Specification documentation for the Functional Genomics Experiment (FuGE) model: Reference manual
Status: FuGE (version 1.0 candidate, final); Reference manual.
Authors:
Andrew R. Jones
School of Computer Science, University of Manchester
Email: ajones@cs.man.ac.uk
Michael Miller
Rosetta Inpharmatics, LLC
Email: Michael_Miller@Rosettabio.com
Paul Spellman
Lawrence Berkeley National Laboratory
Email: PTSpellman@lbl.gov
Angel Pizarro
Institute for Translational Medicine and Therapeutics, University of Pennsylvania
Email: angel@mail.med.upenn.edu
Copyright: These specifications are distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
This document is the reference manual for FuGE version 1. The contents have been generated automatically from the object model.
An entry in this document has the following structure:
Fully qualified class name (abstract) if class is abstract
Inheritance hierarchy:
Class name --> superclass --> superclass
Attributes:
Note: all attributes are converted to an attribute in the XML Schema unless marked *
| Name | Documentation | Data type | Required |
| Name of the attribute | Attribute's documentation | The UML data type of the attribute | Whether the attribute is required (cardinality "1") or not (cardinality "0..1") |
Associations:
Note: abstract associations will be rendered in italic font
| Name | Associated class | Documentation | Multiplicity | Composite |
| Name of the association | Class at the navigable end | The association's documentation | The multiplicity from source end to navigable end | Whether the association is "composite", "aggregate" or "none" |
XML Schema Complex Type specification:
The definition of the corresponding ComplexType (minus documentation) in the XML Schema
|
XML Schema element specification:
The definition of the corresponding Element in the XML Schema
|
Table of contents
FuGE.Bio.ConceptualMolecule.SequenceAnnotationSet
Inheritance hierarchy:
SequenceAnnotationSet --> Identifiable --> Describable
Documentation:
This is used to annotate a set of sequences that share the same
species, type and PolymerType.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| Species |
OntologyTerm |
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.
|
0..* to 0..* |
none |
| Types |
OntologyTerm |
The type of Sequence, e.g. gene, exon, UniGene cluster,
fragment, BAC, EST, etc.
|
0..* to 0..* |
none |
| PolymerType |
OntologyTerm |
A choice of protein, RNA, or DNA.
|
0..* to 0..1 |
none |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Bio.ConceptualMolecule.SequenceAnnotationSetType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.IdentifiableType">
<xsd:sequence>
<xsd:element name="_species" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="OntologyTerm_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="_types" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="OntologyTerm_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="_polymerType" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:attribute name="OntologyTerm_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="SequenceAnnotationSet" type="fuge:FuGE.Bio.ConceptualMolecule.SequenceAnnotationSetType" abstract="false" substitutionGroup="fuge:Identifiable"/>
|
FuGE.Bio.ConceptualMolecule.Sequence
Inheritance hierarchy:
Sequence --> ConceptualMolecule --> Identifiable --> Describable
Documentation:
A Sequence is a representation of a DNA, RNA, or protein
sequence.
Attributes:
| Name | Documentation | Data type | Required |
| length |
The number of residues in the Sequence.
|
int |
false |
| isApproximateLength |
If length not positively known will be true
|
boolean |
false |
| isCircular |
Indicates if the Sequence is circular in nature.
|
boolean |
false |
| sequence |
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.
|
string |
false |
| start |
The start position of the referenced Sequence with respect to a
larger Sequence, such as a complete chromosome, BAC etc.
|
int |
false |
| end |
The end position of the referenced Sequence with respect to a
larger Sequence, such as a complete chromosome, BAC etc.
|
int |
false |
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| SequenceAnnotation |
SequenceAnnotationSet |
Shared annotations for a set of sequences.
|
0..* to 0..1 |
none |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Bio.ConceptualMolecule.SequenceType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Bio.ConceptualMolecule.ConceptualMoleculeType">
<xsd:attribute name="length" type="xsd:int"/>
<xsd:attribute name="isApproximateLength" type="xsd:boolean"/>
<xsd:attribute name="isCircular" type="xsd:boolean"/>
<xsd:attribute name="sequence" type="xsd:string"/>
<xsd:attribute name="start" type="xsd:int"/>
<xsd:attribute name="end" type="xsd:int"/>
<xsd:attribute name="SequenceAnnotationSet_ref" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Sequence" type="fuge:FuGE.Bio.ConceptualMolecule.SequenceType" abstract="false" substitutionGroup="fuge:ConceptualMolecule"/>
|
FuGE.Bio.ConceptualMolecule.ConceptualMolecule (abstract)
Inheritance hierarchy:
ConceptualMolecule --> Identifiable --> Describable
Documentation:
An abstract class for describing database entries of biological
molecules such as DNA and protein sequences, metabolites or
lipids etc.
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Bio.ConceptualMolecule.ConceptualMoleculeType" abstract = "true">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.IdentifiableType">
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="ConceptualMolecule" type="fuge:FuGE.Bio.ConceptualMolecule.ConceptualMoleculeType" abstract="true" substitutionGroup="fuge:Identifiable"/>
|
FuGE.Bio.Investigation.Investigation
Inheritance hierarchy:
Investigation --> Identifiable --> Describable
Documentation:
An Investigation is a self-contained unit of study that contains
one or more types of 'omics technology.
Attributes:
| Name | Documentation | Data type | Required |
| start |
The start point of the investigation.
|
dateTime |
false |
| end |
The end point of the investigation.
|
dateTime |
false |
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| InvestigationComponents |
InvestigationComponent |
The association to the techniques that comprise the
Investigation.
|
1..1 to 0..* |
composite |
| Providers |
ContactRole |
The providers of the Investigation, its data and annotation.
|
0..1 to 0..* |
composite |
| SummaryResults |
HigherLevelAnalysis |
HigherLevelAnalyses performed over data.
|
0..* to 0..* |
none |
| SourceMaterials |
Material |
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.
|
0..* to 0..* |
none |
| Hypothesis |
Description |
The hypothesis being tested in the investigation.
|
0..1 to 0..1 |
composite |
| InvestigationTypes |
OntologyTerm |
The biological design type of the Investigation, such as
toxicity, drug-response, gene knockout etc.
|
0..* to 0..* |
none |
| Conclusion |
Description |
The conclusions of the Investigation.
|
0..1 to 0..1 |
composite |
| InvestigationSummary |
OntologyTerm |
OntologyTerms can be referenced that describe the hypothesis,
conclusion or other summary information about the Investigation.
|
0..* to 0..* |
none |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Bio.Investigation.InvestigationType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.IdentifiableType">
<xsd:sequence>
<xsd:element ref="fuge:InvestigationComponent" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="fuge:ContactRole" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element name="_summaryResults" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="HigherLevelAnalysis_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="_sourceMaterials" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="Material_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="_hypothesis" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="fuge:Description" minOccurs="1" maxOccurs="1"/>
</xsd:sequence>
</xsd:complexType>
</xsd:element>
<xsd:element name="_investigationTypes" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="OntologyTerm_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="_conclusion" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="fuge:Description" minOccurs="1" maxOccurs="1"/>
</xsd:sequence>
</xsd:complexType>
</xsd:element>
<xsd:element name="_investigationSummary" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="OntologyTerm_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
<xsd:attribute name="start" type="xsd:dateTime"/>
<xsd:attribute name="end" type="xsd:dateTime"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Investigation" type="fuge:FuGE.Bio.Investigation.InvestigationType" abstract="false" substitutionGroup="fuge:Identifiable"/>
|
FuGE.Bio.Investigation.InvestigationComponent
Inheritance hierarchy:
InvestigationComponent --> Identifiable --> Describable
Documentation:
An overview of the design using a single omics technique.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| Factors |
Factor |
The description of the factors (TimeCourse, Dosage, etc.) that
segment the Data. The aggregation of Factors is limited to a
single Investigation.
|
0..* to 0..* |
aggregate |
| ReplicateDescription |
Description |
Description of the replicate strategy of the
InvestigationComponent.
|
0..1 to 0..1 |
composite |
| QualityControlDescription |
Description |
Description of the quality control aspects of the
InvestigationComponent.
|
0..1 to 0..1 |
composite |
| NormalizationDescription |
Description |
Description of the normalization strategy of the
InvestigationComponent.
|
0..1 to 0..1 |
composite |
| AllProtocolApplications |
ProtocolApplication |
Complete set of all ProtocolApplications for a given
InvestigationComponent. This allows access to the complete set
of Materials and Data for the component.
|
0..* to 0..* |
none |
| ComponentDesignTypes |
OntologyTerm |
The design of the investigation with respect to a single
technique (InvestigationComponent) e.g. dye swap.
|
0..* to 0..* |
none |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Bio.Investigation.InvestigationComponentType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.IdentifiableType">
<xsd:sequence>
<xsd:element name="_factors" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="Factor_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="_replicateDescription" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="fuge:Description" minOccurs="1" maxOccurs="1"/>
</xsd:sequence>
</xsd:complexType>
</xsd:element>
<xsd:element name="_qualityControlDescription" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="fuge:Description" minOccurs="1" maxOccurs="1"/>
</xsd:sequence>
</xsd:complexType>
</xsd:element>
<xsd:element name="_normalizationDescription" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="fuge:Description" minOccurs="1" maxOccurs="1"/>
</xsd:sequence>
</xsd:complexType>
</xsd:element>
<xsd:element name="_allProtocolApplications" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="ProtocolApplication_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="_componentDesignTypes" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="OntologyTerm_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="InvestigationComponent" type="fuge:FuGE.Bio.Investigation.InvestigationComponentType" abstract="false" substitutionGroup="fuge:Identifiable"/>
|
FuGE.Bio.Investigation.Factor
Inheritance hierarchy:
Factor --> Identifiable --> Describable
Documentation:
Factors are the independent variables of an experiment (e.g.
