Downstream effect - Sc CDC8
Submitted by Val
This is the gene product CDC8 in S. cerevisiae which is thymidylate kinase involved in deoxyribonucleoside biosynthesis. This was annotated directly to "DNA replication" at SGD, and I queried whether it should be annotated to "regulation of DNA replication"
The SGD decision was that this was a legacy annotation and that it was an upstream prcess and the annotation was removed.
For me I am still unclear the best way to annotate this. I think, as it is described as "essential for mitotic and meiotic DNA replication" in the description, there is a cease to annotate to "regulation of replication".
DNA replication is defined as "The cellular metabolic process whereby new strands of DNA are synthesized. The template for replication can either be an existing DNA molecule or RNA"
Maybe we need to invoke David's regulation rules and decide where the process begins and ends and include this in the definition?
I don't know if this would help in this case, even if the process was defined to begin with the binding of the origin recognition process I would still see the availability of building blocks as regulating the elongation?
The big issues are that i) if we decide to implement different rules, the concept of consistent annotation flies out of the window ii) as these annotations are revised, a large number of ISS annotations to the original annotations will remain. iii) If we decide that we do not annotate to downstream processes, we have a mixed bag of annotation; the annotations where we think something could be involved in replication, and the annotations where we know that it is upstream. This makes the paint annotation a LOT more difficult as you would need to say, this is known to be an upstream process, so all of the other annotation based on phenotype, should not be transferred. This would make an argument for not transferring any annotation until there is a sufficient body of knowledge to know that the process is not upstream.
Related example: thioredoxin
Here is another example for DNA replication, but here the previous annotation was to "DNA replication" and the annotation has been moved to "regulation of DNA replication". However, the effect is the similar to CDC8, it appears to be regulating deoxyribonucleotide pools http://www.ncbi.nlm.nih.gov/pubmed/7929110