Cell Cycle

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Summary

The cell cycle terms in GO haven't been touched for a while. There's a number of problems with the current arrangement since the cell cycle is largely based on timing. Along with cell cycle experts, we need to find a better way to model the cell cycle in GO.

NOTE: this is an old page, created to kick off the project and the Content Meeting in Hinxton.


Personnel

GO

  • Val
  • GOEds (Jane, Paola, David, Tanya)
  • Rachael Huntley (UniProt-GOA)
  • Mary Dolan (MGI)

Reactome

  • Bijay Jassal
  • Lisa Matthews

External experts

  • Jacqueline Hayles
  • Takashi Toda
  • Rob De Bruin

Key Issues

Summary from Val:

I had a read through most of the SF items and this is a general flavour of the problems. Problems include:

  1. General inconsistencies: [1] identifies some inconsistencies under cell cycle, and raises the questions
  2. Where does the cell cycle begin and end what do we mean by cell cycle as a process?
  3. Should we separate "cell cycle events " like DNA replication, chromosome segregation, from the cell cycle control system[2]
  4. Problems linking events to timing, because events occur in different phases in different organisms [3]
  5. Should we have phases (S-phase, M-phase, G1 phase which are currently in the process ontology), OR should we only have regulation of cell cycle phase transitions?
  6. A lot of issues arise because we don't have a clear idea where sub processes begin and end. So for instance is spindle elongation part of chromosome segregation? [4] e.g. Chromosome segregation occurs in two phases: chromosomes move towards spindle poles during anaphase A, and spindle poles separate from each other during anaphase B.(PMID: 11309422). But the definition of chromosome segregation in GO ends when the chromosomes reach the spindle poles, suggesting that spindle elongation comes after:

Viruses and the host cell cycle

Currently two separate cell cycle grouping terms in the viral node. Should they be merged or related? (once sorted out what processes are part of the cell cycle, and what processes regulate the cell cycle):

  • modification by virus of host cell cycle regulation ; GO:0019055
  • modulation by virus of host cell cycle ; GO:0060153


SF items

Resources

Cell Cycle Ontology


Papers

Meetings

Cell Cycle Content Meeting (EBI, Hinxton, UK)

Feb. 28th and March 1st 2013.

Link to meeting page: http://wiki.geneontology.org/index.php/Cell_Cycle_Content_Meeting_Feb_2013

Cell Cycle Content Meeting follow-up 27 March 2013

Agenda


Cell Cycle Content Meeting follow-3 (date TBD)

Agenda

Cell Cycle Content Meeting follow-up 12 April 2013

Discussion after GOC Consortium meeting, Churchill College, Cambridge

Minutes


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