PAnnBuilder (version 1.36.0)

pBaseBuilder_DB: Build Data Packages for Primary Protein Database

Description

Given the URL to SwissProt, TREMBL, IPI or NCBI RefSeq protein data, this function creates a SQLite-based annotation data package.

Usage

pBaseBuilder_DB(baseMapType = c("sp","trembl","ipi","refseq"), organism,  prefix, pkgPath, version, author)

Arguments

baseMapType

a character string that can be either "sp", "trembl", "ipi" or "refseq" to indicate which protein database will be used.

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 ".

Value

This function does not return any value.

Details

Build annotation data packages for proteins in primary protein database, including SwissProt, TREMBL, IPI or NCBI RefSeq Database. Basic annotation information will be integrated with protein entries, including protein sequence, description, coding gene, structure, Gene Ontology, KEGG pathway, Pfam doamin and so on.

When baseMapType = "sp", protein data are from UniProtKB/Swiss-Prot. (http://expasy.org/sprot/)

When baseMapType = "trembl", protein data are from UniProtKB/TrEMBL. (http://expasy.org/sprot/)

When baseMapType = "ipi", protein data are from International Protein Index (IPI),and seven organisms are supported: Homo sapiens, Mus musculus, Rattus norvegicus, Danio rerio, Bos taurus, Gallus gallus, Arabidopsis thaliana. (http://http://www.ebi.ac.uk/IPI/IPIhelp.html/)

When baseMapType = "refseq", protein data are from NCBI Reference Sequence, and six organisms are supported: Homo sapiens, Mus musculus, Rattus norvegicus, Danio rerio, Bos taurus, Xenopus tropicalis. (http://www.ncbi.nlm.nih.gov/RefSeq/)

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]>"

if(FALSE){
    # NOTE: THESE PACKAGES ARE NO LONGER AVAILABLE, YOU NEED TO GENERATE
    #       THEM FOLLOWING THE INSTRUCTIONS IN THE VIGNETTE

    # It may take a long time to parse database and build R package.
    # Build annotation data packages "org.Hs.sp.db" for Homo sapiens
    # proteins in SwissProt.
    pBaseBuilder_DB(baseMapType = "sp", organism = "Homo sapiens",  
                    prefix = "org.Hs.sp", pkgPath = pkgPath, version = version, 
                    author = author)                 
    
    # Build annotation data packages "org.Mm.ipi.db" for Mus musculus
    # proteins in IPI.
    pBaseBuilder_DB(baseMapType = "ipi", organism = "Mus musculus",  
                    prefix = "org.Mm.ipi", pkgPath = pkgPath, version = version, 
                    author = author)
                            
    # Build annotation data packages "org.Rn.ref.db" for Rattus norvegicus
    # proteins in NCBI RefSeq.
    pBaseBuilder_DB(baseMapType = "refseq", organism = "Rattus norvegicus",
                    prefix = "org.Rn.ref", pkgPath = pkgPath, version = version,
                    author = author)
}