When working with the biological data, it is recommended (and often required) to properly annotate samples. The annotation information attached to the samples includes information about organism, source, cell type, library preparation protocols and others.
The annotation fields associated with the samples or related sample files are defined in the descriptor schemas. This tutorial describes the descriptor schemas that are attached to the sample objects, raw sequencing reads and differential expressions files.
When a new data object that represents a biological sample (i.e. fastq files, bam files) is uploaded to the database, the unannotated sample ( presample) is automatically created. When annotation is attached to the presample object, this object is automatically converted to the annotated sample. To annotate the sample, we need to define a descriptor schema that will be used for the annotation. Together with the descriptor schema, we need to provide the annotations (descriptors) that populate the annotation fields defined in the descriptor shema. The details of this process are described in the Resolwe SDK documentation.
To annotate raw sequencing reads we have prepared corresponding reads descriptor schema.
To define the default thresholds for
log fold change (FC)
and to describe which samples are used as cases and which as controls in
the calculation of differential expression we have prepared diffexp