Getting stuff right
Early in the evolution of the Sequence Ontology, it was noted (by gadflies like myself) that SO asserts the relationship of mRNA to gene to be the “part of” relationship. This is obviously wrong. An RNA molecule is not part of a DNA molecule. Saying that mRNA is part of a gene is like saying that a CD with some audio chapters from a book is part of that book.
Ontologies are supposed to support formal reasoning: errors in representation will lead inevitably to erroneous results. For instance, if we are reasoning about the chemical composition of a cell using mRNA part_of gene as a constraint, we would conclude falsely that the mass of DNA must always be at least as much as the mass of mRNA, because the mass of a thing is always at least as great as the mass of some specified parts.