An overview of the design using a single omics technique.
The description of the factors (TimeCourse, Dosage, etc.) that segment the Data. The aggregation of Factors is limited to a single Investigation.
Description of the replicate strategy of the InvestigationComponent.
Description of the quality control aspects of the InvestigationComponent.
Description of the normalization strategy of the InvestigationComponent.
The design of the investigation with respect to a single technique (InvestigationComponent) e.g. dye swap.
Complete set of all ProtocolApplications for a given InvestigationComponent. This allows access to the complete set of Materials and Data for the component.
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 x axis represents the distance from the anode (+) to the cathode (-).
T y axis is the matrix length.
The z axis dimensions is the matrix depth.
A specification of the access right (e.g. read or write) that a specified group (SecurityGroup) has on a particular object.
The type of AccessRight allowed on this object e.g. Read, Write etc.
The group of contacts that have the specified access right on an object.
The protocol for one step within an ElectrophoresisProtocol. The referenced parameters capture the details of the step.
DetectingProtocol is for defining how 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
The GenericEquipment used within the DetectionProtocol.
Abstract superclass representing Duration and TimePoints.
The root container for accessing all objects.
A range for the runtime value of a Parameter.
The complete collection of all Data, Dimension and HigherLevelAnalysis objects.
A single dimension of a coordinate system. The DimensionElement class represents the discreet domain values represented in this dimension. A dimension with infinite domain values is not modeled here, for practical reasons.
An instance of an Ontology data property. So an individual of Age might be restricted to a value of 8.
An optional data type attribute which should be either one of the CORBA Any types or one of the XML Schema simple types.
If the Parent Individual is associated with a has_datatype property, instead of stating that property explicity, it could be used as the value of the datatype attribute, or the datatype can be provided as a hint to applications on how to store the value.
The value associated with the DataProperty instance.
A subclass of the abstract Paramter class to represent a parameter that is defined by a controlled vocabulary term.
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)
Abstract superclass for describing gels following electrophoresis.
A reference to the GelLanes defined as part of the Gel substrate that this ElectrophoresedGel came from.
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.
A URI is short for Uniform Resource Identifier.
A URI is a compact sequence of characters that identifies an abstract or physical resource.
The Uniform Resource Indicator for this object.
Base class for instances of Ontology properties
The source ontology or controlled vocabulary list that ontology terms have been obtained from.
A URI that references the location of the ontology.
A Protocol is a parameterizable description of a method. ProtocolApplication is used to specify the ParameterValues of its Protocol's Parameters.
The types of outputs produced by this Protocol e.g. organisms, solutions, data formats etc.
The types of inputs this Protocol can take e.g. organisms, solutions, data formats etc.
OtherGelExperiment captures the ProtocolApplications that should be reported for a type of gel electrophoresis other than 1D or 2D in a GelML file.
Gel2D is the material produced from a Gel2DApplication representing the combination of the two gel substrates and the proteins that have been separated.
A subclass of the abstract Material class, which should be used in conjunction with controlled vocabulary terms describe Materials of any types used in an investigation.
The collection of objects that allow external references.
The resolution of the image.
The unit of resolution.
The value of the resolution.
A single point within a parent dimension.
The use of a protocol with the requisite Parameters and ParameterValues. ProtocolApplications can take Material or Data (or both) as input and produce Material or Data (or both) as output.
When the protocol was applied.
Abstract class with sub-classes that define different specifications of a defaultValue.
A protocol describing the procedure of 2D gel electrophoresis.
Material represents any kind of substance used in an experimental workflow, such as whole organisms, cells, DNA, solutions, compounds and experimental substances (gels, arrays etc.). The Material class can be extended by adding subclasses to model domain specific properties or the relationships to OntologyIndividual can be used to describe the characteristics and type of Material.
Materials can be related to other materials through a directed acyclic graph (represented by ProtocolApplication(s)). Sub-component materials can be represented by the self-association on Material (e.g. Wells within a array)
The characteristics of a Material.
Measures of the quality of the Material.
The type of material used, i.e. RNA, DNA, lipid, phosphoprotein, organism etc.
An Investigation is a self-contained unit of study that contains one or more types of 'omics technology.
The biological design type of the Investigation, such as toxicity, drug-response, gene knockout etc.
