tableList              package:ppiData              R Documentation

_A _l_i_s_t _o_f _t_a_b_l_e_s _f_o_r _t_h_e _d_o_w_n_l_o_a_d_e_d _a_n_d _p_a_r_s_e_d _x_m_l _f_i_l_e_s _f_r_o_m _t_h_e
_I_n_t_A_c_t _d_a_t_a_b_a_s_e

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

     This is a list of tables generated from the a script used to parse
     the xml files from the IntAct data repository.

     tableList is a list that contains six data-frames (tables) that
     records all the various data given by IntAct. The names of these
     six tables are:

     1. "acInfo" 2. "experimentInfo" 3. "ac2xref" 4. "interactionInfo"
     5. "experiment2interaction" 6. "interaction2inteactor"

     The "acInfo" data frame contains 4 columns: "ac", "type",
     "shortLabel", "fullName". They are IntAct accession numbers, types
     (experiment, interaction, or interactor), and short/long names,
     respectively.  The reason to have the second column is because
     IntAct assigns an accession number to each experiment,
     interaction, and interactor. The second column is an indicator
     between these three. The accession numbers in the first column of
     this data frame are those accession numbers in the yeast xml files
     from the IntAct repository.

     There are also 4 columns in the "experimentInfo" data frame:
     "ac","hostOrganism","interactionDetection", and
     "participantDetection". The IntAct accession numbers of
     experiments will be in the first column. The "hostOrganism" column
     is the tax id of the host organism (yeast in this case).  The next
     two columns are the detection methods of the interaction and of
     the participant, respectively.  The values in the 3rd and 4th
     columns are Proteomics Standards Initiative (PSI) Molecular
     Interaction (MI) identification codes. IntAct documents both the
     PSI MI 1.0 as well as PSI MI 2.5 codes.

     The "ac2xref" data frame contains 4 columns: "ac", "db", "id", and
     "secondary". This data frame provides the cross references (among
     several databases) for each IntAct accession number.  The column
     "ac" is the IntAct accession numbers, and the columns "db" and
     "id" are the reference database names and the corresponding
     identification code for that database. The secondary column
     provides secondary id if provided.

     There are also 4 columns in the "interactionInfo" data frame:
     "ac", "interactionType", "confidenceUnit", and "confidenceValue".
     The first column contains all the interaction accession numbers
     among these xml files.  The second column is the type of
     interaction.  The values here are also the PSI MI codes. The third
     and forth columns are the confidence information for this
     interaction.

     There are 2 columns in the "experiment2interaction" data frame:
     "experiment", and "interaction". This data frame tells us the what
     types of interactions were derived from the experiment. Both the
     experiments and the interactions are given by the IntAct accession
     numbers.

     There are 3 columns in the "interaction2inteactor" data frame:
     "interaction", "interactor", and "role". The first column provide
     the type of interaction while the second column provides the
     interactors within the interaction. Both the "interaction" and the
     "interactor" are given by the IntAct accession numbers. The third
     column is the role (bait or prey) of the interactors.

_U_s_a_g_e:

     data(tableList)

_F_o_r_m_a_t:

     The format is: chr "tableList"

_E_x_a_m_p_l_e_s:

     data(tableList)

