Disease Ontology: a backbone for disease semantic integration

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.

[1]  W. Kibbe,et al.  Annotating the human genome with Disease Ontology , 2009, BMC Genomics.

[2]  Gang Feng,et al.  From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations , 2009, Bioinform..

[3]  Seth M. Barribeau,et al.  Immunity and other defenses in pea aphids, Acyrthosiphon pisum , 2010, Genome Biology.

[4]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.

[5]  Ibrahim Emam,et al.  ArrayExpress update—an archive of microarray and high-throughput sequencing-based functional genomics experiments , 2010, Nucleic Acids Res..

[6]  Ana Rath,et al.  WHO International Classification of Diseases (ICD) Revision Process: incorporating rare diseases into the classification scheme: state of art , 2010, Orphanet Journal of Rare Diseases.

[7]  Cynthia L. Smith,et al.  Integrating phenotype ontologies across multiple species , 2010, Genome Biology.

[8]  Jessica A. Turner,et al.  The NIFSTD and BIRNLex Vocabularies: Building Comprehensive Ontologies for Neuroscience , 2008, Neuroinformatics.

[9]  Werner Ceusters,et al.  Foundations for a realist ontology of mental disease , 2010, J. Biomed. Semant..

[10]  Andrew I. Su,et al.  The Gene Wiki: community intelligence applied to human gene annotation , 2009, Nucleic Acids Res..

[11]  Brian D Athey,et al.  The Cell Line Ontology and its use in tagging cell line names in biomedical text. , 2007, AMIA ... Annual Symposium proceedings. AMIA Symposium.

[12]  W. Kibbe,et al.  A collection of bioconductor methods to visualize gene-list annotations , 2010, BMC Research Notes.

[13]  A. Rector,et al.  Relations in biomedical ontologies , 2005, Genome Biology.

[14]  Lynn M. Schriml,et al.  GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database , 2009, Nucleic Acids Res..

[15]  Sherri de Coronado,et al.  NCI Thesaurus: A semantic model integrating cancer-related clinical and molecular information , 2007, J. Biomed. Informatics.

[16]  Giorgio Valle,et al.  The Gene Ontology in 2010: extensions and refinements , 2009, Nucleic Acids Res..

[17]  Mark A. Musen,et al.  Building a biomedical ontology recommender web service , 2010, J. Biomed. Semant..

[18]  Warren A Kibbe,et al.  Mining biomedical data using MetaMap Transfer (MMtx) and the Unified Medical Language System (UMLS). , 2007, Methods in molecular biology.

[19]  Rolf Apweiler,et al.  The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries , 2006, BMC Bioinformatics.

[20]  Carol A. Bocchini,et al.  A new face and new challenges for Online Mendelian Inheritance in Man (OMIM®) , 2011, Human mutation.

[21]  Werner Ceusters,et al.  Toward an Ontological Treatment of Disease and Diagnosis , 2009, Summit on translational bioinformatics.

[22]  Stuart J. Nelson,et al.  The MeSH Translation Maintenance System: Structure, Interface Design, and Implementation , 2004, MedInfo.

[23]  José L. V. Mejino,et al.  A reference ontology for biomedical informatics: the Foundational Model of Anatomy , 2003, J. Biomed. Informatics.

[24]  Mary Shimoyama,et al.  The Rat Genome Database, update 2007—Easing the path from disease to data and back again , 2006, Nucleic Acids Res..

[25]  S. Mundlos,et al.  The Human Phenotype Ontology , 2010, Clinical genetics.

[26]  Alessandro Sette,et al.  The Immune Epitope Database 2.0 , 2009, Nucleic Acids Res..

[27]  J. Childs,et al.  The ascension of wildlife rabies: a cause for public health concern or intervention? , 1995, Emerging infectious diseases.