cMAPKEGGMOLECULE            package:cMAP            R Documentation

_A_n _a_n_n_o_t_a_t_i_o_n _d_a_t_a _f_i_l_e _t_h_a_t _m_a_p_s _c_M_A_P _m_o_l_e_c_u_l_e _i_d_e_n_t_i_f_i_e_r_s _t_o
_d_a_t_a _c_o_n_c_e_r_n_i_n_g _t_h_e _m_o_l_e_c_u_l_e

_D_e_s_c_r_i_p_t_i_o_n:

     cMAPKEGGMOLECULE maps cMAP (NCICB Pathway Interaction Database)
     molecule ids to data about the molecules

_D_e_t_a_i_l_s:

     This is an environment object containing key and value pairs. Keys
     are molecule ids and values are lists of vectors and sublists.
     Each molecule id is mapped to a list that has a type, extid,
     component, and member element.

     The type element is a character string describing what type of
     molecule the key molecule id corresponds to. Potential values for
     type include "protein", "complex", "compound", and "rna".

     The extid element is a named vector of character strings. values
     of the vector are external identifiers corresponding to the key
     molecule id. Names of the vector are abbreviations of the external
     public data sources from which the external ids are obtained.
     Potential values for vector names include "LL" (LocusLink
     identifier), "CA" (CAChemical Abstract number), "GO" (Gene
     Ontology), "KG" (KEGG), etc.

     The component element is a sublist with an id (molecule id of the
     component molecule), location (a GO Cellular Component vocabulary
     indicating the location of the molecule), and activity (an
     abstract term that can be "inactive", "active", "active1",
     "active2") elements. The component element only applies to complex
     molecules. Each complex molecule has a sequence of component
     molecules represented by elements of the sublist. 

     The member element is a named vector of molecule ids for molecules
     that belong to the same protein family as the key molecule id.
     Names of the vector are the key molecule id. 

     Mappings were based on data provided by:

     cMAP: <URL: http://cmap.nci.nih.gov/PW/Download>. Build:
     Unavailable. Downloaded:Tue Oct  4 18:56:42 2005

     Package built: Tue Oct  4 18:56:42 2005

_R_e_f_e_r_e_n_c_e_s:

     cMAP <URL: http://cmap.nci.nih.gov/PW>

_E_x_a_m_p_l_e_s:

         require(cMAP) || stop(paste(cMAP, "unavailable"))
         xx <- as.list(cMAPKEGGMOLECULE)
         if(length(xx) > 0){
             # Get the value of the first key
             xx[[1]]
             # Get the values for multiget for a few keys
             if(length(xx) >= 3){
                 xx[1:3]
             }
         }

