DRAFT

SECTION 2

METATHESAURUS^®

DRAFT

2.0 INTRODUCTION

The Metathesaurus is a very large, multi-purpose, and multi-lingual vocabulary database that contains information about biomedical and health related concepts, their various names, and the relationships among them. Designed for use by system developers, the Metathesaurus is built from the electronic versions of many different thesauri, classifications, code sets, and lists of controlled terms used in patient care, health services billing, public health statistics, indexing and cataloging biomedical literature, and/or basic, clinical, and health services research. These are referred to as the "source vocabularies" of the Metathesaurus. The term Metathesaurus draws on Webster's Dictionary third definition for the prefix "meta," i.e., "more comprehensive, transcending." In a sense, the Metathesaurus transcends the specific thesauri, vocabularies, and classifications it encompasses.

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.

The Metathesaurus is linked to other UMLS Knowledge Sources. All concepts in the Metathesaurus are assigned to at least one semantic type from the Semantic Network (Section 3.0). This provides consistent categorization of all concepts in the Metathesaurus at the relatively general level represented in the Semantic Network. Many of the words and multi-word terms that appear in concept names or strings in the Metathesaurus also appear in the SPECIALIST lexicon (Section 4). The lexical tools (Section 4) are used to generate the word, normalized word, and normalized string indexes to the Metathesaurus. MetamorphoSys (Section 6) is the software tool for customizing the Metathesaurus for specific purposes. It is also the install program for all of the UMLS resources.

2.0.1 Scope of the Metathesaurus

The scope of the Metathesaurus is determined by the combined scope of its source vocabularies. Many relationships (primarily synonymous), concept attributes, and some concept names are added by the NLM during Metathesaurus creation and maintenance, but essentially all the concepts themselves come from one or more of the source vocabularies. With very few exceptions, if none of the source vocabularies contains a concept, that concept will not appear in the Metathesaurus.

2.0.2    Preservation of Content and Meaning from Source Vocabularies

The Metathesaurus reflects and preserves the meanings, concept names, and relationships from its source vocabularies. When two different source vocabularies use the same name for differing concepts, the Metathesaurus represents both of the meanings and indicates which meaning is present in which source vocabulary. When the same concept appears in different hierarchical contexts in different source vocabularies, the Metathesaurus includes all the hierarchies. When conflicting relationships between two concepts appear in different source vocabularies, both views are included in the Metathesaurus. Although specific concept names or relationships from some source vocabularies may be idiosyncratic and lack face validity, they are still included in the Metathesaurus.

In other words, the Metathesaurus does not represent a comprehensive NLM-authored ontology of biomedicine or a single consistent view of the world (except at the high level of the semantic types assigned to all its concepts).

The Metathesaurus preserves the many views of the world present in its source vocabularies because these different views may be useful for different tasks.

Although it preserves all the meanings and content in its source vocabularies, the Metathesaurus stores this information in a single common format.

The native format of each vocabulary is carefully studied and then "inverted" into the common Metathesaurus format. For some vocabularies, this involves representing implied information in a more explicit format. For example, if a source vocabulary stores its preferred concept name as the first occurrence in a list of alternative concept names, that first name is explicitly tagged as the preferred name for that source in the Metathesaurus.

2.0.3 Need to Customize the Metathesaurus

Because it is a multi-purpose resource that includes concepts and terms from many different source vocabularies developed for very different purposes, the Metathesaurus must be customized for effective use in most specific applications. Your decisions about what to include in your customized subset(s) of the Metathesaurus will have a significant effect on its utility in your systems. Vocabulary sources that are essential for some purposes, e.g., LOINC for standard exchange of laboratory data, may be detrimental for others, such as natural language processing. It can also be important to exclude a subset of the concept names found in a vocabulary source that is otherwise useful, e.g., non-standard abbreviations or shortened forms that lack face validity or produce spurious results in natural language processing.

The Metathesaurus contains source vocabularies produced by many different copyright holders. The majority of the content of the Metathesaurus is available for use under the basic (and quite open) terms described in sections 1-11 and 13-16 of the Metathesaurus license. However, some vocabulary producers place additional restrictions on the use of their content as distributed within the Metathesaurus. The various levels of additional restrictions are described in Section 12 of the license. The level that applies to individual vocabularies is recorded in the Appendix to the license in Appendix B.4 to this documentation, and in the MetamorphoSys install and customization program (section 6.0). If a UMLS user already has a separate license for use of one of the source vocabularies, the user’s existing license also applies to that source as distributed within the Metathesaurus. In some cases, UMLS users may have to request permission or negotiate a separate license with a vocabulary producer in order to use that vocabulary in a production system. There may be a charge associated with these separate permissions or license agreements.

The Metathesaurus is designed to facilitate customization. All information in the Metathesaurus is labeled as to its source(s), so it is possible to determine which concept names, attributes, and relationships come from which source vocabularies and which attributes and relationships were added during Metathesaurus construction. The labels allow UMLS users to subset the Metathesaurus by excluding information from specific source vocabularies, including those for which they do not have necessary licenses or permissions. It is also easy to exclude all source vocabularies that have particular restriction levels or all information in particular languages. In addition to identifying the source(s), restriction levels, and language of the information it contains, the Metathesaurus includes various more specific concept name flags and relationship labels that can help UMLS users to exclude content that is not relevant or helpful for particular applications.

MetamorphoSys, the install and customization program distributed with the UMLS (Section 6), makes it easy to generate custom subsets. MetamorphoSys also includes default settings that generate subsets that may be generally useful. MetamorphoSys can be also used to change the default preferred names of concepts (explained in Section 2.2.6); to change the default character set (from 7-bit ASCII to Unicode UTF8); and to include versioned vocabulary source abbreviations in every Metathesaurus file (see section 2.1).

2.0.4 Metathesaurus Release Formats

Metathesaurus users may select from two relational formats: the Rich Release Format (RRF), introduced in 2004, and the Original Release Format (ORF). Both are available as output options of MetamorphoSys, the UMLS install and customization program (Section 6). All Rich Release Format file names have an extension (.RRF). Original Release Format files have no extension. Both formats are described in this documentation (usually abbreviated as RRF and ORF). There is also a White Paper explaining the rationale for the Rich Release Format and a detailed description of the differences between the .RRF files and the Original Format files.

The Rich Release Format has a number of advantages and is the preferred format for new users of the Metathesaurus and for most data creation applications.

2.1 SOURCE VOCABULARY

The Metathesaurus contains concepts, concept names, and other attributes from more than 100 terminologies, classifications, and thesauri, some in multiple editions. There is a concept in the Metathesaurus for each source vocabulary itself, which is assigned the semantic type "Intellectual Product". A special file (MRSAB.RRF and MRSAB in ORF) stores the version of each source vocabulary present in a particular edition of the Metathesaurus. All other Metathesaurus files that reference source vocabularies use "root" or versionless abbreviations, e.g., ICD9CM, not ICD9CM2003, thus avoiding routine wholesale updates to reflect the new versions. If you prefer to have versioned vocabulary source abbreviations in your custom Metathesaurus subset files, MetamorphoSys offers this as an option.

A complete list of the Metathesaurus source vocabularies with their root and versioned source abbreviations appears in Appendix B.4 of this documentation. The list is alphabetized by the abbreviation for that vocabulary source that is used in the Metathesaurus. Appendix B.4 includes the other information including: the number of its concept names that are present in the Metathesaurus, the type of hierarchies or contexts it has (if any), and whether it is one of the small number of source vocabularies that is not routinely updated in the Metathesaurus.

The Metathesaurus source vocabularies include terminologies designed for use in patient-record systems; large disease and procedure classifications used for statistical reporting and billing; 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. A categorized list of the English-language source vocabularies is available.

2.1.1 Inclusion of U.S. Standard Code Sets and Terminologies

The Metathesaurus includes the code sets mandated for use in electronic administrative transactions in the U.S. under the provisions of the Health Insurance Portability and Accountability Act (HIPAA). With the exception of the National Drug Codes (NDC), the Metathesaurus includes all concepts and terms from these code sets. NDC codes available from the Food and Drug Administration are included as attributes of clinical drug concepts present in the FDA National Drug Code Directory (MTHFDA), which is a source vocabulary.

NLM intends to incorporate all clinical terminologies designated as target U.S. government-wide standards by the Consolidated Health Informatics (CHI) initiative and/or recommended as U.S. standards by the National Committee on Vital and Health Statistics. Several of these (e.g., LOINC, SNOMED CT, RxNorm) are already present in the Metathesaurus.

The fact that a vocabulary has been designated as a HIPAA or CHI standard is included in Appendix B.4

2.1.2 Inclusion of Languages Other than English

The Metathesaurus structure can accommodate translations of its source vocabularies into languages other than English. Many translations in many different languages are present in this edition of the Metathesaurus. The Metathesaurus includes many translations of some source vocabularies, e.g., NLM’s Medical Subject Headings (MeSH) and the International Classification of Primary Care; one or a few of others, and, in many cases, only the English version. As previously explained, MetamorphoSys (see Section 6) makes it easy to create a subset of the Metathesaurus that excludes the languages that are not relevant in a particular application.

