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Basal Ganglion product EPIC

Open dosumis opened this issue 5 months ago • 1 comments

State of BG mappings: https://github.com/Cellular-Semantics/WMB_BG_KG/blob/main/reports/BG_mappings_analysis.csv

Old notes might be useful for consensus_anno_old in reference Gsheet

MVP aim (For October 2025 CL release) - All terms must have a CL classification at some level - not necessarily exact, but also ideally something deeper than just neuron, or neuron + NT.

Old tickets to review - still relevant?

  • [ ] #2761

Updates to BG mappings priority list:

  1. Classic GABAergics with 1:1 mappings to mouse

CL edits Priority 1: Terms with no CL mapping in BG or WMB at any level

  • [ ] #3345
    • Subpallium GABA,Cx GABA,ACx MEIS2 GABA,OB Dopa-GABA
  • [Subpallium GABA,Cx GABA,ACx MEIS2 GABA,OB FRMD7 GABA]
  • [Subpallium GABA,F M GABA,CN ONECUT1 GABA,GPi Core]
    • see https://chatgpt.com/share/68c70054-d240-800f-b0bb-9c65a8e4d5d2
  • [Subpallium GABA,F M GABA,F GABA,AMY-SLEA-BNST D1 GABA]
  • [Subpallium GABA,F M GABA,F GABA,AMY-SLEA-BNST GABA]
  • Group: SN GATA3-PAX8 GABA --> subclass: 195 SNr-VTA Pax5 Npas1 Gaba | [https://doi.org/10.3389/fnins.2022.976209]
  • Group: SN GATA3-PVALB GABA --> supertype: 0806 SNr Six3 Gaba_1 | [https://doi.org/10.3389/fnins.2022.976209]
  • [Subpallium GABA,F M GABA,F M GATA3 GABA,SN-VTR-HTH GATA3-TCF7L2 GABA]
  • [Subpallium GABA-Glut,CN GABA-Glut,CN GABA-Glut,GPi Shell]
    • See https://chatgpt.com/share/68c70054-d240-800f-b0bb-9c65a8e4d5d2
  • [x] #3322
  • [x] #3345

Priority2: Terms with CL lineage mapping only

  • [Subpallium GABA,CN LGE GABA,CN MEIS2 GABA,GPe MEIS2-SOX6 GABA]
  • [Subpallium GABA,CN MGE GABA,CN Cholinergic GABA,GPin-BF Cholinergic GABA] Related ticket - might need modifying (CN Chol-GABA may be more appropriate) #3093
  • [Subpallium GABA,CN MGE GABA,CN Cholinergic GABA,STR Cholinergic GABA] #3093
  • [Subpallium GABA,CN MGE GABA,CN Cholinergic GABA,STRd Cholinergic GABA] #3093
  • [Subpallium GABA,CN MGE GABA,CN ST18 GABA,STR-BF TAC3-PLPP4-LHX8 GABA]
  • [Subpallium GABA,F M GABA,CN LHX8 GABA,GPe SOX6-CTXND1 GABA]

Terms with mapping in WMB (to transfer to BG)

TO discuss with BG analysis WG:

BG2WMB_mapping refs BG_path BG_mapped_2_CL BG_CL_mapping WMB_mapped_2_CL WMB_CL_mapping
Group: GPe SOX6-CTXND1 GABA --> supertype: 0247 NDB-SI-MA-STRv Lhx8 Gaba_4 null [Subpallium GABA,F M GABA,CN LHX8 GABA,GPe SOX6-CTXND1 GABA] null null class: 08 CNU-MGE GABA medial ganglionic eminence derived interneuron
  • [ ] Add to agenda for BG analysis WG @ucdnjj

Should be straightforward to transfer

TODO: Edit first column to TRUE when updated on BG taxonomy sheet & in BG taxonomy annotations sheet. Consider appropriate level for addition. For annotations sheet, add annotation transfer evidence to rationale.

