Serialized Form
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Package org.biomage.Array |
arrayIdentifier
java.lang.String arrayIdentifier
- An identifying string, e.g. a barcode.
arrayXOrigin
float arrayXOrigin
- This can indicate the x position on a slide, chip, etc. of the
first Feature and is usually specified relative to the fiducial.
arrayYOrigin
float arrayYOrigin
- This can indicate the y position on a slide, chip, etc. of the
first Feature and is usually specified relative to the fiducial.
originRelativeTo
java.lang.String originRelativeTo
- What the array origin is relative to, e.g. upper left corner,
fiducial, etc.
arrayDesign
ArrayDesign arrayDesign
- The association of a physical array with its array design.
information
ArrayManufacture information
- Association between the manufactured array and the information on
that manufacture.
arrayGroup
ArrayGroup arrayGroup
- Association between an ArrayGroup and its Arrays, typically the
ArrayGroup will represent a slide and the Arrays will be the
manufactured so that they may be hybridized separately on that
slide.
arrayManufactureDeviations
HasArrayManufactureDeviations.ArrayManufactureDeviations_list arrayManufactureDeviations
- Association to classes to describe deviations from the
ArrayDesign.
arrayGroup_list
Array_package.ArrayGroup_list arrayGroup_list
- An array package is a physical platform that contains one or more
arrays that are separately addressable (e.g. several arrays that can
be hybridized on a single microscope slide) or a virtual grouping
together of arrays.
The array package that has been manufactured has information about
where certain artifacts about the array are located for scanning and
feature extraction purposes.
array_list
Array_package.Array_list array_list
- The physical substrate along with its features and their
annotation
arrayManufacture_list
Array_package.ArrayManufacture_list arrayManufacture_list
- Describes the process by which arrays are produced.
barcode
java.lang.String barcode
- Identifier for the ArrayGroup.
arraySpacingX
float arraySpacingX
- If there exist more than one array on a slide or a chip, then the
spacing between the arrays is useful so that scanning / feature
extraction software can crop images representing 1 unique bioassay.
arraySpacingY
float arraySpacingY
- If there exist more than one array on a slide or a chip, then the
spacing between the arrays is useful so that scanning / feature
extraction software can crop images representing 1 unique bioassay.
numArrays
int numArrays
- This attribute defines the number of arrays on a chip or a slide.
orientationMark
java.lang.String orientationMark
- For a human to determine where the top left side of the array is,
such as a barcode or frosted side of the glass, etc.
orientationMarkPosition
ArrayGroup.OrientationMarkPosition orientationMarkPosition
- One of top, bottom, left or right.
width
float width
- The width of the platform
length
float length
- The length of the platform.
fiducials
HasFiducials.Fiducials_list fiducials
- Association to the marks on the Array for alignment for the
scanner.
arrays
HasArrays.Arrays_list arrays
- Association between an ArrayGroup and its Arrays, typically the
ArrayGroup will represent a slide and the Arrays will be the
manufactured so that they may be hybridized separately on that
slide.
substrateType
OntologyEntry substrateType
- Commonly, arrays will be spotted on 1x3 glass microscope slides
but there is nothing that says this must be the case. This
association is for scanners to inform them on the possible different
formats of slides that can contain arrays.
distanceUnit
DistanceUnit distanceUnit
- The unit of the measurement attributes.
manufacturingDate
java.lang.String manufacturingDate
- The date the arrays were manufactured
tolerance
float tolerance
- The allowable error of a feature printed to its intended
position.
arrays
HasArrays.Arrays_list arrays
- Association between the manufactured array and the information on
that manufacture.
arrayManufacturers
HasArrayManufacturers.ArrayManufacturers_list arrayManufacturers
- The person or organization to contact for information concerning
the ArrayManufacture.
qualityControlStatistics
HasQualityControlStatistics.QualityControlStatistics_list qualityControlStatistics
- Information on the quality of the ArrayManufacture.
featureLIMSs
HasFeatureLIMSs.FeatureLIMSs_list featureLIMSs
- Information on the manufacture of the features.
protocolApplications
HasProtocolApplications.ProtocolApplications_list protocolApplications
- The protocols followed in the manufacturing of the arrays.
adjustments
HasAdjustments.Adjustments_list adjustments
- Descriptions of how a Zone has been printed differently than
specified in the ArrayDesign.
featureDefects
HasFeatureDefects.FeatureDefects_list featureDefects
- Description on features who are manufactured in a different
location than specified in the ArrayDesign.
defectType
OntologyEntry defectType
- Indicates the type of defect (e.g. a missing feature or a moved
feature).
positionDelta
PositionDelta positionDelta
- How the feature deviates in position from the ArrayDesign.
feature
Feature feature
- The feature that was manufactured defectively.
fiducialType
OntologyEntry fiducialType
- A descriptive string that indicates the type of a fiducial (e.g.
the chrome border on an Affymetrix array, a laser ablation mark).
distanceUnit
DistanceUnit distanceUnit
- The units the fiducial is measured in.
position
Position position
- The position, relative to the upper left corner, of the fiducial
quality
java.lang.String quality
- A brief description of the quality of the array manufacture
process.
feature
Feature feature
- The feature whose LIMS information is being described.
bioMaterial
BioMaterial bioMaterial
- The BioMaterial used for the feature.
identifierLIMS
DatabaseEntry identifierLIMS
- Association to a LIMS data source for further information on the
manufacturing process.
bioMaterialPlateIdentifier
java.lang.String bioMaterialPlateIdentifier
- The plate from which a biomaterial was obtained.
bioMaterialPlateRow
java.lang.String bioMaterialPlateRow
- The plate row from which a biomaterial was obtained. Specified
by a letter.
bioMaterialPlateCol
java.lang.String bioMaterialPlateCol
- The plate column from which a biomaterial was obtained.