2.2 CONCEPTS, CONCEPT NAMES, AND THEIR IDENTIFIERS

The Metathesaurus is organized by concept. One of its primary purposes is to connect different names for the same concept from many different vocabularies. The Metathesaurus assigns several types of unique, permanent identifiers to the concepts and concept names it contains, in addition to retaining all identifiers that are present in the source vocabularies. The Metathesaurus "concept structure" includes concept names, their identifiers, and key characteristics of these concept names (e.g., language, vocabulary source, name type). The entire concept structure appears in a single file in the Rich Release Format (MRCONSO.RRF). An abbreviated version of the concept structure is split between two files in the Original Format (MRCON and MRSO).

2.2.1 Concepts and Concept Identifiers

A concept is a meaning. A meaning can have many different names. A key goal of Metathesaurus construction is to understand the intended meaning of each name in each source vocabulary and to link all the names from all of the source vocabularies that mean the same thing (the synonyms). This is not an exact science. The construction of the Metathesaurus is based on the assumption that specially trained subject experts can determine synonymy with a degree of accuracy that is highly useful. Metathesaurus editors decide what view of synonymy to represent in the Metathesaurus concept structure. Please note that each source vocabulary’s view of synonymy is also present in the Metathesaurus, irrespective of whether it agrees or disagrees with the Metathesaurus view.

Each concept or meaning in the Metathesaurus has a unique and permanent concept identifier (CUI). The CUI has no intrinsic meaning. In other words, you cannot infer anything about a concept just by looking at its CUI. In principle, the identifier for a concept never changes, irrespective of changes over time in the names that are attached to it in the Metathesaurus or in the source vocabularies.

In actuality, a CUI will be removed from the Metathesaurus when it is discovered that two CUIs actually name the same concept – in other words, when undiscovered synonymy comes to light. In these cases, one of the two CUIs will be retained, all relevant information in the Metathesaurus will be linked to it, and the other CUI will be retired.

Retired CUIs are never re-used. Each edition of the Metathesaurus includes files that detail any such changes from the previous edition. One Metathesaurus file (MRCUI.RRF and MRCUI in ORF) tracks such changes from 1991 to the present, allowing users to determine the fate of any CUI that is no longer present in the Metathesaurus.

2.2.2 Concept Names and String Identifiers

Each unique concept name or string in each language in the Metathesaurus has a unique and permanent string identifier (SUI). Any variation in character set, upper-lower case, or punctuation 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. If the same string, e.g., Cold, has more than one meaning, the string identifier will be linked to more than one concept identifier (CUI).

2.2.3 Atoms and Atom Identifiers

The basic building blocks or "atoms" from which the Metathesaurus is constructed are the concept names or strings from each of the source vocabularies. Each and every occurrence of a string in each source vocabulary is assigned a unique atom identifier (AUI). If exactly the same string appears twice in the same vocabulary, for example, as both the long name and the short name for the same concept or as an alternate name for two different concepts in the same vocabulary source, a unique AUI is assigned for each occurrence. When the same string appears in multiple source vocabularies, it will have AUIs for every time it appears as a concept name in each of those sources. All of these AUIs will be linked to a single string identifier (SUI), since they represent occurrences of the same string. Unlike string identifiers, a single AUI is always linked to a single concept identifier, because each occurrence of a string in a source can only have one meaning.

AUIs appear in the RRF (.RRF files), but not in the ORF.

2.2.4 "Terms" and Lexical Identifiers

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.) English lexical variants are detected using the lvg program, one of the UMLS lexical tools (see Section 4). As similar tools become available for other languages, they may be used to create lexical variant groups in other languages. (In the meantime, the LUI for a non-English string is really another string identifier.)

Like a string identifier, the LUI for an English string may be linked to more than one concept. This occurs when strings that are lexical variants of each other have different meanings. In contrast, each string identifier and each atom identifier can only be linked to a single LUI.

2.2.5 Uses of Concept, String, Atom, and Term Identifiers

In the Metathesaurus, every CUI (concept) is linked to at least one AUI (atom), SUI (string), and LUI (term), but can be linked to many of each of these. Every AUI (atom) is linked to a single SUI (string), a single LUI (term), and a single CUI (concept). Each SUI (string) can be linked to many AUIs (atoms), to a single LUI (term), and to more than one CUI (concept) – although the typical case is one CUI. Each LUI (term) can be linked to many AUIs (atoms), many SUIs (strings), and more than one CUI (concept) – although the typical case is one CUI.

FIGURE 1.

In the abbreviated example in Figure 1, "Atrial Fibrillation" appears as an atom in more than one source vocabulary and has a distinct AUI for each occurrence. Since each of these atoms has an identical string or concept name, they are linked to a single SUI. "Atrial Fibrillations", the plural of "Atrial Fibrillation" has a different string identifier. Since the singular and plural are lexical variants of each other, both are linked to the same LUI.   There is a different LUI and different SUIs and AUIs for "Auricular Fibrillation" and its plural "Auricular Fibrillations." Since "Atrial Fibrillation" and "Auricular Fibrillation" have been judged to have the same meaning, they are linked to the same CUI.

All of these identifiers serve important purposes in building the Metathesaurus, in allowing efficient and accurate customization for specific purposes, and in identifying changes in its concept and concept name coverage over time.

CUIs link all information in the Metathesaurus related to particular concepts. In other words, a CUI can be used to retrieve all the concept names, relationships, and attributes for a particular concept that appear in any Metathesaurus file. CUIs also serve as permanent, publicly available identifiers for biomedical concepts or meanings to which many individual source vocabularies are linked. Users of the Metathesaurus are strongly encouraged to incorporate CUIs in their local applications – to support data exchange and linking and to assist migration between the use of individual source vocabularies should that become necessary in the future.

Users of the Metathesaurus are also encouraged to incorporate SUIs in local applications. Inclusion of SUIs will allow more efficient updating of local systems as new versions of the Metathesaurus are issued.

The value of retaining LUIs in local applications (as opposed to their use in creating the customized version of the Metathesaurus to be used locally) will vary depending on local system approaches to detecting and dealing with minor variations in language.

AUIs link all information in the Metathesaurus related to particular atoms or occurrences of strings in a specific source vocabulary.   AUIs can assist users of the Metathesaurus in identifying those cases in which a source vocabulary’s concept structure differs from that of the Metathesaurus. Many users of the Metathesaurus will have no need to store these identifiers in local applications.

2.2.6 Default Preferred Names for Metathesaurus Concepts

As a convenience for those who build the Metathesaurus, one string from one English term is designated and labeled as the default preferred name of each concept in the Metathesaurus. To avoid laborious selection among alternative terms and strings, selection of the default preferred name for any Metathesaurus concept is based on an order of precedence of all the types of English strings in all the Metathesaurus source vocabularies.   Different types of strings, e.g., preferred terms, cross references, abbreviations, from each vocabulary will have different positions in this order. The factors considered in establishing the default order of precedence include breadth of subject coverage, frequency of update, and the degree to which the source's concept names are used in regular clinical or biomedical discourse. The default order of precedence appears in the MRRANK.RRF, in MRRANK in ORF, and in Appendix B, Section B.5 of this documentation.

The default order of precedence will not be suitable for all applications of the Metathesaurus. MetamorphoSys (Section 6) can be used to change the selection of preferred names to feature terminology from the source vocabularies most appropriate to particular user populations. For example, concept names from SNOMED CT may be preferred in clinical applications, and terminology from MeSH may be preferred in literature retrieval systems.   

2.2.7 Strings with Multiple Meanings

FIGURE 2.

2.2.8     Concept Names added during Metathesaurus Construction

Although the vast majority of concept names present in the Metathesaurus come from one or more of its source vocabularies, some concept names are created during Metathesaurus construction. This occurs in the following circumstances:

A unique name is created for a string with multiple meanings (the case explained in Section 2.2.7),

(b)      A more explicit name is created when none of the source vocabulary names for a concept conveys its meaning adequately,

(c)       An American English variant is generated for a British spelling,

(d)      An equivalent basic Latin ASCII character set string is generated for a string in an extended character set, such as Unicode.

Like all other concept names in the Metathesaurus, names created during Metathesaurus construction are labeled to indicate their source.

2.3 RELATIONSHIPS AND RELATIONSHIP IDENTIFIERS

The Metathesaurus includes many relationships between different concepts (in addition to the synonymous relationships in the Metathesaurus concept structure described in Section 2.2). Most of these relationships come from individual source vocabularies.  Some are added by NLM during Metathesaurus construction. Some have been contributed by Metathesaurus users to support certain types of applications.

