NeXML ISAtab update

[Elliott Hauser]

Hey all.

We've made good progress in the NeXML -> ISAtab tool.

This week I completed:

* Rewriting all of the code to take arbitrary changes to the ISAconfigs

* Splitting out the logical mappings into mappings.xsl (for customization & updating convenience)

* Commenting and documenting mappings.xsl

Did not get done:

* Validation of ISAtab using new config.  Files appear well-formed, but ISA validator is giving me weird errors.  Emails out to Philippe for help with this and I'll also email the ISAtools list

To-do:

* Documentation and how-tos update 

* Merge branches

* Write-up of next steps for MIAPA

* Loose ends & issue documentation

The ISAconfig branch has my latest version.  Feel free to give it a try at yr command line.  The readme should have everything you need for operation, and example files with example output are included.  If you REALLY want to test things, make some arbitrary (but well-formed) changes to the ISA configs and run the transform again.  You'll see header names, etc that you change reflected in the output, meaning the tool is ready for versioned ISAconfigs over time.  Changes to Treebase NeXML can be reflected in mappings.xsl, so the data shows up in the right place.

Let me know if you have any questions.

E

[Rutger Vos]

Wow, great progress! Now I have that nagging feeling again that
TreeBASE's NeXML output needs more work. Thanks.

Best wishes,

Rutger

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--
Dr. Rutger A. Vos
Bioinformaticist
NCB Naturalis
Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the Netherlands
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[Jim Leebens-Mack]

Yes!  Elliott! it is wonderful to see the progress you have made over the summer!

We are refining Phylont as a source of useful concepts for describing tree types, branch length units, etc.  We will keep you all posted as this work moves forward.

Bests,

Jim

  

=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Jim Leebens-Mack
Department of Plant Biology
University of Georgia
Athens, GA 30602-7271

Phone: 706-583-5573
Fax: 706-542-1805
email: jleebe...@plantbio.uga.edu
url: http://www.plantbio.uga.edu/~jleebensmack/JLMmain.html 

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From: Rutger Vos [mailto:rutge...@gmail.com]
To: Elliott Hauser [mailto:ea...@mac.com]
Cc: Phyloinformatics Group [mailto:wg-phyloi...@nescent.org], nexml-...@lists.sourceforge.net, miapa-...@googlegroups.com
Sent: Thu, 26 Jul 2012 07:14:50 -0400
Subject: Re: NeXML ISAtab update