Биоақпараттық және қатысты бағдарламалық құралдардың онлайн жинағы: UMLS жүйесі

Online compendium of Bioinformatics & related software tools
The Unified Medical Language System (UMLS) is a compendium of many controlled vocabularies in the biomedical sciences (created 1986). It provides a mapping structure among these vocabularies and thus allows one to translate among the various terminology systems; it may also be viewed as a comprehensive thesaurus and ontology of biomedical concepts. UMLS further provides facilities for natural language processing. It is intended to be used mainly by developers of systems in medical informatics. UMLS consists of Knowledge Sources (databases) and a set of software tools. The UMLS was designed and is maintained by the US National Library of Medicine, is updated quarterly and may be used for free. The project was initiated in 1986 by Donald A. B. Lindberg, M. D., then Director of the Library of Medicine, and directed by Betsy Humphreys.

The number of biomedical resources available to researchers is enormous. Often this is a problem due to the large volume of documents retrieved when the medical literature is searched. The purpose of the UMLS is to enhance access to this literature by facilitating the development of computer systems that understand biomedical language. This is achieved by overcoming two significant barriers: "the variety of ways the same concepts are expressed in different machine readable sources & by different people" and "the distribution of useful information among many disparate databases & systems".

Users of the system are required to sign a "UMLS agreement" and file brief annual usage reports. Academic users may use the UMLS free of charge for research purposes. Commercial or production use requires copyright licenses for some of the incorporated source vocabularies.

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.

Given the size and complexity of the UMLS and its permissive policy on integrating terms, errors are inevitable. Errors include ambiguity and redundancy, hierarchical relationship cycles (a concept is both an ancestor and descendant to another), missing ancestors (semantic types of parent and child concepts are unrelated), and semantic inversion (the child/parent relationship with the semantic types is not consistent with the concepts). These errors are discovered and resolved by auditing the UMLS. Manual audits can be very time consuming and costly. Researchers have attempted to address the issue through a number of ways. Automated tools can be used to search for these errors. For structural inconsistencies (such as loops), a trivial solution based on the order would work. However, the same wouldn't apply when the inconsistency is at the term or concept level (context specific meaning of a term). This requires an informed search strategy to be used (knowledge representation).

In addition to the knowledge sources, the National Library of Medicine also provides supporting tools.