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]])
         }

