Cell Cycle Content Meeting Feb 2013

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Date: Feb. 28th and March 1st 2013

Location: EBI, Hinxton, UK


Attendees:

Go Editors: Jane Lomax, Paola Roncaglia, David Hill, Tanya Berardini

Valerie Wood, Antonia Lock (PomBase)

Rachael Huntley (UniProt-GOA)

Steve Jupe (Reactome/EBI)

Lisa Matthews (Reactome/New York - attending remotely)

Mary Dolan (MGI - attending remotely)

External experts: Jacqueline Hayles, Takashi Toda, Rob de Bruin


Day 1 (Thursday Feb. 28th)

  • Schedule:

9:30am: Start

10am: Coffee break

12 noon: Lunch

3pm: Coffee break

5pm approx: End

7pm: Group dinner (at the John Barleycorn in Duxford)


  • Program:

Introductions

Overview of GO (David) (David's slides are on Slideshare: http://www.slideshare.net/janelomax3/feb2013-cell-cycle-geneontologydhill?utm_source=ss&utm_medium=upload&utm_campaign=quick-view)

History and current status/structure of the cell cycle ontology node (Jane)

Issues with current GO structure (Val)

Reactome view of cell cycle (Lisa, remotely, approx. 3:30pm) 

 Homepage -> search w/ 'cell cycle' -> pathway browser that can be navigated
Reactome can be very useful in the creation of function-process links.  Keep in mind that Reactome links out to the 
'phase' GO terms and they (and other resources) that use these ids, should have something new for mapping purposes.

Plan: define the transitions, then revisit all the other terms and see how they fit. Perhaps get rid of the 'phase' terms and move them out to a separate, external ontology that can be referred to by the GO terms. 

Note: cell cycle phase transition is not to be used for annotation, tag as subset and add comment not to use.
  • Aims:

1. What does cell cycle mean - define cell cycle v/s cell cycle regulation

2. Define start and end of cell cycle phases

  • Note:

The dbxref for this meeting is:

GOC:mtg_cell_cycle GO content meeting Feb. 28th and Mar. 1st 2013, EBI, with external experts: http://wiki.geneontology.org/index.php/Cell_Cycle_Content_Meeting_Feb_2013


  • General questions:

Do bacteria have a cell cycle? 

Answer: Yes. DNA replication and cytokinesis. No phases.

Day 2 (Friday March 1st)

  • Schedule:

9am: Start

10am: Coffee break

12 noon: Lunch

3pm: Coffee break

5pm approx: End


  • Program:

Cover Ontology SourceForge tickets for category 'cell cycle' (see below for links: http://wiki.geneontology.org/index.php/Cell_Cycle_Content_Meeting_Feb_2013#SourceForge_tickets_.28items_for_discussion.29)

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


SourceForge tickets (items for discussion)

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