Re: [Treebase-devel] NeXML support in TreeBASE2

[Rutger V. <rut...@gm...>]

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