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org.biomage.Array.* (11)org.biomage.ArrayDesign.* (10)org.biomage.AuditAndSecurity.* (7)
org.biomage.BQS.* (2)org.biomage.BioAssay.* (12)org.biomage.BioAssayData.* (21)
org.biomage.BioEvent.* (3)org.biomage.BioMaterial.* (9)org.biomage.BioSequence.* (5)
org.biomage.Common.* (6)

Package Samples:

org.biomage.BQS
org.biomage.AuditAndSecurity
org.biomage.Array
org.biomage.BioAssay
org.biomage.ArrayDesign
org.biomage.BioAssayData
org.biomage.BioEvent
org.biomage.BioMaterial
org.biomage.BioSequence
org.biomage.Common

Classes:

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 ...
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, ...
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 ...
Reporter: 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 ...
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 ...
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.
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.
ArrayGroup: 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.
CompositeCompositeMap: 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.
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.
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.
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.
BioAssayData: 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.
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.
PresentAbsent: Indicates relative presence or absence. From the enumeration AbsoluteCallTypeEnum {Present | Absent | Marginal | No call} or ComparisonCallTypeEnum {Increase I Marginal Increase | Decrease | Marginal Decrease | No change | No Call | Unknown }, as specified by the dataType.
Describable: Abstract class that allows subclasses to inherit the association to Description, for detailed annotations such as Ontology entries and Database references, the association to Audit, for tracking changes, and the association to Security for indicating permissions.
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.
CompositePosition: The location in the compositeSequence target's sequence to which a source compositeSequence maps. The association to MismatchInformation allows the specification, usually for control purposes, of deviations from the CompositeSequence's BioMaterial.
BioSource: The BioSource is the original source material before any treatment events. It is also a top node of the directed acyclic graph generated by treatments. The association to OntologyEntry allows enumeration of a BioSource's inherent properties.
BioSample: BioSamples are products of treatments that are of interest. BioSamples are often used as the sources for other biosamples. The Type attribute describes the role the BioSample holds in the treatment hierarchy. This type can be an extract.
BioMaterial: 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)).
Compound: 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.

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