Re: [GUSDEV] GUS schema to support Genbank features

[Jian Lu <jl...@vb...>]

 So if we want to incorporate a new qualifier "operon" into either 
GeneFeature or Transcript, we have to add it to them. Will GUS consider 
it for future new release?

  <feature name="gene" table="DoTS::GeneFeature" so="gene">
  <qualifier name="allele" />
  <qualifier name="citation" />
  <qualifier name="evidence" />
  <qualifier name="function" />
  <qualifier name="gene" handler="standard" method="gene" />
  <qualifier name="label" />
  <qualifier name="locus_tag" column="source_id" />
  <qualifier name="map" />
  <qualifier name="note" handler="standard" method="note" />
  <qualifier name="old_locus_tag" ignore="true" />
  <qualifier name="operon" ignore="true" />
  <qualifier name="product" />
  <qualifier name="pseudo" column="is_pseudo" />
  <qualifier name="phenotype" />
  <qualifier name="standard_name" />
  <qualifier name="usedin" />
  <qualifier name="db_xref" handler="standard" method="dbXRef" />
  </feature>

Ed Robinson wrote:
> 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
>