Screen Plate Well 2010-04

The Screen Plate Well (SPW) model is designed to support High Content Screening. It is aimed at providing a flexible framework to organise the images that result from such a screen and link to external systems that contain full information about the components and products used. Throughout the model there are several External Identifier strings that can be attached to support this.

The top level of the SPW model has two objects that exist side by side, Screen and Plate. It is important to stress that Plate is not a child of Screen, they are equals. This is necessary to cater for the fact that while a Screen can contain many Plates, a Plate can also be used in more than one Screen. This allows less common scenarios where, for example, there are two screens against two different reagent sets but only one set of control plates that are used in common.

Reagents are children of a Screen and as such are designed to be referenced from each Screen they are part of. It is worth covering the exact meaning of a Reagent within SPW. The storing of detailed information about biological reagents is beyond the scope of the OME model. There are several other system that are designed to handle this type of information. What the Reagent element in SPW provides is useful descriptions and an external reagent identifier that can be used to find detailed information about the reagent in another system. A side effect of this is that any change to an external reagent requires a new SPW reagent. This could be a change of dilution, supplier, or lot-number.

Example

If you have two chemical reagents Monastrol and VX680 that I wish to apply to samples in various concentrations. The Monastrol will be applied at 100, 300, and 900 nM concentrations. The VX680 at 300, 900, 2700 nM concentrations. This requires a total of 6 reagents to be defined in the OME file.

<spw:Screen ...>
    ...
    <spw:Reagent ID="Reagent:001" Description="Monastrol at a 100nM concentration from XYZ Supplier" Name="Monastrol-100nM" ReagentIdentifier="R-XYZ-Mon-100-nm-00345"/>
    <spw:Reagent ID="Reagent:002" Description="Monastrol at a 300nM concentration from XYZ Supplier" Name="Monastrol-300nM" ReagentIdentifier="R-XYZ-Mon-300-nm-01245"/>
    <spw:Reagent ID="Reagent:003" Description="Monastrol at a 900nM concentration from XYZ Supplier" Name="Monastrol-900nM" ReagentIdentifier="R-XYZ-Mon-900-nm-00875"/>
    <spw:Reagent ID="Reagent:004" Description="VX680 at a 300nM concentration from XYZ Supplier" Name="VX680-300nM" ReagentIdentifier="R-XYZ-VX680-300-nm-00256"/>
    <spw:Reagent ID="Reagent:005" Description="VX680 at a 900nM concentration from XYZ Supplier" Name="VX680-900nM" ReagentIdentifier="R-XYZ-VX680-900-nm-00257"/>
    <spw:Reagent ID="Reagent:006" Description="VX680 at a 2700nM concentration from XYZ Supplier" Name="VX680-2700nM" ReagentIdentifier="R-XYZ-VX680-2700-nm-00258"/>
    ...
</spw:Screen>

What is recorded where

What happened to ScreenAcquisition?

In the previous version of the SPW Model the acquisition information was recorded below Screen. During use it was discovered that this did not best reflect the way data was collected. This difference between the structure and the collected data produced a performance bottleneck when dealing with the large structures necessary for HCS data. The decision was taken to rework the model to store the acquisition information on Plate instead. The structure was moved in the model to below Plate and renamed PlateAcquisition.

We also took this opportunity to add Index to WellSample. This records the order of the well samples and should be unique within a given Plate. It does not however have to be sequential so supports the collection of sparse datasets.

Diagram showing structure in the SPW Schema

Within the OME data model Screen, Plate and Image are top level structures. A file can contain multiple instances of these elements.

Each Plate can contain multiple Wells, PlateAcquisitions, and ScreenRefs, i.e. a plate can belong to multiple screens. Each Well in turn can have one (or zero) ReagentRef, and zero or more WellSamples. Each of the well samples defines the location of an image within the well and the time at which the sample started to be collected. It also references the Image itself.

Each Screen contains multiple Reagents, and PlateRefs, i.e. a screen can use many plates. A PlateAcquisition is best viewed as a pass over some or all of the Wells in a Plate - usually associated with some time-point or step in a protocol. It is a collection of individual WellSamples across the ''Plate''s collected between two time points.

Diagram showing structure in the SPW Schema (cross-linked)

The dashed arrows added to the previous diagram show the inter-dependencies between the ''Screen'' branch and the ''Plate'' branch of the schema, as well as the ultimate link to ''Image''.

Diagram showing sample file structure of the SPW Schema

This diagram shows how a typical file would be structured and what objects are normally contained inside each other.

Diagram showing sample file structure of the SPW Schema (cross-linked)

The dashed arrows added to the previous diagram show the inter-dependencies of the objects in the sample file structure. Each dashed line could represent links from several objects of one type to several objects of the second type. The links in the file are accomplished using unique IDs on objects and then References to these IDs from elsewhere in the file.