Suggestions to make valid relationships in the eye table v1.3 (08/05/2023)
Please, add a comment below if you want to address any of the actions to be taken. Please, indicate the number before the comment. IMPORTANT The order of the two classes in these pages is the same as it is found in the tables (e.g. AS4 → AS5)
AS→AS
1 - neuron projection bundle connecting eye with brain → cranial neuron projection bundle
Substitute cranial neuron projection bundle with cranial nerve II UBERON:0000941 (aka optic nerve).
2 - neuron projection bundle connecting eye with brain → retinal neural layer
This will be solved with AS-AS1.
3 - neuron projection bundle connecting eye with brain → sclera
What relationship is expected here?
4 - corneo-scleral junction → basal lamina of epithelium
Needs a NTR 'basal epithelial layer of limbus'.
5 - retina → vasculature of eye
Should be vasculature of retina UBERON:0004864.
6 - lens → suspensory ligament of lens
Correct relationship is continuous_with @anitacaron to add to checks. https://github.com/hubmapconsortium/ccf-validation-tools/issues/221
7 - eye → neuron projection bundle connecting eye with brain
AS-AS1 might solve it.
8 - neuron projection bundle connecting eye with brain → scleral lamina cribrosa
scleral lamina cribrosa is a part of sclera.
9 - neuron projection bundle connecting eye with brain → unmyelinated nerve fiber
It needs a 'has part' relationship.
10 - eye → lamina of spiral limbus
lamina of spiral limbus is a ear structure, not sure why is in this table.
11 - lamina of spiral limbus → corneo-scleral junction
lamina of spiral limbus is a ear structure, not sure why is in this table.
CT→CT
1 - Amacrine Cell → GABAergic interneuron
GABAergic amacrine cell CL:4030027 is more specific and validates.
~~2 - ON-bipolar cell → rod bipolar cell~~
It has been fixed
3 - medium field retinal amacrine cell → wide field retinal amacrine cell
A wide field retinal amacrine cell is not a medium field retinal amacrine cell
4 - neuron → microglial cell
Microglial cell is not a neuron. It can be classified under neural cell or central nervous system macrophage.
5 - neuron → Mueller cell
Müller cell is not a neuron. It can be classified under neural cell, neuron associated cell or glial cell.
AS→CT
1 - iris epithelium → epithelial cell
High level cell.
2 - retina → microglial cell
High level cell.
3 - inner nuclear layer of retina → Amacrine Cell
amacrine cell is all lowercase. inner nuclear layer of retina has part some amacrine cell, and should validate.
4 - outer nuclear layer of retina → retinal cone cell
Missing 'has soma location' some 'outer nuclear layer of retina'.
5 - outer nuclear layer of retina → retinal rod cell
Missing 'has soma location' some 'outer nuclear layer of retina'.
6 - inner nuclear layer of retina → Mueller cell
MCs cover the entire thickness of the retina. The AS should be retine and then it will validate.
7 - vasculature of retina → pericyte
It needs a NTR retinal pericyte.
8 - ganglionic layer of retina → retinal ganglion cell
Need to validate 'has soma location' some retina.
9 - inner nuclear layer of retina → retina horizontal cell
inner nuclear layer of retina has part some retina horizontal cell, and should validate.
10 - inner nuclear layer of retina → retinal bipolar neuron
inner nuclear layer of retina has part some retinal bipolar neuron, and should validate.
11 - inner nuclear layer of retina → ON-bipolar cell
It will be fixed with AS-CT10.
12 - inner nuclear layer of retina → rod bipolar cell
It will be fixed with AS-CT10.
13 - lens nucleus → secondary lens fiber
All lens fibers structures and cells need revision.
14 - lens fiber → primary lens fiber
All lens fibers structures and cells need revision.
15 - anterior stroma of cornea → keratocyte
keratocyte is 'part of' some 'substantia propria of cornea'(UBERON:0001777).
16 - vasculature of retina → retinal blood vessel endothelial cell
it needs a SubclassOf 'part of' some 'vasculature of retina'
17 - inner nuclear layer of retina → A2 amacrine cell
It will be fixed with AS-CT3.
18 - inner nuclear layer of retina → starburst amacrine cell
It will be fixed with AS-CT3.
19 - inner nuclear layer of retina → wide field retinal amacrine cell
It will be fixed with AS-CT3.
20 - lens fiber → lens fiber cell
All lens fibers structures and cells need revision.
21 - lens nucleus → lens fiber cell
All lens fibers structures and cells need revision.
22 - lens cortex → lens fiber cell
All lens fibers structures and cells need revision.
23 - inner nuclear layer of retina → GABAergic interneuron
It will be fixed with AS-CT3 and CT-CT1.
24 - anterior stroma of cornea → telocyte
Looking at this reference, telocytes are not only in the anterior stroma of cornea.
25 - ganglionic layer of retina → Midget ganglion cell of retina
It will be fixed with AS-CT8.
26 - ganglionic layer of retina → Parasol ganglion cell of retina
It will be fixed with AS-CT8.
27 - inner nuclear layer of retina → glycinergic amacrine cell
It will be fixed with AS-CT3.