Specification documentation for the GelML model: Reference manual
Status: GelML (version 1.0 final); Reference manual.
Authors:
Andrew R. Jones
School of Computer Science, University of Manchester
Email: ajones@cs.man.ac.uk
Frank Gibson
School of Computing Science, University of Newcastle upon Tyne,
Email: Frank.Gibson@newcastle.ac.uk
Copyright: Copyright © Proteome Standards Initiative (2007). All Rights Reserved.
This document is the reference manual for GelML version 1 (final). The contents have been generated automatically from the object model.
An entry in this document has the following structure:
Fully qualified class name (abstract) if class is abstract
Inheritance hierarchy:
superclass --> superclass --> Class name
Attributes:
Note: all attributes are converted to an attribute in the XML Schema unless marked *
| Name | Documentation | Data type | Required |
| Name of the attribute | Attribute's documentation | The UML data type of the attribute | Whether the attribute is required (cardinality "1") or not (cardinality "0..1") |
Associations:
Note: abstract associations will be rendered in italic font
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| Name of the association | Class at the navigable end | The association's documentation |
The multiplicity from source end to navigable end | Whether the association is "composite", "aggregate" or "none" |
If this association extends from an abstract association in FuGE, the name of the parent association is shown here; note: the association does not inherit any functionality from the parent association but, for example, could indicate to FuGE-compliant software the role that this association plays |
XML Schema Complex Type specification:
The definition of the corresponding ComplexType (minus documentation) in the XML Schema
|
XML Schema element specification:
The definition of the corresponding Element in the XML Schema
|
Table of contents
Top level XML Schema defintion
<xsd:schema
targetNamespace="http://www.psidev.info/gelml/1.0"
xmlns:xsd="http://www.w3.org/2001/XMLSchema"
xmlns:fuge="fuge.sf.net"
xmlns:gelml="http://www.psidev.info/gelml/1.0"
elementFormDefault="qualified">
<xsd:import namespace="fuge.sf.net" schemaLocation="http://fuge.sourceforge.net/Version1-InProcess/FuGE-v1-InProcess.xsd"/>
|
GelML.GelMLRoot.GelMLMaterialCollection
Inheritance hierarchy:
GelMLMaterialCollection
-->
Describable
Documentation:
Collection class for accessing all GenericMaterial instances
used in GelML.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| AllGenericMaterials |
fuge:GenericMaterial |
All GenericMaterial objects within the GelML file.
|
0..* to 0..* |
composite |
none
|
| AllMeasuredMaterials |
MeasuredMaterial |
All instances of MeasuredMaterial.
|
0..1 to 0..* |
composite |
none
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.GelMLRoot.GelMLMaterialCollectionType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.DescribableType">
<xsd:sequence>
<xsd:element ref="fuge:GenericMaterial" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="gelml:MeasuredMaterial" minOccurs="0" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="GelMLMaterialCollection" type="gelml:GelML.GelMLRoot.GelMLMaterialCollectionType" abstract="false" substitutionGroup="fuge:Describable" />
|
GelML.GelMLRoot.GelMLDataCollection
Inheritance hierarchy:
GelMLDataCollection
-->
Describable
Documentation:
Collection class for accessing all ExternalData instances in
GelML.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| AllData |
fuge:ExternalData |
All ExternalData objects within the GelML file.
|
0..* to 0..* |
composite |
none
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.GelMLRoot.GelMLDataCollectionType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.DescribableType">
<xsd:sequence>
<xsd:element ref="fuge:ExternalData" minOccurs="0" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="GelMLDataCollection" type="gelml:GelML.GelMLRoot.GelMLDataCollectionType" abstract="false" substitutionGroup="fuge:Describable" />
|
GelML.GelMLRoot.GelML
Inheritance hierarchy:
GelML
-->
Identifiable
-->
Describable
Documentation:
The root of the GelML document.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| GelMaterials |
GelMLMaterialCollection |
All GenericMaterials referenced in the GelML document, such as
samples, buffers and solutions.
|
1..1 to 0..1 |
composite |
none
|
| GelMLDataCollection |
GelMLDataCollection |
All the ExternalData within the GelML file, such as Images.
|
1..1 to 0..1 |
composite |
none
|
| GelProtocolCollection |
GelMLProtocolCollection |
The GelMLProtocolCollection in the document.
|
1..1 to 0..1 |
composite |
none
|
| GelExperiments |
GelExperiment |
All GelExperiments in the document.
|
0..* to 0..* |
composite |
none
|
| GelOntologyCollection |
fuge:OntologyCollection |
The complete set of OntologyIndividual and OntologySource
objects referenced in the GelML document.
|
0..1 to 0..1 |
composite |
none
|
| GelAuditCollection |
fuge:AuditCollection |
All Audit objects used in the document: security settings,
contacts etc.
|
0..1 to 0..1 |
composite |
none
|
| GelReferenceCollection |
fuge:ReferenceableCollection |
All referenced objects (BibliographicReference and
DatabaseReference).
|
0..1 to 0..1 |
composite |
none
|
| GelMLProvider |
fuge:Provider |
The provider of the document in terms of the Contact and the
software the produced the document instance.
|
0..* to 0..1 |
composite |
none
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.GelMLRoot.GelMLType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.IdentifiableType">
<xsd:sequence>
<xsd:element ref="gelml:GelMLMaterialCollection" minOccurs="0" maxOccurs="1"/>
<xsd:element ref="gelml:GelMLDataCollection" minOccurs="0" maxOccurs="1"/>
<xsd:element ref="gelml:GelMLProtocolCollection" minOccurs="0" maxOccurs="1"/>
<xsd:element ref="gelml:GelExperiment" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="fuge:OntologyCollection" minOccurs="0" maxOccurs="1"/>
<xsd:element ref="fuge:AuditCollection" minOccurs="0" maxOccurs="1"/>
<xsd:element ref="fuge:ReferenceableCollection" minOccurs="0" maxOccurs="1"/>
<xsd:element ref="fuge:Provider" minOccurs="0" maxOccurs="1"/>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="GelML" type="gelml:GelML.GelMLRoot.GelMLType" abstract="false" substitutionGroup="fuge:Identifiable" />
|
GelML.GelMLRoot.Gel2DExperiment
Inheritance hierarchy:
Gel2DExperiment
-->
GelExperiment
-->
Identifiable
-->
Describable
Documentation:
Gel2DExperiment captures the ProtocolApplications that should be
reported for 2D gel electrophoresis in a GelML file.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| Gel2DApplication |
Gel2DApplication |
The Gel2DApplication within this Gel2DExperiment.
|
0..* to 1..1 |
composite |
none
|
| ElectrophoresisApplications |
ElectrophoresisApplication |
The two ElectrophoresisApplications within this Gel2DExperiment.
|
0..* to 1..* |
composite |
none
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.GelMLRoot.Gel2DExperimentType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:GelML.GelMLRoot.GelExperimentType">
<xsd:sequence>
<xsd:element ref="gelml:Gel2DApplication" minOccurs="1" maxOccurs="1"/>
<xsd:element ref="gelml:ElectrophoresisApplication" minOccurs="1" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Gel2DExperiment" type="gelml:GelML.GelMLRoot.Gel2DExperimentType" abstract="false" substitutionGroup="gelml:GelExperiment" />
|
GelML.GelMLRoot.GelMLProtocolCollection
Inheritance hierarchy:
GelMLProtocolCollection
-->
Describable
Documentation:
Collection class for accessing all Software, Protocol, Equipment
and GenericProtocolApplications.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| AllEquipment |
fuge:Equipment |
All the Equipment used in the document.
|
0..* to 0..* |
composite |
none
|
| AllSoftware |
fuge:Software |
All the Software objects used in the document.
|
0..* to 0..* |
composite |
none
|
| AllProtocols |
fuge:Protocol |
All the Protocol objects used in the document.
|
0..* to 0..* |
composite |
none
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.GelMLRoot.GelMLProtocolCollectionType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.DescribableType">
<xsd:sequence>
<xsd:element ref="fuge:Equipment" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="fuge:Software" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="fuge:Protocol" minOccurs="0" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="GelMLProtocolCollection" type="gelml:GelML.GelMLRoot.GelMLProtocolCollectionType" abstract="false" substitutionGroup="fuge:Describable" />
|
GelML.GelMLRoot.GelExperiment (abstract)
Inheritance hierarchy:
GelExperiment
-->
Identifiable
-->
Describable
Documentation:
Abstract superclass representing the groups of
ProtocolApplications that should be represented in a valid GelML
document.
Attributes:
| Name | Documentation | Data type | Required |
| date |
The date the experiment was initiated on.
|
date |
false |
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| DetectionApplications |
DetectionApplication |
An association to all the DetectionApplications for this
GelExperiment.
|
0..* to 0..* |
composite |
none
|
| ExcisionApplications |
ExcisionApplication |
An association to all the ExcisionApplications for this
GelExperiment.
|
0..* to 0..* |
composite |
none
|
| ImageAcquisitionApplications |
ImageAcquisitionApplication |
An association to all the ImageAcquisitionApplications for this
GelExperiment.
|
0..* to 0..* |
composite |
none
|
| SampleLoadingApplications |
SampleLoadingApplication |
An association to all the SampleLoadingApplications for this
GelExperiment.
|
0..* to 1..* |
composite |
none
|
| GelManufactureApplications |
GelManufactureApplication |
An association to all the GelManufactureApplications for this
GelExperiment.
|
0..* to 0..* |
composite |
none
|
| ElectrophoresisType |
fuge:OntologyTerm |
The experiment type definition, such as "2D-DIGE",
"one-dimensional gel electrophoresis", "two-dimensional gel
electrophoresis" etc.
|
0..* to 0..1 |
none |
none
|
| OtherProtocolApplications |
fuge:GenericProtocolApplication |
All the GenericProtocolApplication objects used in the document.
|
0..* to 0..* |
composite |
none
|
| ExperimentContact |
fuge:ContactRole |
The Contact that is responsible for this experiment.
|
0..* to 0..1 |
composite |
none
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.GelMLRoot.GelExperimentType" abstract = "true">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.IdentifiableType">
<xsd:sequence>
<xsd:element ref="gelml:DetectionApplication" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="gelml:ExcisionApplication" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="gelml:ImageAcquisitionApplication" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="gelml:SampleLoadingApplication" minOccurs="1" maxOccurs="unbounded"/>
<xsd:element ref="gelml:GelManufactureApplication" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element name="_electrophoresisType" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:attribute name="OntologyTerm_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
<xsd:element ref="fuge:GenericProtocolApplication" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="fuge:ContactRole" minOccurs="0" maxOccurs="1"/>
</xsd:sequence>
<xsd:attribute name="date" type="xsd:date"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="GelExperiment" type="gelml:GelML.GelMLRoot.GelExperimentType" abstract="true" substitutionGroup="fuge:Identifiable" />
|
GelML.GelMLRoot.Gel1DExperiment
Inheritance hierarchy:
Gel1DExperiment
-->
GelExperiment
-->
Identifiable
-->
Describable
Documentation:
Gel1DExperiment captures the ProtocolApplications that should be
reported for 1D gel electrophoresis in a GelML file.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| Gel1DApplication |
Gel1DApplication |
The Gel1DApplication within this Gel1DExperiment.
