Review/update major cross-species T-types in neocortex.

[dosumis]

Aim: Review & edit neocortical T-types at 'subclass' level in CL (see lists below) and:

• Dealing with multiple species: add species neutral term and species-specific types for mouse (WMB) & human (Jorstad).
  • For species neutral terms - mention that this is a transcriptomically supported/defined types. Add summary location in dev origins and properties to degree supported by current data.
  • For mouse terms, release via the WMB pipeline.
  • For human - add new subtypes and link these to the relevant dataset on CxG.
  • For species neutral terms (existing) we need to work on new guidance/pattern for definition.
• Neurons defined as T-types, not simply on expression (remove any expression-based EquivalentClass axioms)
• Make specifically neocortical - if justified by data (currently cerebral cortex)
• Review evidence for properties in name and detail this evidence in comment, e.g. what is the evidence for projection pattern and layer specificity of L6 IT - which brain regions were these tested in and by what technique (LLM queries would help - perhaps with a RAG DB in place). With these in place, how safe are classifications/assertions about these properties? relevant reference for projection patterns: https://www.nature.com/articles/s41586-021-03941-1#Fig1

Reference datasets:

Jorstad: Jorstad et al. (2023) Science CxG

.	class	subclass
GABA	MGE	Sst
GABA	MGE	Pvalb
GABA	MGE	Sst Chodl
GABA	MGE	Chandelier
GABA	CGE	Vip
GABA	CGE	Lamp5
GABA	CGE	Sncg
GABA	CGE	Lamp5 Lhx6
GABA	CGE	Pax6
Glut	IT	L2/3 IT
Glut	IT	L5 IT
Glut	IT	L4 IT
Glut	IT	L6 IT Car3
Glut	IT	L6 IT
Glut	non-IT	L5/6 NP
Glut	non-IT	L5 ET
Glut	non-IT	L6 CT
Glut	non-IT	L6b

WMB:

DOI:10.1038/s41586-023-06812-z https://tinyurl.com/2vt7dws4

Class	SubClass
01 IT-ET Glut	007 L2/3 IT CTX Glut
01 IT-ET Glut	004 L6 IT CTX Glut
01 IT-ET Glut	005 L5 IT CTX Glut
01 IT-ET Glut	022 L5 ET CTX Glut
01 IT-ET Glut	006 L4/5 IT CTX Glut
01 IT-ET Glut	001 CLA-EPd-CTX Car3 Glut
02 NP-CT-L6b Glut	032 L5 NP CTX Glut
02 NP-CT-L6b Glut	029 L6b CTX Glut
02 NP-CT-L6b Glut	030 L6 CT CTX Glut
06 CTX-CGE GABA	049 Lamp5 Gaba
06 CTX-CGE GABA	047 Sncg Gaba
06 CTX-CGE GABA	048 RHP-COA Ndnf Gaba
06 CTX-CGE GABA	046 Vip Gaba
07 CTX-MGE GABA	053 Sst Gaba
07 CTX-MGE GABA	050 Lamp5 Lhx6 Gaba
07 CTX-MGE GABA	051 Pvalb chandelier Gaba
07 CTX-MGE GABA	052 Pvalb Gaba

CL content:

• CGE http://purl.obolibrary.org/obo/CL_4023064

  • 
  • Specific issues:
    • Mouse has LAMP5 as CGE, LAMP5 Lhx6 as MGE. More recent data supports the MGE classification
      • [x] #3182
    • Check whether anatomically broader than neocortex (LAMP5 appears to have some population in striatum)

• MGE

  • http://purl.obolibrary.org/obo/CL_4023069
  • 
  • specific issues - pvalb, chandelier pvalb, sst, sst chodl should all be siblings
  • Check whether any are anatomically broader than neocortex (provisionally - yes - at least pan cortical - maybe broader)

• ET http://purl.obolibrary.org/obo/CL_4023009

• IT http://purl.obolibrary.org/obo/CL_0010012

• NP http://purl.obolibrary.org/obo/CL_4023012

• CT http://purl.obolibrary.org/obo/CL_4023013

• [x] Include new specific terms for species specific sst GABA #3242

• [x] #3247

• [x] #3231

[RiveraAndrea83]

Visual comparison of the two:

[RiveraAndrea83]

according to Tasic et al., sst-chodl should be a parent of sst and pvalb