A free text description of an object.
The description.
A reference to a record in a database.
The identifier used to look up the record.
The appropriate version of the accession (if applicable).
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).
A person for which the attributes are self describing.
An instance of an Ontology 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.
A subclass of the abtract Software class for capturing the description of Software used.
The use of a piece of Equipment with the requisite Parameters and ParameterValues.
Manufacturer's identifier for the Equipment.
An abstract class for describing biological molecules such as DNA and protein sequences or metabolites.
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.
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)
Factors are the dependent variables of an experiment (e.g. time, glucose concentration, ...). Note that Factors can be shared by multiple InvestigationComponents.
An Investigation is a self-contained unit of study that contains one or more types of 'omics technology.
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.
A subclass of MaterialMeasurement to be used without being extended in conjunction with GenericProtocolApplication and GenericMaterial to model measured sources of materials.
The interface that is the use of a Parameterizable class.
The equipment (hardware) used in this Protocol. Examples include: computers, scanners, wash stations etc...
Equipment is abstract and should either be extended by subclassing or the GenericEquipment class, a functional version of Equipment, should be used.
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.
The collection of objects that allow external references.
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).
The collection of Audit objects (Security, SecurityGroup and Contacts).
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.
The complete collection of all Data, Dimension and HigherLevelAnalysis objects.
An overview of the design using a single omics technique.
A specification of the access right (e.g. read or write) that a specified group (SecurityGroup) has on a particular object.
The complete set of OntologyIndividual objects referenced in the FuGE document.
The Parameterizable interface encapsulates the association of Parameters with ParameterValues.
A subclass of the abstract Paramter class to represent a parameter that is defined by a controlled vocabulary term.
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.
Represents a segmentation of the data by indexing existing DimensionElements of a Data.
A container for domain-specific analyses performed on data. Subclasses must be created for different domains.
The value of a Parameter.
A single point within a parent dimension. This class should be extended.
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.
Data external to the XML instance document. The location of the data file is given in the association to the URI class.
The complete set of ConceptualMolecule objects and SequenceAnnotation objects.
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.
Relates a DataPartition (subset of Data) from one data set with a DataPartition from another data set, for example for "supporting evidence".
A Protocol is a parameterizable description of a method. ProtocolApplication is used to specify the ParameterValues of its Protocol's Parameters.
Protocol should be extended in data formats. For cases where no extension is developed, the subclass of Protocol, GenericProtocol, should be used to capture experimental protocols.
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.
Organizations are entities like companies, universities, government agencies for which the attributes are self describing.
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.
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.
Base class for instances of Ontology properties
The complete set of all Material objects in the FuGE document.
The complete set of Protocol, Equipment, Software and ProtocolApplication objects in the FuGE document.
A subclass of the abtract Equipment class for capturing the description of Equipment used.
Groups contacts together based on their security privileges.
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
Software represents the software used. Examples of Software include: feature extraction software, clustering software, etc...
Software is abstract and should either be extended by subclassing or the GenericSoftware class, a functional version of Software, should be used.
The version of software used.
ActionApplication mirrors the structure of Actions within Protocols. This allows ActionDeviations to be reported and it can reference sub-ProtocolApplications if they exist.
ActionApplication should not be extended but should be used as it is, for instance to connect different extensions (subclasses) of ProtocolApplication together, following a given Protocol structure.
Represents bibliographic references, including the most common attributes. Note that because a BibliographicReference is Identifiable, a DatabaseEntry can also be specified.
Permission information for an object as to ownership, write and read permissions.
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.
Parameter is abstract and should be extended by subclassing. The GenericParameter class offers the functionality of a parameter defined by a controlled vocabulary term.
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 use of a piece of software with the requisite Parameters and ParameterValues.
An address to a repository.
The version for which a DatabaseReference applies.
The location of the Database.
The root container for accessing all objects.
This is used to annotate a set of sequences that share the same species, type and PolymerType.
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.
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.
A contact is either a person or an organization.
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.
The collection of Investigation and Factor objects in the FuGE document.
A subclass of ProtocolApplication to be used as it is in data formats without being extended.
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 for a Factor
Reference to the database where the DatabaseEntry instance can be found.
The organization a person belongs to.
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.
The parameters for this piece of GenericSoftware.
The underlying hardware.
The data produced by a ProtocolApplication.
The input data for a ProtocolApplication.
PartitionPairs that associate subsets (DataPartition) of the output data with subsets of the input data.
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.
This association should be extended for cases where the entire Material is used in the ProtocolApplication in full and it does not make sense to give a measured quantity of the Material as input.
