\Header{getSrcUrl}{Functions that find the correct url for downloading annotation data}
\alias{getAllUrl}{getSrcUrl}
\alias{getGEOUrl}{getSrcUrl}
\alias{getGOUrl}{getSrcUrl}
\alias{getKEGGUrl}{getSrcUrl}
\alias{getLLUrl}{getSrcUrl}
\alias{getUCSCUrl}{getSrcUrl}
\alias{getUGUrl}{getSrcUrl}
\alias{getYGUrl}{getSrcUrl}
\alias{readURL}{getSrcUrl}
\keyword{datasets}{getSrcUrl}
\begin{Description}\relax
Given a source data name and organism name, the url from which the
source annotation data can be downloaded will be returned.\end{Description}
\begin{Usage}
\begin{verbatim}
getSrcUrl(src = "LL", organism = "human", xml = TRUE, dateOnly = FALSE)
getAllUrl(organism)
getLLUrl()
getUCSCUrl(organism)
getUGUrl(organism)
getGOUrl(xml = TRUE, dateOnly = FALSE) 
getKEGGUrl()
readURL(url)
getGEOUrl()
getYGUrl()
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{src}] A character string for the name of the data source. See
details for valid names
\item[\code{organism}] A character string for the name of the organism of
interests
\item[\code{url}] A character string for the url where the source data can be
downloaded
\item[\code{dateOnly}] A boolean that is set to TRUE if only the built date
of the data souce will be returned or TRUE if the source url will be
returned
\item[\code{xml}] A boolean indicating whether the XML format data file will
be downloaded/processed
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
\code{getAllUrl} finds the urls for all the data source including
LocusLink, UinGene, the Human Geneome Project, Gene Ontology, and
KEGG.

\code{getLLUrl} finds the url fro LocusLink.

\code{getUCSCUrl} finds the url for the Human Genome Project.

\code{getUGUrl} finds the url for UniGene.

\code{getGOUrl} finds the url for Gene Ontology.

\code{getKEGGUrl} finds the url for KEGG.

\code{getGEOUrl} finds the url for GOE (the CGI script)

\code{getYGUrl} gets the url to the ftp site where Yeast Genome data
can be downloaded.

Valid data source names include LL - LocusLink, UG - UniGene, UCSC -
the Human Genome Project, GO - Gene Ontology, KEGG - KEGG, and YG -
Yeast Genome.

Valid organism name include human, mouse, rat, and yeast at this time.\end{Details}
\begin{Value}
\code{getAllUrl} returns a vector of character strings and all the others
return a character string for the url\end{Value}
\begin{Note}\relax
The functions are part of the Buiconductor project at Dana-Farber
Cancer Institute to provide Bioinformatics functionalities through R\end{Note}
\begin{Author}\relax
Jianhau Zhang\end{Author}
\begin{References}\relax
\url{"http://www.ncbi.nlm.nih.gov/LocusLink/statistics.html"},
\url{"ftp://ftp.ncbi.nih.gov/repository/UniGene"},
\url{"http://www.godatabase.org/dev/database/archive/latest"},
\url{"http://www.genome.ad.jp/kegg/kegg2.html"},
\url{ftp://ftp.ncbi.nih.gov/refseq/LocusLink/},
\url{http://www.yeastgenome.org}\end{References}
\begin{SeeAlso}\relax
\code{\Link{getSrcBuilt}}\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
# The source URL may be checnged or the system is down
urls <- getSrcUrl("ALL")
\end{ExampleCode}
\end{Examples}

