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Annotating the human genome with Disease Ontology.

Publication ,  Journal Article
Osborne, JD; Flatow, J; Holko, M; Lin, SM; Kibbe, WA; Zhu, LJ; Danila, MI; Feng, G; Chisholm, RL
Published in: BMC Genomics
July 7, 2009

BACKGROUND: The human genome has been extensively annotated with Gene Ontology for biological functions, but minimally computationally annotated for diseases. RESULTS: 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. CONCLUSION: 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 dramatically increases the coverage of the disease annotation of human genome.

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Published In

BMC Genomics

DOI

EISSN

1471-2164

Publication Date

July 7, 2009

Volume

10 Suppl 1

Issue

Suppl 1

Start / End Page

S6

Location

England

Related Subject Headings

  • Unified Medical Language System
  • Software
  • Humans
  • Genome, Human
  • Databases, Genetic
  • Computational Biology
  • Bioinformatics
  • 32 Biomedical and clinical sciences
  • 31 Biological sciences
  • 11 Medical and Health Sciences
 

Citation

APA
Chicago
ICMJE
MLA
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Osborne, J. D., Flatow, J., Holko, M., Lin, S. M., Kibbe, W. A., Zhu, L. J., … Chisholm, R. L. (2009). Annotating the human genome with Disease Ontology. BMC Genomics, 10 Suppl 1(Suppl 1), S6. https://doi.org/10.1186/1471-2164-10-S1-S6
Osborne, John D., Jared Flatow, Michelle Holko, Simon M. Lin, Warren A. Kibbe, Lihua Julie Zhu, Maria I. Danila, Gang Feng, and Rex L. Chisholm. “Annotating the human genome with Disease Ontology.BMC Genomics 10 Suppl 1, no. Suppl 1 (July 7, 2009): S6. https://doi.org/10.1186/1471-2164-10-S1-S6.
Osborne JD, Flatow J, Holko M, Lin SM, Kibbe WA, Zhu LJ, et al. Annotating the human genome with Disease Ontology. BMC Genomics. 2009 Jul 7;10 Suppl 1(Suppl 1):S6.
Osborne, John D., et al. “Annotating the human genome with Disease Ontology.BMC Genomics, vol. 10 Suppl 1, no. Suppl 1, July 2009, p. S6. Pubmed, doi:10.1186/1471-2164-10-S1-S6.
Osborne JD, Flatow J, Holko M, Lin SM, Kibbe WA, Zhu LJ, Danila MI, Feng G, Chisholm RL. Annotating the human genome with Disease Ontology. BMC Genomics. 2009 Jul 7;10 Suppl 1(Suppl 1):S6.
Journal cover image

Published In

BMC Genomics

DOI

EISSN

1471-2164

Publication Date

July 7, 2009

Volume

10 Suppl 1

Issue

Suppl 1

Start / End Page

S6

Location

England

Related Subject Headings

  • Unified Medical Language System
  • Software
  • Humans
  • Genome, Human
  • Databases, Genetic
  • Computational Biology
  • Bioinformatics
  • 32 Biomedical and clinical sciences
  • 31 Biological sciences
  • 11 Medical and Health Sciences