[Gramene] Questions on TO

[Wang Hongru]

Hello, gramene : )

 

I have downloaded the trait ontology file of the current release from your
ftp site. But there are 5 files, and I do not know what is the difference
between them, and they are:

diversity-arabidopsis-to.txt

diversity-rice-to.txt

TO_Gene_association.txt

TO_Protein_association.txt

to_QTL_association.txt

 

another question is:

I have some regions from rice genome, and I want to annotate these regions
with trait ontology; or at least, I can extract all genes in these regions,
and then annotate the genes with trait ontology.

But I noticed that the files I downloaded does not contain any gene_id
information (such as these from MSU: LOC_Osxxgxxxxx, or these from RAPDB:
Osxxgxxxxxxx). The only clue is DB_Object_IDs, but I do not know how to link
them with gene_ids or physical positions on rice genome.

Is their alternative way to solve this problem? 

 

All the best! 

Merry Christmas .. in advance!~

 

Hongru. 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://brie4.cshl.edu/pipermail/gramene/attachments/20121219/5665e24d/attachment.html>