PO is listed at BRENDA enzyme database

Wed Jul 6 17:07:35 EDT 2005

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 This ontology is no longer maintained and was retired in February 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.
>
>

-- 
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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.
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