From John.Flintham at bbsrc.ac.uk  Fri Jul  1 04:56:24 2005
From: John.Flintham at bbsrc.ac.uk (john flintham (JIC))
Date: Fri, 1 Jul 2005 09:56:24 +0100
Subject: [Fwd: [ geneontology-Curator requests-929957 ] vivipary]
Message-ID: <286D8A554155B54CBFB18EF26EE2F169212F10@jie2ksrv1.jic.bbsrc.ac.uk>

Note maize has a series of "Viviparous" mutants associated with abscisic acid synthesis and signal transduction, some orthologues have been identified in other spp. Pre-harvest sprouting is still a major quality problem for many wheat producers, and also affects other grains including rye, barley, rice, sorghum. PHS is conditional upon environmental triggers, but may be genetically related to vivipary....

-----Original Message-----
From: grains-request at greengenes.cit.cornell.edu
[mailto:grains-request at greengenes.cit.cornell.edu]On Behalf Of Tom Blake
Sent: 28 June 2005 18:27
To: 'Mary Polacco'; 'po-dev at plantontology.org, Pankaj Jaiswal';
'POC-dev'
Cc: 'Jennifer I Clark'; rice-e-net at chanko.lab.nig.ac.jp;
grains at greengenes.cit.cornell.edu
Subject: RE: [Fwd: [ geneontology-Curator requests-929957 ] vivipary]


Hi folks,
   In the small grains, this is called preharvest sprouting.  It's
well-understood, and as Mary suggests is the result of lack of seed dormancy
and a wet harvest environment.  Calling it vivipary won't improve
understanding of the process.  In both barley and wheat the genetics of
dormancy and of preharvest sprouting is pretty well-understood.  
Cheers,
Tom Blake, barley breeder, Montana State University

-----Original Message-----
From: grains-request at greengenes.cit.cornell.edu
[mailto:grains-request at greengenes.cit.cornell.edu] On Behalf Of Mary Polacco
Sent: Tuesday, June 28, 2005 11:04 AM
To: po-dev at plantontology.org, Pankaj Jaiswal; POC-dev
Cc: Jennifer I Clark; rice-e-net at chanko.lab.nig.ac.jp;
grains at greengenes.cit.cornell.edu
Subject: Re: [Fwd: [ geneontology-Curator requests-929957 ] vivipary]

Is there going to be consideration of the related process, dormancy?

> From: Pankaj Jaiswal <pj37 at cornell.edu>
> Reply-To: po-dev at plantontology.org, Pankaj Jaiswal <pj37 at cornell.edu>
> Date: Tue, 28 Jun 2005 09:57:44 -0400
> To: POC-dev <po-dev at plantontology.org>
> Cc: Jennifer I Clark <jenclark at ebi.ac.uk>,
rice-e-net at chanko.lab.nig.ac.jp,
> grains at greengenes.cit.cornell.edu
> Subject: [Fwd: [ geneontology-Curator requests-929957 ] vivipary]
> 
> Hi Everyone,
> 
> I though that some people from the plant community may be interested in
> the discussion on adding a new term VIVIPARY (and its instances ??) in
> the Gene Ontology.
> 
> Please follow the link below on the discussion
>
https://sourceforge.net/tracker/?func=detail&atid=440764&aid=929957&group_id
=3
> 6855
> 
> A couple of questions are:
> 
> #1 whether we need the two instances of a generic term VIVIPARY
> 
> vegetative vivipary (sensu Magnoliophyta)
> non-vegetative vivipary (sensu Magnoliophyta)
> 
> 
> #2 Is there anything called as vegetative vivipary.
> 
> 
> BY definition, in cereal plants or elsewhere, vivipary is defined as
> 
> "A process promoting the germination of embryos while still attached to
> the mother plant. "
> 
> -Pankaj
> 
> 
> 
> 




From jclark at ebi.ac.uk  Fri Jul  1 11:34:40 2005
From: jclark at ebi.ac.uk (Jennifer I Clark)
Date: Fri, 01 Jul 2005 16:34:40 +0100
Subject: [Fwd: [ geneontology-Curator requests-929957 ] vivipary]
In-Reply-To: <286D8A554155B54CBFB18EF26EE2F169212F10@jie2ksrv1.jic.bbsrc.ac.uk>
References: <286D8A554155B54CBFB18EF26EE2F169212F10@jie2ksrv1.jic.bbsrc.ac.uk>
Message-ID: <42C56290.7020203@ebi.ac.uk>

Hi,

Thanks for all this information. It's really a huge help. :-)

 From what you're saying I understand that the thing that we were 
talking about as 'non-vegetative vivipary' is properly called 
'pre-harvest sprouting' amongst certain biologists. Perhaps that should 
be the name of the term? Do you have any more names for it? We can add 
as many names as you can give us just by putting them in a synonyms. The 
synonyms don't have to be exact. We can add absolutely any names that 
will help domain biologists to find the term that they're interested in.

Do you have special names for the kind of vivipary that happens in 
Bryophyllum?

Thanks,

Jen



john flintham (JIC) wrote:

>Note maize has a series of "Viviparous" mutants associated with abscisic acid synthesis and signal transduction, some orthologues have been identified in other spp. Pre-harvest sprouting is still a major quality problem for many wheat producers, and also affects other grains including rye, barley, rice, sorghum. PHS is conditional upon environmental triggers, but may be genetically related to vivipary....
>
>-----Original Message-----
>From: grains-request at greengenes.cit.cornell.edu
>[mailto:grains-request at greengenes.cit.cornell.edu]On Behalf Of Tom Blake
>Sent: 28 June 2005 18:27
>To: 'Mary Polacco'; 'po-dev at plantontology.org, Pankaj Jaiswal';
>'POC-dev'
>Cc: 'Jennifer I Clark'; rice-e-net at chanko.lab.nig.ac.jp;
>grains at greengenes.cit.cornell.edu
>Subject: RE: [Fwd: [ geneontology-Curator requests-929957 ] vivipary]
>
>
>Hi folks,
>   In the small grains, this is called preharvest sprouting.  It's
>well-understood, and as Mary suggests is the result of lack of seed dormancy
>and a wet harvest environment.  Calling it vivipary won't improve
>understanding of the process.  In both barley and wheat the genetics of
>dormancy and of preharvest sprouting is pretty well-understood.  
>Cheers,
>Tom Blake, barley breeder, Montana State University
>
>-----Original Message-----
>From: grains-request at greengenes.cit.cornell.edu
>[mailto:grains-request at greengenes.cit.cornell.edu] On Behalf Of Mary Polacco
>Sent: Tuesday, June 28, 2005 11:04 AM
>To: po-dev at plantontology.org, Pankaj Jaiswal; POC-dev
>Cc: Jennifer I Clark; rice-e-net at chanko.lab.nig.ac.jp;
>grains at greengenes.cit.cornell.edu
>Subject: Re: [Fwd: [ geneontology-Curator requests-929957 ] vivipary]
>
>Is there going to be consideration of the related process, dormancy?
>
>  
>
>>From: Pankaj Jaiswal <pj37 at cornell.edu>
>>Reply-To: po-dev at plantontology.org, Pankaj Jaiswal <pj37 at cornell.edu>
>>Date: Tue, 28 Jun 2005 09:57:44 -0400
>>To: POC-dev <po-dev at plantontology.org>
>>Cc: Jennifer I Clark <jenclark at ebi.ac.uk>,
>>    
>>
>rice-e-net at chanko.lab.nig.ac.jp,
>  
>
>>grains at greengenes.cit.cornell.edu
>>Subject: [Fwd: [ geneontology-Curator requests-929957 ] vivipary]
>>
>>Hi Everyone,
>>
>>I though that some people from the plant community may be interested in
>>the discussion on adding a new term VIVIPARY (and its instances ??) in
>>the Gene Ontology.
>>
>>Please follow the link below on the discussion
>>
>>    
>>
>https://sourceforge.net/tracker/?func=detail&atid=440764&aid=929957&group_id
>=3
>  
>
>>6855
>>
>>A couple of questions are:
>>
>>#1 whether we need the two instances of a generic term VIVIPARY
>>
>>vegetative vivipary (sensu Magnoliophyta)
>>non-vegetative vivipary (sensu Magnoliophyta)
>>
>>
>>#2 Is there anything called as vegetative vivipary.
>>
>>
>>BY definition, in cereal plants or elsewhere, vivipary is defined as
>>
>>"A process promoting the germination of embryos while still attached to
>>the mother plant. "
>>
>>-Pankaj
>>
>>
>>
>>
>>    
>>
>
>
>  
>



