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The OME Data Model specification
Open Microscopy Environment
Screen, Plate, and Well XML Schema
Author: Andrew J Patterson
This element identifies microtiter plates within a screen.
A plate can belong to more than one screen.
The Screen(s) that a plate belongs to are specified by the ScreenRef element.
The Plate ID and Name attributes are required.
The Wells in a plate are numbers from the top-left corner in a grid starting at zero.
i.e The top-left well of a plate is index (0,0)
The Name identifies the plate to the user. It is used much like the
ID, and so must be unique within the document.
A textual annotation of the current state of the plate with respect to the
experiment work-flow; e.g.
1. Seed cell: done; 2. Transfection: done; 3. Gel doc: todo.
The ExternalIdentifier attribute may contain a reference to an external database.
The PlateRef element is a reference to a Plate element.
Screen elements may have one or more PlateRef elements to define the plates that are part of the screen.
Plates may belong to more than one screen.
Reagent is used to describe a chemical or some other physical experimental parameter.
A long description for the reagent
A short name for the reagent
This is a reference to an external (to OME) representation of the Reagent.
It serves as a foreign key into an external database. - It is sometimes refereed to as ExternalIdentifier.
The Screen element is a grouping for Plates.
The required attribute is the Screen's Name and ID - both must be unique within the document.
The Screen element may contain an ExternalRef attribute that refers to an external database.
A description of the screen may be specified in the Description element.
Screens may contain overlapping sets of Plates i.e. Screens and Plates have a many-to-many relationship.
Plates contain one or more ScreenRef elements to specify what screens they belong to.
A pointer to an externally defined protocol, usually in a screening database.
A description of the screen protocol; may contain very detailed information to
reproduce some of that found in a screening database.
A description of the set of reagents; may contain very detailed information to
reproduce some of that information found in a screening database.
A pointer to an externally defined set of reagents, usually in a screening
database/automation database.
A human readable identifier for the screen type; e.g. RNAi, cDNA, SiRNA, etc.
This string is likely to become an enumeration in future releases.
The ScreenRef element is a reference to a Screen element.
Plate elements may have one or more ScreenRef elements to define the screen that a plate belongs to.
Plates may belong to more than one screen.
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.
Time when the last image of this acquisition was collected
Time when the first image of this acquisition was collected
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 only one Plate.
The origin for the row and column identifiers is the top left corner of the plate starting at zero.
i.e The top left well of a plate is index (0,0)
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)
A description of the externally defined identifier for this plate.
The ExternalIdentifier attribute may contain a reference to an external database.
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)
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 is an individual image that has been captured within a Well.
This is the main link to the core Image element
This is redundant and will be removed
The X position of the image within the well
The Y position of the image within the well
The time-point at which the image started to be collected
The ImageRef element is a reference to a OME:Image element.
Note: at present this is only used from SPW. If it is used more
widely in the future it will be moved into the main OME schema.
The WellSampleRef element is a reference to a WellSample element.