Specification documentation for the GelML model: Reference manual

Status: GelML (version 1.0 internal candidate); 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 statement to come

This document is the reference manual for GelML version 1 (September candidate). 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 *

NameDocumentationData typeRequired
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

NameAssociated classDocumentationMultiplicityCompositeExtends association
Name of the associationClass at the navigable endThe association's documentation The multiplicity from source end to navigable endWhether 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="psidev.sf.net/gelml"
    xmlns:xsd="http://www.w3.org/2001/XMLSchema" 
    xmlns:fuge="fuge.sf.net"
     xmlns:gelml="psidev.sf.net/gelml"
    elementFormDefault="qualified">
    
    <xsd:import namespace="fuge.sf.net" schemaLocation="http://fuge.sourceforge.net/Version1Candidate/FuGE-version1-Sept-candidate.xsd"/>

GelML.GelMLRoot.GelMLMaterialCollection

Inheritance hierarchy:

GelMLMaterialCollection --> Describable

Documentation:

Collection class for accessing all GenericMaterial instances used in GelML.

Associations:

NameAssociated classDocumentationMultiplicityCompositeExtends association
AllGenericMaterials fuge:GenericMaterial All GenericMaterial objects within the GelML file. 0..* 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: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:

NameAssociated classDocumentationMultiplicityCompositeExtends 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:

NameAssociated classDocumentationMultiplicityCompositeExtends 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 All OntologyTerms used with the document. 1..1 to 0..1 composite none
GelAuditCollection fuge:AuditCollection All Audit objects used in the document: security settings, contacts etc. 1..1 to 0..1 composite none
GelReferenceCollection fuge:ReferenceableCollection All referenced objects (BibliographicReference and DatabaseEntry). 1..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 none 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:sequence>
   <xsd:attribute name="Provider_ref" type="xsd:string"/>
  </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:

NameAssociated classDocumentationMultiplicityCompositeExtends 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:

NameAssociated classDocumentationMultiplicityCompositeExtends 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
AllGenProtocolApps fuge:GenericProtocolApplication All the GenericProtocolApplication 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:element ref="fuge:GenericProtocolApplication" 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:

NameDocumentationData typeRequired
date The date the experiment was initiated on. date false

Associations:

NameAssociated classDocumentationMultiplicityCompositeExtends 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
ExperimentContact fuge:ContactRole A reference to the responsible person or institutional role that should be contacted about this experiment. 0..1 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: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:

NameAssociated classDocumentationMultiplicityCompositeExtends 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:

NameAssociated classDocumentationMultiplicityCompositeExtends 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 used 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 or the actionTerm association to OntologyTerm can be used to specify how the substance has been used within the protocol.

Attributes:

NameDocumentationData typeRequired
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:

NameAssociated classDocumentationMultiplicityCompositeExtends association
Concentration Concentration The concentration of the substance. 0..1 to 0..1 composite none
Mass Mass The mass of substance used in the protocol. 0..1 to 0..1 composite none
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
VolumeParameter VolumeParameter The volume of the substance. 0..1 to 0..1 composite none

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:

NameAssociated classDocumentationMultiplicityCompositeExtends association
ActionTime TimeParameter The duration or time point that the TemporalSubstanceAction applies to. 0..1 to 1..1 composite none

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 or actionTerm attributes of SubtanceAction are not used, the SubstanceMixtureProtocol represents only the components of the mixture and not the processes applied to them.

Attributes:

NameDocumentationData typeRequired
mixtureName The name of the mixture represented by this protocol. string false

Associations:

NameAssociated classDocumentationMultiplicityCompositeExtends 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 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. A duration parameter. Note: values for absolute or relative time can be 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:

NameAssociated classDocumentationMultiplicityCompositeExtends association
SampleLoadingAction SampleLoadingAction A reference to the SampleLoadingAction. 0..1 to 1..* composite fuge:ProtocolActions
FirstDimension FirstDimensionAction A reference to the FirstDimensionAction. 1..1 to 1..1 composite fuge:ProtocolActions
SecondDimension SecondDimensionAction A reference to the SecondDimensionAction. 1..1 to 1..1 composite fuge:ProtocolActions
InterDimensionAction InterDimensionAction A reference to the Action that defines Protocols applied between the first and second dimension ElectrophoresisProtocols. 0..1 to 0..* composite fuge:ProtocolActions

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: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, and GenericProtocolApplication as its sub-steps, as defined by the referenced Gel2DProtocol.

