ABPkgBuilder            Functions that support a single API for
                        building data packages
EG-class                Class "EG" handles data provided by Entrez
                        Gene
GEO-class               Class "GEO" represents a GEO object that
                        reads/downloads data from the GEO web site
GO-class                Class "GO" a class to handle data from Gene
                        Ontology
GOPkgBuilder            Functions to build a data package using GO
                        data
GOXMLParser             Parse the Gene Ontology OBO XML data file
GP-class                Class "GP" a sub-class of pubRepo to
                        get/process data from GoldenPath
HG-class                Class "HG" a class to represent HomoloGene
                        data source
KEGG-class              Class "KEGG" a sub-class of pubRepo to
                        get/process pathway and enzyme information
KEGGPkgBuilder          A function to make the data package for KEGG
LL-class                Class "LL" a sub-class of pubRepo to handle
                        data from LocusLink
MeSHParser              Function to parse the XML data file form MeSH
SPPkgBuilder            A function to build a data pckage using
                        Swiss-Prot protein data
UG-class                Class "UG" a sub-class of pubRepo to handle
                        data from UniGene
YG-class                Class "YG" a sub-class of pubRepo that
                        reads/downloads data from yeast genomic
addNamespace            Functions to add namespaces for data files or
                        seal the environment objects in the data
                        subdirectory
athPkgBuilder           Functions that build annotation packages for
                        Arbidopsis
cMapPathBuilder         Functions that build a data pacakge using data
                        provided by cMAP
chrLocPkgBuilder        A function to build a data package containing
                        mappings between LocusLink ids and the
                        chromosomal locations of genes represented by
                        the LocusLink ids
cleanSrcObjs            Supporting function that may no of any other
                        usese
cols2Env                Creates a environment object using data from
                        two columns of a matrix
downloadSourceData      Create a local mirror of annotation data
                        sources
fileMuncher             Dynamically create a Perl script to parse a
                        source file base on user specifications
fileToXML               A function to convert a text file to XML.
getChroLocation         Functions to extract data from Golden Path
getDPStats              Functions to read in the statistics about a
                        data package
getKEGGIDNName          Functions to get/process pathway and enzyme
                        data from KEGG
getPubDataGo            Functions to download public domain annotation
                        data sources
getSrcBuilt             Functions that get the built date or number of
                        the source data used for annotation
getSrcUrl               Functions that find the correct url for
                        downloading annotation data
getUGShortName          Functions that produce short versions of
                        organism names used by UniGene or for other
                        purposes
getYeastData            Functions to get/process yeast genome data
homoPkgBuilder          Functions to build a homology data package
                        using data from NCBI
loadFromUrl             Functions to load files from a web site
makeLLDB                Create a lazy loading database for package
                        data files
makeSrcInfo             Functions to make source information available
                        for later use
map2LL                  A function that maps LocusLink ids to other
                        public repository ids and vice versa
print.ABQCList          Prints the quality control results for a given
                        data package in a nice format
pubDataURLs             Public Domain Data Source URLs
pubRepo-class           Class "pubRepo" a generic class for
                        downloading/parsing data provided by various
                        public data repositories
queryGEO                Function to extract a data file from the GEO
                        web site
readSourceUrlConfig     Read a data source URL config file
resolveMaps             Functions to obtain unified mappings for a
                        given set of ids using various sources
sourceURLs              A data file contains urls for data available
                        from various public repositories
unifyMappings           A function to unify mapping result from
                        different sources
wget                    Wrapper for system wget
writeChrLength          Functions that creates binary files for
                        chromosome length and organism
writeHomoXMLData        Functions to parse HomoloGene XML data file
                        and build the homology annotation data package
writeManPage            Functions that write supporting files needed
                        by a data package
writeSourceUrlConfig    Create a source URL config file
writeXMLHeader          A function to write header information to an
                        XML file.
yeastAnn                Functions to annotate yeast genom data
yeastPkgBuilder         Functions to do a data package for yeast
                        genome