From pj37 at cornell.edu  Fri Jul  1 13:19:57 2005
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 01 Jul 2005 13:19:57 -0400
Subject: [Fwd: [ geneontology-Curator requests-929957 ] vivipary]
In-Reply-To: <42C56290.7020203@ebi.ac.uk>
References: <286D8A554155B54CBFB18EF26EE2F169212F10@jie2ksrv1.jic.bbsrc.ac.uk> <42C56290.7020203@ebi.ac.uk>
Message-ID: <42C57B3D.9000008@cornell.edu>

REF: PMID: 10759503
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10759503&dopt=Abstract

# vivipary is a instance of seed_hgermination (on parent plant)

# A correct balance of Gibberellic acid (GA) and Abscisic acid(ABA) is 
required in maturing seed (dormant stage) prevents vivipary.

# GAs stimulate a developmental program leading to vivipary in the 
absence of normal amounts of ABA, and that a reduction of GA content 
re-establishes an ABA/GA ratio appropriate for suppression of 
germination and induction of maturation. In contrast, the induction of a 
GA deficiency did not suppress vivipary.

Therefore here is a suggestion:

In the suggestion, I have considered to use VIVIPARY exclusive to the 
use of plants. Perhaps this may require sensu Mangnoliophyta term if 
users consider that they need a term to represent the similar phenomenon 
from metazoans. Looks like pregnancy is analogous to vivipary. Since 
this is seed specific term you may want to use the words "germination of 
the embryo from a seed" in the definition, thus excluding the so called 
vivipary (vegetative propagation) as seen in bryophyllum.

[i] = is_a (child to parent term relationship)

seed germination GO:0009845
-[i]-negative regulation of seed germination GO:0010187
--[i]-vivipary GO:new


seed dormancy GO:0010162
-[i]-regulation of seed dormancy GO:new
--[i]-positive regulation of seed dormancy GO:new
--[i]-negative regulation of seed dormancy GO:new
----[i]-vivipary GO:new

maintenance of dormancy GO:0010231
This term exists as a child of (seed dormancy GO:0010162) and looks like 
it needs obsoletion, if the above tree under seed dormancy is adopted. 
Basically maintenance of dormancy = positive regulation of dormancy.


response to hormone stimulus GO:0009725
-[i]-response to gibberellic acid and abscisic acid GO:new
----[i]--vivipary GO:new
-[i]--response to abscisic acid stimulus GO:0009737
----[i]--response to gibberellic acid and abscisic acid GO:new
-------[i]--vivipary GO:new
-[i]--response to gibberellic acid stimulus GO:0009739
----[i]--response to gibberellic acid and abscisic acid GO:new
-------[i]--vivipary GO:new

I did not use the XX-acid mediated signalling terms as parent terms 
because the literature does not use the word signalling. Perhaps it is 
but I am not sure.

-Pankaj



From pj37 at cornell.edu  Fri Jul  1 14:06:03 2005
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 01 Jul 2005 14:06:03 -0400
Subject: [rice-e-net] Re: [Fwd: [ geneontology-Curator requests-929957
 ] vivipary]
In-Reply-To: <42C57B3D.9000008@cornell.edu>
References: <286D8A554155B54CBFB18EF26EE2F169212F10@jie2ksrv1.jic.bbsrc.ac.uk> <42C56290.7020203@ebi.ac.uk> <42C57B3D.9000008@cornell.edu>
Message-ID: <42C5860B.3000107@cornell.edu>

 >Comment By: Pankaj Jaiswal (pj37)

Date: 2005-07-01 14:00

Message:
Logged In: YES
user_id=561361

I see your point. Going  by your suggestions, can we have

organismal physiological process GO:0050874
-[i]-vivipary
---[i]-vivipary sensu metazoa
-----[i]-pregnancy GO:0007565
---[i]-vivipary sensu magnoliophyta
-[i]-seed germination GO:0009845
---[i]-vivipary sensu magnoliophyta

It looks kind of odd but it may work.
In my previous suggestion all the terms AKA "vivipary"  can
be replaced with 'vivipary sensu magnoliophyta"

For Jen:
I suggest excluding the bryophyllum type of vivipary from
this . It should be considerd as a vegetative propagation
(is_a asexual reproduction).

-Pankaj

 >Comment By: Karen Christie (kchris)

Date: 2005-07-01 10:32


Hi,

I know this is almost exactly the same comment I made on this
discussion earlier, but we cannot use plain 'vivipary' in a way that 
restricts
it plants. The word has a broader meaning and is applied to animals as
well as plants. Here's the dictionary.com definition for 'viviparous':

vi-vip-a-rous
adj.

Zoology. Giving birth to living offspring that develop within
the mother's body. Most mammals and some other animals are
viviparous.

Botany.  Germinating or producing seeds that germinate before
becoming detached from the parent plant, as in the mangrove.
Producing bulbils or new plants rather than seed, as in the tiger
lily.

http://dictionary.reference.com/search?q=viviparous

Thanks,

-Karen

Pankaj Jaiswal wrote:

