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EntityType and Species Taxonomy in version 14

Dave Middleton
Posted 4 months ago

enter image description here

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POSTED BY: Dave Middleton
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Dave Middleton
Dave Middleton
Posted 3 months ago

@kapio An update of the ResourceFunction has been released. Please run ResourceUpdate["TaxonomyTree"].
POSTED BY: Dave Middleton
Dave Middleton
Dave Middleton
Posted 3 months 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
Dave Middleton
Dave Middleton
Posted 3 months 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
Dave Middleton
Dave Middleton
Posted 3 months 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

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

I don't know, I get the same error you do.
POSTED BY: Ian Ford
Dave Middleton
Dave Middleton
Posted 3 months ago
POSTED BY: Dave Middleton
Dave Middleton
Dave Middleton
Posted 3 months ago
POSTED BY: Dave Middleton

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

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

POSTED BY: Ian Ford
Dave Middleton
Dave Middleton
Posted 3 months 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

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
Dave Middleton
Dave Middleton
Posted 3 months ago
POSTED BY: Dave Middleton
POSTED BY: Moderation Team
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