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")