> REF: PMID: 10759503
> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10759503&dopt=Abstract 
> 
> 
> # vivipary is a instance of seed_hgermination (on parent plant)
> 
> # A correct balance of Gibberellic acid (GA) and Abscisic acid(ABA) is 
> required in maturing seed (dormant stage) prevents vivipary.
> 
> # GAs stimulate a developmental program leading to vivipary in the 
> absence of normal amounts of ABA, and that a reduction of GA content 
> re-establishes an ABA/GA ratio appropriate for suppression of 
> germination and induction of maturation. In contrast, the induction of a 
> GA deficiency did not suppress vivipary.
> 
> Therefore here is a suggestion:
> 
> In the suggestion, I have considered to use VIVIPARY exclusive to the 
> use of plants. Perhaps this may require sensu Mangnoliophyta term if 
> users consider that they need a term to represent the similar phenomenon 
> from metazoans. Looks like pregnancy is analogous to vivipary. Since 
> this is seed specific term you may want to use the words "germination of 
> the embryo from a seed" in the definition, thus excluding the so called 
> vivipary (vegetative propagation) as seen in bryophyllum.
> 
> [i] = is_a (child to parent term relationship)
> 
> seed germination GO:0009845
> -[i]-negative regulation of seed germination GO:0010187
> --[i]-vivipary GO:new
> 
> 
> seed dormancy GO:0010162
> -[i]-regulation of seed dormancy GO:new
> --[i]-positive regulation of seed dormancy GO:new
> --[i]-negative regulation of seed dormancy GO:new
> ----[i]-vivipary GO:new
> 
> maintenance of dormancy GO:0010231
> This term exists as a child of (seed dormancy GO:0010162) and looks like 
> it needs obsoletion, if the above tree under seed dormancy is adopted. 
> Basically maintenance of dormancy = positive regulation of dormancy.
> 
> 
> response to hormone stimulus GO:0009725
> -[i]-response to gibberellic acid and abscisic acid GO:new
> ----[i]--vivipary GO:new
> -[i]--response to abscisic acid stimulus GO:0009737
> ----[i]--response to gibberellic acid and abscisic acid GO:new
> -------[i]--vivipary GO:new
> -[i]--response to gibberellic acid stimulus GO:0009739
> ----[i]--response to gibberellic acid and abscisic acid GO:new
> -------[i]--vivipary GO:new
> 
> I did not use the XX-acid mediated signalling terms as parent terms 
> because the literature does not use the word signalling. Perhaps it is 
> but I am not sure.
> 
> -Pankaj
> 
> 




From matthews at greengenes.cit.cornell.edu  Fri Jul  1 13:44:23 2005
From: matthews at greengenes.cit.cornell.edu (Dave Matthews)
Date: Fri, 1 Jul 2005 13:44:23 -0400 (EDT)
Subject: no automatic mails, please
Message-ID: <200507011744.j61HiN0A026743@greengenes.cit.cornell.edu>

Hi Manfred,

I've removed you from the "grains at greengenes" list.

I think there are probably others on the list who aren't interested
in this discussion about vivipary, or plant ontology in general.  Though
some clearly are.  I would recommend that these folks look at the po-dev
Mailing List Archive, http://www.plantontology.org/mailarch-dev/, or join
the po-dev mailing list.  There are frequently some quite interesting 
discussions.

all the best,
- Dave

> Date: Fri, 01 Jul 2005 11:49:59 +0200
> To: curator at pw.usda.gov
> From: Manfred Heun <manfred.heun at umb.no>
> Subject: no automatic mails, please
> 
> kj?re dave,
> 
> please take my name out from the mailing list so that I will get NO more
> automatic emails from graingenes, since the recent Q & A games are not my
> taste.
> 
> my name and my stuff (map, AFLPs etc) should remain inside the graingenes
> server, selvf?lgelig.
> 
> mvh manfred
> -------------------
> Professor Manfred Heun, Dr. habil., Dr. sc. agr.
> INA, Postboks 5003
> Norwegian University of Life Sciences (UMB)
> N-1432 ?s
> NORWAY
> 
> Phone: +47-64965791
> 
> email: manfred.heun at umb.no
> 
> http://www.umb.no/ina/ansatte/mhe_e.htm
> -------------------



From kirchoff at uncg.edu  Fri Jul  1 16:00:12 2005
From: kirchoff at uncg.edu (Bruce Kirchoff KIRCHOFF)
Date: Fri, 1 Jul 2005 16:00:12 -0400
Subject: Bruce Kirchoff is out of the office.
Message-ID: <OF6B603475.7CEBD2BC-ON85257031.006DE207-85257031.006DE209@uncg.edu>





I will be out of the office starting Thu 06/30/2005 and will not return
until Mon 07/25/2005.

I will check my email only sporatically during this time, and will respond
to your message when I return.



From matthews at greengenes.cit.cornell.edu  Fri Jul  1 13:51:01 2005
From: matthews at greengenes.cit.cornell.edu (Dave Matthews)
Date: Fri, 1 Jul 2005 13:51:01 -0400 (EDT)
Subject: [Fwd: [ geneontology-Curator requests-929957 ] vivipary]
Message-ID: <200507011751.j61Hp1oA026834@greengenes.cit.cornell.edu>

Subject: RE: [Fwd: [ geneontology-Curator requests-929957 ] vivipary]
Date: Fri, 1 Jul 2005 10:52:49 +0100
From: "steve reader \(JIC\)" <steve.reader at bbsrc.ac.uk>
To: <grains-request at greengenes.cit.cornell.edu>

Hello from the UK.
	Not sure if the reasoning is getting a little ahead of itself,
as hinted at in the last comment below - pre-harvest sprouting is the
effect of unusual environment speeding up a natural process, i.e.
germination, and as such is variable from season to season in many
countries. In my view, it's wrong to consider the seasonal shifts in the
genotype x environment interaction as a form of vivipary.
	Like many of the correspondents to the website, I understood
'Vivipary' to have an asexual slant, i.e. to mean the creation of a
young plant in (emanating from) an inflorescence, viz. as in some
grassses and especially the common house plant known as the 'spider
plant'. Similarly, the asexual production of a new plant when a bud is
detached from the parent, as in the onion. These are a means of natural
propagation which happens each season and is under genetic control.
However, their occurrence is independent of normal environmental
influence, yet such seasonal variation may influence survival of the new
plantlets, once produced.
Cheers,
Steve Reader.

Stephen M. Reader, Germplasm Manager,
Wheat Precise Genetic Stocks,
John Innes Centre,
Norwich Research Park,
Colney, Norwich,		Tel:	+44 1603 450613 / 450594
NR4 7UH,			Fax:	+44 1603 450023
UK.			e-mail:	steve.reader at bbsrc.ac.uk

-----Original Message-----
From: grains-request at greengenes.cit.cornell.edu
[mailto:grains-request at greengenes.cit.cornell.edu] On Behalf Of Tom
Blake
Sent: 28 June 2005 18:27
To: 'Mary Polacco'; 'po-dev at plantontology.org, Pankaj Jaiswal';
'POC-dev'
Cc: 'Jennifer I Clark'; rice-e-net at chanko.lab.nig.ac.jp;
grains at greengenes.cit.cornell.edu
Subject: RE: [Fwd: [ geneontology-Curator requests-929957 ] vivipary]


Hi folks,
   In the small grains, this is called preharvest sprouting.  It's
well-understood, and as Mary suggests is the result of lack of seed
dormancy and a wet harvest environment.  Calling it vivipary won't
improve understanding of the process.  In both barley and wheat the
genetics of dormancy and of preharvest sprouting is pretty
well-understood. 
Cheers,
Tom Blake, barley breeder, Montana State University

-----Original Message-----
From: grains-request at greengenes.cit.cornell.edu
[mailto:grains-request at greengenes.cit.cornell.edu] On Behalf Of Mary
Polacco
Sent: Tuesday, June 28, 2005 11:04 AM
To: po-dev at plantontology.org, Pankaj Jaiswal; POC-dev
Cc: Jennifer I Clark; rice-e-net at chanko.lab.nig.ac.jp;
grains at greengenes.cit.cornell.edu
Subject: Re: [Fwd: [ geneontology-Curator requests-929957 ] vivipary]

Is there going to be consideration of the related process, dormancy?

