From cwt6 at cornell.edu  Fri Sep  7 10:43:22 2007
From: cwt6 at cornell.edu (Chih-Wei Tung)
Date: Fri, 7 Sep 2007 10:43:22 -0400
Subject: [Po-dev] Plant Ontology Database Release-September 2007
Message-ID: <5A7863B5-2F12-448B-808A-B8F255E59020@cornell.edu>

Plant Ontology Consortium is happy to announce the release #0907 of  
PO database!
http://www.plantontology.org

* Ontology update
	- 1109 PO terms
	- 32104 annotations
	visit http://www.plantontology.org/docs/release_notes/index.html for  
more details

* New version of PO browser (http://www.plantontology.org/amigo/go.cgi)
	- New interface
	- New users guide
	- New tutorials
	- New feature: added "GO" (Gene Ontology) associations link to  
Arabidopsis genes

* POC Website updates (http://www.plantontology.org/)
	- added "Request PO terms" feature on navigation menu
	- added "POC Outreach Activities" link in "Documentation" page
	- Updated "Mail Archives"
	- Updated "PO website usage statistics"
	- Updated "Tutorials"

* POC and plant community
	- Welcome experts from Medicago, Populus, Rosaceae, Solanaceae,  
Vitis fields to join plant ontology development
		Please email to po-dev at plantontology.org or subscribe po-dev  
mailing list

	- Phenote (a phenotype annotation tool using ontologies http:// 
www.phenote.org/) has added "plant" configuration, plus PO and other  
plant related ontologies for curation.
		Contact Nicole Washington ( NLWashington at lbl.gov ) for more  
information about downloading and using Phenote tool

	- Meet POC members in international conferences
		@ 8th Agricultural Ontology Service (AOS) workshop, Rome, Italy   
Sep 21-22
		@ 5th International Symposium of Rice Functional Genomics, Tsukuba,  
Japan Oct 15-17
		@ 2nd International Biocuration meeting, San Jose, CA Oct 25-28



The Plant Ontology Consortium
web: http:www.plantontology.org
e-mail: po-dev at plantontology.org
submit requests at:
http://sourceforge.net/tracker/?func=add&group_id=76834&atid=835555

	



From cwt6 at cornell.edu  Fri Sep  7 11:43:17 2007
From: cwt6 at cornell.edu (Chih-Wei Tung)
Date: Fri, 7 Sep 2007 11:43:17 -0400
Subject: [Po-dev] Fwd: Terminology of Apple Fruit Tissues
References: <p0623090fc3060bb307af@[132.236.10.73]>
Message-ID: <C70C9480-351B-4E85-B07C-C9CCCE13B28C@cornell.edu>



Begin forwarded message:

> From: "Martin C. Goffinet" <mcg2 at nysaes.cornell.edu>
> Date: September 6, 2007 4:49:37 PM EDT
> To: cwt6 at cornell.edu
> Cc: skb3 at nysaes.cornell.edu
> Subject: Terminology of Apple Fruit Tissues
>
> To Chih-Wei Tung:
>
> Because I am a plant anatomist with some experience in apple fruit  
> structure and development, Professor Susan Brown has forwarded your  
> email to me concerning the terminology of apple fruit tissues.   
> Below and in the attached scan of a few drawings from a 1942 paper,  
> I will try to give you my perspective on this issue.
>
> The "fruit cortex" of apple is specifically the tissue between the  
> skin and the 10 large vascular bundles as seen in an equatorial  
> cross section of the fruit.  The "pith" is that tissue inside these  
> 10 bundles but outside the horseshoe-shaped region (the carpellary  
> tissue) that surrounds each seed locule within the fruit.  We eat  
> both the cortex and pith tissues and consider them to make up the  
> flesh in mature fruit.  In general, the core is the part of the  
> fruit not eaten.  This typically contains the seeds, surrounding  
> leathery pericarp (some would say endocarp), and any adherent  
> softer tissue that may be considered pericarp, as interpreted by  
> those who claim that the pome fruit is a receptacle overarching and  
> embedding five individual carpels.  This is the view taken by the  
> authors of the information in the attached drawings, a view that  
> provides much of the terminology we most use today in describing  
> apple anatomy.  I use this terminology, although I am not a  
> disciple of this school of thought, but it does provide a common  
> language for descriptive purposes.  The two schools of thought of  
> this, for apple, are presented in the review of Charlotte Pratt  
> (C.Pratt. 1988. Apple Flower and Fruit: Morphology and Anatomy.   
> Horticultural Reviews 10: 273-308.).
>
> So, the fruit "cortex" is NOT the same as  "flesh" or "mesocarp,"  
> but is a region that makes up the flesh.  Pericarp, mesocarp,  
> endocarp, and exocarp are simple topographic, descriptive terms  
> that reference the tissue by its position within the fruit.  Cortex  
> thus is a component of the mesocarp, while the skin is described as  
> the exocarp by some authors.
>
> The placenta is a region or zone along each carpel that erupts into  
> the ovules, typically where (during floral development) the two  
> longitudinal margins of each carpel's ovarian region fold and  
> converge upon each other.  In the case of apple, each of the two  
> placental regions of each carpel will develop one ovule that, later  
> on, will develop into a mature seed.   Therefore, the description  
> of the fruit placenta as a "more or less localized region within a  
> fruit to  which seeds are attached" is correct; the placenta cannot  
> be synonymous with fruit core.  The apple fruit has one fruit core  
> but 10 enfolded carpel margins each with a placental region.
>
> I don't know if this helps or confuses you even more.  The  
> interpretation of the pome fruit remains a complicated issue and by  
> no means will there be agreement any time soon.
>
> Sincerely yours,
>
> Martin Goffinet
> Senior Research Associate
>
> -- 
> Martin C. Goffinet, Ph.D.		          Ph: 315-787-2392
> Cornell University		          Fax: 315-787-2216
> Department of Horticultural Sciences	          Web: http:// 
> www.nysaes.cornell.edu/hort/faculty/goffinet/
> New York State Agricultural Experiment Station
> 630 W. North Street
> Geneva, NY 14456?
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From cwt6 at cornell.edu  Fri Sep  7 15:08:47 2007
From: cwt6 at cornell.edu (Chih-Wei Tung)
Date: Fri, 7 Sep 2007 15:08:47 -0400
Subject: Fwd: [Po-dev] Fwd: Terminology of Apple Fruit Tissues
References: <7746E8E0-BE69-4284-9963-2194BCCBBFDB@mobot.org>
Message-ID: <4B3FEA2D-F1E4-4CBE-9A0E-DF586E331298@cornell.edu>