|
0..* to 1..1 |
composite |
none
|
| ElectrophoresisApplication |
ElectrophoresisApplication |
The ElectrophoresisApplication within the Gel1DExperiment.
|
0..* to 1..1 |
composite |
none
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.GelMLRoot.Gel1DExperimentType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:GelML.GelMLRoot.GelExperimentType">
<xsd:sequence>
<xsd:element ref="gelml:Gel1DApplication" minOccurs="1" maxOccurs="1"/>
<xsd:element ref="gelml:ElectrophoresisApplication" minOccurs="1" maxOccurs="1"/>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Gel1DExperiment" type="gelml:GelML.GelMLRoot.Gel1DExperimentType" abstract="false" substitutionGroup="gelml:GelExperiment" />
|
GelML.GelMLRoot.OtherGelExperiment
Inheritance hierarchy:
OtherGelExperiment
-->
GelExperiment
-->
Identifiable
-->
Describable
Documentation:
OtherGelExperiment captures the ProtocolApplications that should
be reported for a type of gel electrophoresis other than 1D or
2D in a GelML file.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| ElectrophoresisApplications |
ElectrophoresisApplication |
The ElectrophoresisApplications within the OtherGelExperiment.
|
0..* to 1..* |
composite |
none
|
| OtherGelApplication |
OtherGelApplication |
The OtherGelApplication within this OtherGelExperiment.
|
0..* to 1..1 |
composite |
none
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.GelMLRoot.OtherGelExperimentType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:GelML.GelMLRoot.GelExperimentType">
<xsd:sequence>
<xsd:element ref="gelml:ElectrophoresisApplication" minOccurs="1" maxOccurs="unbounded"/>
<xsd:element ref="gelml:OtherGelApplication" minOccurs="1" maxOccurs="1"/>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="OtherGelExperiment" type="gelml:GelML.GelMLRoot.OtherGelExperimentType" abstract="false" substitutionGroup="gelml:GelExperiment" />
|
GelML.SelectSubstance.RelativeVolume
Inheritance hierarchy:
RelativeVolume
-->
VolumeParameter
-->
Parameter
-->
Identifiable
-->
Describable
Documentation:
The volume of a substance relative to the medium in which it is
in.
XML Schema Complex Type specification:
<xsd:complexType name="GelML.SelectSubstance.RelativeVolumeType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:GelML.SelectSubstance.VolumeParameterType">
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="RelativeVolume" type="gelml:GelML.SelectSubstance.RelativeVolumeType" abstract="false" substitutionGroup="gelml:VolumeParameter" />
|
GelML.SelectSubstance.VolumeFunction
Inheritance hierarchy:
VolumeFunction
-->
VolumeParameter
-->
Parameter
-->
Identifiable
-->
Describable
Documentation:
VolumeFunction represents a specification of a volume that
changes, for example, over time. The value provided for a
VolumeFunction should use the ComplexValue specification to
represent the function.
XML Schema Complex Type specification:
<xsd:complexType name="GelML.SelectSubstance.VolumeFunctionType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:GelML.SelectSubstance.VolumeParameterType">
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="VolumeFunction" type="gelml:GelML.SelectSubstance.VolumeFunctionType" abstract="false" substitutionGroup="gelml:VolumeParameter" />
|
GelML.SelectSubstance.AbsoluteVolume
Inheritance hierarchy:
AbsoluteVolume
-->
VolumeParameter
-->
Parameter
-->
Identifiable
-->
Describable
Documentation:
An absolute volume parameter.
XML Schema Complex Type specification:
<xsd:complexType name="GelML.SelectSubstance.AbsoluteVolumeType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:GelML.SelectSubstance.VolumeParameterType">
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="AbsoluteVolume" type="gelml:GelML.SelectSubstance.AbsoluteVolumeType" abstract="false" substitutionGroup="gelml:VolumeParameter" />
|
GelML.SelectSubstance.VolumeParameter (abstract)
Inheritance hierarchy:
VolumeParameter
-->
Parameter
-->
Identifiable
-->
Describable
Documentation:
Abstract superclass representing the different formats for
representing the volume of a substance.
XML Schema Complex Type specification:
<xsd:complexType name="GelML.SelectSubstance.VolumeParameterType" abstract = "true">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ParameterType">
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="VolumeParameter" type="gelml:GelML.SelectSubstance.VolumeParameterType" abstract="true" substitutionGroup="fuge:Parameter" />
|
GelML.SelectSubstance.SubstanceAction
Inheritance hierarchy:
SubstanceAction
-->
Action
-->
Identifiable
-->
Describable
Documentation:
An action representing the use of a substance within a protocol.
The substance can be named by free text or using the
OntologyTerm association. The attribute actionText can be used
to specify how the substance has been used within the protocol.
Attributes:
| Name | Documentation | Data type | Required |
| substanceName |
The name of the substance given as free text.
|
string |
false |
| actionText |
A specification of the use of the substance within the parent
protocol.
|
string |
false |
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| Concentration |
Concentration |
The concentration of the substance.
|
0..1 to 0..1 |
composite |
fuge:Parameters
|
| Mass |
Mass |
The mass of substance used in the protocol.
|
0..1 to 0..1 |
composite |
fuge:Parameters
|
| SubstanceCharacteristics |
fuge:OntologyTerm |
The characteristics of the substance.
|
0..* to 0..* |
none |
none
|
| SubstanceType |
fuge:OntologyTerm |
The type of substance, the substance name has not been given as
free text in the SubstanceAction.
|
0..* to 0..1 |
none |
none
|
| Volume |
VolumeParameter |
The volume of the substance.
|
0..1 to 0..1 |
composite |
fuge:Parameters
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.SelectSubstance.SubstanceActionType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ActionType">
<xsd:sequence>
<xsd:element ref="gelml:Concentration" minOccurs="0" maxOccurs="1"/>
<xsd:element ref="gelml:Mass" minOccurs="0" maxOccurs="1"/>
<xsd:element name="_substanceCharacteristics" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="OntologyTerm_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="_substanceType" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:attribute name="OntologyTerm_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
<xsd:element ref="gelml:VolumeParameter" minOccurs="0" maxOccurs="1"/>
</xsd:sequence>
<xsd:attribute name="substanceName" type="xsd:string"/>
<xsd:attribute name="actionText" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="SubstanceAction" type="gelml:GelML.SelectSubstance.SubstanceActionType" abstract="false" substitutionGroup="fuge:Action" />
|
GelML.SelectSubstance.TemporalSubstanceAction
Inheritance hierarchy:
TemporalSubstanceAction
-->
SubstanceAction
-->
Action
-->
Identifiable
-->
Describable
Documentation:
The use of a substance within a protocol at a particular time
point or for a particular duration.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| ActionTime |
TimeParameter |
The duration or time point that the TemporalSubstanceAction
applies to.
|
0..1 to 1..1 |
composite |
fuge:Parameters
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.SelectSubstance.TemporalSubstanceActionType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:GelML.SelectSubstance.SubstanceActionType">
<xsd:sequence>
<xsd:element ref="gelml:TimeParameter" minOccurs="1" maxOccurs="1"/>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="TemporalSubstanceAction" type="gelml:GelML.SelectSubstance.TemporalSubstanceActionType" abstract="false" substitutionGroup="gelml:SubstanceAction" />
|
GelML.SelectSubstance.SubstanceMixtureProtocol
Inheritance hierarchy:
SubstanceMixtureProtocol
-->
Protocol
-->
Parameterizable
-->
Identifiable
-->
Describable
Documentation:
A Protocol representing the creation of a mixture of substances,
for example to be used for specifying the components of buffers,
solutions etc. If the actionText attribute of SubtanceAction is
not used, the SubstanceMixtureProtocol represents only the
components of the mixture and not the processes applied to them.
Attributes:
| Name | Documentation | Data type | Required |
| mixtureName |
The name of the mixture represented by this protocol.
|
string |
false |
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| SelectSubstances |
SubstanceAction |
The Substances used within the SubstanceMixtureProtocol, for
example to define the constituents of a buffer.
|
0..1 to 1..* |
composite |
none
|
| MixtureType |
fuge:OntologyTerm |
The type of mixture e.g. buffer, solution, protein complex etc.
|
0..* to 0..1 |
none |
none
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.SelectSubstance.SubstanceMixtureProtocolType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ProtocolType">
<xsd:sequence>
<xsd:element ref="gelml:SubstanceAction" minOccurs="1" maxOccurs="unbounded"/>
<xsd:element name="_mixtureType" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:attribute name="OntologyTerm_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
<xsd:attribute name="mixtureName" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="SubstanceMixtureProtocol" type="gelml:GelML.SelectSubstance.SubstanceMixtureProtocolType" abstract="false" substitutionGroup="fuge:Protocol" />
|
GelML.SelectSubstance.Duration
Inheritance hierarchy:
Duration
-->
TimeParameter
-->
Parameter
-->
Identifiable
-->
Describable
Documentation:
A duration parameter. Note: values for absolute or relative time
can be specified using the Parameter DefaultValue model.
XML Schema Complex Type specification:
<xsd:complexType name="GelML.SelectSubstance.DurationType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:GelML.SelectSubstance.TimeParameterType">
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Duration" type="gelml:GelML.SelectSubstance.DurationType" abstract="false" substitutionGroup="gelml:TimeParameter" />
|
GelML.SelectSubstance.TimePoint
Inheritance hierarchy:
TimePoint
-->
TimeParameter
-->
Parameter
-->
Identifiable
-->
Describable
Documentation:
A single time point. Note: values for absolute or relative time
can be specified using the Parameter DefaultValue model.
XML Schema Complex Type specification:
<xsd:complexType name="GelML.SelectSubstance.TimePointType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:GelML.SelectSubstance.TimeParameterType">
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="TimePoint" type="gelml:GelML.SelectSubstance.TimePointType" abstract="false" substitutionGroup="gelml:TimeParameter" />
|
GelML.SelectSubstance.TimeParameter (abstract)
Inheritance hierarchy:
TimeParameter
-->
Parameter
-->
Identifiable
-->
Describable
Documentation:
Abstract superclass representing Duration and TimePoints.
XML Schema Complex Type specification:
<xsd:complexType name="GelML.SelectSubstance.TimeParameterType" abstract = "true">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ParameterType">
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="TimeParameter" type="gelml:GelML.SelectSubstance.TimeParameterType" abstract="true" substitutionGroup="fuge:Parameter" />
|
GelML.SelectSubstance.Concentration
Inheritance hierarchy:
Concentration
-->
Parameter
-->
Identifiable
-->
Describable
Documentation:
The Concentration of a substance.
