\HeaderA{GOENTREZID2GO}{Entrez Gene to Gene Ontology (GO) mapping}{GOENTREZID2GO}
\aliasA{GOLOCUSID2GO}{GOENTREZID2GO}{GOLOCUSID2GO}
\keyword{datasets}{GOENTREZID2GO}
\begin{Description}\relax
This data set describes associations between Entrez Gene identifiers
and GO identifiers as reported by NCBI.  The format is an R
environment mapping Entrez Gene identifiers to a list of GO identifiers that are
associated with it.  In addition to the GO identifier. the GO ontology
category and the evidence code (the reason for the association) is
given.
\end{Description}
\begin{Details}\relax
Each Entrez Gene identifier is mapped to a list of lists.  The names on the
outer list are GO identifiers.  Each inner list consists of three named
elements: GOID, Ontology, and Evidence.

The GOID element matches the GO identifier named in the outer list and is
included for convenience when processing the data using \code{lapply}.

The Ontology element indicates which of the three Gene Ontology
categories this identifier belongs to.  The categories are biological
process (BP), cellular component (CC), and molecular function (MF).

The Evidence element contains a code indicating what kind of evidence
supports the association of the GO identifier to the Entrez Gene identifier. The
evidence codes in use include:

IMP - inferred from mutant phenotype  

IGI - inferred from genetic interaction

IPI - inferred from physical interaction  

ISS - inferred from sequence similarity  

IDA - inferred from direct assay  

IEP - inferred from expression pattern  

IEA - inferred from electronic annotation  

TAS - traceable author statement  

NAS - non-traceable author statement  

ND - no biological data available  

IC - inferred by curator

Entrez Gene identifiers for which no GO associations exist are left out of the
environment.

Mappings were based on data provided by:

Entrez Gene:\url{http://gopher5/compbio/annotationSourceData/ftp.ncbi.nlm.nih.gov/gene/DATA/}. Built: Source data downloaded from Entrez Gene on Tue Sep  5 18:42:30 2006

Package built: Tue Sep  5 18:42:30 2006
\end{Details}
\begin{References}\relax
\url{http://www.ncbi.nih.gov/entrez/query.fcgi?db=gene}
\end{References}
\begin{Examples}
\begin{ExampleCode}
library("GO")
## Select an Entrez Gene id
egId <- "10043"
egIdGoData <- GOENTREZID2GO[[egId]]

## Display GO identifiers associated with the Entrez Gene id
sapply(egIdGoData, function(x) x$GOID)

## The ontology categories of the GO identifiers
sapply(egIdGoData, function(x) x$Ontology)

## The evidence codes for the GO identifiers
sapply(egIdGoData, function(x) x$Evidence)
\end{ExampleCode}
\end{Examples}