YEASTGO2PROBE             package:YEAST             R Documentation

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_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]])
         }