> From: Pankaj Jaiswal <pj37 at cornell.edu>
> Reply-To: po-dev at plantontology.org, Pankaj Jaiswal <pj37 at cornell.edu>
> Date: Tue, 28 Jun 2005 09:57:44 -0400
> To: POC-dev <po-dev at plantontology.org>
> Cc: Jennifer I Clark <jenclark at ebi.ac.uk>,
rice-e-net at chanko.lab.nig.ac.jp,
> grains at greengenes.cit.cornell.edu
> Subject: [Fwd: [ geneontology-Curator requests-929957 ] vivipary]
>
> Hi Everyone,
>
> I though that some people from the plant community may be interested
> in the discussion on adding a new term VIVIPARY (and its instances ??)

> in the Gene Ontology.
>
> Please follow the link below on the discussion
>
https://sourceforge.net/tracker/?func=detail&atid=440764&aid=929957&group_id=36855
>
> A couple of questions are:
>
> #1 whether we need the two instances of a generic term VIVIPARY
>
> vegetative vivipary (sensu Magnoliophyta)
> non-vegetative vivipary (sensu Magnoliophyta)
>
>
> #2 Is there anything called as vegetative vivipary.
>
>
> BY definition, in cereal plants or elsewhere, vivipary is defined as
>
> "A process promoting the germination of embryos while still attached
> to the mother plant. "
>
> -Pankaj



From jclark at ebi.ac.uk  Mon Jul  4 10:04:12 2005
From: jclark at ebi.ac.uk (J Clark)
Date: Mon, 04 Jul 2005 15:04:12 +0100
Subject: [Fwd: [ geneontology-Curator requests-929957 ] vivipary]
In-Reply-To: <BE57D4C018CC2642AF256E2FDDA909570D6ECA@exchange1.scri.sari.ac.uk>
References: <BE57D4C018CC2642AF256E2FDDA909570D6ECA@exchange1.scri.sari.ac.uk>
Message-ID: <42C941DC.40506@ebi.ac.uk>

Hi,

How about this as a proposal?

[i]germination
---[i]germination on parent plant ; GO:new

[i]asexual reproduction
---[i]vegetative vivipary (sensu Magnoliophyta) ; GO:new

Term:germination on parent plant
synonym: non-vegetative vivipary (sensu Magnoliophyta)

Term: vegetative vivipary (sensu Magnoliophyta)
synonym: pre-harvest sprouting

Thanks,

Jen






David Marshall wrote:

> preharvest sprouting is of particular interest. There are a number of  advances at the molecular level. It is interesting to place preharvest sprouting in the context of related processes i.e. grain development, "normal germination", dormance and in the case of barley- malting.
>  
> David Marshall
> 
> 	-----Original Message----- 
> 	From: owner-po-dev at plantontology.org on behalf of Tinker, Nicholas 
> 	Sent: Tue 28/06/2005 19:05 
> 	To: Tom Blake; Mary Polacco; po-dev at plantontology.org, Pankaj Jaiswal; POC-dev 
> 	Cc: 
> 	Subject: RE: [Fwd: [ geneontology-Curator requests-929957 ] vivipary]
> 	
> 	
> 
> 	But,
> 	If an ontology defines "vivipary" as a "type of" preharvest sprouting
> 	(or vice-versa) then won't it help the corn people do comparative
> 	genomics with the barley people? 
> 	
> 	>
> 	> Hi folks,
> 	>    In the small grains, this is called preharvest sprouting.  It's
> 	> well-understood, and as Mary suggests is the result of lack of seed
> 	> dormancy
> 	> and a wet harvest environment.  Calling it vivipary won't improve
> 	> understanding of the process.  In both barley and wheat the genetics
> 	of
> 	> dormancy and of preharvest sprouting is pretty well-understood.
> 	> Cheers,
> 	> Tom Blake, barley breeder, Montana State University
> 	>
> 	> -----Original Message-----
> 	> From: grains-request at greengenes.cit.cornell.edu
> 	> [mailto:grains-request at greengenes.cit.cornell.edu] On Behalf Of Mary
> 	> Polacco
> 	> Sent: Tuesday, June 28, 2005 11:04 AM
> 	> To: po-dev at plantontology.org, Pankaj Jaiswal; POC-dev
> 	> Cc: Jennifer I Clark; rice-e-net at chanko.lab.nig.ac.jp;
> 	> grains at greengenes.cit.cornell.edu
> 	> Subject: Re: [Fwd: [ geneontology-Curator requests-929957 ] vivipary]
> 	>
> 	> Is there going to be consideration of the related process, dormancy?
> 	>
> 	> > From: Pankaj Jaiswal <pj37 at cornell.edu>
> 	> > Reply-To: po-dev at plantontology.org, Pankaj Jaiswal
> 	<pj37 at cornell.edu>
> 	> > Date: Tue, 28 Jun 2005 09:57:44 -0400
> 	> > To: POC-dev <po-dev at plantontology.org>
> 	> > Cc: Jennifer I Clark <jenclark at ebi.ac.uk>,
> 	> rice-e-net at chanko.lab.nig.ac.jp,
> 	> > grains at greengenes.cit.cornell.edu
> 	> > Subject: [Fwd: [ geneontology-Curator requests-929957 ] vivipary]
> 	> >
> 	> > Hi Everyone,
> 	> >
> 	> > I though that some people from the plant community may be interested
> 	in
> 	> > the discussion on adding a new term VIVIPARY (and its instances ??)
> 	in
> 	> > the Gene Ontology.
> 	> >
> 	> > Please follow the link below on the discussion
> 	> >
> 	>
> 	https://sourceforge.net/tracker/?func=detail&atid=440764&aid=929957&grou
> 	p_
> 	> id
> 	> =3
> 	> > 6855
> 	> >
> 	> > A couple of questions are:
> 	> >
> 	> > #1 whether we need the two instances of a generic term VIVIPARY
> 	> >
> 	> > vegetative vivipary (sensu Magnoliophyta)
> 	> > non-vegetative vivipary (sensu Magnoliophyta)
> 	> >
> 	> >
> 	> > #2 Is there anything called as vegetative vivipary.
> 	> >
> 	> >
> 	> > BY definition, in cereal plants or elsewhere, vivipary is defined as
> 	> >
> 	> > "A process promoting the germination of embryos while still attached
> 	to
> 	> > the mother plant. "
> 	> >
> 	> > -Pankaj
> 	> >
> 	> >
> 	> >
> 	> >
> 	
> 	
> 	
> 
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> 
> DISCLAIMER:
> 
> This email is from the Scottish Crop Research Institute, but the views 
> expressed by the sender are not necessarily the views of SCRI and its 
> subsidiaries.  This email and any files transmitted with it are confidential 
> to the intended recipient at the e-mail address to which it has been 
> addressed.  It may not be disclosed or used by any other than that addressee.
> If you are not the intended recipient you are requested to preserve this 
> confidentiality and you must not use, disclose, copy, print or rely on this 
> e-mail in any way. Please notify postmaster at scri.sari.ac.uk quoting the 
> name of the sender and delete the email from your system.
> 
> Although SCRI has taken reasonable precautions to ensure no viruses are 
> present in this email, neither the Institute nor the sender accepts any 
> responsibility for any viruses, and it is your responsibility to scan the email 
> and the attachments (if any).



