The interface that is the use of a Parameterizable class.
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.
An overview of the design using a single omics technique.
The duration of this step, the value should be given as, for example, volthours.
A reference to a record in a database.
The identifier used to look up the record.
The appropriate version of the accession (if applicable).
A single location on a gel.
A measurement parameter (e.g. concentration and volume) for the agent applied.
An action to represent the order of the referenced ElectrophoresisProtocol, with respect to other Actions performed within this parent protocol.
The gel substrate used in any dimension of an electrophoresis assay.
The dimension this gel separates in e.g. for 2D electrophoresis, one Gel separationDimension = 1, other Gel separationDimension = 2.
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.
Multiple boundary points can be used to define a location on an image as pairs of X/Y coordinates that entirely surround the location.
X-coordinate of the boundary point.
X-coordinate of the boundary point.
The Parameterizable interface encapsulates the association of Parameters with ParameterValues.
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.
Base class for instances of Ontology properties
Gel2DApplication is the application of a Gel2DProtocol. An instance of Gel2DApplication should reference SampleLoadingApplication, ElectrophoresisApplication, DetectionApplication and GenericProtocolApplication as its sub-steps, as defined by the referenced Gel2DProtocol.
A reference to the ElectrophoreisProtocol performed within the parent protocol.
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.
A protocol for capturing the details of electrophoresis.
Note: [Generalization to Material, is this correct? A Gel Lane is a material I think but it should probably be related to the Gel using an extension of the sub-components association.] A lane on a gel.
The lane number with respect to the parent gel.
A person for which the attributes are self describing.
A specification of the access right (e.g. read or write) that a specified group (SecurityGroup) has on a particular object.
An Investigation is a self-contained unit of study that contains one or more types of 'omics technology.
Data may have associations to the ProtocolApplication that created them. Data may be produced from a Material through the DataAcquisition or from another Data object through the DataTransformation. Examples of Data are gene expression measurements, or phenotypes associated with genetic manipulations. Data is abstract and must be subclassed in an appropriate domain (i.e. microarray or proteomic experiments).
AgentProtocol allows the user to give details about how a stain or label (DetectionAgent) has been applied.
The use of a piece of software with the requisite Parameters and ParameterValues.
The root container for accessing all objects.
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. It is assumed that Detection is taking place on the ElectrophoresedGel referenced from the Gel2DApplication, Gel1DApplication or OtherGelApplication which has referenced DirectDetection.
The collection of Audit objects (Security, SecurityGroup and Contacts).
A subclass of the abtract Equipment class for capturing the description of Equipment used.
The application of a Gel1DProtocol. Gel1DApplication should reference (via ActionApplication) SampleLoadingApplication, ElectrophoresisApplication and DetectionApplication matching the structure of the referenced Gel1DProtocol.
The medium on which proteins are detected in processes such as autoradiography (example photographic film).
A GenericAction represents a step within a GenericProtocol. It allows a reference to a sub-GenericProtocol, user entered text to describe the GenericAction or a term from a controlled vocabulary to be given.
Free text to describe this Action.
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.
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.
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.
Software represents the software used. Examples of Software include: feature extraction software, clustering software, etc...
The version of software used.
Gel1D is the material produced from a Gel1DApplication representing the combination of the gel substrate with the proteins that have been separated and any detection agents applied.
Collection class for accessing all ExternalData instances in GelML.
An abstract superclass such that either the Voltage or Current can be specified in this electrophoresis step.
An instance of an Ontology class.
A sample excised from a gel.
Represents bibliographic references, including the most common attributes. Note that because a BibliographicReference is Identifiable, a DatabaseEntry can also be specified.
This should ultimately be a data set in its own right i.e. a subclass of InternalData with dimensions etc...
Permission information for an object as to ownership, write and read permissions.
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.
An action to represent the order of the referenced ElectrophoresisProtocol, with respect to other Actions performed within this parent protocol.
The value for a Factor
A single point within a parent dimension.
The Application of a protocol that describes the excision of locations on gels.
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.
A free text description of an object.
The description.
Abstract superclass such that either time points (TimePoint) or a duration (Duration) can be supplied.
Circle is for defining a circular location on an image. The X and Y coordinates correspond with the centroid.
X-coordinate of the centroid of the Circle.
Y-coordinate of the centroid of the Circle.
Radius of the Circle in pixels.
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 complete set of all Material objects in the FuGE document.
