Make a cell cycle DNA replication class

[gocentral]

We need to include DNA replication that happens as part of the cell cycle under cell cycle. This needs to work for bacteria, but exclude organelle chromosomes/genomes.

Reported by: jl242

Original Ticket: geneontology/ontology-requests/10102

[gocentral]

Hi Jane,

Assigning this to you as you're owning all of the other cell cycle SF requests, but we can split tickets if you prefer - feel free to assign to me.

Thanks, Paola

Original comment by: paolaroncaglia

[gocentral]

• assigned_to: nobody --> jl242

Original comment by: paolaroncaglia

[gocentral]

Hi Jane, when you do this can you rename any existing terms for starters

1. GO:0033260 DNA replication involved in S phase could be renamed cell cycle DNA replication

2. Some terms are specific for nuclear or bacterial DNA replication and can be moved directly under here (the taxon restraints might help with this, but I don't think it will find everything) pre-replicative complex assembly DNA replication preinitiation complex assembly telomere maintenance via semi-conservative replication etc Do not need to have a parent which is not under the cell cycle node

3. All terms which are required to annotated nuclear or bacterial DNA replication, but are also applicable to mitochondria or plastid/chloroplast need to be replicated under the cell cycle node

Annotation guidelines will be needed for groups to map existing annotations to the more specific terms. I can write these once the terms are migrated and I can see what is what.

Original comment by: ValWood

[gocentral]

Hi Val - going through the points in order:

1. GO:0033260 DNA replication involved in S phase has loads of has_parts e.g. 'DNA replication, synthesis of RNA primer' which are euk-specific. So I'd be reluctant to broaden the meaning of this term by removing them all so it could be used for proks too (remember with has_part the process always has to have all the parts). I seem to remember we were talking about a fairly high-level split into euk/prok anyway, so perhaps we make a new generic DNA replication term, and make this a child like this:

cell cycle DNA replication ---[i] nuclear cell cycle DNA replication ---[i] bacterial-type DNA replication

or we could obsolete GO:0033260 DNA replication involved in S phase and make a new generic term.

Original comment by: jl242

[gocentral]

These are the has_parts for GO:0033260 DNA replication involved in S phase:

GO:0051104 DNA ligation involved in DNA-dependent DNA replication GO:0006270 DNA replication initiation GO:0071163 DNA replication preinitiation complex assembly GO:0006274 DNA replication termination GO:0006269 DNA replication, synthesis of RNA primer GO:0006271 DNA strand elongation involved in DNA replication GO:0006268 DNA unwinding involved in replication GO:0045005 maintenance of fidelity involved in DNA-dependent DNA replication GO:0006267 pre-replicative complex assembly

Original comment by: jl242

[gocentral]

Implemented the above:

New terms:

cell cycle DNA replication ; GO:0044786 bacterial-type DNA replication ; GO:0044787

Renamed:

GO:0033260 DNA replication involved in S phase -> nuclear cell cycle DNA replication

Original comment by: jl242

[gocentral]

• status: open --> closed-accepted
• Group: --> None

Original comment by: jl242