Logo of compfungenJournal's HomeManuscript SubmissionAims and ScopeAuthor GuidelinesEditorial BoardHome
Comp Funct Genomics. 2003 Feb; 4(1): 80–84.
PMCID: PMC2447396

An Upper-Level Ontology for the Biomedical Domain


At the US National Library of Medicine we have developed the Unified Medical Language System (UMLS), whose goal it is to provide integrated access to a large number of biomedical resources by unifying the vocabularies that are used to access those resources. The UMLS currently interrelates some 60 controlled vocabularies in the biomedical domain. The UMLS coverage is quite extensive, including not only many concepts in clinical medicine, but also a large number of concepts applicable to the broad domain of the life sciences. In order to provide an overarching conceptual framework for all UMLS concepts, we developed an upper-level ontology, called the UMLS semantic network. The semantic network, through its 134 semantic types, provides a consistent categorization of all concepts represented in the UMLS. The 54 links between the semantic types provide the structure for the network and represent important relationships in the biomedical domain. Because of the growing number of information resources that contain genetic information, the UMLS coverage in this area is being expanded. We recently integrated the taxonomy of organisms developed by the NLM's National Center for Biotechnology Information, and we are currently working together with the developers of the Gene Ontology to integrate this resource, as well. As additional, standard, ontologies become publicly available, we expect to integrate these into the UMLS construct.

Full Text

The Full Text of this article is available as a PDF (123K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Creating the gene ontology resource: design and implementation. Genome Res. 2001 Aug;11(8):1425–1433. [PMC free article] [PubMed]
  • McCray AT, Nelson SJ. The representation of meaning in the UMLS. Methods Inf Med. 1995 Mar;34(1-2):193–201. [PubMed]
  • Schulze-Kremer S. Ontologies for molecular biology. Pac Symp Biocomput. 1998:695–706. [PubMed]
  • Stevens R, Goble CA, Bechhofer S. Ontology-based knowledge representation for bioinformatics. Brief Bioinform. 2000 Nov;1(4):398–414. [PubMed]
  • Wain Hester M, Bruford Elspeth A, Lovering Ruth C, Lush Michael J, Wright Mathew W, Povey Sue. Guidelines for human gene nomenclature. Genomics. 2002 Apr;79(4):464–470. [PubMed]
  • Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD, Tatusova TA, Rapp BA. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2000 Jan 1;28(1):10–14. [PMC free article] [PubMed]

Articles from Comparative and Functional Genomics are provided here courtesy of Hindawi Publishing Corporation


Save items

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...


  • PubMed
    PubMed citations for these articles

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...