time, glucose concentration, ...). Note that Factors can be
shared by multiple InvestigationComponents.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| FactorValues |
FactorValue |
The FactorValues for this Factor e.g. the time points in a time
course.
|
1..1 to 0..* |
composite |
| FactorType |
OntologyTerm |
The category of a Factor could be biological (time, [glucose])
or methodological (differing cDNA preparation protocols).
|
0..* to 0..1 |
none |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Bio.Investigation.FactorType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.IdentifiableType">
<xsd:sequence>
<xsd:element ref="fuge:FactorValue" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element name="_factorType" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:attribute name="OntologyTerm_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Factor" type="fuge:FuGE.Bio.Investigation.FactorType" abstract="false" substitutionGroup="fuge:Identifiable"/>
|
FuGE.Bio.Investigation.FactorValue
Inheritance hierarchy:
FactorValue --> Describable
Documentation:
The value for a Factor.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| DataPartitions |
DataPartition |
Represents a segmentation of the data by indexing existing
DimensionElements of Data that relate to the FactorValue.
|
0..* to 0..* |
none |
| Value |
Measurement |
Allows a value to be specified for a FactorValue using the
Measurement class, which includes support for storing values as
ontology terms.
|
0..1 to 1..1 |
composite |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Bio.Investigation.FactorValueType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.DescribableType">
<xsd:sequence>
<xsd:element name="_dataPartitions" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="DataPartition_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
<xsd:element ref="fuge:Measurement" minOccurs="1" maxOccurs="1"/>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="FactorValue" type="fuge:FuGE.Bio.Investigation.FactorValueType" abstract="false" substitutionGroup="fuge:Describable"/>
|
FuGE.Bio.Investigation.HigherLevelAnalysis (abstract)
Inheritance hierarchy:
HigherLevelAnalysis --> Identifiable --> Describable
Documentation:
A container for domain-specific analyses performed on data.
Subclasses must be created for different domains.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| SupportingData (abstract) |
Data |
Association to the Data on which the HigherLevelAnalysis has
been performed.
|
0..* to 0..* |
none |
| Hypothesis |
Description |
The hypothesis being tested by the HigherLevelAnalysis
|
0..1 to 0..1 |
composite |
| Conclusion |
Description |
The conclusion reached from the HigherLevelAnalysis.
|
0..1 to 0..1 |
composite |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Bio.Investigation.HigherLevelAnalysisType" abstract = "true">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.IdentifiableType">
<xsd:sequence>
<xsd:element name="_hypothesis" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="fuge:Description" minOccurs="1" maxOccurs="1"/>
</xsd:sequence>
</xsd:complexType>
</xsd:element>
<xsd:element name="_conclusion" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="fuge:Description" minOccurs="1" maxOccurs="1"/>
</xsd:sequence>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="HigherLevelAnalysis" type="fuge:FuGE.Bio.Investigation.HigherLevelAnalysisType" abstract="true" substitutionGroup="fuge:Identifiable"/>
|
FuGE.Bio.Data.Data (abstract)
Inheritance hierarchy:
Data --> Identifiable --> Describable
Documentation:
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.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| Dimensions (abstract) |
Dimension |
The dimensions contained within this Data object.
|
0..* to 0..* |
none |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Bio.Data.DataType" abstract = "true">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.IdentifiableType">
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Data" type="fuge:FuGE.Bio.Data.DataType" abstract="true" substitutionGroup="fuge:Identifiable"/>
|
FuGE.Bio.Data.Dimension (abstract)
Inheritance hierarchy:
Dimension --> Identifiable --> Describable
Documentation:
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.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| DimensionElements (abstract) |
DimensionElement |
The DimensionElements belonging to this Dimension.
|
1..1 to 0..* |
composite |
| DimensionType |
OntologyTerm |
The type of Dimension e.g. "array feature dimension"
|
0..* to 0..1 |
none |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Bio.Data.DimensionType" abstract = "true">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.IdentifiableType">
<xsd:sequence>
<xsd:element name="_dimensionType" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:attribute name="OntologyTerm_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Dimension" type="fuge:FuGE.Bio.Data.DimensionType" abstract="true" substitutionGroup="fuge:Identifiable"/>
|
FuGE.Bio.Data.DimensionElement (abstract)
Inheritance hierarchy:
DimensionElement --> Identifiable --> Describable
Documentation:
A single point within a parent dimension. This class should be
extended.
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Bio.Data.DimensionElementType" abstract = "true">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.IdentifiableType">
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="DimensionElement" type="fuge:FuGE.Bio.Data.DimensionElementType" abstract="true" substitutionGroup="fuge:Identifiable"/>
|
FuGE.Bio.Data.ExternalData
Inheritance hierarchy:
ExternalData --> Data --> Identifiable --> Describable
Documentation:
Data external to the XML instance document. The location of the
data file is given in the location attribute.
Attributes:
| Name | Documentation | Data type | Required |
| location |
The location of the data file.
|
anyURI |
true |
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| ExternalFormatDocumentation |
URI |
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.
|
0..1 to 0..1 |
composite |
| FileFormat |
OntologyTerm |
The format of the ExternalData file, for example "tiff" for
image files.
|
0..* to 0..1 |
none |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Bio.Data.ExternalDataType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Bio.Data.DataType">
<xsd:sequence>
<xsd:element name="_externalFormatDocumentation" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="fuge:URI" minOccurs="1" maxOccurs="1"/>
</xsd:sequence>
</xsd:complexType>
</xsd:element>
<xsd:element name="_fileFormat" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:attribute name="OntologyTerm_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
<xsd:attribute name="location" use="required" type="xsd:anyURI"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="ExternalData" type="fuge:FuGE.Bio.Data.ExternalDataType" abstract="false" substitutionGroup="fuge:Data"/>
|
FuGE.Bio.Data.InternalData (abstract)
Inheritance hierarchy:
InternalData --> Data --> Identifiable --> Describable
Documentation:
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).
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Bio.Data.InternalDataType" abstract = "true">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Bio.Data.DataType">
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="InternalData" type="fuge:FuGE.Bio.Data.InternalDataType" abstract="true" substitutionGroup="fuge:Data"/>
|
FuGE.Bio.Data.DataPartition (abstract)
Inheritance hierarchy:
DataPartition --> Identifiable --> Describable
Documentation:
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.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| DimensionElementSet (abstract) |
DimensionElement |
The DimensionElements segmented by this DataPartition. This
association can be extended if DataPartition has been subclassed
to associate with a specific subclass of Data.
|
0..* to 0..* |
none |
| PartitionedData (abstract) |
Data |
This is a reference to the Data on which this DataPartition is
based. This association can be extended if DataPartition has
been subclassed to associate with a specific subclass of Data.
|
0..* to 1..1 |
none |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Bio.Data.DataPartitionType" abstract = "true">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.IdentifiableType">
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="DataPartition" type="fuge:FuGE.Bio.Data.DataPartitionType" abstract="true" substitutionGroup="fuge:Identifiable"/>
|
FuGE.Bio.Data.PartitionPair (abstract)
Inheritance hierarchy:
PartitionPair --> Describable
Documentation:
Relates a DataPartition (subset of Data) from one data set to
another data set, for example for "supporting evidence".
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| PartitionPairAlgorithm |
Description |
The algorithm that relates the input partitions to the output
partitions.
|
0..1 to 0..1 |
composite |
| InputPartitions (abstract) |
DataPartition |
The DataPartitions corresponding to the InputData for this
PartitionPair. There should be no more than one DataPartition
per set of InputData.
|
0..* to 0..* |
none |
| OutputPartitions (abstract) |
DataPartition |
The DataPartitions corresponding to the OutputData for this
PartitionPair. There should be no more than one DataPartition
per set of OutputData.
|
0..* to 0..* |
none |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Bio.Data.PartitionPairType" abstract = "true">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.DescribableType">
<xsd:sequence>
<xsd:element name="_partitionPairAlgorithm" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="fuge:Description" minOccurs="1" maxOccurs="1"/>
</xsd:sequence>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="PartitionPair" type="fuge:FuGE.Bio.Data.PartitionPairType" abstract="true" substitutionGroup="fuge:Describable"/>
|
FuGE.Bio.Data.GenericInternalData
Inheritance hierarchy:
GenericInternalData --> InternalData --> Data --> Identifiable --> Describable
Documentation:
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).
