Apoptosis: Difference between revisions

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APO-SYS are funding a 9 month position at the EBI for a curator to improve the apoptosis term in GO and annotate papers to apoptotic GO terms, with recruitment beginning as soon as possible.
APO-SYS are funding a 9 month position at the EBI for a curator to improve the apoptosis term in GO and annotate papers to apoptotic GO terms, with recruitment beginning as soon as possible.


Apoptosis GO terms were discussed by members of the APO-SYS consortium at a meeting in Stockholm in 2009. The presentation is here: [http://gocwiki.geneontology.org/images/6/64/APO-SYS_2009.pdf]


==ISSUES AND IDEAS IN PROGRESS==
==ISSUES AND IDEAS IN PROGRESS==

Revision as of 06:47, 16 May 2011

Aim

The aim of this project is to overhaul all the terms related to apoptosis in GO, mainly processes. Term phrasing and tree structures will be standardized, and new terms will be added with the aim of giving a broad coverage for all applicable species.


Background

APO-SYS is an EU-funded consortium of 23 partners, aiming at obtaining major progress in comprehension of apoptosis (and more generally cell death) in human diseases, by combining a series of systems biology approaches.

APO-SYS are funding a 9 month position at the EBI for a curator to improve the apoptosis term in GO and annotate papers to apoptotic GO terms, with recruitment beginning as soon as possible.

Apoptosis GO terms were discussed by members of the APO-SYS consortium at a meeting in Stockholm in 2009. The presentation is here: [1]

ISSUES AND IDEAS IN PROGRESS


Definition of apoptosis ; GO:0006915

  • The first step is to decide where apoptosis begins and ends, and to improve the current GO definition of apoptosis ; GO:0006915. [2]
  • The current definition of apoptosis ; GO:0006915 covers ALL events INCLUDING the signaling events AND the physical death of a cell:

A form of programmed cell death that:

    • BEGINS when a cell receives internal or external signals that trigger the activity of proteolytic caspases,
    • PROCEEDS through a series of characteristic stages typically including rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), and plasma membrane blebbing (but maintenance of its integrity until the final stages of the process), and
    • ENDS with the death of the cell.
  • One idea is to limit 'apoptosis ; GO:0006915' to the death of a cell, and create upstream signaling events that regulate apoptosis. This is similar to how the signaling terms are structured in GO [3], and how Reactome view apoptosis: [4]


anti-apoptosis

  • We need to decide if the term 'anti-apoptosis ; GO:0006916' [5] is required, and if so, how it differs from 'negative regulation of apoptosis ; GO:0043066'.
  • What is 'positive regulation of anti-apoptosis ; GO:0045768'?
  • What is 'negative regulation of anti-apoptosis ; GO:0019987'?



To visualise these ideas, see Paola's presentation from the apoptosis call on May 12th 2011: [6].



Apoptosis Working Group

An apoptosis working group will be set up to discuss apoptosis in GO and the related problems.

Members of the apoptosis working group will be:

  • Samuel Kerrien
  • Emily Dimmer
  • Susan Tweedie
  • Rebecca Foulger
  • Paola Roncaglia


Apoptosis Content Meeting

  • An Apoptosis Content Meeting will be held at the EBI (Hinxton, UK) on Wednesday June 1st 2011.
  • The content meeting will be attended by apoptosis experts (numbers/names TBC) , GO editors and GO annotators, and will precede the 2-day APO-SYS Consortium Meeting (June 2nd and 3rd 2011).
  • Sam Kerrien (Intact) will organise and host the apoptosis content meeting.
  • The meeting will be funded by APO-SYS.
  • The outcome from the apoptosis content meeting will be presented on Friday June 3rd 2011, at the APO-SYS Consortium Meeting.

Content Meeting Attendees

  • Samuel Kerrien
  • Emily Dimmer
  • Susan Tweedie
  • Rebecca Foulger
  • Paola Roncaglia
  • Jane Lomax ?
  • ~5 apoptosis experts


Apoptosis call, May 12th 2011

A call was held with GO curators, editors and apoptosis experts to highlight what needs to be done at the Apoptosis workshop in June.

The presentation Paola gave at the call can be found here [7].

The presentation includes:

  • A brief introduction to GO.
  • A summary of the current arrangement of apoptosis GO terms.
  • Problems identified with the current GO terms and their arrangement.
  • Possible ways to proceed with improving the apoptosis node.

Minutes of the call are in the discussion part of this page.


Annotation Targets

Please see the Reference Genome Apoptosis project page for details on targets currently selected for curation by GO Consortium annotation groups.

SF items

Websites and Resources

APO-SYS Consortium

Apoptosis Journal


Relevant Papers

REVIEWS

Classification of cell death: recommendations of the Nomenclature Committee on Cell Death 2009. Kroemer et al. Cell Death Differ. 2009 Jan;16(1):3-11 PMID:18846107

Systems biology of apoptosis signaling networks. Lavrik IN. Curr Opin Biotechnol. 2010 Aug;21(4):551-5. PMID:20674332

From sentencing to execution--the processes of apoptosis. Moffitt KL, Martin SL, Walker B. J Pharm Pharmacol. 2010 May;62(5):547-62. PMID: 20609056

Where, O death, is thy sting?. A brief review of apoptosis biology. Wyllie AH. Mol Neurobiol. 2010 Aug;42(1):4-9. PMID:20552413

Existing apoptosis structure

This is a snapshot of where 'apoptosis ; GO:0006915' and its children are currently housed in GO: February 9th 2011

An Excel spreadsheet showing all of the apoptosis-related terms currently in the GO (February 2011)

A QuickGO chart view of the main structure of apoptosis terms currently in the GO (February 2011).

  • N.B. this chart does not contain all apoptosis-related terms, please see the Excel spreadsheet above for this list.
  • N.B. Click on the chart to zoom in