From kellogge at msx.umsl.edu  Mon Jul  4 14:29:53 2005
From: kellogge at msx.umsl.edu (kellogge)
Date: Mon, 4 Jul 2005 13:29:53 -0500
Subject: [Fwd: [ geneontology-Curator requests-929957 ] vivipary]
In-Reply-To: <42C941DC.40506@ebi.ac.uk>
References: <BE57D4C018CC2642AF256E2FDDA909570D6ECA@exchange1.scri.sari.ac.uk> <42C941DC.40506@ebi.ac.uk>
Message-ID: <9D052042-ECB9-11D9-ABF3-000D93B827BC@msx.umsl.edu>

Hi Jen -
Pre-harvest sprouting is a synonym of "germination on parent plant",  
not vegetative vivipary.
Toby

On Jul 4, 2005, at 9:04 AM, J Clark wrote:

> Hi,
>
> How about this as a proposal?
>
> [i]germination
> ---[i]germination on parent plant ; GO:new
>
> [i]asexual reproduction
> ---[i]vegetative vivipary (sensu Magnoliophyta) ; GO:new
>
> Term:germination on parent plant
> synonym: non-vegetative vivipary (sensu Magnoliophyta)
>
> Term: vegetative vivipary (sensu Magnoliophyta)
> synonym: pre-harvest sprouting
>
> Thanks,
>
> Jen
>
>
>
>
>
>
> David Marshall wrote:
>
>> preharvest sprouting is of particular interest. There are a number of  
>>  advances at the molecular level. It is interesting to place  
>> preharvest sprouting in the context of related processes i.e. grain  
>> development, "normal germination", dormance and in the case of  
>> barley- malting.
>>  David Marshall
>> 	-----Original Message----- 	From: owner-po-dev at plantontology.org on  
>> behalf of Tinker, Nicholas 	Sent: Tue 28/06/2005 19:05 	To: Tom  
>> Blake; Mary Polacco; po-dev at plantontology.org, Pankaj Jaiswal;  
>> POC-dev 	Cc: 	Subject: RE: [Fwd: [ geneontology-Curator  
>> requests-929957 ] vivipary]
>> 	
>> 	
>> 	But,
>> 	If an ontology defines "vivipary" as a "type of" preharvest sprouting
>> 	(or vice-versa) then won't it help the corn people do comparative
>> 	genomics with the barley people? 	
>> 	>
>> 	> Hi folks,
>> 	>    In the small grains, this is called preharvest sprouting.  It's
>> 	> well-understood, and as Mary suggests is the result of lack of seed
>> 	> dormancy
>> 	> and a wet harvest environment.  Calling it vivipary won't improve
>> 	> understanding of the process.  In both barley and wheat the  
>> genetics
>> 	of
>> 	> dormancy and of preharvest sprouting is pretty well-understood.
>> 	> Cheers,
>> 	> Tom Blake, barley breeder, Montana State University
>> 	>
>> 	> -----Original Message-----
>> 	> From: grains-request at greengenes.cit.cornell.edu
>> 	> [mailto:grains-request at greengenes.cit.cornell.edu] On Behalf Of  
>> Mary
>> 	> Polacco
>> 	> Sent: Tuesday, June 28, 2005 11:04 AM
>> 	> To: po-dev at plantontology.org, Pankaj Jaiswal; POC-dev
>> 	> Cc: Jennifer I Clark; rice-e-net at chanko.lab.nig.ac.jp;
>> 	> grains at greengenes.cit.cornell.edu
>> 	> Subject: Re: [Fwd: [ geneontology-Curator requests-929957 ]  
>> vivipary]
>> 	>
>> 	> Is there going to be consideration of the related process,  
>> dormancy?
>> 	>
>> 	> > From: Pankaj Jaiswal <pj37 at cornell.edu>
>> 	> > Reply-To: po-dev at plantontology.org, Pankaj Jaiswal
>> 	<pj37 at cornell.edu>
>> 	> > Date: Tue, 28 Jun 2005 09:57:44 -0400
>> 	> > To: POC-dev <po-dev at plantontology.org>
>> 	> > Cc: Jennifer I Clark <jenclark at ebi.ac.uk>,
>> 	> rice-e-net at chanko.lab.nig.ac.jp,
>> 	> > grains at greengenes.cit.cornell.edu
>> 	> > Subject: [Fwd: [ geneontology-Curator requests-929957 ] vivipary]
>> 	> >
>> 	> > Hi Everyone,
>> 	> >
>> 	> > I though that some people from the plant community may be  
>> interested
>> 	in
>> 	> > the discussion on adding a new term VIVIPARY (and its instances  
>> ??)
>> 	in
>> 	> > the Gene Ontology.
>> 	> >
>> 	> > Please follow the link below on the discussion
>> 	> >
>> 	>
>> 	https://sourceforge.net/tracker/? 
>> func=detail&atid=440764&aid=929957&grou
>> 	p_
>> 	> id
>> 	> =3
>> 	> > 6855
>> 	> >
>> 	> > A couple of questions are:
>> 	> >
>> 	> > #1 whether we need the two instances of a generic term VIVIPARY
>> 	> >
>> 	> > vegetative vivipary (sensu Magnoliophyta)
>> 	> > non-vegetative vivipary (sensu Magnoliophyta)
>> 	> >
>> 	> >
>> 	> > #2 Is there anything called as vegetative vivipary.
>> 	> >
>> 	> >
>> 	> > BY definition, in cereal plants or elsewhere, vivipary is  
>> defined as
>> 	> >
>> 	> > "A process promoting the germination of embryos while still  
>> attached
>> 	to
>> 	> > the mother plant. "
>> 	> >
>> 	> > -Pankaj
>> 	> >
>> 	> >
>> 	> >
>> 	> >
>> 	
>> 	
>> 	
>> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _  
>> _ _ _
>> DISCLAIMER:
>> This email is from the Scottish Crop Research Institute, but the  
>> views expressed by the sender are not necessarily the views of SCRI  
>> and its subsidiaries.  This email and any files transmitted with it  
>> are confidential to the intended recipient at the e-mail address to  
>> which it has been addressed.  It may not be disclosed or used by any  
>> other than that addressee.
>> If you are not the intended recipient you are requested to preserve  
>> this confidentiality and you must not use, disclose, copy, print or  
>> rely on this e-mail in any way. Please notify  
>> postmaster at scri.sari.ac.uk quoting the name of the sender and delete  
>> the email from your system.
>> Although SCRI has taken reasonable precautions to ensure no viruses  
>> are present in this email, neither the Institute nor the sender  
>> accepts any responsibility for any viruses, and it is your  
>> responsibility to scan the email and the attachments (if any).
>
>
Elizabeth A. Kellogg
E. Desmond Lee and Family Professor of Botanical Studies
Department of Biology
University of Missouri-St. Louis
St. Louis, MO 63121
Tel: 314-516-6217
FAX: 314-516-6233
http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ 
home.html
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From jclark at ebi.ac.uk  Tue Jul  5 04:42:56 2005
From: jclark at ebi.ac.uk (J Clark)
Date: Tue, 05 Jul 2005 09:42:56 +0100
Subject: [Fwd: [ geneontology-Curator requests-929957 ] vivipary]
In-Reply-To: <BE57D4C018CC2642AF256E2FDDA909570D6ECA@exchange1.scri.sari.ac.uk>
References: <BE57D4C018CC2642AF256E2FDDA909570D6ECA@exchange1.scri.sari.ac.uk>
Message-ID: <42CA4810.30600@ebi.ac.uk>

Further comments on vivipary have been posted at

[ 929957 ] vivipary
https://sourceforge.net/tracker/index.php?func=detail&aid=929957&group_id=36855&atid=440764

Any feedback on this would be greatly appreciated.