Begin forwarded message:

> From: Peter Stevens <peter.stevens at mobot.org>
> Date: September 7, 2007 1:18:19 PM EDT
> To: Chih-Wei Tung <cwt6 at cornell.edu>
> Subject: Re: [Po-dev] Fwd: Terminology of Apple Fruit Tissues
>
> OK, I followed you until this paragraph:
>
> So, the fruit "cortex" is NOT the same as  "flesh" or "mesocarp,"  
> but is a region that makes up the flesh.  Pericarp, mesocarp,  
> endocarp, and exocarp are simple topographic, descriptive terms  
> that reference the tissue by its position within the fruit.  Cortex  
> thus is a component of the mesocarp, while the skin is described as  
> the exocarp by some authors.
>
> If the apple fruit is the product of an inferior ovary, whatever  
> the mechanism by which the ovary became inferior (i.e. axial or  
> appendicular), the skin is surely not  the exocarp, which is a term  
> applied to the fruit proper, and similarly the apple cortex is not  
> a component of the mesocarp (if anything, it would be the other way  
> around), and the meso- exo- and endocarps are a tad more than  
> descriptive terms (what terms are not?), but refer specifically to  
> fruits proper, i.e. a carpel/s at the time of dispersal of the seed.
>
> P.
>
>
> On Sep 7, 2007, at 10:43 AM, Chih-Wei Tung wrote:
>
>>
>>
>> Begin forwarded message:
>>
>>> From: "Martin C. Goffinet" <mcg2 at nysaes.cornell.edu>
>>> Date: September 6, 2007 4:49:37 PM EDT
>>> To: cwt6 at cornell.edu
>>> Cc: skb3 at nysaes.cornell.edu
>>> Subject: Terminology of Apple Fruit Tissues
>>>
>>> To Chih-Wei Tung:
>>>
>>> Because I am a plant anatomist with some experience in apple  
>>> fruit structure and development, Professor Susan Brown has  
>>> forwarded your email to me concerning the terminology of apple  
>>> fruit tissues.  Below and in the attached scan of a few drawings  
>>> from a 1942 paper, I will try to give you my perspective on this  
>>> issue.
>>>
>>> The "fruit cortex" of apple is specifically the tissue between  
>>> the skin and the 10 large vascular bundles as seen in an  
>>> equatorial cross section of the fruit.  The "pith" is that tissue  
>>> inside these 10 bundles but outside the horseshoe-shaped region  
>>> (the carpellary tissue) that surrounds each seed locule within  
>>> the fruit.  We eat both the cortex and pith tissues and consider  
>>> them to make up the flesh in mature fruit.  In general, the core  
>>> is the part of the fruit not eaten.  This typically contains the  
>>> seeds, surrounding leathery pericarp (some would say endocarp),  
>>> and any adherent softer tissue that may be considered pericarp,  
>>> as interpreted by those who claim that the pome fruit is a  
>>> receptacle overarching and embedding five individual carpels.   
>>> This is the view taken by the authors of the information in the  
>>> attached drawings, a view that provides much of the terminology  
>>> we most use today in describing apple anatomy.  I use this  
>>> terminology, although I am not a disciple of this school of  
>>> thought, but it does provide a common language for descriptive  
>>> purposes.  The two schools of thought of this, for apple, are  
>>> presented in the review of Charlotte Pratt (C.Pratt. 1988. Apple  
>>> Flower and Fruit: Morphology and Anatomy.  Horticultural Reviews  
>>> 10: 273-308.).
>>>
>>> So, the fruit "cortex" is NOT the same as  "flesh" or "mesocarp,"  
>>> but is a region that makes up the flesh.  Pericarp, mesocarp,  
>>> endocarp, and exocarp are simple topographic, descriptive terms  
>>> that reference the tissue by its position within the fruit.   
>>> Cortex thus is a component of the mesocarp, while the skin is  
>>> described as the exocarp by some authors.
>>>
>>> The placenta is a region or zone along each carpel that erupts  
>>> into the ovules, typically where (during floral development) the  
>>> two longitudinal margins of each carpel's ovarian region fold and  
>>> converge upon each other.  In the case of apple, each of the two  
>>> placental regions of each carpel will develop one ovule that,  
>>> later on, will develop into a mature seed.   Therefore, the  
>>> description of the fruit placenta as a "more or less localized  
>>> region within a fruit to  which seeds are attached" is correct;  
>>> the placenta cannot be synonymous with fruit core.  The apple  
>>> fruit has one fruit core but 10 enfolded carpel margins each with  
>>> a placental region.
>>>
>>> I don't know if this helps or confuses you even more.  The  
>>> interpretation of the pome fruit remains a complicated issue and  
>>> by no means will there be agreement any time soon.
>>>
>>> Sincerely yours,
>>>
>>> Martin Goffinet
>>> Senior Research Associate
>>>
>>> -- 
>>> Martin C. Goffinet, Ph.D.		          Ph: 315-787-2392
>>> Cornell University		          Fax: 315-787-2216
>>> Department of Horticultural Sciences	          Web: http:// 
>>> www.nysaes.cornell.edu/hort/faculty/goffinet/
>>> New York State Agricultural Experiment Station
>>> 630 W. North Street
>>> Geneva, NY 14456
>> <AppleTissue.jpg>
>>
>> _______________________________________________
>> Po-dev mailing list
>> Po-dev at plantontology.org
>> http://mail.plantontology.org/mailman/listinfo/po-dev
>

