[BioSQL-l] FPC maps in the marker database

[Jason Stajich]

I don't think there is much one way or another anymore.  I stopped work 
on those modules quite a long time ago.  I had some hope that Ken's 
CMAP stuff would be able to generally handle lots of different map 
types but it would need someone to dedicate a fair amount of time to 
get the FPC stuff working.

You also might have more luck talking to the FPC module authors about 
their ideas as they probably store stuff in DBs there.

If there is a logical mapping of the FPC stuff into the BioSQL system 
I'm all for it, but as of now the map stuff  it is pretty much just 
remnants.  I also expect the chado guys to integrate some sort of map 
stuff into their models as well since there is a lot of genetic map 
data in most of the model system dbs but I don't know anything about 
their plans.

Maybe would be good if you can talk a little more about the type of 
functionality you really wanted with the DB and that might stir up some 
more memories of what it would take to get it in the system.


-jason

On Jan 7, 2005, at 1:07 PM, Hilmar Lapp wrote:

> The markerdb part of biosql was retired 2 years ago ... I don't know 
> whether Jason (the author of that part) has had any other plans in 
> this direction.
>
> 	-hilmar
>
> On Jan 4, 2005, at 9:01 AM, Bonnie Hurwitz wrote:
>
>> Hi,
>>
>> I was just wondering if anyone is using the markerdb portion of 
>> BioSQL to store FPC maps?  If so, are there any useful load scripts 
>> available?  I also noticed that BioPerl 1.5 will have parsers for FPC 
>> data, is this going to be connected in with BioSQL and the marker 
>> database?
>>
>> Thanks,
>> Bonnie
>>
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>>
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--
Jason Stajich
Duke University
jason at cgt.duhs.duke.edu