[Gmod-help] Re: [Gmod-gbrowse] Custom GBrowse adaptor

[Haiming Wang]

Hi Inna,

In EuPathDB project, inclucding PlasmoDB, ToxoDB, TriTrypDB... We wrote 
a custom database adaptor to let GBrowse communicate with databases in 
GUS schema long time ago. Designed to be more general, SQL queries were 
factored into a separate config file which provides flexibility for 
customization. From our experience, that adatpor works well. However, 
the sites encountered performance slowdown and performance tuning is 
required.

If you're interested, the codes are under gbrowse realease 
/contrib/SynView/cgi-lib/ directory, there is no sample query xml and 
document about how to set it up yet. Please let me know if you want to 
give it a try or have other questions.

Cheers,
-Haiming

-----------------------
Haiming Wang
EuPathDB Group
Center for Tropical & Emerging Global Diseases
University of Georgia
Phone: 706-542-1447
Email: hwang at uga.edu


Rytsareva, Inna (I) wrote:
> Hello, 
>
> Of course, it is easier and faster to write a program to convert the
> contents of the DB to GFF3, but here is a problem - "redundancy" as well
> as we will have 2 similar datasets. And I'm not sure that it's possible
> to write a new adaptor by myself for 1 month. 
>
> Well, I'm thinking about to create GFF3 file on-fly as a temporary file.
> An idea is to write a perl script what parses the DB and creates GFF3
> according with a search query. But it's still an idea and I'm not sure
> that it works.
>
> How do you think, is this implementation possible? 
>  
> Inna Rytsareva
> Discovery Information Management
> Dow AgroSciences
> Indianapolis, IN 
> 317-337-4716
>
> -----Original Message-----
> From: Dave Clements, GMOD Help Desk [mailto:gmodhelp at googlemail.com] 
> Sent: Wednesday, July 15, 2009 4:19 PM
> To: Rytsareva, Inna (I)
> Cc: Gbrowse Mailing List
> Subject: Re: [Gmod-gbrowse] Custom GBrowse adaptor
>
> Hi Inna,
>
> Writing a GBrowse adaptor is a large undertaking.  It is almost always
> easier to write a program to convert the contents of your DB to GFF3,
> then it is to write your own adaptor.
>
> Now, before reading any more, imagine that I typed that paragraph
> several hundred times.  Really, writing a database adaptor is not for
> the faint of heart.
>
>
> However, if you absolutely have to have an adaptor, I would start by
> looking at existing adaptors.  Several are in the gbrowse-adaptors CVS
> project:
>
>   http://gmod.cvs.sourceforge.net/viewvc/gmod/gbrowse-adaptors/
>
> The Chado and BioSql adaptors are probably good places to start.  I
> don't know of any doc on how to write a GBrowse adaptor.
>
> Thanks,
>
> Dave C
>
> On Wed, Jul 15, 2009 at 9:17 AM, Rytsareva, Inna (I)<IRytsareva at dow.com>
> wrote:
>   
>> Hello,
>> As I understood, to get GBrowse to use my custom database (MySQL, not
>>     
> GFF,
>   
>> not Chado), I would need to write my own GBrowse adaptor.
>>
>> How can I get started?
>> Thanks,
>> Inna Rytsareva
>>
>>
>>     
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