mu19ksubaGO2ALLPROBES       package:mu19ksuba       R Documentation

_M_a_p _B_e_t_w_e_e_n _G_e_n_e _O_n_t_o_l_o_g_y (_G_O) _I_d_e_n_t_i_f_i_e_r_s _a_n_d _a_l_l _M_a_n_u_f_a_c_t_u_r_e_r
_I_d_e_n_t_i_f_i_e_r_s _i_n _t_h_e _s_u_b_t_r_e_e

_D_e_s_c_r_i_p_t_i_o_n:

     mu19ksubaGO2ALLPROBES is an R environment that provides mappings
     between a given GO id and all manufactuerer ids annotated at that
     GO term or one of its children in the GO ontology.

_D_e_t_a_i_l_s:

     GO consists of three ontologies-molecular function (MF),
     biological process (BP), and cellular component (CC).  All
     ontologies are structured as directed acyclic graphs (DAGs).  Each
     node in each DAG (tree) is a GO term (id) associated with a named
     vector of manufacturer ids.  The name associated with each
     manufacturer id corresponds to the evidence code for that GO id. 
     This environment mu19ksubaGO2ALLPROBES maps between a given GO id
     and all manufactuerer ids annotated at that GO term or one of its
     children in the GO ontology.  

     The evidence code indicates what kind of evidence supports the
     association between the GO and Entrez Gene ids. Evidence codes
     currently 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 manufacturer id more than once
     but the evidence code can be different. Mappings between Gene
     Ontology ids and Gene Ontology terms and other information are
     available in a separate data package named GO.  

     Mappings were based on data provided by:

     Entrez Gene:<URL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/>. Built:
     Source data downloaded from Entrez Gene on Sun Mar 26 02:34:07
     2006

     Package built Sun Mar 26 02:51:48 2006

_R_e_f_e_r_e_n_c_e_s:

     <URL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/>

_E_x_a_m_p_l_e_s:

         # Convert to a list
         xx <- as.list(mu19ksubaGO2ALLPROBES)
         if(length(xx) > 0){
             # Gets the probe ids for the top 2nd and 3nd GO ids
             goids <- xx[2:3]
             # Gets all the probe ids for the first element of goids
             goids[[1]]
             # Evidence code for the mappings
             names(goids[[1]])
         }

