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ZFA spatial disjointness violations #378
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Some context: these ZFA classes cause problems when imported with bridge axioms to uberon, due to aggressive spatial disjointness axioms in Uberon. In some cases the disjointness axiom (sometimes sourced externally, eg from ABA) needs to be weakened. In other cases, ZFA should be fixed In others, and uberon-ZFA bridging axiom should be fixed. This should be done on a case by case basis - use Elk. For now the temp fix is to suppress expansion of problematic constraints by putting status=pending into the axiom annotation |
Tip: use the DL query tab, write queries of form (part_of some X) and (part_of some Y) where X and Y are spatially disjoint Click on ? next to each query result for an answer |
* Suppressed some neuro spatial disjoitness axioms. Addrsses #378
I am running into this issue again. I am looking at a bunch of unsatisfiable cranial nerves subclasses (most importantly right now 'cranial nerve II' in ZFA, but III, IV and some more have the same problem). Cranial nerve 2 (CN2) is classified as a nerve, which by Uberon, is part of the peripheral nervous system (PNS). CN2 is also classified as part of the 'brain' which is part of the central nervous system. Now, something must be wrong here, but which:
@cmungall @dosumis if you could tell me which of the three are likely to be too tight to be useful, I will create a pull request to having it removed. |
I think PNS CNS spatial disjointness is tempting to add given the classical lit, but is probably untenable for multiple reasons:
@cmungall do you agree that this disjointness should be deleted? Or should we try to support it by applying the various fixes above? |
Cranial nerves should be part of both CNS and PNS imho. |
That definitely rules out the PNS-CNS spatial disjointness axiom. |
@cmungall @dosumis @mellybelly Who else might have a stake in this decision? Or should I just prepare a pull request? |
How urgent is this? I'd like to put a case for the current position. @dosumis makes excellent points in 1-3, these are all covered by separate tickets give me a chance to find these |
The cell bodies of the cranial nerves reside in the brain nuclei. I can't think of any cases where we say different parts of cells are in disjoint systems. |
"The cell bodies of the cranial nerves reside in the brain nuclei." We can support that by using has_soma_location to link cells to brain nuclei. I think we need to do this more generally for neuron in CL (we mostly do this in FBbt although have some legacy issues to clear up). |
@dosumis <https://github.com/dosumis> Motor neurons have cell bodies in the
CNS but their axons are certainly considered to be in the PNS, as those
axons make up considerable parts of peripheral nerves. In addition, the
peripheral axons are surrounded by Schwann cells but in the CNS the axons
are wrapped by oligodendrocytes. This is true for primary sensory afferents
as well but, with a few exceptions, their cell bodies are in the periphery.
I am afraid that the real problem here is that the distinction between the
PNS and the CNS is "fuzzy." This is also true for cranial and spinal nerves.
Robert E. Druzinsky, Ph.D.
Clinical Associate Professor
Dept. of Oral Biology
College of Dentistry
University of Illinois at Chicago
801 S. Paulina
Chicago, IL 60612
druzinsk@uic.edu
Office: 312-996-0406
Lab: 312-996-0629
Website: www.peerj.com/RobertDruzinsky
…On Fri, Sep 21, 2018 at 12:38 PM Chris Mungall ***@***.***> wrote:
Who else might have a stake in this decision
@tgbugs <https://github.com/tgbugs> @ukemi <https://github.com/ukemi>
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I did not mean to suggest that the distinction between cranial and spinal
nerves is not clear (it is, mostly). I meant that the problems determining
what is in the PNS and what is in the CNS are there for both cranial and
spinal nerves. And yes, if the distinction between central and peripheral
is some anatomical boundary (such as the point at which a nerve or nerve
root emerges from the brainstem or spinal cord, then all of those neurons
are in both the CNS and PNS.
Robert E. Druzinsky, Ph.D.
Clinical Associate Professor
Dept. of Oral Biology
College of Dentistry
University of Illinois at Chicago
801 S. Paulina
Chicago, IL 60612
druzinsk@uic.edu
Office: 312-996-0406
Lab: 312-996-0629
Website: www.peerj.com/RobertDruzinsky
…On Fri, Sep 21, 2018 at 2:14 PM Robert Druzinsky ***@***.***> wrote:
@dosumis <https://github.com/dosumis> Motor neurons have cell bodies in
the CNS but their axons are certainly considered to be in the PNS, as those
axons make up considerable parts of peripheral nerves. In addition, the
peripheral axons are surrounded by Schwann cells but in the CNS the axons
are wrapped by oligodendrocytes. This is true for primary sensory afferents
as well but, with a few exceptions, their cell bodies are in the periphery.
