Extending FuGE into other domains

1
Extending FuGE into other domains

• Andrew Jones
• School of Computer Science, University of
  Manchester
• http//fuge.sourceforge.net/

2
FuGE Status

• Functional Genomics Experiment-OM/ML
• Milestone 1 release Sept 2005
• UML (Object Model)
• XML Schema
• Milestone release being tested by MGED for MAGE-2
  
• We are looking at testing it in PSI context
• As a basis for GelML and Gel IML
• For Investigation structure, sample prep etc.

3
mzData

• mzData v 1.05 is the current release
• Question How do we integrate mzData into
  proteome workflows?
• Details of sample prep
• Other separation techniques
• FuGE could be used in different ways
• Giving mzData a context within a workflow OR
• As a basis for future mzData versions

4
Experiment retrofitting mzData

• FuGE can store Software, Equipment, Contact
• mzData has similar concepts
• FuGE has Protocol / ProtocolApplication
• This is the mechanism for storing parameters and
  parameter values
• Slightly different from parameter definition in
  mzData
• There is not always a 11 mapping between mzData
  concept and FuGE concept

5
An mzDataFuGE hybrid format?

• mzData could sub-class from FuGE elements
• Would require some changes in structure
• Some would appear relatively arbitrary
• Few major benefits at this stage, given that
  current structure is being implemented
• May be worth considering for mzData v 2, if FuGE
  is successful in other domains

6
Referencing an mzData file with FuGE
Protocol definition says See ExternalData file
for parameters (rather than storing params in
Protocol)
ProtocolApplication
Protocol
inputMaterial
outputData
Material
ExternalData
mzData file
Material can be used to describe the
sample. This connects the MS data with a
separation workflow
File format definition
Parser will exist to extract data / parameters
from mzData file
7
Referencing an mzData file with FuGE

• ltProtocolApplication identifier"FuGE.ProtocolApp.
  1001" activityDate"24/08/2005"gt
• ltoutputDatagt
• ltData_ref identifier_ref"FuGE.ExternalData.1001
  "/gt
• lt/outputDatagt
• ltinputMaterialsgt
• ltMaterialMeasurementgt
• ltmaterialgt
• ltMaterial_ref identifier_ref"FuGE.Material.10
  01"/gt
• lt/materialgt
• lt/MaterialMeasurementgt
• lt/inputMaterialsgt
• ltprotocolgt
• ltProtocol_ref identifier_ref"FuGE.Protocol.1001
  "/gt
• lt/protocolgt
• lt/ProtocolApplicationgt

8
Referencing an mzData file with FuGE

• ltProtocolApplication identifier"FuGE.ProtocolApp.
  1001" activityDate"24/08/2005"gt
• ltoutputDatagt
• ltData_ref identifier_ref"FuGE.ExternalData.1001
  "/gt
• lt/outputDatagt
• ltinputMaterialsgt
• ltMaterialMeasurementgt
• ltmaterialgt
• ltMaterial_ref identifier_ref"FuGE.Material.10
  01"/gt
• lt/materialgt
• lt/MaterialMeasurementgt
• lt/inputMaterialsgt
• ltprotocolgt
• ltProtocol_ref identifier_ref"FuGE.Protocol.1001
  "/gt
• lt/protocolgt
• lt/ProtocolApplicationgt

• Reference to the Data object that lives elsewhere
  in the document
• ltdatagt
• ltExternalData identifier"FuGE.ExternalData.1001"
  gt
• lturigt
• ltURI uri"c\mzData\mzData1.xml"/gt
• lt/urigt
• ltexternalFormatDocumentationgt
• ltURI uri"http//psidev.sourceforge.net/mzdata.
  html"/gt
•  lt/externalFormatDocumentationgt
• lt/ExternalDatagt
• lt/datagt

9
Referencing an mzData file with FuGE

• Reference to the Protocol object
• ltProtocol identifier"FuGE.Protocol.1001"
  name"Mass Spec Protocol 1"gt
• ltactionsgt
• ltAction actionOrdinal"1" actionText"MS/MS
  performed using the following protocol... See the
  mzData file for instrument and software
  parameters"/gt
• lt/actionsgt
• lt/Protocolgt

