2/13/2006 UMLS® KNOWLEDGE SOURCES February Release 2006AA DOCUMENTATION Section 0: Preface 0.1 Purpose of This Documentation 0.2 Release Schedule 0.3 Audience 0.4 How to Use This Documentation 0.5 What's New for This Version of the UMLS Section 1: Introduction to the UMLS 1.1 Purpose of the UMLS 1.2 Conditions of Use of the UMLS 1.3 Brief Description of the UMLS Knowledge Sources and Associated Tools 1.4 Getting Started 1.5 Sources of Additional Information about the UMLS Section 2: Metathesaurus 2.0 Introduction 2.1 Source Vocabularies 2.2 Concepts, Concept Names, and their Identifiers 2.3 Relationships and Relationship Identifiers 2.4 Attributes and Attribute Identifiers 2.5 Data About the Metathesaurus 2.6 Concept Name Indexes 2.7 File Formats - Metathesaurus Rich Release Format (RRF) and Original Release Format (ORF) 2.8 Character Sets Section 3: Semantic Network 3.0 Introduction 3.1 Overview 3.2 Semantic Network ASCII Relational Format 3.3 Semantic Network ASCII Unit Record Format 3.4 Hierarchies for Semantic Types and Relations in the Semantic Network Section 4: SPECIALIST Lexicon and Lexical Tools Section 5: Using the UMLS Knowledge Source Server (UMLSKS) via the Internet 5.0 Background 5.1 Downloading UMLS Knowledge Sources 5.2 System Architecture 5.3 Querying the UMLSKS 5.4 Gaining Access to the UMLSKS 5.5 UMLSKS Documentation 1 Section 6: MetamorphoSys - the UMLS install and customization program 6.0 Introduction 6.1 MetamorphoSys Requirements 6.2 Starting MetamorphoSys 6.3 Using MetamorphoSys 6.4 Select Default Subset 6.5 Option Tabs 6.6 File Menu 6.7 Edit Menu 6.8 Options (for Advanced Users) 6.9 Reset Menu 6.10 Done; Begin Subset 6.11 API Documentation 6.12 Version Validation 6.13 Getting Help 6.14 Acknowledgments Section 7: UMLS DVD 7.0 Introduction 7.1 Hardware and Software requirements 7.2 Installing from DVD Appendix A. License for Use of the UMLS Metathesaurus A.1 Appendix to the License Agreement for Use of the UMLS®Metathesaurus Appendix B. Metathesaurus Metadata B.1 Columns and Data Elements B.1.1 Columns and Data Elements in Rich Release Format (RRF) B.1.2 Columns and Data Elements in Original Release Format (ORF) B.2 Attribute Names B.3 Abbreviations Used in Data Elements B.4 Source Vocabularies B.5 Source and Term Type Default Order of Precedence and Suppressibility B.6 Release Metadata Documentation Index Section 0 Preface 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 purpose, content, and file structure of the current versions of the three UMLS Knowledge Sources - the Metathesaurus®, the Semantic Network, and the SPECIALIST Lexicon; - why and how to use associated UMLS programs, including: (a) MetamorphoSys, the install program for the three UMLS Knowledge Sources; it also provides a variety of output options, including Rich Release and Original Release Formats, and a choice of preferred character set, to produce custom subsets of the Metathesaurus. (b) the Lexical Programs, which help to deal with inflectional variation (e.g., treat, treats, treating, treatment) in 2 the English language; to convert American English to British English and vice versa, and to map text to concepts in the Metathesaurus; - how to access the UMLS resources via the UMLS Knowledge Source Server via (a) download, (b) an application programming interface (API), or (c) a Web browser. - the DVD-ROM distribution format for the UMLS Knowledge Sources and associated UMLS programs, which is available on 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 2005AC version which was released in November 2005. The next UMLS version will be 2006AA, scheduled to be released in January 2006. 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 How to Use This Documentation 0.4.0 If you are an experienced UMLS user If you have done substantive work with preceding versions of the UMLS resources go directly to Section 0.5, which describes what has been changed for this new version - in the documentation and in the UMLS resources themselves. Section 0.5 will point you to the parts of the documentation that describe any changes to data files, content, or format introduced in this release. 0.4.1 If you are a novice UMLS user If you are new to the UMLS, Section 0.5 won't be particularly relevant (or understandable!), but you should read the rest of Section 0 and all of Section 1 before moving on to other parts of the documentation. Please read this brief overview, which explains what you will find in each section of the documentation. Section 1. Introduction to the UMLS The section explains the purpose of the UMLS, explains the conditions under which you may use the different UMLS components and how these relate to Open Access/Open Source principles, provides a brief description of each of the UMLS components and the relationships between them, describes how to get a feel for what is in each of the UMLS Knowledge Sources, and provides a list of additional reference materials about the UMLS. Section 2. Metathesaurus This section describes the content and structure of the Metathesaurus, a very large concept-oriented database that incorporates many different biomedical and health-related vocabularies, classifications, and coding systems. The Metathesaurus provides a consistent categorization of these concepts by assigning basic semantic types and makes all information from these terminologies accessible in common, fully-specified file formats. The Metathesaurus contains coding systems and vocabularies designated as U.S. standards under the Administrative Simplification provisions of the Health Insurance Portability and Accountability Act of 1996 (HIPAA) and as target U.S. government-wide standards by the Consolidated Health Informatics eGov initiative. Section 3. Semantic Network 3 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, as well as 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 (1) the SPECIALIST Lexicon, a database of syntactic, morphological, and orthographic information for commonly occurring English language words and biomedical vocabulary that is useful for natural language processing applications; and (2) lexical programs, which are designed to assist in detecting and abstracting away from the inflectional, case, and word order variations encountered in natural language. One of these, MMTx (Metamap Transfer), 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 programmer interface, and interactive Web browser. Section 6. MetamorphoSys: the UMLS install and customization program This section describes MetamorphoSys, the install program for all the UMLS Knowledge Sources and the customization program for the Metathesaurus. UMLS users must use MetamorphoSys to install the Knowledge Sources. MetamorphoSys allows users to output data in either the 7-bit ASCII (the default) or Unicode UTF-8 character set. MetamorphoSys provides two file format options (Rich Release or Original Release Format) for the Metathesaurus, and provides a number of other options to customize it in specific applications. Section 7. UMLS DVD This section gives technical specifications for the UMLS DVD-ROM, an alternative method for distribution of UMLS content. The DVD-ROM is available on request to UMLS licensees. Appendices Appendix A includes the text of the License Agreement for Use of the UMLS Metathesaurus and Appendix. Appendix B includes additional information about the Metathesaurus data elements and the source vocabularies in the current Metathesaurus. 0.5 What's New for This Version of the UMLS 0.5.0 Metathesaurus The Metathesaurus now contains more than 1 million concepts and 5 million unique concept names from more than 100 different source vocabularies. In the 2006AA release 22 source vocabularies were updated including HCPCS, Altlink, CPT, and UMDNS. 0.5.1 MetamorphoSys Filter Changes With the 2006AA version of MetamorphoSys, several Filter names have changed. Users who use a configuration file from a previous version may recieve an error notice. Filters that have changed include: The Attributes To Exclude Filter, The Relationships To Exclude Filter, and The Semantic Types To Exclude Filter. 4 MRCXT File removed Users who require the MRCXT file will need to create that file after creating a subset. The information formerly contained in MRCXT is found in MRHIER.RRF.