cMAPCARTAINTERACTION          package:cMAP          R Documentation

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

     cMAPCARTAINTERACTION maps cMAP (NCICB Pathway Interaction
     Database) molecule identifiers to data about the interactions of
     the molecule represented by the identifiers and other 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
     source, process, reversible, condition, and component element.

     The source element is a character string indicating whether the
     interactions between molecules are from a BioCarta or KEGG
     pathway. 

     The process is a character string describing the process the key
     molecule is involved. Potential values include "reaction",
     "modification", "transcription", "translocation", "macroprocess"
     or a more specific subtype of macroprocess including any term from
     the GO Biological Process vocabulary. 

     The reversible element is a boolean indicating whether the
     interaction is reversible. 

     The condition element is a character string indicating the
     biological process the interactions take place. Potential values
     include any term from the GO Biological Process vocabulary.

     The component element contains sublists of vectors. Each key
     molecule identifier has a sequence of component represented by
     elements of the sublist. Each sublist has an identifier (molecule
     identifier of the interacting molecule), edge (indicating the way
     two molecule interact. Potential values include "input", "agent",
     "inhibitor", and "output"), role (the function of the key
     molecule. Potential values include any term from the GO Molecular
     Function vocabulary), location (a GO Cellular Component vocabulary
     indicating the location of the interaction), and activity (an
     abstract term that can be "inactive", "active", "active1",
     "active2") elements.   

     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(cMAPCARTAINTERACTION)
         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]
             }
         }