Attributes:
| Name | Documentation | Data type | Required |
| storage * |
The storage matrix for data as specified by instantiation of
extensions of Dimension and DimensionElement.
|
string[] |
true |
*Attribute is mapped to an element in the XML Schema
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| MatrixEncoding |
OntologyTerm |
The format or data type in which the data matrix is represented
in the storage object of GenericInternalData.
|
0..* to 0..1 |
none |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Bio.Data.GenericInternalDataType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Bio.Data.InternalDataType">
<xsd:sequence>
<xsd:element name="_matrixEncoding" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:attribute name="OntologyTerm_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="storage">
<xsd:simpleType>
<xsd:list itemType="xsd:string"/>
</xsd:simpleType>
</xsd:element>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="GenericInternalData" type="fuge:FuGE.Bio.Data.GenericInternalDataType" abstract="false" substitutionGroup="fuge:InternalData"/>
|
FuGE.Bio.Data.GenericDataPartition
Inheritance hierarchy:
GenericDataPartition --> DataPartition --> Identifiable --> Describable
Documentation:
Represents a segmentation of the data by indexing existing
DimensionElements of a Data
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| PartitionedData |
Data |
This is a reference to the Data on which this DataPartition is
based.
|
0..* to 1..1 |
none |
| DimensionElementSet |
DimensionElement |
The DimensionElements segmented by this DataPartition.
|
0..* to 0..* |
none |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Bio.Data.GenericDataPartitionType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Bio.Data.DataPartitionType">
<xsd:sequence>
<xsd:element name="_dimensionElementSet" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="DimensionElement_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
<xsd:attribute name="Data_ref" use="required" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="GenericDataPartition" type="fuge:FuGE.Bio.Data.GenericDataPartitionType" abstract="false" substitutionGroup="fuge:DataPartition"/>
|
FuGE.Bio.Material.Material (abstract)
Inheritance hierarchy:
Material --> Identifiable --> Describable
Documentation:
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.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| Components (abstract) |
Material |
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.
|
0..* to 0..* |
none |
| Contacts |
ContactRole |
Contact details for the Material. The association to ContactRole
could specify, for example, the creator or provider of the
Material.
|
0..1 to 0..* |
composite |
| MaterialType |
OntologyTerm |
The type of material used, i.e. RNA, DNA, lipid, phosphoprotein,
organism etc.
|
0..* to 0..1 |
none |
| Characteristics |
OntologyTerm |
The characteristics of a Material.
|
0..* to 0..* |
none |
| QualityControlStatistics |
OntologyTerm |
Measures of the quality of the Material.
|
0..* to 0..* |
none |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Bio.Material.MaterialType" abstract = "true">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.IdentifiableType">
<xsd:sequence>
<xsd:element ref="fuge:ContactRole" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element name="_materialType" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:attribute name="OntologyTerm_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="_characteristics" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="OntologyTerm_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="_qualityControlStatistics" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="OntologyTerm_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Material" type="fuge:FuGE.Bio.Material.MaterialType" abstract="true" substitutionGroup="fuge:Identifiable"/>
|
FuGE.Bio.Material.MaterialMeasurement (abstract)
Inheritance hierarchy:
MaterialMeasurement --> Describable
Documentation:
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.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| MeasuredMaterial (abstract) |
Material |
Material that is being measured as the source for a
ProtocolApplication.
|
0..* to 1..1 |
none |
| Measurement |
Measurement |
The value of the measured source of material.
|
1..1 to 0..1 |
composite |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Bio.Material.MaterialMeasurementType" abstract = "true">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.DescribableType">
<xsd:sequence>
<xsd:element ref="fuge:Measurement" minOccurs="0" maxOccurs="1"/>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="MaterialMeasurement" type="fuge:FuGE.Bio.Material.MaterialMeasurementType" abstract="true" substitutionGroup="fuge:Describable"/>
|
FuGE.Bio.Material.GenericMaterial
Inheritance hierarchy:
GenericMaterial --> Material --> Identifiable --> Describable
Documentation:
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.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| Components |
GenericMaterial |
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.
|
0..* to 0..* |
none |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Bio.Material.GenericMaterialType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Bio.Material.MaterialType">
<xsd:sequence>
<xsd:element name="_components" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="GenericMaterial_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="GenericMaterial" type="fuge:FuGE.Bio.Material.GenericMaterialType" abstract="false" substitutionGroup="fuge:Material"/>
|
FuGE.Bio.Material.GenericMaterialMeasurement
Inheritance hierarchy:
GenericMaterialMeasurement --> MaterialMeasurement --> Describable
Documentation:
A subclass of MaterialMeasurement to be used without being
extended in conjunction with GenericProtocolApplication and
GenericMaterial to model measured sources of materials.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| MeasuredMaterial |
Material |
The instance of GenericMaterial or a subclass of Material that
is input to the GenericProtocolApplication.
|
0..* to 1..1 |
none |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Bio.Material.GenericMaterialMeasurementType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Bio.Material.MaterialMeasurementType">
<xsd:attribute name="Material_ref" use="required" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="GenericMaterialMeasurement" type="fuge:FuGE.Bio.Material.GenericMaterialMeasurementType" abstract="false" substitutionGroup="fuge:MaterialMeasurement"/>
|
FuGE.Common.Audit.Person
Inheritance hierarchy:
Person --> Contact --> Identifiable --> Describable
Documentation:
A person for which the attributes are self describing.
Attributes:
| Name | Documentation | Data type | Required |
| lastName |
The Person's last/family name.
|
string |
false |
| firstName |
The Person's first name.
|
string |
false |
| midInitials |
The Person's middle initial.
|
string |
false |
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| Affiliations |
Organization |
The organization a person belongs to.
|
0..* to 0..* |
none |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Audit.PersonType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Audit.ContactType">
<xsd:sequence>
<xsd:element name="_affiliations" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="Organization_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
<xsd:attribute name="lastName" type="xsd:string"/>
<xsd:attribute name="firstName" type="xsd:string"/>
<xsd:attribute name="midInitials" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Person" type="fuge:FuGE.Common.Audit.PersonType" abstract="false" substitutionGroup="fuge:Contact"/>
|
FuGE.Common.Audit.Security
Inheritance hierarchy:
Security --> Identifiable --> Describable
Documentation:
Permission information for an object as to ownership, write and
read permissions.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| Owners |
Contact |
The owner(s) of the security rights on the object.
|
0..* to 0..* |
none |
| SecurityRights |
SecurityAccess |
Specifies which security groups have permission to view the
associated object.
|
1..1 to 0..* |
composite |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Audit.SecurityType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.IdentifiableType">
<xsd:sequence>
<xsd:element name="_owners" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="Contact_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
<xsd:element ref="fuge:SecurityAccess" minOccurs="0" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Security" type="fuge:FuGE.Common.Audit.SecurityType" abstract="false" substitutionGroup="fuge:Identifiable"/>
|
FuGE.Common.Audit.Audit
Inheritance hierarchy:
Audit --> Describable
Documentation:
Tracks information on the Contact that creates or modifies an
object.
Attributes:
| Name | Documentation | Data type | Required |
| date |
The date of a change.
|
dateTime |
true |
| action |
The type of Audit performed, using a value from the AuditAction
enumeration.
|
FuGE.Common.Audit.AuditAction |
true |
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| Performer |
Contact |
The contact for creating or changing the instance referred to by
the Audit.
|
0..* to 0..1 |
none |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Audit.AuditType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.DescribableType">
<xsd:attribute name="date" use="required" type="xsd:dateTime"/>
<xsd:attribute name="action" use="required">
<xsd:simpleType>
<xsd:restriction base="xsd:NMTOKEN">
<xsd:enumeration value="creation"/>
<xsd:enumeration value="modification"/>
<xsd:enumeration value="deletion"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
<xsd:attribute name="Contact_ref" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Audit" type="fuge:FuGE.Common.Audit.AuditType" abstract="false" substitutionGroup="fuge:Describable"/>
|
FuGE.Common.Audit.Organization
Inheritance hierarchy:
Organization --> Contact --> Identifiable --> Describable
Documentation:
Organizations are entities like companies, universities,
government agencies for which the attributes are self
describing.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| Parent |
Organization |
The containing organization (the university or business which a
lab belongs to, etc.)
|
0..* to 0..1 |
none |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Audit.OrganizationType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Audit.ContactType">
<xsd:sequence>
<xsd:element name="_parent" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:attribute name="Organization_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Organization" type="fuge:FuGE.Common.Audit.OrganizationType" abstract="false" substitutionGroup="fuge:Contact"/>
|
FuGE.Common.Audit.SecurityGroup
Inheritance hierarchy:
SecurityGroup --> Identifiable --> Describable
Documentation:
Groups Contacts together based on their security privileges.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| Members |
Contact |
The members of the SecurityGroup.
|
0..* to 1..* |
none |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Audit.SecurityGroupType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.IdentifiableType">
<xsd:sequence>
<xsd:element name="_members" minOccurs="1" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="Contact_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="SecurityGroup" type="fuge:FuGE.Common.Audit.SecurityGroupType" abstract="false" substitutionGroup="fuge:Identifiable"/>
|
FuGE.Common.Audit.Contact (abstract)
Inheritance hierarchy:
Contact --> Identifiable --> Describable
Documentation:
A contact is either a person or an organization.
Attributes:
| Name | Documentation | Data type | Required |
| address |
The address of the Contact.
|
string |
false |
| phone |
The telephone number of the Contact including the suitable area
codes.
|
string |
false |
| email |
The email address of the Contact.
|
string |
false |
| fax |
The fax number of the Contact.
|
string |
false |
| tollFreePhone |
A toll free phone number for the Contact, including suitable
area codes.
|
string |
false |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Audit.ContactType" abstract = "true">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.IdentifiableType">
<xsd:attribute name="address" type="xsd:string"/>
<xsd:attribute name="phone" type="xsd:string"/>
<xsd:attribute name="email" type="xsd:string"/>
<xsd:attribute name="fax" type="xsd:string"/>
<xsd:attribute name="tollFreePhone" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Contact" type="fuge:FuGE.Common.Audit.ContactType" abstract="true" substitutionGroup="fuge:Identifiable"/>
|
FuGE.Common.Audit.ContactRole
Inheritance hierarchy:
ContactRole --> Describable
Documentation:
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.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| Contact |
Contact |
When a ContactRole is used, it specifies which Contact the role
is associated with.
|
0..* to 1..1 |
none |
| Role |
OntologyTerm |
The roles (lab equipment sales, contractor, etc.) the Contact
fills.
|
0..* to 1..1 |
none |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Audit.ContactRoleType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.DescribableType">
<xsd:sequence>
<xsd:element name="_role" minOccurs="1" maxOccurs="1">
<xsd:complexType>
<xsd:attribute name="OntologyTerm_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
<xsd:attribute name="Contact_ref" use="required" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="ContactRole" type="fuge:FuGE.Common.Audit.ContactRoleType" abstract="false" substitutionGroup="fuge:Describable"/>
|
FuGE.Common.Audit.SecurityAccess
Inheritance hierarchy:
SecurityAccess --> Describable
Documentation:
A specification of the access right (e.g. read or write) that a
specified group (SecurityGroup) has on a particular object.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| AccessGroup |
SecurityGroup |
The group of contacts that have the specified access right on an
object.
|
0..* to 1..1 |
none |
| AccessRight |
OntologyTerm |
The type of AccessRight allowed on this object e.g. Read, Write
etc.
|
0..* to 0..1 |
none |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Audit.SecurityAccessType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.DescribableType">
<xsd:sequence>
<xsd:element name="_accessRight" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:attribute name="OntologyTerm_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
<xsd:attribute name="SecurityGroup_ref" use="required" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="SecurityAccess" type="fuge:FuGE.Common.Audit.SecurityAccessType" abstract="false" substitutionGroup="fuge:Describable"/>
|
FuGE.Common.References.BibliographicReference
Inheritance hierarchy:
BibliographicReference --> Identifiable --> Describable
Documentation:
Represents bibliographic references, including the most common
attributes. Note that because a BibliographicReference is
Identifiable, a DatabaseEntry can also be specified.
