GOLOCUSID2ALLGO              package:GO              R Documentation

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_D_e_s_c_r_i_p_t_i_o_n:

     This is an R environment (hash table) mapping LocusLink ids to
     gene ontology information regarding the genes represented by the
     LocusLink identifiers. Gene ontology information includes those
     stated directly by NCBI and those derived based on the directed
     acyclic GO graph defined by Gene Ontology Consortium

_D_e_t_a_i_l_s:

     LocusLink ids are keys and the corresponding GO information are
     values. Association of LocusLink ids to GO information were
     obtained by including those reported by NCBI (specific) and those
     that were derived through the parent-child relations among GO
     nodes on the directed acyclic GO graph. If a given GO node had
     been reported to be associated with a LocusLink id, all the
     offspring of that GO node were considered to be associated with
     the LocusLink id as well. 

     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 GO id
     at this time.

     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(GOLOCUSID2ALLGO)
             # 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)
             }

