About: (Alpha test version 0.1 - Database updated on November 1st 2006, next update: beta version planned f or July 2008)

PhenoGO is a computed database designed for high throughput mining that provides phenotypic and experimental context, such as the cell type, disease, tissue and organ to existing annotations between gene products and Gene Ontology (GO) terms as specified in the Gene Ontology Annotations (GOA) for multiple model organisms. For example of mined derivative, see "Discovery of Protein Interaction Networks Shared by Diseases. Pac Symp Biocomp 12:76-87(2007)

Phenotypic and Experimental (P&E) contexts to identifiers are computationally mapped to general biological ontologies, including:
 • the Cell Ontology (CO),
 • phenotypes from the Unified Medical Language System (UMLS),
 • species from Taxonomy of the National Center for Biotechnology Information (NCBI) taxonomy,
 • specialized ontologies such as Mammalian Phenotype Ontology (MP) and Mouse Anatomy (MA).

Note: PhenoGO is computed using natural language processing (see Pac Sympos Biocomp 11:64-75(2006)), and thus some mappings are inaccurate(see updated coding accuracy AMIA Translational 2008). Some users of Internet Explorer 7.0 may encounter sporadic issues with the website. We recommend using an alternative browser such as Firefox.

1) Download the PhenoGO database (CVS format File)

2) Advanced Query

3) Simple Query: Use semicolons (;) to separate search terms
Look for:
In fields
PubMed ID Gene Accession # Gene Name* Gene Description GO ID
GO Term P&E Contextual ID** P&E Contextual Term*** Source:
showing maximum results. output:

* Gene name =Official gene Name
** P&E Contextual Code = Phenotypic or experimental context identifier from the following ontologies: Cell Ontology, UMLS, NCBI Taxonomy, MP or MA.
*** P&E Contextual Term = Phenotypic or experimental context term from the following ontologies: Cell Ontology, UMLS, NCBI Taxonomy, MP or MA.

Examples:

  • GO Term = "apoptosis"
  • Gene Name = "p53"
  • Context Name = "Cytoplasm"

 

Citing PhenoGO: by design, PhenoGO contains data from the following publicly available primary databases: Flybase, MGI, SGD, WormBase and GO Annotations @ EBI. When using PhenoGO data, please also cite the primary sources. The following citation format is suggested when referring to phenotypic datasets specific to PhenoGO:

Phenotype Context Database for Gene Ontology Annotations (PhenoGO),
Contributors: Lussier YA, Friedman C, Mendon?a E, and Blake J Research Groups
The University of Chicago, Chicago, IL
(www.phenogo.org).
Type in date (month, year) when you retrieve the data cited.

We welcome your feedback! Send mail to: lussier@uchicago.edu

  
  Lussier Research Group | Friedman Research Group | The University of Chicago