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<molgenis name="org.molgenis.omx">
<module name="xgap" label="XGAP module">
<description>
XGAP, taken from https://raw.github.com/joerivandervelde/molgenis-sdk/omx3/src/main/resources/omx3/xgap.xml at 26 sept 2013.
Added: Variant
</description>
<entity name="Track" extends="Characteristic" xref_label="Identifier"></entity>
<entity name="Variant" extends="ObservationTarget" implements="Locus">
<description>A SNP is a special kind of Marker, but can also be seen as a phenotype to map against in some cases. A single-nucleotide polymorphism is a DNA sequence variation occurring when a single nucleotide in the genome (or other shared sequence) differs between members of a biological species or paired chromosomes in an individual.</description>
<field name="MutationPosition" type="int" nillable="true"/>
<field name="CdnaPosition" type="int" nillable="true"/>
<field name="AaPosition" type="int" nillable="true"/>
<field name="VariantLength" type="int" nillable="true"/>
<field name="Event" nillable="true"/>
<field name="NtChange" nillable="true"/>
<field name="Codonchange" nillable="true"/>
<field name="CdnaNotation" nillable="true"/>
<field name="GdnaNotation" nillable="true"/>
<field name="AaNotation" nillable="true"/>
<field name="Exon" nillable="true"/>
<field name="Consequence" nillable="true"/>
<field name="Inheritance" nillable="true"/>
<field name="ReportedSNP" type="bool" nillable="true"/>
<field name="EffectOnSplicing" type="bool" nillable="true"/>
<field name="Pathogenicity" nillable="true"/>
<field name="Gene" nillable="true"/>
<field name="IdMutation" type="int" nillable="true"/>
<field name="DetailsForMutation" type="hyperlink" nillable="true"/>
<field name="Track" type="xref" xref_entity="Track"/>
</entity>
<entity name="Locus" abstract="true">
<description> position. Typical examples of such traits are genes,
probes and markers. Common structure for entities that have a
genomic</description>
<field name="Chromosome" label="Chromosome" type="xref"
xref_entity="Chromosome" nillable="true"
description="Reference to the chromosome this
position belongs to." />
<field name="cM" label="cMPosition" type="decimal" nillable="true"
description="genetic map position in centi morgan (cM)." />
<field name="bpStart" label="Start (5')" type="long" nillable="true"
description="numeric basepair postion (5') on the chromosome" />
<field name="bpEnd" label="End" type="long" nillable="true"
description="numeric basepair postion (3') on the chromosome" />
<field name="Seq" type="text" nillable="true"
description="The FASTA text representation of the sequence." />
<field name="Symbol" type="varchar" nillable="true"
description="todo" />
</entity>
<entity name="Chromosome" extends="ObservationTarget">
<field name="orderNr" type="int" />
<field name="isAutosomal" type="bool" description="Is 'yes' when number of chromosomes is equal in male and female individuals, i.e., if not a sex chromosome."/>
<field name="bpLength" type="int" nillable="true" description="Lenght of the chromsome in base pairs."/>
<field name="Species" label="Species" type="xref" xref_entity="OntologyTerm"
nillable="true"
description="Reference to the species this
chromosome belongs to." />
</entity>
<entity name="NMRBin" extends="ObservationTarget">
<description> Shift of the NMR frequency due to the chemical
environment.</description>
</entity>
<entity name="Clone" extends="ObservationTarget" implements="Locus">
<description> BAC clone fragment.</description>
</entity>
<entity name="DerivedTrait" extends="ObservationTarget">
<description> Any meta trait, eg. false discovery rates, P-values,
thresholds.</description>
</entity>
<!--
EnvironmentalFactor was previously magetab_idf.Factor which was xgap.Factor.
The MAGE-TAB Factor only applies to intended (predefined) experimental
conditions. For example: in a study where we want to find out what causes
a certain disease, the disease is the factor. This is a bit too restrictive
for XGAP/xQTL: we also want to model 'unforeseen' experimental conditions
in the form of environmental factors. For example: the age/diet/weight/
sex/bloodtype of subjects, time of drawing a sample, the day of harvesting
an organ or plant, the lab worker which processed the sample or microarray,
the normalization method used, and so on. The 'factor of interest' can also
be included here, though usually it is simply added as a (binary) phenotype.
For example: a ClassicalPhenotype named 'HasDisease'. EnvironmentalFactor is
a special phenotype (ObservableFeature) because the value of the factor
itself is also 'measured'.
-->
<entity name="EnvironmentalFactor" extends="ObservationTarget">
<description>Experimental conditions,
such as temperature differences, batch effects etc.</description>
</entity>
<entity name="Gene" extends="ObservationTarget" implements="Locus">
<description> Trait annotations specific for genes.</description>
<field name="Symbol" nillable="true"
description="Main symbol this gene is known by (not necessarily unique, in constrast to 'name')" />
<field name="Orientation" type="enum" enum_options="[F,R]"
nillable="true"
description="Orientation of the gene on the genome (F=forward, R=reverse)" />
<field name="Control" type="bool" nillable="true"
description="Indicating whether this is a 'housekeeping' gene that can be used as control." />
</entity>
<entity name="Transcript" extends="ObservationTarget">
<description> Trait annotations specific for transcripts.
</description>
<!-- Question: Is there a specific notation involved that we can create
type for? -->
<field name="Gene" label="Gene" type="xref" xref_entity="Gene"
nillable="true"
description="The gene that produces this protein" />
</entity>
<entity name="Protein" extends="ObservationTarget">
<description> Trait annotations specific for proteins.</description>
<!--
Question: Is there a specific notation involved that we can create
type for?