• ltProtocolApplication identifier"FuGE.ProtocolApp.
  1001" activityDate"24/08/2005"gt
• ltoutputDatagt
• ltData_ref identifier_ref"FuGE.ExternalData.1001
  "/gt
• lt/outputDatagt
• ltinputMaterialsgt
• ltMaterialMeasurementgt
• ltmaterialgt
• ltMaterial_ref identifier_ref"FuGE.Material.10
  01"/gt
• lt/materialgt
• lt/MaterialMeasurementgt
• lt/inputMaterialsgt
• ltprotocolgt
• ltProtocol_ref identifier_ref"FuGE.Protocol.1001
  "/gt
• lt/protocolgt
• lt/ProtocolApplicationgt

10
Referencing an mzData file with FuGE

• ltProtocolApplication identifier"FuGE.ProtocolApp.
  1001" activityDate"24/08/2005"gt
• ltoutputDatagt
• ltData_ref identifier_ref"FuGE.ExternalData.1001
  "/gt
• lt/outputDatagt
• ltinputMaterialsgt
• ltMaterialMeasurementgt
• ltmaterialgt
• ltMaterial_ref identifier_ref"FuGE.Material.10
  01"/gt
• lt/materialgt
• lt/MaterialMeasurementgt
• lt/inputMaterialsgt
• ltprotocolgt
• ltProtocol_ref identifier_ref"FuGE.Protocol.1001
  "/gt
• lt/protocolgt
• lt/ProtocolApplicationgt

ltmaterialsgt ltMaterial identifier"FuGE.Material.1
001" name"Fraction from LC"gt
ltcharacteristicsgtetclt/characteristicsgt
lt/Materialgt lt/materialsgt
11
mzData conclusions

• Referencing an mzData file from FuGE will give
  mass spec data a context in a proteome workflow
• Retrofitting the model is likely to require
  structural changes
• Not likely to be welcomed if it is already being
  implemented
• May be benefits for major future revisions using
  some FuGE concepts
• Will be demonstrated by successful deployment of
  FuGE in other domains

12

• Using FuGE for GelML, Gel IML

13
Existing Gel Models

• PEDRo
• Frank Gibsons gel extension GELI
• Gla-PSI model (Jones 2003)
• AGML (http//bioinformatics.musc.edu/agml/)
• Swiss 2D PAGE
• In-house models from software companies
• and various others that Ive forgotten!
• What features do we want for GelML?

14
Extending FuGE into a gel model

• Concepts of FuGE to understand
• Protocol / ProtocolApplication
• Material
• Data
• Should be extended with more specific types
• Software and Equipment could be extended
• But use of ontology terms may suffice
• Demo models of gel separation and gel data
• Mainly structural, fine details must be worked
  out in PSI context

15
Stage 1 - replace FuGE Root

• ltxscomplexType name"GelMLType"gt
• ltxscomplexContentgt
• ltxsextension base"fugeFuGE.FuGEType/gt
• lt/xscomplexContentgt
• lt/xscomplexTypegt
• ltxselement name"GelML" type"geldataGelMLType"
  abstract"false" substitutionGroup"fugeFuGE"/gt
• This allows GelML to inherit all FuGE
  functionality

16
Stage 2 - represent a gel

• ltxscomplexType name"Gel2DType"gt
• ltxscomplexContentgt
• ltxsextension base"fugeFuGE.Bio.Material.Mater
  ialType"gt
• ltxssequencegt
• ltxselement name"pi_start" type"double"/gt
• ltxselement name"pi_end" type"double"/gt
• ltxselement name"mass_start" type"double"/gt
• ltxselement name"mass_end" type"double"/gt
• lt/xssequencegt
• lt/xsextensiongt
• lt/xscomplexContentgt
• lt/xscomplexTypegt
• ltxselement name"Gel2D" type"gelGel2DType"
  substitutionGroup"fugeMaterial"/gt

17
Stage 2 - represent a gel

• ltxscomplexType name"Gel2DType"gt
• ltxscomplexContentgt
• ltxsextension base"fugeFuGE.Bio.Material.Mater
  ialType"gt
• ltxssequencegt
• ltxselement name"pi_start" type"double"/gt
• ltxselement name"pi_end" type"double"/gt
• ltxselement name"mass_start" type"double"/gt
• ltxselement name"mass_end" type"double"/gt
• lt/xssequencegt
• lt/xsextensiongt
• lt/xscomplexContentgt
• lt/xscomplexTypegt
• ltxselement name"Gel2D" type"gelGel2DType"
  substitutionGroup"fugeMaterial"/gt