Thanks,

Jen



From jitterbug at tesuque.stanford.edu  Wed Jul  6 14:51:03 2005
From: jitterbug at tesuque.stanford.edu (Katica Ilic)
Date: Wed, 6 Jul 2005 11:51:03 -0700
Subject: anatomy ontology ids (fwd) (PR#2849)
Message-ID: <200507061851.j66Ip3KD022833@tesuque.stanford.edu>

Dear Helen,

I am not sure if I completely understand your question, so please tell me if I
missed something.

The following databases, TAIR, Gramene, NASC and BRENDA, all have Plant
Structure Ontology displayed on their web sites. TAIR and Gramene retired their
species-specific anatomical ontologies and switched to using exclusively Plant
Structure Ontology. Therefore,  regardless of whether you perform searches using
one of the browsers from the above databases, or whether you use Ontology
browser at the Plant Ontology Consortium (POC) web site (www.plantontology.org,
and click on the Ontology Browser on the main menu bar), each Plant Structure
Ontology term should have a unique ID, which never changes.

For instance, term 'leaf', has the following id in the Plant Ontology:
PO:0009025 and this ID is clearly displayed in POC, TAIR, Gramene and NASC
browsers.
And yes, you are right, when I used BRENDA search option, I noticed a difference
in term ID prefix, and also, 7 digit-term-id number is shortened (zeros are not
displayed):

Term: leaf 
PlA ID 
9025

What is even more confusing is that BRENDA also displays our old, retired TAIR
anatomy ontology, and there, term 'leaf' has GO prefix and also the old TAIR ID
number (as well as the old definition) - this ontology should be removed from
BRENDA, since it is no longer actively maintained or displayed and is no longer
in use. 

BRENDA also doesn't display the proper name of POC ontology, which is Plant
Structure Ontology. I will contact Christian Ebeling from BRENDA and ask them to
correct the above issues.

Since you also mentioned developmental stages ontology, this ontology is still
species-specific in Gramene and TAIR. At TAIR, we still use Arabidopsis
Developmental Stages Ontology, and term ids have TAIR prefices. Plant Ontology
Consortium is releasing Plant Part Developmental Stages Ontology this summer,
and we at TAIR are planning to adopt this new ontology by the end of the year.

GO id prefix should be associated only with GO terms, coming from three
components of the Gene Ontology.

I hope this help.

Sincerely,

Katica Ilic, TAIR Curator


 
> ---------- Forwarded message ----------
> Date: Wed, 06 Jul 2005 17:06:09 +0100
> From: Helen Parkinson <parkinson at ebi.ac.uk>
> To: curator at arabidopsis.org, Niran Abeygunawardena <niran at ebi.ac.uk>
> Subject: anatomy ontology ids
> 
> Hello TAIR people,
> 
> we are connecting to TAIR for the anatomy and dev stage and and invoking a 
> browser window from our microarray annotation tool. The dev stage ontology 
> looks OK, but the dev stage one has ids of the format
> e.g. leaf ground tissue
> 
> GO ID
> 227
> 
> Is this prefix correct?
> 
> Here's where we are getting it from, I can also contact them if necessary
> 
> http://www.brenda.uni-koeln.de/ontology/arabidopsis_gross_anatomy/tree/index.php4?f[term][value]=Arabidopsis%20anatomy
> 
> Thanks
> 
> Helen
> 
> 
> -- 
> Helen Parkinson, PhD
> Curation Coordinator
> Microarray Informatics Team, EBI
> 
> and
> 
> Seconded Scientific Programme Manager
> NCRI Cancer Informatics Initiative
> www.cancerinformatics.org.uk
> 
> Katica Ilic                             katica at acoma.stanford.edu
The Arabidopsis Information Resource    Tel: (650) 325-1521 ext. 253
Carnegie Institution of Washington      FAX: (650) 325-6857
Department of Plant Biology             URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
U.S.A.



From katica at acoma.Stanford.EDU  Wed Jul  6 17:07:35 2005
From: katica at acoma.Stanford.EDU (katica at acoma.Stanford.EDU)
Date: Wed, 6 Jul 2005 14:07:35 -0700 (PDT)
Subject: PO is listed at BRENDA enzyme database
In-Reply-To: <200501041042.55140.c.ebeling@uni-koeln.de>
References: <200501031926.j03JQ9Uq015483@brie4.cshl.org>
 <200501041042.55140.c.ebeling@uni-koeln.de>
Message-ID: <Pine.LNX.4.62.0507061309420.21344@aztec.stanford.edu>


Hi Christian,

I had contacted you earlier this year regarding Plant Structure Ontology 
that you have downloaded and displayed on your web site.

One of our users has brought to my attention that the ontology term IDs 
and prefices which are displayed on the BRENDA browser are not exactly the 
same as they are in the Plant Ontology.

For instance, term 'leaf', has the following id in the Plant Ontology:
PO:0009025

This ID is clearly displayed in the POC, TAIR, Gramene and NASC Browsers 
(all these databases have their own Plant Ontology browser tools).

Using BRENDA search option, I noticed a difference in term ID prefix, and 
also, 7 digit-term-id number is shortened (zeros are not displayed):

For instance:
Term: leaf
PlA ID
9025

The full and complete term ID for 'leaf' is PO:0009025, and since this is 
the important part of term identity, it would be good to have it displayed 
as 'PO:0009025', as it is on the POC, or any other database using Plant 
Ontologies.

Also, the correct name of the POC ontology on the BRENDA site is 'Plant 
Structure Ontology' and not 'Plant anatomy'.

Since I am the TAIR curator in charge of Plant ontologies, I also noticed 
that you have the old TAIR Arabidopsis anatomy ontology downloaded at 
BRENDA. This ontology is no longer maintained and was retired in February 
2005, when TAIR switched to using exclusively Plant Structure Ontology. 
Among other reasons (for removing Arabidopsis anatomy), it's confusing to 
have both Plant Structure Ontology and Arabidopsis Anatomy Ontology on the 
BRENDA browser, since many terms are duplicated but term IDs are 
different.

Also, how often do you update Plant Ontology files? Do you use POC cvs 
repository or SourceForge to download the most recent files?
The reason I am asking is that the most recent files are in the POC cvs 
repository, and we don't have cron job that would update Sourceforge 
regularly, it's been done manually by one of the POC curator (once a month 
or so).

URL: http://brebiou.cshl.edu/viewcvs/Poc/

I hope that you will find my comments constructive and helpful. We at POC 
are delighted to see our ontologies being displayed and used at several 
database, but at the same time, we are a bit concerned that users may not 
recognize that they are looking at the same ontology, i.e., Plant 
Structure Ontology, regardless of which database they prefer to go to. One 
way of making it easier for them is to make sure that term names and IDs 
are displayed in the standard format, and that each ontology have the same 
name in all databases wherever PO is in use. This summer, we are going to 
release a new ontology, Plant Developmental Stages Ontology, so the 
use of the proper ontology names would eliminate further confusion for users.

