GOTERM                  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_e_r_m_s _d_e_f_i_n_e_d _b_y _G_e_n_e _O_n_t_o_l_o_g_y
_C_o_n_s_o_r_t_i_u_m

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

     This is an R environment (hash table) mapping GO ids to the
     specific terms in defined by Gene Ontology Consortium

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

     GO ids are keys and the corresponding GO terms are values. Each
     value is a GOTerms object with 6 slots (GOID - GO identifier, Term
     - the specific GO ontology term for the GO id, Synonym - other
     synonymous terms, Secondary - secondary GO ids that were merged to
     the primary GO id, Definition - further definition of the GO
     ontology term, Category - the GO ontology category. Can be MF -
     molecular function, CC - cellular component, or BP - biological
     process).

     All the obsolete GO terms are under the nodes "obsolete molecular
     function" (GO:0008369), "obsolete cellular component" (GO id
     GO:0008370), and "obsolete biological process" (GO:0008371). Each
     of these GO ids has a group of GO ids as their direct children
     (nodes directly linked to but below the GO ids along the directed
     acyclic graph defined by GO) with GO terms that were defined by GO
     but are deprecated in the current build. These deprecated GO terms
     were appended by "(obsolete)" when the data package was built. 

     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

     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")
         require("annotate") || stop("annotate unavailable")
         # Convert the environment object to a list
         xx <- as.list(GOTERM)
         if(length(xx) > 0){
             # Get the TERMS for the first elent of xx
             GOID(xx[[1]])
             Term(xx[[1]])
             Synonym(xx[[1]])
             Secondary(xx[[1]])
             Definition(xx[[1]])
         }

