[BioSQL-l] PhyloDB

[Hilmar Lapp]

MJ,

Did you try using the --download option? BTW you can obtain documentation of this and other options by supplying --help on the command line.

	-hilmar

On Oct 7, 2012, at 10:35 PM, Mo_Jun_Shen at bd.com wrote:

> Hi Hilmar, 
> 
> Thank you for your reply. I ever tried to run 'load_itis_taxonomy.pl' to load ITIS taxonomy. But the load_itis_taxonomy.pl  could not work because it needs 'itisMSforTar.sql' to complete the process.  When I run the load_itis_taxonomy.pl, I got error message: 
> 
> failed to open /itisMSforTar.sql for reading: No such file or directory 
> 
> I couldn't find itisMSforTar.sql anywhere. It is neither in BioSQL scripts/sql, nor in ITIS data set.  Can you please advise where I can get itisMSforTar.sql? 
> 
> Thanks, 
> MJ Shen 
> 
> 
> From:	Hilmar Lapp <hlapp at drycafe.net>
> To:	"Mo_Jun_Shen at bd.com" <Mo_Jun_Shen at bd.com>
> Cc:	"biosql-l at lists.open-bio.org" <biosql-l at lists.open-bio.org>
> Date:	09/19/2012 02:20 PM
> Subject:	Re: [BioSQL-l] PhyloDB
> 
> 
> 
> 
> MJ, 
> 
> Apologies for the long time your message was held up in moderation. Was your question resolved meanwhile? There is a script that comes with Biosql that loads the ITIS taxonomy (which essentially consists of 5 trees, one for each "kingdom") into the PhyloDB tables. This may serve as an example for how to get data into those tables. Does this answer your question?
> 
> -hilmar 
> 
> Sent with a tap. 
> 
> On Jul 8, 2012, at 9:06 PM, Mo_Jun_Shen at bd.com wrote:
> 
> Dear  Sir/Madam, 
> 
> I am very interested in PhyloDB in BioSQL for querying taxonomy.  However, I couldn't find scripts or document to describe how to setup data for phyloDB after initiating phyloDB .  Could you please provide guidance?
> 
> Thank you. 
> 
> Best Regards, 
> MJ Shen
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: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
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