Question: is thalamus missing in Uberon?

[aleixpuigb]

In Uberon we have the following terms: dorsal thalamus, ventral thalamus and dorsal plus ventral thalamus.
dorsal plus ventral thalamus has a broad synonym thalamus, and there isn't a term labeled thalamus.
My question is: are thalamus and dorsal plus ventral thalamus different structures (dorsal plus ventral thalamus would be part of thalamus) or are they the same structure?
We can find in the thalamic complex definition a distinction of ventral and dorsal thalamus as separate entities:

A nuclear complex which in mammals consists of four parts, the hypothalamus, epithalamus, ventral thalamus, and dorsal thalamus.

[shawntanzk]

was finding some other thing and saw this ticket lol.
Looks like dorsal plus ventral thalamus is mapped to thalamus in HBA so I assume it is the thalamus - super weird name for it thoguh - maybe it is to disambiguate from thalamic complex which includes more than the thalamus?
see https://www.ebi.ac.uk/ols4/ontologies/pcl/classes/https%253A%252F%252Fpurl.brain-bican.org%252Fontology%252Fhbao%252FHBA_4392

[aleixpuigb]

Consulting Jeremy Miller:

I'm not sure there's a totally straightforward answer since these terms get used variably in the literature. If we follow our own reference atlas, the hierarchy has thalamus comprised of dorsal and ventral thalamic nuclei as well as epithalamus and reticular nucleus, so I'd hesitate to use dorsal thalamus as an exact synonym for thalamus. I'd vote that a parent is created to catch all the edge cases where they don't mean the same thing.

@AvolaAmg, since you have more expertise, do you mind if I assign the creation of thalamus to you?

[issueswiithtissues]

Hi @aleixpuigb, The thalamus is made up of the ventral thalamus (subthalamus) and dorsal thalamus (thalamus) and they are two large bilaterally symmetrical nuclear complexes located anterior and superior to the midbrain. The ventral thalamus includes some visual and motor system nuclei, and the dorsal thalamus includes multiple nuclei or groups of nuclei that are highly interconnected with various parts of the telencephalon. So i guess to answer your question, they are two structures with different nuclei components?

[github-actions]

This issue has not seen any activity in the past 6 months; it will be closed automatically one year from now if no action is taken.

[AvolaAmg]

In light of this discussion a few New Oberon Terms need to be added:
NTR:

label
Thalamus

definition
The thalamus is composed by two grey matter structure of the diencephalon one in each hemisphere. It is located in the center of the brain, above the mesencephalon and the midbrain. The thalamus is a relay center for sensory and motor informations. It is composed of 50–60 nuclei that project to specific cortical areas, each nucleus can receive inputs from multiple cortical regions, creating feedback loops that enhance relevant signals while suppressing irrelevant ones. The organisation of thalamic afferents and efferents is contralateral, influencing both sensory and motor functions.

database cross reference:
PMID: 31194341
PMID: 12192499
PMID: 26618760
PMID: 28450543

logical axioms
part of thalamic complex

move under this new term all the following UBERON terms
dorsal plus ventral thalamus
medullary lamina of thalamus
thalamic eminence

[dosumis]

@AvolaAmg - to work on solution in Feb.