GOBPPARENTS              package:GO.db              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 _t_o _t_h_e_i_r _B_i_o_l_o_g_i_c_a_l _P_r_o_c_e_s_s _P_a_r_e_n_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     This data set describes associations between GO molecular function
     (BP) terms and their direct parent BP terms, based on the directed
     acyclic graph (DAG) defined by the Gene Ontology Consortium. The
     format is an R object mapping the GO BP terms to all direct parent
     terms, where a direct parent term is a more general GO term that
     immediately precedes the given GO term in the DAG.

_D_e_t_a_i_l_s:

     Each GO BP term is mapped to a named vector of GO BP terms. The
     name associated with the parent term will be either _isa_, _hasa_
     or _partof_, where _isa_ indicates that the child term is a more
     specific version of the parent, and _hasa_ and _partof_ indicate
     that the child term is a part of the parent. For example, a
     telomere is part of a chromosome.

     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 (
     ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest ) on
     200803

_R_e_f_e_r_e_n_c_e_s:

     <URL: http://www.geneontology.org/> and <URL:
     http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene>

_E_x_a_m_p_l_e_s:

       # Convert the 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]]])
             Ontology(GOTERM[[goids[1]]])
       }

