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org.biomage.BioMaterial: Javadoc index of package org.biomage.BioMaterial.


Package Samples:

org.biomage.BioMaterial

Classes:

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.
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.
LabeledExtract: LabeledExtracts are special BioSamples that have Compounds which are detectable (these are often fluorescent or reactive moieties).
Treatment: The process by which a biomaterial is created (from source biomaterials). Treatments have an order and an action.
BioMaterialMeasurement: A BioMaterialMeasurement is a pairing of a source BioMaterial and an amount (Measurement) of that BioMaterial.
CompoundMeasurement: A CompoundMeasurement is a pairing of a source Compound and an amount (Measurement) of that Compound.

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