[Gramene] GO Help query (from jenny) (fwd)

[Pankaj Jaiswal (OSU)]

Dear Jenny,

If you go to the Gramene's website www.gramene.org
-select 'ontologies' from the search section on top right corner of the page
-type 'biological_process' and click on the search icon.
-This will take you to the appropriate page e.g 
http://www.gramene.org/db/ontology/search?id=GO:0008150
-Then scroll down the page on above link and look in the 'Associations' 
section.
-You will see the counts for 'Ensembl rice gene (xxxxxxx)', where 
(xxxxxxx) is the unique count of objects/genes annotated with biological 
process terms

In this example there are 23,335 Ensembl rice genes with biological 
process term annotations. Which is about 50% of the total genes. THIS 
DATA IS BASED ON THE ANNOTATIONS PROVIDED BY GRAMENE  FOR THE 
MSU/TIGR-Rice build #5.

The same query can be performed from any of the ontology view pages such 
as the main ontology page
http://www.gramene.org/plant_ontology/
OR
any term detail pages e.g.
http://www.gramene.org/db/ontology/search?id=GO:0008150
All you need to do is select the ontology type and the exact match 
option when available.

Let me know if it helps
Pankaj

Midori Harris wrote:
> Hello Gramene,
> 
> We've received this question on gohelp from a user who needs to know how 
> many genes have products with GO annotations. I hope you can help!
> 
> Thanks,
> Midori
> 
> ---------- Forwarded message ----------
> Date: Sun, 12 Jul 2009 07:46:53 -0700 (PDT)
> From: jenny88844 at hotmail.com
> To: gohelp at genome.stanford.edu
> Subject: GO Help query (from jenny)
> 
> contactName: jenny
> contactEmail: jenny88844 at hotmail.com
> contactText: Honorable professors,
> I am a graduate student. Recently, I tried my best to find out that how 
> many genes in rice genome have a gene ontology item with biological 
> process .The exact number will be helpful to my research. However, when 
> I searched your web, I notice that the result showed "the gene product". 
> I think it may be different between gene and gene products. However, I 
> don't find any information to tell me that the exact number of genes 
> involving in biological process in rice. I hope you can give me some 
> advice. I will be appreciated!
> 
> Thank you.
> _______________________________________________
> Gramene mailing list
> Gramene at brie4.cshl.edu
> http://mail.gramene.org/mailman/listinfo/gramene

-- 
Pankaj Jaiswal
Assistant Professor
Dept. of Botany and Plant Pathology
3082 Cordley Hall
Oregon State University
Corvallis, OR, 97331-2902, USA

Ph.: +1-541-737-8471
Fax: +1-541-737-3573
Web: www.gramene.org
      www.plantontology.org