A Protocol is a parameterizable description of a method. ProtocolApplication is used to specify the ParameterValues of its Protocol's Parameters.
An ordered step within the parent ElectrophoresisProtocol.
A contact is either a person or an organization.
Tracks information on the contact that creates or modifies an object.
The date of a change.
Indicates whether an action is a creation, modification or a deletion.
This is used to annotate a set of sequences that share the same species, type and PolymerType.
The collection of objects that allow external references.
A single entry from an ontology or a controlled vocabulary. If it is a simple controlled vocabulary, the ontologyURI and ontologyTermURI might be undefined and there would be an OntologyIndividual whose name was the property and who had a single DataProperty whose value was the value for the property. For instance, for an OntologyIndividual based on the MO ontology the attributes might be: The identifier is some unique identifier for individuals, possible a UUID, The name would be what is usually called the local name in the Ontology, for instance 'Age' The ontologyTermURI could be 'http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Age', The ontologyURI could be 'http://mged.sourceforge.net/ontologies/MGEDOntology.owl". The OntologyTerm subclasses are instances of Ontology classes and properties, not the actual terms themselves. An OntologyIndividual, if based on an existing Ontology, can be considered a statement that can be validated against the referenced ontology. The subclasses and their associations are based on the Ontology Definition Model, ad/2005-04-13, submitted to the OMG as a response to RFP ad/2003-03-40, Copyright © 2005 DSTC Pty Ltd. Copyright © 2005 IBM Copyright © 2005 Sandpiper Software, Inc under the standard OMG license terms.
An optional URI that can be resolved to the definition of an Ontology
An optional URI that can be resolved to the definition of an Ontology Class or Property
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.
Represents a segmentation of the data by indexing existing DimensionElements of a Data.
The protocol for one step within an ElectrophoresisProtocol. The referenced parameters capture the details of the step.
A single time point.
Abstract superclass to represent applications of a DetectionProtocol. Its subclasses DirectDetection and IndirectDetection capture the application of the procedure.
The collection of Investigation and Factor objects in the FuGE document.
An address to a repository.
The version for which a DatabaseReference applies.
The location of the Database.
An abstract class for describing biological molecules such as DNA and protein sequences or metabolites.
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.
The complete collection of all Data, Dimension and HigherLevelAnalysis objects.
An application of the referenced ElectrophoresisProtocol.
Voltage parameter.
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.
Temperature parameter.
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.
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
An action to represent the order of the referenced DetectionProtocol, with respect to other Actions performed within this parent protocol.
The dimension gel that the referenced Protocol refers to. For a Gel1DProtocol this value need not be given because there is only one Gel.
The value of a Parameter.
A reference to an image file stored in an external location.
The medium proteins are transfered to during Indirect detection of proteins, such as the membrane in a Western blot.
An application of the SampleLoadingProtocol. SampleLoadingApplication defines how a sample was loaded to a gel. If the sample has been loaded onto a GelLane, the LoadGelRegion association should be used to associate with LoadGelLane. To capture loading a first dimension gel onto a second dimension gel, LoadGelRegion should reference the second dimension gel, GelSampleMeasurement should reference the first dimension gel.
A reference to each AgentProtocol for each agent (stain or label etc.) that is applied within this DetectionProtocol.
Data that is internal to an instance XML document. The storage array will typically use pointer arithmatic to access values based on the rank (e.g. number of) Dimensions and their respective sizes (e.g. the number of contained DimensionElements).
Data external to the XML instance document. The location of the data file is given in the association to the URI class.
Abstract superclass for describing gels following electrophoresis.
A container for domain-specific analyses performed on data. Subclasses must be created for different domains.
Abstract superclass representing the different types of method that could be used to identify a location.
Gel2D is the material produced from a Gel2DApplication representing the combination of the two gel substrates, the proteins that have been separated and any detection agents applied.
Organizations are entities like companies, universities, government agencies for which the attributes are self describing.
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).
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.
The use of a piece of Equipment with the requisite Parameters and ParameterValues.
Manufacturer's identifier for the Equipment.
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.
DirectDetection represents the application of a DetectionProtocol in which a detection agent (stain or label) is applied directly to a gel. It is assumed that Detection is taking place on the ElectrophoresedGel referenced from the Gel2DApplication, Gel1DApplication or OtherGelApplication which has referenced DirectDetection.
Collection class for accessing all GenericMaterial instances used in GelML.
