A single entry from an ontology or a controlled vocabulary.
If it is a simple controlled vocabulary, there may be no formal accession for the term. In these cases the local name should be repeated in both term and termAccession. If the term has a value, the OntologyIndividual with have 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 term would be what is usually called the local name in the Ontology, for instance 'Age'
The inherited name attribute should not be used.
The termAccession could be 'http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Age' or a an arbitrary accession if one exists,
The ontologyURI of OntologySource 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.
The ontology term itself, also known as the localname is some ontologies.
The accession number assigned to the ontology term in the source ontology. If there is no explicit accession assigned, then the term (localname) must be repeated (in effect the term is the accession).
A complex default value for the Parameter, such as a term from a controlled list or a function.
The default value for the parameter is given by an ontology term.
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 type of Dimension e.g. "array feature 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.
An atomic defaultValue i.e. one that has a single value.
An atomic default value for the parameter.
Relates a DataPartition (subset of Data) from one data set with a DataPartition from another data set, for example for "supporting evidence".
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.
The collection of objects that allow external references.
A subclass of the abstract Paramter class to represent a parameter that is defined by a controlled vocabulary term.
The name of the parameter.
A Boolean default value for the Parameter
A Boolean default value for the parameter.
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.
Used to define human readable notes for annotating deviations to an Action during the ActionApplication.
Association to the Action that is being performed as recorded by this ActionApplication.
An abstract class for describing biological molecules such as DNA and protein sequences or metabolites.
Factors are the dependent variables of an experiment (e.g. time, glucose concentration, ...). Note that Factors can be shared by multiple InvestigationComponents.
The category of a Factor could be biological (time, [glucose]) or methodological (differing cDNA preparation protocols).
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.
Association from a GenericMaterial to other GenericMaterials that are sub-components (such as wells within an array plate). If a subcomponent undergoes a ProtocolApplication, then the containing GenericMaterial must also be an input to the ProtocolApplication and be output as a new GenericMaterial or version of the GenericMaterial.
An Investigation is a self-contained unit of study that contains one or more types of 'omics technology.
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.
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.
The interface that is the use of a Parameterizable class.
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 type of material used, i.e. RNA, DNA, lipid, phosphoprotein, organism etc.
The characteristics of a Material.
Measures of the quality of the Material.
A subclass of the abtract Equipment class for capturing the description of Equipment used.
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 collection of Investigation and Factor objects in the FuGE document.
A subclass of MaterialMeasurement to be used without being extended in conjunction with GenericProtocolApplication and GenericMaterial to model measured sources of materials.
The instance of GenericMaterial or a subclass of Material that is input to the GenericProtocolApplication.
A range for the runtime value of a Parameter.
The lower end of a range value for the parameter.
The higher end of a range value for the parameter.
The root container for accessing all objects.
The provider of the FuGE document in terms of the Contact and the software the produced the document instance.
The software that produced the document instance.
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 class with sub-classes that define different specifications of a defaultValue.
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.
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 use of a piece of Equipment with the requisite Parameters and ParameterValues.
Manufacturer's identifier for the Equipment.
The underlying hardware.
The complete set of ConceptualMolecule objects and SequenceAnnotation objects.
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.
The data type of the Parameter such as Boolean, integer, String and can include a specification of whether the parameter can accept range or other complex value types.
The Unit of the Parameter
Groups contacts together based on their security privileges.
The members of the SecurityGroup.
Represents bibliographic references, including the most common attributes. Note that because a BibliographicReference is Identifiable, a DatabaseEntry can also be specified.
The complete set of all Material objects in the FuGE document.
The complete set of OntologyIndividual objects referenced in the FuGE document.
Tracks information on the contact that creates or modifies an object.
The date of a change.
The contact for creating or changing the instance referred to by the Audit.
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.
Each Action may be associated with an OntologyTerm that defines that Action.
Free text to describe this 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 Parameterizable interface encapsulates the association of Parameters with ParameterValues.
The type of Equipment, Software or Protocol.
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 container for domain-specific analyses performed on data. Subclasses must be created for different domains.
Association to the Data on which the HigherLevelAnalysis has been performed.
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.
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 abtract Software class for capturing the description of Software used.
Organizations are entities like companies, universities, government agencies for which the attributes are self describing.
The containing organization (the university or business which a lab belongs to, etc.)
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.
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.
A reference to the GenericSoftware used with this GenericProtocol.
A reference to the GenericProtocol used with this GenericEquipment.
The text for that applies to the entire Protocol.
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.
The format of the ExternalData file, for example "tiff" for image files.
The location of the external data file.
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 single point within a parent dimension. This class should be extended.
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).
An address to a repository.
The version for which a DatabaseReference applies.
The location of the Database.
The use of a piece of software with the requisite Parameters and ParameterValues.
The underlying software.
Permission information for an object as to ownership, write and read permissions.
The owner of the security rights on the object.
The source ontology or controlled vocabulary list that ontology terms have been obtained from.
A URI that references the location of the ontology.
A Boolean runtime value for the Parameter.
A Boolean value for the parameter.
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.
A complex runtime value for the Parameter, such as a term from a controlled list or a function.
The value of the parameter. Will have the datatype of its associated Parameter.
The complete collection of all Data, Dimension and HigherLevelAnalysis objects.
The value of a Parameter.
The parameter this value is for.
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 dimensions contained within this Data object.
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.
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.
When the protocol was applied.
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.
An instance of an Ontology class.
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.
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.
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.
A contact is either a person or an organization.
The collection of Audit objects (Security, SecurityGroup and Contacts).
Base class for instances of Ontology properties
The complete set of Protocol, Equipment, Software and ProtocolApplication objects in the FuGE document.
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 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.
The equipment make, usually the organisation that makes the equipment.
The Equipment model.
A range for the default value of a Parameter.
The lower end of a default range value for the parameter.
The higher end of a default range value for the parameter.
This is used to annotate a set of sequences that share the same species, type and PolymerType.
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.
A person for which the attributes are self describing.
The organization a person belongs to.
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.
A free text description of an object.
The description.
An atomic runtime value for the Parameter.
An atomic value for the parameter.
Represents a segmentation of the data by indexing existing DimensionElements of a Data.
The DimensionElements segmented by this DataPartition.
This is a reference to the Data on which this DataPartition is based.
The value for a Factor
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.
A subclass of ProtocolApplication to be used as it is in data formats without being extended.
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.