29.2.15. Bioassays and raw data

Figure 29.16. Bioassays and raw data

Bioassays and raw data

Physical bioassays

A PhysicalBioAssayData item connect the array slides from the Array LIMS part with extracts from the biomaterials part. The creationEvent is used to register which extracts that were used on the bioassay. The relation to slides is a one-to-one relation. A slide can only be used on a single physical bioassay and a bioassay can only use a single slide. The relation is optional from both sides.

Further processing of the bioassay is registered as a series of DerivedBioAssayData items. For microarray experiments the first step is typically a scanning of the hybridization. Information about the software/hardware and protocol used can be registered. Any data files generated by the process can be registered with the FileSetData item. If more than one processsing step is required child derived bioassays can be created that descrive each additional step.

If the root physical bioassay has multiple extracts in multiple positions, the extract property of a derived bioassay is used to link with the extract that the specific derived bioassay represents. If the link is null the derived bioassay represents all extracts on the physical bioassay.

Raw data

A RawBioAssayData object represents the raw data that is produced by analysing the data from the physical bioassay. You may register which software that was used, the protocol and any parameters (through the annotation system).

Files with the analysed data values can be attached to the associated FileSetData object. The platform and, optionally, the variant has information about the file types that can be used for that platform. If the platform file types support metadata extraction, headers, the number of spots, and other information may be automatically extracted from the raw data file(s).

If the platform support it, raw data can also be imported into the database. This is handled by batchers and RawData objects. Which table to store the data in depends on the rawDataType property. The properties shown for the RawData class in the diagram are the mandatory properties. Each raw data type defines additional properties that are specific to that raw data type.

Spot images

Spot images can be created if you have the original image files. BASE can use 1-3 images as sources for the red, green and blue channel respectively. The creation of spotimages requires that x and y coordinates are given for each raw data spot. The scaling and offset values are used to convert the coordinates to pixel coordinates. With this information BASE is able to cut out a square from the source images that, theoretically, contains a specific spot and nothing else. The spot images are gamma-corrected independently and then put together into PNG images that are stored in a zip file.