• Extend from FuGE Material type
• Add whatever attributes required

18
Stage 3 - represent gel separation

• ltxscomplexType name"Gel2DSeparation"gt
• ltxscomplexContentgt
• ltxsextension base"fugeFuGE.Common.Protocol.Pr
  otocolApplicationType"gt
• ltxssequencegt
• ltxselement name"Gel2DUsed"gt
• ltxsannotationgt
• ltxsdocumentationgtA reference to the Gel
  material on which the separation takes place
• lt/xsdocumentationgt
• lt/xsannotationgt
• ltxscomplexTypegt
• ltxssequencegt
• ltxselement name"Gel2D_ref"gt
• ltxscomplexTypegt
• ltxsattribute name"identifier_ref"
  type"xsstring" use"required"/gt
• lt/xscomplexTypegt
• lt/xselementgt
• closing tags

19
Example schema for a gel separation

• ltxscomplexType name"Gel2DSeparation"gt
• ltxscomplexContentgt
• ltxsextension base"fugeFuGE.Common.Protocol.Pr
  otocolApplicationType"gt
• ltxssequencegt
• ltxselement name"Gel2DUsed"gt
• ltxsannotationgt
• ltxsdocumentationgtA reference to the Gel
  material on which the separation takes place
• lt/xsdocumentationgt
• lt/xsannotationgt
• ltxscomplexTypegt
• ltxssequencegt
• ltxselement name"Gel2D_ref"gt
• ltxscomplexTypegt
• ltxsattribute name"identifier_ref"
  type"xsstring" use"required"/gt
• lt/xscomplexTypegt
• lt/xselementgt
• closing tags

• Extend from ProtocolApplication
• This allows definition of input and output
  samples

20
Example schema for a gel separation

• ltxscomplexType name"Gel2DSeparation"gt
• ltxscomplexContentgt
• ltxsextension base"fugeFuGE.Common.Protocol.Pr
  otocolApplicationType"gt
• ltxssequencegt
• ltxselement name"Gel2DUsed"gt
• ltxsannotationgt
• ltxsdocumentationgtA reference to the Gel
  material on which the separation takes place
• lt/xsdocumentationgt
• lt/xsannotationgt
• ltxscomplexTypegt
• ltxssequencegt
• ltxselement name"Gel2D_ref"gt
• ltxscomplexTypegt
• ltxsattribute name"identifier_ref"
  type"xsstring" use"required"/gt
• lt/xscomplexTypegt
• lt/xselementgt
• closing tags

• Reference the details of the gel used

21
Example XML for gel separation

• ltGel2DSeparation xmlns"http//psi.org/gel"
  identifier"PSI.Gel2DSep.1001"gt
• ltinputMaterials xmlns"http//fuge.org/core"gt
• ltMaterialMeasurementgt
• ltmaterialgt
• ltMaterial_ref identifier_ref"PSI.Material.100
  1"/gt
• lt/materialgt
• lt/MaterialMeasurementgt
• lt/inputMaterialsgt
• ltprotocol xmlns"http//fuge.org/core"gt
• ltProtocol_ref identifier_ref"PSI.Protocol.1001"
  /gt
• lt/protocolgt
• ltGel2DUsedgt
• ltGel2D_ref identifier_ref"PSI.Gel2D.1001"/gt
• lt/Gel2DUsedgt
• lt/Gel2DSeparationgt

22
Example XML for gel separation

• ltGel2DSeparation xmlns"http//psi.org/gel"
  identifier"PSI.Gel2DSep.1001"gt
• ltinputMaterials xmlns"http//fuge.org/core"gt
• ltMaterialMeasurementgt
• ltmaterialgt
• ltMaterial_ref identifier_ref"PSI.Material.100
  1"/gt
• lt/materialgt
• lt/MaterialMeasurementgt
• lt/inputMaterialsgt
• ltprotocol xmlns"http//fuge.org/core"gt
• ltProtocol_ref identifier_ref"PSI.Protocol.1001"
  /gt
• lt/protocolgt
• ltGel2DUsedgt
• ltGel2D_ref identifier_ref"PSI.Gel2D.1001"/gt
• lt/Gel2DUsedgt
• lt/Gel2DSeparationgt

• Define input materials for the separation
• Reference to the Material used as input
  specified elsewhere
• ltMaterial identifier"PSI.Material.1001"
  name"protein sample"gt
• ltcharacteristicsgt etc. lt/characteristicsgt
• lt/Materialgt