Attributes:
| Name | Documentation | Data type | Required |
| authors |
The names of the authors of the reference.
|
string |
false |
| publication |
The name of the journal, book etc.
|
string |
false |
| publisher |
The publisher of the publication.
|
string |
false |
| editor |
The editor(s) of the reference.
|
string |
false |
| year |
The year of publication.
|
int |
false |
| volume |
The volume name or number.
|
string |
false |
| issue |
The issue name or number.
|
string |
false |
| pages |
The page numbers.
|
string |
false |
| title |
The title of the BibliographicReference.
|
string |
false |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.References.BibliographicReferenceType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.IdentifiableType">
<xsd:attribute name="authors" type="xsd:string"/>
<xsd:attribute name="publication" type="xsd:string"/>
<xsd:attribute name="publisher" type="xsd:string"/>
<xsd:attribute name="editor" type="xsd:string"/>
<xsd:attribute name="year" type="xsd:int"/>
<xsd:attribute name="volume" type="xsd:string"/>
<xsd:attribute name="issue" type="xsd:string"/>
<xsd:attribute name="pages" type="xsd:string"/>
<xsd:attribute name="title" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="BibliographicReference" type="fuge:FuGE.Common.References.BibliographicReferenceType" abstract="false" substitutionGroup="fuge:Identifiable"/>
|
FuGE.Common.References.Database
Inheritance hierarchy:
Database --> Identifiable --> Describable
Documentation:
An address to a repository.
Attributes:
| Name | Documentation | Data type | Required |
| version |
The version of the Database.
|
string |
false |
| URI |
The location of the Database.
|
anyURI |
false |
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| DatabaseContact |
ContactRole |
Contacts associated with this database, such as hosting
institution, database curators, manager etc.
|
0..1 to 0..* |
composite |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.References.DatabaseType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.IdentifiableType">
<xsd:sequence>
<xsd:element ref="fuge:ContactRole" minOccurs="0" maxOccurs="unbounded"/>
</xsd:sequence>
<xsd:attribute name="version" type="xsd:string"/>
<xsd:attribute name="URI" type="xsd:anyURI"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Database" type="fuge:FuGE.Common.References.DatabaseType" abstract="false" substitutionGroup="fuge:Identifiable"/>
|
FuGE.Common.References.DatabaseReference
Inheritance hierarchy:
DatabaseReference --> Describable
Documentation:
A reference to a record in a database.
Attributes:
| Name | Documentation | Data type | Required |
| accession |
The identifier used to look up the record.
|
string |
true |
| accessionVersion |
The appropriate version of the accession (if applicable).
|
string |
false |
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| Database |
Database |
Reference to the database where the DatabaseEntry instance can
be found.
|
0..* to 1..1 |
none |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.References.DatabaseReferenceType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.DescribableType">
<xsd:attribute name="accession" use="required" type="xsd:string"/>
<xsd:attribute name="accessionVersion" type="xsd:string"/>
<xsd:attribute name="Database_ref" use="required" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="DatabaseReference" type="fuge:FuGE.Common.References.DatabaseReferenceType" abstract="false" substitutionGroup="fuge:Describable"/>
|
FuGE.Common.Description.Description
Inheritance hierarchy:
Description --> Describable
Documentation:
A free text description of an object.
Attributes:
| Name | Documentation | Data type | Required |
| text |
The description.
|
string |
false |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Description.DescriptionType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.DescribableType">
<xsd:attribute name="text" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Description" type="fuge:FuGE.Common.Description.DescriptionType" abstract="false" substitutionGroup="fuge:Describable"/>
|
FuGE.Common.Description.URI
Inheritance hierarchy:
URI --> Describable
Documentation:
A URI is short for Uniform Resource Identifier.
A URI is a compact sequence of characters that identifies an
abstract or physical resource.
Attributes:
| Name | Documentation | Data type | Required |
| location |
The Uniform Resource Indicator for this object.
|
anyURI |
true |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Description.URIType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.DescribableType">
<xsd:attribute name="location" use="required" type="xsd:anyURI"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="URI" type="fuge:FuGE.Common.Description.URIType" abstract="false" substitutionGroup="fuge:Describable"/>
|
FuGE.Common.Description.NameValueType
Inheritance hierarchy:
NameValueType --> Describable
Documentation:
A tuple designed to store data, keyed by a name and type.
Attributes:
| Name | Documentation | Data type | Required |
| name |
The name of the key.
|
string |
false |
| value |
The value of the name.
|
string |
false |
| type |
The type of the key.
|
string |
false |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Description.NameValueTypeType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.DescribableType">
<xsd:attribute name="name" type="xsd:string"/>
<xsd:attribute name="value" type="xsd:string"/>
<xsd:attribute name="type" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="NameValueType" type="fuge:FuGE.Common.Description.NameValueTypeType" abstract="false" substitutionGroup="fuge:Describable"/>
|
FuGE.Common.Protocol.Protocol (abstract)
Inheritance hierarchy:
Protocol --> Parameterizable --> Identifiable --> Describable
Documentation:
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.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| Actions (abstract) |
Action |
Each Protocol may be composed of a number of steps, each of
which is represented by an Action.
|
1..1 to 0..* |
composite |
| Equipment (abstract) |
Equipment |
Hardware used by this protocol.
|
0..* to 0..* |
none |
| Software (abstract) |
Software |
Software used by this Protocol.
|
0..* to 0..* |
none |
| InputTypes |
OntologyTerm |
The types of inputs this Protocol can take e.g. organisms,
solutions, data formats etc.
|
0..* to 0..* |
none |
| OutputTypes |
OntologyTerm |
The types of outputs produced by this Protocol e.g. organisms,
solutions, data formats etc.
|
0..* to 0..* |
none |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Protocol.ProtocolType" abstract = "true">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ParameterizableType">
<xsd:sequence>
<xsd:element name="_inputTypes" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="OntologyTerm_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="_outputTypes" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="OntologyTerm_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Protocol" type="fuge:FuGE.Common.Protocol.ProtocolType" abstract="true" substitutionGroup="fuge:Parameterizable"/>
|
FuGE.Common.Protocol.Parameter (abstract)
Inheritance hierarchy:
Parameter --> Identifiable --> Describable
Documentation:
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.
Attributes:
| Name | Documentation | Data type | Required |
| isInputParam |
An optional Boolean value to determine whether the parameter is
an input (true) or an output (false).
|
boolean |
false |
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| DefaultValue |
Measurement |
The default value for this parameter.
|
0..1 to 0..1 |
composite |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Protocol.ParameterType" abstract = "true">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.IdentifiableType">
<xsd:sequence>
<xsd:element ref="fuge:Measurement" minOccurs="0" maxOccurs="1"/>
</xsd:sequence>
<xsd:attribute name="isInputParam" type="xsd:boolean"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Parameter" type="fuge:FuGE.Common.Protocol.ParameterType" abstract="true" substitutionGroup="fuge:Identifiable"/>
|
FuGE.Common.Protocol.ParameterValue
Inheritance hierarchy:
ParameterValue --> Describable
Documentation:
The value of a Parameter.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| Parameter |
Parameter |
The parameter this value is for.
|
0..* to 1..1 |
none |
| Value |
Measurement |
The runtime value for this Parameter.
|
0..1 to 1..1 |
composite |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Protocol.ParameterValueType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.DescribableType">
<xsd:sequence>
<xsd:element ref="fuge:Measurement" minOccurs="1" maxOccurs="1"/>
</xsd:sequence>
<xsd:attribute name="Parameter_ref" use="required" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="ParameterValue" type="fuge:FuGE.Common.Protocol.ParameterValueType" abstract="false" substitutionGroup="fuge:Describable"/>
|
FuGE.Common.Protocol.ProtocolApplication (abstract)
Inheritance hierarchy:
ProtocolApplication --> ParameterizableApplication --> Identifiable --> Describable
Documentation:
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.