Factors are the dependent variables of an experiment (e.g. time, glucose concentration, ...). Note that Factors can be shared by multiple InvestigationComponents.
The complete set of ConceptualMolecule objects and SequenceAnnotation objects.
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.
A protocol describing the procedure of 1D gel electrophoresis.
ActionApplication mirrors the structure of Actions within Protocols. This allows ActionDeviations to be reported and it can reference sub-ProtocolApplications if they exist.
The equipment (hardware) used in this Protocol. Examples include: computers, scanners, wash stations etc...
A subclass of MaterialMeasurement to be used without being extended in conjunction with GenericProtocolApplication and GenericMaterial to model measured sources of materials.
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.
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.
Groups contacts together based on their security privileges.
The complete set of OntologyIndividual objects referenced in the FuGE document.
The complete set of Protocol, Equipment, Software and ProtocolApplication objects in the FuGE document.
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.
The parameter values for this Parameterizable Application.
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.
Reference to the database where the DatabaseEntry instance can be found.
Measures or attributes for each GelLocation.
The location of the feature.
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.
The ElectrophoresisProtocol performed in the first dimension.
The GelLanes on this Gel.
The physical dimensions of the gel. The term should support values for the three dimensions and units.
The separation range and type of separation performed on this gel. (Example pH range 4-7).
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".
The provider of the Protocol, Equipment or Software.
The set of parameters for the Parameterizable class instance.
Reference to the Gel on which the first dimension separation is performed.
Reference to the Gel on which the second dimension separation is performed.
When a ContactRole is used, it specifies which Contact the role is associated with.
The roles (lab equipment sales, contractor, etc.) the contact fills.
The equipment used in electrophoresis (e.g. power packs, tanks etc.).
The organization a person belongs to.
The group of contacts that have the specified access right on an object.
The type of AccessRight allowed on this object e.g. Read, Write etc.
The association to the techniques that comprise the Investigation.
The providers of the Experiment, its data and annotation.
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 dimensions contained within this Data object.
The type of DetectionAgent applied.
The association to the time parameter is for giving the time and/or duration for which this agent is applied within the DetectionProtocol.
The gel produced by the GelManufactureApplication.
Measured quantities of materials used to create the referenced gel.
The name of this parameter from a controlled vocabulary term.
The underlying software.
The complete set of all Material objects in the FuGE document.
The complete set of ConceptualMolecules
The complete set of BibliographicReferences and Databases.
The collection of Investigation and Factor objects in the FuGE document.
The complete collection of all Data, Dimension and HigherLevelAnalysis objects.
The collection of Audit objects (Security, SecurityGroup and Contacts).
The complete set of Protocol, Equipment, Software and ProtocolApplication objects in the FuGE document.
The complete set of OntologyIndividual objects in the FuGE document.
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.
Reference to the complete set of BibliographicReference objects in the FuGE document.
The complete set of Contacts.
Reference to the complete set of SecurityGroup objects in the FuGE document.
The type of measure e.g. pI / MW
The value for this measure.
The evidence for this measure.
A relationship between GenericSoftware and GenericEquipment to capture that instances of software are specifically associated with instances of equipment.
The gel following the application of a Gel1DProtocol.
The gel material on which this Gel1DProtocol acts.
The protocol used in this Gel1DProtocolApplication.
Each Action may be associated with an OntologyTerm that defines that Action.
Shared annotations for a set of sequences.
Material that is being measured as the source for a ProtocolApplication.
The value of the measured source of material.
ProtocolReference,as the name implies, is a reference to an existing Protocol. It is used to tie together Protocols into complex procedures. For example a "cDNA synthesis" protocol may be broken down into two distinct phases, with the first and second round having distinct default values for common parameters, or defining different sets of parameters, etc.
Associates Equipment and Software together. Indicates that a set of Software run on a single piece of Equipment.
A list of properties associated with the Individual. If based on an external Ontology, the list should be able to be validated against that Ontology.
A reference to the location that this sample was excised from.
The contacts associated with this GelML file such as submitter, lab head, experimenter etc.
Supporting the MIAPE GE, experiment type definition, such as "2D-DIGE", "standard 1D", "standard 2D" etc.
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 evidence or source file for this location set. The referenced file should be in the ginML format when it is finalised.
The image of a gel that these locations refer to.
The type of LocationSet (examples to come).
The owner of the security rights on the object.
Specifies which security groups have permission to view the associated object.
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 ElectrophoresisProtocol performed in the second dimension.
