Genestrace

Phenomic knowledge discovery via structured terminology

Michael N. Cantor, Indra Neil Sarkar, Olivier Bodenreider, Yves A Lussier

Research output: Chapter in Book/Report/Conference proceedingConference contribution

12 Citations (Scopus)

Abstract

The era of applied genomic medicine is quickly approaching accompanied by the increasing availability of detailed genetic information. Understanding the genetic etiology behind complex, multi-gene diseases remains an important challenge. In order to uncover the putative genetic etiology of complex diseases, we designed a method that explores the relationships between two major terminological and ontological resources: the Unified Medical Language System (UMLS) and the Gene Ontology (GO). The UMLS has a mainly clinical emphasis; Gene Ontology has become the standard for biological annotations of genes and gene products. Using statistical and semantic relationships within and between the two resources, we are able to infer relationships between disease concepts in the UMLS and gene products annotated using GO and its associated databases. We validated our inferences by comparing them to the known gene-disease relationships, as defined in the Online Mendelian Inheritance in Man's morbidmap (OMIM). The proof-of-concept methods presented here are unique in that they bypass the ambiguity of the direct extraction of gene or disease term from MEDLINE. Additionally, our methods provide direct links to clinically significant diseases through established terminologies or ontologies. The preliminary results presented here indicate the potential utility of exploiting the existing, manually curated relationships in biomedical resources as a tool for the discovery of potentially valuable new gene-disease relationships.

Original languageEnglish (US)
Title of host publicationProceedings of the Pacific Symposium on Biocomputing 2005, PSB 2005
Pages103-114
Number of pages12
StatePublished - 2005
Externally publishedYes
Event10th Pacific Symposium on Biocomputing, PSB 2005 - Big Island of Hawaii, United States
Duration: Jan 4 2005Jan 8 2005

Other

Other10th Pacific Symposium on Biocomputing, PSB 2005
CountryUnited States
CityBig Island of Hawaii
Period1/4/051/8/05

Fingerprint

Terminology
Data mining
Genes
Ontology
Medicine
Semantics
Availability

ASJC Scopus subject areas

  • Computational Theory and Mathematics
  • Biomedical Engineering

Cite this

Cantor, M. N., Sarkar, I. N., Bodenreider, O., & Lussier, Y. A. (2005). Genestrace: Phenomic knowledge discovery via structured terminology. In Proceedings of the Pacific Symposium on Biocomputing 2005, PSB 2005 (pp. 103-114)

Genestrace : Phenomic knowledge discovery via structured terminology. / Cantor, Michael N.; Sarkar, Indra Neil; Bodenreider, Olivier; Lussier, Yves A.

Proceedings of the Pacific Symposium on Biocomputing 2005, PSB 2005. 2005. p. 103-114.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Cantor, MN, Sarkar, IN, Bodenreider, O & Lussier, YA 2005, Genestrace: Phenomic knowledge discovery via structured terminology. in Proceedings of the Pacific Symposium on Biocomputing 2005, PSB 2005. pp. 103-114, 10th Pacific Symposium on Biocomputing, PSB 2005, Big Island of Hawaii, United States, 1/4/05.
Cantor MN, Sarkar IN, Bodenreider O, Lussier YA. Genestrace: Phenomic knowledge discovery via structured terminology. In Proceedings of the Pacific Symposium on Biocomputing 2005, PSB 2005. 2005. p. 103-114
Cantor, Michael N. ; Sarkar, Indra Neil ; Bodenreider, Olivier ; Lussier, Yves A. / Genestrace : Phenomic knowledge discovery via structured terminology. Proceedings of the Pacific Symposium on Biocomputing 2005, PSB 2005. 2005. pp. 103-114
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