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. If more than one species are provided, this indicates that the identical sequence is found in these species. The type of Sequence, e.g. gene, exon, UniGene cluster, fragment, BAC, EST, etc. A choice of protein, RNA, or DNA. A Sequence is a representation of a DNA, RNA, or protein sequence. The number of residues in the Sequence. If length not positively known will be true Indicates if the Sequence 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 if the actual sequence is not specified here, it can be found through the DatabaseEntry. The start position of the referenced Sequence with respect to a larger Sequence, such as a complete chromosome, BAC etc. The end position of the referenced Sequence with respect to a larger Sequence, such as a complete chromosome, BAC etc. Shared annotations for a set of sequences. An abstract class for describing database entries of biological molecules such as DNA and protein sequences, metabolites or lipids etc. An Investigation is a self-contained unit of study that contains one or more types of 'omics technology. The association to the techniques that comprise the Investigation. The providers of the Investigation, 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 hypothesis being tested in the investigation. The biological design type of the Investigation, such as toxicity, drug-response, gene knockout etc. The conclusions of the Investigation. OntologyTerms can be referenced that describe the hypothesis, conclusion or other summary information about the Investigation. The start point of the investigation. The end point of the investigation. 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. Factors are the independent variables of an experiment (e.g. time, glucose concentration, ...). Note that Factors can be shared by multiple InvestigationComponents. 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 value for a Factor. Represents a segmentation of the data by indexing existing DimensionElements of Data that relate to the FactorValue. Allows a value to be specified for a FactorValue using the Measurement class, which includes support for storing values as ontology terms. A container for domain-specific analyses performed on data. Subclasses must be created for different domains. The hypothesis being tested by the HigherLevelAnalysis The conclusion reached from the HigherLevelAnalysis. Data can be an input to or an output from a ProtocolApplication. Data may be produced from a Material (data acquisition) or from another Data object (data transformation). Examples of Data are gene expression measurements, or phenotypes associated with genetic manipulations. A single dimension of a coordinate system. The DimensionElement class represents the discrete 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 single point within a parent dimension. This class should be extended. Data external to the XML instance document. The location of the data file is given in the location attribute. 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 data file. Data that is internal to an instance XML document. InternalData can be extended with an element that defines a particular encoding or data type for the storage array or the subclass GenericInternalData should be instantiated. The array will typically use pointer arithmetic to access values based on the rank (e.g. number of) Dimensions and their respective sizes (e.g. the number of contained DimensionElements). An abstract class to represents a segmentation of the data by indexing existing DimensionElements of a Data. The class can be extended to reference specific subclasses of DimensionElement. Relates a DataPartition (subset of Data) from one data set to another data set, for example for "supporting evidence". The algorithm that relates the input partitions to the output partitions. Data that is internal to an instance XML document stored in an array with a specified encoding. The array will typically use pointer arithmetic to access values based on the rank (e.g. number of) Dimensions and their respective sizes (e.g. the number of contained DimensionElements). The format or data type in which the data matrix is represented in the storage object of GenericInternalData. The storage matrix for data as specified by instantiation of extensions of Dimension and DimensionElement. 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. 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). These associations are abstract and should be extended to represent these semantics for extensions of ProtocolApplication and 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. MaterialMeasurement represents the quantity of a source Material used in a ProtocolApplication. MaterialMeasurement is abstract and should be extended if a subclass of ProtocolApplication has to be associated with a measured source of a subclass of Material. The value of the measured source of material. A subclass of the abstract Material class, which should be used in conjunction with controlled vocabulary terms to 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. 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 person for which the attributes are self describing. The organization a person belongs to. The Person's last/family name. The Person's first name. The Person's middle initial. Permission information for an object as to ownership, write and read permissions. The owner(s) of the security rights on the object. Specifies which security groups have permission to view the associated object. 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. 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.) Groups Contacts together based on their security privileges. The members of the SecurityGroup. A contact is either a person or an organization. The address of the Contact. The telephone number of the Contact including the suitable area codes. The email address of the Contact. The fax number of the Contact. A toll free phone number for the Contact, including suitable area codes. The role that a Contact plays in an organization or with respect to the associating class. 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 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. Represents bibliographic references, including the most common attributes. Note that because a BibliographicReference is Identifiable, a DatabaseEntry can also be specified. The names of the authors of the reference. The name of the journal, book etc. The publisher of the publication. The editor(s) of the reference. The year of publication. The volume name or number. The issue name or number. The page numbers. The title of the BibliographicReference. An address to a repository. Contacts associated with this database, such as hosting institution, database curators, manager etc. The version of the Database. The location of the Database. 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. A free text description of an object. The description. 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 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 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 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 default value for this parameter. An optional Boolean value to determine whether the parameter is an input (true) or an output (false). The value of a Parameter. The runtime value for this Parameter. The parameter this value is for. 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. ProtocolApplication is abstract and should be subclassed in the development of modular formats. The subclass GenericProtocolApplication can be used without extension. 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. When the protocol was applied. Software used in the Protocol. 