I am afraid that the real problem here is that the distinction between the
PNS and the CNS is "fuzzy." This is also true for cranial and spinal nerves.
Robert E. Druzinsky, Ph.D.
Clinical Associate Professor
Dept. of Oral Biology
College of Dentistry
University of Illinois at Chicago
801 S. Paulina
Chicago, IL 60612
***@***.***
Office: 312-996-0406
Lab: 312-996-0629
Website: www.peerj.com/RobertDruzinsky
On Fri, Sep 21, 2018 at 12:38 PM Chris Mungall ***@***.***>
wrote:
> Who else might have a stake in this decision
> @tgbugs <https://github.com/tgbugs> @ukemi <https://github.com/ukemi>
>
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|
@RDruzinsky nice to see you in my inbox. Do you agree that the cranial nerves should be part of both PNS and CNS? |
Yes, I think that they should be in both.
…On Fri, Sep 21, 2018, 2:28 PM Melissa Haendel ***@***.***> wrote:
@RDruzinsky <https://github.com/RDruzinsky> nice to see you in my inbox.
Do you agree that the cranial nerves should be part of both PNS and CNS?
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Here is my explanation of the current way of modeling this. Let me preface this by saying that of course we can modify the ontology according to consensus. There is no right or wrong answers here, just modeling choices. First, I like simplicity. A definition of the PNS as being the parts of the NS outside the brain and spinal cord is both simple and IMO biologically/anatomically defensible. In particular these kinds of simple pairwise-spatially-disjoint-exhaustive spatial partitions are the norm for atlases, and I assume consistency with atlases is a goal (for more details on what I mean by spatially disjoint see this design pattern on the uberon wiki). Another advantage of simple clear non-subjective divisions is that it makes it easier to represent things in a consistent way. I also think any alternative has undesirable properties. I see 3 alternatives, (a) the dual part-of suggested here, (b) no part-of, and (c) two separate classes I'm not aware of any AO that has nerve (or any structure) that is part of both CNS and of PNS. Note that if we make these assertions this entails some odd things, such as the CNS extending throughout the whole body touching the skin. A query for structures localized to the CNS would necessarily return results for structures localized to nerve endings - this seems undesirable. On top of this, I think having multiple part-of relationships for a single structure along a single axis of classification is a bad smell pattern and has many undesirable structural properties, leading to more hairballs etc. The more common alternative is simply not to make any part-of relationship at all (of course, we would have overlaps relationships, either explicit or implicit, but these are far less useful for common AO use cases). This is what ZFA does, nerve is directly under nervous system. Some subclasses of nerves are asserted to be part-of the PNS, but not all (not sure of the criteria). This means that sometimes queries for PNS will yield incomplete results. I am still open to this proposal, but we need clearer guidelines on when a nerve should be part-of PNS vs just NS. Another option is to have two classes, e.g. "PNS part of nerve" and "nerve plus nerve root". But I think this has some undesirable properties. As for the current representation in Uberon, how do we deal with the issues David mentions? I'll address these in order 2,1,3 2: The optic "nerve". I believe this is the only example in this category. I think this is largely terminological. The current solution to this is outlined here: #298 (comment) 3: Yes, we really need to implement the has_some_part_of solution. This is needed regardless of this issue, as many relationships in CL are simply wrong 1: nerve roots. For more on how we represent this see the nerve root class. Def: A continuation of the neuron projection bundle component of a nerve inside, crossing or immediately outside the central nervous system Editor note: We consider cranial nerve roots to be primarily CNS structures, but model spinal nerve roots as PNS structures, due to the existence of ganglia on the roots. Also some discussion of the FMA representation in #286 So overall there is no logical issue here, and IMO this makes sense biologically. I'm happy to make the decision the community wants but I urge people to think through the issues and look at related documentation and tickets such as #298 |
I think you mean that they overlap both the CNS and PNS? Remember if A part-of B, then every part-of is also a part-of B. |
Here are my preliminary thoughts on this. I too have been bitten by CNS-PNS disjointness in my dealings with the old My thinking is as follows. It is more important to preserve the meaning Nerve roots provide a clear solution to this. So here I agree with Given that part of is used so pervasively for dealing with purely conceptual The idea of constitution helps here because once we see that the nerves Based on the current usage of part of and location, neurons are not part of any Thus the question is how to relate disjoint parts of neurons to Removing the disjointness axioms in one I need to give it more thought, but I suspect that it is possible to model this |
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