ABA inconsistencies

[cmungall]

Using spatial disjointness axioms derived from Allen Brain, the following classes are part of two disjoint regions:

MA:0002742-cerebellar peduncle MA:0000169-brainstem MA:0000198-cerebellum
MA:0001057-trigeminal V mesencephalic nucleus MA:0000195-hindbrain MA:0000207-midbrain
MA:0001053-trigeminal V spinal sensory nucleus MA:0000204-pons MA:0000206-medulla oblongata

(3 out of the whole ontology ain't bad!)

This is assuming the following ABA terms have the obvious equivalents in MA

ABA:BS brainstem
ABA:CB cerebellum
ABA:P Pons
ABA:MY medulla oblongata

NIF had a similar issue with the peduncles. This is what Maryann had to say:

"Although I see that some nomenclatures, e.g., Hof via BAMS, do list the peduncles as part of the cerebellar white matter. But I think we should take it out because volumetrically, as Chris points out, it doesn't fit with cerebellum"

I haven't checked with experts on the others, but some guesses:

I suspect making the trigeminal nucleus part_of pons is too strong (though supported by FMA). NIF has this under Composite part spanning multiple base regional parts of brain which sounds awkward but is a good way of thinking about these structures. The links to pons could be moved down to the principal nucleus and motor nucleus. You'd then have individual structures spatially classified with the generic structure spanning all these.

Original comment by: cmungall

Original Ticket: obo/mouse-anatomy-requests/44

[cmungall]

• labels: --> other request
• priority: 5 --> 7
• assigned_to: nobody --> hayamizu

Original comment by: tfhayamizu

[cmungall]

Appreciate having this looked into and will definitely evaluate this further.

Original comment by: tfhayamizu

[cmungall]

Note the treatment of brainstem is very different in ABA from other AOs.

MA is consistent with FMA, NIF, ZFA, Mesh, wikipedia,... in having the structure:

brain
-- brainstem
-- hindbrain
---- cerebellum

However, ABA has:

basic cell groups and regions
-- cerebellum
-- brainstem
---- hindbrain

Original comment by: cmungall

[cmungall]

RE: MA:0002742-cerebellar peduncle MA:0000169-brainstem MA:0000198-cerebellum
Your reasoning, supported by Maryann, make sense.
I will remove the edge between "cerebellar peduncle" and "cerebellum white matter"

Original comment by: tfhayamizu

[cmungall]

RE:
MA:0001057-trigeminal V mesencephalic nucleus MA:0000195-hindbrain MA:0000207-midbrain
MA:0001053-trigeminal V spinal sensory nucleus MA:0000204-pons MA:0000206-medulla oblongata

As suggested, I will remove the edge between "trigeminal V nucleus" and "pons"

I will also further investigate appropriate part_of parents for:
trigeminal V motor nucleus
trigeminal V prinicipal sensory nucleus
trigeminal V spinal sensory nucleus

Original comment by: tfhayamizu

[cmungall]

trigeminal nucleus notes

Original comment by: tfhayamizu

[cmungall]

• status: open --> closed-accepted

Original comment by: tfhayamizu