Re: Problems with gmod_bulk_load_gff3

Hi Fernando,

I suspect that the problem is that the IDs in your GFF are not the  
primary GO IDs.  For example, GO:0005554 is not a primary id in GO; it  
is an alt_id for GO:0003674.   GO:0042829 is an alt_id for GO: 
0006952.  Unfortunately, the GFF loader doesn't currently do alt_ids.   
This information is typically stored in chado via the cvterm_dbxref  
table, so the loader could be modified to make use of it, but it would  
entail a fair bit of work.  The easier thing to do for the moment  
would be to update the GFF to use current IDs.

Scott

On Jul 8, 2009, at 3:23 PM, fernando bueno wrote:

> Hi!
>
> i have loaded the sequence ontologies on my chado schema with the  
> chado feature properties ontology
> but appears this
> Preparing data for inserting into the chado database
> (This may take a while ...)
> couldn't find GO:0005554 's cvterm_id in cvterm table
> couldn't find GO:0005554 's cvterm_id in cvterm table
> couldn't find GO:0005554 's cvterm_id in cvterm table
> couldn't find GO:0042829 's cvterm_id in cvterm table
> couldn't find GO:0008151 's cvterm_id in cvterm table
> couldn't find GO:0000074 's cvterm_id in cvterm table
> couldn't find GO:0042829 's cvterm_id in cvterm table
>
>
> i don't have idea how to solve it
> your could help me again?
>
>
>
> thank you very much.
>
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Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

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