Investigationally important materials. These are typically a species or set of strains. This might also be a bucket of seawater or a pound of dirt. It is expected that these Materials are referenced by a ProtocolApplication.
The medium on which proteins are detected in processes such as autoradiography (example photographic film).
The complete set of ConceptualMolecule objects and SequenceAnnotation objects.
Represents bibliographic references, including the most common attributes. Note that because a BibliographicReference is Identifiable, a DatabaseEntry can also be specified.
Gel2DExperiment captures the ProtocolApplications that should be reported for 2D gel electrophoresis in a GelML file.
The gel matrix used in any dimension of an electrophoresis assay.
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 association can specify component gels, for example to represent a stacking gel.
The dimension this gel separates in e.g. for 2D electrophoresis, one Gel separationDimension = 1, other Gel separationDimension = 2.
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.
The mass of a substance.
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.
MaterialMeasurement represents the quantity of a source Material used in a MaterialTreatment. The Measurement is represented using an ontology to allow complex specifications of measurements.
The value of the measured source of material.
A Sequence is a representation of a DNA, RNA, or protein sequence.
The number of residues in the biosequence.
If length not positively known will be true
Indicates if the BioSequence is circular in nature.
The actual components of the sequence, for instance, for DNA a string consisting of A,T,C and G.
The attribute is optional and instead of specified here, can be found through the DatabaseEntry.
Shared annotations for a set of sequences.
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.
A free text description of an object.
The description.
An instance of an Ontology object property that restricts the parent individual to its child individual. So an Age individual may be restricted to an Individual unit of years.
Abstract superclass representing the different formats for representing the volume of a substance.
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 X axis.
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 type of substance, the substance name has not been given as free text in the SubstanceAction.
The characteristics of the substance.
The name of the substance given as free text.
A specification of the use of the substance within the protocol.
A reference to a record in a database.
The identifier used to look up the record.
The appropriate version of the accession (if applicable).
Reference to the database where the DatabaseEntry instance can be found.
The Concentration of a substance.
GenericProtocol should be used in conjunction with GenericAction to describe protocols in a data format for cases where no explicit extension of Protocol has been developed.
The equipment (hardware) used in this Protocol. Examples include: computers, scanners, wash stations etc...
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.
A Action is one step of a Protocol. Sets of ordered Actions define the Protocol.
The order by which this Action should occur with respect to the Parent protocol. Note that two Actions with the same actionOrdinal are performed in parallel or the order is not important.
An absolute volume parameter.
A protocol for capturing experiments that cannot be represented by Gel1DProtocol or Gel2DProtocol.
A person for which the attributes are self describing.
The organization a person belongs to.
An address to a repository.
The version for which a DatabaseReference applies.
The location of the Database.
An atomic defaultValue i.e. one that has a single value.
The use of a substance within a protocol at a particular time point or for a particular duration.
A subclass of MaterialMeasurement to be used without being extended in conjunction with GenericProtocolApplication and GenericMaterial to model measured sources of materials.
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.
A range for the default value of a Parameter.
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 complete set of OntologyTerm objects referenced in the document.
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.
The equipment used in electrophoresis (e.g. power packs, tanks etc.).
Buffers other than the running buffer used in the ElectrophoresisProtocol.
The running buffer used in the ElectrophoresisProtocol.
A duration parameter. Note: values for absolute or relative time can be using the Parameter DefaultValue model.
A Parameter is a replaceable value in a Parameterizable class. Examples of Parameters include: scanning wavelength, laser power, centrifuge speed, multiplicative errors, the number of input nodes to a SOM, and PCR temperatures.
The simple data type of the Parameter e.g. Boolean, float, int, String etc.
The role that a Contact plays in an organization. A Contact may have several Roles within scope, and as such, associations to ContactRole allow the use of a Contact in a certain manner. Examples might include a provider, or a data analyst.
The roles (lab equipment sales, contractor, etc.) the contact fills.
When a ContactRole is used, it specifies which Contact the role is associated with.
Abstract superclass representing the groups of ProtocolApplications that should be represented in a valid GelML document.
Supporting the MIAPE GE, experiment type definition, such as "2D-DIGE", "one-dimensional gel electrophoresis", "two-dimensional gel electrophoresis" etc.
The date the experiment was initiated on (see MIAPE 1.1.1).
Circle is for defining a circular location on an image.
