getSrcUrl             package:AnnBuilder             R Documentation

_F_u_n_c_t_i_o_n_s _t_h_a_t _f_i_n_d _t_h_e _c_o_r_r_e_c_t _u_r_l _f_o_r _d_o_w_n_l_o_a_d_i_n_g _a_n_n_o_t_a_t_i_o_n _d_a_t_a

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

     Given a source data name and organism name, the url from which the
     source annotation data can be downloaded will be returned.

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

     getSrcUrl(src, organism = "Homo sapiens", xml = TRUE, dateOnly = FALSE)
     getAllUrl(organism)
     getLLUrl()
     getUCSCUrl(organism, downloadSite)
     getUGUrl(organism)
     getGOUrl(xml = TRUE, dateOnly = FALSE) 
     getKEGGUrl()
     readURL(url)
     getGEOUrl()
     getYGUrl()
     getHGUrl()
     getRefSeqUrl(organism)
     getEGUrl()

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

     src: A character string for the name of the data source. See
          details for valid names

organism: A character string for the name of the organism of interests

     url: A character string for the url where the source data can be
          downloaded

dateOnly: A boolean that is set to TRUE if only the built date of the
          data souce will be returned or TRUE if the source url will be
          returned

     xml: A boolean indicating whether the XML format data file will be
          downloaded/processed

downloadSite: 'downLoadSite' a character string for the url to the
          general downloading site for the human, mouse, and rat data

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

     'getAllUrl' finds the urls for all the data source including
     LocusLink, UinGene, the Human Geneome Project, Gene Ontology, and
     KEGG.

     'getLLUrl' finds the url fro LocusLink.

     'getUCSCUrl' finds the url for the Human Genome Project.

     'getUGUrl' finds the url for UniGene.

     'getGOUrl' finds the url for Gene Ontology.

     'getKEGGUrl' finds the url for KEGG.

     'getGEOUrl' finds the url for GOE (the CGI script)

     'getYGUrl' gets the url to the ftp site where Yeast Genome data
     can be downloaded.

     Valid data source names include LL - LocusLink, UG - UniGene, UCSC
     - the Human Genome Project, GO - Gene Ontology, KEGG - KEGG, and
     YG - Yeast Genome.

     Valid organism name include human, mouse, rat, and yeast at this
     time.

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

     'getAllUrl' returns a vector of character strings and all the
     others return a character string for the url

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

     Jianhau Zhang

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

     <URL: "http://www.ncbi.nlm.nih.gov/LocusLink/statistics.html">,
     <URL: "ftp://ftp.ncbi.nih.gov/repository/UniGene">, <URL:
     "http://www.godatabase.org/dev/database/archive/latest">, <URL:
     "http://www.genome.ad.jp/kegg/kegg2.html">, <URL:
     ftp://ftp.ncbi.nih.gov/refseq/LocusLink/>, <URL:
     http://www.yeastgenome.org>

_S_e_e _A_l_s_o:

     'getSrcBuilt'

