Re: [GUSDEV] GUS schema to support Genbank features

[Ed R. <ero...@ug...>]

The genbank2gus.xml was designed to match all GB features to
tables in GUS.  You shouldn't find any GB feature which is not
in the file.  You may find some feature attributes which are
not in the file.  Feel free to add any attributes you may need.

The mapping of genbank features to gus tables is not one to
one.  GUS was not written to mirror GenBank.  

The genbank2gus.xml file was written as an idealized mapping
for some of the datasets we have seen while working on
ApiComplexan data sets.  As such, the file is a good
suggesstion on how to map GenBank features into GUS.  However,
it is not the final word on how to handle such a mapping. 
Features such as Gene, Exon, and CDS are central to the
working of InsertSequenceFeatures.  Thus, you should probably
leave those features pointing at their respective tables.  If
you want to change one of the other features to point at a
different table, you should feel free to do so.  You should
design a map that allows you to make the best use of the GUS
tables for your own data.

I hope this helps.  If you have any more specific questions
about using the map for your data, please post them.  Data
modeling discussions are always lively.

-ed



---- Original message ----
>Date: Wed, 15 Mar 2006 13:24:11 -0500
>From: Jian Lu <jl...@vb...>  
>Subject: [GUSDEV] GUS schema to support Genbank features  
>To: gus...@li...
>
>Hi GUS,
>
>The GUS 3.5 doesn't support all Genbank features such as
"operon". From 
>the mapping file "genbank2gus.xml", we could see "operon" has
been 
>included in several feature tables.
>Questions:
>1. Does "genbank2gus.xml" contain all Genbank features or will?
>2. How soon GUS schema will support all Genbank features or
at least 
>features within genbank2gus.xml
>3. How will GUS plug-ins support the added Genbank features?
>
>Thanks,
>
>Jian Lu
>VBI
>
>
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-----------------
Ed Robinson
Center for Tropical and Emerging Global Diseases
University of Georgia, Athens, GA 30602
ero...@ug.../(706)542.1447/254.8883