Allows a value to be specified for a FactorValue using an ontology.
Represents a segmentation of the data by indexing existing DimensionElements of a Data.
The set of locations on an image of a gel.
The ElectrophoresedGel from which locations are excised.
The set of locations on a gel as determined by, for instance, a robotic spot picker.
Association from a Material to other Materials that are sub-components (such as wells within an array plate). If a subcomponent undergoes a ProtocolApplication, then the containing Material must also be an input to the ProtocolApplication and be output as a new Material or version of the Material.
Contact details for the Material. The association to ContactRole could specify, for example, the creator or provider of the Material.
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.
The complete set of Materials.
Each Protocol may be composed of a number of steps, each of which is represented by an Action.
Hardware used by this protocol.
Software used by this Protocol.
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.
The contact for creating or changing the instance referred to by the Audit.
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 reference to the SampleLoadingAction.
A reference to the FirstDimensionAction.
A reference to the SecondDimensionAction.
Reference to the complete set of BibliographicReference objects in the FuGE document.
Reference to the complete set of Database objects in the FuGE document.
The DimensionElements segmented by this DataPartition.
A reference to the time point or duration of this step.
Other parameters that are used during this step.
The value at which the Current or Voltage is set at for the duration of this step.
The maximum value of the Current or Voltage for the duration of this step.
The temperature during this step.
The set of Investigations.
Reference to the complete set of Factor objects in the FuGE document.
Reference to the complete set of Dimension objects in the FuGE document.
Reference to the complete set of HigherLevelAnalysis objects in the FuGE document.
Reference to the complete set of Data objects in the FuGE document.
The Gel on which Electrophoresis takes place. The referenced gels must be one of the gels associated as inputs to Gel1DApplication, Gel2DApplication or OtherGelApplication.
The instance(s) of the child Individual restriction on the Parent Individual
The parameter this value is for.
The value of the parameter. Will have the datatype of its associated Parameter.
A measured quantity of the sample loaded onto the gel.
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 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.
A reference to the GelLanes defined as part of the Gel substrate that this ElectrophoresedGel came from.
A relationship between GenericSoftware and GenericEquipment to capture that instances of software are specifically associated with instances of equipment.
Association to the Data on which the HigherLevelAnalysis has been performed.
The containing organization (the university or business which a lab belongs to, etc.)
References to entries in databases.
References to existing literature.
The underlying hardware.
The DefaultValue of a Parameter is to be assumed the proper value when a Parameterizable object has been applied. It may be over-ridden at the time the ParameterizableApplication is instantiated.
The FactorValues for this Factor e.g. the time points in a time course.
The category of a Factor could be biological (time, [glucose]) or methodological (differing cDNA preparation protocols).
Reference to the complete set of ConceptualMolecule objects in the FuGE document.
Reference to the complete set of SequenceAnnotation objects in the FuGE document.
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.
Association to the Action that is being performed as recorded by this ActionApplication.
Used to define human readable notes for annotating deviations to an Action during the ActionApplication.
Association to ProtocolApplication if a hierarchical Protocol has been defined representing the child step of the Protocol.
Associates Equipment and Software together. Indicates that a set of Software run on a single piece of Equipment.
Allows specification of additional ontology entries related to the instance being described that are not directly specified elsewhere.
A list of Audit instances that track changes to the instance of Describable.
Free hand text descriptions.
Information on the security for the instance of the class.
A URI associated with a Describable object.
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.
The members of the SecurityGroup.
The complete set of OntologyIndividuals in the FuGE document.
Reference to all Protocol objects in the FuGE document.
Reference to all Software objects in the FuGE document.
Reference to the complete set of ProtocolApplication objects in the FuGE document.
Reference to all Equipment objects in the FuGE document.
The data produced by a ProtocolApplication.
The input data for a ProtocolApplication.
Association to the Material(s) created as output by this ProtocolApplication. Testing
Association from a ProtocolApplication to a measurement of the quantity of the source (input) Material(s) used.
The protocol that is being used.
Association to the ActionApplication steps that comprise this ProtocolApplication.
The use of software for the application of the protocol.
The use of hardware for the application of the protocol.
Used to define human readable notes for annotating deviations to the protocol on a Protocol-wide level, for example, if the order of execution of Actions was changed in some non-destructive manner.
The people or organizations who performed the protocol. ContactRole could be used to specify the part of the Protocol performed by a particular Contact.