Relationships are expressed in terms of CUIs (in the RRF and ORF) and AUIs (in the RRF only). Metathesaurus relationship files do not include concept names.

In general, the Metathesaurus indicates the author of each relationship, that is, one of the source vocabularies, the Metathesaurus itself, or another supplier.   Some relationships added in the early years of Metathesaurus development (less than 6% of the current total and declining) are attributed to the Metathesaurus, but actually came from specific source vocabularies.

2.3.1 Basic categories of non-synonymous relationships

The Metathesaurus contains non-synonymous relationships between concepts from the same source vocabulary (intra-source vocabulary relationships) and between concepts in different vocabularies (inter-source vocabulary relationships). The Metathesaurus does not include all possible non-synonymous relationships between the concepts it contains.   It includes all relationships present in its source vocabularies and some additional relationships designed to connect related concepts. In general, the relationships asserted by source vocabularies connect closely related concepts, such as those that share some common property or are related by definition. For example, a member of a class of drugs (e.g., penicillin) will be connected to the name for the class (e.g., antibiotics);   a bacterial infection will be connected to the bacterium that causes it. 

2.3.1.1  Intra-Source Relationships

The majority of intra-source relationships are asserted or implied by the individual source vocabularies. Such relationships occur in a source vocabulary’s explicit or implied hierarchical arrangements or contexts, cross-reference structures, rules for applying qualifiers, or connections between different types of names for the same concept (e.g., abbreviations and full forms). The primary Metathesaurus relationships file, that is, MRREL.RRF and MRREL in the ORF) contains the "distance -1" hierarchical relationships, i.e.; immediate parents; immediate child, and immediate sibling relationships; as well as other types of intra-source relationships.

A subset of the contextual or hierarchical relationships are also distributed in a special contexts file (MRCXT.RRF and MRCXT in ORF) to facilitate the construction of user displays. A "computable" representation of the complete hierarchies is provided in MRHIER.RRF (in RRF only). This file represents all sibling relationships even when there are thousands of siblings. Appendix B.4 indicates which source vocabularies have hierarchical contexts, which of these allow concepts to appear in multiple hierarchies, and whether sibling relationships are represented in MRCXT or only in MRHIER.RRF.

Some of the intra-source vocabulary relationships are statistical relationships, which are computed by determining the frequency with which concepts in specific vocabularies co-occur in records in a database. For example, there are co-occurrence relationships for the number of times concepts have co-occurred as key topics within the same articles, as evidenced by the Medical Subject Headings assigned to those articles in the MEDLINE database. Co-occurrence relationships have been also computed for different ICD-9-CM diagnosis codes assigned to the same patients as reflected in a discharge summary database. In contrast to the relationships asserted within source vocabularies, the statistical relationships in the Metathesaurus can connect very different concepts, such as diseases and drugs. There are specific Metathesaurus files for the co-occurrence relationships (MRCOC.RRF and MRCOC in ORF).

2.3.1.2 Inter-Source Relationships

The primary inter-source relationships in the Metathesaurus are the synonymous relationships represented in the Metathesaurus concept structure (Section 2.2).  The Metathesaurus also includes some relationships between non-synonymous concepts from different source vocabularies. Some of these inter-source relationships are generated during Metathesaurus construction to connect specific "orphan" concepts (with few or no ancestors, siblings, or children in their own source vocabularies) to the richer contextual information in another source vocabulary.    Some are supplied by Metathesaurus users who find "like" or "similar" relationships a useful addition to the Metathesaurus’s relatively strict view of synonymy. In both cases, these relationships are distributed in MRREL.RRF and MRREL in ORF.

Many inter-source relationships between non-synonymous concepts are produced through specific efforts to create a mapping between two different source vocabularies. These mappings may be created by an individual source vocabulary producer, by a third party with a particular need for a mapping, or by NLM or under NLM supervision specifically for distribution within the Metathesaurus. The number of NLM-supervised mappings is expected to increase. There are specific Metathesaurus files for mappings in the RRF (MRMAP.RRF and MRSMAP.RRF). A subset of the mappings appear in MRATX in the ORF. Mappings involving SNOMED CT appear in the RRF only.

2.3.2   Relationship Labels

In addition to being identified as to their source, all relationships (outside the basic concept structure) in the Metathesaurus carry a general label (REL), describing their basic nature, such as Broader, Narrower, Child of, Qualifier of, etc. Most of these relationships are either directly asserted in a source vocabulary or are implied by the structure of the source vocabulary. A complete list of the general relationship labels appears MRDOC.RRF and MRDOC in Appendix B.3 in this documentation.

About a quarter of the relationships in the Metathesaurus also carry an additional label (RELA), obtained from a source vocabulary, that explains the nature of the relationship more exactly, such as is a, branch_of, component_of.   The Digital Anatomist vocabulary and RxNorm are examples of source vocabularies that include such relationship labels. A complete list of the additional relationship labels appears in MRDOC.RRF and in Appendix B.3 in this documentation.

2.3.3 Relationship Identifiers

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

Some source vocabularies have their own relationship identifiers. Where they exist, these identifiers are also present in the Metathesaurus.

2.4 ATTRIBUTES AND ATTRIBUTE IDENTIFIERS

In the Metathesaurus, attributes include every discrete piece of information about a concept, an atom, or a relationship that is not (1) part of the basic Metathesaurus concept structure (Section 2.2) or (2) distributed in one of the relationship files (Section 2.3).

2.4.1 Kinds of Attributes

The Metathesaurus includes concept attributes, atom attributes, and relationship attributes.

Concept attributes are added during Metathesaurus construction and apply to all names of a concept. For example, the semantic types "Pathologic Function" and "Finding" are attributes of the concept with the preferred name "Atrial Fibrillation" and are applicable to any atom connected to that concept.

Atom attributes come from a particular source vocabulary. Some of them are of general interest; others are relevant only to a particular source vocabulary. For example, the definition "Disorder of cardiac rhythm characterized by rapid, irregular atrial impulses and ineffective atrial contractions." is an attribute of the atom "Atrial Fibrillation" that comes from the Medical Subject Headings (MeSH).   It may be one of several definitions connected to names of this concept, because the Metathesaurus includes all definitions provided by any of its source vocabularies. Although this particular definition comes from MeSH, it might well be useful in Metathesaurus applications that otherwise do not use MeSH.  In contrast, the date an occurrence of a string (an atom) was added to a source vocabulary applies only to that specific atom. The utility of specific atom attributes will vary considerably for different applications of the Metathesaurus.

Relationship attributes come from a particular source vocabulary and describe special characteristics of particular relationships in that source, e.g., refinability.

The majority of attributes are distributed in MRSAT.RRF and MRSAT in the ORF. In these files, each row contains the name of the attribute, the source of the attribute, and the value of the attribute, in addition to all appropriate identifiers. There are separate files for selected attributes such as the semantic types (MRSTY.RRF and MRSTY in the ORF) and the definitions (MRDEF.RRF and MRDEF in the ORF).

2.4.2 Attribute Identifiers

Each occurrence of each attribute within the Metathesaurus is assigned a unique attribute identifier (ATUI). The appearance or disappearance of ATUIs signals changes in the content of the Metathesaurus, thus ATUIs assist the efficient production of a complete change set for each new version of the Metathesaurus. ATUIs appear only in the RRF, not in the ORF.

2.5   DATA ABOUT THE METATHESAURUS

The Metathesaurus contains a number of files that provide useful "metadata" or data about the Metathesaurus itself. The Metadata files describe (1) characteristics of the current version of the Metathesaurus; (2) changes between the current version and the previous version; and (3) the history of concept identifiers (CUIs) from 1991 to the present.

2.5.1   Characteristics of the Current Metathesaurus

There are discrete Metathesaurus files for:

a)    the names and sizes of every Metathesaurus file (MRFILES.RRF and MRFILES in ORF),

b)    the names and size range of every Metathesaurus data element (MRCOLS.RRF and MRCOLS in ORF),

c)   the possible values for selected data elements that contain a finite set of abbreviated values (MRDOC.RRF only). NOTE: eventually this file will include values for every data element that contains a finite set of abbreviated values

d)   the source vocabularies in the Metathesaurus (MRSAB.RRF and MRSAB in ORF),

e)   the LUIs and SUIs for terms and strings that are known to be ambiguous, that is, to have multiple meanings (to be
 linked to multiple concept identifiers) within the Metathesaurus (AMBIGLUI.RRF and AMBIGSUI.RRF in RRF and AMBIGLUI and AMBIGSUI in ORF),

f)   the order of precedence of vocabulary source and term types that is used to compute the default preferred concept name for each concept in the Metathesaurus (MRRANK.RRF and MRRANK in ORF). NOTE: MetamorphoSys can be used to change this order.

MRCOLS, MRDOC, MRSAB, and MRRANK contain data that do not appear in the actual Metathesaurus content files. The others are computable from the Metathesaurus content files. They are pre-computed and provided in separate files as a convenience to users of the Metathesaurus.

