[BioRuby] Fwd: Re: BioSQL development

[Hilmar Lapp]

Is the issue with GFF3 in the Bioruby to BioSQL mapping, or is somehow  
in the BioSQL schema?

I recall there was a thread on GFF recently which I wasn't able to  
follow, so if the answer is in that thread and isn't easy to sum up  
here, just point me there.

	-hilmar

On Aug 22, 2010, at 6:30 AM, Julian Nordt wrote:

> Hi Rob,
>
> I just wanted to point that there are for sure people that have a  
> greater
> experience in regard to the discussed db-schemas and might give you  
> better
> advice on this topic than I'm able to do. As pointed out I have just
> recently started to work with bioruby. Hence it might be a good idea  
> to
> consider further opinions on this topic.
>
> However I did wanted to reply to you request, as your scenario sounded
> somewhat similar to one of the projects I have to work on.
>
> -- Julian
>
> On Sun, 22 Aug 2010 11:23:52 +0200, Rob Syme <rob.syme at gmail.com>  
> wrote:
>
>> Thanks Toshiaki and Julian,
>>
>> Mapping features from gff may well become an issue. Until Raoul  
>> gets back, I
>> might try and keep the data under the Chado schema as suggested by  
>> Julian.
>> *If* I can get it clean enough, I'll offer it up for incorporation  
>> into
>> bioruby.
>>
>> -r
>>
>>
>> On Sun, Aug 22, 2010 at 4:50 PM, Julian Nordt <ju at ncoffee.de> wrote:
>>
>>> Hi Rob,
>>>
>>> I tried to use the BioSQL part of Bioruby for a webapplication  
>>> based on
>>> rails. With the idea of giving users the capability to upload  
>>> genomes to the
>>> application. However the mapping between BioSQL <-> GFF3 is(?)/ 
>>> were not
>>> figured out completly, which was one of the reasons why I changed my
>>> implementation to CHADO scheme.
>>>
>>>
>>> In regard to your question I did use BioSQL in the following way:
>>>
>>>
>>> def openBioConnection
>>>   Bio::SQL.establish_connection(:adapter  => "mysql",
>>>                                 :host     => "localhost",
>>>                                 :username => "xxx",
>>>                                 :password => "xxx",
>>>                                 :database => "biosql_development")
>>> end
>>>
>>>
>>> def get_sequence(bio_entry_id)
>>>   openBioConnection()
>>>   if !bio_entry_id.blank?
>>>     return Bio::SQL::Biosequence.find_by_bioentry_id(bio_entry_id)
>>>   end
>>> end
>>>
>>>
>>> def setSeqFeatName(id,name)
>>>   seq_feat = Bio::SQL::Seqfeature.find_by_seqfeature_id(id)
>>>   Bio::SQL::Seqfeature.update(seq_feat.id, :display_name => name)
>>> end
>>>
>>> (! This does not mean that it is the correct way or intended way  
>>> of usage
>>> as I'm new to ruby/bioruby !)
>>>
>>> I had to make some small modifications to
>>> bio-1.4.0\lib\bio\io\biosql\ar-biosql.rb and biosql.rb,  
>>> unfortunately I do
>>> not remember where exactly. Mostlikely some changes in regard to the
>>> connection adapter and some changes to tablenames or similiar stuff.
>>>
>>> As you can see in ar-biosql.rb all the "classes" for the biosql  
>>> orm are
>>> already defined, so one does not have to define the classes himself.
>>>
>>> Hope this helps,
>>>
>>> Julian Nordt
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Sun, 22 Aug 2010 08:22:18 +0200, Rob Syme <rob.syme at gmail.com>  
>>> wrote:
>>>
>>> Is there a particular person who has taken charge of the BioSQL  
>>> part of
>>>> Bioruby?
>>>> I just want confirmation that I'm not using it in completely the  
>>>> wrong
>>>> way.
>>>>
>>>> Are the classes designed so that you generate models for an app  
>>>> (a rails
>>>> app, for example) that inherit from the Bio::SQL::whatever? eg:
>>>>
>>>> $ rails g model Biodatabase name:string authority:string  
>>>> description:text
>>>>
>>>> and then in app/model/biodatabase.rb you change:
>>>> class Biodatabase < ActiveRecord::Base
>>>> end
>>>>
>>>> into:
>>>> class Biodatabase < Bio::SQL::Biodatabase # which inherits
>>>> ActiveRecord::Base
>>>> end
>>>>
>>>> If I get a handle on this, I'd be happy to write it up for
>>>> http://bioruby.open-bio.org/wiki/Tutorial#BioSQL
>>>>
>>>> Thanks for all the work by the dev team. Much appreciated - I use  
>>>> bioruby
>>>> almost every day.
>>>> -r
>>>>
>>>> Rob Syme
>>>> _______________________________________________
>>>> BioRuby Project - http://www.bioruby.org/
>>>> BioRuby mailing list
>>>> BioRuby at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioruby
>>>>
>>>>
>>>
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>>>
>
>
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-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================