KEGG Integration

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KEGG Integration

Vallejos, Andrew

I spent some time reading about keys, and simply added primaryIdentifier to the end of the ncbigenenumber key.  

 

key_ncbigenenumber = ncbiGeneNumber, primaryIdentifier

 

That resolved that problem.

 

-Andrew

 

======================

Andrew Vallejos

Web Developer II

Biotechnology and Bioengineering Center

Medical College of Wisconsin

414-955-4104

[hidden email]

 


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Re: KEGG Integration

Richard Smith
Hi Andrew,
That will prevent the error but I'm not sure the genes will merge
correctly.  Genes are created from kegg with the ncbiGeneNumber set
but no primaryIdentifier - so I think adding primaryIdentifier to the
key will mean only genes with no primaryIdentifier will merge.

The real problem is, as you say, that the ensembl source is associating
the same NCBI id with two different ensembl ids.  This happens in a few
cases.

I'm still working on resolving this for metabolicMine, at the moment
I've stopped ensembl from creating NCBI gene ids and am loading genes
from HGNC first which includes mappings to both NCBI and ensembl.  The
HGNC source prevents creation of duplicates.

I don't know yet whether this is the best strategy, but I'll try and
finish it for inclusion in tomorrow's 0.94.1 release.

Cheers,
Richard.




Vallejos, Andrew wrote:

> I spent some time reading about keys, and simply added primaryIdentifier
> to the end of the ncbigenenumber key.  
>
>  
>
> key_ncbigenenumber = ncbiGeneNumber, primaryIdentifier
>
>  
>
> That resolved that problem.
>
>  
>
> -Andrew
>
>  
>
> ======================
>
> Andrew Vallejos
>
> Web Developer II
>
> Biotechnology and Bioengineering Center
>
> Medical College of Wisconsin
>
> 414-955-4104
>
> [hidden email]
>
>  
>
>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev


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