YEASTGO2PROBE             package:YEAST             R Documentation

_M_a_p_p_i_n_g_s _b_e_t_w_e_e_n _G_O _i_d_e_n_t_i_f_i_e_r_s _a_n_d _p_r_o_b_e _i_d_e_n_t_i_f_i_e_r_s
_r_e_p_r_e_s_e_n_t_i_n_g _g_e_n_e_s _t_h_a_t _a_r_e _d_i_r_e_c_t_l_y _a_s_s_o_c_i_a_t_e_d _w_i_t_h _t_h_e _G_O _i_d_s

_D_e_s_c_r_i_p_t_i_o_n:

     The Gene Ontology (GO) Consortium maintains a controlled
     vocabulary of defined terms to describe gene products. Each of the
     terms is assigned a GO id that can be associated with a group of
     genes. YEASTGO2PROBE maps each GO id to the probe identifiers
     representing genes that are associated with the GO ids

_D_e_t_a_i_l_s:

     GO terminologies are presented as a directed acyclic graph with
     root nodes having more general terms than their children nodes.
     YEASTGO2PROBE only maps GO ids to probe ids associated with nodes
     specified by the GO ids but not their children nodes. The mapped
     probe ids are named vectors. Names of the vectors are the evidence
     codes indicating what kind of evidence is found to support the
     association between GO ids and genes.

     The evidence codes in use include: 

     IMP - inferred from mutant phenotype

     IGI - inferred from genetic interaction

     IPI - inferred from physical interaction  

     ISS - inferred from sequence similarity  

     IDA - inferred from direct assay  

     IEP - inferred from expression pattern  

     IEA - inferred from electronic annotation  

     TAS - traceable author statement  

     NAS - non-traceable author statement  

     ND - no biological data available  

     IC - inferred by curator

     A GO id may be mapped to the same probe id more than once but the
     evidence code can be different. Mappings between Gene Ontology ids
     an Gene Ontology terms and other information are available in a
     separate data package named GO. 

     Mappings were based on data provided by:

     LocusLink Yeast Genome:<URL:
     http://www.yeastgenome.org/DownloadContents.shtml>. Built: Yeast
     Genome data are built at various time  intervals. Sources used
     were downloaded  Fri Jan  7 14:56:40 2005  .

     Package built Fri Jan  7 16:12:38 2005

_R_e_f_e_r_e_n_c_e_s:

     <URL: ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz>

_E_x_a_m_p_l_e_s:

         # Convert to a list
         xx <- as.list(YEASTGO2PROBE)
         if(length(xx) > 0){
             # Gets the probe ids for the top 2nd and 3nd GO ids
             goids <- xx[2:3]
             # Gets the probe ids for the first element of goids
             goids[[1]]
             # Evidence code for the mappings
             names(goids[[1]])
         }