Specified by a number.
deltaX
float deltaX
- Deviation from the y coordinate of this feature's position.
deltaY
float deltaY
- Deviation from the y coordinate of this feature's position.
distanceUnit
DistanceUnit distanceUnit
- The unit for the attributes.
defectType
OntologyEntry defectType
- Indicates the type of defect (e.g. a missing zone or a moved
zone).
positionDelta
PositionDelta positionDelta
- How the zone deviates in position from the ArrayDesign.
zone
Zone zone
- Reference to the Zone that was misprinted.
|
Package org.biomage.ArrayDesign |
version
java.lang.String version
- The version of this design.
numberOfFeatures
int numberOfFeatures
- The number of features for this array
protocolApplications
HasProtocolApplications.ProtocolApplications_list protocolApplications
- Describes the application of any protocols, such as the
methodology used to pick oligos, in the design of the array.
featureGroups
HasFeatureGroups.FeatureGroups_list featureGroups
- The grouping of like Features together. Typically for a physical
array design, this will be a single grouping of features whose type
might be PCR Product or Oligo. If more than one technology type
occurs on the array, such as the mixing of Cloned BioMaterial and
Oligos, then there would be multiple FeatureGroups to segregate the
technology types.
reporterGroups
HasReporterGroups.ReporterGroups_list reporterGroups
- The grouping of like Reporter together. If more than one
technology type occurs on the array, such as the mixing of Cloned
BioMaterial and Oligos, then there would be multiple ReporterGroups
to segregate the technology types.
compositeGroups
HasCompositeGroups.CompositeGroups_list compositeGroups
- The grouping of like CompositeSequence together. If more than
one technology type occurs on the array, such as the mixing of
Cloned BioMaterial and Oligos, then there would be multiple
CompositeGroups to segregate the technology types.
designProviders
HasDesignProviders.DesignProviders_list designProviders
- The primary contact for information on the array design
reporterGroup_list
ArrayDesign_package.ReporterGroup_list reporterGroup_list
- Allows specification of the type of Reporter Design Element.
compositeGroup_list
ArrayDesign_package.CompositeGroup_list compositeGroup_list
- Allows specification of the type of Composite Design Element.
arrayDesign_list
ArrayDesign_package.ArrayDesign_list arrayDesign_list
- Describes the design of an gene expression layout. In some cases
this might be virtual and, for instance, represent the output from
analysis software at the composite level without reporters or
features.
compositeSequences
HasCompositeSequences.CompositeSequences_list compositeSequences
- The compositeSequences that belong to this group.
types
HasTypes.Types_list types
- The specific type of a feature, reporter, or composite. A
composite type might be a gene while a reporter type might be a cDNA
clone or an oligo.
species
OntologyEntry species
- The organism from which the biosequences of this group are from.
featureWidth
float featureWidth
- The width of the feature.
featureLength
float featureLength
- The length of the feature.
featureHeight
float featureHeight
- The height of the feature.
technologyType
OntologyEntry technologyType
- The technology type of this design. By specifying a technology
type, higher level analysis can use appropriate algorithms to
compare the results from multiple arrays. The technology type may
be spotted cDNA or in situ photolithography.
featureShape
OntologyEntry featureShape
- The expected shape of the feature on the array: circular, oval,
square, etc.
distanceUnit
DistanceUnit distanceUnit
- The unit for the feature measures.
features
HasFeatures.Features_list features
- The features that belong to this group.
surfaceType
OntologyEntry surfaceType
- The type of surface from a controlled vocabulary that would
include terms such as non-absorptive, absorptive, etc.
zoneGroups
HasZoneGroups.ZoneGroups_list zoneGroups
- In the case where the array design is specified by one or more
zones, allows specifying where those zones are located.
reporters
HasReporters.Reporters_list reporters
- The reporters that belong to this group.
row
int row
- row position in the ZoneGroup
column
int column
- column position in the ZoneGroup.
upperLeftX
float upperLeftX
- Boundary vertical upper left position relative to (0,0).
upperLeftY
float upperLeftY
- Boundary horizontal upper left position relative to (0,0).
lowerRightX
float lowerRightX
- Boundary vertical lower right position relative to (0,0).
lowerRightY
float lowerRightY
- Boundary horizontal lower right position relative to (0,0).
distanceUnit
DistanceUnit distanceUnit
- Unit for the Zone attributes.
spacingsBetweenZonesX
float spacingsBetweenZonesX
- Spacing between zones, if applicable.
spacingsBetweenZonesY
float spacingsBetweenZonesY
- Spacing between zones, if applicable.
zonesPerX
int zonesPerX
- The number of zones on the x-axis.
zonesPerY
int zonesPerY
- The number of zones on the y-axis.
distanceUnit
DistanceUnit distanceUnit
- Unit for the ZoneGroup attributes.
zoneLayout
ZoneLayout zoneLayout
- Describes the rectangular layout of features in the array design.
zoneLocations
HasZoneLocations.ZoneLocations_list zoneLocations
- Describes the location of different zones within the array
design.
numFeaturesPerRow
int numFeaturesPerRow
- The number of features from left to right.
numFeaturesPerCol
int numFeaturesPerCol
- The number of features from top to bottom of the grid.
spacingBetweenRows
float spacingBetweenRows
- Spacing between the rows.
spacingBetweenCols
float spacingBetweenCols
- Spacing between the columns.
distanceUnit
DistanceUnit distanceUnit
- Unit of the ZoneLayout attributes.
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Package org.biomage.AuditAndSecurity |
date
java.util.Date date
- The date of a change.
action
Audit.Action action
- Indicates whether an action is a creation or a modification.
performer
Contact performer
- The contact for creating or changing the instance referred to by
the Audit.
contact_list
AuditAndSecurity_package.Contact_list contact_list
- A contact is either a person or an organization.
securityGroup_list
AuditAndSecurity_package.SecurityGroup_list securityGroup_list
- Groups contacts together based on their security privileges.
security_list
AuditAndSecurity_package.Security_list security_list
- Permission information for an object as to ownership, write and
read permissions.
URI
java.lang.String URI
address
java.lang.String address
phone
java.lang.String phone
tollFreePhone
java.lang.String tollFreePhone
email
java.lang.String email
fax
java.lang.String fax
roles
HasRoles.Roles_list roles
- The roles (lab equipment sales, contractor, etc.) the contact
fills.
parent
Organization parent
- The containing organization (the university or business which a
lab belongs to, etc.)
lastName
java.lang.String lastName
firstName
java.lang.String firstName
midInitials
java.lang.String midInitials
affiliation
Organization affiliation
- The organization a person belongs to.
owner
Contact owner
- The owner of the security rights.
readGroups
HasReadGroups.ReadGroups_list readGroups
- Specifies which security groups have read permission.
writeGroups
HasWriteGroups.WriteGroups_list writeGroups
- Specifies which security groups have write permission.
members
HasMembers.Members_list members
- The members of the Security Group.
title
java.lang.String title
authors
java.lang.String authors
publication
java.lang.String publication
publisher
java.lang.String publisher
editor
java.lang.String editor
year
java.util.Date year
volume
java.lang.String volume
issue
java.lang.String issue
pages
java.lang.String pages
URI
java.lang.String URI
parameters
HasParameters.Parameters_list parameters
- Criteria that can be used to look up the reference in a
repository.
