MEDIC: a practical disease vocabulary used at the Comparative Toxicogenomics Database
Open Access
- 1 January 2012
- journal article
- research article
- Published by Oxford University Press (OUP) in Database: The Journal of Biological Databases and Curation
- Vol. 2012, bar065
- https://doi.org/10.1093/database/bar065
Abstract
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. Database URL:http://ctd.mdibl.org/voc.go?type=diseaseKeywords
This publication has 16 references indexed in Scilit:
- DiseaseComps: a metric that discovers similar diseases based upon common toxicogenomic profiles at CTDBioinformation, 2011
- The curation paradigm and application tool used for manual curation of the scientific literature at the Comparative Toxicogenomics DatabaseDatabase: The Journal of Biological Databases and Curation, 2011
- RGD: A comparative genomics platformHuman Genomics, 2011
- The Comparative Toxicogenomics Database: update 2011Nucleic Acids Research, 2010
- Annotating the human genome with Disease OntologyBMC Genomics, 2009
- Genetic and environmental pathways to complex diseasesBMC Systems Biology, 2009
- The Comparative Toxicogenomics Database facilitates identification and understanding of chemical-gene-disease associations: arsenic as a case studyBMC Medical Genomics, 2008
- Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networksNucleic Acids Research, 2008
- The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queriesBMC Bioinformatics, 2006
- The Unified Medical Language System (UMLS): integrating biomedical terminologyNucleic Acids Research, 2004