GOBPPARENTS                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 _G_O _i_d_e_n_t_i_f_i_e_r_s _o_f _t_h_e_i_r
_d_i_r_e_c_t _p_a_r_e_n_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     This is an R environment (hash table) mapping GO ids to the GO ids
     of their direct parents under biological process (BP). Direct
     parents of a given GO id are those GO ids correponding to all the
     parents nodes that have direct link to the node for the GO id of
     concern based on the directed acyclic graph defined by Gene
     Ontology Consortium. GO terms for parent nodes are more general
     than that of the child nods

_D_e_t_a_i_l_s:

     GO ids are keys and the corresponding parent GO ids are values.
     Values are named vectors of length 1 or greater depending on
     whether the GO id of concern has only one or more parents. The
     name(s) of value(s) is(are) the association code (isa or partof)
     between the GO id and its direct parents.GO ids that do not have
     any parent node are assigned NA as the values.

     Biological process is defined as the broad biological goals, such
     as mitosis or purine metabolism, that are accomplished by ordered
     assemblies of molecular functions as defined by Gene Ontology
     Consortium.

     Mappings were based on data provided:

     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.geneontology.org/> and <URL:
     http://www.ncbi.nlm.nih.gov/LocusLink>

_E_x_a_m_p_l_e_s:

       require("GO", character.only = TRUE) || stop("GO unavailable")
       require("annotate", character.only = TRUE) || stop("annoate unavailable")
       # Convert the environment object to a list
       xx <- as.list(GOBPPARENTS)
       # Remove GO ids that do not have any parent
       xx <- xx[!is.na(xx)]
       if(length(xx) > 0){
          # Get the children GO ids for the first elents of xx
             goids <- xx[[1]]
             # Find out the GO terms for the first parent goid
             GOID(GOTERM[[goids[1]]])
             Term(GOTERM[[goids[1]]])
             Synonym(GOTERM[[goids[1]]])
             Secondary(GOTERM[[goids[1]]])
             Definition(GOTERM[[goids[1]]])
       }

