[Gmod-schema-cmts] schema/chado/chaos-xml/doc chaos-and-chado.html,NONE,1.1

SourceForge Headquarters 225 Broadway Suite 1600 San Diego, CA 92101 +1 (858) 454-5900

Update of /cvsroot/gmod/schema/chado/chaos-xml/doc
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv29209/doc

Added Files:
	chaos-and-chado.html 
Log Message:


--- NEW FILE: chaos-and-chado.html ---
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
  <head>
    <title>Chaos-XML and Chado</title>
    <link rel="stylesheet" type="text/css" href="css/stylesheet.css">
  </head>

  <body>
    <h1>Chaos-XML and Chado</h1> 
    <p>
      Chaos-XML is based on the Chado relational model. For a full
      explanation of the meaning of the elements in Chaos-XML, please
      refer to the Chado documentation
    </p>
    <h2>Chado</h2>
    <p>
      For more details on Chado, see the <a
      href="http://www.gmod.org/schema">GMOD Schema documentation</a>,
      and in particular the module documentation. The <a
      href=""http://www.gmod.org/schema/doc/sequence.html">sequence</a>
      module is the most relevant.
      
    </p>

    <h2>Differences between Chaos XML and the Chado Relational Database Schema</h2>
    <dl>
      <dt>Coordinates</dt>
      <dd>Chaos uses nbeg/nend as opposed to fmin/fmax, as descibed above
      </dd>

      <dt>Dbxref flattening</dt>
      <dd>
        Chaos collapses the normalised chado table "dbxref" into a
        single "dbxrefstr" PCDATA element. See the <a href="dtd/chaos.dtd">DTD</a> for more
        details.
      </dd>

      <dt>Type flattening</dt> 

      <dd>
        Chaos uses a PCDATA element "type" in both feature and
        feature_relationship.
        
        In Chado, types are represented as a foreign key into the
        cvterm table

        In Chaos the type string is implicitly mapped to cvterm with
        the same name as the type, from the Sequence Ontology (SO) CV
      </dd>

      <dt>Organism flattening</dt>
      <dd>Chaos uses an "organismstr" PCDATA element to represent the
        normalised chado table "organism". See the <a href="dtd/chaos.dtd">DTD</a> for more details.
      </dd>
    </dl>
    <hr>
    <address><a href="mailto:cj...@fr...">Chris Mungall</a></address>
<!-- Created: Tue Jun 15 17:44:18 PDT 2004 -->
<!-- hhmts start -->
Last modified: Sun Apr 24 10:01:35 PDT 2005
<!-- hhmts end -->
  </body>
</html>