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Package org.biomage.BioAssay |
channels
HasChannels.Channels_list channels
- Channels can be non-null for all subclasses. For instance,
collapsing across replicate features will create a DerivedBioAssay
that will potentially reference channels.
bioAssayFactorValues
HasBioAssayFactorValues.BioAssayFactorValues_list bioAssayFactorValues
- The values that this BioAssay is associated with for the
experiment.
channel_list
BioAssay_package.Channel_list channel_list
- A channel represents an independent acquisition scheme for the
ImageAcquisition event, typically a wavelength.
bioAssay_list
BioAssay_package.BioAssay_list bioAssay_list
- An abstract class which represents both physical and
computational groupings of arrays and biomaterials.
sourceBioMaterialMeasurements
HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list sourceBioMaterialMeasurements
- The BioSample and its amount used in the BioAssayCreation event.
array
Array array
- The array used in the BioAssayCreation event.
physicalBioAssayTarget
PhysicalBioAssay physicalBioAssayTarget
- The association between the BioAssayCreation event (typically
Hybridization) and the PhysicalBioAssay and its annotation of this
event.
physicalBioAssay
PhysicalBioAssay physicalBioAssay
- The set of treatments undergone by this PhysicalBioAssay.
target
PhysicalBioAssay target
- The PhysicalBioAssay that was treated.
labels
HasLabels.Labels_list labels
- The compound used to label the extract.
type
OntologyEntry type
- The derivation type, for instance collapsed spot replicate,
ratio, averaged intensity, bioassay replicates, etc.
derivedBioAssayData
HasDerivedBioAssayData.DerivedBioAssayData_list derivedBioAssayData
- The data associated with the DerivedBioAssay.
physicalBioAssaySource
PhysicalBioAssay physicalBioAssaySource
- The PhysicalBioAssay used in the FeatureExtraction event.
measuredBioAssayTarget
MeasuredBioAssay measuredBioAssayTarget
- The association between the MeasuredBioAssay and the
FeatureExtraction Event.
URI
java.lang.String URI
- The file location in which an image may be found.
channels
HasChannels.Channels_list channels
- The channels captured in this image.
format
OntologyEntry format
- The file format of the image typically a TIF or a JPEG.
images
HasImages.Images_list images
- The images produced by the ImageAcquisition event.
featureExtraction
FeatureExtraction featureExtraction
- The association between the MeasuredBioAssay and the
FeatureExtraction Event.
measuredBioAssayData
HasMeasuredBioAssayData.MeasuredBioAssayData_list measuredBioAssayData
- The data associated with the MeasuredBioAssay.
physicalBioAssayData
HasPhysicalBioAssayData.PhysicalBioAssayData_list physicalBioAssayData
- The Images associated with this PhysicalBioAssay by
ImageAcquisition.
bioAssayCreation
BioAssayCreation bioAssayCreation
- The association between the BioAssayCreation event (typically
Hybridization) and the PhysicalBioAssay and its annotation of this
event.
bioAssayTreatments
HasBioAssayTreatments.BioAssayTreatments_list bioAssayTreatments
- The set of treatments undergone by this PhysicalBioAssay.
|
Package org.biomage.BioAssayData |
summaryStatistics
HasSummaryStatistics.SummaryStatistics_list summaryStatistics
- Statistics on the Quality of the BioAssayData.
bioAssayDimension
BioAssayDimension bioAssayDimension
- The BioAssays of the BioAssayData.
designElementDimension
DesignElementDimension designElementDimension
- The DesignElements of the BioAssayData.
quantitationTypeDimension
QuantitationTypeDimension quantitationTypeDimension
- The QuantitationTypes of the BioAssayData.
bioDataValues
BioDataValues bioDataValues
- The data values of the BioAssayData.
bioAssayDimension_list
BioAssayData_package.BioAssayDimension_list bioAssayDimension_list
- An ordered list of bioAssays.
designElementDimension_list
BioAssayData_package.DesignElementDimension_list designElementDimension_list
- An ordered list of designElements. It will be realized as one of
its three subclasses.
quantitationTypeDimension_list
BioAssayData_package.QuantitationTypeDimension_list quantitationTypeDimension_list
- An ordered list of quantitationTypes.
bioAssayMap_list
BioAssayData_package.BioAssayMap_list bioAssayMap_list
- The BioAssayMap is the description of how source
MeasuredBioAssays and/or DerivedBioAssays are manipulated
(mathematically) to produce DerivedBioAssays.
quantitationTypeMap_list
BioAssayData_package.QuantitationTypeMap_list quantitationTypeMap_list
- A QuantitationTypeMap is the description of how source
QuantitationTypes are mathematically transformed into a target
QuantitationType.
bioAssayData_list
BioAssayData_package.BioAssayData_list bioAssayData_list
- Represents the dataset created when the BioAssays are created.
BioAssayData is the entry point to the values. Because the actual
values are represented by a different object, BioDataValues, which
can be memory intensive, the annotation of the transformation can be
gotten separate from the data.
value
java.lang.Object value
- The datum value.
bioAssay
BioAssay bioAssay
- The BioAssay associated with the value of the BioAssayDatum.
designElement
DesignElement designElement
- The DesignElement associated with the value of the BioAssayDatum.
quantitationType
QuantitationType quantitationType
- The QuantitationType associated with the value of the
BioAssayDatum.
bioAssays
HasBioAssays.BioAssays_list bioAssays
- The BioAssays for this Dimension
bioAssayMapTarget
DerivedBioAssay bioAssayMapTarget
- The DerivedBioAssay that is produced by the sources of the
BioAssayMap.
sourceBioAssays
HasSourceBioAssays.SourceBioAssays_list sourceBioAssays
- The sources of the BioAssayMap that are used to produce a target
DerivedBioAssay.
bioAssayMaps
HasBioAssayMaps.BioAssayMaps_list bioAssayMaps
- The maps for the BioAssays.
cube
java.lang.Object[][][] cube
- Three dimension array, indexed by the three dimensions to provide
the data for the BioAssayData.
order
BioDataCube.Order order
- The order to expect the dimension. The enumeration uses the
first letter of the three dimensions to represent the six possible
orderings.
bioAssayTupleData
HasBioAssayTupleData.BioAssayTupleData_list bioAssayTupleData
- The collection of BioAssayData tuples.