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From SchaefferM at missouri.edu  Mon Sep 24 17:39:41 2007
From: SchaefferM at missouri.edu (Mary (Polacco) Schaeffer)
Date: Mon, 24 Sep 2007 16:39:41 -0500
Subject: [Po-dev] Questions about associations
Message-ID: <C31D98CD.11AC9%SchaefferM@missouri.edu>

Shuly, Chih-Wei and group.

Getting ready to send in new MaizeGDB associations files and have a few
questions about format since I last did this.

Looking at  the cvs, it seem we are taking in associations to:
    genes
    QTL
    stocks or germplasm (Mutant)
QUESTION: Others? 

It seems on our new, and rather swank interface, that there is a slot for
?sequence? and when null, it states:
      No peptide sequence available.
For example, look up pericarp,
     then the Arabidopsis gene ?CYP707A1?
But, when I look at the record in question at TAIR, it seems there must be
some peptide sequence.
QUESTOIN: So, what is this field all about? OR rather, what must be done to
populate it?

In the same record, there is a column indicating that it has a GO
association?
QUESTION: how does that get into the PO browser?


Is there anything else I should be doing?

     Mary

  
-- 
> Mary Schaeffer, PhD (f/k/a Mary Polacco)
> Geneticist/Curator MaizeGDB
> USDA/ARS Plant Genetics Research Unit
> 203 Curtis Hall
> Adj Assoc Professor
> Division of Plant Sciences
> University of Missouri
> Columbia, MO 65211
> Phone: 573 884 7873
> FAX: 573 884 7850




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From cwt6 at cornell.edu  Mon Sep 24 19:49:05 2007
From: cwt6 at cornell.edu (Chih-Wei Tung)
Date: Mon, 24 Sep 2007 19:49:05 -0400
Subject: [Po-dev] Re: Questions about associations
In-Reply-To: <C31D98CD.11AC9%SchaefferM@missouri.edu>
References: <C31D98CD.11AC9%SchaefferM@missouri.edu>
Message-ID: <3C5D501D-4509-42DB-9D3B-2976B4A75667@cornell.edu>

Hi Mary,

Please find my answers below. You are welcome to add your comments.

Chih-Wei


On Sep 24, 2007, at 5:39 PM, Mary (Polacco) Schaeffer wrote:

> Shuly, Chih-Wei and group.
>
> Getting ready to send in new MaizeGDB associations files and have a  
> few questions about format since I last did this.
>
> Looking at  the cvs, it seem we are taking in associations to:
>     genes
>     QTL
>     stocks or germplasm (Mutant)
> QUESTION: Others?

As described in the association file format page, one of gene,  
transcript, protein, protein structure, complex, germplasm, QTL etc  
are accepted in POC at this moment.  Regarding to "alleles", we  
haven't figured out a best way to store and display this information,  
do you have any maize alleles annotated to PO?

>
> It seems on our new, and rather swank interface, that there is a  
> slot for ?sequence? and when null, it states:
>       No peptide sequence available.
> For example, look up pericarp,
>      then the Arabidopsis gene ?CYP707A1?
> But, when I look at the record in question at TAIR, it seems there  
> must be some peptide sequence.
> QUESTOIN: So, what is this field all about? OR rather, what must be  
> done to populate it?

Right now, we are not planning to bring any sequence information to  
PO browser. This field is a default in AmiGO browser (Shuly can  
confirm this), GOC displays peptide information in this field.

>
> In the same record, there is a column indicating that it has a GO  
> association?
> QUESTION: how does that get into the PO browser?
>

What Shuly did is she retrieved TAIR's gene_associations file from  
GO's website and compared all the gene products to TAIR's gene  
association files (anatomy and temporal) to PO, and extracted all the  
genes that exist in both, associations to GO and to PO.

I just checked GOC database and didn't find any maize gene products,  
are you planning to provide any maize GO annotations to them?

>
> Is there anything else I should be doing?
>
>      Mary

As long as your association files follow the guideline http:// 
www.plantontology.org/docs/otherdocs/assoc-file-format.html, you can  
submit the files any time.

