GOABuilder_DB: Build Data Packages for Proteomics Gene Ontology
In PAnnBuilder: Protein annotation data package builder

Description Usage Arguments Details Value Author(s) Examples

Given the name of organism, this function creates a data package mapping proteins of UniProt to their Gene Ontolgy.

1 2	GOABuilder_DB(organism = "Homo sapiens", prefix, pkgPath, version, author)

`organism`	a character string for the name of the organism of concern. (eg: "Homo sapiens")
`prefix`	the prefix of the name of the data package to be built. (e.g. "hsaSP"). The name of builded package is prefix+".db".
`pkgPath`	a character string for the full path of an existing directory where the built backage will be stored.
`version`	a character string for the version number.
`author`	a list with named elements "authors" containing a character vector of author names and "maintainer" containing the complete character string for the maintainer field, for example, "Jane Doe <jdoe@doe.com>".

Build gene ontology annotation data packages for proteins in Uniprot. GOABuilder_DB employes functions writeGOAData_DB to parse and write data.

Data files in the database will be automatically downloaded to the tmp directory, so enough space is needed for the data files. After downloading, files are parsed by perl, so perl must be installed. It may take a long time to parse database and build R package. Alternatively, we have produced diverse R packages by PAnnBuilder, and you can download appropriate package via http://biosino.org/ .

This function does not return any value.

Hong Li

# Set path, version and author for the package.
pkgPath <- tempdir()
version <- "1.0.0"
author <- list()
author[["authors"]] <- "Hong Li"
author[["maintainer"]] <- "Hong Li <sysptm@gmail.com>"

## It may take a long time to parse database and build R package.
# Build annotation data packages "org.Hs.goa" for Homo sapiens proteomics gene 
# ontology. 
if(interactive()){
    GOABuilder_DB(organism="Homo sapiens",                       
               prefix="org.Hs.goa", pkgPath, version, author)
}