Currently the taxonomic category names are very long and include more information than necessary. For example, "Relative abundance of order data". In the subsetting tab we already have the information that it's relative abundance, and when the user selects it for the app it also says 16S along with it. So it seems that the "relative abundance" and "data" parts of the display name are unnecessary.

Could we please change the display names of these to the taxonomic levels, like how it is on the live site?

Note this is also very helpful for the ranked abundance app, where the display name gets used as an axis name (see below).

I don't think we'll ever use the PostGIS polygon lookup at a lower $max_level than 2 but if we do, these few lines won't affect the @cleaned array.

Currently it's called "Data item". What should we call it instead?

Where B and C both have common ancestor A, the algorithm in ./Load/bin/reconcilePopBioSpecies.pl returns A.

But when you ask for the common ancestor of A and B (in that same hypothetical tree) it returns the parent of A, let's call it Z. It should be A.

Note - when this is fixed we should do a reload of all studies with multiple species assays per sample. This is not a simple EDA query to figure out (it would require a 'count_of_children' derived variable). "Pyretophorus" is one of the offending reconciliation outputs, it is present in VBP0000004 and VBP0000005. Aha... these reconciliation outputs have species qualifier = ambiguous - filtering on that gives us the studies we should reload!

2007-UCDavis-UCLA            VBP0000005    UC Davis/UCLA population dataset
2009-Costantini-Burkina-Faso VBP0000006    Living at the edge: biogeographic patterns of habitat segregation conform to speciation by niche expansion in Anopheles gambiae
2012-Donnelly-M-S-IR         VBP0000004    Genotyping and permethrin-resistance phenotyping of Anopheles gambiae M and S form mosquitoes from Cameroon, Ghana, Uganda and Guinea-Bissau
2012-conn-peru               VBP0000835    Molecular Taxonomy of Anopheles (Nyssorhynchus) benarrochi (Diptera: Culicidae) and Malaria Epidemiology in Southern Amazonian Peru
2016-indian-icemr            VBP0000162    Increasing the potential for malaria elimination by targeting zoophilic vectors
Ag1000G_AR3                  VBP0000163    Natural diversity of the malaria vector Anopheles gambiae

Seen in mbio QA

I would imagine wrapping the text would look better than expanding the box a really really far, but would love to hear other opinions!

Or maybe it is working as planned (downloads may use the variableTree "permissions")

Anyway - it's not ideal - and we should fix. Not sure if front or back end yet.