GOALLENTREZID               package:GO               R Documentation

_A_n_n_o_t_a_t_i_o_n _o_f _G_O _i_d_e_n_t_i_f_i_e_r_s _b_y _a_l_l _t_h_e _c_o_r_r_e_s_p_o_n_d_i_n_g _E_n_t_r_e_z _G_e_n_e
_i_d_e_n_t_i_f_i_e_r_s

_D_e_s_c_r_i_p_t_i_o_n:

     This is an R environment (hash table) mapping GO identifiers to
     all the Entrez Gene identifiers corresponding to the GO
     identifiers and its direct or indirect offspring. The direct or
     indirect offspring of a given GO identifier are the nodes that are
     directly linked to the node for the GO identifier or indirectly
     linked to the GO identifier through nodes that are linked to the
     GO identifier based on the directed acyclic graph defined by Gene
     Ontology Consortium

_D_e_t_a_i_l_s:

     GO identifiers are Keys and the corresponding Entrez Gene
     identifiers are Values. Values are named vectors of length 1 or
     greater depending on whether a given GO identifier can be mapped
     to one or more Entrez Gene identifiers. Names for values are the
     evidence codes for the GO identifier (if an evidence code was
     provided by source data). The evidence codes that are 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

     NA is assigned to GO identifiers that can not be mapped to any
     Entrez Gene identifier at this time.  

     Mappings were based on data provided by:

     Gene Ontology:<URL:
     http://gopher5/compbio/annotationSourceData/archive.godatabase.org
     /latest/>. Built: 08-Aug-2006

     Entrez Gene:<URL:
     http://gopher5/compbio/annotationSourceData/ftp.ncbi.nlm.nih.gov/g
     ene/DATA/>. Built: Source data downloaded from Entrez Gene on Tue
     Sep  5 18:42:30 2006

     Package built: Tue Sep  5 18:42:30 2006

_R_e_f_e_r_e_n_c_e_s:

     <URL: http://www.geneontology.org/> and <URL:
     http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene>

_E_x_a_m_p_l_e_s:

             require("GO") || stop("GO unavailable")
             # Convert the environment object to a list
             xx <- as.list(GOALLENTREZID)
             # Remove GO identifiers that are not mapped to any Entrez Gene identifier
             xx <- xx[!is.na(xx)]
             if(length(xx) > 0){
                     # Get the Entrez Gene identifiers for the first two elents of xx
                     llids  <- xx[1:2]
                     # Get the evidence code llids
                     evds <- sapply(llids, names)
             }