, case, and word order variations encountered in natural language. One of these programs, MetaMap Transfer (MMTx), is specifically designed to map arbitrary terms to concepts in the Metathesaurus, or, equivalently, to discover Metathesaurus concepts within free text.

Section 5. UMLS Knowledge Source Server

This section describes how to access the UMLS resources from the UMLS Knowledge Source Server via download, application programming interface, and interactive Web browser.

Section 6. MetamorphoSys

This section describes MetamorphoSys, the installation program for all the UMLS Knowledge Sources and the customization program for the Metathesaurus. You must use MetamorphoSys to install the Knowledge Sources. MetamorphoSys allows you to output data in either the 7-bit ASCII (the default) or Unicode UTF-8 character set. MetamorphoSys also provides two file format options (Rich Release Format or Original Release Format) for the Metathesaurus, and provides a number of other customization options.

Section 7. UMLS DVD

This section gives technical specifications for the UMLS DVD-ROM, an alternative method for distributing UMLS content. The DVD-ROM is available to UMLS licensees upon request.

Appendices

Appendix A includes the text of the License Agreement for Use of the UMLS Metathesaurus and its appendices.

Appendix B includes additional information about the Metathesaurus data elements and the current source vocabularies.

0.5 What's New for This Version of the UMLS

Release changes are also documented in the What's New section of the README text file included on the DVD.

0.5.0 Metathesaurus

2 new sources and 1 new translation were added:

• Foundational Model of Anatomy (FMA) Ontology,
• MEDCIN, and
• Medical Dictionary for Regulatory Activities Terminology (MedDRA), Czech Edition.

27 English sources and 10 translation sources were updated in this release. This includes MeSH, ICD-9-CM, HUGO, MedDRA, SNOMED CT (English and Spanish), and the NCI Thesaurus. For a complete list of updated sources see: http://www.nlm.nih.gov/archive/20090403/research/umls/updated_sources.html. For more detailed information, see http://www.nlm.nih.gov/archive/20090403/research/umls/updated_sources_expanded.html.

MedlinePlus Health Topics and Japanese Translations of the Medical Subject Headings are now represented in MRHIER.RRF. Their hierarchies can be browsed via either the MetamorphoSys RRF Browser or the UMLSKS Tree Browser.

String unique identifiers (SUIs) now have a maximum length of 9 characters. Previously assigned SUIs retain their 8 character length.

Relationship unique identifiers (RUIs) now have a maximum length of 10 characters. Previously assigned RUIs retain their 9 character length.

Attribute unique identifiers (ATUIs) now have a maximum length of 11 characters. Previously assigned ATUIs retain their 10 character length.

Information on columns and data elements in the Metathesaurus, including SUIs, RUIs and ATUIs are listed in Appendix B.1, Columns and Data Elements, available at: http://www.nlm.nih.gov/archive/20090403/research/umls/metab.html#sb_1.1.

In SNOMED CT Spanish, strings with term type 'MTH*' (i.e. MTH_PT) no longer carry a source asserted atom identifier (SAUI). This field is now blank.

In MRSAB.RRF, the term type list (TTYL) column now has a maximum of 300 characters.

In the Word Index files (e.g., MRXW_SPA.RRF) the WD column length now has a maximum of 500 characters.

The codes for LOINC parts names (LPNs) are now followed by a hyphen plus a single digit. See the following example for Vitamin B2 (from MRCONSO.RRF):

2008AB:
C0035527|ENG|S|L0284721|PF|S0099284|N|A15634064||||LNC|LPN|LP31690-8|Vitamin B2|0|N||

2008AA:
C0035527|ENG|S|L0284721|PF|S0099284|N|A13321409||||LNC|LPN|LP31690|Vitamin B2|0|N||

0.5.1 MetamorphoSys

MetamorphoSys has improved run times across all platforms.

A full Metathesaurus subset now requires 17.7 GB of disk space.

Reported bugs may be viewed on the Release Notes Web page.

0.5.2 UMLS Learning Resources

The new Web-based UMLS Basics Tutorial is available at: http://www.nlm.nih.gov/archive/20090403/research/umls/online%20learning/index.htm.

Users who are new to the UMLS are encouraged to review the New Users' Guide to the UMLS available at: http://www.nlm.nih.gov/archive/20090403/research/umls/new_users.html. This guide includes online demonstrations, step-by-step instructions and a link to UMLS training materials.