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obophenotype / uberon

An ontology of gross anatomy covering metazoa. Works in concert with https://github.com/obophenotype/cell-ontology
http://obophenotype.github.io/uberon/
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Question: is thalamus missing in Uberon? #3171

Open aleixpuigb opened 10 months ago

aleixpuigb commented 10 months ago

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 commented 8 months ago

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 commented 7 months ago

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 commented 7 months ago

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?

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