A framework for annotating human genome in disease context.


Journal Article

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.

Full Text

Duke Authors

Cited Authors

  • Xu, W; Wang, H; Cheng, W; Fu, D; Xia, T; Kibbe, WA; Lin, SM

Published Date

  • 2012

Published In

Volume / Issue

  • 7 / 12

Start / End Page

  • e49686 -

PubMed ID

  • 23251346

Pubmed Central ID

  • 23251346

Electronic International Standard Serial Number (EISSN)

  • 1932-6203

Digital Object Identifier (DOI)

  • 10.1371/journal.pone.0049686


  • eng

Conference Location

  • United States