Associations:

NameAssociated classDocumentationMultiplicityCompositeExtends 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:

NameAssociated classDocumentationMultiplicityCompositeExtends 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:

NameAssociated classDocumentationMultiplicityCompositeExtends 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.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 reference 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 and ElectrophoresisApplication matching the structure of the referenced Gel1DProtocol.

Associations:

NameAssociated classDocumentationMultiplicityCompositeExtends 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:

NameAssociated classDocumentationMultiplicityCompositeExtends 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:ProtocolActions
ElectrophoresisAction ElectrophoresisAction A reference to an action that specifes the performing of Electrophoresis within the Gel1DProtocol. 0..1 to 1..1 composite fuge:ProtocolActions

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: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. The reference to ElectrophoresedGel represents the Gel on which proteins are being detected. If two stainings are done, the destaining should be the first stage of the second staining process.

Associations:

NameAssociated classDocumentationMultiplicityCompositeExtends association
AppliedDetectionProtocol DetectionProtocol The DetectionProtocol that has been run. 0..* to 1..1 none fuge:Protocol
DetectedGel ElectrophoresedGel The instance of Gel2D, Gel1D or OtherGel on which detection has taken place. The referenced object should be an output of Gel2DApplication, Gel1DApplication or OtherGelApplication as appropriate. 0..* to 1..1 none fuge:InputCompleteMaterials

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:attribute name="ElectrophoresedGel_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).

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

Associations:

NameAssociated classDocumentationMultiplicityCompositeExtends association
AdditionalBuffers AddBufferAction The buffers used in the DetectionProtocol. 0..1 to 0..* composite fuge:ProtocolActions
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:ProtocolActions
OtherActions fuge:GenericAction Other actions performed in the DetectionProtocol aside from the specification of the application of the agent and the use of buffers. 0..1 to 0..* composite fuge:ProtocolActions
DetectionEquipment fuge:GenericEquipment Any equipment used in the DetectionProtocol. 0..* to 0..* none none

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:AddBufferAction" minOccurs="0" maxOccurs="unbounded"/>
    <xsd:element ref="gelml:SubstanceAction" minOccurs="1" maxOccurs="unbounded"/>
    <xsd:element ref="fuge:GenericAction" minOccurs="0" 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:sequence>
  </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:

NameAssociated classDocumentationMultiplicityCompositeExtends association
OutputTransferMedium TransferMedium An instance of TransferMedium following the transfer of proteins. 0..1 to 0..1 composite fuge:OutputMaterials
InputTransferMedium TransferMedium The TransferMedium prior to the transfer of proteins. 0..1 to 1..1 composite fuge:InputCompleteMaterials
InputDetectMedium DetectionMedium An instance of DetectionMedium prior to the detection of proteins. 0..1 to 0..1 composite fuge:InputCompleteMaterials
OutputDetectMedium DetectionMedium An instance of DetectionMedium following the detection of proteins. 0..1 to 0..1 composite fuge:OutputMaterials

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 name="_outputMedium" minOccurs="0" maxOccurs="1">
     <xsd:complexType>
      <xsd:sequence>
       <xsd:element ref="gelml:TransferMedium" minOccurs="1" maxOccurs="1"/>
	  </xsd:sequence>
     </xsd:complexType>
    </xsd:element>
    <xsd:element name="_inputTransferMedium" minOccurs="1" maxOccurs="1">
     <xsd:complexType>
      <xsd:sequence>
       <xsd:element ref="gelml:TransferMedium" minOccurs="1" maxOccurs="1"/>
	  </xsd:sequence>
     </xsd:complexType>
    </xsd:element>
    <xsd:element name="_inputDetectMedium" minOccurs="0" maxOccurs="1">
     <xsd:complexType>
      <xsd:sequence>
       <xsd:element ref="gelml:DetectionMedium" minOccurs="1" maxOccurs="1"/>
	  </xsd:sequence>
     </xsd:complexType>
    </xsd:element>
    <xsd:element name="_outputDetectMedium" minOccurs="0" maxOccurs="1">
     <xsd:complexType>
      <xsd:sequence>
       <xsd:element ref="gelml:DetectionMedium" minOccurs="1" maxOccurs="1"/>
	  </xsd:sequence>
     </xsd:complexType>
    </xsd:element>
   </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.

