From feedback_submission at filetta.cshl.edu  Thu Oct 27 10:45:39 2005
From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu)
Date: Thu, 27 Oct 2005 10:45:39 -0400
Subject: Feedback on POC
Message-ID: <200510271445.j9REjd3b022648@filetta.cshl.org>

    *** Feedback from Plant Ontology Live Site ***

refer_to_url: http://www.plantontology.org/index.html

comments: Hello!

I noticed that some obvious "is_a" relationships are missing...

eg: Term "adventitious root epidermis" should have an "is_a" relationship to "root epidermis";
Term "aleurone layer" should, at least (maybe not directly, but through some sub-class) have an "is_a" relationship to "Tissue"; (as far as I know)

Besides, I think that it would be better to rename the Term "obsolete growth and development terms" to "obsolete plant growth and development stage", in order to be consistent with its structural counterpart.

Thanks for reading me.
Bye

name: Fran?ois DELCOUX

email: fdelcoux at ulb.ac.be

organization: ULB (Belgium)

send_feedback: Send your feedback



From jitterbug at plantontology.org  Thu Oct 27 20:56:06 2005
From: jitterbug at plantontology.org (Katica Ilic)
Date: Thu, 27 Oct 2005 20:56:06 -0400
Subject: Feedback on POC (fwd) (PR#89)
Message-ID: <200510280056.j9S0u6wR001785@brie4.cshl.org>

Dear Fran??ois,

Thank you for bringing to our attention an existence of terms in the PO with
missing relationships. We recognized this problem some time ago and have been
trying to solve it. In fact, one of our colleagues, Pankaj Jaiswal, has been
actively working on adding 'is_a' relationships to PO terms. This month, the
ontology release will include updates for some of them, for instance the term
you mentioned 'adventitious root epidermis'. Since there are many terms with
missing 'is_a' relationship, it may take several rounds of ontology updates to
complete this task and have the ontology where all terms would have 'is_a'
relationship.

Regarding your suggestion to include
'obsolete_plant_growth_and_development_stage', this is exactly what we currently
have in PO as the top grouping term for all obsoleted terms in this aspect of
PO. The term you were referring to is just and old term that was obsoleted early
on while we were creating PO. We don???t use, maintain or change names of
obsoleted terms, since they are in the ontology mainly for the historical
prospective and for keeping a record of all the terms entered in the ontology
(no term is ever deleted in PO). 

Thank you for using Plant Ontologies and for contacting us.

Best regards,

Katica Ilic, POC Project Coordinator

> ---------- Forwarded message ----------
> Date: Thu, 27 Oct 2005 10:45:39 -0400
> From: feedback_submission at filetta.cshl.edu
> Reply-To: po-dev at plantontology.org, feedback_submission at filetta.cshl.edu
> To: po-dev <po-dev at plantontology.org>
> Subject: Feedback on POC
> 
>      *** Feedback from Plant Ontology Live Site ***
> 
> refer_to_url: http://www.plantontology.org/index.html
> 
> comments: Hello!
> 
> I noticed that some obvious "is_a" relationships are missing...
> 
> eg: Term "adventitious root epidermis" should have an "is_a" relationship to
> "root epidermis";
> Term "aleurone layer" should, at least (maybe not directly, but through some
> sub-class) have an "is_a" relationship to "Tissue"; (as far as I know)
> 
> Besides, I think that it would be better to rename the Term "obsolete growth
and
> development terms" to "obsolete plant growth and development stage", in order
to
> be consistent with its structural counterpart.
> 
> Thanks for reading me.
> Bye
> 
> name: Fran???s DELCOUX
> 
> email: fdelcoux at ulb.ac.be
> 
> organization: ULB (Belgium)
> 
> send_feedback: Send your feedback
> --1118555204-1981955417-1130439040=:13943--
> 
> 



From SchaefferM at missouri.edu  Fri Oct 28 15:16:27 2005
From: SchaefferM at missouri.edu (Mary (MaizeGDB))
Date: Fri, 28 Oct 2005 14:16:27 -0500
Subject: ? about searching on AMIGO  ATTN SHuly
Message-ID: <BF87E33B.1597E%SchaefferM@missouri.edu>

Shuly,
If, as a user, I want to  look at all the structural terms for a body part,
e.g. root, can I use AMIGO?

I am unable to figure out easily how to do this.
I typed in 'root', with exact match and was able to get the few terms above
the node when I click on the 'show tree' button. What I really wanted was to
explore the terms in the root node.


Second question, if I simply wish to look at all the terms in the anatomy
module that have a match to 'root', can I do this? Currently it seems that
we access all 3 modules at once. If indeed it is not just that I am spastic,
and we can't filter for ontology module, is this an easy filter to aad?

  eg filter on  anatomy
                growth
                development

  mary
 



From katica at acoma.Stanford.EDU  Fri Oct 28 17:54:38 2005
From: katica at acoma.Stanford.EDU (katica at acoma.Stanford.EDU)
Date: Fri, 28 Oct 2005 14:54:38 -0700 (PDT)
Subject: ? about searching on AMIGO ATTN SHuly
In-Reply-To: <BF87E33B.1597E%SchaefferM@missouri.edu>
References: <BF87E33B.1597E%SchaefferM@missouri.edu>
Message-ID: <Pine.LNX.4.62.0510281433340.17244@aztec.stanford.edu>

Hi Mary,

I hope I can provide some help regarding serches in AmiGO. Please see 
below:

On Fri, 28 Oct 2005, Mary (MaizeGDB) wrote:

> Shuly,
> If, as a user, I want to  look at all the structural terms for a body part,
> e.g. root, can I use AMIGO?

