validatePSIMI25           package:RpsiXML           R Documentation

_V_a_l_i_d_a_t_i_n_g _P_S_I-_M_I _2._5 _f_i_l_e _w_i_t_h _M_I_F_2_5 _X_M_L _s_c_h_e_m_a

_D_e_s_c_r_i_p_t_i_o_n:

     The function validates given PSI-MI 2.5 file with MIF25 XML schema
     provided by the Molecular Interactions Workgroup of HUPO
     Proteomics Standards Initiative

_U_s_a_g_e:

     validatePSIMI25(file,
     schema = system.file("extdata/schemas/MIF25.xsd", package = "RpsiXML"),
     ignore.stderr = TRUE)

_A_r_g_u_m_e_n_t_s:

    file: The name or the URL of the file to be validated 

  schema: The schema file of PSI-MI 2.5 file format by default 

ignore.stderr: Whether to print out errors in the console 

_D_e_t_a_i_l_s:

     We advice to set "ignore.stderr=FALSE" for the first time of
     validating. The error number of the file will be printed in the
     console. When the number is not 0, one can set
     "ignore.stderr=TRUE" and see the errors produced during the
     validation.

_V_a_l_u_e:

     The number of errors in validating the file

_N_o_t_e:

     This function sofar depends on the tool "xmllint" bundled with
     libxml2 library. We plan to compile it later to run independent of
     the tool.

_A_u_t_h_o_r(_s):

     Jitao David Zhang <j.zhang@dkfz.de>, Tony Chiang
     <tchiang@ebi.ac.uk>

_R_e_f_e_r_e_n_c_e_s:

     libxml2 library <URL: http://xmlsoft.org/> PSI-MI 2.5 XML schema
     <URL: http://psidev.sourceforge.net/mi/rel25/src/MIF25.xsd>

_E_x_a_m_p_l_e_s:

     okFile <- system.file("extdata/psi25files/intact_2008_test.xml",
                           package="RpsiXML")
     validatePSIMI25(okFile)

