PavlidisLab
data model cleanup
Nothing that the following are not used:
ExperimentalDesign.replicateDescription, qualityControlDescription, normalizationDescription.
ExperimentalDesign.types - this is only used in 9 experiments that were loaded from ArrayExpress, it isn't actually exposed or used for anything (?) so can be deleted (mapping is CHARACTERISTIC.EXPERIMENTAL_DESIGN_FK)
Also unused:
CHARACTERISTIC.BIBLIOGRAPHIC_REFERENCE_FK (BibliographicReference.annotations - already deprecated) CHARACTERISTIC.GENE_SET_FK (GeneSet.characteristics - never used) CHARACTERISTIC.EXPERIMENTAL_FACTOR_FK (ExperimentalFactor.annotations) (Maybe there is some possible use of this)
There may be references to these in query strings (SQL or HQL) that would have to be searched for and removed in addition to stripping out the obvious java code.
The ExperimentalFactor.annotations can be purposed for attributing characteristics and eventually statements to continuous factors. We can add a FactorValue.getAllCharacteristics() that would merge the factor-level and factor-value-level characteristics and use it everywhere we "read" characteristics.
The two other can be removed.
