12/13/95 blh 1/1/96 UMLS KNOWLEDGE SOURCES 7th EXPERIMENTAL Edition - January 1996 DOCUMENTATION 0. Introduction 1. Overview of the UMLS Project 1.1 Purpose 1.2 Development Strategy 1.3 Sources of Additional Information 2. Metathesaurus 2.0 Introduction 2.1 Source Vocabularies 2.2 Organization by Concept 2.2.1 Order of precedence among concept names 2.2.2 Strings with multiple meanings 2.3 Relationships between different Concepts 2.4 Concept, term, and string attributes 2.5 Data Elements 2.5.1 Concept Names 2.5.2 Relationships 2.5.3 Attributes 2.6 Concept Name Indexes 2.6.0 Introduction 2.6.1 Word Index 2.6.1.1 Description 2.6.1.2 Definition of Word 2.6.1.3 Example 2.6.2 Normalized Word Index 2.6.2.1 Description 2.6.2.2 Definition of Normalized Word 2.6.2.3 Example 2.6.3 Normalized String Index 2.6.3.1 Description 2.6.3.2 Definition of Normalized String 2.6.3.3 Example 2.6.4 Word Index Programs 2.7 File Formats 2.7.0 Introduction 2.7.1 ASCII Relational Format 2.7.1.1 General Description of Format 2.7.1.1.1 Data Files 2.7.1.1.2 Ancillary Files 2.7.1.1.2 Columns and Rows 2.7.1.2 Descriptions of Each File 2.7.1.2.1 Relation Relation (MRFILES) 2.7.1.2.2 Attribute Relation (MRCOLS) 2.7.1.2.3 Concept Names (MRCON) 2.7.1.2.4 Related Concepts (MRREL) 2.7.1.2.5 Co-occurring Concepts (MRCOC) 2.7.1.2.6 Simple attributes (MRSAT) 2.7.1.2.7 Definitions (MRDEF) 2.7.1.2.8 Sources (MRSO) 2.7.1.2.9 Semantic Types (MRSTY) 2.7.1.2.10 Concept Contexts (MRCXT) 2.7.1.2.11 Associated Expressions (MRATX) 2.7.1.2.12 Locators (MRLO) 2.7.1.2.13 Word Index 2.7.1.2.14 Normalized Word Index (MRXNW.ENG) 2.7.1.2.15 Normalized String Index (MRXNS.ENG) 2.7.1.2.16 Ambiguous Terms (AMBIG.LUI) 2.7.1.2.17 Ambiguous Strings (AMBIG.SUI) 2.7.2 ASN.1 Format 2.7.2.0 Introduction 2.7.2.1 Data Model 2.7.2.2 List of Files 2.7.2.3 Partial Metathesaurus Specification 2.7.2.4 Partial Metathesaurus Concept Example 3. Semantic Network (see file /UM96_RL1/NET/DOC/NET.DOC) 3.0 Introduction 3.1 Overview 3.2 ASCII Relational Format 3.3 ASCII Unit Record Format 3.4 ASN.1 Format 3.5 Hierarchies and Definitions for Semantic Types and Relationships 3.6 Sample Records 4. SPECIALIST Lexicon and Lexical Programs (see file /UM96_RL2/LEX/DOC/LEX.DOC) 4.0 Introduction 4.1 General Description 4.2 The Scope of the Lexicon 4.3 Lexicon Data Elements 4.4 Lexicon ASCII Relational Tables 4.5 Lexcion Unit Record 4.6 Lexical Databases 4.7 Sample Records 4.8 Lexical Programs 5. Information Sources Map (see file /UM96_RL1/ISM/DOC/ISM.DOC) 5.1 Introduction 5.2 Information Sources Map ASCII Relational Format 5.3 Descriptions of ISM Tables 5.4 List of Current Contents of the ISM 5.5 Changes from the Last Release 5.6 Field Description for ISM Main Records 5.7 Example Record 6. Using the UMLS Knowledge Source Server via the Internet 7. Using the UMLS CD-ROMs 7.1 Content of the CD-ROMs 7.2 Hardware/Software Requirements 8. Differences between the Current and Previous Editions 8.0 Introduction 8.1 Metathesaurus 8.2 Semantic Network 8.3 SPECIALIST Lexicon 8.4 Information Sources Map Appendix A: Experimental Agreement for Use of the UMLS Knowledge Sources Appendix B: Metathesaurus Data Elements and Source Vocabulary Information B.0 Introduction B.1 Data Elements B.1.0 Format of Descriptions B.1.1 Data Element Descriptions B.2 Source Vocabularies and Their Abbreviations B.3 Number of Strings from Each Source B.4 Types of Concept Names in Source Vocabularies and Their Abbreviations B.5 Order of Precedence of Sources and Types of Concept Names APPENDIX C: Abstract Syntax Notation 1 (ASN.1) Format -- General Description and Overview of UMLS ASN.1 Data Model (See file /UM96_AS1/DOC/ASN.DOC) 0. INTRODUCTION TO THE DOCUMENTATION This documentation provides information about the Unified Medical Language System (UMLS ) Knowledge Sources. The Metathesaurus , the Semantic Network, the SPECIALIST Lexicon, and the Information Sources Map are experimental products of the U.S. National Library of Medicine. These Knowledge Sources are designed primarily for use by system developers. They are meant to be consulted and used by search interface programs to interpret and refine user queries, to map the user's terms to appropriate controlled vocabularies and classification schemes, to select relevant information sources, and to assist in structured data creation. They are also useful as reference tools for database builders, librarians and other information professionals. The documentation is arranged as follows: Introduction to the entire UMLS project (Section 1) Metathesaurus (Section 2) Semantic Network (Section 3) SPECIALIST Lexicon and related lexical software tools (Section 4) Information Sources Map (Section 5) Using the UMLS Knowledge Source Server via the Internet (Section 6) Using the UMLS CD-ROMs (Section 7) Differences between the current and previous versions of UMLS Knowledge Sources(Section 8) Some detailed information is included in the Appendices that are referenced in the basic sections of the documentation. To obtain access to the UMLS Knowledge Sources, you must sign an experimental agreement (Appendix A) and send it to: Betsy L. Humphreys UMLS Project Officer National Library of Medicine 8600 Rockville Pike Bethesda, MD 20894 SECTION 1 OVERVIEW OF THE UMLS PROJECT 1.1 Purpose The UMLS project is a long-term NLM research and development effort designed to facilitate the retrieval and integration of information from multiple machine-readable biomedical information sources. The sources of interest include: descriptions of the biomedical literature, clinical records, factual databanks, knowledge-based systems, and directories of people and organizations. Major barriers to effective retrieval and integration of information from these sources include (1) the variety of vocabularies and classifications used in different sources and by different users and (2) the sheer number and wide distribution of potentially relevant information sources. These barriers deter health professionals and researchers from using available machine-readable information and also hamper the development of effective search interfaces that might assist these users. 1.2 Development Strategy The UMLS approach involves the development of machine-readable "Knowledge Sources" that can be used by a wide variety of applications programs to compensate for differences in the way concepts are expressed in different machine-readable sources and by different users, to identify the information sources most relevant to a user inquiry, and to negotiate the telecommunications and search procedures necessary to retrieve information from these sources. The goal is to make it easy for users to link information from patient record systems, bibliographic databases, factual databases, expert systems, etc. The UMLS Knowledge Sources can also assist in health data creation and indexing applications. There are four UMLS Knowledge Sources. The Metathesaurus (Section 2) contains semantic information about biomedical concepts, their various names, and the relationships among them. The Semantic Network (Section 3) is a network of the general categories or semantic types to which all concepts in Metathesaurus have been assigned. The SPECIALIST Lexicon (Section 4) contains syntactic information about biomedical terms and will eventually cover the majority of component terms in the concept names present in the Metathesaurus. A number of lexical programs are distributed with the UMLS Knowledge Sources for use with the Lexicon and the Metathesaurus. The Information Sources Map (Section 5) contains both human-readable and machine-processable information about available sources of machine-readable biomedical information. The UMLS project is directed by an internal NLM research and development team and involves outside research groups funded by contracts and grants. Those currently funded by NLM to conduct UMLS- related research and development include: Lexical Technology, Inc., Massachusetts General Hospital, Brigham and Women's Hospital, the University of Pittsburgh, Columbia University, Stanford University, the Mayo Clinic, and Kaiser-Permanente. More than 600 institutions and individuals throughout the world are currently experimenting with the UMLS Knowledge Sources in a variety of applications. NLM itself makes use of the UMLS Metathesaurus in Internet Grateful Med to enhance MEDLINE searching. The strategy for the development of all UMLS components is to build successive approximations of the capabilities ultimately desired. The current edition of the UMLS Knowledge Sources supersedes the previous edition and includes substantial additional content. 1.3 Sources of Additional Information Current Fact Sheets on the UMLS project, each of the four UMLS Knowledge Sources, the UMLS Knowledge Source Server, and Internet Grateful Med, an NLM interface to MEDLINE that makes use of the UMLS Metathesaurus, are available from NLM's World Wide Web Server: http://www.nlm.nih.gov A good review of the UMLS project appears in: Lindberg DAB, Humphreys BL, McCray AT. The Unified Medical Language System. Meth Inform Med 1993; 32:281-91. The following three articles describe significant additions to the UMLS Knowledge Sources made after the review article was published: McCray AT, Srinivasan S, Browne AC. Lexical Methods for managing variation in biomedical terminologies. Proc Annu Symp Comput Appl Med Care 1994;:235-9. McCray AT, Razi, A. The UMLS Knowledge Source Server. MEDINFO 1995;:144-7. McCray AT, Divita G. ASN.1: Defining a Grammar for the UMLS Knowledge Sources. Proc Annu Symp Comput Appl Med Care 1995;:868-72. Other relevant articles can be retrieved in MEDLINE under the subject heading Unified Medical Language System. SECTION 2 METATHESAURUS 2.0 INTRODUCTION The Metathesaurus is the central vocabulary component of the UMLS. The term Metathesaurus draws on Webster's third definition for the prefix "Meta," i.e., "more comprehensive, transcending." In a sense, the Metathesaurus transcends the specific vocabularies and classifications it encompasses. The Metathesaurus is a database of information on concepts that appear in one or more of a number of different controlled vocabularies and classifications used in the field of biomedicine. In general, the scope of the Metathesaurus is determined by the combined scope of its source vocabularies. The Metathesaurus preserves the meanings, hierarchical connections, and other relationships between terms present in its source vocabularies, while adding certain basic information about each of its concepts and establishing new relationships between concepts and terms from different source vocabularies. 2.1 SOURCE VOCABULARIES The 1996 Metathesaurus contains 252,892 concepts and 542,723 different concept names from 30 vocabularies and classifications, some in multiple editions. (A complete list of the current Metathesaurus source vocabularies appears in Appendix B, Section B.2.) Many of the source vocabularies are included in their entirety; for others the Metathesaurus has partial coverage. (The number of concept names from each source is detailed in Appendix B, Section B.3.) The Metathesaurus source vocabularies include large disease classifications used for clinical data, statistical reporting and billing; terminology used in ambulatory record systems; more narrowly focused vocabularies used to record data related to psychiatry, nursing, medical devices, adverse drug reactions, etc.; disease and finding terminologies from expert diagnostic systems, and some thesauri used in information retrieval. The Metathesaurus structure can incorporate translations of its source vocabularies into languages other than English. The 1996 Metathesaurus includes the French, German, Portuguese, and Spanish translations of NLM's Medical Subject Headings (MeSH). Future editions will include translations of other source vocabularies. 2.2 ORGANIZATION BY CONCEPT 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. Each concept or meaning in the Metathesaurus has a unique concept identifier (CUI) which itself has no intrinsic meaning. Each unique concept name or string in each language in the Metathesaurus has a unique string identifier (SUI). Any variation in upper-lower case is a separate string, with a separate SUI. The same string in different languages (e.g., English and Spanish) will have a different string identifier for each language. For English language entries in the Metathesaurus only, each string is linked to all of its lexical variants or minor variations by means of a common term identifier (LUI). (In the Metathesaurus, therefore, an English "term" is the group of all strings that are lexical variants of each other.) All string and term identifiers are linked to at least one concept identifier. Different terms with the same meaning are linked to the same concept identifier. Thus in the Metathesaurus, strings are linked to terms and both strings and terms are linked to concepts. Concepts (CUIs) Terms (LUIs) Strings (SUIs) C0004238 L0004238 S0016668 (preferred) (preferred) (preferred) Atrial Fibrillation Atrial Fibrillation Atrial Fibrillation Atrial Fibrillations Atrial Fibrillations Auricular Fibrillation S0016669 Auricular Fibrillations (plural variant) Atrial Fibrillations L0004327 S0016899 (synonym) (preferred) Auricular Fibrillation Auricular Auricular Fibrillations Fibrillation S0016900 (plural variant) Auricular Fibrillations FIGURE 1 For example, in Figure 1, the string "Atrial Fibrillation" and its plural "Atrial Fibrillations" have different string identifiers, but are linked to the same term identifier. "Auricular Fibrillation" and its plural "Auricular Fibrillations" are linked to a different term identifier. Since "Atrial Fibrillation" and "Auricular Fibrillation" have been judged to have the same meaning, their different term identifiers are linked to the same concept identifier. For each term, one string is designated as the preferred form. "Atrial Fibrillation" is labelled as the preferred form of its term; "Atrial Fibrillations" is labelled as a plural variant of this preferred form. "Auricular Fibrillation" is labelled as the preferred form of its term; "Auricular Fibrillations" is labelled as a plural variant of this preferred form. One of the terms is designated as the preferred name of the concept. In this case, the "Atrial Fibrillation" term is designated as the preferred term and therefore its preferred form, "Atrial Fibrillation", is the preferred name of the concept in the Metathesaurus. 