org.Sc.sgdGO          package:org.Sc.sgd.db          R Documentation

_M_a_p _b_e_t_w_e_e_n _O_R_F _I_D_s _a_n_d _G_e_n_e _O_n_t_o_l_o_g_y (_G_O)

_D_e_s_c_r_i_p_t_i_o_n:

     org.Sc.sgdGO is an R object that provides mappings between ORF
     identifiers and the GO identifiers that they are  directly
     associated with.

_D_e_t_a_i_l_s:

     Each ORF identifier is mapped to a list of lists.  The names on
     the outer list are GO identifiers.  Each inner list consists of
     three named elements: GOID, Ontology, and Evidence.

     The GOID element matches the GO identifier named in the outer list
     and is included for convenience when processing the data using
     'lapply'.

     The Ontology element indicates which of the three Gene Ontology
     categories this identifier belongs to.  The categories are
     biological process (BP), cellular component (CC), and molecular
     function (MF).

     The Evidence element contains a code indicating what kind of
     evidence supports the association of the GO identifier to the
     Entrez Gene 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

     Mappings between ORF identifiers and GO information were obtained
     through their mappings to ORF identifiers. NAs are assigned to ORF
     identifiers that can not be mapped to any Gene Ontology
     information. Mappings between Gene Ontology identifiers an Gene
     Ontology terms and other information are available in a separate
     data package named GO.

     Mappings were based on data provided by: Yeast Genome (
     ftp://genome-ftp.stanford.edu/pub/yeast/data_download ) on
     2008-Mar29

     For the reverse map org.Sc.sgdGO2ORF, each GO term maps to a named
     vector of ORF identifiers. A GO identifier may be mapped to the
     same ORF identifier more than once but the evidence code can be
     different. Mappings between Gene Ontology identifiers and Gene
     Ontology terms and other information are available in a separate
     data package named GO.

_R_e_f_e_r_e_n_c_e_s:

     <URL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/>

_E_x_a_m_p_l_e_s:

         x <- org.Sc.sgdGO
         # Get the ORF identifiers that are mapped to a GO ID
         mapped_genes <- mappedkeys(x)
         # Convert to a list
         xx <- as.list(x[mapped_genes])
         if(length(xx) > 0) {
             # Try the first one
             got <- xx[[1]]           
             got[[1]][["GOID"]]
             got[[1]][["Ontology"]]
             got[[1]][["Evidence"]]
         }
         # For the reverse map:
         # Convert to a list
         xx <- as.list(org.Sc.sgdGO2ORF)
         if(length(xx) > 0){
             # Gets the ORF ids for the top 2nd and 3nd GO identifiers
             goids <- xx[2:3]
             # Gets the ORF ids for the first element of goids
             goids[[1]]
             # Evidence code for the mappings
             names(goids[[1]])
         }

