anatomy ontology ids (fwd) (PR#2849)

[Helen Parkinson]

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BRENDA, since it is no longer actively maintained or displayed and is no longer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