2.5.2    Changes between the Current Metathesaurus and the Previous Version

Each version of the Metathesaurus contains a set of files that summarize changes from the previous version.

CHANGE/MERGEDCUI.RRF in the RRF (CHANGE/MERGED.CUI in the ORF) documents cases in which two discrete concepts in the previous version of the Metathesaurus are now considered to be synonyms.

CHANGE/MERGEDLUI.RRF in the RRF (CHANGE/MERGED.LUI in the ORF) documents cases in which two discrete terms in the previous version of the Metathesaurus are now identified as lexical variants of each other, based on the current version of luinorm (the program used to compute them).

Three files contain the CUIs, LUIs, and SUIs for Metathesaurus concepts, terms, and strings that appeared in the previous version, but are not in the current version (CHANGE/DELETEDCUI.RRF, CHANGE/DELETEDLUI.RRF, CHANGE/DELETEDSUI.RRF in the RRF and CHANGE/DELETED.CUI, CHANGE/DELETED.LUI, CHANGE/DELETED.SUI in the ORF).

NOTE: In future versions of the Metathesaurus, change files will also be provided for relationships and attributes in the RRF only. The generation of these files is dependent on the relationship and attribute identifiers (RUI and ATUI) introduced in the 2004AA version of the Metathesaurus.

2.5.3    Historical CUIs

The retired CUI file (MRCUI.RRF in RRF and MRCUI in ORF) includes all CUIs present in any previous version of the Metathesaurus, but not in the current version. In general, the file maps the retired CUI to one or more current CUIs.

2.6 CONCEPT NAME INDEXES

2.6.0 INTRODUCTION

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 subelements.  

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; for more information, see the SPECIALIST Lexicon and tools.

2.6.1.3 Word Index 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 subelements.

2.6.2.2 Definition of Normalized Word

The normalization process involves breaking a string into its constituent words, lowercasing each word and converting it to its uninflected form. Normalized words are generated by uninflecting each word and stripping out a small number of stop words. 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 Normalized Word 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", as follows:

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 subelements.

2.6.3.2 Definition of Normalized String

The normalization process involves breaking a string into its constituent words, lowercasing each word, converting each word to its uninflected form, and sorting the words in alphabetic order. Normalized strings are generated by uninflecting each word leaving out a small number of stop words. 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 Normalized String 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 Java. 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 - METATHESAURUS RICH RELEASE FORMAT (RRF) AND ORIGINAL
RELEASE FORMAT (ORF)

2.7.0 INTRODUCTION

Metathesaurus users may select from two relational formats:  the Rich Release Format (RRF), first introduced in 2004, and the Original Release Format (ORF).  Both are available as output options of MetamorphoSys, the UMLS install and customization program (Section 6).

Developers are encouraged to use the RRF, which offers significant advantages in source vocabulary "transparency" (that is,  ability to represent the detailed semantics of each source vocabulary exactly); in the ability to generate complete and accurate change sets between versions of the Metathesaurus; and in more convenient representations of concept name, source, and hierarchical context information.  A more complete discussion of the rationale for the RRF and a detailed description of the differences between the two formats are available.

Neither Metathesaurus format is fully normalized.  By design, there is duplication of data among different files and within certain files.  In particular, relationships 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 specfic applications.

Section 2.7.1 describes the files in the RRF.  Section 2.7.2 describes the files in the ORF.

2.7.1 METATHESAURUS RICH RELEASE FORMAT (RRF)

All file names begin with the letters MR (Metathesaurus Relational) and are followed by letters that denote the file contents (e.g., MRREL=relationships, MRSAB=source abbreviations), and then a file extension .RRF.

All files except MRRANK.RRF are sorted by row.

2.7.1.1 Data Files

The data in each Metathesaurus entry may be represented in more than 20 different "relations" or files. These files correspond to the four logical groups of data elements described in Sections 2.2- 2.5 and the indexes described in Section 2.6 as follows:

Concepts, Concept Names, and their sources (2.2) = MRCONSO.RRF

Attributes (2.3) = MRSAT.RRF, MRDEF.RRF, MRSTY.RRF, MRLO.RRF, MRHIST.RRF

Relationships (2.4) = MRREL.RRF, MRCOC.RRF, MRCXT.RRF, MRHIER.RRF, MRMAP.RRF, MRSMAP.RRF

Data about the Metathesaurus (2.5) = MRFILES.RRF, MRCOLS.RRF, MRDOC.RRF, MRRANK.RRF, MRSAB.RRF, AMBIGLUI.RRF, AMBIGSUI.RRF, CHANGE/MERGEDCUI.RRF, CHANGE/MERGEDLUI.RRF, CHANGE/DELETEDCUI.RRF, CHANGE/DELETEDLUI.RRF, CHANGE/DELETEDSUI.RRF, MRCUI.RRF

Indexes (2.6) = MRXW_BAQ.RRF, MRXW_DAN.RRF, MRXW_DUT.RRF, MRXW_ENG,MRP, MRXW_FIN.RRF, MRXW_FRE.RRF, MRXW_GER.RRF, MRXW_HEB.RRF, MRXW_HUN.RRF, MRXW_ITA.RRF, MRXW_NOR.RRF, MRXW_POR.RRF, MRXW_RUS.RRF, MRXW_SPA.RRF, MRXW_SWE.RRF, MRXNW_ENG.RRF, MRXNS_ENG.RRF

Each file 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 subelement. In general, columns for longer variable length data elements will appear to the right of columns for shorter and/or fixed length data elements. The information for all columns in the files is described in MRCOLS.RRF and in Appendix B.1.1,  Metathesaurus Column Descriptions.

A row contains the values for one or more data elements or logical subelements 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 subelements 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 line termination.

2.7.1.3 Descriptions of Each File

The descriptions of the files appear in the following order:
a) Key data about the Metathesaurus:  Files; Columns or data elements; Documentation that explains the meaning of abbreviations that appear as values in Metathesaurus data elements and attributes,
b) Concept names and their vocabulary sources
c) Attributes
d) Relationships
e) Other data about the Metathesaurus
f) Indexes

Each file description lists the columns or data elements that appear in the file and includes sample rows from the file.

2.7.1.3.1 Files(File = MRFILES.RRF)

There is exactly one row in this file for each physical segment of each logical file. Data elements that appear in multiple files, e.g., CUI, AUI, will have multiple rows in this file.

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

2.7.1.3.2 Data Elements (File = MRCOLS.RRF)

There is exactly one row in this file for each column or data element in each file. Data elements that appear in multiple files, e.g., CUI, AUI, will have multiple rows in this file.  

Sample Records

AUI|Unique identifier for atom||8|8.00|8|MRCONSO.RRF|char(8)|
CODE|Unique Identifier or code for string in source||1|6.4|21|MRCONSO.RRF|varchar(50)|

There is exactly one row in this table for each allowed value of selected data elements or attributes that have a finite number of abbreviations as allowed values. Examples of such data elements include TTY, ATN, TS, STT, REL, RELA.  

  Sample Records

ATN|DDF|expanded_form|Drug Doseform|
ATN|DHJC|expanded_form|HCPCS J-code|

2.7.1.3.4 Concept Names and Sources (File = MRCONSO.RRF)

There is exactly one row in this file for each atom (each occurrence of each unique string or concept name within each source vocabulary) in the Metathesaurus, i.e., there is exactly one row for each unique AUI in the Metathesaurus. Every string or concept name in the Metathesaurus appears in this file, connected to its language, source vocabularies, and its concept identifier. The values of TS, STT, and ISPREF reflect the default order of precedence of vocabulary sources and term types in MRRANK.RRF.

  Sample Records

C0001175|ENG|P|L0001175|VO|S0010340|Y|A0019182||M0000245|D000163|MSH|PM|D000163|
     Acquired Immunodeficiency Syndromes|0|N|| 
C0001175|ENG|S|L0001842|PF|S0011877|N|A2878223|103840012|62479008||SNOMEDCT|PT|62479008|AIDS|4|N||
C0001175|ENG|P|L0001175|VC|S0354232|Y|A2922342|103845019|62479008||SNOMEDCT|SY|62479008|
     Acquired immunodeficiency syndrome|4|Y||
C0001175|FRE|P|L0162173|PF|S0226654|Y|A0248753||||INS|MH|d000163|SIDA|3|N||
C0001175|RUS|P|L0904943|PF|S1108760|Y|A1165232||||RUS|MH|D000163|SPID|3|N||

2.7.1.3.5 Simple Concept and Atom Attributes (File = MRSAT.RRF)

There is exactly one row in this table for each concept, atom, or relationship attribute that does not have a sub-element structure. All Metathesaurus concepts and a minority of Metathesaurus relationships have entries in this file. This file includes all source vocabulary attributes that do not fit into other categories.

