ri16codGO2ALLPROBES        package:ri16cod.db        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:

     ri16codGO2ALLPROBES is an R object 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 object ri16codGO2ALLPROBES 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:

     Gene Ontology (
     ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest ) on
     200803 and Entrez Gene ( ftp://ftp.ncbi.nlm.nih.gov/gene/DATA ) on
     2008-Apr2

_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(ri16codGO2ALLPROBES)
         if(length(xx) > 0){
             # Get the probe identifiers for the top 2nd and 3nd GO identifiers
             goids <- xx[2:3]
             # Get all the probe identifiers for the first element of goids
             goids[[1]]
             # Evidence code for the mappings
             names(goids[[1]])
         }

