GOLOCUSID                 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 _t_h_e _c_o_r_r_e_s_p_o_n_d_i_n_g _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 GO ids to the
     LocusLink ids corresponding to the GO id.

_D_e_t_a_i_l_s:

     GO ids are Keys and the corresponding LocusLink ids are values.
     Values are named vectors of length 1 or greater depending on
     whether a given GO id can be mapped to only one or more LocusLink
     ids. Names for values are the evidence codes for the GO id (if
     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 LocusLink
     id at this time.  

     Only specific mappings (not derived from the directed acyclic
     graph of  Gene Ontology) between GO and LocusLink ids were
     included. Non-specific  mappings (derived from the directed
     acyclic graph of Gene Ontology.  e. g. GO ids are mapped to
     LocusLink ids that are mapped to their  children) are provided by
     a separate environment named GOALLLL. 

     Mappings were based on data provided by:

     Gene Ontology:<URL:
     http://www.godatabase.org/dev/database/archive/2004-09-01/go_20040
     9-termdb.xml.gz>. Built: 2004-09-01

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

