GOMFPARENTS              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 _M_o_l_e_c_u_l_a_r _F_u_n_c_t_i_o_n _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
     (MF) terms and their direct parent MF terms, based on the directed
     acyclic graph (DAG) defined by the Gene Ontology Consortium. The
     format is an R object mapping the GO MF 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 MF term is mapped to a named vector of GO MF 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.

     Molecular function is defined as the tasks performed by individual
     gene products; examples are transcription factor and DNA helicase
     as defined by the Gene Ontology Consortium.

     Mappings were based on data provided by: Gene Ontology (
     ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest ) on
     200708

_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(GOMFPARENTS)
         # Remove GO identifiers that do not have any parent
         xx <- xx[!is.na(xx)]
         if(length(xx) > 0){
             # Get the parent GO identifiers 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]]])
         }

