model.observ.xml Maven / Gradle / Ivy
<?xml version="1.0" encoding="UTF-8"?>
<molgenis name="org.molgenis.omx">
<module name="observ">
<description>
Observ-OM is a model to uniformly describe any phenotypic, genotypic
or
molecular observation. The four core concepts are:
<ul>
<li>
<b>ObservationTarget:</b>
the object we are observing.
<br />
For example: an Individual,
a Panel/Strain, a Sample, a Gene, a
Marker.
</li>
<li>
<b>ObservableFeature:</b>
the question asked or characteristic being
oberveded.
<br />
For example: 'What is height of [Target]?', 'What is genotype of
[Target] at
[Marker]?', 'Has [Target] ever used medicine [X]', 'What
is QTL p-value
association of [Marker] with [Gene Expression]?
</li>
<li>
<b>Protocol:</b>
the procedure of observation
<br />
For example: Food Frequency Questionnaire (FFQ), R/QTL mapping
method,
Genotype array, GWAS protocol.
</li>
<li>
<b>Observation:</b>
the actual act of observation. For example:
'FFQ asked to
[Individual:individual1], 'R/QTL applied to
[Marker:pvv4]',
'Genotype array applied to [Panel:Mouse RIL BxD 1].
Each observation
can have multiple ObservedValue AND be grouped into a DataSet.
</li>
</ul>
</description>
<entity name="Characteristic" implements="Identifiable">
<description> Characteristics are yes-no
statements about things in
the world. These can be used as part of an observation, as
parameter
of ObservableFeature ('measuredCharacteristic'). For
example: 'What
is allele of [Marker]', here the [Marker] is a
characteristic. Also,
Characteristics can be used as target of
observation. Typical
examples are 'Individual' or 'Panel'. But also
'Marker' can be an
Target when asked the question 'QTL p-value for
[phenotype]': here
both target and feature are characteristic, for
example 'leave count'
(phenotype characteristic) and 'PVV4' (marker
characteristic).
</description>
<field name="description" type="text" nillable="true"
description="(Optional) Rudimentary meta data about the observable feature. Use of ontology
terms references to establish unambigious descriptions is recommended" />
</entity>
<entity name="ObservationTarget" extends="Characteristic">
<description> ObservationTarget defines subjects of
observation, such
as Individual, Panel, Sample, etc. For instance: 'target 1' IS A
'Individual'.
</description>
</entity>
<entity name="ObservableFeature" extends="Characteristic">
<description>
ObservableFeature defines anything that can be observed.
<p />
In other words, ObservableFeature are the
questions asked, e.g. 'What
is Height?', 'What is Systolic blood
pressure?', or 'Has blue eyes?'.
<p />
Some questions may
be repeated for multiple characteristics. For
example 'What is [MarkerAllele]
observed?' can be applied to all
elements of a MarkerSet, and 'What
is [medicin codes] uses' can be
applied to a set of Medicine codes. This can be specified using the
measuredCharacteristic field.
<p />
The identifier of ObservableFeature is globally
unique. It is
recommended that
each
ObservableFeature is named
according to a
well-defined ontology
term or database accession.
</description>
<field name="unit" type="xref" xref_entity="OntologyTerm"
nillable="true"
description="(Optional) Reference to the well-defined measurement unit used to observe this feature
(if feature is that concrete). E.g. mmHg" />
<field name="definition" type="xref" xref_entity="OntologyTerm" description="The concept that is being measured in a specific way." nillable="true" />
<field name="dataType" type="enum" default="string"
enum_options="[bool,categorical,date,datetime,decimal,email,enum,file,html,hyperlink,image,int,long,mref,string,text,xref]"
description="(Optional) Reference to the technical data type. E.g. 'int'" />
<field name="temporal" type="boolean" default="false"
description="Whether this feature is time dependent and can have different values when measured
on different times (e.g. weight, temporal=true) or generally only measured once (e.g. birth date,
temporal=false) " />
</entity>
<entity name="Category" extends="Characteristic">
<description>Category is partOf ObservableFeature to define
categories for an
ObservableFeature, such as the categorical
answer codes that are often used in Questionaires.
For example the ObservableFeature 'sex' has
{code_string = 1, label=male} and {code_string
= 2, label=female}.
Category can be linked to well-defined
ontology terms via the
ontologyReference. Category
extends
ObservationElement such that it
can be referenced by
ObservedValue.value.
The Category class maps to
METABASE::Category
</description>
<field name="observableFeature" type="xref" xref_entity="ObservableFeature"
description="The Measurement these permitted values are part of." />
<field name="valueCode" type="string"
description="The value used to store this category in ObservedValue. For example '1', '2'." nillable="true"/>
<field name="definition" type="xref" xref_entity="OntologyTerm" description="The category that is being measured in a specific way." nillable="true" />
<field name="isMissing" type="bool" default="false"
description="whether this value should be treated as missing value." />
</entity>
<entity name="Protocol" extends="Characteristic">
<!-- has name, identifier, description, accession, accessionVersion. Should
be part of a submission -->
<description>
The Protocol class defines parameterizable descriptions
of
(analysis)methods. Examples of protocols are: Questionaires, SOPs,
Assay platforms, Statistical analyses, etc.
