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#8690 APO GO:0006915 apoptosis never_in viridaplantae

closed-accepted
Apoptosis (41)
5
2014-05-13
2011-08-04
No

Hi,

Could you please add in a taxon restriction so that GO:0006915 apoptosis is never applied to gene products in the plant kingdom (Viridiplantae taxon:33090).

Evidence from 'Morphological classification of plant cell deaths' van Doorn et al. Cell Death Differ. 2011 Aug;18(8):1241-6. (PMID:21494263)

I've checked this pass Tanya and Donghui who are happy with this restriction.

Cheers,
Emily

Discussion

  • Paola Roncaglia

    Paola Roncaglia - 2011-08-04

    Hi Emily,
    I've updated category to "Apoptosis" so I can keep track of this along with other apo-related requests. Cheers,
    Paola

     
  • Paola Roncaglia

    Paola Roncaglia - 2011-08-04
    • labels: 2151041 --> Apoptosis
    • assigned_to: nobody --> paolaroncaglia
     
  • Paola Roncaglia

    Paola Roncaglia - 2011-08-11
    • summary: GO:0006915 apoptosis never_in viridaplantae --> APO GO:0006915 apoptosis never_in viridaplantae
     
  • Paola Roncaglia

    Paola Roncaglia - 2011-10-11

    Hi Emily, this is done:

    Added taxon rule to GO:0006915 apoptosis: never_in Viridiplantae

    Note that this taxon rule will still be valid and won't be affected when we soon rename GO:0006915 apoptosis to "apoptotic process" in the GO apoptosis overhaul.

    Thanks,
    Paola

     
  • Paola Roncaglia

    Paola Roncaglia - 2011-10-11
    • status: open --> closed-accepted
     
  • Paola Roncaglia

    Paola Roncaglia - 2014-05-13

    For reference, copying here original email from TAIR curators (Donghui Li and Tanya Berardini) to support this restriction along with the PubMed reference, as stated by Emily in her original request:
    (Emily's question at the bottom, Donghui's reply at the beginning)

    -------- Original Message --------
    Subject: Re: Plant Apoptosis
    Date: Tue, 2 Aug 2011 10:07:30 -0700
    From: Donghui Li donghui@stanford.edu
    To: Emily Dimmer edimmer@ebi.ac.uk
    CC: Tanya Berardini tberardi@acoma.stanford.edu

    Hi Emily,

    The term 'apoptosis' is rarely used by plant biologists. Generally we
    use terms like 'programmed cell death' 'hypersensentive reponse/
    hypersensitive cell death' 'necrosis' etc. Although there have always
    been suggestions that PCD observed in plants is simliar to apoptosis
    in terms of mechanism, but I don't see many uses of 'apoptosis' in
    plant literature. The point made in this article is not a surprise to
    me. Of course, the author left the door open by saying that 'The
    present classification is not static, but will be subject to further
    revision, especially when specific biochemical pathways are better
    defined.'

    I agree that we could create a taxon rule ensuring that 'apoptosis' is
    not applied to plants. Even before this discussion, TAIR generally
    doesn't annotate to 'apoptosis', instead we use 'programmed cell
    death'. Of the 179 annotations to 'apoptosis' currently on TAIR, one
    1 is a manual curation (IGI) by TAIR, 1 by UniProtKB (IC), all the
    rest are IEA/ISS (InterPro, TIGR). We'll remove all IEA/ISS
    annotations and change the other 2 to 'programmed cell death' (Tanya -
    can you please take care of this? Thanks!)

    Best

    Donghui

    On Aug 2, 2011, at 9:29 AM, Emily Dimmer wrote:

    Hi Tanya and Donghui,

    I've just been having a quick read of the following paper that
    strongly suggests that apoptosis does not occur in plants, from
    evaluating plant cell morphology during PCD.
    'Morphological classification of plant cell deaths' van Doorn et al.
    Cell Death Differ. 2011 Aug;18(8):1241-6. (PMID:21494263)

    As I believe that the definition of new apoptotic process term that
    Paola is currently developing, will include some morphological
    criteria for recognising apoptotic cell death, do you feel that there
    be a taxon rule associated with the GO apoptosis term GO:0006915, to
    ensure it is not applied to Viridiplantae GO annotations? At the
    moment there are 10,944 annotations to plant UniProtKB accessions
    created by the InterPro2GO IEA prediction method as well as a few
    manual annotations (Gramene - 1, TAIR - 2, UniProtKB - 57 annotations)
    to this term. Would you suggest that these annotations should be
    redirected to the parent 'programmed cell death' (GO:0012501)?

    Thanks,
    Emily

     

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