[Gmod-gbrowse] [Gmod-help] general questions about data querying

[Scott Cain]

Hi Dave and Ryan,

Right--both Bio::DB::GFF and Bio::DB::SeqFeature::Store support  
querying via the perl API.  You can look at the perldoc for simple  
examples of what can be done, and you can look at this WormBase page:

   http://www.wormbase.org/wiki/index.php/Mining_WormBase_with_Bio::DB::GFF

for more complex examples.  While those examples are using  
Bio::DB::GFF, SeqFeature::Store supports most of the same method calls.

Scott



On Nov 11, 2009, at 5:08 PM, Dave Clements, GMOD Help Desk wrote:

> Hi Ryan,
>
> GFF3 is stored in the Sequence module in Chado, which is fairly well
> documented.  See http://gmod.org/wiki/Chado_Sequence_Module for a
> start.
>
> You *can* query the Bio::DB::SeqFeature::Store directly, but I don't
> think that format is as well documented.  You'll also (I think) have
> to use Perl since features are stored in a binary Perl format.
>
> Dave C.
>
> On Wed, Nov 11, 2009 at 1:51 PM, Ryan Golhar <golharam at umdnj.edu>  
> wrote:
>> Hi Dave.  Thanks for the response.
>>
>> I guess my problem comes down to "I know what I'm looking for", now  
>> I need
>> to scan through the coordinates of the genes to find the ones that  
>> overlap.
>>  I figured I could readily query the database the same way Gbrowse  
>> does to
>> get at the data, is that a correct approach?  I suppose querying the
>> database is a better solution than querying GBrowse as Gbrowse is  
>> just
>> displaying the data from the database, correct?
>>
>> If I load the data into Chado (I currently have it in GFF in  
>> mySQL), then
>> how to I query the database?
>>
>> Once I have all the data processed, I will end up creating a gff  
>> file and
>> displaying it in GBrowse, but I need to get the data first...
>>
>> Ryan
>>
>>
>> Dave Clements, GMOD Help Desk wrote:
>>>
>>> The next best thing is for sites to define their own set of
>>> interesting questions and run some preprocessing on the data to find
>>> regions that are "interesting".  There are several ways to display
>>> and/or link to interesting regions.  There could be a separate page
>>> that lists them; on any feature that is interesting the popup/hover
>>> could have a link to "show other +/- strand overlapping genes".  If
>>> there aren't too many of them you could have a track in the overview
>>> or region areas that shows the interesting areas and then users  
>>> could
>>> zoom in on them.
>>>
>>>
>>> Hmm.  I just reread your email, and you *might* be asking a  
>>> different
>>> question.  Do you want to ask this question in the database itself,
>>> rather than in GBrowse?  To do this, I would load the data into  
>>> Chado
>>> and ask it there.  The databases that usually back GBrowse are built
>>> for speed, rather than for clarity and ad hoc questions.
>>>
>>>
>>> Hopefully, I answered your question, and your next question  
>>> too.  ;-)
>>>
>>> I also encourage anyone else on the list to respond.
>>>
>>> Dave C.
>>>
>>>
>>> On Wed, Nov 11, 2009 at 12:42 PM, Ryan Golhar <golharam at umdnj.edu>  
>>> wrote:
>>>>
>>>> Hi,
>>>>
>>>> I recently installed Gbrowse to view some data I have, but now I'm
>>>> interested in performing a more thorough analysis of the data.  I  
>>>> want to
>>>> identify certain regions of the genome that contain overlapping  
>>>> genes  on
>>>> the plus/minus strand ie one gene on the plus strand and a 2nd  
>>>> gene on
>>>> the
>>>> minus strand overlapping the 1st gene.
>>>>
>>>> I can see one or two of these occurrences in GBrowse, but I don't  
>>>> want to
>>>> do
>>>> this manually.  Is there a way to query the database to find all
>>>> occurrences
>>>> of these?
>>>>
>>>> Ryan
>>>>
>>>
>>>
>>>
>>
>
>
>
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-----------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research