org.EcK12.egGO        package:org.EcK12.eg.db        R Documentation

_M_a_p _b_e_t_w_e_e_n _E_n_t_r_e_z _G_e_n_e _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:

     org.EcK12.egGO is an R object that provides mappings between
     entrez gene identifiers and the GO identifiers that they are 
     directly associated with. This mapping and its reverse mapping do
     NOT associate the child terms from the GO ontology with the gene. 
     Only the directly evidenced terms are represented here.

_D_e_t_a_i_l_s:

     Each Entrez Gene identifier is mapped to a list of lists.  The
     names on the outer list are GO identifiers.  Each inner list
     consists of three named elements: GOID, Ontology, and Evidence.

     The GOID element matches the GO identifier named in the outer list
     and is included for convenience when processing the data using
     'lapply'.

     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 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

     Mappings between entrez gene identifiers and GO information were
     obtained through their mappings to Entrez Gene identifiers. NAs
     are assigned to entrez gene identifiers that can not be mapped to
     any Gene Ontology information. Mappings between Gene Ontology
     identifiers an 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
     200808

     For the reverse map GO2EG, each GO term maps to a named vector of
     entrez gene identifiers. A GO identifier may be mapped to the same
     entrez gene 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.

_R_e_f_e_r_e_n_c_e_s:

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

_S_e_e _A_l_s_o:

     'org.EcK12.egGO2ALLEGS'.

_E_x_a_m_p_l_e_s:

         x <- org.EcK12.egGO
         # Get the entrez gene identifiers that are mapped to a GO ID
         mapped_genes <- mappedkeys(x)
         # Convert to a list
         xx <- as.list(x[mapped_genes])
         if(length(xx) > 0) {
             # Try the first one
             got <- xx[[1]]           
             got[[1]][["GOID"]]
             got[[1]][["Ontology"]]
             got[[1]][["Evidence"]]
         }
         # For the reverse map:
         # Convert to a list
         xx <- as.list(org.EcK12.egGO2EG)
         if(length(xx) > 0){
             # Gets the entrez gene ids for the top 2nd and 3nd GO identifiers
             goids <- xx[2:3]
             # Gets the entrez gene ids for the first element of goids
             goids[[1]]
             # Evidence code for the mappings
             names(goids[[1]])
         }

