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. 2012 Jan;40(Database issue):D940-6.
doi: 10.1093/nar/gkr972. Epub 2011 Nov 12.

Disease Ontology: a backbone for disease semantic integration

Lynn Marie Schriml  1 , Cesar Arze, Suvarna Nadendla, Yu-Wei Wayne Chang, Mark Mazaitis, Victor Felix, Gang Feng, Warren Alden Kibbe
Affiliations

Disease Ontology: a backbone for disease semantic integration

Lynn Marie Schriml et al. Nucleic Acids Res. 2012 Jan.

Abstract

The Disease Ontology (DO) database (http://disease-ontology.org) represents a comprehensive knowledge base of 8043 inherited, developmental and acquired human diseases (DO version 3, revision 2510). The DO web browser has been designed for speed, efficiency and robustness through the use of a graph database. Full-text contextual searching functionality using Lucene allows the querying of name, synonym, definition, DOID and cross-reference (xrefs) with complex Boolean search strings. The DO semantically integrates disease and medical vocabularies through extensive cross mapping and integration of MeSH, ICD, NCI's thesaurus, SNOMED CT and OMIM disease-specific terms and identifiers. The DO is utilized for disease annotation by major biomedical databases (e.g. Array Express, NIF, IEDB), as a standard representation of human disease in biomedical ontologies (e.g. IDO, Cell line ontology, NIFSTD ontology, Experimental Factor Ontology, Influenza Ontology), and as an ontological cross mappings resource between DO, MeSH and OMIM (e.g. GeneWiki). The DO project (http://diseaseontology.sf.net) has been incorporated into open source tools (e.g. Gene Answers, FunDO) to connect gene and disease biomedical data through the lens of human disease. The next iteration of the DO web browser will integrate DO's extended relations and logical definition representation along with these biomedical resource cross-mappings.

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Figures

Figure 1.
Figure 1.
DO web interface with search, navigation and display functions. The disease tree view displays the DO's hierarchical structure and the placement of top level parent nodes expandable to view subgraphs. The fungal infectious disease subgraph with its direct child terms are shown. Term Metadata is displayed for selected terms from the tree view.
Figure 2.
Figure 2.
Term visualization in the DO web-browser. The ‘Visualize’ button on the Metadata page opens a graphical view of DO. Clicking on this button will open a new tab that will display the target node of the visualization (e.g. basidiobolomycosis) [red box], parent node [green box] and sibling leaf nodes [gray box]. Nodes with five or more children are represented by a gold circle containing the number of children. Clicking on a node in the graph will expand the view.
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