23
Example XML for gel separation

• Reference the Protocol that defines this gel
  separation
• ltProtocol identifier"PSI.Protocol.1001"gt
• ltparametersgt
• ltParameter identifier"PSI.Params.1001"
  name"1stStageVoltage"gtlt/Parametergt
• lt/parametersgt
• ltactionsgt
• ltAction actionText"The text for the first
  dimension of the gel separation goes here"
  actionOrdinal"1"/gt
• ltAction actionText"The text for the second
  dimension of the gel separation goes here"
  actionOrdinal"2"/gt
• lt/actionsgt
• lt/Protocolgt

• ltGel2DSeparation xmlns"http//psi.org/gel"
  identifier"PSI.Gel2DSep.1001"gt
• ltinputMaterials xmlns"http//fuge.org/core"gt
• ltMaterialMeasurementgt
• ltmaterialgt
• ltMaterial_ref identifier_ref"PSI.Material.100
  1"/gt
• lt/materialgt
• lt/MaterialMeasurementgt
• lt/inputMaterialsgt
• ltprotocol xmlns"http//fuge.org/core"gt
• ltProtocol_ref identifier_ref"PSI.Protocol.1001"
  /gt
• lt/protocolgt
• ltGel2DUsedgt
• ltGel2D_ref identifier_ref"PSI.Gel2D.1001"/gt
• lt/Gel2DUsedgt
• lt/Gel2DSeparationgt

24
Example XML for gel separation

• Reference the details of the gel used
• ltGel2D xmlnshttp//psi.org/gel
  identifier"PSI.Gel2D.1001"gt
• ltpi_startgt4lt/pi_startgt
• ltpi_endgt7lt/pi_endgt
• ltmass_startgt10000KDalt/mass_startgt
• ltmass_endgt50000KDalt/mass_endgt
• lt/Gel2Dgt

• ltGel2DSeparation xmlns"http//psi.org/gel"
  identifier"PSI.Gel2DSep.1001"gt
• ltinputMaterials xmlns"http//fuge.org/core"gt
• ltMaterialMeasurementgt
• ltmaterialgt
• ltMaterial_ref identifier_ref"PSI.Material.100
  1"/gt
• lt/materialgt
• lt/MaterialMeasurementgt
• lt/inputMaterialsgt
• ltprotocol xmlns"http//fuge.org/core"gt
• ltProtocol_ref identifier_ref"PSI.Protocol.1001"
  /gt
• lt/protocolgt
• ltGel2DUsedgt
• ltGel2D_ref identifier_ref"PSI.Gel2D.1001"/gt
• lt/Gel2DUsedgt
• lt/Gel2DSeparationgt

25
Example XML define output spots

• ltGel2DSeparation xmlns"http//psi.org/gel"
  identifier"PSI.Gel2DSep.1001"gt
• ltoutputMaterials xmlns"http//fuge.org/core"gt
• ltMaterial_ref identifier_ref"PSI.GelSpot1"/gt
• ltMaterial_ref identifier_ref"PSI.GelSpot2"/gt
• ltMaterial_ref identifier_ref"PSI.GelSpot1007"/gt
  
• lt/outputMaterialsgt

• Could also define output materials e.g.
  PhysicalGelSpot
• ltPhysicalGelSpot xmlns"http//psi.org/gel"
  identifier"PSI.GelSpot1"gt
• ltPixelCoordXgt367lt/PixelCoordXgt
• ltPixelCoordYgt2011lt/PixelCoordYgt
• lt/PhysicalGelSpotgt

26
1D Gels

• Gel1D and GelLane defined separately
• GelLane has own ProtocolApplication to reference
  its inputMaterials
• The separation within a lane, produces
  PhysicalBands
• These can go on for further treatment

27
Gel data Gel IML

• Demo model of gel images and spots
• Will demo very simple example here
• More complex gel spot model can be discussed
• Some issues with representing data in XML

28
Representing a gel image

• ltxscomplexType name"GelImageType"gt
• ltxscomplexContentgt
• ltxsextension base"fugeFuGE.Bio.Data.ExternalD
  ataType"gt
• ltxssequencegt
• ltxselement name"PixelXSize" type"int"/gt
• ltxselement name"PixelYSize" type"int"/gt
• lt/xssequencegt
• lt/xsextensiongt
• lt/xscomplexContentgt
• lt/xscomplexTypegt
• ltxselement name"GelImage" type"geldataGelImage
  Type" abstract"false" substitutionGroup"fugeEx
  ternalData"/gt
• FuGE.ExternalData allows a reference to an
  external file
• Could give additional attributes by extending
  this base type