-->
<field name="Gene" label="Gene" type="xref" xref_entity="Gene"
nillable="true"
description="The gene that produces this protein" />
<field name="Transcript" label="Transcript" type="xref" xref_entity="Transcript"
nillable="true"
description="The transcript variant that produces this protein" />
<field name="AminoSequence" label="Sequence" type="text" nillable="true"
description="The aminoacid sequence." />
<field name="Mass" label="Mass" type="decimal" nillable="true"
description="The mass of this metabolite" />
</entity>
<entity name="Metabolite" extends="ObservationTarget">
<description> Trait annotations specific for metabolites.
</description>
<field name="Formula" label="Formula" type="varchar" length="128"
nillable="true" description="The chemical formula of a metabolite." />
<field name="Mass" label="Mass" type="decimal" nillable="true"
description="The mass of this metabolite" />
<field name="Structure" label="Structure" type="text" nillable="true"
description="The chemical structure of a metabolite (in SMILES representation)." />
</entity>
<entity name="Marker" extends="ObservationTarget" implements="Locus">
<description> Trait annotations specific for markers.</description>
<field name="ReportsFor" nillable="true" type="mref"
xref_entity="Marker" description="The marker (or a subclass like 'SNP') this marker (or a subclass like 'SNP') reports for." />
</entity>
<entity name="SNP" extends="Marker">
<description>A SNP is a special kind of Marker, but can also be seen as a phenotype to map against in some cases. A single-nucleotide polymorphism is a DNA sequence variation occurring when a single nucleotide in the genome (or other shared sequence) differs between members of a biological species or paired chromosomes in an individual.</description>
<field name="Status" nillable="true" description="The status of this SNP, eg 'confirmed'."/>
<field name="Polymorphism" nillable="true" type="mref"
xref_entity="Polymorphism" description="The polymorphism that belongs to this SNP." />
</entity>
<entity name="Polymorphism" extends="ObservationTarget">
<description>The difference of a single base discovered between two sequenced individuals.</description>
<field name="Base" type="enum" enum_options="[Reference,A,T,C,G]" nillable="false" description="The affected DNA base. Note that you can select the reference base here." />
<field name="Value" nillable="true" description="The strain/genotype for which this polymorphism was discovered. E.g. 'N2' or 'CB4856'." />
</entity>
<entity name="Probe" extends="ObservationTarget" implements="Locus">
<description> A piece of sequence that reports for the expression of
a gene, typically spotted onto a microarray.</description>
<field name="Mismatch" type="bool"
description="Indicating whether the probe is a match" default="false" />
<field name="ProbeSet" type="xref" nillable="true" xref_entity="ProbeSet"
description="Optional: probeset this probe belongs to (e.g., in Affymetrix assays)." />
<field name="ReportsFor" label="ReportsFor" type="xref" xref_entity="Gene"
nillable="true"
description="The gene this probe reports for." />
</entity>
<entity name="Spot" extends="Probe">
<description>
This is the spot on a microarray.
<br />
Note: We don't distinquish between probes (the sequence) and spots
(the sequence as spotted on the array).
</description>
<field name="x" type="int" description="Row" />
<field name="y" type="int" description="Column" />
<field name="GridX" type="int" description="Meta Row" nillable="true" />
<field name="GridY" type="int" description="Meta Column"
nillable="true" />
<unique fields="X,Y,GridX,GridY" />
</entity>
<entity name="ProbeSet" extends="ObservationTarget" implements="Locus">
<description> A set of Probes. E.g. an Affymetrix probeset has multiple
probes. It implements locus because sometimes you want to give the complete set of probes a range,
for example: indicating that this set of probes spans basepair 0 through 10.000.000 on chromosome 3.
The same information could arguably also be queried from the probes themselves, but if you have 40k probes,
retrieving the same information from only ProbeSet (if annotated so) would be much faster.</description>
</entity>
<entity name="MassPeak" extends="ObservationTarget">
<description> A peak that has been selected within a mass
spectrometry experiment.</description>
<field name="MZ" type="decimal" nillable="true"
description="Mass over charge ratio of this peak." />
<!--
field name="Intensity" type="decimal" optional="true"
description="Intensity of this peak." /
-->
<field name="RetentionTime" type="decimal" nillable="true"
description="The retention-time of this peak in minutes." />
</entity>
<entity name="Sample" extends="ObservationTarget">
<description></description>
<field name="Individual" type="xref" xref_entity="Individual"
nillable="true"
description="The individual from which this sample was taken." />
<field name="Tissue" type="xref" xref_entity="OntologyTerm"
nillable="true"
description="The tissue from which this sample was taken." />
</entity>
<!--entity name="GenericObservationTarget" extends="ObservationTarget">
<description>Generic implementation of ObservationTarget for
applications that choose not to choose subclasses such as Individual
or Panel. NOT NEEDED? ObservationTarget is not abstract</description>
</entity-->
<entity name="PairedSample" extends="ObservationTarget">
<description> A pair of samples labeled for a two-color microarray
experiment.</description>
<field name="Subject1" type="xref" xref_entity="Individual"
description="The first subject" />
<field name="Label1" type="xref" xref_entity="OntologyTerm"
nillable="true"
description="Which channel or Fluorescent labeling is associated with the first subject" />
<field name="Subject2" type="xref" xref_entity="Individual"
description="The second sample" />
<field name="Label2" type="xref" xref_entity="OntologyTerm"
nillable="true"
description="Which channel or Fluorescent labeling is associated with the second subject" />
</entity>
</module>
</molgenis>