  Sample Records

C0001175|L0001175|S0010339|A0019180|AUI|D000163|AT15797077||FX|MSH|AIDS Dementia Complex|N||
C0001175|L0001175|S0354232|A2922342|SAUI|62479008|AT34794876||DESCRIPTIONSTATUS|SNOMEDCT|0|N||
C0001175|L2810384|S3645548|A3814219|SCUI|62479008|AT33494582||CTV3ID|SNOMEDCT|XE0RX|N||
C0001175|L2810384|S3645548|A3814219|SCUI|62479008|AT33652930|\ISPRIMITIVE|SNOMEDCT|0|N||
C0001175|||R19334287|SRUI||AT37098279||REFINABILITY|SNOMEDCT|1|N||

2.7.1.3.6 Definitions (File = MRDEF.RRF)

There is exactly one row in this file for each definition in the Metathesaurus. A definition is an attribute of an atom (an occurrence of a string in a source vocabulary). A few approach 3,000 characters in length.

  Sample Records

2.7.1.3.7 Semantic Types (File = MRSTY.RRF)

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.  The TUI, STN, and STY are all direct links to the UMLS Semantic Network (Section 3).

  Sample Record

C0001175|T047|B2.2.1.2.1|Disease or Syndrome|AT17683839||

2.7.1.3.8.a Locators (File = MRLO.RRF)

Note: NLM intends to eliminate this file from the Metathesaurus with the 2004AB version. Some of the information is outdated and some is duplicative of information contained in other Metathesaurus files, and some is easily obtained from other publicly available sources, e.g., PubMed.

Selected information sources in which atoms from particular source vocabularies were detected.

There is one row in this table for each atom identified as appearing in each of a selected set of machine-readable information sources.

2.7.1.3.8.b History (File = MRHIST.RRF)

This file tracks source-asserted history information. It currently includes SNOMED CT history only.

  Sample Records

C0000294|108821000|SNOMEDCT|20001101|0|CONCEPTSTATUS|0|||
C0000294|108821000|SNOMEDCT|20020731|2|CONCEPTSTATUS|0|FULLYSPECIFIEDNAME CHANGE||
C0000294|1185494016|SNOMEDCT|20020731|0|DESCRIPTIONSTATUS|0|||
C0000294|1461100014|SNOMEDCT|20030131|0|DESCRIPTIONSTATUS|0|||

There is one row in this table for each relationship between concepts or atoms known to the Metathesaurus, with the following exceptions found in other files: co-occurrences found in MRCOC.RRF, and pair-wise mapping relationships between two source vocabularies found in MRMAP.RRF and MRSMAP.RRF

Note that for asymmetrical relationships there is one row for each direction of the relationship. Note also the direction of REL - the relationship which the SECOND concept or atom (with Concept Unique Identifier CUI2 and Atom Unique Identifier AUI2) HAS TO the FIRST concept or atom (with Concept Unique Identifier CUI1 and Atom Unique Identifier AUI1).  

  Sample Records

2.7.1.3.10 Co-occurring Concepts (File = MRCOC.RRF)

This file includes statistical aggregations of co-occurrences of meanings in external data sources. These exist at the AUI level. There are two rows in this table for each pair of atoms 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. Due to the very large number of co-occurrence relationships, they are distributed in a separate file.

  Sample Records 

Co-occurrences are 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 three sources of co-occurrence data: MEDLINE, AI/RHEUM, and CCPSS. From MEDLINE, co-occurrence data was 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 recent MEDLINE data (MED) and one for MEDLINE data from a preceding block of years (MBD); see SOC for date ranges in the current edition. 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 the 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.

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.

In CCPSS, the co-occurrence data is extracted from patient records and includes problem-problem co-occurrences within a patient record as well as problem-modifier co-occurrences.

2.7.1.3.11 "Computable" Hierarchies (File = MRHIER.RRF)

This file contains one row for each hierarchy or context in which each atom appears. If a source vocabulary does not contain hierarchies, its atoms will have no rows in this file. If a source vocabulary is multi-hierarchical (allows the same atom to appear in more than one hierarchy), some of its atoms will have more than one row in this file. MRHIER.RRF provides a complete and compact representation of all hierarchies present in all Metathesaurus source vocabularies. Hierarchical displays can be computed by combining data in this file with data in MRCONSO.RRF. The “distance-1 relationships”, i.e., immediate parent, immediate child, and sibling relationships, represented in MRHIER.RRF also appear in MRREL.RRF. Most of the hierarchical relationships in MRHIER.RRF (excluding some sibling relationships) also appear in a much larger, “pre-computed” format in MRCXT.RRF (Section 2.7.1.3.12). NLM plans to phase out MRCXT.RRF (which has reached an unwieldy size) in favor of providing users with tools that generate hierarchical displays based on MRHIER.RRF and MRCONSO.RRF.

Sample Records

C0001175|A2878223|1|A3316611|SNOMEDCT|isa|A3684559.A2880798.A339606.A3287869.A3316611|||
C0001175|A2878223|2|A3512124|SNOMEDCT|isa|A3684559.A2880798.A3398606.A3287869.A3512124|||
C0001175|A2878223|3|A3696836|SNOMEDCT|isa|A3684559.A2880798.A3398606.A3399957.A3399109.A3144217.A3696836|||
C0001175|A2878223|4|A3512124|SNOMEDCT|isa|A3684559.A2880798.A3398606.A3399957.A3399109.A3512124|||
C0001175|A2878223|5|A3316611|SNOMEDCT|isa|A3684559.A2880798.A3512117.A3082701.A3316611|||
C0001175|A2878223|6|A2888699|SNOMEDCT|isa|A3684559.A2880798.A3512117.A3082701.A3398847.A3398762.A2888699|||
C0001175|A2878223|7|A3316611|SNOMEDCT|isa|A3684559.A2880798.A3512117.A3287869.A3316611|||
C0001175|A2878223|8|A3512124|SNOMEDCT|isa|A3684559.A2880798.A3512117.A3287869.A3512124|||
C0001175|A2988194|1|A2888699|SNOMEDCT|isa|A3684559.A2880798.A3512117.A3082701.A3398847.A3398762.A2888699|||

To find the specific concept names used in a hierarchy, look up the atom identifiers in the AUI and PTR data elements in MRCONSO.RRF.

For most source vocabularies, the value of RELA (if present) applies up the hierarchy to the top or root. In other words, it also applies to the relationship between the atom' s parent and the atom's grandparent, etc. The two exceptions in this version of the Metathesaurus are GO (Gene Ontology) and NIC (Nursing Intervention Classification). Except for GO and NIC atoms, the MRHIER rows for an atom's ancestors (parent, grandparent, etc.) contain no added information except the source asserted hierarchical number or code (HCD). If this is not of interest, there may be no reason to find MRHIER rows for an atom's ancestors.

To find an atom's siblings in a specific context, find all MRHIER.RRF rows that share its SAB, RELA*, and PTR values.

To find an atom's children in a specific context, append a period (.) and the atom's AUI to its PTR and find all MRHIER.RRF rows with its SAB, RELA*, and the expanded PTR.

*The RELA is needed to retrieve correct siblings and children for University of Washington Digital Anatomist (UWDA) hierarchies. Some UWDA atoms appear in multiple hierarchies that are distinguished ONLY by their RELA values.

2.7.1.3.12 Contexts (File = MRCXT.RRF)

This very large file contains pre-computed hierarchical context information (including concept names) intended to facilitate the display of hierarchies present in UMLS source vocabularies. All of the information in this file (plus additional sibling relationships) can be computed by joining the MRHIER.RRF file with MRCONSO.RRF. There can be many rows in this file for each occurrence of an atom in a hierarchy in any of the UMLS source vocabularies - a "context in this discussion. Many Metathesaurus concepts have many atoms with contexts while others may have none. The number of rows per context differs depending on the number of ancestor, sibling, or child terms an atom has in that context. Because some atoms have multiple contexts in the same source, e.g., MeSH, a context number (CXN - e.g., 1,2,3) is used to identify all members of the same context. The CXNs are not global but are created as required for each atom. Each distinct context for a single atom can be retrieved with a CUI-AUI-SAB-CXN key. The "distance-1 relationships, " i.e., the immediate parent, immediate child, and sibling relationships, represented in MRCXT.RRF, are also present in the MRREL.RRF file.

