Repository navigation
fix(CL:4023068): restrict soma location to 'dorsal plus ventral thalamus' (#3791) - #3793
Conversation
… thalamus' in logical definition
The equivalence axiom for thalamic excitatory neuron (CL:4023068) used
has_soma_location some 'thalamic complex' (UBERON:0010225). In Uberon,
'thalamic complex' includes the hypothalamus, so every hypothalamic
glutamatergic cell type was incorrectly being classified as a thalamic
excitatory neuron (e.g. PVH-SO-PVa Otp Glut, PMv-TMv Pitx2 Glut,
MM Foxb1 Glut, LHA Pmch Glut and ~22 other whole mouse brain types).
Swap UBERON:0010225 ('thalamic complex') for UBERON:0001897
('dorsal plus ventral thalamus') in the equivalence axiom, mirror the
change in the text definition, and add a term_tracker_item pointing at
the originating issue.
Fixes part of #3791
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
|
@ai4c-agent please add a parenthetical comment to the definition: "An excitatory neuron that has its soma located in the dorsal plus ventral thalamus." |
|
🤖 Working on it... Follow along: View workflow run — @ai4c-agent |
Per @dosumis's review comment on PR #3793, added a parenthetical to the text definition of 'thalamic excitatory neuron' noting that the 'dorsal plus ventral thalamus' (UBERON:0001897) corresponds to the thalamus in humans. This helps readers who may be more familiar with the human anatomical term understand the scope of the class without having to resolve the Uberon label. Note: the review comment contained an obvious typo ("the thalamus is humans"); applied as "the thalamus in humans". Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
|
Done — pushed The definition of CL:4023068 (
One small call-out: your comment had a typo ("the thalamus is humans"); I applied it as "the thalamus in humans". Let me know if you actually wanted the literal text. Validated with 🤖 Generated by @ai4c-agent
|
1 participant
Summary
Fixes the overly-broad soma-location axiom on thalamic excitatory neuron (CL:4023068), per @dosumis's report in #3791.
The equivalence axiom used
has soma location some 'thalamic complex' (UBERON:0010225). In Uberon,thalamic complexincludes the hypothalamus, so every hypothalamic glutamatergic cell type was being misclassified as athalamic excitatory neuronby the reasoner (22+ WMB types in the issue author's run, e.g.PVH-SO-PVa Otp Glut,PMv-TMv Pitx2 Glut,MM Foxb1 Glut,LHA Pmch Glut).Changes
UBERON:0010225('thalamic complex') →UBERON:0001897('dorsal plus ventral thalamus'), as suggested in the issue.term_tracker_itempointing back to EPIC: axiom errors found while classifying whole mouse brain types (thalamic excitatory neuron, BG primate term parents) #3791.The
rdfs:commentdiscussing associated pathologies was left as-is since it is unrelated to the misclassification bug and the relevant Uberon labels there may need separate consideration once the Uberon thalamus questions (obophenotype/uberon#3171, #3254) are settled.Validated with
robot convert.Addresses one bullet in epic #3791.
🤖 Generated by @ai4c-agent
🤖 Generated with Claude Code