Re: [GUSDEV] GUS schema to support Genbank features

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

First, let me beg an analyst or bilogist to correct me if any
of this is wrong.

Yes, the quick and dirty way would be to incorporate an operon
attribute in your Gene feature and point it towards a
convenient column using "column=".

I also noticed that the genbank2gus.xml map does not have a
table for an operon feature.  If you have operon features, in
addition to operon attributes, you will need to find a
suitable table to store these.  Modify the map as you need to.

Unfortunately, GUS was designed primarily with Eukaryotic
organisms in mind.  There is nothing in GUS that I know of (if
I am wrong, some analyst please correct me) to support
super-gene organizations. If you want to group your genes into
their respective operons, the best way I can see doing that is
to store each operon with it's source_id in some table, and
then store the source_id for each genes operon in some
attribute in your GeneFeature entry.  Then, you can simply
select all of the GeneFeatures with the same source_id to
recover all of the genes in one operon.  The operon itself, if
you store it, will just be a big, long feature on your
NASequence within which you will find many gene records. 
There will be no explicit ordering of genes in this operon via
parent_ids.  You will need to use the gene locations to
determine ordering within the span of an operon.

Unfortunately, there isn't any way to record the order that
genes appear in an operon other than to retrieve their
individual locations.  There is also no hierarchical
organization of super-gene structures in gus. 
InsertSequenceFeatures does support the hierarchy

   gene->mRNA->Exon
             ->CDS->TranslatedAASequence

It does this via the BioPerl unflattener.  However, neither
GUS nor the unflattener supports a hierarchy such as

      ->promoter
Operon->gene.....
      ->gene.....  

Of course, GUS is expandable if someone were inclined to work
on this.....

Hope this is hepful.

-ed


---- Original message ----
>Date: Wed, 15 Mar 2006 14:10:27 -0500
>From: Jian Lu <jl...@vb...>  
>Subject: Re: [GUSDEV] GUS schema to support Genbank features  
>To: Ed Robinson <ero...@ug...>
>Cc: gus...@li...
>
> 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"  />
>  <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
>>   
>
>
>
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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