Chih-Wei





> -- 
>> Mary Schaeffer, PhD (f/k/a Mary Polacco)
>> Geneticist/Curator MaizeGDB
>> USDA/ARS Plant Genetics Research Unit
>> 203 Curtis Hall
>> Adj Assoc Professor
>> Division of Plant Sciences
>> University of Missouri
>> Columbia, MO 65211
>> Phone: 573 884 7873
>> FAX: 573 884 7850
>
>
>

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From cwt6 at cornell.edu  Tue Sep 25 10:49:20 2007
From: cwt6 at cornell.edu (Chih-Wei Tung)
Date: Tue, 25 Sep 2007 10:49:20 -0400
Subject: [Po-dev] Fwd: Terminology of Apple Fruit Tissues
References: <p06230900c316c6b0ac64@[132.236.10.73]>
Message-ID: <22FB3B04-6F68-4C95-AAF8-6D3C720DA11F@cornell.edu>



Begin forwarded message:

> From: "Martin C. Goffinet" <mcg2 at nysaes.cornell.edu>
> Date: September 19, 2007 9:30:49 AM EDT
> To: peter.stevens at mobot.org
> Cc: skb3 at nysaes.cornell.edu, cwt6 at cornell.edu
> Subject: Re: Terminology of Apple Fruit Tissues
>
> To Peter Stevens,
>
> As a rejoiner to your comments at the bottom, I offer up the  
> following comments.  Several botanical dictionaries define cortex  
> as the tissue between the main vascular bundles and the epidermis,  
> whether of the primary construction of a stem, a root, or apple  
> fruit.  Because, in the apple, the cortex is only one of the two  
> main flesh regions (the other being "pith"), one cannot say that  
> the cortex is synonymous with "flesh," but that cortex is a major  
> component of the flesh.  Pericarp is defined as the wall of a  
> fructified ovary -- pretty generic and topographic, as I interpret  
> it.  If pericarp is topographic, then so are the regions defined as  
> composing the pericarp of apple, i.e., endocarp, mesocarp, and  
> exocarp.  These three regions differ vastly among the angiosperms  
> as to what each includes as tissue, thus no specific organogenetic  
> pattern or homology of organs or tissues can be universally defined  
> under those three terms.  I know of no text that applies the term  
> exocarp as the sole definition of the fruit.  Rather, exocarp is  
> universally recognized by botanists as the outer region of the  
> fruit, usually including the epidermis and subjacent hypodermal  
> cell layers.  In the case of apple, the exocarp and skin can be  
> thought of as one and the same, bearing in mind that the skin is  
> composed of very specific cells in apple fruit: waxy cuticle,  
> epidermal cell layer, and a hypodermal layer of several cells.
>
> I don't know if this helps clarify the debate, but if not, please  
> email again.
>
> Martin Goffinet
> ----------------
>
>> Begin forwarded message:
>>
>>> From: Peter Stevens <peter.stevens at mobot.org>
>>> Date: September 7, 2007 1:18:19 PM EDT
>>> To: Chih-Wei Tung <cwt6 at cornell.edu>
>>> Subject: Re: [Po-dev] Fwd: Terminology of Apple Fruit Tissues
>>>
>>> OK, I followed you until this paragraph:
>>>
>>> So, the fruit "cortex" is NOT the same as  "flesh" or "mesocarp,"  
>>> but is a region that makes up the flesh.  Pericarp, mesocarp,  
>>> endocarp, and exocarp are simple topographic, descriptive terms  
>>> that reference the tissue by its position within the fruit.   
>>> Cortex thus is a component of the mesocarp, while the skin is  
>>> described as the exocarp by some authors.
>>>
>>> If the apple fruit is the product of an inferior ovary, whatever  
>>> the mechanism by which the ovary became inferior (i.e. axial or  
>>> appendicular), the skin is surely not  the exocarp, which is a  
>>> term applied to the fruit proper, and similarly the apple cortex  
>>> is not a component of the mesocarp (if anything, it would be the  
>>> other way around), and the meso- exo- and endocarps are a tad  
>>> more than descriptive terms (what terms are not?), but refer  
>>> specifically to fruits proper, i.e. a carpel/s at the time of  
>>> dispersal of the seed.
>>>
>>> P.
>
> -- 
> Martin C. Goffinet, Ph.D.                         Ph: 315-787-2392
> Cornell University                        Fax: 315-787-2216
> Department of Horticultural Sciences              Web: http:// 
> www.nysaes.cornell.edu/hort/faculty/goffinet/
> New York State Agricultural Experiment Station
> 630 W. North Street
> Geneva, NY 14456
>

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From schaefferm at missouri.edu  Tue Sep 25 11:18:36 2007
From: schaefferm at missouri.edu (Schaeffer, Mary L.)
Date: Tue, 25 Sep 2007 10:18:36 -0500
Subject: [Po-dev] RE: Questions about associations
References: <C31D98CD.11AC9%SchaefferM@missouri.edu>
	<3C5D501D-4509-42DB-9D3B-2976B4A75667@cornell.edu>
Message-ID: <47AC1680CE7A8D47ADEA137C742D095D1A61CD@UM-XMAIL07.um.umsystem.edu>


Many Thanks Chih-Wei,
That was most helpful, especially the very quick reply!

Yes we do have alleles annotated to PO. Many  more than genes in fact as most of the annotation is directly to the mostly mutant alleles. Since  you list mutants as acceptable objects for association, I assume you mean alleles other than mutant? 