Sample Records

C0001175|S1911299|A1855909|ICPC2P|B9001|1|ANC|1|ICPC2-Plus|C1140253|A1861145|||||
C0001175|S1911299|A1855909|ICPC2P|B90001|1|ANC|2|BLOOD/BLOOD FORMING ORGANS/IMMUNE
      MECHANISM|C0847039|A1852564|B||||
C0001175|S1911299|A1855909|ICPC2P|B90001|1|ANC|2|Diagnosis/Diseases Component|C0497531|A0916974|7||||  C0001175|S1911299|A1855909|ICPC2P|B90001|1|ANC|3|HIV-INFECTION|AIDS|C0497169|A1852069|B90|||| C0001175|S1911299|A1855909|ICPC2P|B90001|1|CCP||Acquired Immune-Deficiency Syndrome|C0001175|A1855909|B90001||||

2.7.1.3.13 Mappings (File = MRMAP.RRF)

Representations of simple and complex mappings between (1) concept names or (usually) their surrogates (identifiers or codes) from one source vocabulary or from the Metathesaurus and (2) concept names or (usually) their surrogates from another source vocabulary or from the Metathesaurus. This file can accommodate multiple purpose-specific mappings between the same source vocabularies and/or conditional rules for when mappings apply.  Source asserted historical mappings (i.e., mappings between obsolete terms/concepts and current ones) are included here.

2.7.1.3.14 Simple Mappings (File = MRSMAP.RRF)

A simpler representation of most of the mappings in MRMAP.RRF. This file is provided to serve applications which do not require the full richness of the MRMAP.RRF data structure. It does not include entries for mappings that have MAPSUBSETID and MAPRANK values in MRMAP.RRF.

2.7.1.3.15 Source Information (File=MRSAB.RRF)

The UMLS Metathesaurus has "versionless" or "root" Source Abbreviations (SABs) in the data files.  MRSAB.RRF connects the "root" SAB to fully specified version information for the current release. For example, the released SAB for MeSH is now simply "MSH". In MRSAB.RRF, you will see a current versioned SAB, e.g., MSH2003_2002_10_24. MRSAB.RRF allows all other Metathesaurus files to use versionless source abbreviations, so that all rows with no data change between versions remain unchanged. MetamorphoSys can produce files with either the root or versioned SABs so that either form can be available in custom subsets of the Metathesaurus.

There is one row in this file for every version of every source in the current Metathesaurus; eventually there will also be historical informtion with a row for each version of each source that has appeared in any Metathesaurus relese. Note that the field CURVER has the value 'Y' to identify the version in this Metathesaurus release. Future releases of MRSAB.RRF will also contain historical version information in rows with CURVER value 'N'.

The structure of MRSAB.RRF is as follows:

2.7.1.3.16 Concept Name Ranking (File=MRRANK.RRF)

There is exactly one row for each concept name type from each Metathesaurus source vocabulary (each SAB-TTY combination). The RANK and SUPPRES values in the distributed file are those used in Metathesaurus production. Users are free to change these values to suit their needs and preferences, then change the naming precedence and suppressibility by using MetamorphoSys to create a customized Metathesaurus. 

Sample Records

0210|AIR|SY|N|
0209|ULT|PT|N|
0208|CPT|PT|N|

2.7.1.3.17 Ambiguous Term Identifiers (File = AMBIGLUI.RRF)

There is exactly one row in this table for each Lexical Unique Identifier (LUI) that is linked to multiple Concept Unique Identifiers (CUIs); i.e., it identifies those lexical variant classes which have multiple meanings in the Metathesaurus.

In the Metathesaurus, the LUI links all strings within the English language that are identified as lexical variants of each other by the luinorm program found in the UMLS SPECIALIST Lexicon and Tools (see Sections 4). LUIs are assigned irrespective of the meaning of each string. This table may be useful to system developers who wish to make use of the lexical programs in their applications.  

2.7.1.3.18 Ambiguous String Identifiers (File=AMBIGSUI.RRF)

There is exactly one row in this file for each string identifier (SUI) that is linked to multiple concept identifiers (CUI). This file is now in the META directory (use to be in CHANGE directory). 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.

2.7.1.3.19 Metathesaurus Change Files 

There are six files or relations that identify key differences between entries in the previous and the current edition of the Metathesaurus. 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.

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 ends with a vertical bar and line termination.

2.7.1.3.19.1 Deleted Concepts (File=CHANGE/DELETEDCUI.RRF)

There is exactly one row in this table for each reviewed concept that was present in the previous Metathesaurus and is not present in the 2003AC Metathesaurus.

Cols.
PCUI Concept Unique Identifier in the previous Metathesaurus
PSTR Preferred name of this concept in the previous Metathesaurus

2.7.1.3.19.2 Merged Concepts (File=CHANGE/MERGEDCUI.RRF)

There is exactly one row in this table for each released concept in the previous Metathesaurus (CUI1) that was merged into another released concept from the previous Metathesaurus (CUI2). When this merge occurs, the first CUI (CUI1) was retired; this table shows the CUI (CUI2) for the merged concept in this Metathesaurus.

Entries in this file represent concepts pairs that were considered to have different meanings in the previous edition, but which are now identified as synonyms

Cols.
PCUI1 Concept Unique Identifier in the previous Metathesaurus
CUI Concept Unique Identifier in this Metathesaurus in format C#######

2.7.1.3.19.3 Deleted Terms (File=CHANGE/DELETEDLUI.RRF)

There is exactly one row in this table for each Lexical Unique Identifier (LUI) that appeared in the previous Metathesaurus, but does not appear in this Metathesaurus.

Metathesaurus Lexical Unique Identifiers (LUIs) are assigned by the luinorm program, part of LVG program in the UMLS SPECIALIST Lexicon and Tools; see Section 4.

These entries represent the cases where LUIs identified by the previous release's luinorm program, when used to identify lexical variants in the previous Metathesaurus, are no longer found with this release's luinorm on this release's Metathesaurus. This does not necessarily imply the deletion of a string or a concept from the Metathesaurus.

Cols.
PLUI Lexical Unique Identifier in the previous Metathesaurus
PSTR Preferred Name of Term in the previous Metathesaurus

2.7.1.3.19.4 Merged Terms (File=CHANGE/MERGEDLUI.RRF)

There is exactly one row in this file for each case in which strings had different Lexical Unique Identifiers (LUIs) in the previous Metathesaurus yet share the same LUI in this Metathesaurus; a LUI present in the previous Metathesaurus is therefore absent from this Metathesaurus.

Metathesaurus Lexical Unique Identifiers (LUIs) are assigned by the luinorm program, part of the LVG program in the UMLS SPECIALIST Lexicon and Tools; see Section 4.

These entries represent the cases where separate lexical variants as identified by the previous release's luinorm program version are a single lexical variant as identified by this release's luinorm.

Cols.
PLUI Lexical Unique Identifier in the previous Metathesaurus but not present in this Metathesaurus
LUI Lexical Unique Identifier into which it was merged in this Metathesaurus

2.7.1.3.19.5 Deleted Strings (File=CHANGE/DELETEDSUI.RRF)

There is exactly one row in this file for each string in each language that was present in a entry in the previous Metathesaurus and does not appear in this Metathesaurus.

Note that this does not necessarily imply the deletion of a term (LUI) or a concept (CUI) from the Metathesaurus. A string deleted in one language may still appear in the Metathesaurus in another language.

Cols.
PSUI String Unique Identifier in previous Metathesaurus that is not present in this Metathesaurus
PSTR Preferred name of term in previous Metathesaurus that is not present in this Metathesaurus

2.7.1.3.19.6 Retired CUI Mapping (File=MRCUI.RRF)

There are one or more rows in this file for each Concept Unique Identifier (CUI) that existed in any prior release but is not present in the current release. The file includes mappings to current CUIs as synonymous or to one or more related current CUI where possible. If a synonymous mapping cannot be found, other relationships between the CUIs can be created. These relationships can be Broader (RB), Narrower (RN) or Other Related (RO). Some CUIs may be mapped to more than one other CUI using these relationships.

CUIs may be retired when (1) two released concepts are found to be synonyms and so are merged, retiring one CUI; (2) when the concept no longer appears in any source vocabulary and is not 'rescued' by NLM; or (3) where the concept is an acknowledged error in a source vocabulary or determined to be a Metathesaurus production error.

See Sections 2.7.1.3.19, 1 through 5 for files of changes from the last release only, without mappings.

Sample Records:

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.  

  Sample Records from MRXW_ENG.RRF

ENG|anaemia|C0002871|L0280031|S0352688|
ENG|anemia|C0002871|L0002871|S0013742|
ENG|anemias|C0002871|L0002871|S0013787|
ENG|blood|C0002871|L0376533|S0500659|
ENG|cells|C0002871|L0376533|S0500659|

  Sample Records from MRXW_FRE.RRF

FRE|ANEMIE|C0002871|L0162748|S0227229|

2.7.1.3.21 Normalized Word Index (File=MRXNW_ENG.RRF)

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.  

  Sample Records

ENG|anaemia|C0002871|L0280031|S0352688|
ENG|anemia|C0002871|L0002871|S0013742|
ENG|anemia|C0002871|L0002871|S0013787|
ENG|blood|C0002871|L0376533|S0500659|
ENG|cell|C0002871|L0376533|S0500659|

2.7.1.3.22 Normalized String Index (File=MRXNS_ENG.RRF)

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.  

