ProCKSI

= Standardising Results with XML =  

ProCKSI utilises a variety of similarity comparison methods (e.g. USM, MaxCMO, TMaling, ...) producing different similarity measures  (e.g. Zscore, TMscore, RMSD, ...) each. Each of the comparison methods produces output with different formats and additional content such as alignments, rotation matrix, etc. Some of them produce just one output file, others a set of linked HTML files.

== Input ==

Optional tags: '''exclude''' (measure, result), '''log''' (no log is generated if not specified) [[BR]]

Optional attributes: '''description'''

{{{

<job id="ID" description="TEXT">

  <log filename="FILENAME" />

  <input type="structure|tree|contact map|similarity matrix">

    <item id="ID" label="TEXT" filename="FILENAME" />

    :::

    <item id="ID" label="TEXT" filename="FILENAME" />

  </input>  

  <method id="ID" name="TEXT">

    <param name="TEXT">VALUE</param>

    :::

    <param name="TEXT">VALUE</param>

    <exclude>

      <measure>NAME</measure>

      :::

      <measure>NAME</measure>

      <result>NAME</result>

      :::

      <result>NAME</result>

    </exclude>

  </method>

  :::

  <method ...>

    ...

  </method>

</job>

}}}

The data used as an input could be protein structures, similarity trees, contact maps or similarity matrices. All specified methods should be able to operate on given data files. This dependency could be verified automatically using XML Schema.

== Output ==

Optional tags: '''log''', '''message''', '''similarity''' (used only if output is a ''comparison'') [[BR]]

Optional attributes: '''description''', '''node''', '''start''', '''end''', '''ref_id''' (only if output type is ''composition''), '''ref_id2''' (only if output type is not ''comparison'')

{{{

<job id="ID" description="TEXT" node="TEXT" start="TIME" end="TIME">

  <log filename="FILENAME" />

  <message type="error|warning|info">TEXT</message>

  :::

  <message type="error|warning|info">TEXT</message>

  <input type="structure|tree|contact map|similarity matrix">

    <item id="ID" label="TEXT" filename="FILENAME" />

    :::

    <item id="ID" label="TEXT" filename="FILENAME" />

  </input>  

  <parameters>

    <method id="ID" name="NAME">

      <parameter name="TEXT">VALUE</parameter>

      :::

      <parameter name="TEXT">VALUE</parameter>

    </method>

    :::

    <method ...>

      ...

    </method>

  </parameters>

  <output type="transformation|comparison|composition" ref_id="" ref_id2=" ">

    <method id="ID">

      <message type="error|warning|info">TEXT</message>

      :::

      <message type="error|warning|info">TEXT</message>

      <similarity measure="NAME">VALUE</similarity>

      :::

      <similarity measure="NAME">VALUE</similarity>

      <file type="TEXT" label="TEXT" name="FILENAME" />

      :::

      <file type="TEXT" label="TEXT" name="FILENAME" />

    <method>

  </output>

  :::

  <output ...>

    ...

  </output>

</job>

}}}

Message being an error, warning or additional information could be passed on a global or a method level. Input data and parameters defined in the input file could be repeated in the output if needed (self-contained output). Output could be a 1->1 transformation (e.g. structure -> contact map), a 2->1 comparison (e.g. 2*structure -> similarity measure) or N->1 composition (e.g. N*tree -> total tree or N*similarity matrix -> consensus similarity matrix). The results other than similarity measures for a pair of proteins are stored in external files and are just referenced from the XML file.

The alignment data could be described in the XML file, as there is no single format used by all programs. This yet to be decided.