Best,

Katica Ilic, POC Project Coordinator



On Tue, 4 Jan 2005, Christian Ebeling wrote:

> Dear Katica Ilic,
>
> thanks for your hints. I changed the ontology name ( to  "Plant structure" )
> and the source/webpage link name ( to "Plant Ontology Consortium").
>
> Yours sincerely
> Christian Ebeling
>
> Am Montag, 3. Januar 2005 20:26 schrieb Katica Ilic:
>> Dear Christian,
>>
>> Thank you for downloading the Plant Ontology to your local browser at the
>> BRENDA enzyme database (URL:www.brenda.uni-koeln.de). I have a minor
>> comment for the web page where all the ontologies are listed, just as
>> clarification:
>>
>> The ontology is Plant Ontology, and not the Plant Ontology Consortium (to
>> be more specific, it is the Plant Structure Ontology), while the web source
>> is Plant Ontology Consortium. If you could just swap these two around, I
>> would appreciate it.
>>
>> Best Regards,
>>
>> Katica Ilic, POC Project Coordinator
>>
>>> Date: Wed, 22 Dec 2004 15:11:04 +0100
>>> From: Christian Ebeling <c.ebeling at uni-koeln.de>
>>> Reply-To: po-dev at plantontology.org, Christian Ebeling
>>
>> <c.ebeling at uni-koeln.de>
>>
>>> To: go at geneontology.org, Henning.Hermjakob at ebi.ac.uk,
>>
>> po-dev at plantontology.org,
>>
>>>      pheno at informatics.jax.org, maria at genome.stanford.edu,
>>
>> gramene at gramene.org,
>>
>>>      curator at arabidopsis.org
>>> Subject: Your ontology is listed at BRENDA enzyme database
>>>
>>> Dear curator of an ontology,
>>>
>>> we want inform you that we have integrated in our ontology browser and
>>> "Fulltext Search" engine 9 new ontologies. I inform you because your
>>> email address was listed on http://obo.sourceforge.net/cgi-bin/table.cgi
>>> as contact to your ontology.
>>>
>>> We list your ontology with a link to your webpage and an email contact.
>>>
>>> Please don't hesitate to contact me if you have found any malfunctions or
>>> if you have any suggestions.
>>>
>>> Yours sincerely
>>> Christian
>>> --
>>> Christian Ebeling
>>> www.brenda.uni-koeln.de
>>> Zuelpicher Str. 47
>>> 50674 Cologne
>>> Germany
>>
>> Katica Ilic, TAIR Curator,	     E-mail: katica at acoma.stanford.edu
>> The Arabidopsis Information Resource	Tel: (650) 325-1521 ext. 253
>> Carnegie Institution of Washington	Fax: (650) 325-6857
>> Department of Plant Biology	        URL: http://arabidopsis.org/
>> 260 Panama St.
>> Stanford, CA 94305, U.S.A.
>
>

-- 
--------------------------------------------------------------------------
Katica Ilic             		katica at acoma.stanford.edu
The Arabidopsis Information Resource 	Tel: (650) 325-1521 ext. 253
Carnegie Institution of Washington 	FAX: (650) 325-6857
Department of Plant Biology 		URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
U.S.A.
--------------------------------------------------------------------------



From parkinson at ebi.ac.uk  Thu Jul  7 05:11:06 2005
From: parkinson at ebi.ac.uk (Helen Parkinson)
Date: Thu, 07 Jul 2005 10:11:06 +0100
Subject: anatomy ontology ids (fwd) (PR#2849)
In-Reply-To: <200507061851.j66Ip3KD022833@tesuque.stanford.edu>
References: <200507061851.j66Ip3KD022833@tesuque.stanford.edu>
Message-ID: <42CCF1AA.7020305@ebi.ac.uk>

Dear Katica,

thanks for the fast response. Clearly the source of our problem is that 
Brenda are displaying the old ontology with the wrong ids. Should I 
contact them about this or do you have a contact there? The sw that I am 
testing is about to go to production and I would really rather they fix 
the ontology than I have to get the code changed.

Thanks again,

Helen



Katica Ilic wrote:

>Dear Helen,
>
>I am not sure if I completely understand your question, so please tell me if I
>missed something.
>
>The following databases, TAIR, Gramene, NASC and BRENDA, all have Plant
>Structure Ontology displayed on their web sites. TAIR and Gramene retired their
>species-specific anatomical ontologies and switched to using exclusively Plant
>Structure Ontology. Therefore,  regardless of whether you perform searches using
>one of the browsers from the above databases, or whether you use Ontology
>browser at the Plant Ontology Consortium (POC) web site (www.plantontology.org,
>and click on the Ontology Browser on the main menu bar), each Plant Structure
>Ontology term should have a unique ID, which never changes.
>
>For instance, term 'leaf', has the following id in the Plant Ontology:
>PO:0009025 and this ID is clearly displayed in POC, TAIR, Gramene and NASC
>browsers.
>And yes, you are right, when I used BRENDA search option, I noticed a difference
>in term ID prefix, and also, 7 digit-term-id number is shortened (zeros are not
>displayed):
>
>Term: leaf 
>PlA ID 
>9025
>
>What is even more confusing is that BRENDA also displays our old, retired TAIR
>anatomy ontology, and there, term 'leaf' has GO prefix and also the old TAIR ID
>number (as well as the old definition) - this ontology should be removed from
>BRENDA, since it is no longer actively maintained or displayed and is no longer
>in use. 
>
>BRENDA also doesn't display the proper name of POC ontology, which is Plant
>Structure Ontology. I will contact Christian Ebeling from BRENDA and ask them to
>correct the above issues.
>
>Since you also mentioned developmental stages ontology, this ontology is still
>species-specific in Gramene and TAIR. At TAIR, we still use Arabidopsis
>Developmental Stages Ontology, and term ids have TAIR prefices. Plant Ontology
>Consortium is releasing Plant Part Developmental Stages Ontology this summer,
>and we at TAIR are planning to adopt this new ontology by the end of the year.
>
>GO id prefix should be associated only with GO terms, coming from three
>components of the Gene Ontology.
>
>I hope this help.
>
>Sincerely,
>
>Katica Ilic, TAIR Curator
>
>
> 
>  
>
>>---------- Forwarded message ----------
>>Date: Wed, 06 Jul 2005 17:06:09 +0100
>>From: Helen Parkinson <parkinson at ebi.ac.uk>
>>To: curator at arabidopsis.org, Niran Abeygunawardena <niran at ebi.ac.uk>
>>Subject: anatomy ontology ids
>>
>>Hello TAIR people,
>>
>>we are connecting to TAIR for the anatomy and dev stage and and invoking a 
>>browser window from our microarray annotation tool. The dev stage ontology 
>>looks OK, but the dev stage one has ids of the format
>>e.g. leaf ground tissue
>>
>>GO ID
>>227
>>
>>Is this prefix correct?
>>
>>Here's where we are getting it from, I can also contact them if necessary
>>
>>http://www.brenda.uni-koeln.de/ontology/arabidopsis_gross_anatomy/tree/index.php4?f[term][value]=Arabidopsis%20anatomy
>>
>>Thanks
>>
>>Helen
>>
>>
>>-- 
>>Helen Parkinson, PhD
>>Curation Coordinator
>>Microarray Informatics Team, EBI
>>
>>and
>>
>>Seconded Scientific Programme Manager
>>NCRI Cancer Informatics Initiative
>>www.cancerinformatics.org.uk
>>
>>Katica Ilic                             katica at acoma.stanford.edu
>>    
>>
>The Arabidopsis Information Resource    Tel: (650) 325-1521 ext. 253
>Carnegie Institution of Washington      FAX: (650) 325-6857
>Department of Plant Biology             URL: http://arabidopsis.org/
>260 Panama St.
>Stanford, CA 94305
>U.S.A.
>  
>