compositeSequences
HasCompositeSequences.CompositeSequences_list compositeSequences
- The CompositeSequences for this Dimension.
producerTransformation
Transformation producerTransformation
- The association between the DerivedBioAssayData and the
Transformation event that produced it.
designElementMaps
HasDesignElementMaps.DesignElementMaps_list designElementMaps
- The maps for the DesignElements.
containedFeatures
HasContainedFeatures.ContainedFeatures_list containedFeatures
- The features for this dimension.
quantitationTypes
HasQuantitationTypes.QuantitationTypes_list quantitationTypes
- The QuantitationTypes for this Dimension.
targetQuantitationType
QuantitationType targetQuantitationType
- The QuantitationType whose value will be produced from the values
of the source QuantitationType according to the Protocol.
sourcesQuantitationType
HasSourcesQuantitationType.SourcesQuantitationType_list sourcesQuantitationType
- The QuantitationType sources for values for the transformation.
quantitationTypeMaps
HasQuantitationTypeMaps.QuantitationTypeMaps_list quantitationTypeMaps
- The maps for the QuantitationTypes.
reporters
HasReporters.Reporters_list reporters
- The reporters for this dimension.
bioAssayDataSources
HasBioAssayDataSources.BioAssayDataSources_list bioAssayDataSources
- The BioAssayData sources that the Transformation event uses to
produce the target DerivedBioAssayData.
derivedBioAssayDataTarget
DerivedBioAssayData derivedBioAssayDataTarget
- The association between the DerivedBioAssayData and the
Transformation event that produced it.
quantitationTypeMapping
QuantitationTypeMapping quantitationTypeMapping
- The collection of mappings for the QuantitationTypes.
designElementMapping
DesignElementMapping designElementMapping
- The collection of mappings for the DesignElements.
bioAssayMapping
BioAssayMapping bioAssayMapping
- The collection of mappings for the BioAssays.
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Package org.biomage.BioEvent |
protocolApplications
HasProtocolApplications.ProtocolApplications_list protocolApplications
- The applied protocols to the BioEvent.
|
Package org.biomage.BioMaterial |
qualityControlStatistics
HasQualityControlStatistics.QualityControlStatistics_list qualityControlStatistics
- Measures of the quality of the BioMaterial.
characteristics
HasCharacteristics.Characteristics_list characteristics
- Innate properties of the biosource, such as genotype, cultivar,
tissue type, cell type, ploidy, etc.
materialType
OntologyEntry materialType
- The type of material used, i.e. rna, dna, lipid, phosphoprotein,
etc.
treatments
HasTreatments.Treatments_list treatments
- This association is one way from BioMaterial to Treatment. From
this a BioMaterial can discover the amount and type of BioMaterial
that was part of the treatment that produced it.
compound_list
BioMaterial_package.Compound_list compound_list
- A Compound can be a simple compound such as SDS (sodium dodecyl
sulfate). It may also be made of other Compounds in proportions
using CompoundMeasurements to enumerate the Compounds and their
amounts such as LB (Luria Broth) Media.
bioMaterial_list
BioMaterial_package.BioMaterial_list bioMaterial_list
- BioMaterial is an abstract class that represents the important
substances such as cells, tissues, DNA, proteins, etc...
Biomaterials can be related to other biomaterial through a directed
acyclic graph (represented by treatment(s)).
bioMaterial
BioMaterial bioMaterial
- A source BioMaterial for a treatment.
measurement
Measurement measurement
- The amount of the BioMaterial.
type
OntologyEntry type
- The Type attribute describes the role the BioSample holds in the
treatment hierarchy. This type can be an extract.
sourceContact
Contact sourceContact
- The BioSource's source is the provider of the biological material
(a cell line, strain, etc...). This could be the ATTC (American
Tissue Type Collection).
isSolvent
boolean isSolvent
- A Compound may be a special case Solvent.
merckIndex
OntologyEntry merckIndex
- The Merck Index of this Compound.
componentCompounds
HasComponentCompounds.ComponentCompounds_list componentCompounds
- The Compounds and their amounts used to create this Compound.
compound
Compound compound
- A Compound to be used to create another Compound.
measurement
Measurement measurement
- The amount of the Compound.
labels
HasLabels.Labels_list labels
- Compound used to label the extract.
order
int order
- The chronological order in which a treatment occurred (in
relation to other treatments). More than one treatment can have the
same chronological order indicating that they happened (or were
caused to happen) simultaneously.
action
OntologyEntry action
- The event that occurred (e.g. grow, wait, add, etc...). The
actions should be a recommended vocabulary
actionMeasurement
Measurement actionMeasurement
- Measures events like duration, centrifuge speed, etc.
compoundMeasurements
HasCompoundMeasurements.CompoundMeasurements_list compoundMeasurements
- The compounds and their amounts used in the treatment.
sourceBioMaterialMeasurements
HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list sourceBioMaterialMeasurements
- The BioMaterials and the amounts used in the treatment
|
Package org.biomage.BioSequence |
length
int length
- The number of residues in the biosequence.
isApproximateLength
boolean isApproximateLength
- If length not positively known will be true
isCircular
boolean isCircular
- Indicates if the BioSequence is circular in nature.
sequence
java.lang.String 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 instead of specified here, can be
found through the DatabaseEntry.
sequenceDatabases
HasSequenceDatabases.SequenceDatabases_list sequenceDatabases
- References an entry in a species database, like GenBank, UniGene,
etc.
ontologyEntries
HasOntologyEntries.OntologyEntries_list ontologyEntries
- Ontology entries referring to common values associated with
BioSequences, such as gene names, go ids, etc.
polymerType
OntologyEntry polymerType
- A choice of protein, RNA, or DNA.
type
OntologyEntry type
- The type of biosequence, i.e. gene, exon, UniGene cluster,
fragment, BAC, EST, etc.
species
OntologyEntry species
- The organism from which this sequence was obtained.
seqFeatures
HasSeqFeatures.SeqFeatures_list seqFeatures
- Association to annotations for subsequences. Corresponds to the
GenBank Frame Table.
bioSequence_list
BioSequence_package.BioSequence_list bioSequence_list
- A BioSequence is a representation of a DNA, RNA, or protein
sequence. It can be represented by a Clone, Gene, or the sequence.
basis
SeqFeature.Basis basis
- How the evidence for a SeqFeature was determined.
regions
HasRegions.Regions_list regions
- Association to classes that describe the location with the
sequence of the SeqFeature.
strandType
java.lang.String strandType
- Indicates the direction and/or type of the SeqFeature, i.e.
