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<?xml version="1.0" encoding="utf-8"?>
<book xmlns="http://docbook.org/ns/docbook"
xmlns:xi="http://www.w3.org/2001/XInclude">
<info>
<title>domagi manual</title>
<copyright><year>2026</year><holder>Arun Isaac</holder></copyright>
</info>
<chapter>
<title>Database Schema</title>
<para>domagi uses a SQL schema with the following four tables to represent a pangenome.</para>
<variablelist>
<varlistentry>
<term>segment</term>
<listitem><para>entity representing pangenome segments</para></listitem>
</varlistentry>
<varlistentry>
<term>link</term>
<listitem><para>many-to-many relation between segments representing pangenome links</para></listitem>
</varlistentry>
<varlistentry>
<term>path</term>
<listitem><para>entity representing pangenome paths</para></listitem>
</varlistentry>
<varlistentry>
<term>path_segment</term>
<listitem><para>many-to-many relation mapping paths to segments associating them with the path at a certain coordinate</para></listitem>
</varlistentry>
</variablelist>
<para>The schema and the entity relationship diagram are visualized in <xref linkend="schema" /> and <xref linkend="er" /> respectively.</para>
<figure xml:id="schema">
<title>domagi database schema</title>
<mediaobject>
<imageobject>
<imagedata fileref="schema.svg" scale="80" />
</imageobject>
</mediaobject>
</figure>
<figure xml:id="er">
<title>domagi entity relationship diagram in Chen's notation</title>
<mediaobject>
<imageobject>
<imagedata fileref="er.svg" scale="90" />
</imageobject>
</mediaobject>
</figure>
</chapter>
<reference>
<title>Reference</title>
<xi:include href="domagi-build.dbk" />
<xi:include href="domagi-chop.dbk" />
<xi:include href="domagi-crush.dbk" />
<xi:include href="domagi-depth.dbk" />
<xi:include href="domagi-extract.dbk" />
<xi:include href="domagi-matrix.dbk" />
<xi:include href="domagi-overlap.dbk" />
<xi:include href="domagi-paths.dbk" />
<xi:include href="domagi-stats.dbk" />
<xi:include href="domagi-view.dbk" />
</reference>
</book>
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