Re: [Treebase-devel] analysis metadata in TreeBASE, some experiments

[Rutger V. <R....@re...>]

It looks like the example file was blocked by the mailman software so
I committed it to the nexml examples directory. Here it is:
http://nexml.svn.sourceforge.net/viewvc/nexml/trunk/nexml/examples/treebase-record.xml?revision=1697&view=markup

On Mon, Jun 13, 2011 at 1:37 PM, Rutger Vos <R....@re...> wrote:
> Hi all,
>
> over the weekend I did some experimentation with how additional
> metadata having to do with phylogenetic analyses stored by TreeBASE
> could be serialized. Attached is the result as produced by a test case
> that I committed to the TreeBASE source.
>
> For context, here is how TreeBASE sees the world: every submission to
> TreeBASE consists of the results of one or more analyses. Each
> analysis consists of one or more analysis steps. For each step, we
> store the "algorithm" (e.g. neighbor joining) and the "software" (e.g.
> PAUP). Optional additional metadata can consist of a textual
> description of the algorithm, a version number and URL of the software
> and a text string containing analysis step commands (perhaps something
> like a PAUP block).
>
> Every analysis step has input and output data. These data can be trees
> and matrices. The set of taxa in the input must be a superset of the
> taxa in the output (i.e. some sort of taxon pruning is allowed, but
> new taxa cannot be introduced during an analysis step). All data
> that's accessible to third parties (i.e. all public, non-embargoed
> data) must be the input or output of at least one analysis step, i.e.
> we don't allow orphaned data in completed submissions.
>
> In the attached example, I'm annotating the study (i.e. the root of
> the nexml document) to specify the permanent URLs of any associated
> analyses, and I annotate those analysis URLs with their respective
> analysis steps, specifying their PURLs and any additional metadata as
> described above. This is shown in lines 3-13.
>
> Then, for every data object I specify for which analysis step(s) it is
> the input and/or output (a data object can be both input and output if
> analysis steps are chained together). This is shown in line 448 for a
> character state matrix and line 1849 for a tree.
>
> This is all highly experimental but I figured I'd share at as a
> discussion piece for refining actual implementation of MIAPA
> annotations.
>
> Rutger
>
> --
> Dr. Rutger A. Vos
> School of Biological Sciences
> Philip Lyle Building, Level 4
> University of Reading
> Reading, RG6 6BX, United Kingdom
> Tel: +44 (0) 118 378 7535
> http://rutgervos.blogspot.com
>



-- 
Dr. Rutger A. Vos
School of Biological Sciences
Philip Lyle Building, Level 4
University of Reading
Reading, RG6 6BX, United Kingdom
Tel: +44 (0) 118 378 7535
http://rutgervos.blogspot.com