GOALLLOCUSID               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 ids to all the
     Entrez Gene ids corresponding to the GO id and its direct or
     indirect offspring. The direct or indirect offspring of a given GO
     id are the nodes that are directly linked to the node for the GO
     id or indirectly linked to the GO id through nodes that are linked
     to the GO id based on the directed acyclic graph defined by Gene
     Ontology Consortium

_D_e_t_a_i_l_s:

     GO ids are Keys and the corresponding Entrez Gene ids are Values.
     Values are named vectors of length 1 or greater depending on
     whether a given GO id can be mapped to one or more Entrez Gene
     ids. Names for values are the evidence codes for the GO id (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 ids that can not be mapped to any Entrez Gene
     id at this time.  

     Mappings were based on data provided by:

     Gene Ontology:<URL:
     http://gopher5/compbio/annotationSourceData/archive.godatabase.org
     /latest/>. Built: 200509

     Entrez Gene:<URL:
     http://gopher5/compbio/annotationSourceData/ftp.ncbi.nlm.nih.gov/g
     ene/DATA/>. Built: Source data downloaded from Entrez Gene on Fri
     Sep 30 02:51:32 2005

     Package built: Fri Sep 30 02:51:32 2005

_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(GOALLLOCUSID)
             # Remove GO ids that are not mapped to any Entrez Gene id
             xx <- xx[!is.na(xx)]
             if(length(xx) > 0){
                     # Get the Entrez Gene ids for the first two elents of xx
                     llids  <- xx[1:2]
                     # Get the evidence code llids
                     evds <- sapply(llids, names)
             }

