PhenoGO

an integrated resource for the multiscale mining of clinical and biological data.

Lee T. Sam, Eneida A. Mendonça, Jianrong Li, Judith Blake, Carol Friedman, Yves A Lussier

Research output: Contribution to journalArticle

20 Citations (Scopus)

Abstract

The evolving complexity of genome-scale experiments has increasingly centralized the role of a highly computable, accurate, and comprehensive resource spanning multiple biological scales and viewpoints. To provide a resource to meet this need, we have significantly extended the PhenoGO database with gene-disease specific annotations and included an additional ten species. This a computationally-derived resource is primarily intended to provide phenotypic context (cell type, tissue, organ, and disease) for mining existing associations between gene products and GO terms specified in the Gene Ontology Databases Automated natural language processing (BioMedLEE) and computational ontology (PhenOS) methods were used to derive these relationships from the literature, expanding the database with information from ten additional species to include over 600,000 phenotypic contexts spanning eleven species from five GO annotation databases. A comprehensive evaluation evaluating the mappings (n = 300) found precision (positive predictive value) at 85%, and recall (sensitivity) at 76%. Phenotypes are encoded in general purpose ontologies such as Cell Ontology, the Unified Medical Language System, and in specialized ontologies such as the Mouse Anatomy and the Mammalian Phenotype Ontology. A web portal has also been developed, allowing for advanced filtering and querying of the database as well as download of the entire dataset http://www.phenogo.org.

Original languageEnglish (US)
JournalBMC Bioinformatics
Volume10 Suppl 2
DOIs
StatePublished - 2009
Externally publishedYes

Fingerprint

Ontology
Mining
Databases
Resources
Genes
Phenotype
Annotation
Unified Medical Language System
Natural Language Processing
Gene
Web Portal
Gene Ontology
Comprehensive Evaluation
Cell
Anatomy
Natural Language
Mouse
Genome
Filtering
Entire

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computer Science Applications

Cite this

PhenoGO : an integrated resource for the multiscale mining of clinical and biological data. / Sam, Lee T.; Mendonça, Eneida A.; Li, Jianrong; Blake, Judith; Friedman, Carol; Lussier, Yves A.

In: BMC Bioinformatics, Vol. 10 Suppl 2, 2009.

Research output: Contribution to journalArticle

Sam, Lee T. ; Mendonça, Eneida A. ; Li, Jianrong ; Blake, Judith ; Friedman, Carol ; Lussier, Yves A. / PhenoGO : an integrated resource for the multiscale mining of clinical and biological data. In: BMC Bioinformatics. 2009 ; Vol. 10 Suppl 2.
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