Of course, that's why AmiGO is made for searches and queries.
If you type in 'root' and choose 'exact match' only one term will show up, 
that is, 'root'.

To view the ontology tree, you need to click on the little tree icon next 
to the term name (it is blue icon, while the term name itself is green).
Whan shows up is exactly what you described, ontology lineage for the term 
'root' all the way up to the very top node. The children terms of the root 
would not show up at this point. If you want to further expand the tree, 
and view all the children terms under the node of your interest, you need 
to click on the 'plus sign' that is displeyed next to the term name of the 
node you want to expand. Then, keep clicking till you see all 
granular terms under the node(s) you have chosen.


> I am unable to figure out easily how to do this.
> I typed in 'root', with exact match and was able to get the few terms above
> the node when I click on the 'show tree' button. What I really wanted was to
> explore the terms in the root node.
Ontology tutorials that Leonore created are very helpful for tricks on how
to navigate through the PO.

Ontology tutorials that Leonore created and we put up on the POC web 
site are very helpful for 'tricks' on how to navigate through the PO.

> Second question, if I simply wish to look at all the terms in the anatomy
> module that have a match to 'root', can I do this? Currently it seems that
> we access all 3 modules at once. If indeed it is not just that I am spastic,
> and we can't filter for ontology module, is this an easy filter to aad?

We had discussion about improving the searches in AmiGO last summer, and 
again this fall, and a few suggestions for improvements came from me (I 
believe) - I did suggest filtering the search options by Ontology 
aspect, that is, search in 'structure ontology', growth stages, or 
developmental stages'. Shuly is in contact with GO people who are in 
charge of AmiGO maintenence, since we decided to work with them on these 
improvements.

I hope this helps.

Best,

Katica

--------------------------------------------------------------------------
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 SchaefferM at missouri.edu  Fri Oct 28 19:13:42 2005
From: SchaefferM at missouri.edu (Mary (MaizeGDB))
Date: Fri, 28 Oct 2005 18:13:42 -0500
Subject: ? about searching on AMIGO ATTN SHuly
In-Reply-To: <Pine.LNX.4.62.0510281433340.17244@aztec.stanford.edu>
Message-ID: <BF881AD6.1598E%SchaefferM@missouri.edu>

Thanks Katica,
I did do  this, (ie click on the plus) but it never came up on my browser,
although there were hints that something might eventually come up, as
another window popped up but never had any results in it. I will try
patience.

The reason I wrote this email is because I asked a student working on root
QTL in maize to evaluate the terms in the PO and he gave up right away. He
had the same impression that I did, that the terms under root, at some time
previous to today, did  come up more readily.

I will try on other browsers - we were both using explorer, but one on a MAc
and one one a PC.

 mary

> From: katica at acoma.stanford.edu
> Date: Fri, 28 Oct 2005 14:54:38 -0700 (PDT)
> To: POC-dev <po-dev at plantontology.org>, "Mary (MaizeGDB)"
> <SchaefferM at missouri.edu>
> Subject: Re: ? about searching on AMIGO ATTN SHuly
> 
> The children terms of the root
> would not show up at this point. If you want to further expand the tree,
> and view all the children terms under the node of your interest, you need
> to click on the 'plus sign' that is displeyed next to the term name of the
> node you want to expand. Then, keep clicking till you see all
> granular terms under the node(s) you have chosen.



From kellogge at msx.umsl.edu  Sat Oct 29 15:52:45 2005
From: kellogge at msx.umsl.edu (kellogge)
Date: Sat, 29 Oct 2005 14:52:45 -0500
Subject: ? about searching on AMIGO ATTN SHuly
In-Reply-To: <BF881AD6.1598E%SchaefferM@missouri.edu>
References: <BF881AD6.1598E%SchaefferM@missouri.edu>
Message-ID: <96d8f1c06733dce0084e1d8e58932947@msx.umsl.edu>

I just tried it in Safari on a Mac G5 and it worked OK.
Toby

On Oct 28, 2005, at 6:13 PM, Mary (MaizeGDB) wrote:

> Thanks Katica,
> I did do  this, (ie click on the plus) but it never came up on my 
> browser,
> although there were hints that something might eventually come up, as
> another window popped up but never had any results in it. I will try
> patience.
>
> The reason I wrote this email is because I asked a student working on 
> root
> QTL in maize to evaluate the terms in the PO and he gave up right 
> away. He
> had the same impression that I did, that the terms under root, at some 
> time
> previous to today, did  come up more readily.
>
> I will try on other browsers - we were both using explorer, but one on 
> a MAc
> and one one a PC.
>
>  mary
>
>> From: katica at acoma.stanford.edu
>> Date: Fri, 28 Oct 2005 14:54:38 -0700 (PDT)
>> To: POC-dev <po-dev at plantontology.org>, "Mary (MaizeGDB)"
>> <SchaefferM at missouri.edu>
>> Subject: Re: ? about searching on AMIGO ATTN SHuly
>>
>> The children terms of the root
>> would not show up at this point. If you want to further expand the 
>> tree,
>> and view all the children terms under the node of your interest, you 
>> need
>> to click on the 'plus sign' that is displeyed next to the term name 
>> of the
>> node you want to expand. Then, keep clicking till you see all
>> granular terms under the node(s) you have chosen.
>
>
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/services/kellogg/
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