At this time there are no GO annotations, other than electronic for maize, but not in MaizeGDB, but other places (PlantGDB, TIGR) and none are not at the GO place.

Looking at the format page for associations, it is not clear how you wish the growth/anatomy/development sorted out. It seems that  you wish them handled separatedly,ie 3 different files, or aspects, but to use only 2 codes in the aspect column: A (anatomy) or G(growth, development).
QUESTION: is that what you mean? Or can I lump the growth and development together since they are both aspect='G'?

 mary


-----Original Message-----
From: Chih-Wei Tung [mailto:cwt6 at cornell.edu]
Sent: Mon 9/24/2007 6:49 PM
To: Schaeffer, Mary L.
Cc: Shuly Avraham; po-dev at plantontology.org
Subject: Re: Questions about associations
 
Hi Mary,

Please find my answers below. You are welcome to add your comments.

Chih-Wei


On Sep 24, 2007, at 5:39 PM, Mary (Polacco) Schaeffer wrote:

> Shuly, Chih-Wei and group.
>
> Getting ready to send in new MaizeGDB associations files and have a  
> few questions about format since I last did this.
>
> Looking at  the cvs, it seem we are taking in associations to:
>     genes
>     QTL
>     stocks or germplasm (Mutant)
> QUESTION: Others?

As described in the association file format page, one of gene,  
transcript, protein, protein structure, complex, germplasm, QTL etc  
are accepted in POC at this moment.  Regarding to "alleles", we  
haven't figured out a best way to store and display this information,  
do you have any maize alleles annotated to PO?

>
> It seems on our new, and rather swank interface, that there is a  
> slot for 'sequence' and when null, it states:
>       No peptide sequence available.
> For example, look up pericarp,
>      then the Arabidopsis gene 'CYP707A1'
> But, when I look at the record in question at TAIR, it seems there  
> must be some peptide sequence.
> QUESTOIN: So, what is this field all about? OR rather, what must be  
> done to populate it?

Right now, we are not planning to bring any sequence information to  
PO browser. This field is a default in AmiGO browser (Shuly can  
confirm this), GOC displays peptide information in this field.

>
> In the same record, there is a column indicating that it has a GO  
> association?
> QUESTION: how does that get into the PO browser?
>

What Shuly did is she retrieved TAIR's gene_associations file from  
GO's website and compared all the gene products to TAIR's gene  
association files (anatomy and temporal) to PO, and extracted all the  
genes that exist in both, associations to GO and to PO.

I just checked GOC database and didn't find any maize gene products,  
are you planning to provide any maize GO annotations to them?

>
> Is there anything else I should be doing?
>
>      Mary

As long as your association files follow the guideline http:// 
www.plantontology.org/docs/otherdocs/assoc-file-format.html, you can  
submit the files any time.

Chih-Wei





> -- 
>> Mary Schaeffer, PhD (f/k/a Mary Polacco)
>> Geneticist/Curator MaizeGDB
>> USDA/ARS Plant Genetics Research Unit
>> 203 Curtis Hall
>> Adj Assoc Professor
>> Division of Plant Sciences
>> University of Missouri
>> Columbia, MO 65211
>> Phone: 573 884 7873
>> FAX: 573 884 7850
>
>
>





From msachs at uiuc.edu  Tue Sep 25 11:27:14 2007
From: msachs at uiuc.edu (Marty Sachs)
Date: Tue, 25 Sep 2007 10:27:14 -0500
Subject: [Po-dev] RE: Questions about associations
In-Reply-To: <47AC1680CE7A8D47ADEA137C742D095D1A61CD@UM-XMAIL07.um.umsystem.edu>
References: <C31D98CD.11AC9%SchaefferM@missouri.edu>
	<3C5D501D-4509-42DB-9D3B-2976B4A75667@cornell.edu>
	<47AC1680CE7A8D47ADEA137C742D095D1A61CD@UM-XMAIL07.um.umsystem.edu>
Message-ID: <p06240804c31ed8812373@[130.126.89.70]>

At 10:18 AM -0500 9/25/07, Schaeffer, Mary L. wrote:
>I assume you mean alleles other than mutant?

Huh?  All alleles differ from each other due to mutation.  Many may 
not be induced by a researcher in a lab setting, but natural allelic 
variation is also due to mutation.

	-Marty


From pj37 at cornell.edu  Tue Sep 25 11:53:15 2007
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Tue, 25 Sep 2007 11:53:15 -0400
Subject: [Po-dev] RE: Questions about associations
In-Reply-To: <p06240804c31ed8812373@[130.126.89.70]>
References: <C31D98CD.11AC9%SchaefferM@missouri.edu>	<3C5D501D-4509-42DB-9D3B-2976B4A75667@cornell.edu>	<47AC1680CE7A8D47ADEA137C742D095D1A61CD@UM-XMAIL07.um.umsystem.edu>
	<p06240804c31ed8812373@[130.126.89.70]>
Message-ID: <46F92EEB.4040204@cornell.edu>

Marty Sachs wrote:
> At 10:18 AM -0500 9/25/07, Schaeffer, Mary L. wrote:
>> I assume you mean alleles other than mutant?
> 
> Huh?  All alleles differ from each other due to mutation.  Many may not 
> be induced by a researcher in a lab setting, but natural allelic 
> variation is also due to mutation.
> 
>     -Marty
> _______________________________________________
> Po-dev mailing list
> Po-dev at plantontology.org
> http://mail.plantontology.org/mailman/listinfo/po-dev
> 

If I remember it correctly, this came up for discussion at the 2006 POC 
meeting at PAG. Chih-wei can you dig out the notes from the meeting?

