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obophenotype / cell-ontology

An ontology of cell types
https://obophenotype.github.io/cell-ontology/
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BG taxonomy class level terms to add/map #2626

Open dosumis opened 1 month ago

dosumis commented 1 month ago

Terms to Map/Add for class level BG taxonomy

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
- [ ] https://github.com/obophenotype/cell-ontology/issues/2752
- [ ] https://github.com/obophenotype/cell-ontology/issues/2753
- [ ] https://github.com/obophenotype/cell-ontology/issues/2754
- [ ] https://github.com/obophenotype/cell-ontology/issues/2756
- [ ] https://github.com/obophenotype/cell-ontology/issues/2759
- [ ] https://github.com/obophenotype/cell-ontology/issues/2760
- [x] https://github.com/obophenotype/cell-ontology/issues/2761
- [ ] https://github.com/obophenotype/cell-ontology/issues/2771
### Tasks
dosumis commented 1 month ago

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 commented 6 days ago

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)

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 commented 6 days ago

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 commented 6 days ago

@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 commented 5 days ago

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

In DHBA it has

image

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 commented 1 day ago

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 commented 11 hours ago

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?