psimi25Source-class         package:RpsiXML         R Documentation

_C_l_a_s_s "_p_s_i_m_i_2_5_S_o_u_r_c_e"

_D_e_s_c_r_i_p_t_i_o_n:

     A class representing data source compatible with PSI-MI 2.5 XML
     data exchange format

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form 'new("psimi25Source",
     ...)'

_S_l_o_t_s:


     '_l_a_b_e_l': Object of class '"character"', a meaningful unique label
          of the database, does not necessarily have to be the
          identifier used in the PSI-MI files. The value is advised to
          be overwritten by the objects

     '_s_o_u_r_c_e_D_b': Object of class '"character"', the character string
          used in the PSI-MI files to identify the source database. The
          value must be overwritten by the object, depending on the
          database identifier used in the PSI-MI file.

     '_u_n_i_p_r_o_t_S_y_m_b_o_l': Object of class '"character"', the identifier of
          UniProf reference in "primaryRef" or "secondaryRef"
          attributes of the interactors, telling the parser where to
          find UniProt symbol of the interactors. The value must be
          overwritten by the objects.

     '_p_a_r_s_e_E_x_p_e_r_i_m_e_n_t': Object of class '"function"', the function to
          parse experiment from the PSI-MI 2.5 file. Except for special
          need this function should not be overwritten by the objects,
          since it parses the experiment node strictly according the
          PSI-MI standard 

     '_p_a_r_s_e_I_n_t_e_r_a_c_t_o_r': Object of class '"function"', the function to
          parse interactor from the PSI-MI 2.5 file. Except for special
          need this function should not be overwritten by the objects,
          since it parses the interactor node strictly according the
          PSI-MI standard  

     '_p_a_r_s_e_C_o_m_p_l_e_x': Object of class '"function"', the function to
          parse complex from the PSI-MI 2.5 file. Except for special
          need this function should not be overwritten by the objects,
          since it parses the complex node strictly according the
          PSI-MI standard 

_M_e_t_h_o_d_s:


     _p_a_r_s_e_C_o_m_p_l_e_x 'signature(x = "psimi25Source")': parse complex node
          of PSI-MI 2.5 file 

     _p_a_r_s_e_E_x_p_e_r_i_m_e_n_t 'signature(x = "psimi25Source")': parse experiment
          node of PSI-MI 2.5 file

     _p_a_r_s_e_I_n_t_e_r_a_c_t_o_r 'signature(x = "psimi25Source")': parse interactor
          node of PSI-MI 2.5 file

     _s_o_u_r_c_e_D_b 'signature(x = "psimi25Source")': returns the source
          database

     _u_n_i_p_r_o_t 'signature(x = "psimi25Source")': returns the uniprot
          identifier of the PSI-MI 2.5 XML file 

_N_o_t_e:

     In case of a new data repository, you can first try creating a new
     object of the class with 'label', 'sourceDb' and 'uniprotSymbol'
     adjusted as needed. Try parsing a function with this new
     psimi25Source object. In case of warnings or errors, it may mean
     that the file provided is not strictly compatible with PSI-MI 2.5
     data exchange format standard, please then contact the data
     provider.

     By 02.06.08, six sources have been registered in the release
     version of 'RpsiXML':  BIOGRID.PSIMI25, DIP.PSIMI25, HPRD.PSIMI25,
     INTACT.PSIMI25,, MINT.PSIMI25,MIPS.PSIMI25. Along the development
     we will implement more data sources under PSI-MI 25 standard.

_A_u_t_h_o_r(_s):

     Jitao David Zhang <j.zhang@dkfz.de>

_S_e_e _A_l_s_o:

     'parsePsimi25Interaction', 'parsePsimi25Complex',
     'psimi25XML2Graph'

_E_x_a_m_p_l_e_s:

     showClass("psimi25Source")

