MEDIC: a practical disease vocabulary used at the Comparative Toxicogenomics Database

Department of Bioinformatics, The Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672, USA.
Database The Journal of Biological Databases and Curation (Impact Factor: 3.37). 01/2012; 2012:bar065. DOI: 10.1093/database/bar065
Source: PubMed


The Comparative Toxicogenomics Database (CTD) is a public resource that promotes understanding about the effects of environmental chemicals on human health. CTD biocurators manually curate a triad of chemical–gene, chemical–disease and gene–disease relationships from the scientific literature. The CTD curation paradigm uses controlled vocabularies for chemicals, genes and diseases. To curate disease information, CTD first had to identify a source of controlled terms. Two resources seemed to be good candidates: the Online Mendelian Inheritance in Man (OMIM) and the ‘Diseases’ branch of the National Library of Medicine's Medical Subject Headers (MeSH). To maximize the advantages of both, CTD biocurators undertook a novel initiative to map the flat list of OMIM disease terms into the hierarchical nature of the MeSH vocabulary. The result is CTD’s ‘merged disease vocabulary’ (MEDIC), a unique resource that integrates OMIM terms, synonyms and identifiers with MeSH terms, synonyms, definitions, identifiers and hierarchical relationships. MEDIC is both a deep and broad vocabulary, composed of 9700 unique diseases described by more than 67 000 terms (including synonyms). It is freely available to download in various formats from CTD. While neither a true ontology nor a perfect solution, this vocabulary has nonetheless proved to be extremely successful and practical for our biocurators in generating over 2.5 million disease-associated toxicogenomic relationships in CTD. Other external databases have also begun to adopt MEDIC for their disease vocabulary. Here, we describe the construction, implementation, maintenance and use of MEDIC to raise awareness of this resource and to offer it as a putative scaffold in the formal construction of an official disease ontology.
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Available from: Allan Peter Davis, Jul 20, 2015
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    • "The user has to provide the presumptive (or known) Mendelian disorder associated to the sample, the mode of inheritance and the platform used for exome target enrichment. The disease has to be chosen using a fixed vocabulary implementing the MEDIC hierarchical disease ontology [23] including all child terms to MeSH ID D009358: "Congenital, Hereditary, and Neonatal Diseases and Abnormalities". The disease list can be searched by directly typing the specific OMIM ID [1] or a keyword and the auto-completion function will automatically retreive all the available matching terms. "
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