GOCCPARENTS                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 _t_o _t_h_e_i_r _C_e_l_l_u_l_a_r _C_o_m_p_o_n_e_n_t _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
     (CC) terms and their direct parent CC terms, based on the directed
     acyclic graph (DAG) defined by the Gene Ontology Consortium. The
     format is an R environment mapping the GO CC 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 CC term is mapped to a named vector of GO CC 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.

     Cellular component is defined as the subcellular structures,
     locations, and macromolecular complexes; examples include nucleus,
     telomere, and origin recognition complex as defined b y Gene
     Ontology Consortium.

     Mappings were based on data provided:

     Gene Ontology:<URL:
     http://gopher5/compbio/annotationSourceData/archive.godatabase.org
     /latest/>. Built: 08-Aug-2006

     Package built: Tue Sep  5 18:42:30 2006

_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:

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