whether it is in the 5' or 3' direction, is double stranded, etc.
subregions
HasSubregions.Subregions_list subregions
- Regions within the SeqFeature.
coordinate
SequencePosition coordinate
- At which base pairs or amino acid this SeqFeature begins and
ends.
start
int start
- The location of the base, for nucleotides, that the SeqFeature
starts.
end
int end
- The location of the base, for nucleotides, that the SeqFeature
ends.
|
Package org.biomage.Common |
descriptions
HasDescriptions.Descriptions_list descriptions
- Free hand text descriptions. Makes available the associations of
Description to an instance of Describable.
auditTrail
HasAuditTrail.AuditTrail_list auditTrail
- A list of Audit instances that track changes to the instance of
Describable.
security
Security security
- Information on the security for the instance of the class.
propertySets
HasPropertySets.PropertySets_list propertySets
- Allows specification of name/value pairs. Meant to primarily
help in-house, pipeline processing of instances by providing a place
for values that aren't part of the specification proper.
identifier
java.lang.String 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.
name
java.lang.String name
- The potentially ambiguous common identifier.
auditAndSecurity_package
AuditAndSecurity_package auditAndSecurity_package
- Specifies classes that allow tracking of changes and information
on user permissions to view the data and annotation.
description_package
Description_package description_package
- The classes in this package allow a variety of references to
third party annotation and direct annotation by the experimenter.
measurement_package
Measurement_package measurement_package
- The classes of this package provide utility information on the
quantities of other classes to each other.
bQS_package
BQS_package bQS_package
- Allows a reference to an article, book or other publication to be
specified for searching repositories.
bioEvent_package
BioEvent_package bioEvent_package
- An abstract class representing an event that takes sources of
some type to produce a target of some type. Each of the realized
subclasses determines the type of the sources and the target. The
association to a protocol application allows specification of how
the event was performed.
protocol_package
Protocol_package protocol_package
- Provides a relatively immutable class, Protocol, that can
describe a generic laboratory procedure or analysis algorithm, for
example, and an instance class, ProtocolApplication, which can
describe the actual application of a protocol. The
ProtocolApplication provides values for the replaceable parameters
of the Protocol and, through the Description association of
Describable, any variation from the Protocol.
bioMaterial_package
BioMaterial_package bioMaterial_package
- The classes in this package describe how a BioSource is treated
to obtain the BioMaterial (typically a LabeledExtract) that is used
by a BioAssayCreation in combination with an Array to produce a
PhysicalBioAssay. A set of treatments are typically linear in time
but can form a Directed Acyclic Graph.
bioSequence_package
BioSequence_package bioSequence_package
- Describes a known gene or sequence. BioAssays typically seek to
identify what BioSequences are expressed in a BioMaterial after
treatments, the expression level measured from the association
between the BioMaterial and the Array. The Array's Features
typically provide known locations for this association to occur.
Most often, the Reporter and CompositeSequence are known and the
presence or absence of a particular BioSequence in the BioMaterial
is based on whether there as been an association to the
DesignElement targeted for it. Some other experiments may not know
the DesignElement's target but can discover it with known properties
of the BioSequences in the BioMaterial.
designElement_package
DesignElement_package designElement_package
- The classes of this package are the contained classes of the
ArrayDesign and describe through the DesignElements what is intended
to be at each location of the Array. The Feature describes an
intended location on the Array, the Reporter the Oligo, Clone, PCR
Product that is on a Feature and the CompositeSequence which
combines Reporters or CompositeSequences into what the child
DesignElements are meant to represent biologically, e.g. a Gene,
Exon, SpliceVariant, etc.
arrayDesign_package
ArrayDesign_package arrayDesign_package
- Describes a microarray design that can be printed and then, in
the case of gene expression, hybridized. An array design consists
of several features (also called spots) in which reporter sequences
are placed. Many features may have the same reporter replicated and
a reporter may be specified in one or more array designs.
The nature of the reporter's biosequence placed on a spot will
depend on the technology. Two well-known technologies differ
significantly-spotter arrays draw material from a well and place a
spot on the array whereas in situ oligo arrays are created through
the synthesis of many, short (~20-100mer) nucleotide sequences onto
the features.
Reporters can be grouped together into CompositeSequences, typically
representing a gene or one or more splice variants in gene
expression experiments.
There are then two distinct ways that DesignElements are grouped.
The one described in the ArrayDesign package by FeatureGroup,
ReporterGroup and CompositeGroup is by technology type, that is, one
might want to segregate the controls to a Group and all the
non-controls to another. Or if PCR Product and Oligos are both
used on an array they would likely be in different groups. The
grouping described in the DesignElement package by the mappings
relates the Features to the Reporter, the Reporters to
CompositeSequence, and at higher levels, CompositeSequences to
CompositeSequence.
array_package
Array_package array_package
- Describes the process of creating arrays from array designs.
Includes information on how arrays are grouped together, if
relevant, how an array deviates from its array design both in layout
and per feature and potentially contains references to LIMS data
that might contain more detail on the BioMaterial used to create the
reporters.
bioAssay_package
BioAssay_package bioAssay_package
- Provides classes that contain information and annotation on the
event of joining an Array with a BioMaterial preparation, the
acquisition of images and the extraction of data on a per feature
basis from those images. The derived classes of BioAssay represent
the base PhysicalBioAssays which lead to the production of Images,
the MeasuredBioAssay which is associated with the set of
quantitations produced by FeatureExtraction, and DerivedBioAssay
(see BioAssayData package) which groups together BioAssays that have
been analyzed together to produce further refinement of the
quantitations.
The design of this package and the related BioAssayData package was
driven by the following query considerations and the desire to
return as little data as necessary to satisfy a query. Often, the
first set of queries for experiments below the Experiment level will
want to discover the why of an experiment and this is captured in
the BioAssay class through its FactorValue, BioEvent and Description
associations. This separates it from the data but allows an
overview of the experiment hierarchy. The BioAssayData class
association to BioDataValues is optional only to allow queries on
them to discover the how of the experiment through the association
to the transformation and mappings of the three BioAssayData
dimensions and the protocols used. Once a researcher, for instance,
has narrowed down the experiments of interest then the actual data,
represented by the BioDataValues, can be downloaded. Because these
data can be in the hundreds of megabytes to gigabytes range, it was
considered desirable to be able to return information and annotation
on the experiment without the data.
quantitationType_package
QuantitationType_package quantitationType_package
- This Package defines the classes for quantitations, such as
measured and derived signal, error, and pvalue. The subclasses of
StandardQuantitationType will be the best fit from FeatureExtraction
or Transformation Protocol for the values obtained. Other values
can be specified using SpecializedQuantitationType.
bioAssayData_package
BioAssayData_package bioAssayData_package
- The classes defined here provide data and the information and
annotation on the derivation of that data. Some of the scenarios
that might occur are the following.
