moe430aGO2ALLPROBES         package:moe430a         R Documentation

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_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:

     moe430aGO2ALLPROBES is an R environment that provides mappings
     between a given GO identifier and all manufactuerer identifiers
     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 identifiers.  The name associated with each
     manufacturer id corresponds to the evidence code for that GO
     identifier.  This environment moe430aGO2ALLPROBES maps between a
     given GO identifier and all manufactuerer identifiers 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 identifiers. 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 identifier may be mapped to the same manufacturer identifier
     more than once but the evidence code can be different. Mappings
     between Gene Ontology identifiers 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 Thu Mar 15 19:40:34
     2007

     Package built Thu Mar 15 20:05:07 2007

_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(moe430aGO2ALLPROBES)
         if(length(xx) > 0){
             # Gets the probe identifiers for the top 2nd and 3nd GO identifiers
             goids <- xx[2:3]
             # Gets all the probe identifiers for the first element of goids
             goids[[1]]
             # Evidence code for the mappings
             names(goids[[1]])
         }