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 type of material used, i.e. RNA, DNA, lipid, phosphoprotein, organism etc.
The characteristics of a Material.
Measures of the quality of the Material.
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).
The association to the techniques that comprise the Investigation.
The providers of the Experiment, its data and annotation.
HigherLevelAnalyses performed over data.
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 biological design type of the Investigation, such as toxicity, drug-response, gene knockout etc.
The instance of GenericMaterial or a subclass of Material that is input to the GenericProtocolApplication.
The parameter values for this Parameterizable Application.
Associates Equipment and Software together. Indicates that a set of Software is run on a piece of Equipment.
This association can be used to specify sub-components of a "parent" Equipment instance. The cardinality allows pieces of Equipment to be associated with more than one parent, for example allowing the re-use different parts.
If a Protocol makes use of a "parent" Equipment and EquipmentParts, all of the sub-component Equipment instances must also be directly referenced from the Protocol using the ProtocolEquipment association.
The Equipment model.
The equipment make, usually the organisation that makes the equipment.
The DimensionElements belonging to this Dimension.
The type of Dimension e.g. "array feature dimension"
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 dimensions contained within this Data object.
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 contact for creating or changing the instance referred to by the Audit.
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.
Reference to the complete set of DataPartitions.
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.
Complete set of all ProtocolApplications for a given InvestigationComponent. This allows access to the complete set of Materials and Data for the component.
The design of the investigation with respect to a single technique (InvestigationComponent) e.g. dye swap.
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 complete set of OntologyTerms in the FuGE document.
The provider of the Protocol, Equipment or Software.
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 set of parameters for the Parameterizable class instance.
Shared annotations for a set of sequences.
The DimensionElements segmented by this DataPartition.
This is a reference to the Data on which this DataPartition is based.
Association to the Data on which the HigherLevelAnalysis has been performed.
The parameter this value is for.
The value of the parameter. Will have the datatype of its associated Parameter.
When a ContactRole is used, it specifies which Contact the role is associated with.
The roles (lab equipment sales, contractor, etc.) the contact fills.
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.
The format of the ExternalData file, for example "tiff" for image files.
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 DataPartitions corresponding to the InputData for this PartitionPair. There should be no more than one DataPartition per set of InputData.
The DataPartitions corresponding to the OutputData for this PartitionPair. There should be no more than one DataPartition per set of OutputData.
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 inputs this Protocol can take e.g. organisms, solutions, data formats etc.
The types of outputs produced by this Protocol e.g. organisms, solutions, data formats etc.
The actions performed within a GenericProtocol.
A reference to the GenericSoftware used with this GenericProtocol.
A reference to the GenericProtocol used with this GenericEquipment.
The parameters defined for the GenericProtocol.
The containing organization (the university or business which a lab belongs to, etc.)
Each Action may be associated with an OntologyTerm that defines that Action.
This is an instantiation of the ProtocolReference association for associating complex, hierarchical protocols together. A GenericAction can reference substeps within the parent GenericProtocol. The substeps can be further instances of GenericProtocol, or defined subclasses of Protocol.
The complete set of Materials.
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 parameters for this piece of GenericEquipment.
An association between a parent GenericEquipment and its parts. If a GenericProtocol utilises GenericEquipment and its parts, both the parent and child GenericEquipment instances should be referenced.
The members of the SecurityGroup.
Associates Equipment and Software together. Indicates that a set of Software is run on a piece of Equipment.
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.
The owner of the security rights on the object.
Specifies which security groups have permission to view the associated object.
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 name of the parameter and its data type such as Boolean, float, integer etc.
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 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.
The underlying software.
Contacts associated with this database, such as hosting institution, database curators, manager etc.
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.
The organism from which this sequence was obtained.
The type of Sequence, e.g. gene, exon, UniGene cluster, fragment, BAC, EST, etc.
A choice of protein, RNA, or DNA.
References to entries in databases.
References to existing literature.
The instance(s) of the child Individual restriction on the Parent Individual
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.
The set of Investigations.
Reference to the complete set of Factor objects in the FuGE document.
Measured sources of material that are inputs to this GenericProtocolApplication.
The instances of GenericData that are inputs to the GenericProtocolApplication.
The Data produced from the GenericProtocolApplication.
The instances of GenericMaterial or a subclass of Material that are produced from the GenericProtocolApplication.
A reference to the GenericProtocol or subclass of Protocol that has been used with this GenericProtocolApplication.
Material that is being measured as the source for a ProtocolApplication.
The value of the measured source of material.
Represents a segmentation of the data by indexing existing DimensionElements of a Data.
Allows a value to be specified for a FactorValue using an ontology.