FeatureExtraction of a single PhysicalBioAssay produces
MeasuredBioAssayData that has a single BioAssay on the
BioAssayDimension, typically the Features described in the
ArrayDesign on the DesignElementDimension, and the Quantitations
associated with the application of a FeatureExtraction protocol on
the QuantitationDimension.
An error model transformation might be applied that doesn't change
the BioAssayDimension or the DesignElementDimension but likely
changes the QuantitationDimension. A transformation on replicate
Reporters or CompositeSequences might be applied on the single
BioAssay that would change the DesignElementDimension and the
QuantitationDimension both. Replicate and Control BioAssays might
be added to the BioAssayDimension and a transformation could change
the BioAssayDimension and the QuantitationDimension but not change
the DesignElementDimension to produce a new DerivedBioAssayData. Or
some combination of the above transformations could be performed at
once to change all three dimensions.
Because the classes derive from Describable, the Experimenter can
provide as much detail at each level of the class hierarchy as
desired.
experiment_package
Experiment_package experiment_package
- Represents the container for a hierarchical grouping of
BioAssays. Can have the end results of Clustering Analysis
specified and, through the ExperimentDesign, a description and
annotation of the overall design of the experiment and what it was
to show.
higherLevelAnalysis_package
HigherLevelAnalysis_package higherLevelAnalysis_package
- Describes the results of performing analysis on the result of the
BioAssayData from an Experiment.
modelToClass
org.biomage.Common.MAGEJava.ModelNameToClassMap modelToClass
- Instantiate the ModelNameToClassMap
name
java.lang.String name
- The name of the key.
value
java.lang.String value
- The value of the name.
type
java.lang.String type
- The type of the key.
propertySets
HasPropertySets.PropertySets_list propertySets
- Allows nested specification of name/value pairs
|
Package org.biomage.Description |
version
java.lang.String version
- The version for which a DatabaseReference applies.
URI
java.lang.String URI
- The location of the Database.
contacts
HasContacts.Contacts_list contacts
- Information on the contacts for the database
accession
java.lang.String accession
- The identifier used to look up the record.
accessionVersion
java.lang.String accessionVersion
- The appropriate version of the accession (if applicable).
URI
java.lang.String URI
- The location of the record.
type
OntologyEntry type
- The type of record (e.g. a protein in SwissProt, or a yeast
strain in SGD).
database
Database database
- Reference to the database where the DataEntry instance can be
found.
text
java.lang.String text
- The description.
externalReference
ExternalReference externalReference
- Specifies where the described instance was originally obtained
from.
annotations
HasAnnotations.Annotations_list annotations
- Allows specification of ontology entries related to the instance
being described.
databaseReferences
HasDatabaseReferences.DatabaseReferences_list databaseReferences
- References to entries in databases.
bibliographicReferences
HasBibliographicReferences.BibliographicReferences_list bibliographicReferences
- References to existing literature.
database_list
Description_package.Database_list database_list
- An address to a repository.
exportedFromServer
java.lang.String exportedFromServer
- The originating server for the object, a network address or
common name.
exportedFromDB
java.lang.String exportedFromDB
- Name of the database, if applicable, that the object was exported
from.
exportID
java.lang.String exportID
- The identifier of the object at the originating source.
exportName
java.lang.String exportName
- The name of the object at the originating source.
category
java.lang.String category
- The category to which this entry belongs.
value
java.lang.String value
- The value for this entry in this category.
description
java.lang.String description
- The description of the meaning for this entry.
ontologyReference
DatabaseEntry ontologyReference
- Many ontology entries will not yet have formalized ontologies.
In those cases, they will not have a database reference to the
ontology.
In the future it is highly encouraged that these ontologies be
developed and ontologyEntry be subclassed from DatabaseReference.
|
Package org.biomage.DesignElement |
compositeSequence
CompositeSequence compositeSequence
- A map to the compositeSequences that compose this
CompositeSequence.
compositePositionSources
HasCompositePositionSources.CompositePositionSources_list compositePositionSources
- Association to the CompositeSequences that compose this
CompositeSequence and where those CompositeSequences occur.
composite
CompositeSequence composite
- A source CompositeSequence that is part of a target
CompositeSequence
mismatchInformation
HasMismatchInformation.MismatchInformation_list mismatchInformation
- Differences in how the contained compositeSequence matches its
target compositeSequence's sequence.
biologicalCharacteristics
HasBiologicalCharacteristics.BiologicalCharacteristics_list biologicalCharacteristics
- The annotation on the BioSequence this CompositeSequence
represents. Typically the sequences will be a Genes, Exons, or
SpliceVariants.
reporterCompositeMaps
HasReporterCompositeMaps.ReporterCompositeMaps_list reporterCompositeMaps
- A map to the reporters that compose this CompositeSequence.
compositeCompositeMaps
HasCompositeCompositeMaps.CompositeCompositeMaps_list compositeCompositeMaps
- A map to the compositeSequences that compose this
CompositeSequence.
controlType
OntologyEntry controlType
- If the design element represents a control, the type of control
it is (normalization, deletion, negative, positive, etc.)
compositeSequence_list
DesignElement_package.CompositeSequence_list compositeSequence_list
- A collection of Reporter or CompositeSequence Design Elements,
annotated through the association to BioSequence.
reporter_list
DesignElement_package.Reporter_list reporter_list
- A Design Element that represents some biological material (clone,
oligo, etc.) on an array which will report on some biosequence or
biosequences. The derived data from the measured data of its
Features represents the presence or absence of the biosequence or
biosequences it is reporting on in the BioAssay.
Reporters are Identifiable and several Features on the same array
can be mapped to the same reporter as can Features from a different
ArrayDesign. The granularity of the Reporters independence is
dependent on the technology and the intent of the ArrayDesign.
Oligos using mature technologies can in general be assumed to be
safely replicated on many features where as with PCR Products there
might be the desire for quality assurence to make reporters one to
one with features and use the mappings to CompositeSequences for
replication purposes.
compositeCompositeMap_list
DesignElement_package.CompositeCompositeMap_list compositeCompositeMap_list
- A CompositeCompositeMap is the description of how source
CompositeSequences are transformed into a target CompositeSequence.