XML Schema Complex Type specification:
<xsd:complexType name="GelML.SelectSubstance.ConcentrationType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ParameterType">
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Concentration" type="gelml:GelML.SelectSubstance.ConcentrationType" abstract="false" substitutionGroup="fuge:Parameter" />
|
GelML.SelectSubstance.Mass
Inheritance hierarchy:
Mass
-->
Parameter
-->
Identifiable
-->
Describable
Documentation:
The mass of a substance.
XML Schema Complex Type specification:
<xsd:complexType name="GelML.SelectSubstance.MassType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ParameterType">
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Mass" type="gelml:GelML.SelectSubstance.MassType" abstract="false" substitutionGroup="fuge:Parameter" />
|
GelML.Gel2DProtocol.Gel2D
Inheritance hierarchy:
Gel2D
-->
ElectrophoresedGel
-->
Material
-->
Identifiable
-->
Describable
Documentation:
Gel2D is the material produced from a Gel2DApplication
representing the combination of the two gel substrates and the
proteins that have been separated.
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Gel2DProtocol.Gel2DType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:GelML.Gel.ElectrophoresedGelType">
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Gel2D" type="gelml:GelML.Gel2DProtocol.Gel2DType" abstract="false" substitutionGroup="gelml:ElectrophoresedGel" />
|
GelML.Gel2DProtocol.Gel2DProtocol
Inheritance hierarchy:
Gel2DProtocol
-->
Protocol
-->
Parameterizable
-->
Identifiable
-->
Describable
Documentation:
A protocol describing the procedure of 2D gel electrophoresis.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| SampleLoadingAction |
SampleLoadingAction |
A reference to the SampleLoadingAction.
|
0..1 to 1..* |
composite |
fuge:Actions
|
| FirstDimension |
FirstDimensionAction |
A reference to the FirstDimensionAction.
|
1..1 to 1..1 |
composite |
fuge:Actions
|
| SecondDimension |
SecondDimensionAction |
A reference to the SecondDimensionAction.
|
1..1 to 1..1 |
composite |
fuge:Actions
|
| InterDimensionAction |
InterDimensionAction |
A reference to the Action that defines Protocols applied between
the first and second dimension ElectrophoresisProtocols.
|
0..1 to 0..* |
composite |
fuge:Actions
|
| DetectionAction |
DetectionAction |
The DetectionAction that references the DetectionProtocol
applied within the Gel2DProtocol.
|
0..1 to 0..* |
composite |
fuge:Actions
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Gel2DProtocol.Gel2DProtocolType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ProtocolType">
<xsd:sequence>
<xsd:element ref="gelml:SampleLoadingAction" minOccurs="1" maxOccurs="unbounded"/>
<xsd:element ref="gelml:FirstDimensionAction" minOccurs="1" maxOccurs="1"/>
<xsd:element ref="gelml:SecondDimensionAction" minOccurs="1" maxOccurs="1"/>
<xsd:element ref="gelml:InterDimensionAction" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="gelml:DetectionAction" minOccurs="0" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Gel2DProtocol" type="gelml:GelML.Gel2DProtocol.Gel2DProtocolType" abstract="false" substitutionGroup="fuge:Protocol" />
|
GelML.Gel2DProtocol.Gel2DApplication
Inheritance hierarchy:
Gel2DApplication
-->
ProtocolApplication
-->
ParameterizableApplication
-->
Identifiable
-->
Describable
Documentation:
Gel2DApplication is the application of a Gel2DProtocol. An
instance of Gel2DApplication should reference
SampleLoadingApplication, ElectrophoresisApplication,
DetectionApplications and GenericProtocolApplication as its
sub-steps, as defined by the referenced Gel2DProtocol.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| OutputGel2D |
Gel2D |
The instance of Gel2D representing the combination of the two
gel substrates and the proteins that have been separated.
|
1..1 to 1..1 |
composite |
fuge:OutputMaterials
|
| InputFirstDimension |
Gel |
Reference to the Gel on which the first dimension separation is
performed.
|
0..1 to 1..1 |
composite |
fuge:InputCompleteMaterials
|
| InputSecondDimension |
Gel |
Reference to the Gel on which the second dimension separation is
performed.
|
0..1 to 1..1 |
composite |
fuge:InputCompleteMaterials
|
| Gel2DProtocol |
Gel2DProtocol |
The Gel2DProtocol that has been run.
|
0..* to 1..1 |
none |
fuge:Protocol
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Gel2DProtocol.Gel2DApplicationType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ProtocolApplicationType">
<xsd:sequence>
<xsd:element ref="gelml:Gel2D" minOccurs="1" maxOccurs="1"/>
<xsd:element name="_inputFirstDimension" minOccurs="1" maxOccurs="1">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="gelml:Gel" minOccurs="1" maxOccurs="1"/>
</xsd:sequence>
</xsd:complexType>
</xsd:element>
<xsd:element name="_inputSecondDimension" minOccurs="1" maxOccurs="1">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="gelml:Gel" minOccurs="1" maxOccurs="1"/>
</xsd:sequence>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
<xsd:attribute name="Gel2DProtocol_ref" use="required" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Gel2DApplication" type="gelml:GelML.Gel2DProtocol.Gel2DApplicationType" abstract="false" substitutionGroup="fuge:ProtocolApplication" />
|
GelML.Gel2DProtocol.FirstDimensionAction
Inheritance hierarchy:
FirstDimensionAction
-->
Action
-->
Identifiable
-->
Describable
Documentation:
An action to represent the order of the referenced
ElectrophoresisProtocol, with respect to other Actions performed
within this parent protocol.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| FirstDimensionProtocol |
ElectrophoresisProtocol |
The ElectrophoresisProtocol performed in the first dimension.
|
0..* to 1..1 |
none |
fuge:ChildProtocol
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Gel2DProtocol.FirstDimensionActionType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ActionType">
<xsd:attribute name="ElectrophoresisProtocol_ref" use="required" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="FirstDimensionAction" type="gelml:GelML.Gel2DProtocol.FirstDimensionActionType" abstract="false" substitutionGroup="fuge:Action" />
|
GelML.Gel2DProtocol.SecondDimensionAction
Inheritance hierarchy:
SecondDimensionAction
-->
Action
-->
Identifiable
-->
Describable
Documentation:
An action to represent the order of the referenced
ElectrophoresisProtocol, with respect to other Actions performed
within this parent protocol.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| SecondDimensionProtocol |
ElectrophoresisProtocol |
The ElectrophoresisProtocol performed in the second dimension.
|
0..* to 1..1 |
none |
fuge:ChildProtocol
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Gel2DProtocol.SecondDimensionActionType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ActionType">
<xsd:attribute name="ElectrophoresisProtocol_ref" use="required" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="SecondDimensionAction" type="gelml:GelML.Gel2DProtocol.SecondDimensionActionType" abstract="false" substitutionGroup="fuge:Action" />
|
GelML.Gel2DProtocol.DetectionAction
Inheritance hierarchy:
DetectionAction
-->
Action
-->
Identifiable
-->
Describable
Documentation:
An action to represent the order of the referenced
DetectionProtocol, with respect to other Actions performed
within this parent protocol.
Attributes:
| Name | Documentation | Data type | Required |
| dimension * |
If proteins have been detected on both the first and second
dimension gel, the dimension attribute should be used to
distinguish the DetectionProtocols.
|
int |
false |
*Attribute is mapped to an element in the XML Schema
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| DetectionProtocol |
DetectionProtocol |
The DetectionProtocol referenced from this Action.
|
0..* to 1..1 |
none |
none
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Gel2DProtocol.DetectionActionType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ActionType">
<xsd:element name="dimension" type="xsd:int" minOccurs="0" maxOccurs="1"/>
<xsd:attribute name="DetectionProtocol_ref" use="required" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="DetectionAction" type="gelml:GelML.Gel2DProtocol.DetectionActionType" abstract="false" substitutionGroup="fuge:Action" />
|
GelML.Gel1DProtocol.Gel1D
Inheritance hierarchy:
Gel1D
-->
ElectrophoresedGel
-->
Material
-->
Identifiable
-->
Describable
Documentation:
Gel1D is the material produced from a Gel1DApplication
representing the combination of the gel substrate with the
proteins that have been separated. Gel1D should be referenced by
a DetectionApplication to describe any detection agents that
have been applied.
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Gel1DProtocol.Gel1DType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:GelML.Gel.ElectrophoresedGelType">
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Gel1D" type="gelml:GelML.Gel1DProtocol.Gel1DType" abstract="false" substitutionGroup="gelml:ElectrophoresedGel" />
|
GelML.Gel1DProtocol.Gel1DApplication
Inheritance hierarchy:
Gel1DApplication
-->
ProtocolApplication
-->
ParameterizableApplication
-->
Identifiable
-->
Describable
Documentation:
The application of a Gel1DProtocol. Gel1DApplication should
reference (via ActionApplication) SampleLoadingApplication,
ElectrophoresisApplication and DetectionApplication matching the
structure of the referenced Gel1DProtocol.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| OutputGel1D |
Gel1D |
The gel following the application of a Gel1DProtocol.
|
1..1 to 1..1 |
composite |
fuge:OutputMaterials
|
| InputGel |
Gel |
The gel material on which this Gel1DProtocol acts.
|
0..1 to 1..1 |
composite |
fuge:InputCompleteMaterials
|
| Gel1DProtocol |
Gel1DProtocol |
The protocol used in this Gel1DProtocolApplication.
|
0..* to 1..1 |
none |
fuge:Protocol
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Gel1DProtocol.Gel1DApplicationType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ProtocolApplicationType">
<xsd:sequence>
<xsd:element ref="gelml:Gel1D" minOccurs="1" maxOccurs="1"/>
<xsd:element name="_inputGel" minOccurs="1" maxOccurs="1">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="gelml:Gel" minOccurs="1" maxOccurs="1"/>
</xsd:sequence>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
<xsd:attribute name="Gel1DProtocol_ref" use="required" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Gel1DApplication" type="gelml:GelML.Gel1DProtocol.Gel1DApplicationType" abstract="false" substitutionGroup="fuge:ProtocolApplication" />
|
GelML.Gel1DProtocol.Gel1DProtocol
Inheritance hierarchy:
Gel1DProtocol
-->
Protocol
-->
Parameterizable
-->
Identifiable
-->
Describable
Documentation:
A protocol describing the procedure of 1D gel electrophoresis.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| SampleLoadingAction |
SampleLoadingAction |
The action that specifies how SampleLoadingProtocols are used
within the Gel1DProtocol. The dimension attribute of
SampleLoadingAction is not normally required here.
|
0..1 to 1..* |
composite |
fuge:Actions
|
| ElectrophoresisAction |
ElectrophoresisAction |
A reference to an action that specifes the performing of
Electrophoresis within the Gel1DProtocol.
