Unified Medical Language System

The Metathesaurus forms the base of the UMLS and comprises over 1 million biomedical concepts and 5 million concept names, all of which stem from the over 100 incorporated controlled vocabularies and classification systems. Some examples of the incorporated controlled vocabularies are CPT, ICD-10, MeSH, SNOMED CT, DSM-IV, LOINC, WHO Adverse Drug Reaction Terminology, UK Clinical Terms, RxNorm, Gene Ontology, and OMIM (see full list).

The Metathesaurus is organized by concept, and each concept has specific attributes defining its meaning and is linked to the corresponding concept names in the various source vocabularies. Numerous relationships between the concepts are represented, for instance hierarchical ones such as "isa" for subclasses and "is part of" for subunits, and associative ones such as "is caused by" or "in the literature often occurs close to" (the latter being derived from Medline).

The scope of the Metathesaurus is determined by the scope of the source vocabularies. If different vocabularies use different names for the same concept, or if they use the same name for different concepts, then this will be faithfully represented in the Metathesaurus. All hierarchical information from the source vocabularies is retained in the Metathesaurus. Metathesaurus concepts can also link to resources outside of the database, for instance gene sequence databases.

Each concept in the Metathesaurus is assigned one or more semantic types (categories), which are linked with one another through semantic relationships.[3] The semantic network is a catalog of these semantic types and relationships. This is a rather broad classification; there are 127 semantic types and 54 relationships in total.

The major semantic types are organisms, anatomical structures, biologic function, chemicals, events, physical objects, and concepts or ideas. The links among semantic types define the structure of the network and show important relationships between the groupings and concepts. The primary link between semantic types is the "isa" link, establishing a hierarchy of types. The network also has 5 major categories of non-hierarchical (or associative) relationships, which constitute the remaining 53 relationship types. These are "physically related to", "spatially related to", "temporally related to", "functionally related to" and "conceptually related to".[3]

The information about a semantic type includes an identifier, definition, examples, hierarchical information about the encompassing semantic type(s), and associative relationships. Associative relationships within the Semantic Network are very weak. They capture at most some-some relationships, i.e. they capture the fact that some instance of the first type may be connected by the salient relationship to some instance of the second type. Phrased differently, they capture the fact that a corresponding relational assertion is meaningful (though it need not be true in all cases).

An example of an associative relationship is "may-cause", applied to the terms (smoking, lung cancer) would yield: smoking "may-cause" lung cancer.

The SPECIALIST Lexicon contains information about common English vocabulary, biomedical terms, terms found in MEDLINE and terms found in the UMLS Metathesaurus. Each entry contains syntactic (how words are put together to create meaning), morphological (form and structure) and orthographic (spelling) information. A set of Java programs use the lexicon to work through the variations in biomedical texts by relating words by their parts of speech, which can be helpful in web searches or searches through an electronic medical record.

Entries may be one-word or multiple-word terms. Records contain four parts: base form (i.e. "run" for "running"); parts of speech (of which Specialist recognizes eleven); a unique identifier; and any available spelling variants. For example, a query for "anesthetic" would return the following:[4]

{ base=anaesthetic
      spelling_variant=anesthetic
      entry=E0008769
          cat=noun
          variants=reg
}
{ base=anaesthetic
      spelling_variant=anesthetic
      entry=E0008770
          cat=adj
          variants=inv
          position=attrib(3)
}

The SPECIALIST lexicon is available in two formats. The "unit record" format can be seen above, and comprises slots and fillers. A slot is the element (i.e. "base=" or "spelling variant=") and the fillers are the values attributable to that slot for that entry. The "relational table" format is not yet normalized and contain a great deal of redundant data in the files.