Explain rooted tree vs. "biologically correct" root (curation tool)

[jimallman]

Email from @rgazis:

Even though I rooted the tree (as in the publication) and selected the ingroup. Under trees it says "tree root: arbitrary (not biologically correct)". The same happens with the other studies.

[jimallman]

To make this more clear, I've made the root-setting clickable in the tree list (this is subtle, since it's not really an error):

Clicking this brings up the tree-popup to the Properties tab. If the user is just viewing the study, this shows an expanded explanation of arbitrary rooting:

A curator who's editing the tree will see the root-setting widget highlighted as we've done for internal node labeling elsewhere:

[jimallman]

This is available for review on devtree. @rgazis, does this address your concerns?

[jar398]

I'm not too keen on "arbitrary". In fact the root may not be arbitrary - it could actually be the correct one by coincidence, and it is at least likely to b one that is chosen methodically (if 'incorrectly'), not arbitrarily, by an algorithm. I would say in this situation that the correct (biological) root is unknown (to the app), not recorded (in phylesystem), not available (to us), or not curated (by any of our curators). This leads to something like

Biological root is
o confirmed by curator
o not confirmed (displayed root could be arbitrary)

[jimallman]

not confirmed (displayed root could be arbitrary)

Thanks, will do. As a bonus, this more accurately reflects the logic of the app.

[jimallman]

These changes are live on devtree for review.

[jimallman]

NOTE that this is causing a problem on devtree. Tree popup disappears immediately from this URL:
https://devtree.opentreeoflife.org/curator/study/edit/694?tab=trees

[jimallman]

Fixed, merged to master.