PAnnBuilder (version 1.36.0)

intBuilder_DB: Build Data Package for Interaction

Description

Given the URL to protein-protein or domain-domain interaction database, this function creates a SQLite-based annotation data package.

Usage

intBuilder_DB(src=c("geneint","intact","mppi","3DID","DOMINE"),  prefix, pkgPath, version, author)

Arguments

src

a character string to indicate which protein-protein or domain-domain interaction database will be used.

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 ".

Value

This function does not return any value.

Details

Build annotation data packages for protein-protein or domain-domain interaction. Supported databases are: "geneint": ftp://ftp.ncbi.nih.gov/gene/GeneRIF/interactions.gz ; "intact": http://www.ebi.ac.uk/intact ; "mppi": http://mips.gsf.de/proj/ppi ; "3DID": interacting protein domains of known three-dimensional structure, http://3did.embl.de ; "DOMINE": http://domine.utdallas.edu/cgi-bin/Domine ;

intBuilder_DB employes functions writeGENEINTData_DB, writeINTACTData_DB, writeMPPIData_DB, write3DIDData_DB and writeDOMINEData_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://www.biosino.org/PAnnBuilder.

Examples

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

## It may take a long time to parse database and build R package.
if(interactive()){
    # Build annotation data package "int.geneint" for interaction data from NCBI.
    intBuilder_DB(src="geneint", 
    prefix="int.geneint", pkgPath, version, author) 
    
    # Build annotation data package "int.intact" for IntAct database.
    intBuilder_DB(src="intact", 
    prefix="int.intact", pkgPath, version, author) 
    
    # Build annotation data package "int.mppi" for interaction data from MIPS.
    intBuilder_DB(src="mppi", 
    prefix="int.mppi", pkgPath, version, author) 
    
    # Build annotation data package "int.did" for 3DID database.
    intBuilder_DB(src="3DID", 
    prefix="int.did", pkgPath, version, author) 
    
    # Build annotation data package "int.domine" for DOMINE database.
    intBuilder_DB(src="DOMINE", 
    prefix="int.domine", pkgPath, version, author) 
}