GOLOCUSID2GO               package:GO               R Documentation

_A_n_n_o_t_a_t_i_o_n _o_f _L_o_c_u_s_L_i_n_k _i_d_e_n_t_i_f_i_e_r_s _b_y _s_p_e_c_i_f_i_c _g_e_n_e _o_n_t_o_l_o_g_y
_i_n_f_o_r_m_a_t_i_o_n _f_o_r _g_e_n_e_s _r_e_p_r_e_s_e_n_t_e_d _b_y _t_h_e _L_o_c_u_s_L_i_n_k _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 LocusLink ids to
     specific gene ontology information regarding genes represented by
     the LocusLink identifiers. Specific gene ontology infomation
     include the associations between LocusLink ids and GO information
     reported by NCBI

_D_e_t_a_i_l_s:

     LocusLink ids are keys and the corresponding GO information are
     values. Each locusLink id is mapped to a list with one (mapped to
     none or one GO id) or more (mapped to more than one GO ids) sub
     lits. Each sub list contains three elements named "GOID",
     "Ontology", and "Evidence". The value for element "GOID" gives the
     Gene Ontology identifier the key LocusLink id  corresponds to. The
     value for element "Ontology" can be an abbreviation of MF (mocular
     function), BP (biological process),or CC (cellular component) for
     the GO category the GO id belongs to. The values for element
     "Evidence" contains an evidence code indicating what kind of
     evidence is found to support the association of the GO id to the
     LocusLink 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

     NA is assigned to LocusLink id that can not be mapped to any gene
     ontology information. 

     Mappings were based on data provided by:

     LocusLink:<URL:
     ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz>. Built:
     January 10, 2005

     Package built: Mon Jan 10 19:19:56 2005

_R_e_f_e_r_e_n_c_e_s:

     <URL: http://www.ncbi.nlm.nih.gov/LocusLink>

_E_x_a_m_p_l_e_s:

             require("GO") || stop("GO unavailable")
             # Convert the environment object to a list
             xx <- as.list(GOLOCUSID2GO)
             # Remove LocusLink ids that are not mapped to any GO id
             xx <- xx[!is.na(xx)]
             if(length(xx) > 0){
                     # Get the GO ids for the first two elents of xx
                     goids  <- xx[1:2]
                     # Get the evidence code goids
                     evds <- sapply(goids, names)
             }

