Re: [Treebase-devel] analysis steps capture in NeXML served by TreeBASE

[Hilmar L. <hl...@ne...>]

I guess the NeXML example file should then be documented so as not to be mistaken as a sample of something one would actually obtain from TreeBASE.

	-hilmar

On Jun 20, 2012, at 4:20 PM, Rutger Vos wrote:

> Hi Hilmar,
> 
> that example file was generated using this unit test:
> 
> http://treebase.svn.sourceforge.net/viewvc/treebase/trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlAnalysisConverterTest.java?revision=1095&view=markup
> 
> I am very sorry but I don't have the time right now to deploy this on
> TreeBASE, but it wouldn't be hard to do - it would need to be folded
> into the document writer here:
> 
> http://treebase.svn.sourceforge.net/viewvc/treebase/trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentWriter.java?revision=1095&view=markup
> 
> Cheers,
> 
> Rutger
> 
> On Wed, Jun 20, 2012 at 6:04 PM, Hilmar Lapp <hl...@ne...> wrote:
>> There is an example NeXML file in the examples folder that suggests that it is reproduced from TreeBASE (and its study number is actually a valid one):
>> 
>> http://nexml.org/nexml/examples/treebase-record.xml
>> 
>> However, this differs significantly from the one returned by TreeBASE for this study:
>> 
>> http://purl.org/phylo/treebase/phylows/study/TB2:S794?format=nexml
>> 
>> Specifically, the analysis input and output connections between trees and matrices are gone in the TreeBASE-produced version. This is rather unfortunate (at least from a MIAPA standpoint), because there doesn't seem to be any other way to connect characters and trees through an analysis with one as the input and the other as the output. Although Both characters and trees elements reference otus elements, referencing the same otus element doesn't have to mean that they are connected through one analysis.
>> 
>> Are there plans to also capture the analysis input/output in the TreeBASE NeXML?
>> 
>>        -hilmar
>> --
>> ===========================================================
>> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
>> ===========================================================
>> 
>> 
>> 
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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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-- 
===========================================================
: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
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