Radius of the Circle in pixels.
Permission information for an object as to ownership, write and read permissions.
The owner of the security rights on the object.
The value for a Factor
Allows a value to be specified for a FactorValue using an ontology.
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.
A tuple designed to store data, keyed by a name and type.
The name of the key.
The value of the name.
The type of the key.
Collection class for accessing all Software, Protocol, Equipment and GenericProtocolApplications.
ActionApplication mirrors the structure of Actions within Protocols and allows ActionDeviations to be reported.
RULE:
If an Action references a sub-Protocol, an ActionApplication must be created and reference a sub-ProtocolApplication of the corresponding type (or GenericProtocolApplication) to mirror the Protocol structure.
ActionApplications can be (but need not be) created for simple Actions.
Association to the Action that is being performed as recorded by this ActionApplication.
Association to ProtocolApplication if a hierarchical Protocol has been defined representing the child step of the Protocol.
The Gel output from an OtherGelApplication representing the combination of gel substrates and proteins separated.
A single boundary point used in a BoundaryPointSet.
X-coordinate of the boundary point.
X-coordinate of the boundary point.
The medium proteins are transfered to during Indirect detection of proteins, such as the membrane in a Western blot.
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 use of a piece of software with the requisite Parameters and ParameterValues.
The underlying software.
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 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.
The collection of Audit objects (Security, SecurityGroup and Contacts).
Collection class for accessing all GenericMaterial instances used in GelML.
Collection class for accessing all ExternalData instances in GelML.
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.
Input material can be to an electrophoresed gel but could also be various other kinds of material e.g. TransferMedium or DetectionMedium.
Abstract class that allows subclasses to inherit associations that enable objects to be given a text description, additional annotations as Ontology entries, a URI, associations to Audit for tracking changes, and the association to Security for indicating permissions.
A list of Audit instances that track changes to the instance of Describable.
Free hand text descriptions.
A URI associated with a Describable object.
Allows specification of additional ontology entries related to the instance being described that are not directly specified elsewhere.
Allows specification of name, value, type triples. Meant to primarily help in-house, pipeline processing of instances by providing a place for values that are not part of the specification proper.
Information on the security for the instance of the class.
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.
A subclass of ProtocolApplication to be used as it is in data formats without being extended.
Extends_outputMaterials@
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.
A measured quantity of Material loaded onto the Gel. If no measurement is given, it is assumed that the entire quantity of material was loaded.
The sample loaded onto the gel. This will be either a reference to a protein sample modelled as GenericMaterial or a reference to another Gel if one gel is loaded onto the other.
The estimated or know pH range of a gel that separates substances based on their isoelectric point.
This is used to annotate a set of sequences that share the same species, type and PolymerType.
A choice of protein, RNA, or DNA.
The type of Sequence, e.g. gene, exon, UniGene cluster, fragment, BAC, EST, etc.
The organism from which this sequence was obtained.
A complex runtime value for the Parameter, such as a term from a controlled list or a function.
A measured value, property or annotation about a GelLocation, such as predicted MW or pI.
The value for this measure.
The evidence for this measure, such as molecular weight markers, mass spectrometry etc.
An atomic runtime value for the Parameter.
Data external to the XML instance document. The location of the data file is given in the association to the URI class.
A URI to access documentation and tools to interpret the external format of the ExternalData instance. For example, XML Schema or static libraries (APIs) to access binary formats.
Other classes in the model can be specified as sub-classes, inheriting from Identifiable. Identifiable gives classes a unique identifier within the scope and a name that need not be unique. Identifiable also provides a mechanism for annotating objects with BibliographicReference(s) and DatabaseEntry(s).
References to existing literature.
An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
The potentially ambiguous common identifier.
A protocol describing the procedure of 1D gel electrophoresis.
The Parameterizable interface encapsulates the association of Parameters with ParameterValues.
The type of a Protocol, Equipment or Software. Examples of types include: RNA extraction, mass spectrometer, image analysis etc... Note that the type association can be used for annotating complex protocols with terms such as "assay" or "phase".
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.
A Boolean default value for the Parameter
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.
An abstract class for describing biological molecules such as DNA and protein sequences or metabolites.
Represents a segmentation of the data by indexing existing DimensionElements of a Data.
The DimensionElements segmented by this DataPartition.
A single location on a gel.