anatomy ontology ids (fwd) (PR#2849)

[Katica Ilic]

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BRENDA, since it is no longer actively maintained or displayed and is no longer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