getSrcBuilt            package:AnnBuilder            R Documentation

_F_u_n_c_t_i_o_n_s _t_h_a_t _g_e_t _t_h_e _b_u_i_l_t _d_a_t_e _o_r _n_u_m_b_e_r _o_f _t_h_e _s_o_u_r_c_e _d_a_t_a
_u_s_e_d _f_o_r _a_n_n_o_t_a_t_i_o_n

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

     Given a data source name and organism, the built date or number of
     the annotation source data will be returned. The built date or
     number is provided by the data source through its web site.

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

     getSrcBuilt(src = "LL", organism = "human")
     getLLBuilt(url = "http://www.ncbi.nlm.nih.gov/LocusLink/statistics.html")
     getUGBuilt(organism, url = "ftp://ftp.ncbi.nih.gov/repository/UniGene")
     getUCSCBuilt(organism)
     getGOBuilt(url = "http://www.godatabase.org/dev/database/archive/latest")
     getKEGGBuilt(url = "http://www.genome.ad.jp/kegg/kegg2.html")
     getYGBuilt()
     getHGBuilt()

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

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

organism: A character string for the name of the organism of interests.
          See details for valid names

     url: A character string for the url from which built information
          can be obtained

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

     'getLLBuilt' finds the built data for LocusLink from the
     statistics page.

     'getUGBuilt' finds the built data for UniGene from the Xx.info
     file, where Xx is the short organism name (e.g. Hs for human)

     'getUCSCBuilt' finds the built data for the Human Genome Project
     from the folder for the latest release.

     'getGOBuilt' finds the built data for Gene Ontology from the
     timestamp for the -ont.xml.gz file.

     'getKEGGBuilt' finds the built data for KEGG from kegg2.html page
     (Release version and date)

     'YGBuilt' gets built information for Yeast Genome data.

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

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

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

     All functions return a string for the built information

_N_o_t_e:

     The functions are part of the Bioconductor project at Dana-Farber
     Cancer Institute to provide Bioinformatics functionalities through
     R

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

     Jianhua 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:

     'getSrcUrl'

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

     # Get built information for LocusLink
     ll <- getSrcBuilt(src = "LL")
     ug <- getSrcBuilt(src = "UG", organism = "Mouse")
     yg <- getYGBuilt()
     ll
     ug
     yg

