Annotating the Human Genome with Disease Ontology
Authors John D. Osborne, Jared Flatow, Michelle Holko, Simon M. Lin, Lihua (Julie) Zhu, Maria I. Danila, Gang Feng, Warren A. Kibbe and Rex L. Chisholm
Northwestern University Biomedical Informatics Core (NUBIC), Chicago, IL 60611

The human genome has been extensively annotated with Gene Ontology for biological functions, but minimally computationally annotated for diseases. We used the Unified Medical Language System (UMLS) MetaMap Transfer tool (MMTx) to discover gene-disease relationships from the GeneRIF database. We utilized a comprehensive subset of UMLS, which is disease-focused and structured as a directed acyclic graph (the Disease Ontology), to filter and interpret results from MMTx. The results were validated against the Homayouni gene collection using recall and precision measurements. We compared our results with the widely used Online Mendelian Inheritance in Man (OMIM) annotations. The validation data set suggests a 91% recall rate and 97% precision rate of disease annotation using GeneRIF, in contrast with a 22% recall and 98% precision using OMIM. Our thesaurus-based approach allows for comparisons to be made between disease containing databases and allows for increased accuracy in disease identification through synonym matching. The much higher recall rate of our approach demonstrates that annotating human genome with disease ontology and GeneRIF for diseases increases the coverage of the disease annotation of human genome.

Correspondence to Simon Lin
Tel: (+1) 312 503 2353
Fax: (+1) 312-503-5388
Publication URL Link to the journal's website. TBA
Publication Citation TBA

disease ontology, generif, automated genome annotation

Supplemental Information
Description File Name
Disease-Gene Mappings (tab separated) do_rif.human.txt (10/24/08, 16 M)
Supplemental Database do_rif.db (12/04/08, 11 M)
Supplemental Database Schema do_rif_db_schema.pdf (10/24/08, 18 K)
GeneRIFs generifs_basic (10/10/08 60 M)
About this webpage
Created 10-24-2008. Last updated 12-04-2008.