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 identifiers 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 identifiers and values are lists of vectors and
     sublists. Each molecule identifier 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 identifier 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 identifier. Names of the vector are abbreviations of the
     external public data sources from which the external identifiers
     are obtained. Potential values for vector names include "LL"
     (Entrez Gene identifier), "CA" (CAChemical Abstract number), "GO"
     (Gene Ontology), "KG" (KEGG), etc.

     The component element is a sublist with an identifier (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 identifiers for
     molecules that belong to the same protein family as the key
     molecule identifier. Names of the vector are the key molecule
     identifier. 

     Mappings were based on data provided by:

     cMAP: <URL: http://cmap.nci.nih.gov/PW/Download>. Build:
     Unavailable. Downloaded:Tue Sep 12 16:52:56 2006

     Package built: Tue Sep 12 16:52:56 2006

_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]
             }
         }

