[Gmod-help] Problems with gmod_bulk_load_gff3 again

[Scott Cain]

Hello Fernando,

There are two possibilities:

1. You didn't load the Gene Ontology correctly

2. The GFF file refers to GO ids that aren't in the current version of  
GO.

I suspect the problem is a subset of number 2.  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.

As a side note, it would be good if you addressed further questions of  
this sort to the schema mailing list, <https://lists.sourceforge.net/lists/listinfo/gmod-schema 
 > as there are many people who read that list that could provide  
useful input.

Scott

On Jul 8, 2009, at 2:09 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.
>
>
>
> Fernando

-----------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research