DO

DO provides a standardized ontology of human diseases to support consistent disease annotation, phenotype description, and semantic integration with biomedical vocabularies such as MeSH, ICD, SNOMED CT, NCI Thesaurus, and OMIM.

Key Features:

• Standardized ontology: Database version 3, revision 2510 encompassing 8,043 inherited, developmental, and acquired human diseases.
• Disease descriptors: Represents disease names, synonyms, definitions, phenotype characteristics, Disease Ontology Identifiers (DOIDs), and cross-references.
• Graph database: Implements a graph database structure for knowledge representation.
• Full-text contextual search: Provides Lucene-based full-text contextual searching over names, synonyms, definitions, DOIDs, and cross-references with support for complex Boolean queries.
• Semantic integration: Performs extensive cross-mapping and integration with MeSH, ICD, NCI Thesaurus, SNOMED CT, and OMIM.
• Ontological cross-mappings: Provides ontological cross-mappings between DO, MeSH, and OMIM, with integration exemplified by GeneWiki.

Scientific Applications:

• Disease annotation: Used for disease annotation in Array Express, NIF, and IEDB.
• Standard representation in ontologies: Serves as the standard disease representation in IDO, Cell Line Ontology, NIFSTD Ontology, Experimental Factor Ontology, and Influenza Ontology.
• Cross-resource integration: Enables ontological cross-mapping between DO, MeSH, and OMIM and integration with resources such as GeneWiki.
• Tool integration: Incorporated into open-source tools including Gene Answers and FunDO to link gene and disease biomedical data.

Methodology:

Implements a graph database structure, Lucene-based full-text contextual search supporting complex Boolean queries over names, synonyms, definitions, DOIDs and cross-references, and explicit cross-mapping integration with MeSH, ICD, NCI Thesaurus, SNOMED CT, and OMIM.