29
Example Gel Image XML

• ltdatagt
• ltGelImage xmlns"http//psi.org/geldata"
  identifier"PSI.GelImage.1001"gt
• lturi xmlns"http//fuge.org/core"gt
• ltURI uri"MouseExperimentGel1001.tiff"/gt
• lt/urigt
• ltPixelXSizegt3200lt/PixelXSizegt
• ltPixelYSizegt4200lt/PixelYSizegt
• lt/GelImagegt
• lt/datagt

Note Pixel sizes are in fact redundant (this
could be deduced from image)
30
Sample XML for Gel Spots
ltGelSpotGroup xmlns"http//psi.org/geldata"
identifier"PSI.Dimension.1001"gt
ltdimensionElements xmlns"http//fuge.org/core"
gt ltDimensionElement
identifier"PSI.GelSpot.1001"/gt
ltDimensionElement identifier"PSI.GelSpot.10
02"/gt ltDimensionElement
identifier"PSI.GelSpot.1003"/gt
ltDimensionElement identifier"PSI.GelSpot.10
04"/gt ltDimensionElement
identifier"PSI.GelSpot.1005"/gt
ltDimensionElement identifier"PSI.GelSpot.10
06"/gt ltDimensionElement
identifier"PSI.GelSpot.1007"/gt
lt/dimensionElementsgt
lt/GelSpotGroupgt ltSpotMeasures
xmlns"http//psi.org/geldata" identifier"PSI.Dim
ension.1002"gt
ltdimensionElements xmlns"http//fuge.org/core"gt
ltSpotYCoord
xmlns"http//psi.org/geldata" identifier"PSI.DE.
1001"/gt ltSpotXCoord
xmlns"http//psi.org/geldata" identifier"PSI.DE.
1002"/gt ltSpotArea
xmlns"http//psi.org/geldata" identifier"PSI.DE.
1003"/gt ltSpotVolume
xmlns"http//psi.org/geldata" identifier"PSI.DE.
1004"/gt lt/dimensionElementsgt
lt/SpotMeasuresgt
ltDimension identifier"PSI.Dimension.1003"
name"Gel Dimension"gt
ltdimensionElementsgt
ltDimensionElement identifier"PSI.Gel.1" name"1
hour time point"/gt
ltDimensionElement identifier"PSI.Gel.2" name"2
hour time point"/gt
ltDimensionElement identifier"PSI.Gel.3" name"4
hour time point"/gt
lt/dimensionElementsgt
lt/Dimensiongt lt/dimensionsgt
ltdatagt ltGelDataSet
xmlns"http//psi.org/geldata" identifier"PSI.Gel
DataSet.1001" storage"
Matrix of values goes here or
matrix could be in an external file
"gt ltdimension
xmlns"http//fuge.org/core"gt
ltDimension_ref identifier_ref"PSI.Dimension.1
001"/gt ltDimension_ref
identifier_ref"PSI.Dimension.1002"/gt
ltDimension_ref identifier_ref"PSI.Dim
ension.1003"/gt lt/dimensiongt
lt/GelDataSetgt
31
Ways to take this forward

• For separation (GelML)
• Decide what additional attributes and
  associations required
• Extend ProtocolApplication and Material
• For Gel IML
• Extend Data, Dimension, DimensionElement
• These give facilities for linking to
  Investigation structure
• We have some demo models of these parts
• Important Involve software manufacturers!

32
UML or XSD?

• Depends on expertise of developers
• FuGE exists as UML and XML Schema
• XML Schema auto-generated from UML
• Can build UML and output XML Schema
• OR
• Extend directly from XML Schema
• Need weekly conference call involving interested
  participants

33
Benefits of using FuGE

• Format gets model of Investigation for free
• Method for linking experimental factors to Data
  dimensions
• Protocol system is very flexible
• E.g. for storing sample prep details
• Ontology reference system works for simple term
  list and complex concepts
• Future integration with other omics

34

• . some other issues for discussion

35
Issues with multidimensional data in XML

• 2 ways of representing multi-dimensional data in
  XML
• Option 1 Define data dimensions in XML and store
  data in a non-XML multi-dimensional array
• Need more than just an XML parser to understand
  the data values
• Option 2 Define data dimensions and store values
  with the leaf elements (DimensionElements)
• For large data sets, XML is a highly inefficient
  structure for representing multi-dimensional data

