- A probe represents a physical reporter. It exists only because
the same reporter acquired from different sources may in fact
be different (because of contamination or whatnot).
- It points to a reporter, and is immutable.
2. Plate geometry and mapping
- A plate geometry describes how the way wells are laid out on a plate.
- The number of rows and columns is all the information stored
about a geometry (for now, at least).
- A plate mapping defines how wells from a list of N plates of
one geometry can be mapped over to a list of M plates of another
(or the same) geometry.
3. Plate type
- A plate type describes a particular type or use of microtiter
plate, such as "PCR plate".
- A plate type has a geometry.
- For each plate type there are a number of plate event types.
Each event type has a name and points to a protocol type.
- A plate represents a physical microtiter plate, possibly only at
some stage in its existence.
- A plate is of a plate type, and may have events correspondig to
this type's event types. For each event, there is a protocol of
the event type's protocol type. Also, each event has a date and
- A plate consists of wells. Each well has a row and column
coordinate, and these must be within the limits set by the plate
geometry. Wells cannot be added or removed once the plate has
- Each well may be associated with a probe
- A well may have a parent, which has to have the same
probe reporter as
the well itself.
- A plate P may have an ordered list of parents. This list must
include all plates which contain wells which are the parents of
wells on the plate P.
- The position in the list of parent plates corresponds to the
order of N in the plate mapping discussed in the section on
- If a plate was created using a plate mapping, it should point
to that mapping and know which of the M created plates it was.
- Wells can be annotated.
- [implementation note] To facilitate searches on well
annotations it may be necessary to maintain a table with all
ancestor/descendant well pairs. The trees of wells are expected
to be shallow enough to prevent this from being problematic.
- [note] It's sometimes necessary to identify plates
by name, but this should be solved without requiring plate names to
be unique (this was a source of problems in BASE 1).
- [clarification] Plates can be created from scratch, or
from a set of existing plates (using a plate mapping). The most
common case is that a plate is created from a single plate of
the same geometry, with wells being mapped to the same coordinates.
- A plate cannot have fewer wells than its geometry indicates.
wells are missing when a plate is created, the reporter whose
reporter id is an empty string should be used for the missing
5. Array design
- An array design describes a particular microarray design; what
sits where on what kind of substrate.
- An array design needs a number of description fields, as given
- Array designs can be annotated. Some MIAME-mandated properties
have MGED ontologies, and these should be used if possible.
- A list of plates may be associated with an array design. These
plates are the ones that were/should be used in printing slides
of this array design.
- An array design will at some point get a set of features.
A feature maps a position on the array to a reporter, and possibly
also to a specific plate well. The position is most generally
specified as metarow/metacolumn/row/column.
- If an array design is associated with plates, its features are
created when a print map is added to it. A print map maps
plate wells to feature positions. Each feature created in this way
will point to the plate well it was created from, as well as to
the well's probe's reporter. If the print map contains enough
information for this, plates may be associated with the array
design as the print map is being added.
- An array design not associated with plates may have its features
created from a mapping from positions to reporters.
- Once an array design has had features added to it, it is not
possible to remove the features, nor to change the association
with plates. However, features should be removed if not used.
- It should be possible to store the print map (or other file used
to create the features) together with the array design.
- All coordinates in an array design must have features.
6. Affymetrix data
- An array design may describe an Affymetrix chip, and if it
does a special flag should be set.
- Affy probesets should be represented by reporters in BASE.
- An affyprobe may have a sequence, or nothing at all except
an internal id.
- There is a table which connects affyprobes to reporters.
Each row tells whether the affyprobe is a perfect match or
mismatch, what number it has in the list of probes for this
probeset (so that pm/mm pairs can be identified), and what
feature defines its position. Also, since
an entire reporter may be replicated, should there also be a
number identifying what replicate the affyprobe belongs to?
- Features need to be added before the affy-specific data.
If a feature is only used for one reporter (which is expected
to always be the case), it should point to that reporter.
If a feature is used for more than one probeset, it may point
to the reporter whose reporter id is the empty string.
7. Array batch
- An array batch describes a batch or single print run for one
- It should be possible to record factors affecting the array
slide quality, such as the temperature during printing.
This may be done through annotations.
- Array batches can be created for array designs which do not
yet have features, but user interfaces should warn the user
that the feature adding still needs to be done. As feature
creation cannot be undone, the array batch will need to be
recreated if the feature adding goes bad (if the print map
is wrong, for instance).
8. Array slide
- Each array batch consists of a number of individual array
slides, which are identified by a barcode.
- Array slides can be added to an existing array batch at any
- An array slide may be associated with a hybridization. Only one
slide may be associated with a single hybridization.
- An array slide may be dissociated from its hybridization at
- Array slides may be flagged as having been physically destroyed
without having been used, in which case they may not be connected
- It would be useful to enforce barcode uniqueness, but it would
cause problems with the deleting/undeleting of array slides, and
so it's the users' responsibility to keep barcodes unique.