Classify Instruments Batch II (#476)

* Add instrument class relationships for multiple vendors

New instrument class terms:
- MS:1003922 tandem time-of-flight (TOF/TOF)
- MS:1003923 magnetic sector ion trap

New vendor GC-MS parent terms:
- MS:1003918 LECO GC-MS system model
- MS:1003919 JEOL GC-MS system model
- MS:1003920 PerkinElmer GC-MS system model
- MS:1003921 Varian GC-MS system model

Instrument classifications added (34 total):
- LECO: 10 instruments (TOF)
- IonSpec: 6 instruments (FT-ICR)
- Finnigan MAT: 8 instruments (magnetic sector, quadrupole, triple quadrupole)
- Applied Biosystems: 4 instruments (TOF, TOF/TOF)
- Varian: 2 instruments (ion trap)
- Ionicon Analytik, JEOL, IONTOF, PerkinElmer: 1 each

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Remove verification comment from Pegasus IV term

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Remove vendor-specific GC-MS system model terms

Removed intermediate vendor GC-MS parent terms and reparented
instruments directly to MS:1003734 (gas chromatography mass
spectrometry system model):
- MS:1003918 LECO GC-MS system model
- MS:1003919 JEOL GC-MS system model
- MS:1003920 PerkinElmer GC-MS system model
- MS:1003921 Varian GC-MS system model

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Remove remaining vendor-specific GC-MS system model terms

Removed Agilent and Shimadzu GC-MS parent terms and reparented
instruments directly to MS:1003734 (gas chromatography mass
spectrometry system model):
- MS:1003735 Shimadzu GC-MS system model
- MS:1003914 Agilent GC-MS system model

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Remove MS:1003734 GC-MS system model term

Reparented all 33 GC-MS instruments directly to MS:1003733
(gas chromatography mass spectrometry system).

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Change GC-MS instrument relationships from is_a to part_of

These MS instruments are standalone components that pair with
separate GC systems, not subtypes of GC-MS systems. Using part_of
better represents this modular relationship.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Revert "Change GC-MS instrument relationships from is_a to part_of"

This reverts commit 866b0a4.

* Refactor instrument class hierarchy to separate analyzer types from instruments

Create 6 new instrument class terms (MS:1003924-MS:1003929) for single-analyzer
instruments, remove is_a instrument class from the original mass analyzer type
terms, rename 12 hybrid instrument class terms with "instrument" suffix, redirect
59 instrument model is_a references to the new instrument parents, and harmonize
all 18 instrument class children definitions for consistent style.

* correction to 1x is-a def

* update is_a for termID clash fix

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Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>
Co-authored-by: Joshua Klein <mobiusklein@gmail.com>

Author: 3 people