DNA synthesis/DNA replication question

[hattrill]

Hullo!

Looking at the annotation of replicative polymerases.

The current structure of the ontology means we want to annotate with: GO:0006261 DNA-dependent DNA replication
we have to remember to also co-annotate with: GO:0090592 DNA synthesis involved in DNA replication so that it can be found under DNA biosynthetic process and DNA replication

As many of these mutants are lethal, there is a lot of in vitro experiments - and so not many chances to annotate the experimental work with GO:1904860 | DNA biosynthetic process involved in mitotic DNA replication which "bags" both branches.

There may be a very good reason why not, but any chance of a:

DNA synthesis involved in DNA-dependent DNA replication??

[hattrill]

Adding to this, if one were to annotate to -mitochondrial DNA replication we have to remember to co-annotate with a biosynthesis branch term:

[ValWood]

I think "mitochondrial DNA replication" could go under biosynthesis.

The reason for the difference in nuclear replication is that not all replication is biosynthetic. I can't remember why (@mah11 will know). To me now this seems odd but I think it is that some of the subprocesses are not biosynthetic processes (possibly something to do with primer degradation during removal caused TPVs?).

If this is the case, i can't think of any immediate reason why "mitochondrial DNA replication" cannot go directly under "DNA synthesis involved in DNA replication" (giving it the DNA biosyntheic process parent) , because it's all equivalent to "leading strand synthesis"

[mah11]

The reason for the difference in nuclear replication is that not all replication is biosynthetic

No; it's that DNA replication involves more than just DNA synthesis.

The same may be true for mitochondrial DNA replication, at least in some systems. I don't know it well, but a brief search suggests that different mechanisms exist, e.g.

https://academic.oup.com/jb/article/164/3/183/5040786 http://www.biochemsoctrans.org/content/45/2/513

[ValWood]

I still think this is odd. To all intents and purposes DNA replication is a biosynthetic process. Which "parts" are not biosynthesis?

[mah11]

primers are made of RNA

[ValWood]

Got it. So DNA replication is part of "cellular biosynthetic process", but not part_of DNA biosynthesis.

[hattrill]

So the "involved in" might be a good fudge? e.g. DNA synthesis involved in DNA-dependent DNA replication DNA synthesis involved inmitochondrial DNA replication

It would be helpful to users coming from a top-down query point-of-view.

[mah11]

So DNA replication is part of "cellular biosynthetic process",

I don't know the intended scope of that grouping term, so I'm not in a position to comment.

[ValWood]

In these cases I think it is clearer if the terms are worded

DNA-dependent DNA replication, DNA synthesis

this matches GO:0006269 DNA replication, synthesis of RNA primer

and it is clearer that this is a sub-part of the process.

To me, DNA synthesis involved in DNA-dependent DNA replication just looks confusing....

[srengel]

i agree that this term isn't great and could turn users off: DNA synthesis involved in DNA-dependent DNA replication

[hattrill]

As long as the inheritance works, I don't mind!

[sjm41]

@vanaukenk, others: any more views/progress on this one? I'm particularly keen to have "mitochondrial DNA replication (GO:0006264)" put under the "DNA biosynthetic process (GO:0071897)" branch (see Val's comment above). Thanks, Steven

[vanaukenk]

@sjm41

As @hattrill suggested, how about we create the new term, 'DNA synthesis involved in mitochondrial DNA replication' and position it in the ontology as follows:

is_a DNA biosynthetic process (GO:0071897) part_of mitochondrial DNA replication (GO:0006264) -DNA synthesis involved in mitochondrial DNA replication (GO:new)

and defined as: "Any DNA biosynthetic process that is involved in mitochondrial DNA replication."

We could use Midori's two reviews above as definition xrefs, but I'm happy to add more papers if you have some from your curation.

[sjm41]

Thanks @vanaukenk - this approach sounds good. But wouldn't the new term be a is_a child of "DNA synthesis involved in DNA replication" (GO:0090592) rather than "DNA biosynthetic process" (GO:0071897)? (see Helen's screenshot in her second post above).

Then the new term would be a 'sister' term to the existing "DNA biosynthetic process involved in mitotic DNA replication" (GO:1904860).

On that note, it would be good to use the same wording for these two sister terms - e.g. use "DNA synthesis involved in..." for both.

[vanaukenk]

@sjm41

Yes, you're right about the more granular parent, and the wording for all of the terms should be the same, although it looks like we have both versions throughout this part of the ontology with some terms having synonyms and not others.

@ukemi - do you have opinions on which language should prevail: 'DNA biosynthetic process' vs 'DNA synthesis' ?

[ukemi]

It's kind of a toss-up. I think the community uses DNA synthesis more that biosynthesis, but to keep internally consistent in the ontology with other terms, biosynthesis would be more appropriate. Our general rule is to use what is used by the community and then make a synonym for people who are searching across the ontology.

[ukemi]

Pubmed: "DNA synthesis" ~45,500 "DNA biosynthesis" ~34,000

[vanaukenk]

Thanks, @ukemi For these child terms, I'll go with "DNA synthesis" and make sure all of the appropriate synonyms are there.