2.2.1 ORDER OF PRECEDENCE AMONG CONCEPT NAMES To avoid laborious selection among alternative terms and forms of terms, selection of the preferred term for any Metathesaurus concept and the preferred form of any Metathesaurus term is based on an order of precedence of Metathesaurus source vocabularies that takes into consideration the various types of strings in each vocabulary, e.g., preferred names, cross references, abbreviations. The order of precedence used appears in Appendix B, Section B.5. 2.2.2 STRINGS WITH MULTIPLE MEANINGS In a relatively small number of cases, the same string may name different concepts, usually in different Metathesaurus source vocabularies. In the abbreviated example below, in one vocabulary the string "Cold" is a name for the temperature. In another vocabulary, "Cold" is an alternate name for the "Common cold". As a result the string "Cold" and its unique string identifier are linked to two different concepts in the Metathesaurus. As illustrated in Figure 2, two distinct "Cold" strings, "Cold <1>" and "Cold <2>", have been created for the Metathesaurus to give each meaning a unique name. Each of these strings is linked to only one concept. The plain string "Cold" has an explicit "ambiguous string" indicator in the Metathesaurus and is linked to both of the qualified strings. In future editions of the Metathesaurus, a different approach to distinguishing the strings is likely to be adopted, e.g., "Cold (temperature)", " Cold (disease)". Concepts (CUIs) Terms (LUIs) Strings (SUIs) C0009264 L0009264 S0007170 Cold <1> Cold <1> Cold <1> Cold Cold <2> Cold S0026353 Cold C0009443 L0009443 S0007171 Common Cold Common Cold Cold <2> Cold Cold <2> S0026747 Common Cold FIGURE 2 2.3 RELATIONSHIPS BETWEEN DIFFERENT CONCEPTS The Metathesaurus also represents several types of relationships between different concepts. Many relationships are derived directly from the source vocabularies. For example, the fact that there is a relationship between "Atrial Fibrillation" and "Arrhythmia" is derived from the hierarchical tree structures in the Medical Subject Headings (MeSH). The exact nature of the relationship, i.e., "Atrial Fibrillation" is a "Arrhythmia", is not present in MeSH, but was added during the construction of the Metathesaurus. Relationships between concepts from different source vocabularies were also created during Metathesaurus construction. For example, the COSTAR concept "Paroxysmal Atrial Fibrillation" is identified in the Metathesaurus as having a narrower-than relationship to "Atrial Fibrillation", a concept that is present in MeSH, ICD-9-CM, SNOMED, and COSTAR. 2.4 CONCEPT, TERM, AND STRING ATTRIBUTES All other pieces of information in the Metathesaurus are either attributes of a concept, attributes of a term, or attributes of a string. For example, the semantic type "Disease or Syndrome" and the definition "Disorder of cardiac rhythm characterized by rapid, irregular atrial impulses and ineffective atrial contractions." are attributes of the concept with the preferred name "Atrial Fibrillation". The eponym label attached to the term "Sturge-Weber Syndrome" is a term attribute. The various sources of the string "Atrial Fibrillation" e.g., SNM2|PT|F-73570, ICD91|PT|427.31, are string attributes. The structure of the Metathesaurus distribution files facilitates access to concept relationships and to string, term, and concept attributes, irrespective of the string used as a point of entry. 2.5 DATA ELEMENTS 2.5.0 INTRODUCTION The Metathesaurus has three logical groups of data elements, which are briefly described in the following sections. A complete description of each data element appears in Appendix B, Section B.1, which is arranged alphabetically by data element abbreviation, e.g., CUI. 2.5.1 CONCEPT NAMES These data elements establish the synonymous relationships among all Metathesaurus strings and terms that have the same meaning. In other words, these elements connect all the different names for the same concept that are known to the Metathesaurus and specify certain characteristics of each name. The concept name data elements are as follows: CUI Unique Identifier for Concept LUI Unique Identifier for Term TS Term Status LAT Language of Term SUI Unique Identifier for String STT String Type STR String 2.5.2 RELATIONSHIPS These data elements describe relationships between different Metathesaurus concepts or meanings. By definition, these are non- synonymous relationships, although the combination of concepts represented in an Associated Expression may have a meaning equivalent to the single concept to which the expression is linked. Relationships may be derived from the Metathesaurus source vocabularies or be added expressly for the Metathesaurus. The relationship data elements are as follows: REL Related Concepts COC Co-occurring Concepts ATX Associated Expressions 2.5.3 ATTRIBUTES These data elements provide additional information that helps to define the meaning of a concept and explain how it has been used in various information sources; identify special kinds of terms, e.g., eponym, acronym, tradename, laboratory number, that may require special handling in information retrieval and natural language processing applications; or provide information about the source(s) of the unique strings in the Metathesaurus. There are more than 50 attribute data elements in the Metathesaurus. A few examples are listed below. See Appendix B, Section B.1 for a complete list. Concept Attributes, e.g, DEF Definition STY Semantic Type CXT Hierarchical context RN Registry Number Term Attribute LT Lexical Tag String Attributes, e.g., SO Source of String 2.6 CONCEPT NAME INDEXES 2.6.0 INTRODUCTION To assist system developers in building applications that retrieve all strings or concept names which include specific words or groups of words, three indexes to the concept names are provided: a Word Index, a Normalized Word Index (for English words only), and a Normalized String Index (for English strings only). The indexes are described in sections 2.6.2, 2.6.3, and 2.6.4 respectively. To make the distinctions among them clearer, the descriptions include words or strings that would appear in each index for the following set of Metathesaurus concept names: Lung Diseases, Obstructive (C0024117, L0024117, S0058463) Obstructive Lung Diseases (C0024117, L0024117, S0068169) Lung Disease, Obstructive (C0024117, L0024117, S0058458) Obstructive Lung Disease (C0024117, L0024117, S0068168) 2.6.1 WORD INDEX 2.6.1.1 Description The word index connects each individual word in any Metathesaurus string to all its related string, term, and concept identifiers. There are separate word index files for each language in the Metathesaurus. There is one entry for each word found in each unique string in each language. Each entry has five sub-elements. 1. Abbreviation of language of word (see LAT data element for allowed values, in Appendix B, Section B.1) 2. Lower-case word 3. CUI 4. LUI 5. SUI 2.6.1.2 Definition of a Word For the purpose of creating this index, a word is defined as a token containing only alphanumeric characters with length one or greater. 2.6.1.3 Example For the four concept names listed in section 2.6.0, the word index will contain multiple entries for each of the following words: disease, diseases, lung, obstructive. Two of the entries generated for the names "Lung Disease, Obstructive" and Obstructive Lung Disease" are shown below: ENG|disease|C0024117|L0024117|S0058458 ENG|disease|C0024117|L0024117|S0068168 2.6.2 NORMALIZED WORD INDEX 2.6.2.1 Description The normalized word index connects each individual normalized English word to all its related string, term, and concept identifiers. There is one entry for each normalized word found in each unique English string. There are no entries for other languages in this index. Each entry has five sub-elements. 1. Abbreviation of language of normalized word (always ENG in this edition of the Metathesaurus) 2. Lower-case, normalized word 3. CUI 4. LUI 5. SUI 2.6.2.2 Definition of Normalized Word The normalization process involves breaking a string into its constituent words, lower-casing each word and converting it to its canonical form. Canonical forms are generated by uninflecting each word, stripping a small number of stop words, and looking the uninflected words up in an equivalence class table. The uninflected forms are generated using the SPECIALIST lexicon if the words appear in the lexicon, otherwise they are generated algorithmically. 2.6.2.3 Example For the four concept names listed in section 2.6.0 the normalized word index will contain multiple entries for each of the following words: disease, lung, obstructive. Since the normalized word index contains base forms only, it does not contain entries for the plural "diseases". In this index, therefore, all four concept names are linked to the normalized word "disease", e.g., ENG|disease|C0024117|L0024117|S0058458 ENG|disease|C0024117|L0024117|S0058463 ENG|disease|C0024117|L0024117|S0068168 ENG|disease|C0024117|L0024117|S0068169 2.6.3 NORMALIZED STRING INDEX 2.6.3.1 Description The normalized string index connects the normalized form of a Metathesaurus string to all its related string, term, and concept identifiers. There is one entry for each unique (non-normalized) English string. There are no entries for other languages in this index. Each entry has five sub-elements. 1. Abbreviation of language of normalized string (always ENG in this edition of the Metathesaurus) 2. Lower-case normalized string 3. CUI 4. LUI 5. SUI 2.6.3.2 Definition of Normalized String The normalization process involves breaking a string into its constituent words, lower-casing each word, converting each word to its canonical form, and sorting the words in alphabetic order. Canonical forms are generated by uninflecting each word, stripping a small number of stop words, and looking the uninflected words up in an equivalence class table. The uninflected forms are generated using the SPECIALIST lexicon if the words appear in the lexicon, otherwise they are generated algorithmically. 2.6.3.3 Example Since the four concept names listed in section 2.6.0 are composed of the same set of normalized words, the Normalized String Index will contain four entries for a single string: disease lung obstructive, in which the component normalized words appear in alphabetical order. The complete set of Normalized String Index entries generated by the four concept names is as follows: ENG|disease lung obstructive|C0024117|L0024117|S0058458 ENG|disease lung obstructive|C0024117|L0024117|S0058463 ENG|disease lung obstructive|C0024117|L0024115|S0068168 ENG|disease lung obstructive|C0024117|L0024117|S0068169 2.6.4 WORD INDEX PROGRAMS The programs that generate these indexes are written in C and were developed to run under Unix. They may be of use to system developers who are developing their own interfaces to the UMLS data or for other purposes. Section 4 includes information about these and other lexical programs provided with the UMLS Knowledge Sources. 2.7 FILE FORMATS 2.7.0 INTRODUCTION The Metathesaurus data are distributed in two physical formats: an ASCII Relational Format (Section 2.7.1) and an ASN.1 (Abstract Syntax Notation) Format (2.7.2). A general explanation of ASN.1 and the ASN.1 tools provided with the UMLS Metathesaurus appears in Appendix C. 2.7.1 ASCII RELATIONAL FORMAT 2.7.1.1 General Description The Metathesaurus relational format is not fully normalized. By design, there is duplication of data among different relations and within certain relations. In particular, links between different Metathesaurus concepts appear twice (e.g., from entry A to entry B and from entry B to entry A). Developers will need to make their own decisions about the extent to which this redundancy should be retained, reduced, or increased for their specific applications. All file names in the relational format begin with the letters MR. If a single file would exceed 32 megabytes it is divided into 32 megabyte segments of up to 32 megabytes and consecutive numbers are appended to the file names for the segments, e.g., MRCOC01, MRCOC02. All files are sorted from left to right in ascending order by contents of the columns. 2.7.1.1.1 Data Files The data is each Metathesaurus entry are represented in up to 13 different "relations" or files. These files correspond to the 3 logical groups of data elements described in Section 2.5 and the indexes described in Section 2.6 as follows: Metathesaurus Concept Names (2.5.1) = MRCON Relationships between Different Concept Names(2.5.2) = MRREL, MRCOC Attributes (2.5.3)= MRSAT, MRDEF, MRSTY, MRCXT, MRATX, MRLO, MRSO Indexes (2.6) = MRXW.ENG, MRXW.FRE, MRXW.GER, MRXW.POR, MRXW.SPA, MRXNW.ENG,MRXNS.ENG Each of these relations or files contains the information from all Metathesaurus entries for a given subset of the data elements described in Appendix B, Section B.1. 2.7.1.1.2 Ancillary Files There are 4 ancillary files: MRFILES describes the size of the 13 data files. MRCOLS describes the columns or data elements in the 13 data files. AMBIG.LUI contains all "ambiguous" term identifiers in the Metathesaurus. AMBIG.SUI contains all "ambiguous" string identifiers in the Metathesaurus. The latter two files provide a convenient way to identify all Metathesaurus terms and strings that have more than one meaning in Metathesaurus source vocabularies. 2.7.1.1.3 Columns and Rows Each relation or named table of data values has by definition a fixed number of columns; the number of rows depends on the content of a particular version of the Metathesaurus. A column is a sequence of all the values in a given data element or logical sub-element. In general, columns for longer variable length data elements will appear to the right of columns for shorter and/or fixed length data elements. With the exception of the columns in MRFILES and MRCOLS, the information in all columns in the relational files is described in Appendix B, Section B.1, Metathesaurus Data Elements, under the data element name given in the file description or in each column description. If data items described as logical sub-elements in Appendix B are stored in separate columns in the relational format, this is stated in the file description. A row contains the values for one or more data elements or logical sub-elements for one Metathesaurus entry. Depending on the nature of the data elements involved, each Metathesaurus entry may have one or more rows in a given file. The values for the different data elements or logical sub-elements represented in the row are separated by vertical bars (|). If an optional element is blank, the vertical bars are still used to maintain the correct positioning of the subsequent elements. Each row is terminated by a vertical bar and a carriage return followed by a line feed. (|). 