There are four types of biomaterials:
All four types of are derived from the base class
The reason for this is that they all share common functionality such as pooling
and events. By using a common base class we do not have to create duplicate
classes for keeping track of events and parents.
MeasuredBioMaterialData class is used as a base
class for the other three biomaterial types. It introduces quantity
measurements and can store original and remaining quantities. They are
both optional. If an original quantity has been specified the core
automatically calculates the remaining quantity based on the events a
biomaterial participates in.
All measured biomaterial have at least one event associated with them, the creation event, which holds information about the creation of the biomaterial. A measured biomaterial can be created in three ways:
From a single item of the parent type. Biosource is the parent type of
samples, sample is the parent type of extracts, and extract is the
parent type of labeled extracts. In this case the
pooled property is
and the parent is specified in the parent property.
If the parent is not a
BioSourceData this information
is duplicated, with the addition of an optional used quantity value, in the
sources collection of the
object representing the creation event. It is the responsibility of the
core to make sure that everything is properly synchronized and that
remaining quantities are calculated.
From one or more items of the same type, i.e pooling.
In this case the pooled property is
and the parent property is null. All source
biomaterials are contained in the sources collection.
The core is still responsible for keeping everything synchronized and to
update remaining quantities.
As a standalone biomaterial without parents.
Biomaterial (except biosource) may optionally be placed on
BioPlateData:s. A bioplate is something
that collects multiple biomaterial as a unit. A bioplate typically has a
determines the number of locations on the plate (
A single well can hold a single biomaterial at a time.
The bioplate must be of a specific
The type can be used to put limitations on how the plate can be used. For example,
it can be limited to a single type of biomaterial. It is also possible to lock wells
so that the biomaterial in them can't be changed. Supported lock modes are:
Unlocked: Wells are unlocked and the biomaterial may be changed any number of times.
Locked-after-move: The well is locked after it has been used one time and the biomaterial that was put in it has been moved to another plate.
Locked-after-add: The well is locked after biomaterial has been put into it. It is not possible to remove the biomaterial.
Locked-after-create: The well is locked once it has been created. Biomaterial must be put into wells before the plate is saved to the database.
An event represents something that happened to one or more biomaterials, for example
the creation of another biomaterial. The
holds information about entry and event dates, protocols used, the user who is
responsible, etc. There are three types of events represented by the eventType
Creation event: This event represents the creation of a (measured) biomaterial. The sources collection contains information about the biomaterials that were used to create the new biomaterial. If the biomaterial is a pooled biomaterial all sources must be of the same type. Otherwise there can only be one source of the parent type. These rules are maintained by the core.
Hybridization event: This event represents the creation of a hybridization. This event type is needed because we want to keep track of quantities for labeled extracts. This event has a hybridization as a product instead of a biomaterial. The sources collection can only contain labeled extracts.
Other event: This event represents some other important information about a single biomaterial that affected the remaining quantity. This event type doesn't have any sources.
It is also possible to register events that applies to one or more
bioplates using the
class holds information about each plate that is part of the event. The role
property is a textual description of what happened to the plate. Eg. a move event, may have one
source plate and one destination plate. It is
recommended (but not required) that all biomaterial that are affected by the plate event
are linked via a
BioMaterialEventData to a
This will make it easier to keep track of the history of individual biomaterial items.
Biomaterial events that are linked in this way are also automatically updated if the
bioplate event is modified (eg. selecting a protocol, event date, etc.).