To avoid this controversy of natural variations vs induced variation we 
can simply use 'variation' or 'variant' instead of mutant/allele. In any 
case, the best to start is map the variant annotations to the gene and 
use the WITH column in the association file to effectively that an 
annotation to PO term to a gene is based on the inference derived from 
(WITH) allele (in your case).

Pl take a look at the association file format section of 
http://plantontology.org/docs/otherdocs/assoc-file-format.html
there in the column-8 one can enter the allele symbol suggesting that 
the maize gene annotation to PO term is derived from allele so and so.

I will be happy to talk to you guys sometime on Friday afternoon.

Pankaj


From SchaefferM at missouri.edu  Tue Sep 25 12:45:54 2007
From: SchaefferM at missouri.edu (Mary (Polacco) Schaeffer)
Date: Tue, 25 Sep 2007 11:45:54 -0500
Subject: [Po-dev] RE: Questions about associations
In-Reply-To: <p06240804c31ed8812373@[130.126.89.70]>
Message-ID: <C31EA572.11B29%SchaefferM@missouri.edu>

Marty, 
If you read the association file format info they talk about MUTANTS - so I
was assuming it did not include naturally occuring alleles - and I wished to
be clear if  PO is making a distinction between say diversity alleles as
from the Panzea project, and those that were induced to perturb the system.

So, the question reqmains - are we? Either way works for me,

    m

On 9/25/07 10:27 AM, "Marty Sachs" <msachs at uiuc.edu> wrote:

> At 10:18 AM -0500 9/25/07, Schaeffer, Mary L. wrote:
>> I assume you mean alleles other than mutant?
> 
> Huh?  All alleles differ from each other due to mutation.  Many may
> not be induced by a researcher in a lab setting, but natural allelic
> variation is also due to mutation.
> 
> -Marty




From SchaefferM at missouri.edu  Tue Sep 25 13:30:05 2007
From: SchaefferM at missouri.edu (Mary (Polacco) Schaeffer)
Date: Tue, 25 Sep 2007 12:30:05 -0500
Subject: [Po-dev] RE: Questions about associations
In-Reply-To: <46F92EEB.4040204@cornell.edu>
Message-ID: <C31EAFCD.11B30%SchaefferM@missouri.edu>

On 9/25/07 10:53 AM, "Pankaj Jaiswal" <pj37 at cornell.edu> wrote:

> Pl take a look at the association file format section of
> http://plantontology.org/docs/otherdocs/assoc-file-format.html
> there in the column-8 one can enter the allele symbol suggesting that
> the maize gene annotation to PO term is derived from allele so and so.
> 
> I will be happy to talk to you guys sometime on Friday afternoon.

This Fri is out for me - but next one would be ok if it seems we need to
talk. 

With well-studied genes there will be many alleles annotated to a PO term.
Is the PO database is OK taking in multiple rows that differ only in the
'column 8' listing of alleles?
  m




From msachs at uiuc.edu  Tue Sep 25 13:31:38 2007
From: msachs at uiuc.edu (Marty Sachs)
Date: Tue, 25 Sep 2007 12:31:38 -0500
Subject: [Po-dev] RE: Questions about associations
In-Reply-To: <C31EA572.11B29%SchaefferM@missouri.edu>
References: <C31EA572.11B29%SchaefferM@missouri.edu>
Message-ID: <p06240807c31ef1fc1c42@[130.126.89.70]>

Mary,

My point was, what's the difference?  In this day of DNA sequence 
analysis, a single bp substitution difference is a scorable 
phenotypic difference (regardless of whether this occurred in nature 
or by EMS mutagenesis).  The allelic differences observed in Maize 
Diversity/Panzea project are all due to mutation.  In terms of 
morphological phenotypes, what is the difference between the D8 
allele, which is naturally occurring, and the D9 allele which was 
induced?  Both result in dwarf plants.

My point is there should be no distinction in how variant alleles are treated.

	-Marty

At 11:45 AM -0500 9/25/07, Mary (Polacco) Schaeffer wrote:
>Marty,
>If you read the association file format info they talk about MUTANTS - so I
>was assuming it did not include naturally occuring alleles - and I wished to
>be clear if  PO is making a distinction between say diversity alleles as
>from the Panzea project, and those that were induced to perturb the system.
>
>So, the question reqmains - are we? Either way works for me,
>
>     m
>
>On 9/25/07 10:27 AM, "Marty Sachs" <msachs at uiuc.edu> wrote:
>
>>  At 10:18 AM -0500 9/25/07, Schaeffer, Mary L. wrote:
>>>  I assume you mean alleles other than mutant?
>>
>>  Huh?  All alleles differ from each other due to mutation.  Many may
>>  not be induced by a researcher in a lab setting, but natural allelic
>>  variation is also due to mutation.
>>
>>  -Marty



From cwt6 at cornell.edu  Tue Sep 25 14:47:33 2007
From: cwt6 at cornell.edu (Chih-Wei Tung)
Date: Tue, 25 Sep 2007 14:47:33 -0400
Subject: [Po-dev] RE: Questions about associations
In-Reply-To: <C31EAFCD.11B30%SchaefferM@missouri.edu>
References: <C31EAFCD.11B30%SchaefferM@missouri.edu>
Message-ID: <7050BF31-6760-469D-A523-85E61157CBED@cornell.edu>

Hi Mary,

I am wondering if it is a practical way to display many alleles in  
POC database? I just looked at this maize gene, adh1, it has 575  
variations/alleles (http://www.maizegdb.org/cgi-bin/ 
displaylocusrecord.cgi?id=12021, http://www.maizegdb.org/cgi-bin/ 
locusvarreport.cgi?id=12021).

