XSD/DTD for Chado-XML

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XSD/DTD for Chado-XML

dmgood11
I’m looking at a possibly out of date wiki page concerning Chado-XML (http://gmod.org/wiki/Chado_XML) and noticed a reference to:

  “...the DTD/XSD/RNG/RNC [TODO], in the dtd/ directory.”

does a DTD/XSD document exist in the current (or recent or any) chado distribution? All I found were some xsl files in the ./chado-xml directory.

 

thanks,
-David


--
David M. Goodstein, Ph.D.
Phytozome Group Lead
Plant and Computational Genomics Group
Joint Genome Institute - U.S. Dept. of Energy
Center for Integrative Genomics - UC Berkeley


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Re: XSD/DTD for Chado-XML

Chris Mungall
Hi David,

AFAICR, the structure of Chado-XML was always derived from the
relational schema using the generic XORT transform. I'm not sure that a
XSD or Relax generator was ever written. What's this for? The original
XML-based infrastructure for Chado is less used than Perl and Java based
object layers, which may be a batter target for what you're doing. I'm
back at the JGI the week after next, we can discuss more then.

On 13 Jun 2014, at 23:33, David Goodstein wrote:

> I'm looking at a possibly out of date wiki page concerning Chado-XML (
> http://gmod.org/wiki/Chado_XML) and noticed a reference to:
>
> "...the DTD/XSD/RNG/RNC [TODO], in the dtd/ directory."
>
> does a DTD/XSD document exist in the current (or recent or any) chado
> distribution? All I found were some xsl files in the ./chado-xml
> directory.
>
>
>
> thanks,
> -David
>
>
> --
> David M. Goodstein, Ph.D.
> Phytozome Group Lead
> Plant and Computational Genomics Group
> Joint Genome Institute - U.S. Dept. of Energy
> Center for Integrative Genomics - UC Berkeley
> ------------------------------------------------------------------------------
> HPCC Systems Open Source Big Data Platform from LexisNexis Risk
> Solutions
> Find What Matters Most in Your Big Data with HPCC Systems
> Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
> Leverages Graph Analysis for Fast Processing & Easy Data Exploration
> http://p.sf.net/sfu/hpccsystems_______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema

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Find What Matters Most in Your Big Data with HPCC Systems
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Re: XSD/DTD for Chado-XML

dmgood11
I’m probably thinking a bit too “old school”, but my plan was to use the Chado-XML to populate a number of JAXB classes (previously defined via the apparently non-existent Chado-XML.xsd), and then sub-class those to make a bunch of biologist-friendly objects that are a little more Ensembl-y and a little less SO-y.  At this point they would not be modified and written back to Chado.  I expect I might be reinventing the wheel here, so will be good to talk next week.

-David



On Fri, Jun 13, 2014 at 4:42 PM, Chris Mungall <[hidden email]> wrote:
Hi David,

AFAICR, the structure of Chado-XML was always derived from the relational schema using the generic XORT transform. I'm not sure that a XSD or Relax generator was ever written. What's this for? The original XML-based infrastructure for Chado is less used than Perl and Java based object layers, which may be a batter target for what you're doing. I'm back at the JGI the week after next, we can discuss more then.


On 13 Jun 2014, at 23:33, David Goodstein wrote:

I'm looking at a possibly out of date wiki page concerning Chado-XML (
http://gmod.org/wiki/Chado_XML) and noticed a reference to:

"...the DTD/XSD/RNG/RNC [TODO], in the dtd/ directory."

does a DTD/XSD document exist in the current (or recent or any) chado
distribution? All I found were some xsl files in the ./chado-xml directory.



thanks,
-David


--
David M. Goodstein, Ph.D.
Phytozome Group Lead
Plant and Computational Genomics Group
Joint Genome Institute - U.S. Dept. of Energy
Center for Integrative Genomics - UC Berkeley
------------------------------------------------------------------------------
HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
Find What Matters Most in Your Big Data with HPCC Systems
Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
Leverages Graph Analysis for Fast Processing & Easy Data Exploration
http://p.sf.net/sfu/hpccsystems_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema



--
David M. Goodstein, Ph.D.
Phytozome Group Lead
Plant and Computational Genomics Group
Joint Genome Institute - U.S. Dept. of Energy
Center for Integrative Genomics - UC Berkeley


------------------------------------------------------------------------------
HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
Find What Matters Most in Your Big Data with HPCC Systems
Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
Leverages Graph Analysis for Fast Processing & Easy Data Exploration
http://p.sf.net/sfu/hpccsystems
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema