title: A framework for annotating human genome in disease context.
abstract: Identification of gene-disease association is crucial to understanding disease mechanism. A rapid increase in biomedical literatures, led by advances of genome-scale technologies, poses challenge for manually-curated-based annotation databases to characterize gene-disease associations effectively and timely. We propose an automatic method-The Disease Ontology Annotation Framework (DOAF) to provide a comprehensive annotation of the human genome using the computable Disease Ontology (DO), the NCBO Annotator service and NCBI Gene Reference Into Function (GeneRIF). DOAF can keep the resulting knowledgebase current by periodically executing automatic pipeline to re-annotate the human genome using the latest DO and GeneRIF releases at any frequency such as daily or monthly. Further, DOAF provides a computable and programmable environment which enables large-scale and integrative analysis by working with external analytic software or online service platforms. A user-friendly web interface (doa.nubic.northwestern.edu) is implemented to allow users to efficiently query, download, and view disease annotations and the underlying evidences.
authors.affiliation: The Department of Electronics and Information Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China.
authors.forename: Wei
authors.initials: W
authors.lastname: Xu
authors.forename: Huisong
authors.initials: H
authors.lastname: Wang
authors.forename: Wenqing
authors.initials: W
authors.lastname: Cheng
authors.forename: Dong
authors.initials: D
authors.lastname: Fu
authors.forename: Tian
authors.initials: T
authors.lastname: Xia
authors.forename: Warren A
authors.initials: WA
authors.lastname: Kibbe
authors.forename: Simon M
authors.initials: SM
authors.lastname: Lin
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D020022:Genetic Predisposition to Disease; D015894:Genome, Human; D006801:Humans; D012984:Software; D018875:Vocabulary, Controlled