For instance, several CompositeSequences could represent different
sequence regions for a Gene and could be mapped to different
CompositeSequences, each representing a different splice variant for
that Gene.
reporterCompositeMap_list
DesignElement_package.ReporterCompositeMap_list reporterCompositeMap_list
- A ReporterCompositeMap is the description of how source Reporters
are transformed into a target CompositeSequences. For instance,
several reporters that tile across a section of a chromosome could
be mapped to a CompositeSequence.
featureReporterMap_list
DesignElement_package.FeatureReporterMap_list featureReporterMap_list
- A FeatureReporterMap is the description of how source features
are transformed into a target reporter. These would map replicate
features for a reporter to the reporter.
controlFeatures
HasControlFeatures.ControlFeatures_list controlFeatures
- Associates features with their control features.
controlledFeatures
HasControlledFeatures.ControlledFeatures_list controlledFeatures
- Associates features with their control features.
position
Position position
- The position of the feature on the array, relative to the top,
left corner.
zone
Zone zone
- A reference to the zone this feature is in.
featureLocation
FeatureLocation featureLocation
- Location of this feature relative to a grid.
featureGroup
FeatureGroup featureGroup
- The features that belong to this group.
feature
Feature feature
- The feature the FeatureInformation is supplying information for.
mismatchInformation
HasMismatchInformation.MismatchInformation_list mismatchInformation
- Differences in how the feature matches the reporter's sequence,
typical examples is the Affymetrix probe pair where one of the
features is printed with a mismatch to the other feature's perfect
match.
row
int row
- row position in the Zone
column
int column
- column position in the Zone.
reporter
Reporter reporter
- Associates features with their reporter.
featureInformationSources
HasFeatureInformationSources.FeatureInformationSources_list featureInformationSources
- Typically, the features on an array that are manufactured with
this reporter's BioSequence.
startCoord
int startCoord
- Offset into the sequence that the mismatch occurs.
newSequence
java.lang.String newSequence
- The sequence that replaces the specified sequence starting at
start_coord.
replacedLength
int replacedLength
- Length of the original sequence that is replaced. A deletion is
specified when the length of the newSequence is less than the
replacedLength.
x
float x
- The horizontal distance from the upper left corner of the array.
y
float y
- The vertical distance from the upper left corner of the array.
distanceUnit
DistanceUnit distanceUnit
- The units of the x, y positions.
immobilizedCharacteristics
HasImmobilizedCharacteristics.ImmobilizedCharacteristics_list immobilizedCharacteristics
- The sequence annotation on the BioMaterial this reporter
represents. Typically the sequences will be an Oligo Sequence,
Clone or PCR Primer.
warningType
OntologyEntry warningType
- Similar to failType but indicates a warning rather than a
failure.
failTypes
HasFailTypes.FailTypes_list failTypes
- If at some time the reporter is determined to be failed this
indicts the failure (doesn't report on what it was intended to
report on, etc.)
featureReporterMaps
HasFeatureReporterMaps.FeatureReporterMaps_list featureReporterMaps
- Associates features with their reporter.
compositeSequence
CompositeSequence compositeSequence
- A map to the reporters that compose this CompositeSequence.
reporterPositionSources
HasReporterPositionSources.ReporterPositionSources_list reporterPositionSources
- Association to the reporters that compose this CompositeSequence
and where those reporters occur.
reporter
Reporter reporter
- A reporter that comprises part of a CompositeSequence.
mismatchInformation
HasMismatchInformation.MismatchInformation_list mismatchInformation
- Differences in how the reporter matches its compositeSequence's
sequence.
|
Package org.biomage.Experiment |
providers
HasProviders.Providers_list providers
- The providers of the Experiment, its data and annotation.
analysisResults
HasAnalysisResults.AnalysisResults_list analysisResults
- The results of analyzing the data, typically with a clustering
algorithm.
bioAssayData
HasBioAssayData.BioAssayData_list bioAssayData
- The collection of BioAssayDatas for this Experiment.
bioAssays
HasBioAssays.BioAssays_list bioAssays
- The collection of BioAssays for this Experiment.
experimentDesign
ExperimentDesign experimentDesign
- The association to the description and annotation of the
Experiment, along with the grouping of the top-level BioAssays.
experiment_list
Experiment_package.Experiment_list experiment_list
- The Experiment is the collection of all the BioAssays that are
related by the ExperimentDesign.
category
OntologyEntry category
- The category of an ExperimentalFactor could be biological (time,
[glucose]) or a methodological factor (differing cDNA preparation
protocols).
factorValues
HasFactorValues.FactorValues_list factorValues
- The pairing of BioAssay FactorValues with the ExperimentDesign
ExperimentFactor.
types
HasTypes.Types_list types
- Classification of an experiment. For example 'normal vs.
diseased', 'treated vs. untreated', 'time course', 'tiling', etc.
topLevelBioAssays
HasTopLevelBioAssays.TopLevelBioAssays_list topLevelBioAssays
- The organization of the BioAssays as specified by the
ExperimentDesign (TimeCourse, Dosage, etc.)
experimentalFactors
HasExperimentalFactors.ExperimentalFactors_list experimentalFactors
- The description of the factors (TimeCourse, Dosage, etc.) that
group the BioAssays.
qualityControlDescription
Description qualityControlDescription
- Description of the quality control aspects of the Experiment.
normalizationDescription
Description normalizationDescription
- Description of the normalization strategy of the Experiment.
replicateDescription
Description replicateDescription
- Description of the replicate strategy of the Experiment.
experimentalFactor
ExperimentalFactor experimentalFactor
- The pairing of BioAssay FactorValues with the ExperimentDesign
ExperimentFactor.
measurement
Measurement measurement
- The measured value for this factor.
|
Package org.biomage.HigherLevelAnalysis |
clusterBioAssayData
BioAssayData clusterBioAssayData
- The BioAssayData whose values were used by the cluster algorithm.
nodes
HasNodes.Nodes_list nodes
- The nodes of the cluster.
bioAssayDataCluster_list
HigherLevelAnalysis_package.BioAssayDataCluster_list bioAssayDataCluster_list
- A mathematical method of higher level analysis whereby
BioAssayData are grouped together into nodes.
nodes
HasNodes.Nodes_list nodes
- Nested nodes of the BioAssayDataCluster.
nodeContents
HasNodeContents.NodeContents_list nodeContents
- The contents of the node, expressed as either a one, two or three
dimensional object.
