Collection class for accessing all GenericMaterial instances used in GelML. Collection class for accessing all ExternalData instances in GelML. The root of the GelML document.

The provider of the document in terms of the Contact and the software the produced the document instance.

Gel2DExperiment captures the ProtocolApplications that should be reported for 2D gel electrophoresis in a GelML file. Collection class for accessing all Software, Protocol, Equipment and GenericProtocolApplications. Abstract superclass representing the groups of ProtocolApplications that should be represented in a valid GelML document. The experiment type definition, such as "2D-DIGE", "one-dimensional gel electrophoresis", "two-dimensional gel electrophoresis" etc. The date the experiment was initiated on. Gel1DExperiment captures the ProtocolApplications that should be reported for 1D gel electrophoresis in a GelML file. OtherGelExperiment captures the ProtocolApplications that should be reported for a type of gel electrophoresis other than 1D or 2D in a GelML file. The volume of a substance relative to the medium in which it is in. 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. An absolute volume parameter. Abstract superclass representing the different formats for representing the volume of a substance. 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. The characteristics of the substance. The type of substance, the substance name has not been given as free text in the SubstanceAction. The name of the substance given as free text. A specification of the use of the substance within the parent protocol. The use of a substance within a protocol at a particular time point or for a particular duration. 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. The type of mixture e.g. buffer, solution, protein complex etc. The name of the mixture represented by this protocol. A duration parameter. Note: values for absolute or relative time can be using the Parameter DefaultValue model. A single time point. A duration parameter. Note: values for absolute or relative time can be using the Parameter DefaultValue model. Abstract superclass representing Duration and TimePoints. The Concentration of a substance. The mass of a substance. Gel2D is the material produced from a Gel2DApplication representing the combination of the two gel substrates and the proteins that have been separated. A protocol describing the procedure of 2D gel electrophoresis. 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. Reference to the Gel on which the first dimension separation is performed. Reference to the Gel on which the second dimension separation is performed.

The Gel2DProtocol that has been run.

An action to represent the order of the referenced ElectrophoresisProtocol, with respect to other Actions performed within this parent protocol.

The ElectrophoresisProtocol performed in the first dimension.

An action to represent the order of the referenced ElectrophoresisProtocol, with respect to other Actions performed within this parent protocol.

The ElectrophoresisProtocol performed in the second dimension.

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. The application of a Gel1DProtocol. Gel1DApplication should reference (via ActionApplication) SampleLoadingApplication and ElectrophoresisApplication matching the structure of the referenced Gel1DProtocol. The gel material on which this Gel1DProtocol acts.

The protocol used in this Gel1DProtocolApplication.

A protocol describing the procedure of 1D gel electrophoresis. 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.

The DetectionProtocol that has been run.

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.

The medium on which proteins are detected in processes such as autoradiography (example photographic film). 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 Any equipment used in the DetectionProtocol. DirectDetection represents the application of a DetectionProtocol in which a detection agent (stain or label) is applied directly to a gel. 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. An instance of TransferMedium following the transfer of proteins. The TransferMedium prior to the transfer of proteins. An instance of DetectionMedium prior to the detection of proteins. An instance of DetectionMedium following the detection of proteins. The medium proteins are transfered to during Indirect detection of proteins, such as the membrane in a Western blot. The protocol for one step within an ElectrophoresisProtocol. The referenced parameters capture the details of the step. 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. The electrical setting that the parameter value applies to, such as: hold, maximum, gradient and so on. A reference to the ElectrophoreisProtocol performed within the parent protocol.

A reference to the ElectrophoresisProtocol

An application of the referenced ElectrophoresisProtocol.

The ElectrophoresisProtocol that is applied.

The Gel on which Electrophoresis takes place. The referenced gels must be one of the gels associated as inputs to Gel1DApplication, Gel2DApplication or OtherGelApplication.

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. Buffers other than the running buffer used in the ElectrophoresisProtocol. The running buffer used in the ElectrophoresisProtocol. Temperature parameter. 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.

The specification of the buffer and its components.

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. The x-coordinate of the starting position of the chain code. The y-coordinate of the starting position of the chain code. 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. A single boundary point used in a BoundaryPointSet. x-coordinate of the boundary point. y-coordinate of the boundary point. Circle is for defining a circular location on an image. Radius of the Circle in pixels. A sample excised from a gel. These materials can be referenced by formats modelling other techniques, such as mass spectrometry.

