compose metadata stanza for scaling

[arlin]

The dev portal now shows scaled trees. However, the metadata report does not say anything about the scaling method. Instead it refers to "inference method" which says something like "induced_subtree from synthetic tree with ID opentree9.1". We need to extend this to include a description of the scaling, for the median, SDM and OT methods.

The resulting text could be something like "The induced_subtree from synthetic tree with ID opentree9.1 was scaled by the Supertree Distance Method (SDM) yada yada yada"

To do

• compose a sentence for median
• compose a sentence for SDM
• compose a sentence for OT method
• design a way to combine this with the topology description.

[LunaSare]

Median inference method: Multiple chronograms with some or all species found in OToL tree store are summarized by calculating the median age of overlapping nodes into a distant matrix and then applying a clustering method such as UPGMA.

SDM inference method: Multiple chronograms with some or all species found in OToL tree store are summarized using the Supertree Distance Method (SDM)

OT method: The induced_subtree from synthetic tree with ID opentree9.1 scaled with OToL scaling service.

[LunaSare]

Where exactly goes the topology description?

[arlin]

@LunaSare, go to the dev portal, get a tree, then click on the "metadata" tab. This is the part that we need to fix. It has a slot for tree inference method but not for scaling.

This is because the metadata model is based on the MIAPA checklist (https://github.com/evoinfo/miapa/blob/master/checklist/MIAPA-checklist.md), which did not imagine this use-case. So, it does not have separate slots for "topology" and "scaling". It has slots for "tree inference method" and for "branch lengths". We can (1) create a slot for scaling; (2) put scaling methods in branch lengths; or (3) put scaling methods in "tree inference". Which is best?

Let's do the redesign first, then return to finish this issue. I have opened another ticket, #314, for a redesign. It would be great if you are available to brainstorm on that. The general idea is to document the trees.