Core entities. Generic structure for describing data matrices such as genotype result, gene expression measurement, QTL calculation, etc. Describes the biological material or subject which is being 'measured' by an Data set.
For example an 'Sample' extends from Item, which makes it possible that a microarray-assay Data set such sample (as DataElement can reference any Item).
An DimensionElement is always linked to a single one Investigation. Generic data structure for aiming the values of a data set as described in Data. Each DataElement describes a cell in a data matrix of rows (from) and columns (to), e.g., in "dataset X" it was measured that geneX (col) relates to geneZ (row). A DataElement for storing decimal data. Store text data Subject variants. A variant or subtype of animal, plant, virus or bacteria. Biological individuals. A pair of samples labeled for a two-color microarray experiment. Trait variants. Common structure for entities that have a genomic position. Typical examples of such traits are genes, probes and markers. Traits that are being measured. Traits can be very diverse. The specifics of these traits can be added, as for example in a "Gene" (Gene extends Trait). Trait annotations specific for genes. Trait annotations specific for proteins. Trait annotations specific for metabolites. Trait annotations specific for classical phenotypes. Quantitative treats that are part of a protocol. E.g. microarray probes, marker set. Trait annotations specific for markers. A piece of sequence that reports for the expression of a gene, typically spotted onto a microarray. This is the spot on a microarray.
Note: We don't distinquish between probes (the sequence) and spots (the sequence as spotted on the array). A set of Probes. E.g. Affymetrix probeset has multiple probes. A peak that has been selected within a mass spectrometry experiment.