If most of maize genes have such huge amount of alleles, I think  
providing a external link to MaizeGDB should be sufficient.  I  
searched POC database,  "MaizeGDB:12021" link in this page http:// 
www.plantontology.org/amigo/go.cgi? 
view=details&search_constraint=gp&session_id=9624b1190744163&gp=12021  
didn't direct me to the proper page in MaizeGDB.  Does MaizeGDB have  
stable URL ID to link back to POC?

Here is one example that GOC link back to Flybase, and users can find  
all the alleles in Flybase page (http://amigo.geneontology.org/cgi- 
bin/amigo/go.cgi? 
search_constraint=gp&view=details&session_id=762b1190743889&gp=FBgn00032 
05, click "FB:FBgn0003205", it points to http:// 
flybase.bio.indiana.edu/reports/FBgn0003205.html)


Chih-Wei



On Sep 25, 2007, at 1:30 PM, Mary (Polacco) Schaeffer wrote:

> On 9/25/07 10:53 AM, "Pankaj Jaiswal" <pj37 at cornell.edu> wrote:
>
>> Pl take a look at the association file format section of
>> http://plantontology.org/docs/otherdocs/assoc-file-format.html
>> there in the column-8 one can enter the allele symbol suggesting that
>> the maize gene annotation to PO term is derived from allele so and  
>> so.
>>
>> I will be happy to talk to you guys sometime on Friday afternoon.
>
> This Fri is out for me - but next one would be ok if it seems we  
> need to
> talk.
>
> With well-studied genes there will be many alleles annotated to a  
> PO term.
> Is the PO database is OK taking in multiple rows that differ only  
> in the
> 'column 8' listing of alleles?
>   m
>
>
> _______________________________________________
> Po-dev mailing list
> Po-dev at plantontology.org
> http://mail.plantontology.org/mailman/listinfo/po-dev



From SchaefferM at missouri.edu  Tue Sep 25 15:59:22 2007
From: SchaefferM at missouri.edu (Mary (Polacco) Schaeffer)
Date: Tue, 25 Sep 2007 14:59:22 -0500
Subject: [Po-dev] RE: Questions about associations
In-Reply-To: <7050BF31-6760-469D-A523-85E61157CBED@cornell.edu>
Message-ID: <C31ED2CA.11B4B%SchaefferM@missouri.edu>

Hi Chih-Wei,

If it works best for you, I can restrict to one (column 8, for a gene assoc
file) and where possible,  list an allele that is maintained by Marty at the
Stock Center. 

As FYI, most loci with associations  inferred from phenotype (IMP)  have one
or two alleles that have associations to one or more anatomy terms.  A few
do have hundreds of alleles.  Currently, there are a total of some 16,292
alleles associated to PO body_parts by evidence code IMP; these in turn
represent some 4268 genes and QTL.

Re links to MaizeGDB ? there is a stable link: provided 2-3 years ago ? not
sure where the link you have below came from?

> We have a hyperlink prefix that works for any ID in MaizeGDB, regardless
> of
> object type:
>
> http://www.maizegdb.org/cgi-bin/id_search.cgi?id=
>

http://www.maizegdb.org/cgi-bin/id_search.cgi?id=12327

>

Let me know if this works for you,

     mary






On 9/25/07 1:47 PM, "Chih-Wei Tung" <cwt6 at cornell.edu> wrote:

> Hi Mary,
> 
> I am wondering if it is a practical way to display many alleles in
> POC database? I just looked at this maize gene, adh1, it has 575
> variations/alleles (http://www.maizegdb.org/cgi-bin/
> displaylocusrecord.cgi?id=12021, http://www.maizegdb.org/cgi-bin/
> locusvarreport.cgi?id=12021).
> 
> If most of maize genes have such huge amount of alleles, I think
> providing a external link to MaizeGDB should be sufficient.  I
> searched POC database,  "MaizeGDB:12021" link in this page http://
> www.plantontology.org/amigo/go.cgi?
> view=details&search_constraint=gp&session_id=9624b1190744163&gp=12021
> didn't direct me to the proper page in MaizeGDB.  Does MaizeGDB have
> stable URL ID to link back to POC?
> 
> Here is one example that GOC link back to Flybase, and users can find
> all the alleles in Flybase page (http://amigo.geneontology.org/cgi-
> bin/amigo/go.cgi?
> search_constraint=gp&view=details&session_id=762b1190743889&gp=FBgn00032
> 05, click "FB:FBgn0003205", it points to http://
> flybase.bio.indiana.edu/reports/FBgn0003205.html)
> 
> 
> Chih-Wei
> 
> 
> 
> On Sep 25, 2007, at 1:30 PM, Mary (Polacco) Schaeffer wrote:
> 
>> On 9/25/07 10:53 AM, "Pankaj Jaiswal" <pj37 at cornell.edu> wrote:
>> 
>>> Pl take a look at the association file format section of
>>> http://plantontology.org/docs/otherdocs/assoc-file-format.html
>>> there in the column-8 one can enter the allele symbol suggesting that
>>> the maize gene annotation to PO term is derived from allele so and
>>> so.
>>> 
>>> I will be happy to talk to you guys sometime on Friday afternoon.
>> 
>> This Fri is out for me - but next one would be ok if it seems we
>> need to
>> talk.
>> 
>> With well-studied genes there will be many alleles annotated to a
>> PO term.
>> Is the PO database is OK taking in multiple rows that differ only
>> in the
>> 'column 8' listing of alleles?
>>   m
>> 
>> 
>> _______________________________________________
>> Po-dev mailing list
>> Po-dev at plantontology.org
>> http://mail.plantontology.org/mailman/listinfo/po-dev
> 