  Sample Records

ENG|anaemia|C0002871|L0280031|S0352688|
ENG|anaemia unspecified|C0002871|L0696700|S0803315|
ENG|anemia|C0002871|L0002871|S0013787|

2.7.2 METATHESAURUS ORIGINAL RELEASE FORMAT (ORF)

All files except MRRANK are sorted by row.

2.7.2.1. Data Files

The data in each Metathesaurus entry may be represented in more than 20 different "relations" or files. These files correspond to the four logical groups of data elements described in Section 2.2 - 2.5 and the indexes described in Section 2.6 as follows:

Metathesaurus Concept Names and their sources (2.7.2.2) = MRCON, MRSO
Attributes (2.7.2.3) MRSAT, MRDEF, MRSTY, MRLO
Relationships between Different Concept Names (2.7.2.4) = MRREL, MRCOC, MRATX, MRCXT
Data about the Metathesaurus (2.7.2.5)=MRSAB, MRRANK, AMBIG.LUI, AMBIG.SUI, DELETED.CUI, MERGED.CUI, DELETED.LUI, MERGED.LUI, DELETED.SUI, MRCUI
Indexes (2.7.2.6) = MRXW.BAQ, MRXW.DAN, MRXW.DUT, MRXW.ENG, MRXW.FIN, MRXW.FRE, MRXW.GER, MRXW.HEB, MRXW.HUN, MRXW.ITA, MRXW.NOR, MRXW.POR, MRXW.RUS, MRXW.SPA, MRXW.SWE, MRXNW.ENG, MRXNS.ENG

The AMBIG* files provide a convenient way to identify all Metathesaurus terms and strings that have more than one meaning in Metathesaurus source vocabularies.

2.7.2.2 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 subelement. In general, columns for longer variable length data elements will appear to the right of columns for shorter and/or fixed length data elements. The information for all columns in the ORF files is described in Appendix B.1.2,  ORF Columns or Data Elements

A row contains the values for one or more data elements or logical subelements 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 subelements 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 line termination.

2.7.2.3 Descriptions of Each File

The descriptions of the files appear in the following order:

1. Key data about the Metathesaurus: Files, Columns or data elements
2. Concept names and their vocabulary sources
3. Attributes
4. Relationships
5. Other data about the Metathesaurus
6. Indexes

2.7.2.3.1 Files (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:  

  Sample Records

MRATX|Associated Expressions|CUI,SAB,REL,ATX|4|7295|442571|
MRCOC|Co-occurring Concepts|CUI1,CUI2,SAB,COT,COF,COA|6|9061980|343331578|
MRCOLS|Attribute Relation|COL,DES,REF,MIN,AV,MAX,FIL, DTY|8|115|5728|

2.7.2.3.2 Data Elements (File = MRCOLS)

There is exactly one row in this file for each column or data element in each file in the relational format.  

  Sample Records

ATN|Attribute name||2|3.15|7|MRSAT|varchar(20)|
ATV|Attribute value||1|9.71|3634|MRSAT|varchar(4000)|
ATX|Associated expression||5|35.89|242|MRATX|varchar(300)|

2.7.2.3.3 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 in the Metathesaurus. Any difference in upper-lower case, word order, etc. creates a different unique string.  

  Sample Records

C0002871|ENG|P|L0002871|PF|S0013742|Anemia|0|
C0002871|ENG|P|L0002871|VP|S0013787|Anemias|0|
C0002871|ENG|P|L0002871|VC|S0352787|ANEMIA|0|
C0002871|ENG|P|L0002871|VC|S0414880|anemia|0|
C0002871|ENG|P|L0002871|VO|S0470197|Anemia, NOS|3|
C0002871|ENG|S|L0280031|PF|S0803242|Anaemia|3|

2.7.2.3.4 Vocabulary Sources (File = MRSO)

The vocabulary source(s) for a concept, term, and string.

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.  

  Sample Records

C0002871|L0002871|S0013742|CCS|MD|4.1|0|
C0002871|L0002871|S0013742|ICPCPAE|PT|B82005|3|
C0002871|L0002871|S0013742|LCH|PT|U000235|0|
C0002871|L0002871|S0013742|MSH|MH|D000740|0|
C0002871|L0002871|S0013742|MTH|PT|U000161|0|
C0002871|L0002871|S0013742|MTH|PT|U000164|0|
C0002871|L0002871|S0013742|PSY|PT|02450|3|
C0002871|L0002871|S0013742|RCDAE|PT|XM05A|3|

The information in MRSO can be used in combination with MRCON to determine whether a particular concept, name, or code is present in a particular source, and in what form it appears.

Note: In the RRF, the concept name and vocabulary source information appear in a single file, MRCONSO.RRF.

2.7.2.3.5 Simple Concept 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.  

  Sample Records

C0002871|L0002871|S0013742|D000740|MMR|MSH|19960610|
C0002871|L0002871|S0013742|D000740|MN|MSH|C15.378.71|
C0002871|L0002871|S0013742|D000740|TH|MSH|POPLINE (1994)|
C0002871|L0002871|S0414880|208/04453|SOS|PDQ|secondary related condition|
C0002871|L0002871|S0470197|DC-10010|SIC|SNMI|285.9|

2.7.2.3.6 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.  

  Sample Records

C0002871|MSH|A reduction in the number of circulating erythrocytes or in the quantity of hemoglobin.|

2.7.2.3.7 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.  

  Sample Record

    C0002871|T047|Disease or Syndrome|

2.7.2.3.8 Locators (File = MRLO)

Note: NLM intends to eliminate this file from the Metathesaurus effective with the 2004AB version. Some of the information is outdated and some is duplicative of information contained in other Metathesaurus files.

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.

These columns are described in the appendix:

2.7.2.3.9 Related Concepts (File = MRREL)

There is one row in this table for each relationship between Metathesaurus concepts known to the Metathesaurus, with the following exceptions found in other files: co-occurrences found in MRCOC; Locator information in MRLO; and Associated Expressions found in MRATX.

Note that for asymmetrical relationships there is one row for each direction of the relationship. Note also the direction of REL - the relationship which the SECOND concept (with Concept Unique Identifier CUI2) HAS TO the FIRST concept (with Concept Unique Identifier CUI1).  

  Sample Records

   C0002871|CHD|C0002891|isa|MSH|MSH||
     Anemia, Neonatal (C0002891) 
       has CHILD REL and isa RELA 
         to Anemia (C0002871)

   
   C0002871|RB|C0221016||MTH|MTH||
     [Red blood cell disorder, NOS (C0221016) 
       has broader REL 
         to Anemia (C0002871)]

   C0002871|RL|C0002886|mapped_to|SNMI|SNMI||
     [Anemia, Macrocytic (C0002886)
       has like relationship
        to Anemia (C0002871)]

   C0002871|RO|C0002886|clinically_associated_with|CCPSS|CCPSS||

     [Megaloblastic anemia due to folate deficiency, NOS (C0151482)
       has clinically_associated_with relationship 
         to Anemia (C0002871)]

2.7.2.3.10 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. Due to the very large number of co-occurrence relationships, they are distributed in a separate file.  

  Sample Records

    C0002871||MED|LQ|1||
    C0002871|C0000530|MBD|L|2|CI=1,EN=1,ME=1,PA=1|
    C0002871|C0000727|MBD|L|1|BL=1,ET=1|
    C0002871|C0000737|MBD|L|1|ET=1|
    C0002871|C0000772|MBD|L|2|CN=2|

Co-occurrences are 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 three sources of co-occurrence data: MEDLINE, AI/RHEUM, and CCPSS. From MEDLINE, co-occurrence data was 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 recent MEDLINE data (MED) and one for MEDLINE data from a preceding block of years (MBD); see SOC for date ranges in the current edition. 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 the 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.

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.

In CCPSS, the co-occurrence data is extracted from patient records and includes problem-problem co-occurrences within a patient record as well as problem-modifier co-occurrences.

2.7.2.3.11 Concept contexts (File = MRCXT)

There are rows in this file for each occurrence of a concept in a hierarchy in any of the UMLS source vocabularies - a "context" in this discussion. Many Metathesaurus concepts have multiple contexts while others may 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 (CXN - e.g., 1, 2, 3) is used to identify all members of the same context. The CXNs are not global but are created as required for each concept. Since some concepts have multiple contexts in the same vocabulary with the same SUI, each distinct context can be retrieved with a CUI-SUI-SAB-CXN key. The "distance-1 relationships," i.e., the immediate parent, immediate child, and sibling relationships, represented in this file are also present in the MRREL file.

(Note: The RELA was incorrectly called REL in versions before 2001.)  