A reference to the location that this sample was excised from.

The Application of a protocol that describes the excision of locations on gels. The set of locations on an image of a gel. The set of locations on a gel as determined by, for instance, a robotic spot picker at runtime.

The ElectrophoresedGel from which locations are excised.

The Protocol applied for excision. Note that equipment and software used should be provided using the associations from GenericProtocol to GenericEquipment and GenericSoftware.

Abstract superclass representing the different types of method that could be used to identify a location. Added for M2 A single location on a gel. 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. A measured value, property or annotation about a GelLocation, such as predicted MW or pI. The evidence for this measure, such as molecular weight markers, mass spectrometry etc. LocationSet represents a set of locations on a gel image. The evidence or source file for this location set. The referenced file should be in the GelInfoML format when it is finalised. The type of LocationSet e.g. ImageSet, GelSet.

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.

The image of a gel that these locations refer to.

Rectangle is for defining a rectangular location on an image. The X/Y coordinates correspond with the upper left corner of the rectangle. The X-Coordinate of the upper left corner of the rectangle. The Y-Coordinate of the upper left corner of the rectangle. The size of the rectangle along the X axis. The size of the rectangle along the Y axis. 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. Abstract superclass for describing gels following electrophoresis. A reference to the GelLanes defined as part of the Gel substrate that this ElectrophoresedGel came from. The gel matrix used in any dimension of an electrophoresis assay. The association can specify component gels, for example to represent a stacking gel. The percentage acrylamide in the gel. Any additional substances other than those specified by defined classes should be reported here. 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. The dimension this gel separates in e.g. for 2D electrophoresis, one Gel separationDimension = 1, other Gel separationDimension = 2. A lane on a gel. The lane number with respect to the parent gel. The application of a protocol that defines how a gel was produced. The gel produced by the GelManufactureApplication.

The protocol applied in the GelManufactureApplication.

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. The unit of the Dimensions. The x axis represents the distance from the anode (+) to the cathode (-). The y axis is the matrix length. The z axis dimensions is the matrix depth. The separation range of the gel. This can use the RangeValue or ComplexValue specification. The type of separation range, e.g. logarithmic, linear etc. The estimated or know pH range of a gel that separates substances based on their isoelectric point. The estimated or known range of a gel that separates substances by their molecular weight. A gel range other than molecular weight or pH by which proteins are separated. The type of separation performed i.e. the biophysical property that is separated on. 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). Ratio of bisacrylamide (i.e. value =97 if ratio is 97:3) Ratio of bisacrylamide (i.e. value =3 if ratio is 97:3) An action to represent the order of the referenced SampleLoadingProtocol, with respect to other Actions performed within this parent protocol. Optional lane number attribute for specifying the intended lane that this protocol should be applied to. The gel dimension that the referenced SampleLoadingProtocol refers to. Note, this is not required in the context of Gel1DProtocol.

A reference to the SampleLoadingProtocol.

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).

The SampleLoadingProtocol that has been applied.

The gel onto which the sample was loaded. The gel must be an instance of Gel referenced from Gel1DApplication, Gel2DApplication or OtherGelApplication.

The lane on which the sample was loaded.

A Protocol defining how samples are loaded onto a Gel or GelLanes. Any parameters related to the SampleLoadingProtocol. Any equipment used in the SampleLoadingProtocol. 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. 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.

A reference to the GenericProtocol performed between the dimensions specified.

The Gel output from an OtherGelApplication representing the combination of gel substrates and proteins separated. 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. The gels on which separations are performed. The Gel(s) output from an OtherGelApplication representing the combination of gel substrates and proteins separated.

The OtherGelProtocol that is applied.

A protocol for capturing experiments that cannot be represented by Gel1DProtocol or Gel2DProtocol. An action to represent the order of the referenced ElectrophoresisProtocol, with respect to other Actions performed within this parent protocol. 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.

The ElectrophoresisProtocol performed in this dimension.

A reference to an image file stored in an external location. The channel or wavelength at which the image was scanned. The value of the resolution of the Image. The image bit-depth e.g. 8 bit, 16 bit. The x-axis dimension of the image in pixels. The y-axis dimension of the image in pixels. 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.

The Image produced from ImageAcquisitionApplication.

The protocol describing this image acquisition (scanning) procedure.

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.