gahgu95bGO             package:gahgu95b             R Documentation

_M_a_p _b_e_t_w_e_e_n _c_u_s_t_o_m _p_r_o_b_e_s_e_t _I_D_s _a_n_d _G_e_n_e _O_n_t_o_l_o_g_y (_G_O)

_D_e_s_c_r_i_p_t_i_o_n:

     gahgu95bGO is an R environment that provides mappings between
     custom probeset identifiers and the GO identifiers that they are
     directly associated with.

_D_e_t_a_i_l_s:

     Each custom probeset identifier is mapped to a list of lists.  The
     names on the outer list are GO identifiers.  Each inner list
     contains of five named elements: GOID, Ontology, Term, Evidence
     and PMIDS.

     The GOID element matches the GO identifier named in the outer
     list.

     The Ontology element indicates which of the three Gene Ontology
     categories this identifier belongs to.  The categories are
     biological process (BP), cellular component (CC), and molecular
     function (MF).

     The Term element indicates the name of GO cathegory correspoding
     to the GO identifier named in the outer list.

     The Evidence element contains a code indicating what kind of
     evidence supports the association of the GO identifier to the
     Entrez Gene id. 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

     The PMIDS element indicates the Pubmed IDs of references in the
     literature, if relevant, obtained from EntrezGene.

     NAs are assigned to probe identifiers that can not be mapped to
     any Gene Ontology information. Other information concerning Gene
     Ontology classification are available in a separate data package
     named GO.

     Mappings were based on data provided by:

     GeneCards database - www.genecards.org

     Package built Tue Feb 26 00:10:11 2008

_R_e_f_e_r_e_n_c_e_s:

     <URL: www.genecards.org>

_E_x_a_m_p_l_e_s:

         # Convert to a list
         xx <- as.list(gahgu95bGO)
         # Remove all the NAs
         xx <- xx[!is.na(xx)]
         if(length(xx) > 0){
                 # Try the first one
                 got <- xx[[1]]           
                 got[[1]][["GOID"]]
                 got[[1]][["Ontology"]]
                 got[[1]][["Evidence"]]

         }

