getSrcUrl            package:PAnnBuilder            R Documentation

_G_e_t _t_h_e _U_r_l _a_n_d _R_e_l_e_a_s_e _i_n_f_o_r_m_a_t_i_o_n _f_o_r _D_i_v_e_r_s_e _D_a_t_a_b_a_s_e_s

_D_e_s_c_r_i_p_t_i_o_n:

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

_U_s_a_g_e:

     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()

_A_r_g_u_m_e_n_t_s:

     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 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. 

_D_e_t_a_i_l_s:

     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.

_V_a_l_u_e:

     '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.

_A_u_t_h_o_r(_s):

     Hong Li

_R_e_f_e_r_e_n_c_e_s:

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

_E_x_a_m_p_l_e_s:

     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")
     }