36
Option 1 Data Dimensions for gel electrophoresis
Matrix of values
Data
ordered
Dimension (Variables)
Dimension (Gel Spots)
Dimension (Spot Measures)
ordered
ordered
ordered
DE (1h)
DE (Intensity)
DE (Spot1)
DE (2h)
DE (XCoord)
DE (Spot2)
DE (4h)
DE (YCoord)
DE (Spot3)

DE (Area)
DE (Spot3000)
37
Option 1 Data Dimensions for gel electrophoresis
Result is 3011 references 3 dimensions 3
variables 3000 spots 4 spot measures 1 to
matrix of values Coordinates define where in
matrix to find value e.g. 1 hour time point,
spot 255, Area is at position 1.255.4
Matrix of values
Data
ordered
Dimension (Variables)
Dimension (Gel Spots)
Dimension (Spot Measures)
ordered
ordered
ordered
DE (1h)
DE (Intensity)
DE (Spot1)
DE (2h)
DE (XCoord)
DE (Spot2)
Note This does not imply that spots with the
same ID number on different gels correspond with
each other. We need a different mechanism for
this!
DE (4h)
DE (YCoord)
DE (Spot3)

DE (Area)
DE (Spot3000)
38
Option 2 Data Dimensions for gel electrophoresis
Data
DE (Intensity) Value
DE (XCoord) Value
DE (Spot1)
DE (1h)
DE (Spot2)
DE (2h)
DE (YCoord) Value
DE (Spot3)
DE (4h)
DE (Spot3000)
DE (Area) Value
39
Option 2 Data Dimensions for gel electrophoresis
Result is 36000 references 3 variables X 3000
spots X 4 spot measures Values defined with the
DimensionElements As data volumes become larger,
or the number of dimensions increase, using pure
XML is a highly inefficient structure for
representing this kind of data.
Imagine extra variables are being tested Time
course (4 time points), drug dose (5 doses) and
strain (5), average of 3000 gel spots, say 4 spot
measures This is 4 X 5 X 5 X 3000 X 4 1.2
million references The XML parser would be very
slow!! Compared with 3018 references in the
first case This works because the data matrix
can be loaded into memory and can have direct
access to positions.
Data
DE (Intensity) Value
DE (XCoord) Value
DE (Spot1)
DE (1h)
DE (Spot2)
DE (2h)
DE (YCoord) Value
DE (Spot3)
DE (4h)
DE (Spot3000)
DE (Area) Value
40
Restriction vs. Extension

• Note FuGE is supposed to be used by extending
  core classes
• i.e. giving additional attributes or associations
• May be cases where we want to restrict parts of
  FuGE
• E.g. may not want a type of ProtocolApplication
  to have input or output data
• Problem is that there is no good way of doing
  this in XML or UML or code!
• xsrestriction is not well supported for complex
  types
• May be best to do this with documentation

41
Use of general relationships vs. specific

• Example ProtocolApplication has input and output
  materials
• Is a Gel2D an inputMaterial or do we want a
  specific association from GelSeparation?
• Do we want a typed output SeparatedGel, for use
  with a defined scanning event etc.
• Do we want to use outputMaterials association for
  SeparatedGel or a new specific association?
• Should outputMaterials include gel spots
• These are all discussion issues

42
Some other issues to solve

• How to relate spots across gels
• May also be measures associated with these values
  (ratios, relative abundance, confidence
  indicators etc.)
• This could be another Data object that contains
  some of the same Dimensions
• How to relate different channels on a DIGE gel

43
Related Spots across gels
Matrix of values
Data
ordered
Dimension (RelatedSpots)
Dimension (SingleSpots)
Dimension (Spot Measures)
ordered
ordered
ordered
SingleSpot1
RelatedSpotGroup 1
CompositeArea
RelatedSpotGroup 2
CompVolume
Typical value of SingleSpot SpotGroup1.123 i.e.
this is a reference to how to find the single
spot in the other data set
SingleSpot2
RelatedSpotGroup 3
SingleSpot3
44
Related Spots across gels

• For the microarray case, is it implied that the
  features match across dimensions this is not
  true for gel electrophoresis
• One way to define it is to specify a list of
  composite spots

45
DIGE data in FuGE
Matrix of values
Data
ordered
Dimension (DIGE Conditions)
Dimension (DIGESingleSpots)
Dimension (Spot Measures)
ordered
Spot1
Condition 1
Area
Spot2
Condition 2
Volume
Spot3
Ratio
Composite SpotID