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:

NameAssociated classDocumentationMultiplicityCompositeExtends 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. A measurement can be specified as an atomic value, a range or a complex value. If a range is specifed the following convention MUST be followed, lowValue refers the start measurement in time and highValue refers to end measurement in time.

Associations:

NameAssociated classDocumentationMultiplicityCompositeExtends 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:

NameAssociated classDocumentationMultiplicityCompositeExtends 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:

NameAssociated classDocumentationMultiplicityCompositeExtends 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:

NameAssociated classDocumentationMultiplicityCompositeExtends association
OtherBuffers AddBufferAction Buffers other than the running buffer used in the ElectrophoresisProtocol. 0..1 to 0..* composite fuge:ProtocolActions
ElectrophoresisEquipment fuge:GenericEquipment 0..* to 0..* none fuge:ProtocolEquipment
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:ProtocolActions
RunningBuffer AddBufferAction The running buffer used in the ElectrophoresisProtocol. 0..1 to 0..1 composite fuge:ProtocolActions

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 name="_otherBuffers" minOccurs="0" maxOccurs="1">
     <xsd:complexType>
      <xsd:sequence>
       <xsd:element ref="gelml:AddBufferAction" minOccurs="1" maxOccurs="unbounded"/>
	  </xsd:sequence>
     </xsd:complexType>
    </xsd:element>
    <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:element name="_runningBuffer" minOccurs="0" maxOccurs="1">
     <xsd:complexType>
      <xsd:sequence>
       <xsd:element ref="gelml:AddBufferAction" minOccurs="1" maxOccurs="1"/>
	  </xsd:sequence>
     </xsd:complexType>
    </xsd:element>
   </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 DetectionProtocol by reference to a SubstanceMixtureProtocol that represents the buffer and optionally the method of producing the buffer.

Associations:

NameAssociated classDocumentationMultiplicityCompositeExtends 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 directional steps. See chainCode documentation for this encoding.

Attributes:

NameDocumentationData typeRequired
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.Point

Inheritance hierarchy:

Point --> Describable

Documentation:

A single boundary point used in a BoundaryPointSet.

Attributes:

NameDocumentationData typeRequired
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.Excision.Circle

Inheritance hierarchy:

Circle --> FeatureLocation --> Describable

Documentation:

Circle is for defining a circular location on an image.

Attributes:

NameDocumentationData typeRequired
pixelRadius Radius of the Circle in pixels. int false

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" 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:

NameAssociated classDocumentationMultiplicityCompositeExtends 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:

NameAssociated classDocumentationMultiplicityCompositeExtends association
InputImageLocations LocationSet The set of locations on an image of a gel. 0..1 to 1..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="1" 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 (abstract)

Inheritance hierarchy:

FeatureLocation --> Describable

Documentation:

Abstract superclass representing the different types of method that could be used to identify a location.

Attributes:

NameDocumentationData typeRequired
centroidX Added for M2 int false
centroidY int false

XML Schema Complex Type specification:

<xsd:complexType name="GelML.Excision.FeatureLocationType" abstract = "true">
 <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="true" substitutionGroup="fuge:Describable" />

GelML.Excision.GelLocation

Inheritance hierarchy:

GelLocation --> Identifiable --> Describable

Documentation:

A single location on a gel.

Associations:

NameAssociated classDocumentationMultiplicityCompositeExtends 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 1..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="1" 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:

NameAssociated classDocumentationMultiplicityCompositeExtends 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:

NameAssociated classDocumentationMultiplicityCompositeExtends 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:

NameDocumentationData typeRequired
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:

NameAssociated classDocumentationMultiplicityCompositeExtends 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.Gel.ElectrophoresedGel (abstract)

Inheritance hierarchy:

ElectrophoresedGel --> Material --> Identifiable --> Describable

Documentation:

Abstract superclass for describing gels following electrophoresis.

