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Proposed cleanup of specimen hierarchy

Open sebastianduesing opened this issue 4 months ago • 1 comments

Closes #1821. This pull request is a reorganization & cleanup of the specimen hierarchy to fix issues identified during the COB workshop. Changes are as follows:

  • Some terms from the specimen branch that should have been in the template were not. This PR moves all subclasses of "specimen" into the specimen template.
  • Unlike most other templates, the specimen template did not have a dedicated column for parent class. Instead, all of its axiom columns were formatted as "specimen and _______". This PR removes the "specimen and" part of those columns and adds a column for parent class.
  • This PR makes all terms for specimens from an organism asserted subclasses of "specimen from organism".
  • Some logic changes were made during the process of moving terms into the template; these are primarily the result of translating unnecessarily complicated or redundant axioms into the standard template forms. I've done my best to ensure the template axiomatization captures what the original axiomatization was intended to capture.
  • An axiom adapted from the process "collecting specimen from organism" was added to "specimen from organism" to facilitate logical linkage between those two terms & terms referencing either of them.
  • I made no other changes to specimen terms when moving them into the templates except for a limited number of cases of specimens referencing anatomical parts from Uberon. OBI has many specimen terms that follow a pattern of "{anatomical part} specimen", all of which have similar axioms referencing the anatomical part from which the specimen was derived. There were a small number of terms that had no such axiom despite it being clear which anatomical part they were intended to reference in such an axiom. In these cases, I added the appropriate axiom. Most used terms already imported into OBI that just were not referenced in the term's logic. For one, "cloacal specimen", the term "cloaca" was not already imported, so I imported it.

sebastianduesing avatar Oct 09 '24 21:10 sebastianduesing