Re: [Treebase-devel] NeXML support in TreeBASE2

[William P. <wil...@ya...>]

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