children of the nucler DNA replication etc and has_part

[gocentral]

In the new arrangement http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0033260#term=children

...all of the existing DNA replication terms have has_part links to the new term under the cell cycle node. This is fine ontologically, but for annotation purposes in order to make these annotation appear under the cell cycle node (which is the purpose of the rearrangement for enrichment etc), we will need explicit specific terms, because annotations do not propagate over has_part

e.g nuclear cell cycle DNA replication initiation etc. for all of the terms which belong under more than one node (some terms can move directly under one of the new terms, for example "telomere maintenance via semi-conservative replication" can move under nuclear cell cycle DNA replication )

Once the new terms in place, to make the annotations to DNA replication be included in the "cell cycle" gene set, MODs will need to migrate each existing "DNA replication" annotation to one of the new specific terms (I will put this in the annotation recommendations)

v

Reported by: ValWood

Original Ticket: geneontology/ontology-requests/10177

[gocentral]

• labels: --> cell cycle
• assigned_to: Jane Lomax

Original comment by: paolaroncaglia

[gocentral]

I see what you mean. So it looks like these two:

pre-replicative complex assembly ; GO:0006267 telomere maintenance via semi-conservative replication ; GO:0032201

can go directly under 'nuclear cell cycle DNA replication'.

These ones:

DNA ligation involved in DNA-dependent DNA replication DNA replication initiation DNA replication preinitiation complex assembly DNA replication termination DNA replication, synthesis of RNA primer DNA strand elongation involved in DNA replication DNA unwinding involved in replication maintenance of fidelity involved in DNA-dependent DNA replication

will all require bacterial and nuclear subtypes.

Although actually thinking about it, all of the above processes are common to both prok and nuclear replication...how about we just make a cell cycle subtype e.g. 'DNA ligation involved in cell cycle DNA-dependent DNA replication' and not the prok and nuclear subtypes? Or do you think that would that look inconsistent?

Original comment by: jl242

[gocentral]

It would be a bit inconsistent. especially if people might use the bacterial or nuclear subtypes they wouldn't get the complete gene list

for e.g ideally for fission yeast the annotations to

nuclear cell cycle DNA replication x cell cycle DNA replication x and DNA replication x

should always be identical

... this is the sort of check I would make to check everything is as specific as possible.

Sorry!

Original comment by: ValWood

[gocentral]

Okay, think this is all done now. I've also removed the has_parts from nuclear cell cycle DNA replication.

Original comment by: jl242

[gocentral]

• status: open --> closed-accepted

Original comment by: jl242