2.7.1.2 Descriptions of Each File 2.7.1.2.1 Relation Relation (File = MRFILES) There is exactly one row in this file for each physical segment of the files in the relational format. The columns or data elements in the file are: Cols. FIL- Physical FILENAME DES- Descriptive File Name FMT- Comma separated list of COL, in order CLS- # of COLUMNS RWS- # of ROWS BTS- Size in Bytes 2.7.1.2.2 Attribute Relation (File = MRCOLS) There is exactly one row in this file for each column or data element in each file in the relational format. Cols. COL- Column or data element name DES- Descriptive Name REF- Documentation Section Number MIN- Minimum Length, Characters AV- Average Length MAX- Maximum Length, Characters FIL- Physical FILENAME in which this field occurs 2.7.1.2.3 Concept Names (File = MRCON) There is exactly one row in this file for each meaning of each unique string in the Metathesaurus, i.e., there is exactly one row for each unique CUI-SUI combination. Any difference in upper-lower case, word order, etc. creates a different unique string. Cols. CUI - Unique identifier for concept LAT - Language of Term TS - Term status LUI - Unique identifier for term STT - String type SUI - Unique identifier for string STR - String 2.7.1.2.4 Related Concepts (File = MRREL) There are two rows in this table for each relationship between Metathesaurus concepts (except co-occurrence relationships) that is known to the Metathesaurus--one row for each direction of the relationship. All of the specific columns in this file are described as logical sub-elements in the REL description in Appendix B. Cols. CUI1 - Unique identifier of first concept REL - Relationship of second to first concept CUI2 - Unique identifier of second concept RELA - Relationship attribute SAB - Abbreviation of the source of relationship SL - Source of relationship labels MG - Machine-generated and unverified indicator (optional) 2.7.1.2.5 Co-occurring Concepts (File = MRCOC) There are two rows in this table for each pair of concepts that co- occur in each information source represented -- one for each direction of the relationship. (Note that the COA data may be different for each direction of the relationship.) Many Metathesaurus concepts have no entries in this file. The columns in this file are described as logical sub-elements in the REL description in Appendix B. Due to the very large number of co- occurrence relationships, they are distributed in a separate file. Cols. CUI1 - Unique identifier of first concept (3.3.1.1) CUI2 - Unique identifier of second concept (3.3.1.1) SAB - Abbreviation of the Source of co-occurrence information (3.3.2.2) if applicable COT - Type of co-occurrence (3.3.2.2) COF - Frequency of co-occurrence (3.3.2.2), if applicable COA - Attributes of co-occurrence (3.3.2.2), if applicable 2.7.1.2.6 Simple Concept, Term and string attributes (File = MRSAT) There is exactly one row in this table for each concept, term and string attribute that does not have a sub-element structure. All Metathesaurus concepts have entries in this file. Cols. CUI - Unique identifier for concept or, for LT element only, LUI for term LUI - Unique identifier for term (optional) SUI - Unique identifier for String (optional) SCD - Unique identifier or code for entry in the source of the attribute, e.g., for all attributes derived from MeSH, the MeSH unique identifier This is a sub-element of SO. (optional) ATN - Attribute name. Possible values (all described in Appendix B, Section B.1) are: AM, AN, CX, DA, DC, DE, DQ, DS, DX, DY, EC, EV, EZ, FR, GM , HN, II, LA, LT, LU, M66, M75, M80, M85, M89,MDA, MED, MMR, MN, MR, NA, NAT, NH, NSR, OL, PA, PDA, PI, PM, PX, QA, QE, QG, QS, QT, RN, RR, SB, SCT, SIC, SMX, SOS, SRC, ST, TH SAB - Abbreviation of the source of the attribute (This is a sub- element of SO. Allowed values are listed in Appendix B, Section B.2) ATV - Attribute value - described under specific attribute name above in Appendix B, Section B.1) A few AN values exceed 1,000 characters. 2.7.1.2.7 Definitions (File = MRDEF) There is exactly one row in this file for each definition in the Metathesaurus. A few definitions approach 3,000 characters in length. Cols. CUI - Unique identifier for concept SAB - Abbreviation of the source of the definition DEF - Definition 2.7.1.2.8 Sources (File = MRSO) There is exactly one row in this file for each source of each string in the Metathesaurus. All Metathesaurus concepts have entries in this file. Cols. CUI - Unique Identifier for concept LUI - Unique identifier for term SUI - Unique identifier for string SAB - Source abbreviation (This is a sub-element of SO. See Appendix B, Section B.1. Allowed values are listed in Appendix B, Section B.2) TTY - Term type in that source (This is a sub-element of SO. Allowed values are listed in Appendix B., Section B.3) SCD - Unique Identifier or code for string in that source (This is a sub-element of SO). 2.7.1.2.9 Semantic Types (File = MRSTY) There is exactly one row in this file for each semantic type assigned to each concept. All Metathesaurus concepts have at least one entry in this file. Many have more than one entry. Cols. CUI - Unique identifier of concept TUI - Unique identifier of Semantic type (This is a sub-element of STY in Appendix B, Section B.1) The valid values are defined in the Semantic Network. STY- Semantic type. The valid values are defined in the Semantic Network. 2.7.1.2.10 Concept contexts (File = MRCXT) There are rows in this file for each hierarchical context in which a concept appears in any of the UMLS source vocabularies. Many Metathesaurus concepts have multiple contexts; many have none. The number of rows per context differs depending on the number of ancestor, sibling, or child terms the concept has in that context. Because some concepts have multiple contexts in the same source (e.g., MeSH), a context number (e.g., 1,2,3) is used for all members of the same context. The "distance-1 relationships" i.e., the immediate parent, immediate children, and sibling relationships, represented in this file are also present in the MRREL file (See REL element in Appendix B, Section B.1). The description of the CXN, CXL, RNK, CXS, HCD, and XS sub-elements appears under the CXT element in Appendix B, Section B.1. Cols. CUI - Unique identifier of concept SUI - Unique identifier for string used in this context SAB -Source abbreviation (This is a sub-element of SO. Allowed values are listed in Appendix B, Section B.2) SCD - Unique Identifier or code for string in that source (This is a sub-element of SO). CXN - Context number (To distinguish multiple contexts in the same source) CXL - Context member label, i.e., ANC for ancestor of this concept, CCP for concept, SIB for sibling of this concept, CHD for child of this concept. RNK - For rows with a CXL value of ANC, the rank of the ancestors (e.g., a value of 1 denotes the most remote ancestor in the hierarchy) CXS - String for context member. CUI2 - Unique concept identifier of context member (may be empty if context member is not yet in the Metathesaurus). HCD - Hierarchical number or code of context member in this source (optional). REL - Relationship of concept to parent, if applicable and known. The valid values are the relationships defined in the Semantic Network. XC - For rows with a CXL of CON, SIB or CHD and an SAB of MSH96, plus(+) sign indicating that the concept has children in this context, if applicable 2.7.1.2.11 Associated Expressions (File = MRATX) There is one row in this table for each vocabulary expression (i.e., combination of terms from a specific Metathesaurus source vocabulary) identified as having a identified relationship to a concept in the Metathesaurus. The majority of Metathesaurus entries have no entries in this table, but the number of ATXs increases with each edition of the Metathesaurus. Cols. CUI - Unique identifier of concept to which the expression is related SAB - Abbreviation of source of terms in expression (This is a sub-element of SO. Allowed values are listed in Appendix B, Section B.1) REL - Relationship of meaning of expression to main concept (a sub-element of ATX, described in Appendix B.1) ATX - Associated expression (has a complex internal syntax which is described in Appendix B, Section B.1) 2.7.1.2.12 Locators (File = MRLO) There is one row in this table for each Metathesaurus concept identified as appearing in each of a selected set of a machine-readable information sources. If the same concept is identified as appearing in more than one of these information sources (e.g., MEDLINE, DXPLAIN, QMR), it will have multiple rows in this table. Some Metathesaurus entries have no entries in this file. ISN, FR, UN, SNA, and SOUI are described as sub-elements of LO in Appendix B, Section B.1. Cols. CUI - Unique identifier of concept ISN - Name of information source or database in which concept appears FR - Frequency count of number of occurrences of concept in the information source (optional) UN - Meaning of frequency (optional) SUI - Unique identifier of string if name used in information source appears in MRCON (optional) SNA - Actual name that occurs in the information source if not otherwise present in the Metathesaurus (optional) SOUI - Unique identifier of record in which the concept appears in source (optional) 2.7.1.2.13 Word Index (File = MRXW.ENG, MRXW.FRE, MRXW.GER, MRXW.POR, MRXW.SPA) There is one row in these tables for each word found in each unique Metathesaurus string (ignoring upper-lower case). All Metathesaurus entries have entries in the word index. The entries are sorted in ASCII order. Cols. LAT - Abbreviation of language of the string in which the word appears WD - Word in lower-case CUI - Concept identifier LUI - Term identifier SUI - String identifier 2.7.1.2.14 Normalized Word Index (File=MRXNW.ENG) There is one row in this table for each normalized word found in each unique English-language Metathesaurus string. All English-language Metathesaurus entries have entries in the normalized word index. There are no normalized string indexes for other languages in this edition of the Metathesaurus. Cols. LAT - Abbreviation of language of the string in which the word appears (always ENG in this edition of the Metathesaurus) NWD - Normalized word in lower-case (described in Section 2.6.2.1) CUI - Concept identifier LUI - Term identifier SUI - String identifier 2.7.1.2.15 Normalized String Index (File=MRXNS.ENG) There is one row in this table for each normalized string found in each unique English-language Metathesaurus string (ignoring upper-lower case). All English-language Metathesaurus entries have entries in the normalized string index. There are no normalized word indexes for other languages in this edition of the Metathesaurus. Cols. LAT - Abbreviation of language of the string (always ENG in this edition of the Metathesaurus) NSTR - Normalized string in lower-case (described in Section 2.6.3.1) CUI - Concept identifier LUI - Term identifier SUI - String identifier 2.7.1.2.16 Ambiguous Term Identifiers (File = AMBIG.LUI) There is exactly one row in this table for each term identifier (LUI) that is linked to multiple concept identifiers (CUI). In the Metathesaurus, the LUI links all strings within the English language that are lexical variants of each other, irrespective of the meaning of each string. This table may be useful to system developers who make use of the LUI in their applications or in local data files. Cols. LUI in L####### format CUIs to which the term identifier is linked, separated by commas, e.g., C########,C######## 2.7.1.2.17 Ambiguous String Identifiers (File=AMBIG.SUI) There is exactly one row in this file for each string identifier (SUI) that is linked to multiple concept identifiers (CUI). In the Metathesaurus, there is only one SUI for each unique string within each language, even if the string has multiple meanings. This table is only of interest to system developers who make use of the SUI in their applications or in local data files. Cols. SUI in S######## format CUIs to which the string identifier is linked, separated by commas, e.g., C#######,C####### 2.7.2 ASN.1 FORMAT All four Knowledge Sources have been released in the ASN.1 (Abstract Syntax Notation One) format. ASN.1 provides a consistent description of the data in the Knowledge Sources, and it provides a grammar of the data so that it is possible to validate the data, uncovering any inconsistencies in the process. Further, ASN.1 is used within the Z39.50 protocol, an emerging standard for information retrieval applications. The ASN.1 standard comprises two ISO international standards, one that specifies the basic language and another one that specifies the basic encoding rules for transmitting data in ASN.1 format. The Basic Encoding Rules were designed to minimize data size at the possible expense of encoding and decoding time and CPU cycles. There is an effort to develop certain extensions to the Basic Encoding Rules, and these may address efficiency issues as well as issues of data security. An ASN.1 specification is built by using a set of predefined types such as integers, sets, sequences, strings, and the boolean values true and false. New types are defined using these building blocks, allowing the description of an arbitrarily complex set of data. In the following a partial specification and an example are given. See Appendix C for a fuller description of the ASN.1 format. 