Attributes:
| Name | Documentation | Data type | Required |
| activityDate |
When the protocol was applied.
|
dateTime |
false |
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| OutputData (abstract) |
Data |
The data produced by a ProtocolApplication.
|
0..1 to 0..* |
none |
| InputData (abstract) |
Data |
The input data for a ProtocolApplication.
|
0..* to 0..* |
none |
| PartitionPairs (abstract) |
PartitionPair |
PartitionPairs that associate subsets (DataPartition) of the
output data with subsets of the input data.
|
1..1 to 0..* |
composite |
| OutputMaterials (abstract) |
Material |
Association to the Material(s) created as output by this
ProtocolApplication.
|
0..1 to 0..* |
none |
| InputMaterials (abstract) |
MaterialMeasurement |
Association from a ProtocolApplication to a measurement of the
quantity of the source (input) Material(s) used.
|
1..1 to 0..* |
composite |
| Protocol (abstract) |
Protocol |
The protocol that is being used.
|
0..* to 1..1 |
none |
| ActionApplications |
ActionApplication |
Association to the ActionApplication steps that comprise this
ProtocolApplication.
|
1..1 to 0..* |
composite |
| SoftwareApplications |
SoftwareApplication |
The use of software for the application of the protocol.
|
1..1 to 0..* |
composite |
| EquipmentApplications |
EquipmentApplication |
The use of hardware for the application of the protocol.
|
1..1 to 0..* |
composite |
| ProtocolDeviation |
Description |
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.
|
0..1 to 0..1 |
composite |
| Performers |
ContactRole |
The people or organizations who performed the protocol.
ContactRole could be used to specify the part of the Protocol
performed by a particular Contact.
|
0..1 to 0..* |
composite |
| InputCompleteMaterials (abstract) |
Material |
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.
|
0..1 to 0..* |
none |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Protocol.ProtocolApplicationType" abstract = "true">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ParameterizableApplicationType">
<xsd:sequence>
<xsd:element ref="fuge:ActionApplication" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="fuge:SoftwareApplication" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="fuge:EquipmentApplication" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element name="_protocolDeviation" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="fuge:Description" minOccurs="1" maxOccurs="1"/>
</xsd:sequence>
</xsd:complexType>
</xsd:element>
<xsd:element ref="fuge:ContactRole" minOccurs="0" maxOccurs="unbounded"/>
</xsd:sequence>
<xsd:attribute name="activityDate" type="xsd:dateTime"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="ProtocolApplication" type="fuge:FuGE.Common.Protocol.ProtocolApplicationType" abstract="true" substitutionGroup="fuge:ParameterizableApplication"/>
|
FuGE.Common.Protocol.Software (abstract)
Inheritance hierarchy:
Software --> Parameterizable --> Identifiable --> Describable
Documentation:
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 without extension.
Attributes:
| Name | Documentation | Data type | Required |
| version |
The version of Software used.
|
string |
false |
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| Software2Equipment (abstract) |
Equipment |
Associates Equipment and Software together. Indicates that a
set of Software is run on a piece of Equipment.
|
0..* to 0..* |
none |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Protocol.SoftwareType" abstract = "true">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ParameterizableType">
<xsd:attribute name="version" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Software" type="fuge:FuGE.Common.Protocol.SoftwareType" abstract="true" substitutionGroup="fuge:Parameterizable"/>
|
FuGE.Common.Protocol.Equipment (abstract)
Inheritance hierarchy:
Equipment --> Parameterizable --> Identifiable --> Describable
Documentation:
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.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| Software2Equipment (abstract) |
Software |
Associates Equipment and Software together. Indicates that a
set of Software is run on a piece of Equipment.
|
0..* to 0..* |
none |
| EquipmentParts (abstract) |
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
Equipment association.
|
0..* to 0..* |
none |
| Make |
OntologyTerm |
The equipment make, usually the organization that makes the
equipment.
|
0..* to 0..1 |
none |
| Model |
OntologyTerm |
The Equipment model.
|
0..* to 0..1 |
none |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Protocol.EquipmentType" abstract = "true">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ParameterizableType">
<xsd:sequence>
<xsd:element name="_make" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:attribute name="OntologyTerm_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="_model" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:attribute name="OntologyTerm_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Equipment" type="fuge:FuGE.Common.Protocol.EquipmentType" abstract="true" substitutionGroup="fuge:Parameterizable"/>
|
FuGE.Common.Protocol.EquipmentApplication
Inheritance hierarchy:
EquipmentApplication --> ParameterizableApplication --> Identifiable --> Describable
Documentation:
The use of a piece of Equipment with the requisite Parameters
and ParameterValues.
Attributes:
| Name | Documentation | Data type | Required |
| serialNumber |
Manufacturer's identifier for the Equipment.
|
string |
false |
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| AppliedEquipment |
Equipment |
The Equipment that was used in the ProtocolApplication.
|
0..* to 1..1 |
none |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Protocol.EquipmentApplicationType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ParameterizableApplicationType">
<xsd:attribute name="serialNumber" type="xsd:string"/>
<xsd:attribute name="Equipment_ref" use="required" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="EquipmentApplication" type="fuge:FuGE.Common.Protocol.EquipmentApplicationType" abstract="false" substitutionGroup="fuge:ParameterizableApplication"/>
|
FuGE.Common.Protocol.SoftwareApplication
Inheritance hierarchy:
SoftwareApplication --> ParameterizableApplication --> Identifiable --> Describable
Documentation:
The use of a piece of software with the requisite Parameters and
ParameterValues.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| AppliedSoftware |
Software |
The Software that was used in the ProtocolApplication.
|
0..* to 1..1 |
none |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Protocol.SoftwareApplicationType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ParameterizableApplicationType">
<xsd:attribute name="Software_ref" use="required" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="SoftwareApplication" type="fuge:FuGE.Common.Protocol.SoftwareApplicationType" abstract="false" substitutionGroup="fuge:ParameterizableApplication"/>
|
FuGE.Common.Protocol.Parameterizable (abstract)
Inheritance hierarchy:
Parameterizable --> Identifiable --> Describable
Documentation:
The Parameterizable interface encapsulates the association of
Parameters with ParameterValues.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| Provider |
ContactRole |
The provider of the Protocol, Equipment or Software.
|
0..1 to 0..* |
composite |
| Parameters (abstract) |
Parameter |
The set of parameters for the Parameterizable class instance.
|
0..1 to 0..* |
composite |
| Types |
OntologyTerm |
The type of Equipment, Software or Protocol.
|
0..* to 0..* |
none |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Protocol.ParameterizableType" abstract = "true">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.IdentifiableType">
<xsd:sequence>
<xsd:element ref="fuge:ContactRole" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element name="_types" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="OntologyTerm_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Parameterizable" type="fuge:FuGE.Common.Protocol.ParameterizableType" abstract="true" substitutionGroup="fuge:Identifiable"/>
|
FuGE.Common.Protocol.ParameterizableApplication (abstract)
Inheritance hierarchy:
ParameterizableApplication --> Identifiable --> Describable
Documentation:
The interface that is the use of a Parameterizable class.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| ParameterValues |
ParameterValue |
The parameter values for this Parameterizable Application.
|
1..1 to 0..* |
composite |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Protocol.ParameterizableApplicationType" abstract = "true">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.IdentifiableType">
<xsd:sequence>
<xsd:element ref="fuge:ParameterValue" minOccurs="0" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="ParameterizableApplication" type="fuge:FuGE.Common.Protocol.ParameterizableApplicationType" abstract="true" substitutionGroup="fuge:Identifiable"/>
|
FuGE.Common.Protocol.Action (abstract)
Inheritance hierarchy:
Action --> Identifiable --> Describable
Documentation:
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.
Attributes:
| Name | Documentation | Data type | Required |
| actionOrdinal |
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.
|
int |
false |
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| ChildProtocol (abstract) |
Protocol |
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.
|
0..1 to 0..1 |
none |
| Parameters (abstract) |
Parameter |
The parameters for this Action.
|
0..1 to 0..* |
composite |
| ParameterPairs (abstract) |
ParameterPair |
An abstract association to demonstrate that Actions can have
ParameterPairs. This association should be extended if a
particular subclass of Action can have ParameterPairs.
|
1..1 to 0..* |
composite |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Protocol.ActionType" abstract = "true">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.IdentifiableType">
<xsd:attribute name="actionOrdinal" type="xsd:int"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Action" type="fuge:FuGE.Common.Protocol.ActionType" abstract="true" substitutionGroup="fuge:Identifiable"/>
|
FuGE.Common.Protocol.ActionApplication
Inheritance hierarchy:
ActionApplication --> ParameterizableApplication --> Identifiable --> Describable
Documentation:
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.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| Action |
Action |
Association to the Action that is being performed as recorded by
this ActionApplication.
|
0..* to 1..1 |
none |
| ActionDeviation |
Description |
Used to define human readable notes for annotating deviations to
an Action during the ActionApplication.
|
0..1 to 0..1 |
composite |
| ChildProtocolApplication |
ProtocolApplication |
Association to ProtocolApplication if a hierarchical Protocol
has been defined representing the child step of the Protocol.
|
0..1 to 0..1 |
none |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Protocol.ActionApplicationType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ParameterizableApplicationType">
<xsd:sequence>
<xsd:element name="_actionDeviation" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="fuge:Description" minOccurs="1" maxOccurs="1"/>
</xsd:sequence>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
<xsd:attribute name="Action_ref" use="required" type="xsd:string"/>
<xsd:attribute name="ProtocolApplication_ref" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="ActionApplication" type="fuge:FuGE.Common.Protocol.ActionApplicationType" abstract="false" substitutionGroup="fuge:ParameterizableApplication"/>
|
FuGE.Common.Protocol.GenericProtocol
Inheritance hierarchy:
GenericProtocol --> Protocol --> Parameterizable --> Identifiable --> Describable
Documentation:
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.