-- 
Helen Parkinson, PhD
Curation Coordinator
Microarray Informatics Team, 
EBI

and

Seconded Scientific Programme Manager
NCRI Cancer Informatics Initiative
www.cancerinformatics.org.uk




From jitterbug at tesuque.stanford.edu  Thu Jul  7 14:10:05 2005
From: jitterbug at tesuque.stanford.edu (Katica Ilic)
Date: Thu, 7 Jul 2005 11:10:05 -0700
Subject: anatomy ontology ids (fwd) (PR#2849)
Message-ID: <200507071810.j67IA5eW028340@tesuque.stanford.edu>

Dear Helen,

You are very welcome. Let me know if you need anything else. I already contacted
Christian Ebeling from BRENDA yesterday, and asked him to remove TAIR Anatomy
ontology from their browser and to use proper prefix in the term IDs for the PO
terms; haven't heard from him yet. I'll keep you updated. For the time being you
can still use PO and TAIR terms displayed at BRENDA, just specify 'Plant
Structure Ontology', in fact, Plant anatomy is what they have there (I asked for
the name change too) and Arabidopsis Developmental Stage Ontology, and that
would be sufficient to avoid confusion.The latter one should have TAIR in the
prefix; however they don't have any, so I'll ask Christian to add these prefices
to Arabidopsis dev stage terms.   

Helen, I want to ask you for a little favor. We are conducting a user survey at
the Plant Onotlogy Consortium, and I would like to know how you and people at
EBI are using Plant Ontology terms. If you call just briefly describe it, I
would appreciate it very much.

Thanks,

Katica

> Dear Katica,
> 
> thanks for the fast response. Clearly the source of our problem is that 
> Brenda are displaying the old ontology with the wrong ids. Should I 
> contact them about this or do you have a contact there? The sw that I am 
> testing is about to go to production and I would really rather they fix 
> the ontology than I have to get the code changed.
> 
> Thanks again,
> 
> Helen
> 
> 
> 
> Katica Ilic wrote:
> 
>>Dear Helen,
>>
>>I am not sure if I completely understand your question, so please tell me if
I
>>missed something.
>>
>>The following databases, TAIR, Gramene, NASC and BRENDA, all have Plant
>>Structure Ontology displayed on their web sites. TAIR and Gramene retired
their
>>species-specific anatomical ontologies and switched to using exclusively
Plant
>>Structure Ontology. Therefore,  regardless of whether you perform searches
> using
>>one of the browsers from the above databases, or whether you use Ontology
>>browser at the Plant Ontology Consortium (POC) web site
(www.plantontology.org,
>>and click on the Ontology Browser on the main menu bar), each Plant Structure
>>Ontology term should have a unique ID, which never changes.
>>
>>For instance, term 'leaf', has the following id in the Plant Ontology:
>>PO:0009025 and this ID is clearly displayed in POC, TAIR, Gramene and NASC
>>browsers.
>>And yes, you are right, when I used BRENDA search option, I noticed a
> difference
>>in term ID prefix, and also, 7 digit-term-id number is shortened (zeros are
not
>>displayed):
>>
>>Term: leaf 
>>PlA ID 
>>9025
>>
>>What is even more confusing is that BRENDA also displays our old, retired
TAIR
>>anatomy ontology, and there, term 'leaf' has GO prefix and also the old TAIR
ID
>>number (as well as the old definition) - this ontology should be removed from
>>BRENDA, since it is no longer actively maintained or displayed and is no
longer
>>in use. 
>>
>>BRENDA also doesn't display the proper name of POC ontology, which is Plant
>>Structure Ontology. I will contact Christian Ebeling from BRENDA and ask them
> to
>>correct the above issues.
>>
>>Since you also mentioned developmental stages ontology, this ontology is
still
>>species-specific in Gramene and TAIR. At TAIR, we still use Arabidopsis
>>Developmental Stages Ontology, and term ids have TAIR prefices. Plant
Ontology
>>Consortium is releasing Plant Part Developmental Stages Ontology this summer,
>>and we at TAIR are planning to adopt this new ontology by the end of the
year.
>>
>>GO id prefix should be associated only with GO terms, coming from three
>>components of the Gene Ontology.
>>
>>I hope this help.
>>
>>Sincerely,
>>
>>Katica Ilic, TAIR Curator
>>
>>
>> 
>>  
>>
>>>---------- Forwarded message ----------
>>>Date: Wed, 06 Jul 2005 17:06:09 +0100
>>>From: Helen Parkinson <parkinson at ebi.ac.uk>
>>>To: curator at arabidopsis.org, Niran Abeygunawardena <niran at ebi.ac.uk>
>>>Subject: anatomy ontology ids
>>>
>>>Hello TAIR people,
>>>
>>>we are connecting to TAIR for the anatomy and dev stage and and invoking a 
>>>browser window from our microarray annotation tool. The dev stage ontology 
>>>looks OK, but the dev stage one has ids of the format
>>>e.g. leaf ground tissue
>>>
>>>GO ID
>>>227
>>>
>>>Is this prefix correct?
>>>
>>>Here's where we are getting it from, I can also contact them if necessary
>>>
>>>http://www.brenda.uni-koeln.de/ontology/arabidopsis_gross_anatomy/tree/index.php4?f[term][value]=Arabidopsis%20anatomy
>>>
>>>Thanks
>>>
>>>Helen
>>>
>>>
>>>-- 
>>>Helen Parkinson, PhD
>>>Curation Coordinator
>>>Microarray Informatics Team, EBI
>>>
>>>and
>>>
>>>Seconded Scientific Programme Manager
>>>NCRI Cancer Informatics Initiative
>>>www.cancerinformatics.org.uk
>>>
>>>Katica Ilic                             katica at acoma.stanford.edu
>>>    
>>>
>>The Arabidopsis Information Resource    Tel: (650) 325-1521 ext. 253
>>Carnegie Institution of Washington      FAX: (650) 325-6857
>>Department of Plant Biology             URL: http://arabidopsis.org/
>>260 Panama St.
>>Stanford, CA 94305
>>U.S.A.
>>  
>>
> 
> -- 
> Helen Parkinson, PhD
> Curation Coordinator
> Microarray Informatics Team, 
> EBI
> 
> and
> 
> Seconded Scientific Programme Manager
> NCRI Cancer Informatics Initiative
> www.cancerinformatics.org.uk
> 
> 
> 



From jclark at ebi.ac.uk  Fri Jul 29 06:39:20 2005
From: jclark at ebi.ac.uk (J Clark)
Date: Fri, 29 Jul 2005 11:39:20 +0100
Subject: Gene Ontology Terms
In-Reply-To: <42C15758.8030205@cornell.edu>
References: <42C15758.8030205@cornell.edu>
Message-ID: <42EA0758.60804@ebi.ac.uk>

Hi,

We are adding some terms to the Gene Ontology to cover processes related to 
vivipary and somatic embryogenesis and I would be very interested to have some 
feedback from the members of this list. Would it be possible to take a look at 
the discussion threads on these topics and let me know what you think?

[ 1247346 ] somatic embryogenesis
https://sourceforge.net/tracker/index.php?func=detail&aid=1247346&group_id=36855&atid=440764

[ 929957 ] vivipary
https://sourceforge.net/tracker/index.php?func=detail&aid=929957&group_id=36855&atid=440764

For those who do not have sourceforge passwords I would be very pleased to 
receive comments by e-mail.

Thanks,

Jen