2.7.2.1 Data Model The ASN.1 data model is a hierarchical model rather than a relational model. An important feature of this model is the specification of concepts, terms, and strings as hierarchical structures. Because of the large size of the Metathesaurus, the ASN.1 specification of the Metathesaurus splits co-occurring concepts out into a separate module. Three types of indexes to Metathesaurus concept names are provided: word indexes in various languages, a normalized word index, and a normalized string index. These indexes connect each word, normalized English word, and normalized English string to all their related string, term, and concept identifiers. A cross reference between ASN.1 fields and relational fields is being distributed in lieu of duplicating the entire Metathesaurus data element documentation. Refer to the Metathesaurus documentation for the semantics of the contents of each ASN.1 field. C source programs containing objects and object methods associated with the ASN.1 version of the Metathesaurus are being distributed as well. The objects and object methods are intended as aids to system developers. The objects and object methods were created using the NCBI toolkit, and are dependent upon the toolkit's libraries. The character case of the enumerated object strings in the object loader files (meta.l) have been put into upper case for the Metathesaurus release. This will allow printing the values from enumerated fields in upper case, as they appear in the data documentation. This is only relevant when using the distributed object methods to print to text files. 2.7.2.2 The ASN.1 release of the Metathesaurus consists of the following files: META01.DAT Concepts (ASN.1 Encoded Data) META02.DAT Cooccurrences (ASN.1 Encoded Data) META03.DAT English Normalized Word Index (ASN.1 Data) META04.DAT English Normalized String Index (ASN.1 Data) META05.DAT English Word Index (ASN.1 Encoded Data) META06.DAT French Word Index (ASN.1 Encoded Data) META07.DAT Spanish Word Index (ASN.1 Encoded Data) META08.DAT Portuguese Word Index (ASN.1 Encoded Data) META09.DAT German Word Index (ASN.1 Encoded Data) META.ASN ASN.1 Specification for the Metathesaurus META.H ASN.1 header file for the Metathesaurus META.L ASN.1 loader file for the Objects and Methods META_OBJ.H ASN.1 header file for the Objects and Methods META_OBJ.C ASN.1 C file for the Objects and Methods META.REF Cross Reference of Relational format with ASN MAKEFILE Example Makefile to make the object methods 2.7.2.3 Partial Metathesaurus Specification UMLS-concept ::= SEQUENCE { name VisibleString, cui VisibleString, definitions SET OF UMLS-definition, semantic-types SET OF UMLS-semantic-type, umls-terms SET OF UMLS-term, related-concepts SET OF Related-concept } UMLS-definition ::= SEQUENCE { sab Source-abbreviation, def VisibleString } UMLS-semantic-type ::= SEQUENCE { tui VisibleString, name Semantic-type-name } UMLS-term ::= SEQUENCE { name VisibleString, lui VisibleString, language Language, lexical-tags SET OF Lexical-tag, umls-strings SET OF UMLS-string term-status Term-status } UMLS-string ::= SEQUENCE { name VisibleString, sui VisibleString, umls-string-type Umls-string-type, sources SET OF Source, } Source ::= SEQUENCE { sab Source-abbreviation, term-type Source-term-type, source-string-uid VisibleString } Related-concept ::= SEQUENCE { related-concept-cui VisibleString, relation Relation, relationship-attribute VisibleString, sab Source-abbreviation } 2.7.2.4 Partial Metathesaurus Concept Example UMLS-metathesaurus-module ::= { Concepts { { name "Achromia parasitica" , cui "C0001083" , definitions { { sab DOR27 , def "a variant of tinea versicolor occurring in dark-skinned infants, particularly in the tropics, which begins in the diaper region and spreads rapidly, causing marked depigmentation of the skin. Dorland's Illustrated Medical Dictionary 27th edition; entry for achromia parasitica." } } , semantic-types { { tui "T047" , name Disease or Syndrome } } , umls-terms { { name "Achromia parasitica" , lui "L0001083" , language ENG , lexical-tags { } , umls-strings { { name "Achromia parasitica" , sui "S0003566" , umls-string-type PF , sources { { sab DOR27 , term-type DT , source-string-uid "U000086" } , { sab SNM2 , term-type SY , source-string-uid "D-0587" } } } , { name "Achromia, parasitica" , sui "S0219364" , umls-string-type VW , sources { { sab ICD91 , term-type IT , source-string-uid "111.0" } } } } , term-status P } } , related-concepts { { related-concept-cui "C0040262" , relation RR , relationship-attribute "O" , sab MTH } } } } } SECTION 3 - see /UM96_RL1/NET/DOC/NET.DOC SECTION 4 - see /UM96_RL2/LEX/DOC/LEX.DOC SECTION 5 - see /UM96_RL1/ISM/DOC/ISM.DOC 6. Using the UMLS Knowledge Source Server Background The UMLS Knowledge Source Server is an evolving tool for providing Internet access to the information stored in the UMLS Knowledge Sources. The purpose of the Knowledge Source Server is to make the UMLS data more accessible to users, and in particular to systems developers. The system architecture is based on the client-server paradigm wherein remote site users send their requests to a centrally managed server at the U.S. National Library of Medicine. The client programs can run on platforms supporting the TCP/IP communication protocol. Access to the system is provided through a command-line interface, through an Application Programming Interface (API), and through the World Wide Web (WWW). Querying the Knowledge Source Server Metathesaurus The Knowledge Source Server allows the user to request information about particular Metathesaurus concepts, including, for example, attributes such as the concept's definition, its semantic types, the concepts that are related to it, etc. It also allows the user to request information about the attributes themselves, for example, by asking for all the concepts that have been assigned to a particular semantic type, or by asking for all the terms that have a particular lexical tag. Basic concept information includes the Metathesaurus unique identifier of the concept, the preferred name for the concept, and the names and sources of all terms that comprise that concept. Additional concept information often includes a definition and the source of that definition. Semantic type information is also included. Information about the hierarchical contexts of Metathesaurus concepts is easily available in the system. Related concepts are easily found, as well. If a user were interested in information about a particular term within a concept, then the results could be limited in that way. Term level information includes the syntactic category of the term and any lexical tags it might have, i.e., whether it is an abbreviation or acronym, eponym, lab number, or trade name. Co-occurrence data are included for MeSH and AI-RHEUM terminology. An important perspective on the Metathesaurus is source-specific data. It is possible to query the server by limiting the query to a particular vocabulary. For example, the user may wish to see the ancestors or descendents for a term in just a particular vocabulary, or the user may wish to see just the synonyms for a particular term in a particular vocabulary. Attributes may be queried in the system. Thus, all concepts with a particular semantic type, all terms with a particular syntactic category, all terms from a particular source vocabulary, and all terms with a particular lexical tag may be found. Searching for all concepts with a particular semantic type will, for example, give the user a good idea of the coverage of the Metathesaurus in a subject domain. Semantic Network The Semantic Network contains information about semantic types and their relationships. The implementation of the network module computes the relationships between semantic types using the inheritance property of the network type hierarchy. Information in the Semantic Network can be queried in terms of two semantic types and the relationship between them. Individual queries are specified by providing the known types or relations and leaving out the unknowns. The system then retrieves the corresponding values for the unknowns. For example, if the user wished to know what types are related by a particular relation, then the user would indicate only the relationship name and all the semantic type pairs linked by that relationship would be retrieved. The user might also wish to know if a particular relationship holds between a pair of types. It is possible to retrieve all the relations between a pair of types. For example, "treats", "prevents", and "complicates" would be listed, among others, as potential relationships between drugs and diseases. It is also possible to retrieve an exhaustive list of all related types in the network. In addition, queries can be made about the definition, unique identifier, tree number, ancestors, parents, children, descendents, and siblings of a semantic type or relation. SPECIALIST Lexicon The Knowledge Source Server provides access to lexical records in the SPECIALIST lexicon. The SPECIALIST lexicon is an English language lexicon containing many biomedical terms. The lexicon entry for each word or term records syntactic, morphological, and orthographic information. Currently the lexicon contains some 65,000 records, with approximately 130,000 forms. Lexical entries may be single or multi-word terms. Lexical information includes syntactic category, inflectional variation (e.g., singular and plural for nouns, the conjugations of verbs, the positive, comparative, and superlative for adjectives and adverbs), and allowable complementation patterns (i.e., the objects and other arguments that verbs, nouns, and adjectives can take). Information Sources Map The Knowledge Source Server provides access to the data stored in the Information Sources Map (ISM). The ISM contains records for computerized sources of biomedical information. It provides descriptive data about the information sources such as scope, probable utility, and access conditions. The information sources are varied and include bibliographic databases, diagnostic expert systems, and factual databases. Gaining Access to the UMLS Knowledge Source Server Access to the UMLS Knowledge Source Server is available to anyone who has signed the UMLS experimental agreement. Address a mail message to umlsks@nlm.nih.gov, stating that you have signed the experimental agreement, and provide the IP address of the computer you will be using to access the server. Information about using each of the three interfaces will be sent to you after receipt of your mail message. SECTION 7 USING THE UMLS CD-ROMS 7.1 Contents of the CD-ROMS The 1996 experimental edition of the UMLS Knowledge Sources comprises four CD-ROMs which together contain: two different physical formats of the UMLS Metathesaurus, and files that summarize the significant differences between this version and its immediate predecessor; three different physical formats of the Semantic Network; two formats of the Information Sources Map; three different physical formats for the SPECIALIST lexicon; and a set of Lexical programs for use with the UMLS Knowledge Sources. The contents of each disc are as follows: Disc 1: ISO 9660 (Disc Name = UM96_RL1) - Relational files Top level directory is UM96_RL1, with these subdirectories; there is documentation for each in a subdirectory named DOC: ISM: Information Sources Map in ASCII relational format; and Information Sources Map documentation in ASCII format META: Metathesaurus in ASCII relational format, except for co-occurrence data which is on Disc 2; Metathesaurus documentation in ASCII format; and files identifying significant differences from previous edition in the CHANGE subdirectory. NET: Semantic Network in ASCII Relational Format and unit record formats; and Semantic Network documentation in ASCII format Disc 2: ISO 9660 (Disc Name = UM96-RL2) - Relational Files Top level directory is UM96_RL2, with these subdirectories: LEX: SPECIALIST Lexicon in ASCII relational and Unit Record formats; related Lexical programs in C source code; and SPECIALIST documentation in ASCII format MRCOO: Metathesaurus Co-occurrence data in ASCII Relational format. Disc 3: ISO 9660 (Disc Name = UM96_AS1) ASN.1 - files and programs Top level directory is UM96_AS1, with ASN.1 Binary encoded data for the Information Sources Map, the Semantic Network, and the Metathesaurus, except the Co-occurrences. There are these subdirectories: DOC: An overview document on ASN.1 and sample files for each ASN.1 encoded knowledge source. NCBI: NCBI ASN.1 Toolkit Disc 4: ISO 9660 (Disc Name = UM96_AS2) ASN.1 Metathesaurus Co-occurrences and Specialist Lexicon Top level directory is UM96_AS2, with these subdirectories: LEX: The ASN.1 encoded SPECIALIST Lexicon. META: The ASN.1 encoded meta co-occurrences. 7.2 Hardware/Software Requirements 7.2.1 ISO 9660 Relational Data Discs (UM96_RL1, UM96_RL2) There are no executable files on these discs. Any machine equipped to read ISO 9660 CD-ROM discs will be able to access these Discs. CD-ROM hardware and software to read ISO 9660 discs is available for the IBM PC, Apple Macintosh, Unix, and many other environments. To use the ISO 9660 CD-ROM data disc in the Macintosh environment, an Apple Startup document named "Foreign File Access" and an Apple document named "ISO 9660 File Access" are required. All ASCII Relational and Unit Record files have lines terminated by (0D 0A hexadecimal, 13 10 decimal). This is the ISO 9660 and MS-DOS standard, and includes both the Unix and the Macintosh standard line terminators. If your software cannot use the data with these line terminators or convert or eliminate unneeded characters, then a filter program may be required. The ASCII files containing all 1996 Metathesaurus data elements total more than 800 megabytes. Please note that these files are distribution formats structured to allow developers to select data elements and create data representations which meet their own needs. Your information needs and your performance requirements will determine the data representation, hardware requirements, and software environment needed for your application. It is possible to extract a useful subset of data from the 1996 Metathesaurus to create an application in a modest hardware and software environment. Some applications and approaches to using Metathesaurus information may be demanding even for quite large systems. The most direct method of accessing 1996 Metathesaurus information in the ASCII files is to read the CD-ROM files into the database management system of your choice, where you may select data elements to create your desired data representation. In many cases, this will need to be done in steps constrained by disk space and software limitations. To assist in this process, the co-occurrence files have been segmented. The Semantic Network files total approximately 700 kilobytes. The Information Sources Map files total approximately one megabyte. The SPECIALIST Lexicon files and programs total approximately 80 megabytes. 