Attributes:
| Name | Documentation | Data type | Required |
| protocolText |
The text that applies to the entire Protocol.
|
string |
false |
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| Software |
GenericSoftware |
A reference to the GenericSoftware used with this
GenericProtocol.
|
0..* to 0..* |
none |
| Equipment |
GenericEquipment |
A reference to the GenericProtocol used with this
GenericEquipment.
|
0..* to 0..* |
none |
| Parameters |
GenericParameter |
The parameters defined for the GenericProtocol.
|
0..1 to 0..* |
composite |
| Actions |
Action |
The actions performed within a GenericProtocol.
|
0..1 to 0..* |
composite |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Protocol.GenericProtocolType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ProtocolType">
<xsd:sequence>
<xsd:element name="_software" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="GenericSoftware_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="_equipment" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="GenericEquipment_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
<xsd:element ref="fuge:GenericParameter" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="fuge:Action" minOccurs="0" maxOccurs="unbounded"/>
</xsd:sequence>
<xsd:attribute name="protocolText" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="GenericProtocol" type="fuge:FuGE.Common.Protocol.GenericProtocolType" abstract="false" substitutionGroup="fuge:Protocol"/>
|
FuGE.Common.Protocol.GenericAction
Inheritance hierarchy:
GenericAction --> Action --> Identifiable --> Describable
Documentation:
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.
Attributes:
| Name | Documentation | Data type | Required |
| actionText |
Free text to describe this Action.
|
string |
false |
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| ActionTerm |
OntologyTerm |
Each GenericAction may be associated with an OntologyTerm that
defines that GenericAction.
|
0..* to 0..1 |
none |
| ChildProtocol |
Protocol |
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.
|
0..1 to 0..1 |
none |
| Parameters |
GenericParameter |
The parameters belonging to the GenericAction.
|
0..1 to 0..* |
composite |
| ParameterPairs |
ParameterPair |
ParameterPairs owned by the GenericAction. The TargetParameter
should reference a Parameter owned by a child Protocol which is
also referenced by the GenericAction.
|
1..1 to 0..* |
composite |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Protocol.GenericActionType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ActionType">
<xsd:sequence>
<xsd:element name="_actionTerm" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:attribute name="OntologyTerm_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
<xsd:element ref="fuge:GenericParameter" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="fuge:ParameterPair" minOccurs="0" maxOccurs="unbounded"/>
</xsd:sequence>
<xsd:attribute name="actionText" type="xsd:string"/>
<xsd:attribute name="Protocol_ref" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="GenericAction" type="fuge:FuGE.Common.Protocol.GenericActionType" abstract="false" substitutionGroup="fuge:Action"/>
|
FuGE.Common.Protocol.GenericSoftware
Inheritance hierarchy:
GenericSoftware --> Software --> Parameterizable --> Identifiable --> Describable
Documentation:
A subclass of the abstract Software class for capturing the
description of Software used.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| Software2Equipment |
GenericEquipment |
Associates GenericEquipment with GenericSoftware to indicate
that instances of software are run on piece(s) of Equipment.
|
0..* to 0..* |
none |
| Parameters |
GenericParameter |
The parameters for this piece of GenericSoftware.
|
0..1 to 0..* |
composite |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Protocol.GenericSoftwareType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.SoftwareType">
<xsd:sequence>
<xsd:element name="_equipment" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="GenericEquipment_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
<xsd:element ref="fuge:GenericParameter" minOccurs="0" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="GenericSoftware" type="fuge:FuGE.Common.Protocol.GenericSoftwareType" abstract="false" substitutionGroup="fuge:Software"/>
|
FuGE.Common.Protocol.GenericEquipment
Inheritance hierarchy:
GenericEquipment --> Equipment --> Parameterizable --> Identifiable --> Describable
Documentation:
A subclass of the abstract Equipment class for capturing the
description of Equipment used.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| Software2Equipment |
GenericSoftware |
Associates GenericEquipment with GenericSoftware to indicate
that instances of software are run on piece(s) of Equipment.
|
0..* to 0..* |
none |
| Parameters |
GenericParameter |
The parameters for this piece of GenericEquipment.
|
0..1 to 0..* |
composite |
| EquipmentParts |
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.
|
0..* to 0..* |
none |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Protocol.GenericEquipmentType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.EquipmentType">
<xsd:sequence>
<xsd:element name="_software" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="GenericSoftware_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
<xsd:element ref="fuge:GenericParameter" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element name="_equipmentParts" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="GenericEquipment_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="GenericEquipment" type="fuge:FuGE.Common.Protocol.GenericEquipmentType" abstract="false" substitutionGroup="fuge:Equipment"/>
|
FuGE.Common.Protocol.GenericParameter
Inheritance hierarchy:
GenericParameter --> Parameter --> Identifiable --> Describable
Documentation:
A subclass of the abstract Parameter class to represent a
parameter that is defined by a controlled vocabulary term.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| ParameterType |
OntologyTerm |
The name of the parameter.
|
0..* to 0..1 |
none |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Protocol.GenericParameterType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ParameterType">
<xsd:sequence>
<xsd:element name="_parameterType" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:attribute name="OntologyTerm_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="GenericParameter" type="fuge:FuGE.Common.Protocol.GenericParameterType" abstract="false" substitutionGroup="fuge:Parameter"/>
|
FuGE.Common.Protocol.GenericProtocolApplication
Inheritance hierarchy:
GenericProtocolApplication --> ProtocolApplication --> ParameterizableApplication --> Identifiable --> Describable
Documentation:
A subclass of ProtocolApplication to be used as it is in data
formats without being extended.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| InputMaterials |
GenericMaterialMeasurement |
Measured sources of material that are inputs to this
GenericProtocolApplication.
|
0..1 to 0..* |
composite |
| InputData |
Data |
The instances of GenericData that are inputs to the
GenericProtocolApplication.
|
0..* to 0..* |
none |
| OutputData |
Data |
The Data produced from the GenericProtocolApplication.
|
0..1 to 0..* |
none |
| OutputMaterials |
Material |
The instances of GenericMaterial or a subclass of Material that
are produced from the GenericProtocolApplication.
|
0..1 to 0..* |
none |
| Protocol |
Protocol |
A reference to the GenericProtocol or subclass of Protocol that
has been used with this GenericProtocolApplication.
|
0..* to 1..1 |
none |
| InputCompleteMaterials |
Material |
Whole Materials that are inputs to the
GenericProtocolApplication.
|
0..* to 0..* |
none |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Protocol.GenericProtocolApplicationType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Protocol.ProtocolApplicationType">
<xsd:sequence>
<xsd:element ref="fuge:GenericMaterialMeasurement" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element name="_inputData" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="Data_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="_outputData" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="Data_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="_outputMaterials" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="Material_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="_inputCompleteMaterials" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="Material_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
<xsd:attribute name="Protocol_ref" use="required" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="GenericProtocolApplication" type="fuge:FuGE.Common.Protocol.GenericProtocolApplicationType" abstract="false" substitutionGroup="fuge:ProtocolApplication"/>
|
FuGE.Common.Protocol.ParameterPair
Inheritance hierarchy:
ParameterPair --> Describable
Documentation:
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.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| TargetParameter |
Parameter |
A Parameter that is an input to a process which has been an
output from another process.
|
0..* to 1..1 |
none |
| SourceParameter |
Parameter |
A Parameter that is output from one process which will be input
to another process.
|
0..* to 1..1 |
none |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Protocol.ParameterPairType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.DescribableType">
<xsd:sequence>
<xsd:element name="_targetParameter" minOccurs="1" maxOccurs="1">
<xsd:complexType>
<xsd:attribute name="Parameter_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="_sourceParameter" minOccurs="1" maxOccurs="1">
<xsd:complexType>
<xsd:attribute name="Parameter_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="ParameterPair" type="fuge:FuGE.Common.Protocol.ParameterPairType" abstract="false" substitutionGroup="fuge:Describable"/>
|
FuGE.Common.Ontology.OntologyIndividual
Inheritance hierarchy:
OntologyIndividual --> OntologyTerm --> Identifiable --> Describable
Documentation:
An instance of an Ontology class.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| Properties |
OntologyProperty |
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.
|
0..1 to 0..* |
composite |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Ontology.OntologyIndividualType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Ontology.OntologyTermType">
<xsd:sequence>
<xsd:element ref="fuge:OntologyProperty" minOccurs="0" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="OntologyIndividual" type="fuge:FuGE.Common.Ontology.OntologyIndividualType" abstract="false" substitutionGroup="fuge:OntologyTerm"/>
|
FuGE.Common.Ontology.OntologyProperty (abstract)
Inheritance hierarchy:
OntologyProperty --> OntologyTerm --> Identifiable --> Describable
Documentation:
Base class for instances of Ontology properties
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Ontology.OntologyPropertyType" abstract = "true">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Ontology.OntologyTermType">
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="OntologyProperty" type="fuge:FuGE.Common.Ontology.OntologyPropertyType" abstract="true" substitutionGroup="fuge:OntologyTerm"/>
|
FuGE.Common.Ontology.DataProperty
Inheritance hierarchy:
DataProperty --> OntologyProperty --> OntologyTerm --> Identifiable --> Describable
Documentation:
An instance of an Ontology data property. So an individual of
Age might be restricted to a value of 8.
