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EntityType and Species Taxonomy in version 14

Posted 1 month ago

enter image description here

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POSTED BY: Dave Middleton
15 Replies
Posted 15 days ago

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: enter image description here

Mathematica Online: enter image description here

Mathematica 13.3. Windows running in a Citrix session: enter image description here

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.

POSTED BY: Dave Middleton
Posted 14 days ago

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"]]

enter image description here

POSTED BY: Dave Middleton

POSTED BY: Ian Ford
Posted 18 days ago

Thanks Ian, for the suggestion.

POSTED BY: Dave Middleton
Posted 18 days ago

The sharks taxonomy can be visualized as a tree, starting with a single species i.e. the great white shark as so:

ResourceFunction["TaxonomyTree"][
 Entity["TaxonomicSpecies", "CarcharodonCarcharias::k6mys"], 
 "Depth" -> 7]

enter image description here

POSTED BY: Dave Middleton

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.

enter image description here

POSTED BY: Kapio Letto
Posted 18 days ago

Dear Kapio, you're not confused; the error is odd as you copied the same expression as I did. You should be able to get all the way up to the "cartilaginous fishes, before we enter into "sibling taxa territory" at larger "Depth" values:

ResourceFunction["TaxonomyTree"][
 Entity["TaxonomicSpecies", "CarcharodonCarcharias::k6mys"], 
 "Depth" -> 9]

enter image description here

Thanks for letting me know; I will look into this. Maybe the entity framework was unable to to retrieve some data during your evaluation.

POSTED BY: Dave Middleton
Posted 13 days ago

@kapio An update of the ResourceFunction has been released. Please run ResourceUpdate["TaxonomyTree"].

POSTED BY: Dave Middleton

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?

POSTED BY: Ian Ford

@Ian, do you have some idea why did I get that error? -- See my comment above.

POSTED BY: Kapio Letto

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

POSTED BY: Ian Ford
Posted 18 days ago

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.

POSTED BY: Dave Middleton

Thanks for the explanation. If NestGraph gives a non-tree for a given function and initial value, NestTree would still give a tree but would have duplicate branches, so I see why it makes sense to first build a graph.

POSTED BY: Ian Ford
Posted 17 days ago

Well, this is embarrassing. The resource function works fine on my desktop installation where I removed any possible local resource object when testing on random entities and tree depths. However, I get the same error when I try it on Mathematica Online or the Citrix app of Mathematica. I will contact the WRT to put the function back into review status until this has been sorted.

POSTED BY: Dave Middleton

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