|
0..1 to 1..1 |
composite |
fuge:Actions
|
| DetectionAction |
DetectionAction |
The DetectionAction that references the DetectionProtocol
applied within the Gel1DProtocol.
|
0..1 to 0..* |
composite |
fuge:Actions
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Gel1DProtocol.Gel1DProtocolType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ProtocolType">
<xsd:sequence>
<xsd:element ref="gelml:SampleLoadingAction" minOccurs="1" maxOccurs="unbounded"/>
<xsd:element ref="gelml:ElectrophoresisAction" minOccurs="1" maxOccurs="1"/>
<xsd:element ref="gelml:DetectionAction" minOccurs="0" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Gel1DProtocol" type="gelml:GelML.Gel1DProtocol.Gel1DProtocolType" abstract="false" substitutionGroup="fuge:Protocol" />
|
GelML.Detection.DetectionApplication (abstract)
Inheritance hierarchy:
DetectionApplication
-->
ProtocolApplication
-->
ParameterizableApplication
-->
Identifiable
-->
Describable
Documentation:
Abstract superclass to represent applications of a
DetectionProtocol. Its subclasses DirectDetection and
IndirectDetection capture the application of the procedure. If
two stainings are done, the destaining should be the first stage
of the second staining process, as represented in the
DetectionProtocol.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| AppliedDetectionProtocol |
DetectionProtocol |
The DetectionProtocol that has been run.
|
0..* to 1..1 |
none |
fuge:Protocol
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Detection.DetectionApplicationType" abstract = "true">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ProtocolApplicationType">
<xsd:attribute name="DetectionProtocol_ref" use="required" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="DetectionApplication" type="gelml:GelML.Detection.DetectionApplicationType" abstract="true" substitutionGroup="fuge:ProtocolApplication" />
|
GelML.Detection.DetectionMedium
Inheritance hierarchy:
DetectionMedium
-->
Material
-->
Identifiable
-->
Describable
Documentation:
The medium on which proteins are detected in processes such as
autoradiography (example photographic film). The type of
material should be captured by the inherited MaterialType
association.
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Detection.DetectionMediumType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Bio.Material.MaterialType">
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="DetectionMedium" type="gelml:GelML.Detection.DetectionMediumType" abstract="false" substitutionGroup="fuge:Material" />
|
GelML.Detection.DetectionProtocol
Inheritance hierarchy:
DetectionProtocol
-->
Protocol
-->
Parameterizable
-->
Identifiable
-->
Describable
Documentation:
The process by which proteins are to be detected on a gel,
either by a direct process e.g. staining or by an indirect
process e.g. Western blot. The type of protocol should be
specified using the types association inherited from Protocol
Attributes:
| Name | Documentation | Data type | Required |
| protocolText |
The text of the detection protocol.
|
string |
false |
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| ApplyAgent |
SubstanceAction |
The detection agent used in the DetectionProtocol. If the
duration or time point of the agent application is to be
specifed, this should be done using TemporalSubstanceAction
(subclass of SubstanceAction).
|
0..1 to 1..* |
composite |
fuge:Actions
|
| DetectionEquipment |
fuge:GenericEquipment |
Any equipment used in the DetectionProtocol.
|
0..* to 0..* |
none |
fuge:Equipment
|
| Buffers |
AddBufferAction |
The buffers used with the DetectionProtocol.
|
0..1 to 0..* |
composite |
fuge:Actions
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Detection.DetectionProtocolType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ProtocolType">
<xsd:sequence>
<xsd:element ref="gelml:SubstanceAction" minOccurs="1" maxOccurs="unbounded"/>
<xsd:element name="_detectionEquipment" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="GenericEquipment_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
<xsd:element ref="gelml:AddBufferAction" minOccurs="0" maxOccurs="unbounded"/>
</xsd:sequence>
<xsd:attribute name="protocolText" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="DetectionProtocol" type="gelml:GelML.Detection.DetectionProtocolType" abstract="false" substitutionGroup="fuge:Protocol" />
|
GelML.Detection.DirectDetection
Inheritance hierarchy:
DirectDetection
-->
DetectionApplication
-->
ProtocolApplication
-->
ParameterizableApplication
-->
Identifiable
-->
Describable
Documentation:
DirectDetection represents the application of a
DetectionProtocol in which a detection agent (stain or label) is
applied directly to a gel.
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Detection.DirectDetectionType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:GelML.Detection.DetectionApplicationType">
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="DirectDetection" type="gelml:GelML.Detection.DirectDetectionType" abstract="false" substitutionGroup="gelml:DetectionApplication" />
|
GelML.Detection.IndirectDetection
Inheritance hierarchy:
IndirectDetection
-->
DetectionApplication
-->
ProtocolApplication
-->
ParameterizableApplication
-->
Identifiable
-->
Describable
Documentation:
IndirectDetection represents the application of a
DetectionProtocol in which a detection agent (stain or label) is
applied to a TransferMedium (e.g. a membrane) following proteins
being transfered from a gel. Subsequently, the proteins may be
detected on a DetectionMedium, such as photographic film.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| TransferMedium |
TransferMedium |
The TransferMedium medium used in an indirect detection process,
such as an immobilizing membrane used in a Western blot.
|
0..1 to 1..1 |
composite |
fuge:InputCompleteMaterials
|
| DetectionMedium |
DetectionMedium |
The DetectionMedium used in an IndirectDetection process.
|
0..1 to 0..1 |
composite |
fuge:InputCompleteMaterials
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Detection.IndirectDetectionType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:GelML.Detection.DetectionApplicationType">
<xsd:sequence>
<xsd:element ref="gelml:TransferMedium" minOccurs="1" maxOccurs="1"/>
<xsd:element ref="gelml:DetectionMedium" minOccurs="0" maxOccurs="1"/>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="IndirectDetection" type="gelml:GelML.Detection.IndirectDetectionType" abstract="false" substitutionGroup="gelml:DetectionApplication" />
|
GelML.Detection.TransferMedium
Inheritance hierarchy:
TransferMedium
-->
Material
-->
Identifiable
-->
Describable
Documentation:
The medium proteins are transfered to during Indirect detection
of proteins, such as the membrane in a Western blot. The type of
material should be captured by the inherited MaterialType
association.
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Detection.TransferMediumType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Bio.Material.MaterialType">
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="TransferMedium" type="gelml:GelML.Detection.TransferMediumType" abstract="false" substitutionGroup="fuge:Material" />
|
GelML.Electrophoresis.ElectrophoresisStep
Inheritance hierarchy:
ElectrophoresisStep
-->
Action
-->
Identifiable
-->
Describable
Documentation:
The protocol for one step within an ElectrophoresisProtocol. The
referenced parameters capture the details of the step.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| ElectricParameter |
ElectricalParameter |
The value at which the current, voltage or power is set at for
the duration of this step.
|
0..1 to 1..1 |
composite |
fuge:Parameters
|
| StepTime |
TimeParameter |
The duration or time point of this ElectrophoresisStep with
respect to the ElectrophoresisProtocol.
|
0..1 to 0..1 |
composite |
fuge:Parameters
|
| OtherParameters |
fuge:GenericParameter |
Other parameters that are used during this step.
|
0..1 to 0..* |
composite |
fuge:Parameters
|
| StepTemperature |
Temperature |
The temperature during this step.
|
0..1 to 0..1 |
composite |
fuge:Parameters
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Electrophoresis.ElectrophoresisStepType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ActionType">
<xsd:sequence>
<xsd:element ref="gelml:ElectricalParameter" minOccurs="1" maxOccurs="1"/>
<xsd:element ref="gelml:TimeParameter" minOccurs="0" maxOccurs="1"/>
<xsd:element ref="fuge:GenericParameter" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="gelml:Temperature" minOccurs="0" maxOccurs="1"/>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="ElectrophoresisStep" type="gelml:GelML.Electrophoresis.ElectrophoresisStepType" abstract="false" substitutionGroup="fuge:Action" />
|
GelML.Electrophoresis.ElectricalParameter
Inheritance hierarchy:
ElectricalParameter
-->
Parameter
-->
Identifiable
-->
Describable
Documentation:
A class to represent the current, voltage, power or volthours
etc. in each step.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| ElectricalSetting |
fuge:OntologyTerm |
The electrical setting that the parameter value applies to, such
as: hold, maximum, gradient and so on.
|
0..* to 0..1 |
none |
none
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Electrophoresis.ElectricalParameterType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ParameterType">
<xsd:sequence>
<xsd:element name="_electricalSetting" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:attribute name="OntologyTerm_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="ElectricalParameter" type="gelml:GelML.Electrophoresis.ElectricalParameterType" abstract="false" substitutionGroup="fuge:Parameter" />
|
GelML.Electrophoresis.ElectrophoresisAction
Inheritance hierarchy:
ElectrophoresisAction
-->
Action
-->
Identifiable
-->
Describable
Documentation:
A reference to the ElectrophoreisProtocol performed within the
parent protocol.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| ElectrophoresisProtocol |
ElectrophoresisProtocol |
A reference to the ElectrophoresisProtocol
|
0..* to 1..1 |
none |
fuge:ChildProtocol
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Electrophoresis.ElectrophoresisActionType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ActionType">
<xsd:attribute name="ElectrophoresisProtocol_ref" use="required" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="ElectrophoresisAction" type="gelml:GelML.Electrophoresis.ElectrophoresisActionType" abstract="false" substitutionGroup="fuge:Action" />
|
GelML.Electrophoresis.ElectrophoresisApplication
Inheritance hierarchy:
ElectrophoresisApplication
-->
ProtocolApplication
-->
ParameterizableApplication
-->
Identifiable
-->
Describable
Documentation:
An application of the referenced ElectrophoresisProtocol.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| ElectrophoresisProtocol |
ElectrophoresisProtocol |
The ElectrophoresisProtocol that is applied.
|
0..* to 1..1 |
none |
fuge:Protocol
|
| ElectrophoresisGel |
Gel |
The Gel on which Electrophoresis takes place. The referenced
gels must be one of the gels associated as inputs to
Gel1DApplication, Gel2DApplication or OtherGelApplication.
|
0..* to 1..1 |
none |
fuge:InputCompleteMaterials
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Electrophoresis.ElectrophoresisApplicationType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ProtocolApplicationType">
<xsd:attribute name="ElectrophoresisProtocol_ref" use="required" type="xsd:string"/>
<xsd:attribute name="Gel_ref" use="required" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="ElectrophoresisApplication" type="gelml:GelML.Electrophoresis.ElectrophoresisApplicationType" abstract="false" substitutionGroup="fuge:ProtocolApplication" />
|
GelML.Electrophoresis.ElectrophoresisProtocol
Inheritance hierarchy:
ElectrophoresisProtocol
-->
Protocol
-->
Parameterizable
-->
Identifiable
-->
Describable
Documentation:
A protocol for capturing the details of electrophoresis. The
running conditions applied to the gel should be given in terms
of voltages versus time/kilovolt hours, (or appropriate
measurements) and temperature. The voltage mode profile (eg.
step and hold, or gradient) should be given as ontology terms on
ElectricalParameter.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| Buffers |
AddBufferAction |
Buffers other than the running buffer used in the
ElectrophoresisProtocol.
|
0..1 to 0..* |
composite |
fuge:Actions
|
| ElectrophoresisEquipment |
fuge:GenericEquipment |
Any equipment used during electrophoresis, such as gel tanks or
power packs.
|
0..* to 0..* |
none |
fuge:Equipment
|
| ProtocolTemperature |
Temperature |
The temperature at which the entire protocol is performed at.
