GOENTREZID                package:GO                R Documentation

_G_e_n_e _O_n_t_o_l_o_g_y (_G_O) _t_o _E_n_t_r_e_z _G_e_n_e _M_a_p_p_i_n_g

_D_e_s_c_r_i_p_t_i_o_n:

     This data set gives mappings between GO identifiers and Entrez
     Gene identifiers as reported by NCBI. The format is an R
     environment mapping GO identifiers to a vector of Entrez Gene
     identifiers that are associated with it. In addition to the Entrez
     Gene identifier. the evidence code (the reason for the
     association) is also given.

_D_e_t_a_i_l_s:

     Each GO identifier is mapped to a named vector of Entrez Gene
     identifiers. The name associated with each Entrez Gene identifier
     corresponds to the evidence code for that GO identifier. 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

     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(GOENTREZID)
         # Remove GO identifiers that are not mapped to any Entrez Gene id
         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)
         }