YEASTGO                package:YEAST                R Documentation

_M_a_p_p_i_n_g_s _b_e_t_w_e_e_n _p_r_o_b_e _i_d_e_n_t_i_f_i_e_r_s _a_n_d _G_e_n_e _O_n_t_o_l_o_g_y _i_n_f_o_r_m_a_t_i_o_n

_D_e_s_c_r_i_p_t_i_o_n:

     The Gene Ontology Consortium maintains a controlled vocabulary of
     defined terms to describe gene products. YEASTGO maps probe
     identifiers to Gene Ontology information including the ids,
     evidence codes, and ontology categories of the terms for the genes
     represented by the probe ids.

_D_e_t_a_i_l_s:

     Each probe id is mapped to a list containing one (mapped to none
     or one set of GO information) or more (mapped to more than one
     sets of GO information) elements. When a probe id is mapped to at
     lest one set of GO information, each element of the list contains
     a sub list of three elements named "GOID", "Ontology", and
     "Evidence". The value for element "GOID" gives the Gene Ontology
     identifier the key probe id corresponds to. The value for element
     "Ontology" can be an abbreviation of MF (mocular function), BP
     (biological process), or CC (cellular component) for the GO
     ontology category the GO id belongs to. The value for element
     "Evidence" contains an evidence code indicating what kind of
     evidence is found to support the association of the GO id to the
     gene represented by the key probe id.

     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

     Mappings between probe ids and GO information were obtained
     through their mappings to LocusLink ids. NAs are assigned to probe
     identifiers that can not be mapped to any Gene Ontology
     information. 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:

     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 

     Gene Ontology:<URL:
     http://www.godatabase.org/dev/database/archive/2004-09-01/go_20040
     9-termdb.xml.gz>. Built: 2004-09-01

     Package built Fri Jan  7 16:12:38 2005

_E_x_a_m_p_l_e_s:

         # Convert to a list
         xx <- as.list(YEASTGO)
         # Remove all the NAs
         xx <- xx[!is.na(xx)]
         if(length(xx) > 0){
                 # Try the firest one
                 got <- xx[[1]]           
                 got[[1]][["GOID"]]
                 got[[1]][["Ontology"]]
                 got[[1]][["Evidence"]]

         }