7.2.2 ASN.1 Discs (UM96_AS1, UM96_AS2) The two disks contain the ASN.1 Binary Encoded files along with C source files, C header files and ASN.1 specification files. The discs can be read by any system which can read ISO 9660. In addition, the NCBI toolkit for manipulating ASN.1 encoded data is included. The tool kit is distributed in three formats, a compressed tar file for the Unix community and self extracting archives for the DOS and Mac communities. The toolkit supports other platforms as well, (see the NCBI documentation for specifics.) An ANSI C compiler is required to build the toolkit and the C source files associated with the ASN.1 binary encoded files. Additional information about the ASN.1 versions of the UMLS Knowledge Sources may be found in the DOC directory on Disc 3. SECTION 8 DIFFERENCES BETWEEN THE CURRENT AND PREVIOUS EDITION OF THE UMLS KNOWLEDGE SOURCES 8.0 General Introduction Beginning with the 1996 edition, new releases of the UMLS Knowledge Sources will be released early in the calendar year, rather than in the summer. This change allows applications that use the MeSH terminology in the UMLS Metathesaurus, e.g., NLM's Internet Grateful Med, to have access to the most current MeSH terminology that is being used in MEDLINE. Effective with the 1996 edition, NLM is no longer distributing browser applications for the Metathesaurus and the Semantic Network on the UMLS CDs. UMLS users may now use any World Wide Web client to browse the content of all four UMLS Knowledge Sources on the UMLS Knowledge Source Server (Section 6). An html encoded version of the documentation is also available on the server. Changes to each of the four UMLS Knowledge Sources are described in the following sections. Users of the Metathesaurus should pay particular attention to changes in the format of relationships (REL) which have been introduced to permit specific relationship attributes to be attached to any type of relationship. 8.1 Metathesaurus 8.1.0 Introduction The 1996 edition of the Metathesaurus includes about 30,000 concepts that were not present in the previous edition and several thousand additional definitions. New in 1996 Metathesaurus are: the complete disease axis of SNOMED International; more cancer terminology from PDQ (Physician Data Query); more disease and findings vocabulary from the COSTAR ambulatory record system; the German translation of the Medical Subject Headings (MeSH); and updates to a number of the vocabularies already present in the Metathesaurus. All concepts new to the Metathesaurus can be retrieved by searching the DA element for values that begin with 1996. The format of the year in the DA (Date of entry) and MR (Major revision date) elements has been changed from 2 to 4 digits. Pointers to the HSTAT electronic full-text versions of clinical practice guidelines sponsored by the Agency for Health Care Policy and Research have been added to the Metathesaurus locator data (LO). The format of REL has been changed. The general relationships RR (Reviewed Relationship) and UR (Unreviewed Relationship) have been eliminated. They have been replaced by RB (Related - Broader), RN, (Related - Narrower), RO (Related - Other), and RL (Related -- Alike or similar for "quasi-synonyms"). Any relationship may now have a specific relationship attribute taken from the set of all relationships allowed in the Semantic Network. The changes to REL will necessitate modifications to programs that extract or make use of UMLS relationship data. Details of the new format appear in the description of REL in Appendix B, Section B.1. Several new attributes have been added to the Metathesaurus for information from SNOMED International, the Neuronames Brain Hierarchy, and PDQ. See descriptions of PDA (PDQ Abbreviation or Short Name), NA (Neuronames Abbreviation), NAT (Neuronames Anatomy Type), NSR (Neuronames Species Restriction), SIC (SNOMED ICD-9-CM Reference), and SMX (SNOMED Multi-axial coding) in Appendix B, Section B.1. Information stored in the PA attribute (MeSH Pharmacological Action) is now also expressed as an "is-a" relationship between a specific drug and a class of drugs having the same pharmacologic action. Some concepts present in the 1995 Metathesaurus have been deleted from 1996 version; the majority of these are concepts from the MeSH supplementary chemical file that were mentioned once in a MEDLINE citation some time ago, but have not reappeared. In some cases, the preferred name of a Metathesaurus concept has changed, with the former preferred form retained as a synonym or lexical variant. Some lexical variants have been added; others have been deleted. 8.1.1 Metathesaurus Change Files 8.1.1.1 Introduction There are five files or relations that identify key differences between reviewed entries in the 1995 and the 1996 editions of the Metathesaurus. They are in the subdirectory called CHANGE in META directory on Disc 1 and are also accessible on the UMLS Knowledge Source Server. Developers can use these special files to determine whether there have been changes that affect their applications. The usefulness of individual files will depend on how data from the Metathesaurus have been linked or incorporated in a particular application. 8.1.1.2 General Description of the Files Each relation or named table of data has a fixed number of columns and variable number of rows. A column is a sequence of all the values in a given data element. A row contains the values for two or more data elements for one entry. The values for the different data elements in the row are separated by vertical bars (|). Each row is terminated by a vertical bar and a carriage return followed by a line feed. | The descriptions of the specific data elements in these files can be found in Appendix B, Section B.1. 8.1.1.3 DELETED CONCEPTS (File=DELETED.CUI) There is exactly one row in this table for each reviewed concept that was present in 1995 Metathesaurus and is not present in the 1996 Metathesaurus. Cols. CUI in 1995 Metathesaurus in format C######### Preferred name in 1995 Metathesaurus 8.1.1.4 MERGED CONCEPTS (File=MERGED.CUI) There is exactly one row in this table for each reviewed concept from the 1995 Metathesaurus that was merged with a different concept in the 1996 Metathesaurus. Entries in this file represent concepts that were considered distinct in the 1995 edition, but are now identified as synonyms of other concepts. Cols. CUI in 1995 Metathesaurus in format C####### CUI in 1996 Metathesaurus in format C####### 8.1.1.5 DELETED TERMS (File=DELETED.LUI) There is exactly one row in this table for each term identifier that appeared in a reviewed entry in the 1995 Metathesaurus, but does not appear in a reviewed entry in the 1996 Metathesaurus. An entry in this file signifies a term (in any of its lexical variations) that appeared in 1995 Metathesaurus has been deleted, and the unique identifier for the term has also been deleted. This does not necessarily imply the deletion of a concept from the Metathesaurus. Cols. LUI in 1995 Metathesaurus Preferred Name of Term in 1995 Metathesaurus. 8.1.1.6 MERGED TERMS There is exactly one row in this file for each case in which terms had different term identifiers (LUI) in the 1995 Metathesaurus and in the 1996 Metathesaurus have the same unique term identifier. An LUI present in 1995 Metathesaurus is therefore absent from the 1996 Metathesaurus. These entries represent lexical variants that were not identified as such in 1995 and have been fixed for 1996. Cols. LUI in 1995 Metathesaurus that is not present in 1995 Metathesaurus LUI in 1996 Metathesaurus into which it was merged} 8.1.1.6 DELETED STRINGS (File=DELETED.SUI) There is exactly one row in this file for each string in each language that was present in a reviewed entry in the 1995 Metathesaurus and does not appear in the 1996 Metathesaurus. This does not necessarily imply the deletion of a term or a concept from the Metathesaurus. A string deleted in one language may still appear in the Metathesaurus in another language. Cols. Three character abbreviation of language of string that has been deleted. SUI in 1995 Metathesaurus that is not present in the 1995 Metathesaurus String in 1995 Metathesaurus that is not present in the 1995 Metathesaurus 8.2 Semantic Network The 1996 edition of the Semantic Network has two new semantic types, "Receptors" and "Neoplastic Process". One new relationship, "analyzes" (inverse "analyzed by")has been added to the Network. 8.3 SPECIALIST Lexicon and Lexical Programs The 1996 edition of the SPECIALIST Lexicon contains approximately 80,000 records, 15,000 more than in the 1995 release. The majority of these new records reflect additional terminology from the UMLS Metathesaurus. 8.4 Information Sources Map The 1996 edition of the Information Sources Map contains records for several new databases. Two records for databases that are no longer available have been deleted. Major changes to the Information Sources Map are planned for the 1997 edition. APPENDIX B METATHESAURUS DATA ELEMENTS AND SOURCE VOCABULARY INFORMATION B.0 INTRODUCTION This appendix contains descriptions of the Metathesaurus data elements (Section B.1), a listing of the vocabularies and classifications that are the sources of concepts and terms in the Metathesaurus with the source abbreviations used in the Metathesaurus data (Section B.2), a listing of the types of concept names that appear in the source vocabularies with the type abbreviations used in the Metathesaurus, e.g., preferred term, entry term (Section B.3), and the order of precedence of sources and types of concept names used to determine the preferred name in the Metathesaurus (Section B.4). Appendix B provides supporting details for section 2 of the documentation. Section 2 contains many references to this Appendix. B.1 METATHESAURUS DATA ELEMENTS B.1.O Introduction All data elements in the Metathesaurus are described in this section. The descriptions are arranged alphabetically by data element abbreviation. Mandatory data elements are marked by an asterisk *, i.e., every concept has at least one occurrence of these elements. All others are optional. Data elements created explicitly for the Metathesaurus are marked by (M); all others were derived from one or more of the source vocabularies (See Section B.2 for a list of the sources). The designation "Repeating Element" indicates that the data element may have multiple values for a single concept, term, or string. B.1.1 Data element Descriptions ================= AM Ambiguous string indicator (M) A single character: A An indicator that the string is ambiguous, i.e., has more than one meaning in the Metathesaurus. (See Section 2.2.2 and Figure 2 in this documentation.) An ambiguous string has multiple entries in the Metathesaurus. These entries have the same string (SUI) and term (LUI) identifiers, but different concept identifiers (CUI). ================= AN MeSH Annotation Variable length alphanumeric string that may contain punctuation. An informative MeSH note written primarily for indexers or catalogers that may also be useful in explaining the use of a MeSH term to online searchers. ================= ATX Associated Expression (M) Repeating element with three sub-elements. 1. Abbreviation (as defined in Section B.2) for the source of the vocabulary used in the expression 2. Type of Relationship Valid Values for Type of Relationship: B - Broader N - Narrower O - Other S - Synonymous U - Unspecified 3. Vocabulary expression Several different formats of the expression are possible. a.)
/ or
// or b.) Individual Main Headings and/or Main Heading and subheading combinations coordinated by the Boolean operators, (i.e., AND, OR, AND NOT). The vocabulary terms in the expression are included in less than and greater than signs <> to distinguish them from Boolean operators. Parentheses are used as necessary to clarify the meaning of boolean OR expressions. Examples: / AND ( OR ) AND Coordinated expressions of multiple terms from a Metathesaurus source vocabulary that are related to the concept. In the 1995 Metathesaurus, these expressions are constructed of MeSH, Library of Congress Subject Headings, or Omaha System terms. Information in this element can be used to construct a MeSH or LCSH search related to the concept represented in the Metathesaurus entry or to determine the correct relationships between different concepts in the Omaha System. Note that parentheses are used in these expressions to clarify the Boolean expression and punctuation is used to distinguish the vocabulary terms from the Boolean operators. The punctuation will probably have to be removed before the expressions can be used in a search. Depending on the system being searched, the expression may have to be divided into multiple search statements to achieve the desired search result. In the case of MeSH expressions, it may be necessary to EXPLODE one or more terms in the expression to get the desired search result. In the case of LCSH expressions, some of the subheadings are followed by "etc." indicating that other similar subheadings may be used. Note that the LCSH expressions represent combinations actually used by the Library of Congress in cataloging books. They have been mapped to their closest MeSH equivalents. ================= COC Co-occurring concepts (M) Repeating element; with a variable number of sub-elements 1. CUI of first concept 2. CUI of second concept or null value 3. Source of co-occurrence information 4. Type of co-occurrence 5. Frequency of co-occurrence 6. Attributes of co-occurrence relationship (optional) Valid Values for Source of Co-occurrence: MED - MEDLINE for the period 1992 - 1995 MBD - MEDLINE for the period 1985 - 1991 AIR - AI/RHEUM Valid Values for Type of Co-occurrence: L - co-occurrence of primary or main subject headings in citations to the published literature LQ - second concept occurs as a qualifier of the first in citations to the published literature LQB- second concept is qualified by the first in citations to the published literature KP - positive association in Knowledge Base KN - negative association in Knowledge Base, e.g., a finding that is inconsistent with a disease. Attributes of co-occurrence relationship For MED and MBD sources only Subheading data for co-occurring concept. Multiple values separated by commas. Abbreviation of MeSH subheading applied to first concept when it co- occurs with the second concept or <> (indicating no subheading) = Frequency of application of this subheading to first concept when it