Review thalamus terms and relationship to commonly used terms for human anatomy

[dosumis]

In the table below user_slabel terms comes from some preliminary work on the HDCA. The rest of the table shows potential mappings

FMA	FMA_label	s	slabel	user_slabel	Notes
		UBERON:0001897	dorsal plus ventral thalamus	Thalamus	Should Thalamus map to general term dorsal + ventral thalamus, or just to dorsal thalamus (FMA mapping)
FMA:62007	Thalamus	UBERON:0004703	dorsal thalamus	Thalamus
FMA:62010	Subthalamus	UBERON:0001900	ventral thalamus	Prethalamus	Synonym on ventral thalamus, also FMA mapping. Wikipedia has prethalamus as a synonym of subthalamus
FMA:62010	Subthalamus	UBERON:0001900	ventral thalamus	Subthalamus	FMA name mapping

Relevant defs/commentary from Uberon:

CC @issueswiithtissues - could you clarify your intent for the term prethalamus?

[issueswiithtissues]

Hi David When annotating, ‘prethalamus’ my intention was to describe that this area is the more ventral part of the thalamus. Gene expression expressed genes slightly different diencephalon, so didn’t label it as diencephalon, but prethalamus. Hope this helps Nana-Jane Postdoctoral Scientist Haniffa Lab (T298) Cellular Genetics Wellcome Sanger Institute Wellcome Genome Campus Hinxton, Cambridge [signature_2226353234] From: David Osumi-Sutherland ***@***.***> Reply to: obophenotype/uberon ***@***.***> Date: Monday, 15 April 2024 at 15:39 To: obophenotype/uberon ***@***.***> Cc: Nana-Jane Chipampe ***@***.***>, Mention ***@***.***> Subject: [obophenotype/uberon] Review thalamus terms and relationship to commonly used terms for human anatomy (Issue #3254) [EXT] In the table below user_slabel terms comes from some preliminary work on the HDCA. The rest of the table shows potential mappings FMA FMA_label s slabel user_slabel Notes UBERON:0001897 dorsal plus ventral thalamus Thalamus Should Thalamus map to general term dorsal + ventral thalamus, or just to dorsal thalamus (FMA mapping) FMA:62007 Thalamus UBERON:0004703 dorsal thalamus Thalamus FMA:62010 Subthalamus UBERON:0001900 ventral thalamus Prethalamus Synonym on ventral thalamus, also FMA mapping. Wikipedia has prethalamus as a synonym of subthalamus FMA:62010 Subthalamus UBERON:0001900 ventral thalamus Subthalamus FMA name mapping Relevant defs/commentary from Uberon: image.png (view on web) [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_obophenotype_uberon_assets_112839_a8404950-2D39ef-2D40ad-2Da963-2Dc012f8499041&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=QpLmyvpTrMMJft6n-cCTOv5mX_PuzoToR56eoHvl-0E&m=w4KSkMSh4_j6KDO1wN_4AxnIWaI3esu6-lLvLjSiNmpZVAl86uT_2MU2sMbX4c1d&s=ajPxZAgq84Dv13LZrIZqINTDAW2W1lNRsZUf4FlbqN0&e=> image.png (view on web) [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_obophenotype_uberon_assets_112839_fd2d3315-2D9cf2-2D43cf-2Da250-2D59429519c73e&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=QpLmyvpTrMMJft6n-cCTOv5mX_PuzoToR56eoHvl-0E&m=w4KSkMSh4_j6KDO1wN_4AxnIWaI3esu6-lLvLjSiNmpZVAl86uT_2MU2sMbX4c1d&s=pAj-XkEG2lVu221tW-ZlIgLtW4NZfq5Xd2kE2fm5xOo&e=> CC @issueswiithtissues [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_issueswiithtissues&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=QpLmyvpTrMMJft6n-cCTOv5mX_PuzoToR56eoHvl-0E&m=w4KSkMSh4_j6KDO1wN_4AxnIWaI3esu6-lLvLjSiNmpZVAl86uT_2MU2sMbX4c1d&s=yBmaWXQa55hET8rp18q7CMM8ODtfeH0sJKmNy3LsSIY&e=> - could you clarify your intent for the term prethalamus? — Reply to this email directly, view it on GitHub [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_obophenotype_uberon_issues_3254&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=QpLmyvpTrMMJft6n-cCTOv5mX_PuzoToR56eoHvl-0E&m=w4KSkMSh4_j6KDO1wN_4AxnIWaI3esu6-lLvLjSiNmpZVAl86uT_2MU2sMbX4c1d&s=Rkn9SPuA1bnOQVRl0V-RMHx1efm-0XOT9W6YIjHI7tc&e=>, or unsubscribe [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_BDFRONEYYFHXB6JJQDT3B7DY5PRB7AVCNFSM6AAAAABGHQB3PWVHI2DSMVQWIX3LMV43ASLTON2WKOZSGI2DGOBVHA3TIMI&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=QpLmyvpTrMMJft6n-cCTOv5mX_PuzoToR56eoHvl-0E&m=w4KSkMSh4_j6KDO1wN_4AxnIWaI3esu6-lLvLjSiNmpZVAl86uT_2MU2sMbX4c1d&s=d-S-mKI8oO7hix33Y_ixYwb2gaBql5vnqSDOcx0HXvo&e=>. You are receiving this because you were mentioned.Message ID: ***@***.***>

…

-- The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA

[aleixpuigb]

Related to #3171

[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.

[dosumis]

@AvolaAmg please can you add to the sprint board