[Gmod-help] Re: [Gmod-schema] Problems to Insert a Genbank in Chado

[Scott Cain]

Hi Don,

I added a mapping for pseudoCDS to pseudogenic_exon, but it is less  
clear to me that the mature_peptide should map straight to peptide, so  
I didn't add that mapping.  Does anyone have a suggested term for  
automatic mapping?

Scott

On Aug 26, 2009, at 3:57 PM, Don Gilbert wrote:

>
> Fernando (and Scott),
> Those type conversions for Genbank > GFF/SO are handled in the bioperl
> Bio/SeqFeature/Tools/TypeMapper.pm
> "mature_peptide" used to be a SO term, maybe they dropped it.
> NCBI keeps adding new "pseudoXXX" feature types that usually map to
> SO "pseudogenic_XXX" types, but check for CDS, and use as Scott  
> suggests
> pseudogenic_exon as a good alternate.
> - Don
>
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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