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From cwt6 at cornell.edu  Tue Sep 25 16:41:03 2007
From: cwt6 at cornell.edu (Chih-Wei Tung)
Date: Tue, 25 Sep 2007 16:41:03 -0400
Subject: [Po-dev] RE: Questions about associations
In-Reply-To: <C31ED2CA.11B4B%SchaefferM@missouri.edu>
References: <C31ED2CA.11B4B%SchaefferM@missouri.edu>
Message-ID: <287762D4-1A3F-4174-8F15-F085824A91D2@cornell.edu>

Hi Mary,

This sounds great, thank you for being supportive.

The link I mention here is the gene(or locus) page link in MaizeGDB,  
e.g. http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi? 
id=12021.  Is this page URL a stable link? We would like to provide  
this link in the POC annotation detail page (http:// 
www.plantontology.org/amigo/go.cgi? 
view=details&search_constraint=gp&session_id=4263b1190752135&gp=12021),  
the current linkout to MaizeGDB is not working properly.

Chih-Wei


On Sep 25, 2007, at 3:59 PM, Mary (Polacco) Schaeffer wrote:

> Hi Chih-Wei,
>
> If it works best for you, I can restrict to one (column 8, for a  
> gene assoc file) and where possible,  list an allele that is  
> maintained by Marty at the Stock Center.
>
> As FYI, most loci with associations  inferred from phenotype (IMP)   
> have one or two alleles that have associations to one or more  
> anatomy terms.  A few do have hundreds of alleles.  Currently,  
> there are a total of some 16,292 alleles associated to PO  
> body_parts by evidence code IMP; these in turn represent some 4268  
> genes and QTL.
>
> Re links to MaizeGDB ? there is a stable link: provided 2-3 years  
> ago ? not sure where the link you have below came from?
>
> > We have a hyperlink prefix that works for any ID in MaizeGDB,  
> regardless
> > of
> > object type:
> >
> > http://www.maizegdb.org/cgi-bin/id_search.cgi?id=
> >
>
> http://www.maizegdb.org/cgi-bin/id_search.cgi?id=12327
>
> >
>
> Let me know if this works for you,
>
>      mary
>
>
>
>
>
>
> On 9/25/07 1:47 PM, "Chih-Wei Tung" <cwt6 at cornell.edu> wrote:
>
> > Hi Mary,
> >
> > I am wondering if it is a practical way to display many alleles in
> > POC database? I just looked at this maize gene, adh1, it has 575
> > variations/alleles (http://www.maizegdb.org/cgi-bin/
> > displaylocusrecord.cgi?id=12021, http://www.maizegdb.org/cgi-bin/
> > locusvarreport.cgi?id=12021).
> >
> > If most of maize genes have such huge amount of alleles, I think
> > providing a external link to MaizeGDB should be sufficient.  I
> > searched POC database,  "MaizeGDB:12021" link in this page http://
> > www.plantontology.org/amigo/go.cgi?
> >  
> view=details&search_constraint=gp&session_id=9624b1190744163&gp=12021
> > didn't direct me to the proper page in MaizeGDB.  Does MaizeGDB have
> > stable URL ID to link back to POC?
> >
> > Here is one example that GOC link back to Flybase, and users can  
> find
> > all the alleles in Flybase page (http://amigo.geneontology.org/cgi-
> > bin/amigo/go.cgi?
> >  
> search_constraint=gp&view=details&session_id=762b1190743889&gp=FBgn000 
> 32
> > 05, click "FB:FBgn0003205", it points to http://
> > flybase.bio.indiana.edu/reports/FBgn0003205.html)
> >
> >
> > Chih-Wei
> >
> >
> >
> > On Sep 25, 2007, at 1:30 PM, Mary (Polacco) Schaeffer wrote:
> >
> >> On 9/25/07 10:53 AM, "Pankaj Jaiswal" <pj37 at cornell.edu> wrote:
> >>
> >>> Pl take a look at the association file format section of
> >>> http://plantontology.org/docs/otherdocs/assoc-file-format.html
> >>> there in the column-8 one can enter the allele symbol  
> suggesting that
> >>> the maize gene annotation to PO term is derived from allele so and
> >>> so.
> >>>
> >>> I will be happy to talk to you guys sometime on Friday afternoon.
> >>
> >> This Fri is out for me - but next one would be ok if it seems we
> >> need to
> >> talk.
> >>
> >> With well-studied genes there will be many alleles annotated to a
> >> PO term.
> >> Is the PO database is OK taking in multiple rows that differ only
> >> in the
> >> 'column 8' listing of alleles?
> >>   m
> >>
> >>
> >> _______________________________________________
> >> Po-dev mailing list
> >> Po-dev at plantontology.org
> >> http://mail.plantontology.org/mailman/listinfo/po-dev
> >

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