Associations:

NameAssociated classDocumentationMultiplicityCompositeExtends 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

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: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:

NameDocumentationData typeRequired
separationDimension The dimension this gel separates in e.g. for 2D electrophoresis, one Gel separationDimension = 1, other Gel separationDimension = 2. int false

Associations:

NameAssociated classDocumentationMultiplicityCompositeExtends 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
AcrylBisacrylamide AcrylBisAcrylamide The acrylamide:bisacrylamide ratio in the gel. 1..1 to 0..1 composite none
AdditionalSubstances fuge:GenericMaterial Any additional substances other than those specified by defined classes should be reported here. 0..1 to 0..* none fuge:Components
Model fuge:OntologyTerm The model number of the gel. In 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
GelRange GelRange The separation range and type of separation performed on this gel. (Example pH range 4-7). 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:AcrylBisAcrylamide" minOccurs="0" maxOccurs="1"/>
    <xsd:element name="_additionalSubstances" minOccurs="0" maxOccurs="unbounded"> 
     <xsd:complexType>
      <xsd:attribute name="GenericMaterial_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:element ref="gelml:GelRange" minOccurs="0" maxOccurs="1"/>
   </xsd:sequence>
   <xsd:attribute name="separationDimension" type="xsd:int"/>
  </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:

NameDocumentationData typeRequired
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:

NameAssociated classDocumentationMultiplicityCompositeExtends 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). z = the matrix depth. All dimensions should be given in milimetres.

Attributes:

NameDocumentationData typeRequired
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:

NameAssociated classDocumentationMultiplicityCompositeExtends 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.GelRange (abstract)

Inheritance hierarchy:

GelRange --> Describable

Documentation:

The separation range of the gel. This can use the RangeValue or ComplexValue specification.

Associations:

NameAssociated classDocumentationMultiplicityCompositeExtends 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.GelRangeType" 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:extension>
 </xsd:complexContent>
</xsd:complexType>

XML Schema element specification:

<xsd:element name="GelRange" type="gelml:GelML.Gel.GelRangeType" abstract="true" substitutionGroup="fuge:Describable" />

GelML.Gel.PHRange

Inheritance hierarchy:

PHRange --> GelRange --> Describable

Documentation:

The estimated or know 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.GelRangeType">
  </xsd:extension>
 </xsd:complexContent>
</xsd:complexType>

XML Schema element specification:

<xsd:element name="PHRange" type="gelml:GelML.Gel.PHRangeType" abstract="false" substitutionGroup="gelml:GelRange" />

GelML.Gel.MolWeightRange

Inheritance hierarchy:

MolWeightRange --> GelRange --> 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.GelRangeType">
  </xsd:extension>
 </xsd:complexContent>
</xsd:complexType>

XML Schema element specification:

<xsd:element name="MolWeightRange" type="gelml:GelML.Gel.MolWeightRangeType" abstract="false" substitutionGroup="gelml:GelRange" />

GelML.Gel.OtherGelRange

Inheritance hierarchy:

OtherGelRange --> GelRange --> Describable

Documentation:

A gel range other than molecular weight or pH by which proteins are separated.

Associations:

NameAssociated classDocumentationMultiplicityCompositeExtends 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.GelRangeType">
   <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:GelRange" />

GelML.Gel.AcrylBisAcrylamide

Inheritance hierarchy:

AcrylBisAcrylamide --> Describable

Documentation:

Describes the acrylamide:bisacrylamide ratio. 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).

