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