Note a value should either be provided here or on individual
steps (not on both).
|
0..1 to 0..1 |
composite |
fuge:Parameters
|
| ElectophoresisSteps |
ElectrophoresisStep |
The steps that comprise the ElectrophoresisProtocol.
|
1..1 to 1..* |
composite |
fuge:Actions
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Electrophoresis.ElectrophoresisProtocolType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ProtocolType">
<xsd:sequence>
<xsd:element ref="gelml:AddBufferAction" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element name="_electrophoresisEquipment" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="GenericEquipment_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
<xsd:element ref="gelml:Temperature" minOccurs="0" maxOccurs="1"/>
<xsd:element ref="gelml:ElectrophoresisStep" minOccurs="1" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="ElectrophoresisProtocol" type="gelml:GelML.Electrophoresis.ElectrophoresisProtocolType" abstract="false" substitutionGroup="fuge:Protocol" />
|
GelML.Electrophoresis.Temperature
Inheritance hierarchy:
Temperature
-->
Parameter
-->
Identifiable
-->
Describable
Documentation:
Temperature parameter.
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Electrophoresis.TemperatureType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ParameterType">
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Temperature" type="gelml:GelML.Electrophoresis.TemperatureType" abstract="false" substitutionGroup="fuge:Parameter" />
|
GelML.Electrophoresis.AddBufferAction
Inheritance hierarchy:
AddBufferAction
-->
Action
-->
Identifiable
-->
Describable
Documentation:
An action to represent the use of buffers in the Protocol by
reference to a SubstanceMixtureProtocol that represents the
buffer and optionally the method of producing the buffer.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| SubstanceMixtureProtocol |
SubstanceMixtureProtocol |
The specification of the buffer and its components.
|
0..* to 1..1 |
none |
fuge:ChildProtocol
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Electrophoresis.AddBufferActionType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ActionType">
<xsd:attribute name="SubstanceMixtureProtocol_ref" use="required" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="AddBufferAction" type="gelml:GelML.Electrophoresis.AddBufferActionType" abstract="false" substitutionGroup="fuge:Action" />
|
GelML.Excision.BoundaryChain
Inheritance hierarchy:
BoundaryChain
-->
FeatureLocation
-->
Describable
Documentation:
A boundary chain is a notation for specifying an arbitrarily
shaped location on an image. A starting point is given
(startXCoordinate and startYCoordinate) and a set of directional
steps. See chainCode documentation for this encoding.
Attributes:
| Name | Documentation | Data type | Required |
| startXCoordinate |
The x-coordinate of the starting position of the chain code.
|
int |
true |
| startYCoordinate |
The y-coordinate of the starting position of the chain code.
|
int |
true |
| chainCode |
A chain code denotes the shape of feature using directional
steps of one pixel, starting from the specified X and Y
coordinates. Each step is encoded using the following
convention:
0 = E; 1 = NE; 2 = N; 3 = NW; 4 = W; 5 = SW; 6 = S; 7 = SE; See
the specification document for a diagram.
In-house representations of GelML are free to use a compression
algorithm over the chain code, such as run length encoding, but
for data exchange the code should be uncompressed as shown in
the example (since entire data files can be compressed using Zip
or Gz for data transfer).
Note: In XML Schema, the chainCode is represented as an
xs:integer, which covers the infinite set of integers. Care
should be taken when mapping to other platforms, such as Java,
i.e. this will not map to a Java Integer.
|
integer |
true |
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Excision.BoundaryChainType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:GelML.Excision.FeatureLocationType">
<xsd:attribute name="startXCoordinate" use="required" type="xsd:int"/>
<xsd:attribute name="startYCoordinate" use="required" type="xsd:int"/>
<xsd:attribute name="chainCode" use="required" type="xsd:integer"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="BoundaryChain" type="gelml:GelML.Excision.BoundaryChainType" abstract="false" substitutionGroup="gelml:FeatureLocation" />
|
GelML.Excision.Circle
Inheritance hierarchy:
Circle
-->
FeatureLocation
-->
Describable
Documentation:
Circle is for defining a circular location on an image.
Attributes:
| Name | Documentation | Data type | Required |
| pixelRadius |
Radius of the Circle in pixels.
|
int |
true |
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Excision.CircleType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:GelML.Excision.FeatureLocationType">
<xsd:attribute name="pixelRadius" use="required" type="xsd:int"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Circle" type="gelml:GelML.Excision.CircleType" abstract="false" substitutionGroup="gelml:FeatureLocation" />
|
GelML.Excision.ExcisedSample
Inheritance hierarchy:
ExcisedSample
-->
Material
-->
Identifiable
-->
Describable
Documentation:
A sample excised from a gel. These materials can be referenced
by formats modelling other techniques, such as mass
spectrometry.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| SourceLocation |
GelLocation |
A reference to the location that this sample was excised from.
|
0..1 to 1..1 |
none |
none
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Excision.ExcisedSampleType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Bio.Material.MaterialType">
<xsd:attribute name="GelLocation_ref" use="required" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="ExcisedSample" type="gelml:GelML.Excision.ExcisedSampleType" abstract="false" substitutionGroup="fuge:Material" />
|
GelML.Excision.ExcisionApplication
Inheritance hierarchy:
ExcisionApplication
-->
ProtocolApplication
-->
ParameterizableApplication
-->
Identifiable
-->
Describable
Documentation:
The Application of a protocol that describes the excision of
locations on gels.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| InputImageLocations |
LocationSet |
The set of locations on an image of a gel.
|
0..1 to 0..1 |
composite |
fuge:InputData
|
| OutputSamples |
ExcisedSample |
The samples produced from excision.
|
1..1 to 0..* |
composite |
fuge:OutputMaterials
|
| SourceGel |
ElectrophoresedGel |
The ElectrophoresedGel from which locations are excised.
|
0..* to 1..1 |
none |
fuge:InputCompleteMaterials
|
| InputGelLocations |
LocationSet |
The set of locations on a gel as determined by, for instance, a
robotic spot picker at runtime.
|
0..1 to 0..1 |
composite |
fuge:InputData
|
| ExcisionProtocol |
fuge:GenericProtocol |
The Protocol applied for excision. Note that equipment and
software used should be provided using the associations from
GenericProtocol to GenericEquipment and GenericSoftware.
|
0..* to 1..1 |
none |
fuge:Protocol
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Excision.ExcisionApplicationType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ProtocolApplicationType">
<xsd:sequence>
<xsd:element name="_inputImageLocations" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="gelml:LocationSet" minOccurs="1" maxOccurs="1"/>
</xsd:sequence>
</xsd:complexType>
</xsd:element>
<xsd:element ref="gelml:ExcisedSample" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element name="_inputGelLocations" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="gelml:LocationSet" minOccurs="1" maxOccurs="1"/>
</xsd:sequence>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
<xsd:attribute name="ElectrophoresedGel_ref" use="required" type="xsd:string"/>
<xsd:attribute name="GenericProtocol_ref" use="required" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="ExcisionApplication" type="gelml:GelML.Excision.ExcisionApplicationType" abstract="false" substitutionGroup="fuge:ProtocolApplication" />
|
GelML.Excision.FeatureLocation
Inheritance hierarchy:
FeatureLocation
-->
Describable
Documentation:
Abstract superclass representing the different types of method
that could be used to identify a location.
Attributes:
| Name | Documentation | Data type | Required |
| centroidX |
The centroid position on the x-axis of the image.
|
int |
false |
| centroidY |
The centroid position on the y-axis of the image.
|
int |
false |
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Excision.FeatureLocationType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.DescribableType">
<xsd:attribute name="centroidX" type="xsd:int"/>
<xsd:attribute name="centroidY" type="xsd:int"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="FeatureLocation" type="gelml:GelML.Excision.FeatureLocationType" abstract="false" substitutionGroup="fuge:Describable" />
|
GelML.Excision.GelLocation
Inheritance hierarchy:
GelLocation
-->
Identifiable
-->
Describable
Documentation:
A single location on a gel.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| Measures |
LocationMeasure |
Measures or attributes for each GelLocation.
|
1..1 to 0..* |
composite |
none
|
| Location |
FeatureLocation |
The location of the feature.
|
1..1 to 0..1 |
composite |
none
|
| MappedLocation |
GelLocation |
This is for mapping a Location from one set to another, for
example for mapping a gel coordinate to an image coordinate for
a robotic spot picker.
|
0..1 to 0..1 |
none |
none
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Excision.GelLocationType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.IdentifiableType">
<xsd:sequence>
<xsd:element ref="gelml:LocationMeasure" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="gelml:FeatureLocation" minOccurs="0" maxOccurs="1"/>
<xsd:element name="_mappedLocation" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:attribute name="GelLocation_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="GelLocation" type="gelml:GelML.Excision.GelLocationType" abstract="false" substitutionGroup="fuge:Identifiable" />
|
GelML.Excision.LocationMeasure
Inheritance hierarchy:
LocationMeasure
-->
Describable
Documentation:
A measured value, property or annotation about a GelLocation,
such as predicted MW or pI.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| Evidence |
fuge:OntologyTerm |
The evidence for this measure, such as molecular weight markers,
mass spectrometry etc.
|
0..* to 0..1 |
none |
none
|
| Measurement |
fuge:Measurement |
The value for this measure.
|
0..1 to 1..1 |
composite |
none
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Excision.LocationMeasureType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.DescribableType">
<xsd:sequence>
<xsd:element name="_evidence" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:attribute name="OntologyTerm_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
<xsd:element ref="fuge:Measurement" minOccurs="1" maxOccurs="1"/>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="LocationMeasure" type="gelml:GelML.Excision.LocationMeasureType" abstract="false" substitutionGroup="fuge:Describable" />
|
GelML.Excision.LocationSet
Inheritance hierarchy:
LocationSet
-->
InternalData
-->
Data
-->
Identifiable
-->
Describable
Documentation:
LocationSet represents a set of locations on a gel image.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| GelLane |
GelLane |
A reference to the lane of a gel from which locations are being
excised. A gel lane should only be supplied if appropriate, e.g.
if this is a Gel1D.
|
0..* to 0..1 |
none |
none
|
| GelLocations |
GelLocation |
The set of GelLocations.
|
1..1 to 0..* |
composite |
none
|
| SourceImage |
Image |
The image of a gel that these locations refer to.
|
0..* to 0..1 |
none |
none
|
| LocationEvidence |
fuge:ExternalData |
The evidence or source file for this location set. The
referenced file should be in the GelInfoML format when it is
finalised.
|
0..* to 0..1 |
none |
none
|
| SetType |
fuge:OntologyTerm |
The type of LocationSet e.g. ImageSet, GelSet.
|
0..* to 0..1 |
none |
none
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Excision.LocationSetType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Bio.Data.InternalDataType">
<xsd:sequence>
<xsd:element ref="gelml:GelLocation" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element name="_locationEvidence" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:attribute name="ExternalData_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="_setType" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:attribute name="OntologyTerm_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
<xsd:attribute name="GelLane_ref" type="xsd:string"/>
<xsd:attribute name="Image_ref" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="LocationSet" type="gelml:GelML.Excision.LocationSetType" abstract="false" substitutionGroup="fuge:InternalData" />
|
GelML.Excision.Rectangle
Inheritance hierarchy:
Rectangle
-->
FeatureLocation
-->
Describable
Documentation:
Rectangle is for defining a rectangular location on an image.
