Re: [Treebase-devel] NeXML support in TreeBASE2

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

Well you don't need a triple store for that - BioSQL for example could  
store the data. BioSQL is weakly typed, though, so yes, that's a  
difference. We'll fix that.

	-hilmar

On Aug 10, 2009, at 4:35 PM, Rutger Vos wrote:

> Is TreeBASE (to some extent) a triple store? No. But it would be nice
> if it could collaborate with one. I'd love to talk about some sort of
> community effort to make that work. But for now TreeBASE is strictly
> based on a strongly typed relational schema, so you can understand
> that it can't capture phenoscape annotations.
>
> On Fri, Aug 7, 2009 at 6:22 AM, William Piel<wil...@ya...>  
> wrote:
>>
>> On Aug 6, 2009, at 10:54 AM, Hilmar Lapp wrote:
>>
>>> I understand that TreeBASE2 can now output NeXML. However, can it
>>> also ingest and store the contents of NeXML?
>>
>> no.
>>
>>> More specifically, can TreeBASE2 ingest and store arbitrary metadata
>>> attached to trees, nodes, and matrix cells?
>>
>> no -- only the standard pre-colon and post-colon vaules; and for each
>> tree, a fixed set of metadata (tree quality, tree type, etc) plus
>> values that authors are free to enter whatever they want (tree title,
>> label, comments, etc).
>>
>>> We would be very interested in this in the context of the Phenoscape
>>> project (http://phenoscape.org) where we create NeXML files with the
>>> phylogenetic character data and tree with embedded formal phenotype
>>> assertions that are attached to matrix cells. Is it possible to
>>> submit these files to TreeBASE2, and to get those back out, e.g.,
>>> using the REST API?
>>
>> TreeBASE2 uses a headless version of Mesquite to parse nexus files.  
>> If
>> a module is developed to parse NeXML into Mesquite, that would be one
>> way to bring NeXML into TreeBASE2. Alternatively, we would need to
>> write a NeXML parser. Our schema is largely designed to capture data
>> that are transportable via nexus files -- for matrix files that means
>> character labels and state labels. If "phenoscape assertions" can be
>> coded as character labels and state labels, then there should be no
>> problem storing them in TreeBASE.
>>
>> bp
>>
>>
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>
>
>
> -- 
> NOTE: I will soon lose my UBC email address, please start using my
> gmail address instead (rut...@gm...)
>
> Dr. Rutger A. Vos
> Department of zoology
> University of British Columbia
> http://www.nexml.org
> http://rutgervos.blogspot.com

-- 
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: Hilmar Lapp  -:-  Durham, NC  -:- hlapp at duke dot edu :
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