co-occurs with the second Example (in the Relational format): C0004238|C0003811|MED|L|7|CO=1,DT=4,EP=1,ET=2,PP=2,TH=1| C0015967|C0026691|AIR|KP||| Concepts that occur together in the same "entries" in some information source. The relationships represented here are obtained from machine-manipulation of the information source. Co-occurrence relationships may exist between similar concepts (e.g., "Atrial Fibrillation" and "Arrhythmia") or between very different concepts that nevertheless have some important connection in the field of biomedicine (e.g., "Atrial Fibrillation" and "Digoxin"), or between a primary concept and a qualifier e.g., "Lithotripsy" and "instrumentation". A co-occurrence relationship can exist between two concepts that have no other apparent relationship, although the frequency of such co-occurrences will be small. In the current Metathesaurus, there are two sources of co-occurrence data: MEDLINE and AI-RHEUM. From MEDLINE, co-occurrence data were computed for concepts that were designated as principal or main points in the same journal article i.e., the co-occurrence counts do not include articles in which either or both of the concepts were present and indexed in MEDLINE but not designated as main points. (A concept is considered to be a main point if the * is attached to the main heading or any of its subheadings.) Two overall frequencies of MEDLINE co- occurrence are provided: one for MEDLINE data from 1992 - 1995 and one for MEDLINE data from 1985 through 1991. Separate counts are provided for the frequencies with which the first concept was qualified by different MeSH qualifiers or by no qualifier at all when it co- occurred with second concept. There are separate entries for each direction of the co-occurrence relationship. The related subheading occurrence information in each entry belongs to the first concept in the entry and is therefore different for each direction of the relationship. (See also LO). In addition to the specific qualifier information associated with two co-occurring concepts, this element also includes in entries with LQ and LQB values for type of co-occurrence) totals for the number of times each main concept was qualified by a specific subheading or by no subheading. The AI/RHEUM co-occurrence data represent the co-occurrence of diseases and findings in the AI/RHEUM knowledge base, i.e., the diseases that co-occur with a particular finding and the findings that co-occur with a particular disease. Each disease/finding pair can co- occur only once in the AI/RHEUM knowledge base. Because of the large amount of MEDLINE co-occurrence data, in both the relational and ASN.1 formats the co-occurrence data are distributed on different discs from the remainder of the Metathesaurus data. ================= CUI Unique Identifier for Concept * (M) The letter C followed by 7 digits. The unique identifier for the Metathesaurus concept to which a term and string are linked. The number remains the same across versions of the Metathesaurus irrespective of the term designated as the preferred name of the concept. This facilitates file maintenance and management. In the Metathesaurus distribution formats all data elements are linked to the concept(s) to which they belong. ================= CX Consider Also Note (MeSH only) Variable length alphabetic string. Other word roots or prefixes that should be consulted for concepts related to this MeSH concept, e.g., the value for "Heart" is "consider also terms at cardi-and myocardi-". ================= CXT Context Repeating element. The specific format varies depending on the physical format. (See Sections 2.7.1.2.__ and __________) Hierarchical contexts for the concept from various Metathesaurus source vocabularies, including ancestors (in order from most remote to closest), siblings, and children. The hierarchical contexts are available for display to users as an aid to understanding the scope of concepts and to refining search strategies. Some of the hierarchical relationships present in the CXT are also represented in REL. ================= DA Date of entry * (M) YYYYMMDD, e.g., 19920830 The date of entry of the concept into the Metathesaurus. ================= DC MeSH Descriptor class A single numeric character. Valid Values: l = an Index Medicus descriptor 2 = a citation type descriptor (English Abstract) 3 = a check tag descriptor, e.g., HUMAN 4 = a geographic descriptor 5 = a "non-MeSH" descriptor, e.g., PATIENT CARE MANAGEMENT (NON-MeSH), which is part of a MeSH hierarchy but is never actually assigned as an indexing term in MEDLINE or other NLM databases. In the Metathesaurus such MeSH terms have a type of HT. The type of MeSH term the concept name represents. ================= DE MeSH Descriptor Entry Version Variable length alphabetic string. A short form for a MeSH term used primarily in MEDLINE record creation and maintenance. ================= DEF Definition Repeating element. Two sub-elements 1. Abbreviation of the source of the definition (see Section B.2 for valid values) 2. Variable length string with alpha characters, punctuation, and in some cases numerics Narrative description(s) of the meaning of the concept. The majority of the definitions come from MeSH or Dorland's Illustrated Medical Dictionary, 27th edition (DOR27), but there are also definitions from a number of other sources. The definitions created specifically for the Metathesaurus have a source value of MTH. Definitions were created specifically for the Metathesaurus only when needed to distinguish among different meanings of the same string. Note that some definitions may be several thousand characters long. See also SOS Scope Statement. ================= DQ Date Qualifier Established (MeSH only) YYMMDD The date the qualifier became available for indexing MEDLARS citations. ================= DS MeSH Descriptor Sort Version Variable length alphanumeric string. The form needed for proper sequencing of the concept name, if the name could not be sequenced properly by the sort algorithms used in the MeSH publications, e.g., MC - Antithrombin III DS - Antithrombin 03 ================= DX MeSH Date major descriptor established YYMMDD The first day of the Index Medicus publication month in which the descriptor (in any form) was available for searching as a major descriptor. ================= DY MeSH Date minor descriptor established YYMMDD The first day of the Index Medicus publication month in which the descriptor (in any form) was available for searching as a minor descriptor. ================= EC MeSH Entry combination Variable length alpha numeric string with two sub-elements,separated by a colon (:) 1. Two character abbreviation for MeSH subheading 2. MeSH main heading An invalid MeSH main heading/subheading combination that is a cross reference to a single MeSH main heading or a main heading/subheading combination that should be used in its place. ================= EV MeSH Entry term abbreviation Variable length alphanumeric string. A short form for a MeSH entry term or cross reference used primarily in MEDLINE record creation and maintenance. ================= EZ SNOMED International Enzyme Commission Number A numeric string with embedded periods. Description: The International Union of Biochemists Enzyme Commission number for an enzyme concept, if present in SNOMED International. This number is an alias for the concept name and can be used to retrieve information about the concept from some databases. Enzyme commission numbers may also appear in the RN field, preceded by the designation EC. In future editions of the Metathesaurus, all Enzyme commission numbers are likely to be consolidated in this attribute. ================= FR MeSH Frequency Numeric value For MeSH supplementary chemicals only, the number of times the chemical has been identified in articles indexed in MEDLINE as of ________________. ================= GM MeSH Grateful Med Note Variable length alphanumeric string. A note designed to help Grateful Med users avoid a common misuse of the MeSH heading to which it is attached. ================= HN MeSH History Note Variable length alpha-numeric string with punctuation. In general, the year when the current form of the MeSH term was established as a major and/or minor descriptor. The minor descriptor entry data appears in parentheses. Other brief information about history of the MeSH heading and its cross-references may follow the year data. MeSH terms that have been used continuously as major descriptors since 1963 do not have dates in this element. 72 (68) 83 76 (75) 89; was /occurrence 1966-88 The information in this field can be used to determine whether a MeSH term will appear in early MEDLINE backfiles and to find out how to search a concept in MEDLINE before its current term was introduced into MeSH. See also the PI element. ================= II MeSH Indexing Information One or more MeSH main headings or Main heading/subheading combinations. For MeSH chemical terms (Term Type=NM), MeSH headings that may be relevant to articles that are also assigned the NM term. The information in this field helps to define the NM and suggests other related search terms. ================= LA MeSH Language Code Three alphabetic characters Valid Values: The USMARC language codes. The MARC language code for a MeSH heading that is the name of a language. e.g., MC - ICELANDIC LA - ICE ================= LAT Language of Term* (M) Three alpha characters Valid values: ENG - English FRE - French GER - German POR - Portuguese SPA - Spanish The USMARC (Machine-Readable Cataloging) abbreviation for the language of the term. In the 1996 Metathesaurus English, French, German Portuguese, and Spanish terms are present. ================= LO Locator (M) Repeating element with 4 sub-elements: 1. Name of information source or database in which concept appears 2. Frequency of appearance in source (optional) 3. Meaning of Frequency Data (optional) 4. Metathesaurus SUI of string used in the source or the actual string used in that source (if not otherwise present in the Metathesaurus) (optional) 5. SOUI unique identifier of record in which concept appears in source (optional) Valid Values for Name of information source Health Devices Alerts - (ECRI) (1996) Health Product Comparison System -(ECRI) (1996) MEDLINE -(National Library of Medicine) - will be followed by an indication of the applicable range of years of MEDLINE data. DXPLAIN -a Diagnostic prompting system (Massachusetts General Hospital)(1996) HSTAT- Health Services and Technology Assessment Text (National Library of Medicine) (1996)- only a subset of the full-text documents in this database, i.e., the clinical practice guidelines sponsored by the Agency for Health Care Policy and Research have LO data in this edition of the Metathesaurus. OMIM -Online Mendelian Inheritance in Man (Victor McKusick, Johns Hopkins University) (1996) PDQ -Physician Data Query System (National Cancer Institute) (1996) QMR -Quick Medical Reference (University of Pittsburgh) (1996) AI/RHEUM -AI/RHEUM (National Library of Medicine) ( 1996) Valid Value for Meaning of Frequency Data *CITATIONS - indexed citations in which this concept was designated a primary point. Guidelines - number of guidelines in which this concept is an important topic. Examples: MEDLINE (1992-1995)|12|*CITATIONS| QMR||| DXPLAIN||| Selected information sources in which the Metathesaurus concept was detected. The Metathesaurus does not contain all concepts appearing in some of these information sources, and some Metathesaurus concepts present in these sources may not be flagged as such if the concept is represented in the information source by a term or concept name not present in the Metathesaurus. In some cases the source name is followed by: the frequency of occurrence in that source, the precise meaning of the frequency data, (e.g., whether it refers to a number of citations, etc.). Information in this element can be used to determine which of a limited repertoire of sources contain detected information closely related to the concept. System developers are encouraged to add data for local information sources to this element to support local applications. Data for additional nationally available sources may be included in subsequent versions of the Metathesaurus. For MEDLINE segments only, if the frequency sub-element is blank, the term did not appear as a principal point in any MEDLINE citations for that segment. ================= LT Lexical Tag (M) Repeating element. A three-character alpha code. The majority of terms with lexical tag data have only one tag value. Valid Values: ABB - abbreviation LAB - Lab number ABX - Embedded abbreviation NAM - Proper Name ACR - Acronym NON - NO special tag ACX - Embedded acronym TRD - Trade name EPO - Eponym A tag indicating whether a term falls into any of several special types. The purpose of this tag is to indicate terms that are not generally appropriate for stemming and other natural language techniques. Terms linked to concepts with a status attribute of U(unreviewed) generally do not carry lexical tag data. NLM's intention is eventually to remove these tags from the Metathesaurus and to represent them in the SPECIALIST Lexicon instead. ================= LU MeSH Language Usage The letter C. For MeSH language qualifiers only, an indication that the language is used in cataloging records only and will not appear in MEDLINE or other indexing records. For example, the language qualifier GREEK, CLASSICAL is used in cataloging only and therefore has the value C in this element. ================= LUI Unique Identifier for Term * (M) The letter L followed by 7 digits. The unique identifier for the term of which a string is one form. The number remains the same across versions of the Metathesaurus irrespective of the selection of the preferred form of the term or of the concept to which the term is linked. ================= M## (M66, M75, M80, M85, M90, MED) MEDLINE Backfile Postings (MeSH only) Numeric value followed by another numeric value preceded by an asterisk (*); one of the two values may be absent, indicating no occurrences. Six data elements which give the number of times a MeSH term has been used in MEDLINE and each of its backfiles on the NLM system as of ________. (The date ranges for each file may be found in their records in the UMLS Information Sources Map.) For MeSH main headings, each element has two values: the total occurrences and the occurrences in which the term was