The X/Y coordinates correspond with the upper left corner of the
rectangle.
Attributes:
| Name | Documentation | Data type | Required |
| xCoordinate |
The X-Coordinate of the upper left corner of the rectangle.
|
int |
true |
| yCoordinate |
The Y-Coordinate of the upper left corner of the rectangle.
|
int |
true |
| pixelXSize |
The size of the rectangle along the X axis.
|
int |
true |
| pixelYSize |
The size of the rectangle along the Y axis.
|
int |
true |
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Excision.RectangleType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:GelML.Excision.FeatureLocationType">
<xsd:attribute name="xCoordinate" use="required" type="xsd:int"/>
<xsd:attribute name="yCoordinate" use="required" type="xsd:int"/>
<xsd:attribute name="pixelXSize" use="required" type="xsd:int"/>
<xsd:attribute name="pixelYSize" use="required" type="xsd:int"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Rectangle" type="gelml:GelML.Excision.RectangleType" abstract="false" substitutionGroup="gelml:FeatureLocation" />
|
GelML.Excision.BoundaryPointSet
Inheritance hierarchy:
BoundaryPointSet
-->
FeatureLocation
-->
Describable
Documentation:
A set of boundary points defining a location on a gel. The
BoundaryPoints are inclusive i.e. each point defines the
boundary and part of the location.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| BoundaryPoints |
Point |
The individual boundary points that define the location on the
gel.
|
1..1 to 1..* |
composite |
none
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Excision.BoundaryPointSetType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:GelML.Excision.FeatureLocationType">
<xsd:sequence>
<xsd:element ref="gelml:Point" minOccurs="1" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="BoundaryPointSet" type="gelml:GelML.Excision.BoundaryPointSetType" abstract="false" substitutionGroup="gelml:FeatureLocation" />
|
GelML.Excision.Point
Inheritance hierarchy:
Point
-->
Describable
Documentation:
A single boundary point used in a BoundaryPointSet.
Attributes:
| Name | Documentation | Data type | Required |
| xCoordinate |
x-coordinate of the boundary point.
|
int |
true |
| yCoordinate |
y-coordinate of the boundary point.
|
int |
true |
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Excision.PointType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.DescribableType">
<xsd:attribute name="xCoordinate" use="required" type="xsd:int"/>
<xsd:attribute name="yCoordinate" use="required" type="xsd:int"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Point" type="gelml:GelML.Excision.PointType" abstract="false" substitutionGroup="fuge:Describable" />
|
GelML.Gel.ElectrophoresedGel (abstract)
Inheritance hierarchy:
ElectrophoresedGel
-->
Material
-->
Identifiable
-->
Describable
Documentation:
Abstract superclass for describing gels following
electrophoresis.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| GelLaneReference |
GelLane |
A reference to the GelLanes defined as part of the Gel substrate
that this ElectrophoresedGel came from.
|
0..1 to 0..* |
none |
none
|
| SeparationRange |
SeparationRange |
The separation range and type of separation performed on this
gel. (Example pH range 4-7).
|
1..1 to 0..* |
composite |
none
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Gel.ElectrophoresedGelType" abstract = "true">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Bio.Material.MaterialType">
<xsd:sequence>
<xsd:element name="_gelLaneReference" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="GelLane_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
<xsd:element ref="gelml:SeparationRange" minOccurs="0" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="ElectrophoresedGel" type="gelml:GelML.Gel.ElectrophoresedGelType" abstract="true" substitutionGroup="fuge:Material" />
|
GelML.Gel.Gel
Inheritance hierarchy:
Gel
-->
Material
-->
Identifiable
-->
Describable
Documentation:
The gel matrix used in any dimension of an electrophoresis
assay.
Attributes:
| Name | Documentation | Data type | Required |
| separationDimension |
The dimension this gel separates in e.g. for 2D electrophoresis,
one Gel separationDimension = 1, other Gel separationDimension =
2.
|
int |
false |
| batchNumber |
The manufacturer's batch number for the gel.
|
string |
false |
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| GelLanes |
GelLane |
The GelLanes on this Gel.
|
1..1 to 0..* |
composite |
fuge:Components
|
| ComponentGels |
Gel |
The association can specify component gels, for example to
represent a stacking gel.
|
0..1 to 0..* |
composite |
fuge:Components
|
| PercentAcrylamide |
fuge:Measurement |
The percentage acrylamide in the gel.
|
0..1 to 0..1 |
composite |
none
|
| CrossLinkerRatio |
AcrylamideToCrossLinker |
The acrylamide:bisacrylamide ratio in the gel.
|
1..1 to 0..1 |
composite |
none
|
| OtherGelConstituents |
MeasuredMaterial |
Other constituents of the gel (not specified elsewhere) with
measurements, such as the concentration of SDS.
|
0..1 to 0..* |
none |
fuge:Components
|
| Model |
fuge:OntologyTerm |
The model number of the gel. If no suitable CV of model numbers
exist, the model number is encoded as the term and as the
termAccession. The OntologySource is the URI of the company
producing the gel.
|
0..* to 0..1 |
none |
none
|
| GelDimensions |
Dimensions |
The physical dimensions of the gel. The term should support
values for the three dimensions and units.
|
1..1 to 0..1 |
composite |
none
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Gel.GelType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Bio.Material.MaterialType">
<xsd:sequence>
<xsd:element ref="gelml:GelLane" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element name="_componentGels" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="gelml:Gel" minOccurs="1" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:complexType>
</xsd:element>
<xsd:element name="_percentAcrylamide" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="fuge:Measurement" minOccurs="1" maxOccurs="1"/>
</xsd:sequence>
</xsd:complexType>
</xsd:element>
<xsd:element ref="gelml:AcrylamideToCrossLinker" minOccurs="0" maxOccurs="1"/>
<xsd:element name="_otherGelConstituents" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="MeasuredMaterial_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="_model" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:attribute name="OntologyTerm_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
<xsd:element ref="gelml:Dimensions" minOccurs="0" maxOccurs="1"/>
</xsd:sequence>
<xsd:attribute name="separationDimension" type="xsd:int"/>
<xsd:attribute name="batchNumber" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Gel" type="gelml:GelML.Gel.GelType" abstract="false" substitutionGroup="fuge:Material" />
|
GelML.Gel.GelLane
Inheritance hierarchy:
GelLane
-->
Material
-->
Identifiable
-->
Describable
Documentation:
A lane on a gel.
Attributes:
| Name | Documentation | Data type | Required |
| laneNumber |
The lane number with respect to the parent gel.
|
int |
true |
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Gel.GelLaneType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Bio.Material.MaterialType">
<xsd:attribute name="laneNumber" use="required" type="xsd:int"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="GelLane" type="gelml:GelML.Gel.GelLaneType" abstract="false" substitutionGroup="fuge:Material" />
|
GelML.Gel.GelManufactureApplication
Inheritance hierarchy:
GelManufactureApplication
-->
ProtocolApplication
-->
ParameterizableApplication
-->
Identifiable
-->
Describable
Documentation:
The application of a protocol that defines how a gel was
produced.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| ProductGel |
Gel |
The gel produced by the GelManufactureApplication.
|
0..1 to 1..1 |
none |
fuge:OutputMaterials
|
| InputGelMaterials |
fuge:GenericMaterialMeasurement |
Measured quantities of materials used to create the referenced
gel.
|
0..1 to 0..* |
composite |
fuge:InputMaterials
|
| GelManufactureProtocol |
fuge:GenericProtocol |
The protocol applied in the GelManufactureApplication.
|
0..* to 1..1 |
none |
fuge:Protocol
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Gel.GelManufactureApplicationType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ProtocolApplicationType">
<xsd:sequence>
<xsd:element name="_productGel" minOccurs="1" maxOccurs="1">
<xsd:complexType>
<xsd:attribute name="Gel_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
<xsd:element ref="fuge:GenericMaterialMeasurement" minOccurs="0" maxOccurs="unbounded"/>
</xsd:sequence>
<xsd:attribute name="GenericProtocol_ref" use="required" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="GelManufactureApplication" type="gelml:GelML.Gel.GelManufactureApplicationType" abstract="false" substitutionGroup="fuge:ProtocolApplication" />
|
GelML.Gel.Dimensions
Inheritance hierarchy:
Dimensions
-->
Describable
Documentation:
The measurements must be in the form of the Cartesian Coordinate
system (x,y,z). According to the standard image orientation
described in section 7.1.6 of the MIAPE document
x represents the distance from the anode (+) to the cathode (-).
For example in an IPG strip x = the strip length, for a standard
slab gel, x = the width and z = the matrix depth.
All dimensions should be given in milimetres.
Attributes:
| Name | Documentation | Data type | Required |
| x |
The x axis represents the distance from the anode (+) to the
cathode (-).
|
float |
true |
| y |
The y axis is the matrix length.
|
float |
true |
| z |
The z axis dimensions is the matrix depth.
|
float |
true |
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| DimensionUnit |
fuge:OntologyTerm |
The unit of the Dimensions.
|
0..* to 1..1 |
none |
none
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Gel.DimensionsType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.DescribableType">
<xsd:sequence>
<xsd:element name="_dimensionUnit" minOccurs="1" maxOccurs="1">
<xsd:complexType>
<xsd:attribute name="OntologyTerm_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
<xsd:attribute name="x" use="required" type="xsd:float"/>
<xsd:attribute name="y" use="required" type="xsd:float"/>
<xsd:attribute name="z" use="required" type="xsd:float"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Dimensions" type="gelml:GelML.Gel.DimensionsType" abstract="false" substitutionGroup="fuge:Describable" />
|
GelML.Gel.SeparationRange (abstract)
Inheritance hierarchy:
SeparationRange
-->
Describable
Documentation:
The separation range of the gel. This can use the RangeValue or
ComplexValue specification.
