BG taxonomy class level terms to add/map

[dosumis]

Terms to Map/Add for class level BG taxonomy

• 'CN MGE LAMP5 GABA',
• 'CN CGE VIP GABA',
• 'SN PVALB GABA',
• 'CN LHX6 LHX8 GABA',
• 'STR D1 MSN GABA', Not needed as all MSN are in STR
• 'STR Granular GABA',
• 'STR D2 MSN GABA', Not needed as all MSN are in STR
• 'GP PVALB GABA',
• 'STR Hybrid MSN GABA',
• 'TH MEIS2 GABA',
• 'BN MEIS2 GABA',
• 'SN STH GABA',
• 'STR SST GABA',
• 'STR Cholinergic GABA',
• 'BG PVALB GABA',
• 'BG Glut',
• 'TH Glut',
• 'SN TH Dopa',
• 'GP GABA Glut'

Anatomy based on abbreviations in DHBA/HBA:

CN - (DHBA) "cerebral nuclei"; id "DHBA:10331"; "CN"; "http://atlas.brain-map.org/atlas?atlas=138322603#structure=10331"
SN - (DHBA) "substantia nigra"; "DHBA:12251"; "SN"; "http://atlas.brain-map.org/atlas?atlas=138322603#structure=12251"
STR - (DHBA) "striatum"; "DHBA:10333"; "STR"; "http://atlas.brain-map.org/atlas?atlas=138322603#structure=10333"
GP - (DHBA) "globus pallidus"; "DHBA:10342"; "GP"; "http://atlas.brain-map.org/atlas?atlas=138322603#structure=10342"
TH - (HBA) "thalamus"; "TH"; database_cross_reference "http://atlas.brain-map.org/atlas?atlas=265297125#structure=4392" (DHBA uses this for "medial division of PPHC (area TH)")
BN - (HBA) "basal nuclei (basal ganglia)"; "DHBA:10332"; "BN"; "http://atlas.brain-map.org/atlas?atlas=138322603#structure=10332"
BG - (HBA) "basal ganglia"; "BG"; "http://atlas.brain-map.org/atlas?atlas=265297125#structure=4276" (DHBA uses BG to refer to band of Giacomini)

Tasks

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1. caudal ganglionic eminence derived GABAergic neuron of the cerebral nuclei #2752
   BICAN new term request +2
   
2. medial ganglionic eminence derived GABAergic neuron of the cerebral nuclei #2753
   +0
   
3. NTR grouping term: caudal ganglionic eminence derived neuron #2754
   BICAN +1
   
4. NTR lateral ganglionic eminence derived GABAerigic neuron of the cerebral nuclei #2756
   +0
   
5. NTR medial ganglionic eminenence derived LAMP5 GABAergic neuron of the cerebral nuclei #2759
   +0
   
6. NTR caudal ganglionic eminence derived VIP GABAergic neuron of the ceregral nuclei #2760
   +0
   
7. NTR PVALB GABAergic neuron of the substantia nigra #2761
   +0
   
8. NTR glutametergic neuron of the basal ganglia #2771
   BICAN new term request +2
   
9. adjust definition of thalamic excitatory neuron #2795
   BICAN new term request +2
   
10. NTR SST GABAergic interneuron of the striatum #2797
    BICAN new term request +2
    

Tasks

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[dosumis]

Some redundancy with #26 - although this refers to an earlier version of the taxonomy.

Note - as the latest BG taxonomy has no MSN, no D1 or D2, CL becomes the source for definition, description of these general classes. I suspect there are more like this and that they are a good place for CL to add value.

[AvolaAmg]

In light of this consensus data, a few adjustments need to be carried out in the cell ontology to incorporate new terms.

New Terms Requests on the CL ontology (more to add but these are the ones that can be added relatively straight away)

• GABA-Glut neuron
• Subpallium derived GABAergic neurons
• Basal Ganglia Glutamatergic neurons
• caudal ganglionic eminence derived GABAergic neuron of the cerebral nuclei
• medial ganglionic eminence derived GABAergic neuron of the cerebral nuclei
• lateral ganglionic eminence derived GABAerigic neuron of the cerebral nuclei
• ImOligo (reference Jakel et al., 2019)
• LAMP5 GABAergic neuron of the cerebral nuclei
• VIP GABAergic neuron of the cerebral nuclei
• LHX6 LHX8 GABAergic neuron of the cerebral nuclei
• PVALB GABA of the globus pallidus
• PVALB GABA of the substantia nigra
• MEIS2 GABAergic neurons (a general one for the whole brain)
• Basal Nuclei MEIS2 GABA
• Dopaminergic neurons of the substantia nigra and thalamus
• HDC Histaminergic neurons of the Substantia nigra and subthalamus
• VIP GABAergic neurons of the striatum
• TAC3 PLPP4 GABAergic neurons of the striatum
• globus pallidus internal segment Shell neurons
• globus pallidus internal segment core neurons
• PVALB GATA3 GABAergic neurons of the substantial nigra
• PAX8 GABAergic neurons of the substantia nigra and subthalamic area
• SST chodl GABAergic neurons of the striatum
• PTHLH GABAerggic neurons of the striatum

Discussion

find a CL term that generally refers to immune cells, one that generally refers to OPC-Oligodendrocyte cells and one that refers to Vascular cells
Discussion:
BG Glut, refer to them just as glutametergic neurons (general term)
CN CGE GABA: probably just create a general term for the whole brain rather than for just the location so we can recycle this CL term in the future
Will continue to keep track of the chances and link CL tickets to this tracker

[addiehl]

The CL term that generally refers to immune cells is 'leukocyte' CL:0000738, which already includes 'immune cell' as a related synonym.

'leukocyte' is the ancestor to all major immune cell types, i.e. lymphocytes (T cells, B cells, innate lymphoid cells), dendritic cells, monocytes and macrophages, mast cells, and granulocytes. The reason we haven't made 'immune cell' an exact synonym is that there are a few cell types of non-hematopoietic lineages that play significant roles in the functioning of the immune system, such as follicular dendritic cells (which are not at all like the other dendritic cells), the endothelial cells of the high endothelial venues and a few others like M cells. These non-hematopoietic "immune" cells are all cells found in very particular anatomical locations, and are thus unlikely to be the cells that are identified as immune cells in any kind of transcriptional analysis.

[dosumis]

@AvolaAmg - do you think we will need superclasses to cover SST CHODL GABA, LAMP5 GABA etc independent of region?
Does the Whole mouse brain support groupings like that?

[dosumis]

General issue - Cerebral nuclei in Uberon has no children (subClassOf or part_of).

In DHBA it has

i.e. it covers the basal ganglion. This fits with the draft taxonomy:

Subpallium GABA	CN CGE GABA	CN CGE VIP GABA	STR VIP GABA

(STR= striatum)

1. Make Uberon ticket to update Uberon
2. In the meantime we will need to rely on manual classification of CN neuronal subtypes by location.

[AvolaAmg]

so far there I cannot find any literature evidence that specifically focuses on neurons that are specifically in the cerebral nuclei and they are derived from Caudal, Medial and Lateral ganglionic evidence. Additional literature research will be needed from BICAN to define these cell types

[dosumis]

It may be that the evidence for dev origin is entirely from transcriptional similarity. I think best to check with Nelson & Morgan.

Can you link related Uberon ticket here?

[AvolaAmg]

obophenotype/uberon#3171
obophenotype/uberon#3176
obophenotype/uberon#3254