Review eye 1.3 AS-AS log

[dosumis]

	s	slabel	user_slabel	o	olabel	user_olabel	row_number	deltaIC
0	UBERON:0034713	cranial neuron projection bundle	cranial neuron projection bundle	UBERON:0004904	neuron projection bundle connecting eye with brain	neuron projection bundle connecting eye with brain	68	35.4785
1	UBERON:0003902	retinal neural layer	retinal neural layer	UBERON:0004904	neuron projection bundle connecting eye with brain	neuron projection bundle connecting eye with brain	67	27.1852
3	UBERON:0001773	sclera	sclera	UBERON:0004904	neuron projection bundle connecting eye with brain	neuron projection bundle connecting eye with brain	66	18.5758
10	UBERON:0000482	basal lamina of epithelium	basal epithelium	UBERON:0006761	corneo-scleral junction	corneoscleral limbus	74	2.22955
27	UBERON:0002203	vasculature of eye	vasculature of eye	UBERON:0000966	retina	retina	32	nan
41	UBERON:0006762	suspensory ligament of lens	ciliary zonules	UBERON:0000965	lens	lens	59	nan
44	UBERON:0004904	neuron projection bundle connecting eye with brain	neuron projection bundle connecting eye with brain	UBERON:0000970	eye	eye	64	nan
45	UBERON:0004904	neuron projection bundle connecting eye with brain	neuron projection bundle connecting eye with brain	UBERON:0000970	eye	eye	65	nan
46	UBERON:0035966	scleral lamina cribrosa	scleral lamina cribrosa	UBERON:0004904	neuron projection bundle connecting eye with brain	neuron projection bundle connecting eye with brain	65	nan
47	UBERON:0004904	neuron projection bundle connecting eye with brain	neuron projection bundle connecting eye with brain	UBERON:0000970	eye	eye	66	nan
48	UBERON:0004904	neuron projection bundle connecting eye with brain	neuron projection bundle connecting eye with brain	UBERON:0000970	eye	eye	67	nan
49	UBERON:0004904	neuron projection bundle connecting eye with brain	neuron projection bundle connecting eye with brain	UBERON:0000970	eye	eye	68	nan
50	UBERON:0004904	neuron projection bundle connecting eye with brain	neuron projection bundle connecting eye with brain	UBERON:0000970	eye	eye	70	nan
51	UBERON:0006136	unmyelinated nerve fiber	unmyelinated nerve fiber	UBERON:0004904	neuron projection bundle connecting eye with brain	neuron projection bundle connecting eye with brain	70	nan
52	UBERON:0002276	lamina of spiral limbus	lamina of spiral limbus	UBERON:0000970	eye	eye	74	nan
53	UBERON:0006761	corneo-scleral junction	corneoscleral limbus	UBERON:0002276	lamina of spiral limbus	lamina of spiral limbus	74	nan

[dosumis]

UBERON:0034713	cranial neuron projection bundle	cranial neuron projection bundle	UBERON:0004904	neuron projection bundle connecting eye with brain	neuron projection bundle connecting eye with brain

neuron projection bundle connecting eye with brain --> cranial nerve II (AKA optic nerve). This should then validate.

2. Lots of connections for optic nerve:

UBERON:0004904	neuron projection bundle connecting eye with brain	neuron projection bundle connecting eye with brain	UBERON:0000970	eye	eye
retinal neural layer	retinal neural layer	UBERON:0004904	neuron projection bundle connecting eye with brain	neuron projection bundle connecting eye with brain
UBERON:0035966	scleral lamina cribrosa	scleral lamina cribrosa	UBERON:0004904	neuron projection bundle connecting eye with brain	neuron projection bundle connecting eye with brain.

Update Uberon term as 1.

• [ ] Looks like some of these should have some kind of connected_to relationship in Uberon. https://github.com/obophenotype/uberon/issues/2852 retinal neural layer connected_to optic nerve. scleral lamina cribrosa overlaps with optic nerve.

UBERON:0001773	sclera	sclera	UBERON:0004904	neuron projection bundle connecting eye with brain	neuron projection bundle connecting eye with brain

• [ ] Add adjacent_to relationship Hard to know what type of relationship was expected. sclera is adjacent_to some optic nerve

UBERON:0000482	basal lamina of epithelium	basal epithelium	UBERON:0006761	corneo-scleral junction	corneoscleral limbus

• [ ] NTR 'basal epithelial layer of limbus' Generic term in specific location. Is there a case for adding a specific basal lamina term to Uberon? 'Limbal stem cell' is part_of some 'basal epithelial layer of limbus' . Both terms need to be added.

UBERON:0002203	vasculature of eye	vasculature of eye	UBERON:0000966	retina	retina

• [ ] Table error - should be vasculature of retina UBERON:0004864 . Request change. Comment from Ellen:

  we are striving to remove all generic "vasculature of X" type entries from all tables in favor of any blood vasculature that already has a "part of" relationship to structures.

UBERON:0006762	suspensory ligament of lens	ciliary zonules	UBERON:0000965	lens	lens

• [ ] Correct relationship is continuous_with @anitacaron to add to checks. https://github.com/hubmapconsortium/ccf-validation-tools/issues/221

UBERON:0006136	unmyelinated nerve fiber	unmyelinated nerve fiber	UBERON:0004904	neuron projection bundle connecting eye with brain	neuron projection bundle connecting eye with brain

May be fixed by updating Uberon term

• [ ] check classification in Uberon

UBERON:0002276	lamina of spiral limbus	lamina of spiral limbus	UBERON:0000970	eye	eye
UBERON:0006761	corneo-scleral junction	corneoscleral limbus	UBERON:0002276	lamina of spiral limbus	lamina of spiral limbus

Incorrect Uberon term UBERON:0002276 - is in the ear!

• [ ] Ask experts what they intended here.

[emquardokus]

@aleixpuigb we are striving to remove all generic "vasculature of X" type entries from all tables in favor of any blood vasculature that already has a "part of" relationship to structures. This has not yet been executed for this table.

[aleixpuigb]

Thank you for the update, @emquardokus!

[aleixpuigb]

This ticket is substituted by the feedback reports.