This is a nice function. I haven't looked too closely at the code, but I saw that you construct a Graph object and then convert it to a Tree object using GraphTree. Is there a complication with constructing it directly using NestTree, like you do in this post?

A new version of the ResourceFunction will become available soon. This version as been rewritten and no longer uses the child-taxa property iteratively. This version of TaxonomyTree relies on the TaxonomicSequence and the SpeciesList properties. These properties give results reliably across different installations e.g. cloud, Citrix on a PC.

Version 1.0.0 employed the child-taxa entity property iteratively as a way to traverse the taxonomy tree. Unfortunately, the child-taxa property may not yield any results on some platforms, causing the ResourceFunction to fail.

Comparison of child-taxa resolution performance

My PC, Windows:

Mathematica Online:

Mathematica 13.3. Windows running in a Citrix session:

Of course I tested version 1.0.0 on my PC without any issues, but for other platforms it will not work. I don't think this is how the TaxonomicSpecies entities are supposed to work, so I may report this to Wolfram Support.

Cool. But I got an error, see image. Also starting entity looks like ""great white shark" not some general shark. I might be confused. Cool post.

Thanks Ian.

Feel free to give me any feedback on the code. I am still learning about the Tree syntax and the new TaxonomicSpecies entities. I used Graphs as they are so easy to create with rules and rules are also easy to manipulate. The nested structure in trees adds a layer of complexity. On the other hand, once I have a tree, they are very comfortable to analyze.

My use case for the ResourceFunction is:

1. Use one known species and retrieve its taxonomy, visualized as a tree. If the Entity is a species-taxon: Ability to move up the taxa by a set number of levels. If the Entity is at a higher taxon: Ability to move down the taxa, where the entity's taxon is the root.
2. Compare the taxonomy of two or more different species by exploiting the TaxonomicSequence.

For use case 2 I assumed every TaxonomicSequence is complete and consistent. It's not always the case. I was unable to create a RulesTree from the start as it turned out: is wasn't a tree. The issue can be shown in my "berrries" example. A graph showed me why: some vertices had an InDegree > 1, and this is simple to identify and correct in a graph.

In use case 1, the same issue may exist, and I did not have a proper solution for NestTree when I created the function. For example NestGraph Entity["TaxonomicSpecies", "Lonicera::3gqqp"] resulted in a graph that was not a tree. However, I believe NestTree may offer a solution after all as this works just fine

children[ent : Entity["TaxonomicSpecies", _]] := 
  Replace[ent[
    EntityProperty["TaxonomicSpecies", 
     "ChildTaxa"]], _Missing -> {}];
children[_] = {};
NestTree[children, Entity["TaxonomicSpecies", "Lonicera::3gqqp"], 2, 
 TreeLayout -> Left, TreeElementLabelFunction -> All -> CommonName, 
 MaxDisplayedChildren -> Infinity]

I will rewrite some of the code of TaxonomyTree in future also with new insights I have on the taxonomic structure in the entity framework.

I don't know, I get the same error you do.

In the meantime (before the update), this expression should show you the sharks phyletic group in a taxonomy tree:

ResourceFunction["TaxonomyTree"][
 EntityClass[
   "TaxonomicSpecies", {EntityProperty["TaxonomicSpecies", 
      "PhyleticGroups"] -> Entity["SpeciesPhyleticGroup", "Shark"]}][
  "Entities"]]