issueswiithtissues
commented
4 months ago 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
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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?
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aleixpuigb
In the table below user_slabel terms comes from some preliminary work on the HDCA. The rest of the table shows potential mappings
Relevant defs/commentary from Uberon:
CC @issueswiithtissues - could you clarify your intent for the term prethalamus?