Each protocol has a
unique identifier.
Protocol has an association to OntologyTerm to
represent the type of
protocol.
</description>
<field name="ProtocolType" nillable="true" type="xref"
xref_entity="OntologyTerm" description="classification of protocol" />
<field name="subprotocols" type="mref" xref_entity="Protocol" nillable="true" description="Subprotocols of this protocol"/>
<field name="Features" type="mref" nillable="true" xref_entity="ObservableFeature"
description="parameters (in/out) that are used or produced by this protocol." />
</entity>
<entity name="DataSet" extends="Characteristic">
<description>Container for one or more observations that are measured
using the same protocol and by the same performer(s). The dataset
may be a file (having the same
identifier) but in most cases it is a
data table consisting of rows (Observation).
This entity replaces
ProtocolApplication.
</description>
<field name="ProtocolUsed" type="xref" xref_entity="Protocol"
description="Reference to the protocol that is being used (if available)" />
<field auto="true" name="startTime" type="datetime"
description="time when the protocol started." />
<field auto="true" name="endTime" type="datetime" nillable="true"
description="(Optional) time when the protocol ended." />
</entity>
<entity name="ObservationSet" implements="Autoid">
<description>In practice: Observation is one row within a DataSet.
</description>
<field name="partOfDataSet" type="xref" xref_entity="DataSet"
description="DataSet this ValueSet is part of." />
<field name="Time" type="datetime" description="Time of this observationSet" nillable="true" />
<unique fields="partOfDataSet,Time" description="No single secondary key" />
</entity>
<entity name="ObservedValue" implements="Autoid">
<description>
Generic storage of values as part of one observation
event. Values are atomatic observations,
e.g.,
length (feature) of
individual 1 (valueset.target)
= 179cm (value).
Values can also be
qualified by some characteristic,
e.g., QTL
p-value (feature)
between
phenotype 'leaf count'
(characteristic) and
marker 'PVV4'
(valueset.target) =
0.1^10+3 (value).
</description>
<field name="ObservationSet" type="xref" xref_entity="ObservationSet"
description="Reference to the observation. For example a particular patient visit or the application of a microarray or the calculation of a QTL model" />
<field name="Feature" type="xref" xref_entity="ObservableFeature"
description="References the ObservableFeature that this observation was made on. For example 'probe123'." />
<!-- removed: <field name="Characteristic" nillable="true" type="xref"
xref_entity="Characteristic" description="Is brother of [characteristic], or Average of [height]" /> -->
<field name="Value" type="xref" xref_entity="Value" nillable="true" description="The value observed" />
</entity>
</module>
<module name="observ.target">
<entity name="Species" extends="OntologyTerm">
<description>Ontology terms for species. E.g. Arabidopsis thaliana.
DISCUSSION: should we avoid subclasses of OntologyTerm and instead
make a 'tag' filter on terms so we can make pulldowns context
dependent (e.g. to only show particular subqueries of ontologies).
</description>
</entity>
<entity name="Individual" extends="ObservationTarget">
<description> The Individuals class defines the subjects that are
used
as observation target. The Individual class maps to
XGAP:Individual
and PaGE:Individual. Groups of individuals can be
defined via
Panel.
</description>
<field name="Mother" type="xref" nillable="true" xref_entity="Individual"
description="Refers to the mother of the individual." />
<field name="Father" type="xref" nillable="true" xref_entity="Individual"
description="Refers to the father of the individual." />
</entity>
<entity name="Panel" extends="ObservationTarget">
<!-- panel has: identifier, description, accessions -->
<description>The Panel class defines groups of individuals based on
cohort design, case/controls, families, etc. For instance:
'LifeLines
cohort', 'middle aged man', 'recombinant mouse inbred Line
dba x b6'
or 'Smith family'. A Panel can act as a single
ObservationTarget.
For example: average height (Measurement) in the
LifeLines cohort
(Panel) is 174cm (ObservedValue). The Panel class
maps to XGAP:Strain and PaGE:Panel
classes. In METABASE this is
assumed there is one panel per study.
</description>
<field name="PanelType" type="xref" xref_entity="OntologyTerm"
nillable="true"
description="Indicate the type of Panel (example: Sample panel, AssayedPanel, Natural=wild type, Parental=parents of a cross, F1=First generation of cross, RCC=Recombinant congenic, CSS=chromosome substitution)" />
<field name="NumberOfIndividuals" type="int" />
<field name="Species" type="xref" nillable="true" xref_entity="Species"
description="The species this panel is an instance of/part of/extracted from." />
<field name="Individuals" type="mref" xref_entity="Individual"
nillable="true" description="The list of individuals in this panel" />
</entity>
<entity name="PanelSource" implements="Autoid">
<!-- todo: this should probably be a subclass of protocolApplication? -->
<!-- experimental -->
<description>PanelSources is partOf Panel to define how panels are
related panels, founder panels,
such as overlap,
selection criteria,
getting assayed panel from a
sample panel, etc.
