#106 [CARO] should midbrain-hindbrain be a line?

open
nobody
None
2
2013-12-11
2013-07-24
No
 is_a CARO:0000007 ! immaterial anatomical entity
  is_a ZFA:0001689 ! anatomical line
   is_a ZFA:0000042 ! midbrain hindbrain boundary *** 

is this correct?

This creates problems here

[Term]
id: ZFA:0001341
name: intervening zone
namespace: zebrafish_anatomy
def: "A zone of delayed differentiation at the midbrain hindbrain boundary.  The IZ separates midbrain from anterior hindbrain neuronal clusters and has been described in all vertebrates." [ZFIN:ZDB-PUB-030307-1]
synonym: "IZ" EXACT []
xref: TAO:0001341
xref: ZFIN:ZDB-ANAT-060131-19
is_a: ZFA:0001478  ! anatomical cluster
relationship: develops_from ZFA:0001342 ! presumptive intervening zone
relationship: end ZFS:0000000 ! Unknown
relationship: part_of ZFA:0000042 ! midbrain hindbrain boundary
relationship: start ZFS:0000026 ! Segmentation:14-19 somites

material entities can't be part of immaterial ones; a physical structure with mass can't be part of ab abstraction like a line.

Note: although the OE reasoner is very limited in it's ability to detect these kinds of issues, the boolean query capability is very powerful. You can find cases like this by querying for anything with a part_of path to "anatomical line" and is_a path to anatomical structure.

In general you should be careful using classes that are not anatomical structures. Abstractions such as lines tend to be named anchor points. You may have little need for them in ZFA. They should probably be suppressed from user views and most of the time in annotation - certainly gene expression (something can be expressed around a line but not in it). An exception is for phenotypes. It is easier to describe "increased inter-eye distance" using a monadic quality and an abstract line (interpupillary distance) than with a relational quality.

I think CARO needs to include a class like this (from the FMA originally):

[Term]
id: UBERON:0007651 ! anatomical junction
name: anatomical junction
def: "Anatomical structure in which parts of two or more anatomical structures establish physical continuity with one another or intermingle their component parts. Examples: gastroesophageal junction, line alba, knee joint.[FMA]" [FMA:5898]
subset: upper_level
xref: FMA:5898 ! anatomical junction
xref: SCTID:91833003 ! Anatomical junction
is_a: UBERON:0000477 ! anatomical cluster

This is a physical thing and better for junctions such as those along the neuraxis or gut tube.

I think the hindbrain-midbrain boundary is one of these. The fact it has "isthmus" as an exact syn supports this - the isthmus is very much a structure I think.

Discussion

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