agGO2ALLPROBES              package:ag              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:

     agGO2ALLPROBES 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 agGO2ALLPROBES 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:

     Tair: <URL:
     ftp://ftp.arabidopsis.org/home/tair/Microarrays/Affymetrix/affy_AG_array_elements-2006-07-14.txt>
     Tair: <URL:
     ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR_sequenced_genes>
     Tair: <URL:
     ftp://ftp.arabidopsis.org/home/tair/User_Requests/LocusPublished.02022007>
     Built: N/A

     Package built Fri Aug 24 17:42:16 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(agGO2ALLPROBES)
         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]])
         }

