Glossary for Metaphrase Java API [Up to Overview]

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Association:

The superset of Cooccurrence and Relation. Each Association is a directional link between two Concepts, concept1() and concept2(). For every Association instance there is a corresponding "inverse" instance relating concept2 to concept1.
See Class COM.Lexical.Metaphrase.Association

Atom:

Each occurrence of a name in a particular source is called an atom. The source the atom comes from may associate atoms with a code; a group of atoms in a source that all have the same code is referred to as a partition of that source. Each atom is placed in one concept, which represents the meaning of that atom (i.e., the meaning of the name in the source). When the same name occurs in more than one source, each occurrence is considered a distinct atom and, depending on the usage in the different sources, different atoms with the same name may be assigned to different concepts.
See Class COM.Lexical.Metaphrase.Atom

Code:

A code is an identifier, such as "D1-234", assigned to one or more atoms by a source. Codes are often just numbers, though some sources use mnemonic codes composed of words or word fragments. A source may assign the same code to more than one name to specify, e.g., that those names may be used interchangeably for the purposes of that source.

Concept:

A concept represents a semantic unit or "meaning" in the Metaphrase thesaurus and may be named by one or more names. The particular names associated with a given concept will change over time, and concepts may occasionally be removed; but the meaning of the concept with a given conceptID will never change, and there will be only one conceptID for each meaning named in the thesaurus.
See Class COM.Lexical.Metaphrase.Concept.

Concept Element:

A type which subsumes Atom, SemanticType, Definition, and Relationship. Concept elements can be moved, deleted, and added (various methods in GoodEnoughUpdate).
See Interface COM.Lexical.Metaphrase.ConceptElement

Concept ID:

A string, such as "C0012345", used to identify a particular concept. This can be thought of as that concept's "name that never changes."

Cooccurrence:

Cooccurrences are a directional link between two concepts that occur together in some source entry. Currently their are two sources of coocurring information: MEDLINE and AIRHEUM.
See the UMLS documentation on coourrences for a full description.
See Class COM.Lexical.Metaphrase.Cooccurrence

CUI:

A CUI is a Concept Unique Identifier from the UMLS Metathesaurus. A CUI is a Concept ID consisting of the letter C followed by 7 digits; a concept in the Metaphrase thesaurus that does not occur in the Metathesaurus will still have a Concept ID, but that Concept ID would not be a CUI (i.e., it would not be found in the Metathesaurus).

Definition:

A textual definition from some identified authoritative source, describing a concept from that source.
See Class COM.Lexical.Metaphrase.Definition

Good Enough Update:

The Java interface that specifies the methods for modifying the content of the Metaphrase Thesaurus.
See COM.Lexical.Metaphrase.GoodEnoughUpdate

Hierarchical Element:

Some sources place their terms in a hierarchical structure, and they may place the same term in multiple locations in such a hierarchy. A hierarchical element represents a particular location of a particular term in a source hierarchy. A hierarchical element generally has links to its ancestors, siblings, and children, all of which are themselves hierarchical elements in the same source hierarchy.
See Class COM.Lexical.Metaphrase.HierarchicalElement

Lexical Navigation:

Lexical navigation, or lexical matching, means getting from a string to one or more authoritative names which share "significant" lexemes, i.e., words or word bases. We say that such names are lexically related to each other. For example, "degenerative joint disease" is lexically related to "Joints, Knee", since they share the lexeme "joint". Of course, a closer lexical match would be "Joint disease, NOS", and an even better one would be "Disease, joint, degenerative", which is lexically equivalent--it contains exactly the same set of lexemes. Metaphrase suggests authoritative names for a given string by retrieving a list of the most lexically related names. Compare Semantic Navigation.
See Class COM.Lexical.Metaphrase.Match

LUI:

The Lexical class Unique Identifier of a name. Lexical classes comprise a set of names that are lexical variants, as determined by the norm program.
See Class COM.Lexical.Metaphrase.Term,
See also Class COM.Lexical.Metaphrase.Atom

Merge:

In thesaurus creation/editing, to take a given concept and make it subsidiary to and wholly contained within another concept. Inverse operation of split.
See Class COM.Lexical.Metaphrase.RMIUpdater

Metathesaurus:

See UMLS Metathesaurus.