WMB CL mapping transferred to BG BG2WMB_mapping refs BG_path BG_mapped_2_CL BG_CL_mapping WMB_mapped_2_CL WMB_CL_mapping
FALSE Group: LAMP5-CXCL14 GABA --> subclass: 049 Lamp5 Gaba null [Subpallium GABA,CN CGE GABA,CN LAMP5-CXCL14 GABA,LAMP5-CXCL14 GABA] null null subclass: 049 Lamp5 Gaba lamp5 GABAergic cortical interneuron
FALSE Group: VIP GABA --> subclass: 046 Vip Gaba [https://doi.org/10.1038/s41586-020-2874-8] [Subpallium GABA,CN CGE GABA,CN VIP GABA,VIP GABA] null null subclass: 046 Vip Gaba VIP GABAergic cortical interneuron
FALSE Group: LAMP5-LHX6 GABA --> supertype: 0203 Lamp5 Lhx6 Gaba_1 null [Subpallium GABA,CN MGE GABA,CN LAMP5-LHX6 GABA,LAMP5-LHX6 GABA] null null subclass: 050 Lamp5 Lhx6 Gaba Lamp5 Lhx6 neuron
FALSE Group: STR SST-CHODL GABA --> subclass: 056 Sst Chodl Gaba [https://doi.org/10.1038/s41586-020-2874-8] [Subpallium GABA,CN MGE GABA,STR SST-CHODL GABA,STR SST-CHODL GABA] null null subclass: 056 Sst Chodl Gaba sst chodl GABAergic cortical interneuron
FALSE Group: STR LYPD6-RSPO2 GABA --> supertype: 0212 Pvalb Gaba_8 null [Subpallium GABA,CN MGE GABA,STR RSPO2 GABA,STR LYPD6-RSPO2 GABA] null null subclass: 052 Pvalb Gaba pvalb GABAergic cortical interneuron
FALSE Group: STR SST-RSPO2 GABA --> supertype: 0228 Sst Gaba_15 null [Subpallium GABA,CN MGE GABA,STR RSPO2 GABA,STR SST-RSPO2 GABA] null null subclass: 053 Sst Gaba sst GABAergic cortical interneuron
FALSE Group: STR SST-ADARB2 GABA --> subclass: 053 Sst Gaba null [Subpallium GABA,CN MGE GABA,STR SST GABA,STR SST-ADARB2 GABA] null null subclass: 053 Sst Gaba sst GABAergic cortical interneuron

Terms to review mapping

See all no_bg_cl_mapping: False in https://github.com/Cellular-Semantics/WMB_BG_KG/blob/main/reports/BG_mappings_analysis.csv

BG_mapped_2_CL BG_CL_mapping
Subclass: M Dopa substantia nigra dopaminergic neuron
Group: SN-VTR CALB1 Dopa substantia nigra dopaminergic neuron
  • [ ] #3344

-Change Subclass: M Dopa --> midbrain dopaminergic neuron

  • Is this appropriate Group: SN-VTR CALB1 Dopa --> substantia nigra dopaminergic neuron - or do we need something that covers both SN & VTR (ventral tegmental region of midbrain)

These terms may have been added to CL too early based on more preliminary work on CL. Are they still appropriate?

BG_mapped_2_CL BG_CL_mapping
Group: STRv D2 MSN nucleus accumbens shell and olfactory tubercle D2 medium spiny neuron
Group: STRv D1 NUDAP MSN RXFP1-positive interface island D1-medium spiny neuron
Group: STRv D1 MSN nucleus accumbens shell and olfactory tubercle D1 medium spiny neuron
Group: STR FS PTHLH-PVALB GABA striatal pthlh-expressing interneuron
Group: STR TAC3-PLPP4 GABA TAC3-positive striatal interneuron

Potential CL Mappings to add to WMB based on BG<->WMB AT

For each - Check localization, DRD1/2 expression on ABC atlas & ask for feedback on adding mapping.

  • Group: OT D1 ICj --> subclass: 060 OT D3 Folh1 Gaba --> Island of Calleja granule cell
  • Group: STRd D1 Matrix MSN --> supertype: 0267 STR D1 Gaba_3 --> Island of Calleja granule cell
  • Group: STRd D1 Striosome MSN --> supertype: 0268 STR D1 Gaba_4 --> striosomal D1 medium spiny neuron
  • Group: STRd D2 Matrix MSN --> supertype: 0277 STR D2 Gaba_4  --> matrix D2 medium spiny neuron
  • Group: STRd D2 Striosome MSN --> supertype: 0279 STR D2 Gaba_6 --> striosomal D2 medium spiny neuron
  • Group: STR D1D2 Hybrid MSN --> subclass: 063 STR D1 Sema5a Gaba --> D1/D2-hybrid medium spiny neuron

Ask Cindy Van Velthoven & Zizhen

dosumis avatar Sep 14 '25 16:09 dosumis

have checked and made this true in WMB consensus. Group: OT D1 ICj --> subclass: 060 OT D3 Folh1 Gaba --> Island of Calleja granule cell.

Need to create a better definition and update CL term

RiveraAndrea83 avatar Nov 18 '25 11:11 RiveraAndrea83