Sample Records

 C0002871|S0013742|MSH|D000740|1|ANC|1|MeSH|C0220876||||
 C0002871|S0013742|MSH|D000740|1|ANC|2|Diseases (MeSH Category)|C0012674|C|||
 C0002871|S0013742|MSH|D000740|1|ANC|3|Hemic and Lymphatic Diseases|C0018981|C15|||
 C0002871|S0013742|MSH|D000740|1|ANC|4|Hematologic Diseases|C0018939|C15.378|isa||
 C0002871|S0013742|MSH|D000740|1|CCP||Anemia|C0002871|C15.378.71|isa|+|
 C0002871|S0013742|MSH|D000740|1|CHD||Anemia, Aplastic|C0002874|C15.378.71.85|isa|+|
 C0002871|S0013742|MSH|D000740|1|SIB||Blood Protein Disorders|C0005830|C15.378.147|isa|+|
 C0002871|S0013742|MSH|D000740|1|CHD||Anemia, Hemolytic|C0002878|C15.378.71.141|isa|+|

2.7.2.3.12 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 relationship to a concept in the Metathesaurus. The majority of Metathesaurus entries have no entries in this table.  

  Sample Records

C0001207|MSH|S|<Acromegaly> AND <Gigantism>|
C0001296|LCH|U|<Insurance>/<Statistics>|
C0001355|MSH|S|<Kidney Failure, Acute> AND <Kidney Papillary Necrosis>|

2.7.2.3.13 Source Information (File=MRSAB)

The UMLS Metathesaurus has "versionless" or "root" Source Abbreviations (SABs) in the data files.  MRSAB connects the "root" SAB to fully specified version information for the current release. For example, the released SAB for MeSH is now simply "MSH". In MRSAB, you will find the current versioned SAB, e.g., MSH2003_2002_10_24. MetamorphoSys can produce files with either the root or versioned SABs so that either form can be utilized by a user.

There is one row in this file for every version of every source in the current Metathesaurus; when complete, there will also be historical information with a row for each version of each source that has appeared in any Metathesaurus release. Note that the field CURVER has the value 'Y' to identify the version in this Metathesaurus release.  Future releases of MRSAB will also contain historical version information in rows with CURVER value 'N'.

MRSAB allows all other Metathesaurus files to use versionless source abbreviations, so that rows with no data change between versions also remain unchanged.

2.7.2.3.14 Concept Name Ranking (File=MRRANK)

There is exactly one row for each concept name type from each Metathesaurus source vocabulary (each SAB-TTY combination). The RANK and SUPPRES values in the distributed file are those used in Metathesaurus production. Users are free to change these values to suit their needs and preferences, then change the naming precedence and suppressibility (TS in MRCON) by using MetamorphoSys to create a customized Metathesaurus. 

  Sample Records

0210|AIR|SY|N|
0209|ULT|PT|N|
0208|CPT|PT|N|

2.7.2.3.15 Ambiguous Term Identifiers (File = AMBIG.LUI)

There is exactly one row in this table for each Lexical Unique Identifier (LUI) that is linked to multiple Concept Unique Identifiers (CUIs); i.e., it identifies those lexical variant classes which have multiple meanings in the Metathesaurus.

In the Metathesaurus, the LUI links all strings within the English language that are identified as lexical variants of each other by the luinorm program found in the UMLS SPECIALIST Lexicon and Tools (see section 4). LUIs are assigned irrespective of the meaning of each string. This table may be useful to system developers who wish to make use of the lexical programs in their applications.  

2.7.2.3.16 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). This file is now in the META directory (use to be in CHANGE directory). 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.

2.7.2.3.17 Metathesaurus Change Files

There are six files or relations that identify key differences between entries in the previous and the current edition of the Metathesaurus.  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.

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 ends with a vertical bar and line termination.

2.7.2.3.17.1 Deleted Concepts (File=DELETED.CUI)

There is exactly one row in this table for each reviewed concept that was present in the previous Metathesaurus and is not present in the current Metathesaurus.

Cols.
CUI Concept Unique Identifier in the previous Metathesaurus
STR Preferred name of this concept in the previous Metathesaurus

2.7.2.3.17.2 Merged Concepts (File=MERGED.CUI)

There is exactly one row in this table for each released concept in the previous Metathesaurus (CUI1) that was merged into another released concept from the previous Metathesaurus (CUI2). When this merge occurs, the first CUI (CUI1) was retired; this table shows the CUI (CUI2) for the merged concept in this Metathesaurus.

Entries in this file represent concepts pairs that were considered to have different meanings in the previous edition, but which are now identified as synonyms

Cols.
CUI1 Concept Unique Identifier in the previous Metathesaurus
CUI2 Concept Unique Identifier in this Metathesaurus in format C#######

2.7.2.3.17.3 Deleted Terms (File=DELETED.LUI)

There is exactly one row in this table for each Lexical Unique Identifier (LUI) that appeared in the previous version of Metathesaurus, but does not appear in this version.

Metathesaurus Lexical Unique Identifiers (LUIs) are assigned by the luinorm program, part of LVG program in the UMLS SPECIALIST Lexicon and Tools; see Sections 4 in this manual.

These entries represent the cases where LUIs identified by the previous release's luinorm program, when used to identify lexical variants in the previous Metathesaurus, are no longer found with this release's luinorm on this release's Metathesaurus. This does not necessarily imply the deletion of a string or a concept from the Metathesaurus.

Cols.
LUI Lexical Unique Identifier in the previous Metathesaurus
STR Preferred Name of Term in the previous Metathesaurus

2.7.2.3.17.4 Merged Terms (File=MERGED.LUI)

There is exactly one row in this file for each case in which strings had different Lexical Unique Identifiers (LUIs) in the previous Metathesaurus yet share the same LUI in this Metathesaurus; a LUI present in the previous Metathesaurus is therefore absent from this Metathesaurus.

Metathesaurus Lexical Unique Identifiers (LUIs) are assigned by the luinorm program, part of the LVG program in the UMLS SPECIALIST Lexicon and Tools; see Sections 4 and 4.8 in this manual.

These entries represent the cases where separate lexical variants as identified by the previous release's luinorm program version are a single lexical variant as identified by this release's luinorm.

Cols.
LUI Lexical Unique Identifier in the previous Metathesaurus but not present in this Metathesaurus
LUI Lexical Unique Identifier into which it was merged in this Metathesaurus

2.7.2.3.17.5 Deleted Strings (File=DELETED.SUI)

There is exactly one row in this file for each string in each language that was present in a entry in the previous Metathesaurus and does not appear in this Metathesaurus.

Note that this does not necessarily imply the deletion of a term (LUI) or a concept (CUI) from the Metathesaurus. A string deleted in one language may still appear in the Metathesaurus in another language.

Cols.
SUI String Unique Identifier in previous Metathesaurus that is not present in this Metathesaurus
LAT Three character abbreviation of language of string that has been deleted.
STR Preferred name of term in previous Metathesaurus that is not present in this Metathesaurus.

2.7.2.3.17.6 Retired CUI Mapping (File=MRCUI)

There are one or more rows in this file for each Concept Unique Identifier (CUI) that existed in any prior release but is not present in the current release. The file includes mappings to current CUIs as synonymous or to one or more related current CUI where possible. If a synonymous mapping can not be found, other relationships between the CUIs can be created. These relationships can be Broader (RB), Narrower (RN) or Other Related (RO). Some CUIs may be mapped to more than one other CUI using these relationships.

CUIs may be retired when (1) two released concepts are found to be synonyms and so are merged, retiring one CUI; (2) when the concept no longer appears in any source vocabulary and is not 'rescued' by NLM; or (3) where the concept is an acknowledged error in a source vocabulary or determined to be a Metathesaurus production error.

See the META/CHANGE files, especially MERGED.CUI and DELETED.CUI, for the changes from the last release only, without mappings.

Sample Records:
C0079138|2001|DEL||Y|
C0079138|2001|RO|C0037440|Y|
C0079151|1993|DEL||N|
C0079158|1997|SY|C0009081||
C0079167|1997|SY|C0010042|N|

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.  

  Sample Records from MRXW.ENG

ENG|anaemia|C0002871|L0280031|S0352688|
ENG|anemia|C0002871|L0002871|S0013742|
ENG|anemias|C0002871|L0002871|S0013787|
ENG|blood|C0002871|L0376533|S0500659|
ENG|cells|C0002871|L0376533|S0500659|

  Sample Records from MRXW.FRE

FRE|ANEMIE|C0002871|L0162748|S0227229|

2.7.2.3.19 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.  

  Sample Records

ENG|anaemia|C0002871|L0280031|S0352688|
ENG|anemia|C0002871|L0002871|S0013742|
ENG|anemia|C0002871|L0002871|S0013787|
ENG|blood|C0002871|L0376533|S0500659|
ENG|cell|C0002871|L0376533|S0500659|

2.7.2.3.20 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.  

  Sample Records

ENG|anaemia|C0002871|L0280031|S0352688|
ENG|anaemia unspecified|C0002871|L0696700|S0803315|
ENG|anemia|C0002871|L0002871|S0013787|