Name:

An [english] word or phrase which is used in a source to name a concept. A name may occur in multiple sources; each such occurrence is an atom.
See Class COM.Lexical.Metaphrase.Atom

Neighborhood:

The [semantic] neighborhood of a concept is the set of concepts which are directly related to it.
See method Concept.neighborhoodAtoms(Source)

Norm:

A program supplied with the UMLS Metathesaurus which converts any given term to a corresponding "normalized" string or "norm form". Different terms that are lexical variants will generally have the same norm form. E.g., the term "Alzheimer's Disease" and the term "disease, alzheimer" both have the norm form "alzheimer disease".

Partition:

Partitions are source-specific concept groups. They allow sources to group atoms according to their world-view, which may be different from how the Metathesaurus groups atoms into concepts. A partition is identified by a code assigned by the source.
See Class COM.Lexical.Metaphrase.Partition

Preferred name:

The name of the atom from the highest precedence source and termgroup in a concept.

Preferred form:

The name of the atom from the highest precedence source and termgroup in a lexical class.

Precedence:

An ordering of the set of all termgroups of all sources in the Metaphrase thesaurus, used to select the preferred name of concepts.

Relation:

The relations are part of the UMLS Semantic Network. Each Relationship in the thesaurus may optionally specify a relationship attribute (rela), which is either a name or an inverse of a Relation. For full list of included Relations see Relations.htm.
See Class COM.Lexical.Metaphrase.Relation.

Relationship:

A specified directional link between two Concepts. Each relationship comes from some source, although this source is often the Metathesaurus (SAB="MTH"). For every relationship relating concept1 and concept2, there is a a corresponding "inverse" relationship relating concept2 and concept1. Relationships are used for semantic navigation. Relationships may specify generic "relatedness" or may specify a particular kind of relationship such as "caused_by" or "part_of" (see Relation).
See Class COM.Lexical.Metaphrase.Relationship

Semantic Navigation:

Semantic navigation means getting from one concept to other concepts with similar or related meanings. Unlike lexical navigation, semantic navigation is independent of word forms. Semantic navigation is supported by an extensive, though necessarily incomplete, knowledge base of binary relationships among concepts.
See also Relationships.

Semantic Type:

An attribute of a concept placing it in one of about 130 categories of similar concepts. Examples include "Disease or Syndrome", "Anatomical Structure", and "Organic Chemical". In the Metaphrase Thesaurus, one or more semantic types are assigned to every concept. For a full list of UMLS Semantic Types see SemanticTypes.htm
See Class COM.Lexical.Metaphrase.SemanticType

Source:

A version of a local or external authoritative terminology, such as SNOMED (the Systematized Nomenclature of Human and Veterinary Medicine) or ICD-9-CM (The International Classification of Diseases: 9th revision, Clinical Modification).
See Class COM.Lexical.Metaphrase.Source

Split:

In thesaurus creation/editing, to extract an atom or set of atoms from a concept and make it an independent concept. Compare Merge.
See Class COM.Lexical.Metaphrase.RMIUpdater

Subsource:

Represents a named portion or version of a source. Of the sources in the Metaphrase Thesaurus, only READ and CPT have subsources.
See Class COM.Lexical.Metaphrase.Subsource

Term:

The lexical index unit of Metaphrase. Conceptually, a term represents a unit of medical language. In implementation, it corresponds to a set of atoms which all belong to the same Concept and the same lexical class (i.e., have the same LUI). E.g., there are two terms in version 2.0 of the Metaphrase Thesaurus with the name "Cold" (<cold temperature> and <Common Cold>), and another with the name "COLD" (<Chronic Obstructive Airway Disease>) which is also in the same lexical class. More commonly, there is only one term associated with any given name (i.e., most names are unambiguous).
Note: in common usage, especially within the context of a single source, the intended meaning is often somewhat different, often corresponding instead to either name or atom as defined here.
See Class COM.Lexical.Metaphrase.Term

Termgroup:

A two-letter code specifying a subset of the terms in a source. Atoms (commonly called "terms" by the source authors) are grouped into termgroups such as "preferred term" (PT), "synonym" (SY), or "abbreviation" (AB).

UMLS Metathesaurus:

The Unified Medical Language System Metathesaurus, a large thesaurus of concepts which is maintained annually by the National Library of Medicine. The 1999 Metathesaurus (the tenth annual version, available January 1999) includes over 625,000 concepts containing over a million terms taken from more than 40 authoritative sources. Note that some of the sources included in the Metathesaurus have restrictions on their use; however, 55% of the concepts in the 1999 Metathesaurus are named by at least one unrestricted source.

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