Information on Screen Plate Well

The screen plate well 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 provide links to the 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 SWP. 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 SWP 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

Attachment Level	Information Recorded	Description
Plate
	ID	This is used by the system to identify the plate.
	Name	This is chosen by the user to identify the plate.
	Description	A free text description
	Status	The current state of the plate in the experiment work-flow.
	ExternalIdentifier	This is a identifier for the plate used by an external system. This may be a barcode printed on the plate by the manufacturer.
Reagent
	ID	This is used by the system to identify the reagent
	Description	A long description for the reagent
	Name	A short name for the reagent
	ReagentIdentifier	This is a reference to an external (to OME) representation of the Reagent. It serves as a foreign key into an external database.
Screen
	ID	This is used by the system to identify the screen
	Name	This is chosen by the user to identify the screen
	ProtocolIdentifier	A pointer to an externally defined protocol, usually in a screening database.
	ProtocolDescription	A description of the screen protocol; may contain very detailed information to reproduce some of that found in a screening database.
	ReagentSetDescription	A description of the set of reagents; may contain very detailed information to reproduce some of that information found in a screening database.
	ReagentSetIdentifier	A pointer to an externally defined set of reagents, usually in a screening database/automation database.
	Type	A human readable identifier for the screen type; e.g. RNAi, cDNA, SiRNA, etc.
ScreenAcquisition		ScreenAcquisition is used to describe a single acquisition run for a screen. Since Screens are abstract, this object is used to record the set of images acquired in a single acquisition run. The Images for this run are linked to ScreenAcquisition through WellSample.
	ID
	EndTime	Time when the last image of this acquisition was collected
	StartTime	Time when the first image of this acquisition was collected
Well		A Well is a component of the Well/Plate/Screen construct to describe screening applications. A Well has a number of WellSample elements that link to the Images collected in this well. The ReagentRef links any Reagents that were used in this Well. A well is part of one or more Plates. The origin for the row and column identifiers is the top left corner of the plate starting at zero.
	ID
	Column	This is the column index of the well, the origin is the top left corner of the plate with the first column of cells being column zero. i.e top left is (0,0)
	ExternalDescription	A description of the externally defined identifier for this plate.
	ExternalIdentifier	A pointer to an externally defined identifier for this plate.
	Row	This is the row index of the well, the origin is the top left corner of the plate with the first row of wells being row zero. i.e top left is (0,0)
	Type	A human readable identifier for the screening status. e.g. empty, positive control, negative control, control, experimental, etc. This string is likely to become an enumeration in future releases.
WellSample		WellSample is an individual image that has been captured within a Well.
	ID
	Index	This is redundant and will be removed (The ImageRef is used to identify the specific Image)
	PosX	The X position of the image within the well
	PosY	The Y position of the image within the well
	Timepoint	The time-point at which the image started to be collected

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

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

The dashed arrows added to the previous diagram show the interdependencies 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 interdependencies 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.