Q: multi-cell-part structure

[cmungall]

Def: A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part.

This is a useful class for many of the layers of the nervous system, e.g.

http://neurolex.org/wiki/Category:Cell_layer

Here is the challenge. I believe the majority of these layers are MCPSs. They consist of cell bodies and cell processes. However, when drawing out the boundaries of a layer on an atlas, one minor deviation would result in (effectively) the same structure S being classified as a MCPS in one scheme and being ComplementOf(MCPS) in another, due to the strict no-complete-cells criterion.

From a practical perspective it's very hard (even for the experienced neuroanatomist, I would wager) to look at a named cell layer region and assign it to a MCPS class.

This is just in one species (and even one atlas?) at one point in time. Extending in ontogenic and phylogenetic time seems even more difficult.

On the other hand, I think there are strong benefits. Despite the difficulty, it seems that this would be very useful for making precise developmental (and homological) associations between layers. But hard... do we need a simpler solution on the road to perfection?

Maybe we just make the stronger statement, and treat the relationship between atlas and class as overlaps?

It would be valid for most of these cell layers to say anatomical structure and 'composed primarily of' 'MCPS'. i.e. adding a few cells to the mix wouldn't change the classification. But it doesn't feel satisfactory.

Also: change def to say 'part' not 'component'

[cmungall]

also: fbbt passes, but if our axioms are complete then the following cells should be marked as unsats, as they are part of a MC{C,P}S.

    is_a FBbt:00007060 ! multi-cell-component structure
     is_a FBbt:00005139 ! neuropil 
      po FBbt:00003648 ! large field neuron
      po FBbt:00007392 ! projection neuron
      po FBbt:00100502 ! adult neuropil associated glial cell

Presumably in FBbt, the part_ofs should be changed to soma_part_of?

[dosumis]

Yep. Seem to remember this being a deliberate hack. Will check implications
for classification under x intrinsic neutron.
On 3 Dec 2014 20:37, "Chris Mungall" notifications@github.com wrote:

also: fbbt passes, but if our axioms are complete then the following cells
should be marked as unsats, as they are part of a MC{C,P}S.

is_a FBbt:00007060 ! multi-cell-component structure
 is_a FBbt:00005139 ! neuropil
  po FBbt:00003648 ! large field neuron
  po FBbt:00007392 ! projection neuron
  po FBbt:00100502 ! adult neuropil associated glial cell

Presumably in FBbt, the part_ofs should be changed to soma_part_of?

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#10 (comment).

[cmungall]

Of course, the fbbt jenkins job passes as it's configured to use Elk.

We can derive from

SubClassOf
'connected anatomical structure'
and ('has part' only (not (cell)))
and ('has component' min 2 'cell part')

A weaker but valid (I think) axiom:

cell DisjointWith part_of some MCPS

[dosumis]

From a practical perspective it's very hard (even for the experienced neuroanatomist, I would wager) to look at a named cell layer region and assign it to a MCPS class.

I can see the problem - I think this is a much bigger issue for vertebtrate nervous systems than for arthropod ones. Arthropods are much easier as all of the soma are located in the rind. Perhaps we should be making compound structural classes with has_predominant_part ? Need to think through use cases.

[dosumis]

Also note - 2 possibly uses of the term 'laminar' - straight translation => flat, but also often used by biologists to mean 'consisting of layers'. Need to be careful to keep these distinct.

[cmungall]

Morphologists may use it in the sense of 'flat'. cc @wdahdul

Also possible confusion: if laminar is 'consisting of layers', then each of the layers (laminae) are not themselves laminar, it's only the mereological sum that is laminar?

[dosumis]

layered http://en.wikipedia.org/wiki/Laminar_organization
flat http://en.wikipedia.org/wiki/Leaf_shape