GOMFPARENTS                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 _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 environment 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:<URL:
     http://gopher5/compbio/annotationSourceData/archive.godatabase.org
     /latest/>. Built: 200509

     Package built: Fri Sep 30 02:51:32 2005

_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(GOMFPARENTS)
         # Remove GO ids that do not have any parent
         xx <- xx[!is.na(xx)]
         if(length(xx) > 0){
             # Get the parent 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]]])
             Category(GOTERM[[goids[1]]])
         }