Loading human genomic data into Chado

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Loading human genomic data into Chado

dgpinheiro
Hi,

  I'm a novice user of Chado, so I need some help to load the current available human genomic data in there. Initially, I have three questions:
  1) Is there a Chado database storing human genomic data?
  2) Is there any gff files ready to load the human genomic data in there?
  3) How can I convert the NCBI NT contigs and chromosomes from Genbank files to Chado database? Is bp_genbank2gff3.pl reliable?

Thanks,
Daniel
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Re: Loading human genomic data into Chado

Scott Cain
Hi Daniel,

Questions about Chado are best sent to the schema mailing list, cc'ed
here.  I'll answer inline below.

Scott


On Wed, Dec 8, 2010 at 7:23 AM, Daniel Guariz Pinheiro
<[hidden email]> wrote:
> Hi,
>
>   I'm a novice user of Chado, so I need some help to load the current
> available human genomic data in there. Initially, I have three questions:
>   1) Is there a Chado database storing human genomic data?

Not that I know of, but I wouldn't be surprised if someone had done it.

>   2) Is there any gff files ready to load the human genomic data in there?

Not that I know of.

>   3) How can I convert the NCBI NT contigs and chromosomes from Genbank
> files to Chado database? Is bp_genbank2gff3.pl reliable?

bp_genbank2gff3.pl works reasonably well, but dealing with the
variablility in Genbank files can be quite difficult, so the output
needs to be cleaned up sometimes.  The good news is that anything in
RefSeq should work reasonably well.

May I ask why you want to put human data into Chado?  That is, what is
your plan for it once it's in there?

Scott


>
> Thanks,
> Daniel
> ------------------------------------------------------------------------------
> What happens now with your Lotus Notes apps - do you make another costly
> upgrade, or settle for being marooned without product support? Time to move
> off Lotus Notes and onto the cloud with Force.com, apps are easier to build,
> use, and manage than apps on traditional platforms. Sign up for the Lotus
> Notes Migration Kit to learn more. http://p.sf.net/sfu/salesforce-d2d
> _______________________________________________
> Gmod-devel mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>
>



--
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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

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