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 without extension. The version of Software used. The equipment (hardware) used in the 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 organization that makes the equipment. The Equipment model. The use of a piece of Equipment with the requisite Parameters and ParameterValues. Manufacturer's identifier for the Equipment. The Equipment that was used in the ProtocolApplication. The use of a piece of software with the requisite Parameters and ParameterValues. The Software that was used in the ProtocolApplication. The Parameterizable interface encapsulates the association of Parameters with ParameterValues. The provider of the Protocol, Equipment or Software. The type of Equipment, Software or Protocol. The interface that is the use of a Parameterizable class. The parameter values for this Parameterizable Application. An Action is one step of a Protocol. Sets of ordered Actions define the Protocol. Action is abstract and can be extended to specify particular types of steps within a subclass of 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. ActionApplication mirrors the structure of Actions within Protocols and allows ActionDeviations to be reported. RULE: If an Action references a childProtocol, an ActionApplication must be created and reference a childProtocolApplication 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. Association to ProtocolApplication if a hierarchical Protocol has been defined representing the child step of the Protocol. GenericProtocol should be used with GenericAction, GenericParameter or protocolText 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 parameters defined for the GenericProtocol. The actions performed within a GenericProtocol. The text that applies to the entire Protocol. 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 GenericAction may be associated with an OntologyTerm that defines that GenericAction. The parameters belonging to the GenericAction. ParameterPairs owned by the GenericAction. The TargetParameter should reference a Parameter owned by a child Protocol which is also referenced by the GenericAction. Free text to describe this Action. This is an instantiation of the ChildProtocol 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. A subclass of the abstract Software class for capturing the description of Software used. Associates GenericEquipment with GenericSoftware to indicate that instances of software are run on piece(s) of Equipment. The parameters for this piece of GenericSoftware. A subclass of the abstract Equipment class for capturing the description of Equipment used. Associates GenericEquipment with GenericSoftware to indicate that instances of software are run on piece(s) of Equipment. 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. A subclass of the abstract Parameter class to represent a parameter that is defined by a controlled vocabulary term. The name of the parameter. A subclass of ProtocolApplication to be used as it is in data formats without being extended. 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. Whole Materials that are inputs to the GenericProtocolApplication. A reference to the GenericProtocol or subclass of Protocol that has been used with this GenericProtocolApplication. A pairing of an output parameter from a Protocol (SourceParameter) with an input parameter to a separate Protocol (TargetParameter) to indicate that the ParameterValue will be the same. A Parameter that is an input to a process which has been an output from another process. A Parameter that is output from one process which will be input to another process. An instance of an Ontology class. 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. Base class for instances of Ontology properties 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 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. The instance(s) of the child OntologyIndividuals referenced by the parent OntologyIndividual. 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 will 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 term would be what is usually called the local name in the Ontology, for instance 'Age'; The termAccession could be 'http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Age' or a an arbitrary accession if one exists; The identifier is a unique identifier for individuals in the scope of the FuGE instance; The inherited name attribute should not be used; 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 local name in 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 (i.e. the term is the unique accession). The source ontology or controlled vocabulary list that ontology terms have been obtained from. The source ontology or controlled vocabulary list that ontology terms have been obtained from. A URI that references the location of the ontology. 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 URI, Annotations, PropertySets and Descriptions associations inherited from Describable should only be used to capture additional information where the model contains no other structures that could be used to capture the information. 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. 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 entries in databases. 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, such as a human-readable name for the instance. An atomic value i.e. one that has a single value. An atomic default value for the parameter. A Boolean value. A Boolean default value for the parameter. A complex default value for the Parameter, such as a term from a controlled list or a function. A value given by an ontology term. A range value. Ontology terms can be used the define the semantics of the lower and upper limit in the range, for example the inclusivity of the values or what the values correspond to in the annotated object. The lower limit of a range value. The upper limit of a range value. Abstract superclass representing different methods of supplying a value or measurement. The Unit of Measurement. The data type of the Parameter such as Boolean, integer, String. The complete set of Protocol, Equipment, Software and ProtocolApplication objects in the FuGE document. Reference to all Protocol objects in the FuGE document. Reference to all Software objects in the FuGE document. Reference to all ProtocolApplication objects in the FuGE document. Reference to all Equipment objects in the FuGE document. The collection of Investigation and Factor objects in the FuGE document. Reference to all Investigation objects in the FuGE document. Reference to the complete set of Factor objects in the FuGE document. The collection of objects that allow external references. 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 complete collection of all Data, Dimension, DataPartition and HigherLevelAnalysis objects. 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 complete set of ConceptualMolecule objects and SequenceAnnotationSet objects. 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 complete set of OntologyIndividual and OntologySource objects referenced in the FuGE document. The complete set of OntologyTerms in the FuGE document. The complete set of OntologySources in the FuGE document. The complete set of all Material objects in the FuGE document. The complete set of Materials. The collection of Audit objects (Security, SecurityGroup and Contacts). Reference to the complete set of Security objects in the FuGE document. The complete set of Contacts. Reference to the complete set of SecurityGroup objects in the FuGE document. The provider of the FuGE document in terms of the Contact and the software the produced the document instance. The Contact that provided the document instance. The Software that produced the document instance. The root container for accessing all objects. The complete set of all Material objects in the FuGE document. The complete set of ConceptualMolecule objects and SequenceAnnotationSet objects. 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, DataPartition 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 Provider of the FuGE document