Attributes:
| Name | Documentation | Data type | Required |
| dataType |
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.
|
string |
false |
| value |
The value associated with the DataProperty instance.
|
string |
false |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Ontology.DataPropertyType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Ontology.OntologyPropertyType">
<xsd:attribute name="dataType" type="xsd:string"/>
<xsd:attribute name="value" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="DataProperty" type="fuge:FuGE.Common.Ontology.DataPropertyType" abstract="false" substitutionGroup="fuge:OntologyProperty"/>
|
FuGE.Common.Ontology.ObjectProperty
Inheritance hierarchy:
ObjectProperty --> OntologyProperty --> OntologyTerm --> Identifiable --> Describable
Documentation:
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.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| Content |
OntologyIndividual |
The instance(s) of the child OntologyIndividuals referenced by
the parent OntologyIndividual.
|
0..1 to 1..* |
composite |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Ontology.ObjectPropertyType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Ontology.OntologyPropertyType">
<xsd:sequence>
<xsd:element ref="fuge:OntologyIndividual" minOccurs="1" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="ObjectProperty" type="fuge:FuGE.Common.Ontology.ObjectPropertyType" abstract="false" substitutionGroup="fuge:OntologyProperty"/>
|
FuGE.Common.Ontology.OntologyTerm (abstract)
Inheritance hierarchy:
OntologyTerm --> Identifiable --> Describable
Documentation:
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.
Attributes:
| Name | Documentation | Data type | Required |
| term |
The ontology term itself, also known as the local name in some
ontologies.
|
string |
true |
| termAccession |
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).
|
string |
true |
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| OntologySource |
OntologySource |
The source ontology or controlled vocabulary list that ontology
terms have been obtained from.
|
0..* to 0..1 |
none |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Ontology.OntologyTermType" abstract = "true">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.IdentifiableType">
<xsd:attribute name="term" use="required" type="xsd:string"/>
<xsd:attribute name="termAccession" use="required" type="xsd:string"/>
<xsd:attribute name="OntologySource_ref" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="OntologyTerm" type="fuge:FuGE.Common.Ontology.OntologyTermType" abstract="true" substitutionGroup="fuge:Identifiable"/>
|
FuGE.Common.Ontology.OntologySource
Inheritance hierarchy:
OntologySource --> Identifiable --> Describable
Documentation:
The source ontology or controlled vocabulary list that ontology
terms have been obtained from.
Attributes:
| Name | Documentation | Data type | Required |
| ontologyURI |
A URI that references the location of the ontology.
|
anyURI |
true |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Ontology.OntologySourceType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.IdentifiableType">
<xsd:attribute name="ontologyURI" use="required" type="xsd:anyURI"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="OntologySource" type="fuge:FuGE.Common.Ontology.OntologySourceType" abstract="false" substitutionGroup="fuge:Identifiable"/>
|
FuGE.Common.Describable (abstract)
Inheritance hierarchy:
Describable
Documentation:
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.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| AuditTrail |
Audit |
A list of Audit instances that track changes to the instance of
Describable.
|
0..1 to 0..* |
composite |
| Descriptions |
Description |
Free hand text descriptions.
|
0..1 to 0..* |
composite |
| Security |
Security |
Information on the security for the instance of the class.
|
0..* to 0..1 |
aggregate |
| URI |
URI |
A URI associated with a Describable object.
|
0..1 to 0..1 |
composite |
| Annotations |
OntologyTerm |
Allows specification of additional ontology entries related to
the instance being described that are not directly specified
elsewhere.
|
0..* to 0..* |
none |
| PropertySets |
NameValueType |
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.
|
0..1 to 0..* |
composite |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.DescribableType" abstract = "true">
<xsd:sequence>
<xsd:element name="_auditTrail" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="fuge:Audit" minOccurs="1" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:complexType>
</xsd:element>
<xsd:element name="_descriptions" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="fuge:Description" minOccurs="1" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:complexType>
</xsd:element>
<xsd:element name="_uri" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="fuge:URI" minOccurs="1" maxOccurs="1"/>
</xsd:sequence>
</xsd:complexType>
</xsd:element>
<xsd:element name="_annotations" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="OntologyTerm_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="_propertySets" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="fuge:NameValueType" minOccurs="1" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
<xsd:attribute name="Security_ref" type="xsd:string"/>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Describable" type="fuge:FuGE.Common.DescribableType" abstract="true"/>
|
FuGE.Common.Identifiable (abstract)
Inheritance hierarchy:
Identifiable --> Describable
Documentation:
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).
Attributes:
| Name | Documentation | Data type | Required |
| identifier |
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.
|
string |
true |
| name |
The potentially ambiguous common identifier, such as a
human-readable name for the instance.
|
string |
false |
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| DatabaseReferences |
DatabaseReference |
References to entries in databases.
|
0..1 to 0..* |
composite |
| BibliographicReferences |
BibliographicReference |
References to existing literature.
|
0..* to 0..* |
none |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.IdentifiableType" abstract = "true">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.DescribableType">
<xsd:sequence>
<xsd:element ref="fuge:DatabaseReference" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element name="_bibliographicReferences" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="BibliographicReference_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
<xsd:attribute name="identifier" use="required" type="xsd:string"/>
<xsd:attribute name="name" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Identifiable" type="fuge:FuGE.Common.IdentifiableType" abstract="true" substitutionGroup="fuge:Describable"/>
|
FuGE.Common.Measurement.AtomicValue
Inheritance hierarchy:
AtomicValue --> Measurement --> Describable
Documentation:
An atomic value i.e. one that has a single value.
Attributes:
| Name | Documentation | Data type | Required |
| value |
An atomic default value for the parameter.
|
string |
true |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Measurement.AtomicValueType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Measurement.MeasurementType">
<xsd:attribute name="value" use="required" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="AtomicValue" type="fuge:FuGE.Common.Measurement.AtomicValueType" abstract="false" substitutionGroup="fuge:Measurement"/>
|
FuGE.Common.Measurement.BooleanValue
Inheritance hierarchy:
BooleanValue --> Measurement --> Describable
Documentation:
A Boolean value.
Attributes:
| Name | Documentation | Data type | Required |
| value |
A Boolean default value for the parameter.
|
boolean |
true |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Measurement.BooleanValueType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Measurement.MeasurementType">
<xsd:attribute name="value" use="required" type="xsd:boolean"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="BooleanValue" type="fuge:FuGE.Common.Measurement.BooleanValueType" abstract="false" substitutionGroup="fuge:Measurement"/>
|
FuGE.Common.Measurement.ComplexValue
Inheritance hierarchy:
ComplexValue --> Measurement --> Describable
Documentation:
A complex default value for the Parameter, such as a term from a
controlled list or a function.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| Value |
OntologyTerm |
A value given by an ontology term.
|
0..* to 1..1 |
none |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Measurement.ComplexValueType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Measurement.MeasurementType">
<xsd:sequence>
<xsd:element name="_value" minOccurs="1" maxOccurs="1">
<xsd:complexType>
<xsd:attribute name="OntologyTerm_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="ComplexValue" type="fuge:FuGE.Common.Measurement.ComplexValueType" abstract="false" substitutionGroup="fuge:Measurement"/>
|
FuGE.Common.Measurement.Range
Inheritance hierarchy:
Range --> Measurement --> Describable
Documentation:
A range value.
Attributes:
| Name | Documentation | Data type | Required |
| lowerLimit |
The lower limit of a range value.
|
string |
true |
| upperLimit |
The upper limit of a range value.
|
string |
true |
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| RangeDescriptors |
OntologyTerm |
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.
|
0..* to 0..* |
none |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Measurement.RangeType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.Measurement.MeasurementType">
<xsd:sequence>
<xsd:element name="_rangeDescriptors" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="OntologyTerm_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
<xsd:attribute name="lowerLimit" use="required" type="xsd:string"/>
<xsd:attribute name="upperLimit" use="required" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Range" type="fuge:FuGE.Common.Measurement.RangeType" abstract="false" substitutionGroup="fuge:Measurement"/>
|
FuGE.Common.Measurement.Measurement (abstract)
Inheritance hierarchy:
Measurement --> Describable
Documentation:
Abstract superclass representing different methods of supplying
a value or measurement.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| Unit |
OntologyTerm |
The Unit of Measurement.
|
0..* to 0..1 |
none |
| DataType |
OntologyTerm |
The data type of the Parameter such as Boolean, integer, String.
|
0..* to 0..1 |
none |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Common.Measurement.MeasurementType" abstract = "true">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.DescribableType">
<xsd:sequence>
<xsd:element name="_unit" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:attribute name="OntologyTerm_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="_dataType" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:attribute name="OntologyTerm_ref" use="required" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Measurement" type="fuge:FuGE.Common.Measurement.MeasurementType" abstract="true" substitutionGroup="fuge:Describable"/>
|
FuGE.Collection.ProtocolCollection
Inheritance hierarchy:
ProtocolCollection --> Describable
Documentation:
The complete set of Protocol, Equipment, Software and
ProtocolApplication objects in the FuGE document.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| Protocols |
Protocol |
Reference to all Protocol objects in the FuGE document.
|
0..* to 0..* |
composite |
| AllSoftware |
Software |
Reference to all Software objects in the FuGE document.
|
0..* to 0..* |
composite |
| ProtocolApplications |
ProtocolApplication |
Reference to all ProtocolApplication objects in the FuGE
document.
|
0..* to 0..* |
composite |
| AllEquipment |
Equipment |
Reference to all Equipment objects in the FuGE document.
|
0..* to 0..* |
composite |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Collection.ProtocolCollectionType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.DescribableType">
<xsd:sequence>
<xsd:element ref="fuge:Protocol" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="fuge:Software" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="fuge:ProtocolApplication" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="fuge:Equipment" minOccurs="0" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="ProtocolCollection" type="fuge:FuGE.Collection.ProtocolCollectionType" abstract="false" substitutionGroup="fuge:Describable"/>
|
FuGE.Collection.InvestigationCollection
Inheritance hierarchy:
InvestigationCollection --> Describable
Documentation:
The collection of Investigation and Factor objects in the FuGE
document.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| Investigations |
Investigation |
Reference to all Investigation objects in the FuGE document.
