molgenis_db.xml

<?xml version="1.0" encoding="UTF-8"?>
	<!--
		DOCTYPE molgenis PUBLIC "MOLGENIS 1.0"
		"http://molgenis.sourceforge.net/dtd/molgenis_v_1_0.dtd"
	-->
<molgenis name="example" label="My MOLGENIS">
	<description>This is an minimal example database to show how MOLGENIS works.
		The purpose of this example database is to administrate experiment, samples,
		traits and measurements. The name='example' will result in a Java package
		'example' being generated.</description>
	<!-- abstract data types -->
	<entity name="Identifiable" abstract="true">
		<description>For modeling purposes only (denoted by abstract='true', this
			entity defines fields id and name centrally.</description>
		<field name="Id" type="autoid" description="autogenerated id number (autoid)" />
		<field name="Name" unique="true" readonly="true"
			description="unique, user provided name string" />
	</entity>
	<!-- experiment structure -->
	<entity name="Experiment" implements="Identifiable" xref_label="Name">
		<description>Summary of an experiment.</description>
		<field name="Description" type="text" nillable="true"
			description="Optional description text" />
		<field name="CreationDate" type="date" auto="true"
			description="Creation date, with an automatic default to 'today'" />
	</entity>
	<!-- sample description structure -->
	<entity name="Sample" implements="Identifiable">
		<description>Samples that are part of an experiment.</description>
		<field name="Experiment" type="xref" xref_field="Experiment.Id"
			xref_label="Name"
			description="Samples are part-of one experiment (by cross reference to Experiment.id)" />
		<field name="Species" default="Arabidopsis thaliana" description="Species, default to Arabidopsis" />
		<field name="Tissue" nillable="true" description="Optional specification of tissue" />
		<field name="Sex" type="enum" enum_options="[male,female,unknown]"
			description="Fixed choice on Sex" />
		<field name="SampleTime" type="datetime" auto="true" />
		<unique fields="Experiment,Name"/>
	</entity>
	<entity name="SpecialSample" extends="Sample">
		<field name="detail" />
	</entity>
	<!-- trait description structure -->
	<entity name="Trait" implements="Identifiable">
		<description>Traits that are studied in this experiment.</description>
		<field name="Molecular" type="bool"
			description="Indication whether this is a molecular trait" />
		<field name="Experiment" type="xref" xref_field="Experiment.Id"
			xref_label="Name"
			description="Traits are defined per experiment (by cross reference to Experiment.id)" />
	</entity>
	<!-- trait description structure -->
	<entity name="Data">
		<description>Data values (observations) of a measurement. Note: Data doesn't
			inherit from Identifiable because it has no unique name.</description>
		<field name="Id" type="autoid" description="autogenerated id number" />
		<field name="Experiment" type="xref" xref_field="Experiment.Id"
			xref_label="Name" description="Measurements are part-of one experiment" />
		<field name="Sample" type="xref" xref_field="Sample.Id" xref_label="Experiment_Name,Name"
			description="The sample this measurement is on" />
		<field name="Trait" type="xref" xref_field="Trait.Id" xref_label="Name"
			description="The trait this measurement is on" />
		<field name="Value" description="The value measured/calculated" />
		<unique fields="Experiment,Sample,Trait" description="There can be only one value per Sample X Trait" />
	</entity>
	<entity name="AggregateData">
				<description>Data on multiple samples in one go.</description>
		<field name="Id" type="autoid" description="autogenerated id number" />
		<field name="Experiment" type="xref" xref_field="Experiment.Id"
			xref_label="Name" description="Measurements are part-of one experiment" />
		<field name="Samples" type="mref" xref_field="Sample.Id" xref_label="Name"
			description="The samples this measurement is on" />
		<field name="Trait" type="xref" xref_field="Trait.Id" xref_label="Name"
			description="The trait this measurement is on" />
		<field name="Value" description="The value measured/calculated" />
	</entity>
</molgenis>