Cell Cycle Content Meeting follow-up 27 March 2013: Difference between revisions

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  * Propose we add a soft check and a comment, "not to be used for direct annotation", and refer to the existing part of children for reannotation
  * Propose we add a soft check and a comment, "not to be used for direct annotation", and refer to the existing part of children for reannotation
  * Defs currently make these sound like processes, redefine as phases?
  * Defs currently make these sound like processes, redefine as phases?
* outstanding question: although this is currently a little odd, because although mitosis has a nuclear division parent, meiosis meiosis I and meiosis II don't....maybe the meiosis terms are a little broader and encompass MORE than nuclear division ? although maybe this is confusion between a "meiotic cell cycle" and "meiosis".... I'm not sure.....anyone else know?


===SF tickets===
===SF tickets===

Revision as of 14:58, 23 March 2013

Meeting report

  • Work through comments

Discussion items

  • Merges of the checkpoint terms. To demerge or not.
  • Regulation between checkpoint signaling and checkpoint response (signaling is_a positive regulation of response?)
  • Regulation between checkpoint signaling and phase transition (signaling is_a negative regulation of phase transition?)
  • Regulation between checkpoint and phase transition (checkpoint is_a negative regulation of phase transition?)


Phase terms

Merge of phase terms Previous e-mail from Jane

1. The relationship between the phases and other cell cycle processes. David OS has suggested that we could continue to use part_of, or when part_of is too strong use happens_during (also starts_during and ends_during). But I got the sense during the meeting that we wanted to steer away from using part_of between processes and phases and make the phases both is_a and part_of disjoint from the rest of bp? The main part_of children are currently the cell cycle transitions.

 * Val: I feel *very strongly* that they should all be happens_during.

I think we should stick with this *unless* anyone can find an annotation where this is not true...

2. How to handle phases that are also processes. It's possible to frame some phases as processes, indeed some phases are defined this way e.g. metaphase. Would we want these to be represented under both 'cell cycle phase' and 'cell cycle process' and have two separate terms? Or do we decide which should be phases and which should be processes and just split them up?

3. Do we want to make this node generic for all phases in GO, and use it to house some of the e.g. developmental phases there? How might that look e.g.:

* biological process
** [i] cell cycle phase
*** [i] developmental phase

etc

TO DO

* I have asked Chris for a list of direct annotations
* Propose we add a soft check and a comment, "not to be used for direct annotation", and refer to the existing part of children for reannotation
* Defs currently make these sound like processes, redefine as phases?
  • outstanding question: although this is currently a little odd, because although mitosis has a nuclear division parent, meiosis meiosis I and meiosis II don't....maybe the meiosis terms are a little broader and encompass MORE than nuclear division ? although maybe this is confusion between a "meiotic cell cycle" and "meiosis".... I'm not sure.....anyone else know?

SF tickets

  • regulation of CDK activity [1]