Attributes:

NameDocumentationData typeRequired
acrylamide Ratio of bisacrylamide (i.e. value =97 if ratio is 97:3) float true
bisacrylamide Ratio of bisacrylamide (i.e. value =3 if ratio is 97:3) float true

XML Schema Complex Type specification:

<xsd:complexType name="GelML.Gel.AcrylBisAcrylamideType" abstract = "false">
 <xsd:complexContent>
  <xsd:extension base="fuge:FuGE.Common.DescribableType">
   <xsd:attribute name="acrylamide" use="required" type="xsd:float"/>
   <xsd:attribute name="bisacrylamide" use="required" type="xsd:float"/>
  </xsd:extension>
 </xsd:complexContent>
</xsd:complexType>

XML Schema element specification:

<xsd:element name="AcrylBisAcrylamide" type="gelml:GelML.Gel.AcrylBisAcrylamideType" abstract="false" substitutionGroup="fuge:Describable" />

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:

NameDocumentationData typeRequired
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:

NameAssociated classDocumentationMultiplicityCompositeExtends 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, GelSampleMeasurement should reference the first dimension gel and SampleLoadingApplication references the second dimension Gel (as LoadedGel).

Associations:

NameAssociated classDocumentationMultiplicityCompositeExtends 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.

Associations:

NameAssociated classDocumentationMultiplicityCompositeExtends association
SubstanceActions SubstanceAction An optional description of the substances that can be loaded with this protocol (the actual instances of the sample will be described by the SampleLoadingApplication). 0..1 to 0..* composite fuge:ProtocolActions
SampleLoadingParameters fuge:GenericParameter Any parameters related to the SampleLoadingProtocol. 0..1 to 0..* none fuge:Parameters
SampleLoadingActions fuge:GenericAction Actions describing steps unrelated to the sample within this protocol (which should be described using SubstanceAction). 0..1 to 0..* composite fuge:ProtocolActions
SampleLoadingEquipment fuge:GenericEquipment Any equipment used in the SampleLoadingProtocol. 0..* to 0..* none none
SampleLoadingBuffer AddBufferAction 0..1 to 0..1 composite none

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 ref="gelml:SubstanceAction" minOccurs="0" maxOccurs="unbounded"/>
    <xsd:element name="_sampleLoadingParameters" minOccurs="0" maxOccurs="unbounded"> 
     <xsd:complexType>
      <xsd:attribute name="GenericParameter_ref" use="required" type="xsd:string"/>
     </xsd:complexType>
    </xsd:element>
    <xsd:element ref="fuge:GenericAction" 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:element ref="gelml:AddBufferAction" minOccurs="0" maxOccurs="1"/>
   </xsd:sequence>
  </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:

NameDocumentationData typeRequired
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:

NameAssociated classDocumentationMultiplicityCompositeExtends 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, ElectrophoresisApplicationand GenericProtocolApplication as its sub-steps, as defined by the referenced OtherGelProtocol.

Associations:

NameAssociated classDocumentationMultiplicityCompositeExtends 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:

NameAssociated classDocumentationMultiplicityCompositeExtends association
SampleLoadingAction SampleLoadingAction The SampleLoadingActions within the OtherGelProtocol. 0..1 to 0..* composite fuge:ProtocolActions
ElectrophoresisAction DimensionAction A reference to DimensionAction that captures the ElectrophoresisProtocols performed in various dimensions of the separation. 0..1 to 1..* composite fuge:ProtocolActions
InterDimensionActions InterDimensionAction A reference to InterDimensionAction for protocols performed between the dimension separations. 0..1 to 0..* composite fuge:ProtocolActions

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: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:

NameDocumentationData typeRequired
dimension The dimension that the referenced electrophoresis protocol occurs in. This value does not need to be given for a Gel1DProtocol as there is only one dimension. int false

Associations:

NameAssociated classDocumentationMultiplicityCompositeExtends association
ElectrophoresisProtocol ElectrophoresisProtocol The ElectrophoresisProtocol performed in this dimension. 0..* to 1..1 none none

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:

NameDocumentationData typeRequired
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:

NameAssociated classDocumentationMultiplicityCompositeExtends 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:

NameAssociated classDocumentationMultiplicityCompositeExtends association
ProductImage Image The Image produced from ImageAcquisitionApplication. 0..1 to 1..1 none none
ImageAcquisitionProtocol fuge:GenericProtocol The protocol describing this image acquisition (scanning) procedure. 0..* to 1..1 none none
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 none

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="GenericProtocol_ref" use="required" type="xsd:string"/>
   <xsd:attribute name="Material_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" />