Attributes:
| Name | Documentation | Data type | Required |
| dimension |
The dimension separation that the range refers to.
|
int |
true |
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| RangeValue |
fuge:Measurement |
The value of the Gel range. This should use the Range type in
FuGE.
|
0..1 to 0..1 |
composite |
none
|
| RangeType |
fuge:OntologyTerm |
The type of separation range, e.g. logarithmic, linear etc.
|
0..* to 0..1 |
none |
none
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Gel.SeparationRangeType" abstract = "true">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.DescribableType">
<xsd:sequence>
<xsd:element ref="fuge:Measurement" minOccurs="0" maxOccurs="1"/>
<xsd:element name="_rangeType" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:attribute name="OntologyTerm_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
<xsd:attribute name="dimension" use="required" type="xsd:int"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="SeparationRange" type="gelml:GelML.Gel.SeparationRangeType" abstract="true" substitutionGroup="fuge:Describable" />
|
GelML.Gel.PHRange
Inheritance hierarchy:
PHRange
-->
SeparationRange
-->
Describable
Documentation:
The estimated or known pH range of a gel that separates
substances based on their isoelectric point.
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Gel.PHRangeType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:GelML.Gel.SeparationRangeType">
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="PHRange" type="gelml:GelML.Gel.PHRangeType" abstract="false" substitutionGroup="gelml:SeparationRange" />
|
GelML.Gel.MolWeightRange
Inheritance hierarchy:
MolWeightRange
-->
SeparationRange
-->
Describable
Documentation:
The estimated or known range of a gel that separates substances
by their molecular weight.
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Gel.MolWeightRangeType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:GelML.Gel.SeparationRangeType">
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="MolWeightRange" type="gelml:GelML.Gel.MolWeightRangeType" abstract="false" substitutionGroup="gelml:SeparationRange" />
|
GelML.Gel.OtherGelRange
Inheritance hierarchy:
OtherGelRange
-->
SeparationRange
-->
Describable
Documentation:
A gel range other than molecular weight or pH by which proteins
are separated.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| SeparationType |
fuge:OntologyTerm |
The type of separation performed i.e. the biophysical property
that is separated on.
|
0..* to 1..1 |
none |
none
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Gel.OtherGelRangeType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:GelML.Gel.SeparationRangeType">
<xsd:sequence>
<xsd:element name="_separationType" minOccurs="1" maxOccurs="1">
<xsd:complexType>
<xsd:attribute name="OntologyTerm_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="OtherGelRange" type="gelml:GelML.Gel.OtherGelRangeType" abstract="false" substitutionGroup="gelml:SeparationRange" />
|
GelML.Gel.AcrylamideToCrossLinker
Inheritance hierarchy:
AcrylamideToCrossLinker
-->
Describable
Documentation:
Describes the acrylamide:crosslinker ratio, where the
crosslinker type is given by an ontology term (e.g.
bisacrylamide). The values stored in the attributes can be
represented as a simple ratio (e.g. 37.5:1) or as percentages
out of 100 (97:3). If a monomer other than acrylamide has been
used, this object should not be used and the components should
be specified as additional substances.
Attributes:
| Name | Documentation | Data type | Required |
| acrylamide |
The ratio of acrylamide (i.e. value =97 if ratio is 97:3)
|
float |
true |
| crossLinker |
The ratio of crosslinker (i.e. value =3 if ratio is 97:3)
|
float |
true |
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| CrossLinkerType |
fuge:OntologyTerm |
The name of the crosslinker used in the gel.
|
0..* to 1..1 |
none |
none
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Gel.AcrylamideToCrossLinkerType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.DescribableType">
<xsd:sequence>
<xsd:element name="_crossLinkerType" minOccurs="1" maxOccurs="1">
<xsd:complexType>
<xsd:attribute name="OntologyTerm_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
<xsd:attribute name="acrylamide" use="required" type="xsd:float"/>
<xsd:attribute name="crossLinker" use="required" type="xsd:float"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="AcrylamideToCrossLinker" type="gelml:GelML.Gel.AcrylamideToCrossLinkerType" abstract="false" substitutionGroup="fuge:Describable" />
|
GelML.Gel.MeasuredMaterial
Inheritance hierarchy:
MeasuredMaterial
-->
Material
-->
Identifiable
-->
Describable
Documentation:
A subclass of Material for associating a quantity with a
material description.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| Measurement |
fuge:Measurement |
The quantity of material.
|
0..1 to 0..1 |
composite |
none
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.Gel.MeasuredMaterialType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Bio.Material.MaterialType">
<xsd:sequence>
<xsd:element ref="fuge:Measurement" minOccurs="0" maxOccurs="1"/>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="MeasuredMaterial" type="gelml:GelML.Gel.MeasuredMaterialType" abstract="false" substitutionGroup="fuge:Material" />
|
GelML.SampleLoading.SampleLoadingAction
Inheritance hierarchy:
SampleLoadingAction
-->
Action
-->
Identifiable
-->
Describable
Documentation:
An action to represent the order of the referenced
SampleLoadingProtocol, with respect to other Actions performed
within this parent protocol.
Attributes:
| Name | Documentation | Data type | Required |
| laneNumber |
Optional lane number attribute for specifying the intended lane
that this protocol should be applied to.
|
int |
false |
| dimension |
The gel dimension that the referenced SampleLoadingProtocol
refers to. Note, this is not required in the context of
Gel1DProtocol.
|
int |
false |
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| SampleLoadingProtocol |
SampleLoadingProtocol |
A reference to the SampleLoadingProtocol.
|
0..* to 1..1 |
none |
fuge:ChildProtocol
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.SampleLoading.SampleLoadingActionType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ActionType">
<xsd:attribute name="laneNumber" type="xsd:int"/>
<xsd:attribute name="dimension" type="xsd:int"/>
<xsd:attribute name="SampleLoadingProtocol_ref" use="required" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="SampleLoadingAction" type="gelml:GelML.SampleLoading.SampleLoadingActionType" abstract="false" substitutionGroup="fuge:Action" />
|
GelML.SampleLoading.SampleLoadingApplication
Inheritance hierarchy:
SampleLoadingApplication
-->
ProtocolApplication
-->
ParameterizableApplication
-->
Identifiable
-->
Describable
Documentation:
An application of the SampleLoadingProtocol.
SampleLoadingApplication defines how a sample was loaded to a
gel.
To capture loading a first dimension gel onto a second dimension
gel, GenericMaterialMeasurement should reference the first
dimension gel and SampleLoadingApplication references the second
dimension Gel (as LoadedGel).
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| LoadingProtocol |
SampleLoadingProtocol |
The SampleLoadingProtocol that has been applied.
|
0..* to 1..1 |
none |
fuge:Protocol
|
| LoadedGel |
Gel |
The gel onto which the sample was loaded. The gel must be an
instance of Gel referenced from Gel1DApplication,
Gel2DApplication or OtherGelApplication.
|
0..* to 1..1 |
none |
fuge:InputCompleteMaterials
|
| LoadedGelLane |
GelLane |
The lane on which the sample was loaded.
|
0..* to 0..1 |
none |
fuge:InputCompleteMaterials
|
| InputSample |
fuge:GenericMaterialMeasurement |
A measured quantity of the sample loaded onto the gel. For a 1D
gel, the inputs are protein samples using GenericMaterial.
For a 2D gel, the input to first dimension Gel is a protein
sample using GenericMaterial. The input to the second dimension
can be protein samples e.g. MW markers (GenericMaterial) and /
or the first dimension gel (Gel).
A Measurement value is only required for protein samples.
|
0..1 to 0..* |
composite |
fuge:InputMaterials
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.SampleLoading.SampleLoadingApplicationType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ProtocolApplicationType">
<xsd:sequence>
<xsd:element ref="fuge:GenericMaterialMeasurement" minOccurs="0" maxOccurs="unbounded"/>
</xsd:sequence>
<xsd:attribute name="SampleLoadingProtocol_ref" use="required" type="xsd:string"/>
<xsd:attribute name="Gel_ref" use="required" type="xsd:string"/>
<xsd:attribute name="GelLane_ref" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="SampleLoadingApplication" type="gelml:GelML.SampleLoading.SampleLoadingApplicationType" abstract="false" substitutionGroup="fuge:ProtocolApplication" />
|
GelML.SampleLoading.SampleLoadingProtocol
Inheritance hierarchy:
SampleLoadingProtocol
-->
Protocol
-->
Parameterizable
-->
Identifiable
-->
Describable
Documentation:
A Protocol defining how samples are loaded onto a Gel or
GelLanes.
Attributes:
| Name | Documentation | Data type | Required |
| protocolText |
The details of the SampleLoadingProtocol as free text.
|
string |
false |
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| LoadingBuffer |
AddBufferAction |
The loading buffer of the sample.
|
0..* to 0..1 |
composite |
fuge:Actions
|
| SampleLoadingParameters |
fuge:GenericParameter |
Any parameters related to the SampleLoadingProtocol.
|
0..1 to 0..* |
composite |
fuge:Parameters
|
| SampleLoadingEquipment |
fuge:GenericEquipment |
Any equipment used in the SampleLoadingProtocol.
|
0..* to 0..* |
none |
fuge:Equipment
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.SampleLoading.SampleLoadingProtocolType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ProtocolType">
<xsd:sequence>
<xsd:element name="_loadingBuffer" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="gelml:AddBufferAction" minOccurs="1" maxOccurs="1"/>
</xsd:sequence>
</xsd:complexType>
</xsd:element>
<xsd:element ref="fuge:GenericParameter" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element name="_sampleLoadingEquipment" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="GenericEquipment_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
<xsd:attribute name="protocolText" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="SampleLoadingProtocol" type="gelml:GelML.SampleLoading.SampleLoadingProtocolType" abstract="false" substitutionGroup="fuge:Protocol" />
|
GelML.OtherGelProtocol.InterDimensionAction
Inheritance hierarchy:
InterDimensionAction
-->
Action
-->
Identifiable
-->
Describable
Documentation:
The Action represent a reference to a Protocol for the stages
that occur between electrophoresis over particular dimensions
and an ordering of the reference with respect to other Actions
performed within the parent Protocol.
Attributes:
| Name | Documentation | Data type | Required |
| preDimension |
The dimension that this procedure precedes. This attribute is
not required for within a Gel2DProtocol as it is assumed that
this specifies a Protocol prior to dimension 2.
|
int |
false |
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| InterDimensionProtocol |
fuge:Protocol |
A reference to the GenericProtocol performed between the
dimensions specified.
|
0..* to 1..1 |
none |
fuge:ChildProtocol
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.OtherGelProtocol.InterDimensionActionType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ActionType">
<xsd:attribute name="preDimension" type="xsd:int"/>
<xsd:attribute name="Protocol_ref" use="required" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="InterDimensionAction" type="gelml:GelML.OtherGelProtocol.InterDimensionActionType" abstract="false" substitutionGroup="fuge:Action" />
|
GelML.OtherGelProtocol.OtherGel
Inheritance hierarchy:
OtherGel
-->
ElectrophoresedGel
-->
Material
-->
Identifiable
-->
Describable
Documentation:
The Gel output from an OtherGelApplication representing the
combination of gel substrates and proteins separated.