designated a principal concept, preceded by an asterisk. For subheadings, only the total postings are given. This is the only source of information in the Metathesaurus on the frequency of use of MeSH headings in MEDLINE prior to 1985 and on the total frequency of use of MeSH headings in MEDLINE from 1966 to January 1995. See also LO. ================= MDA MeSH date of entry YYMMDD The date the term was added to the MeSH file, which is prior to the date the term became available for indexing and searching MEDLARS citations. Terms that have been part of MeSH for many years may have no value in this element. ================= MG Machine Generated and unverified indicator ================= MMR MeSH revision date YYMMDD The date of the last major revision to the term's MeSH record. ================= MN MeSH Tree Number Repeating element. Variable length alphanumeric string with imbedded periods. The hierarchical number for the concept in the MeSH tree structures. This number also appears in the HCD sub-element of the REL and CXT elements. ================= MR Major revision date (M) YYMMDD The date the Metathesaurus entry for the concept underwent any revision in content. ================= NA Neuronames Abbreviation One or more alphabetic characters A short abbreviation for a concept name in the Neuronames thesaurus. ================= NAT Neuronames Anatomy Type A single character. Valid Values: S -- superficial V -- volumetric An indication of the type of anatomy represented by a Neuronames concept name. ================= NH Non-Human Flag (M) A single character: Y. An indication that the concept does not apply to human beings, used only when the concept's Semantic type(s) could imply the contrary. For example, the concept BEAK and CLAW are assigned the Semantic type"Body Part, Organ, or Organ Component", but do not apply to human beings. Concepts do not carry the non- human flag if their semantic types are obviously non-human (e.g., "Medical Device", "Hazardous or Poisonous Substance"). This element can indicate when special search restrictions are appropriate or that a concept may be inappropriate to the user's search. ================= NSR Neuronames Species Restriction A single character. Valid Values: H -- human only M -- macaque only An indication that a Neuronames concept applies only to humans or only to macaques. Most Neuronames concepts apply to both and have no species restriction. ================= OL MeSH Online Note Variable length alphanumeric string with punctuation. Information helpful to online searchers of MEDLINE, especially when the history of a term or cross-reference has implications for online searching. This is a potential source of useful information for rules for search interface programs. ================= PA MeSH Pharmacologic Action The pharmacologic action of MeSH main headings (MH) for drugs and supplementary chemical names (NM). The information in this element is also represented by an "is-a" relationship between the MH or NM concept and the MeSH concept name for the class of drugs with a particular pharmacologic action. ================= PDA PDQ Short Name or Abbreviation An alphanumeric string with embedded blanks. An abbreviated name for a PDQ concept. ================= PI MeSH Previous Indexing Repeating element. MeSH heading or heading/subheading combination(s) followed by a date range in parentheses (YY-YY). The MeSH headings or main heading/subheading combination that may be used to search for MEDLINE citations indexed before the concept was introduced into MeSH. Each entry is followed by a year or range of years as a guide to the period when the term in the PI field should be searched. The appropriate boolean logic for the PI terms is not provided. The searcher must make the decision whether to AND or OR the terms supplied when multiple terms are present. ================= PM Public MeSH note Variable length alphanumeric. Combines key information from the HN and PI elements in a format that is printed in the MeSH publications. ================= PX MeSH Pre-Explosion Three sub-elements. PX/Name of pre-explode/MeSH hierarchical number. An indication of whether there is a pre-stored MEDLINE search on the NLM system for the MeSH Main heading or subheading and all of its children in the MeSH hierarchical structure. Pre-explodes have been created to allow more rapid and efficient combined searches of specific terms and all their descendants. In most cases the name of the pre-explode is the same as the preferred name of the concept, in a few cases it is different. When used in actual searches pre-explodes must be entered as follows: Name of pre-explode (PX) On NLM's online system, use of a pre-explode is faster and cheaper than using the EXPLODE command. ================= QA MeSH Topical Qualifier Abbreviation Two alphabetic characters. For MeSH subheadings (Term Type=SH), an abbreviation that may be used in place of the full text of the abbreviation in searching on NLM's system and possibly on other systems offering NLM data. ================= QE MeSH Qualifier Entry Version Variable length alphabetic string A short form for a MeSH qualifier. ================= QG MeSH Qualifier Usage The letter C. An indication that a MeSH subheading is used only in cataloging. The absence of this element for a string with a source of MSH SH means that the subheading is used in both indexing and cataloging. This element indicates whether a particular subheading will appear in MEDLINE or not. ================= QS MeSH Qualifier Sort Version Alphabetic string. The form of the subheading needed for proper alphabetic sequencing when the subheading cannot be sequenced properly by the sort algorithms used in the MeSH publications. ================= QT MeSH Qualifier Type A single numeric character. Valid Values: l = a topical qualifier, e.g., DRUG THERAPY 3 = a time qualifier, e.g., 19 CENT. 4 = a geographic qualifier, e.g., FRANCE 5 = a language qualifier, e.g., GERMAN The type of MeSH subheading. Only topical subheadings (QT=1) will appear in MEDLINE or other NLM article citation files. Any type of subheading may appear in CATLINE and AVLINE, NLM's catalog files. ================= REL - Related Concepts Repeating element; with seven sub-elements 1. CUI of first concept 2. Relation of second to first concept 3. CUI of second concept 4. Relationship attribute 5. Source of relationship 6. Source of relationship labels 7. Imprecise relationship indicator (optional) Valid Values for Relation: RB - has a broader relationship, either derived from at least one Metathesaurus source vocabulary or identified during Metathesaurus construction RN - has a narrower relationship, either derived from at least one Metathesaurus source vocabulary or identified during Metathesaurus construction RO - has relationship other than synonymous, narrower, or broader, either derived from at least one Metathesaurus source vocabulary or identified during Metathesaurus construction RL - the two concepts are similar or "alike". In the current edition of the Metathesaurus, all relationships with this attribute link MeSH supplementary chemicals. A number of the concepts linked by this relationship are probably synonymous and may be linked to a single concept identifier in future editions of the Metathesaurus. In future editions of the Metathesaurus, this Relation will be used for "quasi-synonyms", such as "Hypertension" and "High Blood Pressure", which are sometimes used synonymously, but have distinct meanings in some circumstances. When RL is used for quasi-synonyms, the Relationship Attribute will provide the exact nature of the Relationship between the two concepts. PAR - has parent relationship in a Metathesaurus source vocabulary CHD - has child relationship in a Metathesaurus source vocabulary SIB - has sibling relationship in a Metathesaurus source vocabulary AQ - is an allowed qualifier for the first concept in a Metathesaurus source vocabulary QB - can be qualified by the first concept in a Metathesaurus source vocabulary Valid Values for Relationship attribute Any of the relationships defined in the UMLS Semantic Network. Examples include, "is a", "part of", "manifestation of" or no value for unspecified relationships. The large majority of relationships have no relationship attribute, although the number with such attributes is increasing. Valid Values for Source of Relationship: Any source vocabulary abbreviation (see Section B.2). This is the source of the information that there is some relationship between the two concepts. Valid Values for Source of Relationship Labels: Any source vocabulary abbreviation (see Section B.2). This is the source of the information about the specific nature of the relationship, i.e., RB, RN, or RO and any Relationship attribute values. In many cases, this is the same as the source of the relationship. In some cases, the particular nature of the relationship was added in Metathesaurus construction and the Source of Relationship Labels is MTH. Valid Value for Imprecise Relationship Indicator: The single character G. This indicator is used when the Relationship Labels have been machine-generated for the Metathesaurus based on ambiguous information from a source and have not been subsequently reviewed. There is therefore a possibility that the nature of the relationship has been labelled incorrectly. In the current version of the Metathesaurus, all relationships will this indicator involve MeSH supplementary chemicals. Examples (in the relational format): C0006500|CHD|C0007689|Part_of|MSH96|MTH| C1510822|RB|C2228511||MTH|MTH| C0000963|RL|C0209941||MSH96|MTH|G| Relationships between different concepts, derived from a source vocabulary's explicit hierarchy (see also CXT), from the cross-reference structure of a source vocabulary, from information about allowed qualifiers in a source vocabulary, from the lexical matching techniques used to build the Metathesaurus, or added to the Metathesaurus during human review. With the exception of the qualifier relationships, the concepts linked in this data element are usually similar or closely related, e.g., two body parts, two diseases, a manifestation and a disease, an organism and the disease it causes, a chemical and its salt. There are separate entries for each direction of the relationship, i.e., one entry for "Atrial Fibrillation" as a child of "Arrhythmia" and another entry for "Arrhythmia" as a parent of "Atrial Fibrillation". Some concepts linked that are linked by the RL relationship may be determined to be synonyms in future editions of the Metathesaurus. ================= RN Registry Number A series of numbers and hyphens (any leading zeros in an RN are dropped) or a series of numbers and periods, preceded by EC The Chemical Abstracts Service Registry number for a chemical or the Enzyme Commission number for an enzyme. (See also EZ.) This number is an alias for the concept name and can be used to retrieve information about the concept from a number of chemical and toxicological databases. ================= RR Related Registry Number Repeating element; with two sub-elements. Registry number (Relationship to concept in parentheses). e.g., 80551-64-0 (sulfate) The Chemical Abstracts Registry numbers for salts, optical isomers, or isotope-labelled versions of the concept followed by the relationship of this RR to the RN (in parentheses.) Applies to chemicals only. These numbers can be used as links to information in a number of chemical and toxicological databases. ================= SB SNOMED International subset indicator A one or two character code including letters and/or an asterisk. Valid Values: * - can code using two T codes or G code for laterality B - Bethesda system (Morphology) IC - ICDO (Oncology) related N - Nursing N*- Nursing, provisional U - Ultrastructure (Morphology) V - Veterinary V*- Veterinary AND can code using two T codes or G code for laterality (Topography) A tag indicating that a SNOMED International term belongs to one of a number of special categories. ================= SCT Syntactic Category or Part of Speech * (M) Repeating element - Alpha string that may include a slash (/). Valid Values: noun/noun phrase - virtually all Metathesaurus concepts carry this value verb/verb phrase adjective/adjective phrase adverb/adverb phrase The name of the syntactic category to which the concept belongs. Metathesaurus entries with a status of U carry a default value of "noun/noun phrase". This element may be useful for natural language processing applications. ================= SIC SNOMED ICD-9-CM Reference Repeating element; a numeric string which may have embedded periods. The ICD-9-CM code or codes listed as relevant to the meaning of the concept in SNOMED International. In future editions of the Metathesaurus some of the information contained in this element will probably be represented as relationships (REL) between Metathesarus concepts. ================= SL Source of relationship labels ================= SMX SNOMED Multi-axial coding An alphanumeric string that includes hyphens, parentheses, and sometimes ellipsis. Additional SNOMED International codes or truncated codes that cover aspects of the SNOMED International concept to which they are attached. ================= SO Source of String * (M) Repeating element, with three subsections separated by vertical bars (|). 