|
0..* to 0..* |
composite |
| FactorCollection |
Factor |
Reference to the complete set of Factor objects in the FuGE
document.
|
0..* to 0..* |
composite |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Collection.InvestigationCollectionType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.DescribableType">
<xsd:sequence>
<xsd:element ref="fuge:Investigation" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="fuge:Factor" minOccurs="0" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="InvestigationCollection" type="fuge:FuGE.Collection.InvestigationCollectionType" abstract="false" substitutionGroup="fuge:Describable"/>
|
FuGE.Collection.ReferenceableCollection
Inheritance hierarchy:
ReferenceableCollection --> Describable
Documentation:
The collection of objects that allow external references.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| AllBibliographicReferences |
BibliographicReference |
Reference to the complete set of BibliographicReference objects
in the FuGE document.
|
0..* to 0..* |
composite |
| AllDatabases |
Database |
Reference to the complete set of Database objects in the FuGE
document.
|
0..* to 0..* |
composite |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Collection.ReferenceableCollectionType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.DescribableType">
<xsd:sequence>
<xsd:element ref="fuge:BibliographicReference" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="fuge:Database" minOccurs="0" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="ReferenceableCollection" type="fuge:FuGE.Collection.ReferenceableCollectionType" abstract="false" substitutionGroup="fuge:Describable"/>
|
FuGE.Collection.DataCollection
Inheritance hierarchy:
DataCollection --> Describable
Documentation:
The complete collection of all Data, Dimension, DataPartition
and HigherLevelAnalysis objects.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| AllDimensions |
Dimension |
Reference to the complete set of Dimension objects in the FuGE
document.
|
0..* to 0..* |
composite |
| HigherLevelAnalyses |
HigherLevelAnalysis |
Reference to the complete set of HigherLevelAnalysis objects in
the FuGE document.
|
0..* to 0..* |
composite |
| AllData |
Data |
Reference to the complete set of Data objects in the FuGE
document.
|
0..* to 0..* |
composite |
| AllDataPartitions |
DataPartition |
Reference to the complete set of DataPartitions.
|
0..* to 0..* |
composite |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Collection.DataCollectionType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.DescribableType">
<xsd:sequence>
<xsd:element ref="fuge:Dimension" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="fuge:HigherLevelAnalysis" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="fuge:Data" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="fuge:DataPartition" minOccurs="0" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="DataCollection" type="fuge:FuGE.Collection.DataCollectionType" abstract="false" substitutionGroup="fuge:Describable"/>
|
FuGE.Collection.ConceptualMoleculeCollection
Inheritance hierarchy:
ConceptualMoleculeCollection --> Describable
Documentation:
The complete set of ConceptualMolecule objects and
SequenceAnnotationSet objects.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| ConceptualMolecules |
ConceptualMolecule |
Reference to the complete set of ConceptualMolecule objects in
the FuGE document.
|
0..* to 0..* |
composite |
| AllSequenceAnnotations |
SequenceAnnotationSet |
Reference to the complete set of SequenceAnnotation objects in
the FuGE document.
|
0..* to 0..* |
composite |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Collection.ConceptualMoleculeCollectionType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.DescribableType">
<xsd:sequence>
<xsd:element ref="fuge:ConceptualMolecule" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="fuge:SequenceAnnotationSet" minOccurs="0" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="ConceptualMoleculeCollection" type="fuge:FuGE.Collection.ConceptualMoleculeCollectionType" abstract="false" substitutionGroup="fuge:Describable"/>
|
FuGE.Collection.OntologyCollection
Inheritance hierarchy:
OntologyCollection --> Describable
Documentation:
The complete set of OntologyIndividual and OntologySource
objects referenced in the FuGE document.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| OntologyTerms |
OntologyTerm |
The complete set of OntologyTerms in the FuGE document.
|
0..* to 0..* |
composite |
| OntologySources |
OntologySource |
The complete set of OntologySources in the FuGE document.
|
0..* to 0..* |
composite |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Collection.OntologyCollectionType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.DescribableType">
<xsd:sequence>
<xsd:element ref="fuge:OntologyTerm" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="fuge:OntologySource" minOccurs="0" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="OntologyCollection" type="fuge:FuGE.Collection.OntologyCollectionType" abstract="false" substitutionGroup="fuge:Describable"/>
|
FuGE.Collection.MaterialCollection
Inheritance hierarchy:
MaterialCollection --> Describable
Documentation:
The complete set of all Material objects in the FuGE document.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| Materials |
Material |
The complete set of Materials.
|
0..* to 0..* |
composite |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Collection.MaterialCollectionType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.DescribableType">
<xsd:sequence>
<xsd:element ref="fuge:Material" minOccurs="0" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="MaterialCollection" type="fuge:FuGE.Collection.MaterialCollectionType" abstract="false" substitutionGroup="fuge:Describable"/>
|
FuGE.Collection.AuditCollection
Inheritance hierarchy:
AuditCollection --> Describable
Documentation:
The collection of Audit objects (Security, SecurityGroup and
Contacts).
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| SecurityCollection |
Security |
Reference to the complete set of Security objects in the FuGE
document.
|
0..* to 0..* |
composite |
| AllContacts |
Contact |
The complete set of Contacts.
|
0..* to 0..* |
composite |
| SecurityGroups |
SecurityGroup |
Reference to the complete set of SecurityGroup objects in the
FuGE document.
|
0..* to 0..* |
composite |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Collection.AuditCollectionType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.DescribableType">
<xsd:sequence>
<xsd:element ref="fuge:Security" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="fuge:Contact" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="fuge:SecurityGroup" minOccurs="0" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="AuditCollection" type="fuge:FuGE.Collection.AuditCollectionType" abstract="false" substitutionGroup="fuge:Describable"/>
|
FuGE.Collection.Provider
Inheritance hierarchy:
Provider --> Identifiable --> Describable
Documentation:
The provider of the FuGE document in terms of the Contact and
the software the produced the document instance.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| ProducingSoftware |
Software |
The Software that produced the document instance.
|
0..* to 0..1 |
none |
| Provider |
ContactRole |
The Contact that provided the document instance.
|
0..* to 0..1 |
composite |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Collection.ProviderType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.IdentifiableType">
<xsd:sequence>
<xsd:element ref="fuge:ContactRole" minOccurs="0" maxOccurs="1"/>
</xsd:sequence>
<xsd:attribute name="Software_ref" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="Provider" type="fuge:FuGE.Collection.ProviderType" abstract="false" substitutionGroup="fuge:Identifiable"/>
|
FuGE.Collection.FuGE
Inheritance hierarchy:
FuGE --> Identifiable --> Describable
Documentation:
The root container for accessing all objects.
Associations:
| Name | Associated class | Documentation | Multiplicity | Composite |
| MaterialCollection |
MaterialCollection |
The complete set of all Material objects in the FuGE document.
|
0..1 to 0..1 |
composite |
| ConceptualMoleculeCollection |
ConceptualMoleculeCollection |
The complete set of ConceptualMolecule objects and
SequenceAnnotationSet objects.
|
0..1 to 0..1 |
composite |
| ReferenceableCollection |
ReferenceableCollection |
The complete set of BibliographicReferences and Databases.
|
0..1 to 0..1 |
composite |
| InvestigationCollection |
InvestigationCollection |
The collection of Investigation and Factor objects in the FuGE
document.
|
0..1 to 0..1 |
composite |
| DataCollection |
DataCollection |
The complete collection of all Data, Dimension, DataPartition
and HigherLevelAnalysis objects.
|
0..1 to 0..1 |
composite |
| AuditCollection |
AuditCollection |
The collection of Audit objects (Security, SecurityGroup and
Contacts).
|
0..1 to 0..1 |
composite |
| ProtocolCollection |
ProtocolCollection |
The complete set of Protocol, Equipment, Software and
ProtocolApplication objects in the FuGE document.
|
0..1 to 0..1 |
composite |
| OntologyCollection |
OntologyCollection |
The complete set of OntologyIndividual objects in the FuGE
document.
|
0..1 to 0..1 |
composite |
| Provider |
Provider |
The Provider of the FuGE document
|
0..* to 0..1 |
composite |
XML Schema Complex Type specification:
<xsd:complexType name="FuGE.Collection.FuGEType" abstract = "false">
<xsd:complexContent>
<xsd:extension base="fuge:FuGE.Common.IdentifiableType">
<xsd:sequence>
<xsd:element ref="fuge:MaterialCollection" minOccurs="0" maxOccurs="1"/>
<xsd:element ref="fuge:ConceptualMoleculeCollection" minOccurs="0" maxOccurs="1"/>
<xsd:element ref="fuge:ReferenceableCollection" minOccurs="0" maxOccurs="1"/>
<xsd:element ref="fuge:InvestigationCollection" minOccurs="0" maxOccurs="1"/>
<xsd:element ref="fuge:DataCollection" minOccurs="0" maxOccurs="1"/>
<xsd:element ref="fuge:AuditCollection" minOccurs="0" maxOccurs="1"/>
<xsd:element ref="fuge:ProtocolCollection" minOccurs="0" maxOccurs="1"/>
<xsd:element ref="fuge:OntologyCollection" minOccurs="0" maxOccurs="1"/>
<xsd:element ref="fuge:Provider" minOccurs="0" maxOccurs="1"/>
</xsd:sequence>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
|
XML Schema element specification:
|
<xsd:element name="FuGE" type="fuge:FuGE.Collection.FuGEType" abstract="false" substitutionGroup="fuge:Identifiable"/>
|