XML Schema Complex Type specification:
<xsd:complexType name="GelML.OtherGelProtocol.OtherGelType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:GelML.Gel.ElectrophoresedGelType">
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="OtherGel" type="gelml:GelML.OtherGelProtocol.OtherGelType" abstract="false" substitutionGroup="gelml:ElectrophoresedGel" />
|
GelML.OtherGelProtocol.OtherGelApplication
Inheritance hierarchy:
OtherGelApplication
-->
ProtocolApplication
-->
ParameterizableApplication
-->
Identifiable
-->
Describable
Documentation:
OtherGelApplication is the application of an OtherGelProtocol.
An instance of OtherApplication should reference (via
ActionApplication) SampleLoadingApplication,
ElectrophoresisApplication, DetectionApplication and
GenericProtocolApplication as its sub-steps, as defined by the
referenced OtherGelProtocol.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| OtherGelProtocol |
OtherGelProtocol |
The OtherGelProtocol that is applied.
|
0..* to 1..1 |
none |
fuge:Protocol
|
| InputGels |
Gel |
The gels on which separations are performed.
|
0..1 to 1..* |
composite |
fuge:InputCompleteMaterials
|
| OutputGels |
OtherGel |
The Gel(s) output from an OtherGelApplication representing the
combination of gel substrates and proteins separated.
|
0..1 to 0..* |
composite |
fuge:OutputMaterials
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.OtherGelProtocol.OtherGelApplicationType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ProtocolApplicationType">
<xsd:sequence>
<xsd:element name="_inputGels" minOccurs="1" maxOccurs="1">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="gelml:Gel" minOccurs="1" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:complexType>
</xsd:element>
<xsd:element name="_outputGels" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="gelml:OtherGel" minOccurs="1" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
<xsd:attribute name="OtherGelProtocol_ref" use="required" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="OtherGelApplication" type="gelml:GelML.OtherGelProtocol.OtherGelApplicationType" abstract="false" substitutionGroup="fuge:ProtocolApplication" />
|
GelML.OtherGelProtocol.OtherGelProtocol
Inheritance hierarchy:
OtherGelProtocol
-->
Protocol
-->
Parameterizable
-->
Identifiable
-->
Describable
Documentation:
A protocol for capturing experiments that cannot be represented
by Gel1DProtocol or Gel2DProtocol.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| SampleLoadingAction |
SampleLoadingAction |
The SampleLoadingActions within the OtherGelProtocol.
|
0..1 to 0..* |
composite |
fuge:Actions
|
| ElectrophoresisAction |
DimensionAction |
A reference to DimensionAction that captures the
ElectrophoresisProtocols performed in various dimensions of the
separation.
|
0..1 to 1..* |
composite |
fuge:Actions
|
| InterDimensionActions |
InterDimensionAction |
A reference to InterDimensionAction for protocols performed
between the dimension separations.
|
0..1 to 0..* |
composite |
fuge:Actions
|
| DetectionAction |
DetectionAction |
DetectionAction(s) which reference DetectionProtocols that occur
with the OtherGelProtocol.
|
0..1 to 0..* |
composite |
fuge:Actions
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.OtherGelProtocol.OtherGelProtocolType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ProtocolType">
<xsd:sequence>
<xsd:element ref="gelml:SampleLoadingAction" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="gelml:DimensionAction" minOccurs="1" maxOccurs="unbounded"/>
<xsd:element ref="gelml:InterDimensionAction" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="gelml:DetectionAction" minOccurs="0" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="OtherGelProtocol" type="gelml:GelML.OtherGelProtocol.OtherGelProtocolType" abstract="false" substitutionGroup="fuge:Protocol" />
|
GelML.OtherGelProtocol.DimensionAction
Inheritance hierarchy:
DimensionAction
-->
Action
-->
Identifiable
-->
Describable
Documentation:
An action to represent the order of the referenced
ElectrophoresisProtocol, with respect to other Actions performed
within this parent protocol.
Attributes:
| Name | Documentation | Data type | Required |
| dimension |
The dimension that the referenced electrophoresis protocol
occurs in.
|
int |
false |
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| ElectrophoresisProtocol |
ElectrophoresisProtocol |
The ElectrophoresisProtocol performed in this dimension.
|
0..* to 1..1 |
none |
fuge:ChildProtocol
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.OtherGelProtocol.DimensionActionType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ActionType">
<xsd:attribute name="dimension" type="xsd:int"/>
<xsd:attribute name="ElectrophoresisProtocol_ref" use="required" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="DimensionAction" type="gelml:GelML.OtherGelProtocol.DimensionActionType" abstract="false" substitutionGroup="fuge:Action" />
|
GelML.ImageAcquisition.Image
Inheritance hierarchy:
Image
-->
ExternalData
-->
Data
-->
Identifiable
-->
Describable
Documentation:
A reference to an image file stored in an external location.
Attributes:
| Name | Documentation | Data type | Required |
| bitDepth |
The image bit-depth e.g. 8 bit, 16 bit.
|
int |
false |
| dimensionX |
The x-axis dimension of the image in pixels.
|
int |
false |
| dimensionY |
The y-axis dimension of the image in pixels.
|
int |
false |
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| Channel |
fuge:Measurement |
The channel or wavelength at which the image was scanned.
|
0..1 to 0..1 |
composite |
none
|
| Resolution |
fuge:Measurement |
The value of the resolution of the Image.
|
0..1 to 0..1 |
composite |
none
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.ImageAcquisition.ImageType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Bio.Data.ExternalDataType">
<xsd:sequence>
<xsd:element name="_channel" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="fuge:Measurement" minOccurs="1" maxOccurs="1"/>
</xsd:sequence>
</xsd:complexType>
</xsd:element>
<xsd:element name="_resolution" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="fuge:Measurement" minOccurs="1" maxOccurs="1"/>
</xsd:sequence>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
<xsd:attribute name="bitDepth" type="xsd:int"/>
<xsd:attribute name="dimensionX" type="xsd:int"/>
<xsd:attribute name="dimensionY" type="xsd:int"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Image" type="gelml:GelML.ImageAcquisition.ImageType" abstract="false" substitutionGroup="fuge:ExternalData" />
|
GelML.ImageAcquisition.ImageAcquisitionApplication
Inheritance hierarchy:
ImageAcquisitionApplication
-->
ProtocolApplication
-->
ParameterizableApplication
-->
Identifiable
-->
Describable
Documentation:
An application of a protocol (GenericProtocol) describing the
scanning of a material to produce an Image. In this context it
is expected that the Material would be an ElectrophoresedGel,
TransferMedium or DetectionMedium.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| ProductImage |
Image |
The Image produced from ImageAcquisitionApplication.
|
0..1 to 1..1 |
none |
fuge:OutputData
|
| InputSubstrate |
fuge:Material |
The Input material to image acquisition.
In a 1D Gel experiment, if the gel is scanned after
electrophoresis, this should reference the Gel1D produced by
Gel1DApplication. In a 2D Gel experiment, if the gel is scanned
after electrophoresis, this should reference the Gel2D produced
by Gel2DApplication. If an image is aquired of a TransferMedium
or DetectionMedium, this should reference an instance that is
referenced by IndirectDetection as OutputTransferMedium or
OutputDetectionMedium.
|
0..* to 1..1 |
none |
fuge:InputCompleteMaterials
|
| ImageAcquisitionProtocol |
ImageAcquisitionProtocol |
The protocol describing this image acquisition procedure, such
as scanning or photography.
|
0..* to 1..1 |
none |
fuge:Protocol
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.ImageAcquisition.ImageAcquisitionApplicationType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ProtocolApplicationType">
<xsd:attribute name="Image_ref" use="required" type="xsd:string"/>
<xsd:attribute name="Material_ref" use="required" type="xsd:string"/>
<xsd:attribute name="ImageAcquisitionProtocol_ref" use="required" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="ImageAcquisitionApplication" type="gelml:GelML.ImageAcquisition.ImageAcquisitionApplicationType" abstract="false" substitutionGroup="fuge:ProtocolApplication" />
|
GelML.ImageAcquisition.ImageAcquisitionProtocol
Inheritance hierarchy:
ImageAcquisitionProtocol
-->
Protocol
-->
Parameterizable
-->
Identifiable
-->
Describable
Documentation:
A protocol describing image acquisition.
Attributes:
| Name | Documentation | Data type | Required |
| protocolText |
The details of the SampleLoadingProtocol as free text.
|
string |
false |
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite | Extends association |
| Equipment |
fuge:GenericEquipment |
The Equipment used for image acquisition.
|
0..* to 1..* |
none |
fuge:Equipment
|
| Software |
fuge:GenericSoftware |
The software used for image acquisition.
|
0..* to 0..* |
none |
fuge:Software
|
| CalibrationSteps |
fuge:GenericAction |
Descriptions of calibration performed during image acquisition.
|
0..1 to 0..* |
composite |
fuge:Actions
|
| AutoCalibration |
AutoCalibration |
A parameter to represent whether auto-calibration was performed.
|
1..1 to 1..1 |
composite |
fuge:Parameters
|
| AcquisitionParameters |
fuge:GenericParameter |
Any parameters in the ImageAcquisitionProtocol.
|
0..1 to 0..* |
composite |
fuge:Parameters
|
XML Schema Complex Type specification:
<xsd:complexType name="GelML.ImageAcquisition.ImageAcquisitionProtocolType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ProtocolType">
<xsd:sequence>
<xsd:element name="_equipment" minOccurs="1" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="GenericEquipment_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="_software" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="GenericSoftware_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="_calibrationSteps" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="fuge:GenericAction" minOccurs="1" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:complexType>
</xsd:element>
<xsd:element ref="gelml:AutoCalibration" minOccurs="1" maxOccurs="1"/>
<xsd:element ref="fuge:GenericParameter" minOccurs="0" maxOccurs="unbounded"/>
</xsd:sequence>
<xsd:attribute name="protocolText" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="ImageAcquisitionProtocol" type="gelml:GelML.ImageAcquisition.ImageAcquisitionProtocolType" abstract="false" substitutionGroup="fuge:Protocol" />
|
GelML.ImageAcquisition.AutoCalibration
Inheritance hierarchy:
AutoCalibration
-->
Parameter
-->
Identifiable
-->
Describable
Documentation:
A parameter to represent whether auto-calibration was performed.
This should use BooleanValue (subclass of Measurement).
XML Schema Complex Type specification:
<xsd:complexType name="GelML.ImageAcquisition.AutoCalibrationType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ParameterType">
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="AutoCalibration" type="gelml:GelML.ImageAcquisition.AutoCalibrationType" abstract="false" substitutionGroup="fuge:Parameter" />
|