1. SAB Abbreviation for source vocabulary 2. TTY Abbreviation for entity type in source 3. SCD Unique identifier in source OR unique identifier generated for Metathesaurus Valid source abbreviations: included in Section B.2. Valid entity type abbreviations: included in Section B.4. e.g., MSH96|MH|D000735 The vocabulary source(s) for the string. The information in the SO can be used to determine whether a particular concept is present in a particular source (and in what form) and to extract from the Metathesaurus the terms appropriate for searching information sources that have been indexed by specific vocabularies or classifications. In the case of the COSTART vocabulary, the third sub-element is actually an abbreviation composed of alphabetic characters and, in some cases, a space. ================= SOS Scope Statement Two sub-elements 1. Abbreviation of the source of the statement 2. Variable length string with alpha character, punctuation, and in some cases diacritics Details about the scope of a concept in a particular source vocabulary. The Metathesaurus contains scope statements from a number of source vocabularies. ================= SRC MeSH Literature source of chemical name Variable length alphanumeric string. Description: A citation to an article in a journal indexed for MEDLINE in which the chemical has been identified. ================= ST Concept Attributes Status * (M) One alpha character Valid Values: R-Reviewed U-Unreviewed The review status of the concept attributes (**list the set********). If human review of the concept attributes has been completed, the status is R. If human review has not been completed, the status is U. The majority of entries for concepts derived solely from the MeSH supplementary chemical file have a status of U. Note: Interconcept relationships in the Metathesaurus also carry a status of reviewed or unreviewed. (See REL) ================= STR String * Variable length string that includes alpha characters and may also include numerics, punctuation, or any character in the Metathesaurus character set. A unique string or concept name that appears in one or more of the Metathesaurus source vocabularies. Any variation in upper-lower case is a separate string. The same string in different languages (e.g., English, Spanish) will have a different string identifier for each language. ================= STT String Type* (M) Three characters, that may include one or two trailing blanks, as required. Valid values PF - Preferred form of term OR V - followed by one or more of the following, in this order: C - varies from the preferred term only in upper-lower case W - contains same words as the preferred form, disregarding order and punctuation S - Singular of the preferred form P - Plural of the preferred form O - other variant of the preferred form An indication of whether the string is the preferred form of the term or a variant of that form. Variant tags (e.g., W,S,P) were assigned by computer algorithm. NOTE: The Metathesaurus does not necessarily include all possible variants of each of its terms, e.g., not every term has the associated singular form. It includes only those variants that are actually present in the Metathesaurus source vocabularies. MeSH includes a more complete set of lexical variants for its terms than the other Metathesaurus source vocabularies do. Future versions of the Metathesaurus are likely to include a more complete set of variants. The algorithm used to identify lexical variants in the Metathesaurus is described in Section 4 and appears, as a C program, in the LEX directory on Disc 2. ================= STY Semantic Type * (M) Repeating Element with the two sub-elements. 1. TUI Unique identifier for Semantic Type 2. STY Semantic type Valid Values for Unique identifiers The identifiers in the UMLS Semantic Network. Valid Values for Semantic Types: The semantic types in the UMLS Semantic Network. The basic category or categories to which the concept belongs, (e.g., Acquired Immunodeficiency Syndrome is a "Disease or Syndrome".) Unreviewed concepts from the MeSH supplementary chemical files inherit the structural, or in some cases, the functional chemical types of the MeSH headings to which they are mapped. In addition, the semantic type "Pharmacologic Substance" may be assigned to these concepts based on information in the PA (Pharmacologic Action) data element. The Semantic type(s) are the link between the Metathesaurus and the UMLS Semantic Network. They are also one of the links between the Metathesaurus and the UMLS Information Sources Map. Application programs may be able to use the Semantic type information to determine the general topics of interest in a particular user query. Semantic types can also be employed to access related information from the Semantic Network and the Information Sources Map for use in interacting with a user to refine a query and to select appropriate information sources to search. ================= SUI Unique Identifier for String* The letter S followed by 7 digits The unique identifier for each string in the Metathesaurus. This number remains the same across versions of the Metathesaurus. Each SUI is linked to a single LUI that represents the group of all strings that are lexical variants of each other. In cases where a single string can name multiple concepts, an SUI will be linked to multiple CUIs in the Metathesaurus. ================= TH MeSH Thesaurus ID Repeating element. Alphanumeric string. Identifies thesauri other than MeSH in which the MeSH heading or cross-reference is included. Provides additional, less specific SO information. ================= TS Term Status * (M) One alpha character Valid values: P-Preferred Name S-Synonym An indication of whether the term is the preferred name of the concept to which it is linked, or a synonym of the preferred name. There is a separate preferred name for each language. B.2. VOCABULARY SOURCE ABBREVIATIONS ACR92 - Index for radiological diagnoses: including diagnostic ultrasound. Rev. 3rd ed. Reston (VA): American College of Radiology; 1986. AIR93 - AI/RHEUM. Bethesda, (MD): National Library of Medicine, 1993. BRMP96- Descritores em Ciencias da Saude.[Portuguese translation of MeSH] Latin American and Caribbean Center on Health Sciences Information. BIREME/PAHO/WHO, Sao Paulo, Brazil, 1996. BRMS96- Descriptores en Ciencias de la Salud. [Spanish translation of MeSH}] Latin American and Caribbean Center on Health Sciences Information. BIREME/PAHO/WHO, Sao Paulo, Brazil, 1996. COS89 - COSTAR (Computer-Stored Ambulatory Records) of Massachusetts General Hospital, 1989. - (List of terms that occur frequently at 3 COSTAR sites, supplied by Massachusetts General Hospital) COS92 - COSTAR (Computer-Stored Ambulatory Records) of Massachusetts General Hospital, 1992. - (List of terms that occur frequently at 3 COSTAR sites, supplied by Massachusetts General Hospital) COS93 - COSTAR (Computer-Stored Ambulatory Records) of Massachusetts General Hospital, 1993. - (List of terms that occur frequently at 3 COSTAR sites, supplied by Massachusetts General Hospital) COS95 - COSTAR (Computer-Stored Ambulatory Records) of Massachusetts General Hospital, 1995. - (List of terms that occur frequently at 3 COSTAR sites, supplied by Massachusetts General Hospital) CPM93- Columbia Presbyterian Medical Center Medical Entities Dictionary. New York; Columbia Presbyterian Medical Center, 1993. CSP94 - CRISP thesaurus. Bethesda (MD): National Institutes of Health, Division of Research Grants, Research Documentation Section; 1994. CPT89 - Physicians' current procedural terminology: CPT. 4th ed. Chicago (IL): American Medical Association; 1989. CST93 - COSTART: coding symbols for thesaurus of adverse reaction terms. Rockville (MD): Food and Drug Administration, Center for Drug Evaluation and Research; 1993. DMD96 German translation of the MeSH. Cologne, Germany: Deutsches Institut fuer Medizinische Dokumentation und Information, 1996. DOR27 - Dorland's Illustrated Medical Dictionary. 27th. ed. Philadelphia: Saunders; 1988. DSM3R - Diagnostic and statistical manual of mental disorders: DSM-III-R. 3rd ed. rev. Washington (DC): American Psychiatric Association; 1987. DSM4 - Diagnostic and statistical manual of mental disorders: DSM-IV. Washington (DC): American Psychiatric Association; 1994. DXP94 - DXplain, an expert diagnosis program, developed by Massachusetts General Hospital. HHC93- Saba, Virginia. Home Health Care Classification of Nursing Diagnoses and Interventions. Washington, D.C., Georgetown University, 1993. ICD89 - The International Classification of Diseases: 9th revision, Clinical Modification: ICD-9-CM. 3rd ed. Washington (DC): Health Care Financing Administration; 1989. ICD91 - The International Classification of Diseases: 9th revision, Clinical Modification: ICD-9-CM. 4th ed. Washington (DC): Health Care Financing Administration; 1991. INS95 - Thesaurus Biomedical Francais/Anglais. [French translation of MeSH]. Paris: Institut National de la Sante et Recherche Medicale, 1995. LCH90 - Library of Congress subject headings. 12th ed. Washington (DC): Library of Congress; 1989. MCM92 - List of epidemiology terms submitted by McMaster University MIM93 - Online Mendelian Inheritance in Man MSH96 - Medical subject headings. Bethesda (MD): National Library of Medicine; 1996. MTH - UMLS Metathesaurus NAN94 - Carroll-Johnson, Rose Mary, editor. Classification of nursing diagnoses: proceedings of the 10th conference; 1994. NEU95 - Bowden, Douglas M., Martin, Richard F., Dubach, Joev G. Neuronames Brain Hierarchy. Seattle; University of Washington, Primate Information Center; 1995. NIC93- McCloskey, Joanne C.; Bulechek, Gloria M., editors. Nursing interventions classification (NIC): Iowa intervention project. St. Louis (MO): Mosby-Year Book; 1992. NIC94- McCloskey, Joanne C.; Bulechek, Gloria M., editors. Nursing interventions classification (NIC): Iowa intervention project. St. Louis (MO): Mosby-Year Book; 1994. OMS94 - Martin, Karen S., Scheet, Nancy J. The Omaha System: Applications for Community Health Nursing. Philadelphia; W.B. Saunders, 1992. (with 1994 corrections) PDQ95 - Physician Data Query Online System. National Cancer Institute, 1995. PSY94 - Thesaurus of Psychological Index Terms. Washington, D.C. American Psychological Association, 1994. SNM2 - Cote, Roger A., editor. Systematized nomenclature of medicine. 2nd ed. Skokie (IL): College of American Pathologists; 1979. SNOMED update, 1982. Skokie (IL): College of American Pathologists; 1982. SNMI95 - Cote, Roger A., editor. Systemized Nomenclature of Human and Veterinary Medicine: SNOMED International. Northfield, IL: College of American Pathologists; Schaumburg, IL: American Veterinary Medical Association; 1995. SRC - Names of source terminologies included in the Metathesaurus. ULT93- Bell, Douglas. Ultrasound Structured Attribute Reporting. UltraSTAR. Boston: Brigham & Womens Hospital, 1993. UMD96 - Universal medical device nomenclature system: product category thesaurus. Plymouth Meeting (PA): ECRI; 1996. WHO93- WHO Adverse Drug Reaction Terminology. WHOART. Uppsala, Sweden; WHO Collaborating Centre for International Drug Monitoring, 1993. B.3 NUMBER OF STRINGS FROM EACH SOURCE ACR92 122 AIR93 685 BRMP96 30516 BRMS96 30950 COS89 776 COS92 735 COS93 626 COS95 1324 CPM93 536 CPT89 557 CSP94 6461 CST93 5583 DMD96 17997 DOR27 7061 DSM3R 467 DSM4 490 DXP94 10113 HHC93 333 ICD89 484 ICD91 34331 INS96 25379 LCH90 6292 MCM92 43 MIM93 250 MSH96 273426 MTH 3995 NAN94 135 NEU95 783 NIC93 601 NIC94 466 OMS94 539 PDQ95 4271 PSY94 4331 SNM2 29131 SNMI95 78080 SRC 102 ULT93 84 UMD96 8052 WHO93 3293 Total Counts ------------ Concepts: 252,892 Terms: 416,111 Strings: 542,722 Source Strings: 589,400 B.4 CONCEPT NAME TYPES NOTE: In the following list "term" is used in the sense that it is used in the relevant source vocabulary. By the Metathesaurus definition, all types of concept names are strings. AB - Abbreviation in any source vocabulary AD - Adjectives in SNOMED International. CE - Entry "term" to MeSH Supplementary Chemical "Term" DI - Disease Name DQ - Qualifier for a diagnosis in the Home Health Care Classification of Nursing Diagnoses and Interventions DT - Definitional term, present in the Metathesaurus because of its connection to a Dorland's definition or to a definition created especially for the Metathesaurus. EA - Expanded CPT abbreviation - these exact terms do not appear in CPT; the expansion was done to assist in lexical matching used to construct Meta-1 EN - MeSH Non-Print entry "term" EP - Entry "term" ET - MeSH entry "term" FI - Finding Name GQ - MeSH Geographic Qualifier GT - COSTART Glossary "term" HC - Nursing Interventions Classification hierarchical class HT - Hierarchical term; in MeSH a "(Non MeSH)" term established to allow an accurate hierarchy, but not assigned in indexing. A MTH/HT is a string created to facilitate Metathesaurus mapping by dropping the "(Non MeSH)" from a MSH/HT. IN - Name for an intervention IQ - Qualifier for an intervention in the Home Health Care Classification of Nursing Diagnoses and Interventions IT - Index "term", i.e., derived from the index to any non-MeSH source vocabulary LQ - MeSH language qualifier MH - MeSH Main Heading MM - Metathesaurus string created to distinguish different meanings of the same lexical string. MT - An alternate form of a concept name from one of the source vocabularies created for the Metathesaurus NM - MeSH Supplementary Chemical "Term", a name of a substance N1 - Chemical Abstracts Service Type 1 name of a chemical OS - System-Organ class in the WHO Adverse Reaction Terminology PD - Preferred name for a diagnosis in the Home Health Care Classification of Nursing Diagnoses and Interventions PI - Preferred name for an intervention in the Home Health Care Classification of Nursing Diagnoses and Interventions PM - Machine permutation of a MeSH "term" PQ - Qualifier for a problem in the Omaha System PR - Name of a problem in the Omaha System PT - Designated Preferred name in any non-MeSH source vocabulary RT - Designated Related "Term" in any source vocabulary RX - Alternate name of preferred name in SNOMED SI - Name of a sign or symptom of a problem in the Omaha System SY - Designated Synonym in any non-Mesh source vocabulary TG - Name of the target of an intervention in the Omaha System TQ - MeSH topical qualifier TT - ICD-9-CM Table Term XQ - Alternate name for a MeSH qualifier B.5 ORDER OF PRECEDENCE OF SOURCE CONCEPT NAMES NOTE: The precedence of an MTH|MM (e.g., Cold <1>) varies. It immediately precedes the highest ranking Source|Type of Name of the ambiguous string that caused it to be created. MTH|HT MSH96|MH MSH96|HT MSH96|TQ MSH96|GQ MSH96|LQ MSH96|EP MSH96|EN MSH96|XQ MSH96|NM MSH96|N1 MSH96|CE DSM4|PT DSM3R|PT SNMI95|PT SNMI95|HT SNM2|PT SNMI95|RT SNM2|RT SNMI95|SY SNMI95|AD SNM2|SY SNM2|RX CPM93|PT NEU95|PT UMD96|PT UMD96|ET UMD96|RT CST93|PT WHO93|SY WHO93|OS WHO93|HT WHO93|PT WHO93|IT AIR93|HT AIR93|FI AIR93|DI AIR93|SY ULT93|PT ICD91|PT ICD89|PT CPT89|PT MIM93|PT PDQ95|PT PDQ95|RT DSM4|HT DSM3R|HT SNM2|HT ICD91|HT CPT89|HT HHC93|PD HHC93|PI HHC94|HT NIC94|PT NIC94|SY NAN94|PT NAN92|PT NAN94|SY NAN92|SY NAN94|RT NAN92|RT OMS94|MT OMS94|PR OMS94|TG OMS94|HT OMS94|PQ OMS94|IN OMS94|SI NIC93|RT NIC94|HT HHC93|DQ HHC93|IQ COS95|PT COS93|PT COS92|PT COS89|PT DXP94|DI DXP94|FI DXP94|SY MCM92|PT MCM92|RT MTH|PT MTH|SY MTH|RT DSM3R|SY DSM3R|RT ICD91|IT CST93|GT ICD89|IT ICD91|TT PSY94|PT PSY94|ET LCH90|PT ACR92|PT ICD89|AB CPT89|AB CPT89|EA MSH96|PM CSP94|PT MTH|DT DOR27|DT BRMP96|MH BRMS96|MH DMD96|MH INS96|MH INS96|SY SRC|PT SRC|SY