nodeValue
HasNodeValue.NodeValue_list nodeValue
- Values or measurements for this node that may be produced by the
clustering algorithm. Typical are distance values for the nodes.
bioAssayDimension
BioAssayDimension bioAssayDimension
- The relevant BioAssays for this NodeContents from the
BioAssayData.
designElementDimension
DesignElementDimension designElementDimension
- The relevant DesignElements for this NodeContents from the
BioAssayData.
quantitationDimension
QuantitationTypeDimension quantitationDimension
- The relevant QuantitationTypes for this NodeContents from the
BioAssayData.
name
java.lang.String name
- The name for this value.
value
java.lang.Object value
- The value for this NodeValue.
type
OntologyEntry type
- The type of value, distance, etc.
scale
OntologyEntry scale
- The scale (linear, log10, ln, etc.) of the value.
dataType
OntologyEntry dataType
- The data type of the any element.
|
Package org.biomage.Interface |
|
Package org.biomage.Measurement |
unitNameCV
ConcentrationUnit.UnitNameCV unitNameCV
unitNameCV
DistanceUnit.UnitNameCV unitNameCV
unitNameCV
MassUnit.UnitNameCV unitNameCV
type
Measurement.Type type
- The type of measurement, for instance if the measurement is five
feet, it can be either absolute (five feet tall) or change (five
feet further along).
value
java.lang.Object value
- The value of the measurement. kindCV (and otherKind) determine
with Unit the datatype of value.
kindCV
Measurement.KindCV kindCV
- One of the enumeration values to determine the controlled
vocabulary of the value.
otherKind
java.lang.String otherKind
- Name of the controlled vocabulary if it isn't one of the Unit
subclasses.
unit
Unit unit
- The Unit associated with the Measurement.
unitNameCV
QuantityUnit.UnitNameCV unitNameCV
unitNameCV
TemperatureUnit.UnitNameCV unitNameCV
unitNameCV
TimeUnit.UnitNameCV unitNameCV
unitName
java.lang.String unitName
- The name of the unit.
unitNameCV
VolumeUnit.UnitNameCV unitNameCV
|
Package org.biomage.Protocol |
model
java.lang.String model
- The model (number) of a piece of hardware.
make
java.lang.String make
- The make of the Hardware (its manufacturer).
type
OntologyEntry type
- The type of a piece of Hardware. Examples include: scanner, wash
station...
softwares
HasSoftwares.Softwares_list softwares
- Associates Hardware and Software together.
hardwareManufacturers
HasHardwareManufacturers.HardwareManufacturers_list hardwareManufacturers
- Contact for information on the Hardware.
serialNumber
java.lang.String serialNumber
- Manufacturer's identifier for the Hardware.
hardware
Hardware hardware
- The underlying hardware.
unit
Unit unit
- Unit the value is associated with
dataType
OntologyEntry dataType
- The type of data generated by the parameter i.e. Boolean, float,
etc...
URI
java.lang.String URI
- Where an instantiated Parameterizable is located.
parameterTypes
HasParameterTypes.ParameterTypes_list parameterTypes
- The description of the parameters for the Parameterizable class
instance.
parameterValues
HasParameterValues.ParameterValues_list parameterValues
- The parameter values for this Parameterizable Application.
value
java.lang.Object value
- The value of the parameter. Will have the datatype of its
associated Parameter.
parameterType
Parameter parameterType
- The parameter this value is for.
text
java.lang.String text
- The text description of the Protocol.
title
java.lang.String title
- The title of the Protocol
type
OntologyEntry type
- The type of a Protocol, a user should provide/use a recommended
vocabulary. Examples of types include: RNA extraction, array
washing, etc...
hardwares
HasHardwares.Hardwares_list hardwares
- Hardware used by this protocol.
softwares
HasSoftwares.Softwares_list softwares
- Software used by this Protocol.
hardware_list
Protocol_package.Hardware_list hardware_list
- Hardware represents the hardware used. Examples of Hardware
include: computers, scanners, wash stations etc...
software_list
Protocol_package.Software_list software_list
- Software represents the software used. Examples of Software
include: feature extraction software, clustering software, etc...
protocol_list
Protocol_package.Protocol_list protocol_list
- A Protocol is a parameterizable description of a method.
ProtocolApplication is used to specify the ParameterValues of it's
Protocol's Parameters.
activityDate
java.lang.String activityDate
- When the protocol was applied.
hardwareApplications
HasHardwareApplications.HardwareApplications_list hardwareApplications
- The use of hardware for the application of the protocol.
softwareApplications
HasSoftwareApplications.SoftwareApplications_list softwareApplications
- The use of software for the application of the protocol.
performers
HasPerformers.Performers_list performers
- The people who performed the protocol.
protocol
Protocol protocol
- The protocol that is being used.
type
OntologyEntry type
- The type of a piece of Software. Examples include: feature
extractor...
hardware
Hardware hardware
- Associates Hardware and Software together.
softwares
HasSoftwares.Softwares_list softwares
- Software packages this software uses, i.e. operating system, 3rd
party software packages, etc.
softwareManufacturers
HasSoftwareManufacturers.SoftwareManufacturers_list softwareManufacturers
- Contact for information on the software.
version
java.lang.String version
- The version of the software.
releaseDate
java.util.Date releaseDate
- When the software was released.
software
Software software
- The underlying software.
|
Package org.biomage.QuantitationType |
targetQuantitationType
QuantitationType targetQuantitationType
- The association between a ConfidenceIndicator and the
QuantitationType its is an indicator for.
isBackground
boolean isBackground
- Indicates whether the quantitation has been measured from the
background or from the feature itself.
channel
Channel channel
- The optional channel associated with the QuantitationType.
scale
OntologyEntry scale
- Indication of how to interpret the value. From a suggested
vocabulary of {LINEAR | LN | LOG2 |LOG10 | FOLD_CHANGE | OTHER}
dataType
OntologyEntry dataType
- The specific type for the quantitations. From a controlled
vocabulary of {float, int, boolean, etc.}
confidenceIndicators
HasConfidenceIndicators.ConfidenceIndicators_list confidenceIndicators
- The association between a ConfidenceIndicator and the
QuantitationType its is an indicator for.
quantitationType_list
QuantitationType_package.QuantitationType_list quantitationType_list
- A method for calculating a single datum of the matrix (e.g. raw
intensity, background, error).
|
Package org.biomage.tools.xmlutils |
Copyright (C) 2002 The MicroArray Gene Expression Database group (MGED) All rights reserved.