PAnnBuilder (version 1.36.0)

getSrcUrl: Get the Url and Release information for Diverse Databases

Description

Given the abbreviation of databases, these functions gets the url of data file, and get the version/release of the database.

Usage

speciesNorganism()
organism2species(organism) 
organism2alias(organism)
getShortSciName(organism)
organism2taxID(organism)
taxID2organism(taxID)
.srcUrls(name)
getSrcUrl(src, organism = "")
getALLUrl(organism)
getSrcBuilt(src, organism = "")
getALLBuilt(organism)
getSrcSQUrl(src,organism)
getSrcSQBuilt(src,organism)
getSPUrl()
getTREMBLUrl()
getIPIUrl(organism)
getREFSEQUrl(organism)
getGOUrl()
getGOAUrl(organism)
getGENEINTUrl()
getINTACTUrl()
getMPPIUrl()
get3DIDUrl()
getDOMINEUrl()
getDBSUBLOCUrl()
getBACELLOUrl()
getINTERPROUrl()
getPFAMUrl()
getSCOPUrl()
getHOMOLOGENEUrl()
getINPARANOIDUrl(organism)
getPEPTIDEATLASUrl(organism)
getSYSPTMUrl()
getSYSBODYFLUIDUrl()
getSPSQUrl()
getTREMBLSQUrl()
getIPISQUrl(organism)
getREFSEQSQUrl(organism)
getSPBuilt()
getTREMBLBuilt()
getIPIBuilt(organism)
getREFSEQBuilt(organism)
getGOABuilt(organism)
getGENEINTBuilt()
getINTACTBuilt()
getMPPIBuilt()
get3DIDBuilt()
getDOMINEBuilt()
getDBSUBLOCBuilt()
getBACELLOBuilt()
getINTERPROBuilt()
getPFAMBuilt()
getSCOPBuilt()
getHOMOLOGENEBuilt()
getINPARANOIDBuilt()
getPEPTIDEATLASBuilt(organism)
getSYSPTMBuilt()
getSYSBODYFLUIDBuilt()

Arguments

src

a character string to indicate which database will be used. Possible values are: sp, trembl, ipi, refseq, go, goa, geneint, intact, mppi, 3did, domain, dbsubloc, bacello, interpro, pfam, scop, homologene, inparanoid, peptideatlas, sysptm, sysbodyfulid, prosite or ALL.

organism

a character string for the name of the organism of concern. (eg: "Homo sapiens")

taxID

a integer for the taxonomy identifier. (eg: 1906)

name

a character string to indicate data source. Possible values are: SP, IPI, REFSEQ, KEGG, Gene, GO, GOA, geneint, intact, MPPI, 3DID, DOMINE, DBsubloc, Bacello, Interpro, Pfam, SCOP, Homologene, Inparanoid, PeptideAtlas, SysPTM, Sys-BodyFulid or TAX.

Value

getSrcUrl return a character string to indicate the url of data file.getSrcBuilt return a character string to indicate the release/ version of the database.

Details

These functions are the results of an effort to get url and release/version for diverse databases. Some functions are improved from previous package "AnnBuilder". Functions developped to convert multiple names for organism: speciesNorganism return a three-column matrix. organism2species() and organism2alias() employ speciesNorganism() to get organism and alias used in IPI database. organism2species use speciesNorganism() to convert organism to their species name. organism2alias use speciesNorganism() to convert organism to their alias name. getShortSciName get 3-character short name, eg: "Hsa". organism2taxID convert organism to taxID, eg: 9606 for "Homo sapiens". taxID2organism convert taxID to organism, eg: "Homo sapiens" for 9606. Functions developped to get url and release information for data file: .srcUrls get basic web address for the given database. getSrcUrl get url for the data file based on .srcUrls(). getALLUrl get all available urls in this package. getSrcBuilt get version/release information based on .srcUrls. getALLBuilt get release information for databases in getALLUrl. getSrcSQUrl get url for protein sequence files. getSrcSQBuilt get release information for protein sequence files.

References

Zhang, J., Carey, V., Gentleman, R. (2003) An extensible application for assembling annotation for genomic data.Bioinformatics 19(1), 155-156.

Examples

if(interactive()){
    # Get urls of all related databases  for "Homo sapiens".
    getALLUrl("Homo sapiens")
    
    # Get version/release information of all related databases for "Homo sapiens".
    getALLBuilt ("Homo sapiens")
}