anatomy ontology ids (fwd) (PR#2849)

[Katica Ilic]

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
> 
> 
>