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Introduction
Biomedical resources including gene, protein sequence databases, literature, and ontologies are abundant. These resources have terminology in common consisting of the names of proteins, genes, molecular functions, and diseases. The terminology is present in various controlled vocabularies and nomenclatures. However, only common terminology does not mean that all resources have standard vocabularies and are interoperable. One of the salient features of the Unified Medical Language System® (UMLS®), when evaluated against other terminology, is the presence of knowledge sources (Bodenreider, 2004).
This study discusses the approach of Unified Medical Language System® (UMLS®) that covers the most of the biomedical domain.
UMLS (Unified Medical Language System)
Background
The UMLS was developed by US National Library of Medicine and can be said to be the largest repository of biomedical vocabularies. The UMLS covers 900,000 concepts from over 60 families of biomedical vocabularies, consisting of over 2 million names. The vocabularies incorporated in the UMLS knowledge sources consists of Gene Ontology, NCBI taxonomy, OMIM the Medical Subject Headings (MeSH), and the Digital Anatomist Symbolic Knowledge Base. Additionally, the UMLS also provides tools for customizing the knowledge sources for creating name variants and creating MetaMap for mining the text (Bodenreider, 2004).
Knowledge Sources and Development Tools
The UMLS knowledge sources are regularly updated. The vocabularies are free for research purposes, but users need to sign a license agreement before using. The knowledge sources can be obtained on a CD‐ROM or downloaded via FTP. All the Knowledge Sources are accessible through the Internet from NLM servers. The UMLS Knowledge Sources are Metathesaurus®, Semantic Network, and SPECIALIST Lexicon. The knowledge sources have their own Lexical Tools, customization programs, and MetamorphoSys installation. NLM updates the UMLS every year in May and November. UMLS products are available to U.S. and international researchers and users. A License Agreement is required to be signed. The use and distribution restrictions of the UMLS contents are described in the agreement. Some vocabularies of the Metathesaurus might have separate agreements.
Applications & Examples of UMLS Implementation
The UMLS has a variety of uses at different institutions. It is used for information retrieval and creating research and patient data. The UMLS is also useful for controlled communication between systems. The UMLS Metathesaurus is the largest thesaurus of biomedical knowledge. This knowledge has been useful for several applications including decision support systems, information retrieval, management of patient records, and data mining. The users of UMLS based applications include PubMed, Enterprise Vocabulary Services, Indexing Initiative, and ClinicalTrials.gov. A highly configurable program for mapping biomedical text to concepts in the UMLS Metathesaurus is MetaMap (Aronson, 2001).
Future Implications of UMLS on Healthcare Applications
There is an upward trend of UMLS usage in Healthcare institutions and universities. Genomics is leading the industry and supporting genomic concepts the NLM must incorporate more genomic-based terminologies into the UMLS. The UMLS subject range is already exhaustive and includes most topics. The agency of Healthcare Research and Quality have been able to develop several customized applications based on UMLS as it is free to use (Chen, Perl, Geller, & Cimino, 2007).
Additional Information and Relevant Links
National Library of Medicine: http://www.nlm.nih.gov/pubs/factsheets/umls.html
NLM Fact Sheets: http://www.nlm.nih.gov/pubs/factsheets/factsheets.html
http://www.nlm.nih.gov/pubs/factsheets/factsubj.html
Conclusion
UMLS is beneficial for mapping source terminologies. The leading categories of UMLS use are Information Retrieval, Terminology Research and Translation and Natural Language Processing. The correctness and design of the UMLS terminology are most important and relevant audit must be performed to safeguard its authenticity.
References
Aronson, A. R. (2001). Effective mapping of biomedical text to the UMLS Metathesaurus:
the MetaMap program. In Proceedings of the AMIA Symposium (p. 17).
American Medical Informatics Association.
Bodenreider, O. (2004). The unified medical language system (UMLS):
integrating biomedical terminology. Nucleic acids research, 32(suppl 1), D267-D270.
Chen, Y., Perl, Y., Geller, J., & Cimino, J. J. (2007). Analysis of a study of the users, uses,
and future agenda of the UMLS. Journal of the American Medical Informatics
Association, 14(2), 221-231.
