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

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

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