</description>
<field name="CurrentPanel" type="xref" xref_entity="Panel"
description="Panel for which these sources are defined." />
<field name="SourcePanel" type="xref" xref_entity="Panel"
description="Source that contributed individuals to current panel" />
<field name="NumberOfIndividuals" type="int" nillable="true"
description="Number of individuals lifted over from this source" />
<field name="SelectionCriteria" type="text"
description="Inclusion/exclusion criteria used to select these individuals from source into current panel" />
</entity>
<entity name="Ontology" implements="Identifiable">
<description> Ontology defines a reference to an ontology or
controlled vocabulary from which well-defined and stable (ontology)
terms can be obtained. Each Ontology should have a unique identifer,
for instance: Gene Ontology, Mammalian Phenotype, Human Phenotype
Ontology, Unified Medical Language System, Medical Subject Headings,
etc. Also a abbreviation is required, for instance: GO, MP, HPO,
UMLS, MeSH, etc. Use of existing ontologies/vocabularies is
recommended to harmonize phenotypic feature and value descriptions.
But one can also create a 'local' Ontology. The Ontology class maps
to FuGE::Ontology, MAGE-TAB::TermSourceREF.
</description>
<field auto="false" name="ontologyAccession" type="string"
nillable="true"
description="A accession that uniquely identifies the ontology (typically an acronym). E.g. GO, MeSH, HPO." />
<field nillable="true" auto="false" name="ontologyURI" type="hyperlink"
description="(Optional) A URI that references the location of the ontology." />
</entity>
<entity name="OntologyTerm" extends="Characteristic">
<description>
OntologyTerm defines a single entry (term) from an
ontology or a controlled vocabulary (defined by Ontology). The
identifier is the ontology term is unique. E.g. 'NCI:Antigen Gene'.
Other data entities can reference to this OntologyTerm to harmonize
naming of concepts. If no suitable ontology term exists then one can
define new terms locally (in which case there is no formal accession
for the term limiting its use for cross-Investigation queries).
</description>
<field auto="false" name="ontology" type="xref" nillable="true"
description="(Optional) The source ontology or controlled vocabulary list that ontology terms have been obtained from."
xref_entity="Ontology" />
<field nillable="true" auto="false" name="termAccession" type="varchar"
description="(Optional) The accession number assigned to the ontology term in its source ontology. If empty it is assumed to be a locally defined term. " />
<field nillable="true" auto="false" name="definition" type="string"
description="(Optional) The definition of the term." />
<unique fields="ontology,termAccession"
description="The term accession is unique within an Ontology" />
</entity>
<entity name="Accession" extends="OntologyTerm">
<description>
An external identifier for an annotation. For example:
name='R13H8.1', ontology='ensembl' or name='WBgene00000912',
ontology='wormbase'.
</description>
</entity>
</module>
<module name="observ.value">
<entity name="Value" implements="Autoid">
<description></description>
</entity>
<entity name="BoolValue" extends="Value">
<description></description>
<field name="Value" type="bool" />
</entity>
<entity name="CategoricalValue" extends="Value">
<description></description>
<field name="Value" type="xref" xref_entity="Category" />
</entity>
<entity name="DateValue" extends="Value">
<description></description>
<field name="Value" type="date" />
</entity>
<entity name="DateTimeValue" extends="Value">
<description></description>
<field name="Value" type="datetime" />
</entity>
<entity name="DecimalValue" extends="Value">
<description></description>
<field name="Value" type="decimal" />
</entity>
<entity name="EmailValue" extends="Value" decorator="org.molgenis.omx.decorators.EmailValueDecorator">
<description></description>
<field name="Value" type="email" />
</entity>
<entity name="HtmlValue" extends="Value">
<description></description>
<field name="Value" type="text" />
</entity>
<entity name="HyperlinkValue" extends="Value" decorator="org.molgenis.omx.decorators.HyperlinkValueDecorator">
<description></description>
<field name="Value" type="hyperlink" />
</entity>
<entity name="IntValue" extends="Value">
<description></description>
<field name="Value" type="int" />
</entity>
<entity name="LongValue" extends="Value">
<description></description>
<field name="Value" type="long" />
</entity>
<entity name="MrefValue" extends="Value">
<description></description>
<field name="Value" type="mref" xref_entity="Characteristic" />
</entity>
<entity name="StringValue" extends="Value">
<description></description>
<field name="Value" type="string" />
</entity>
<entity name="TextValue" extends="Value">
<description></description>
<field name="Value" type="text" />
</entity>
<entity name="XrefValue" extends="Value">
<description></description>
<field name="Value" type="xref" xref_entity="Characteristic" />
</entity>
</module>
</molgenis>
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