inner ear foramen part_of nervous system?

[cerivs]

    is_a ZFA:0000396 ! nervous system
      po ZFA:0000282 ! sensory system
       is_a ZFA:0001138 ! vestibuloauditory system
        po ZFA:0000217 ! inner ear
         po ZFA:0005415 ! inner ear foramen *** 

Each individual relationship is in itself on the surface fine, but the entailment is that there is a foramen in the nervous system, which is unusual.

In uberon, we make the relationship between sensory system and nervous system overlaps.

What you do in ZFA depends on how you rate false +ves vs false -ves. People querying for genes expressed in the nervous system should get back mostly NS genes (and foramens are unlikely to get annotated for gene expression - you don't express genes in spaces). But for phenotype reasoning we end up with inner ear foramen phenotypes being NS phenotypes, which is not what we want.

Original comment by: cmungall

[cerivs]

Seealso : https://github.com/obophenotype/uberon/issues/370

Original comment by: cmungall

[cerivs]

Currently we are restricted to part_of, is_a and develops from relationships. Will revisit when more relationships are available.

Original comment by: cerivs

[cerivs]

All sensory systems that have neuronal and non-neuronal structures as part_of will have this issue. One strategy might be to have a neural and non-neural component to the systems, shuffling the parts between the appropriate parent such that the neural parts resolve to part_of nervous system and the structural parts resolve to non-neural parts.

Original comment by: ybradford

[cerivs]

I like this idea.

You needn't necessarily have the non-neural component class, but I think it's cleaner that way.

On Tue, Nov 5, 2013 at 2:40 PM, Yvonne Bradford < yvonne_bradford@users.sf.net> wrote:

All sensory systems that have neuronal and non-neuronal structures as part_of will have this issue. One strategy might be to have a neural and non-neural component to the systems, shuffling the parts between the appropriate parent such that the neural parts resolve to part_of nervous system and the structural parts resolve to non-neural parts.

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\ [zebrafish-anatomy-zfa-term-requests:#116] inner ear foramen part_of nervous system?**

Status: open Created: Tue Nov 05, 2013 03:37 AM UTC by Chris Mungall Last Updated: Tue Nov 05, 2013 07:13 PM UTC Owner: nobody

    is_a ZFA:0000396 ! nervous system
      po ZFA:0000282 ! sensory system
       is_a ZFA:0001138 ! vestibuloauditory system
        po ZFA:0000217 ! inner ear
         po ZFA:0005415 ! inner ear foramen ***

Each individual relationship is in itself on the surface fine, but the entailment is that there is a foramen in the nervous system, which is unusual.

In uberon, we make the relationship between sensory system and nervous system overlaps.

What you do in ZFA depends on how you rate false +ves vs false -ves. People querying for genes expressed in the nervous system should get back mostly NS genes (and foramens are unlikely to get annotated for gene expression - you don't express genes in spaces). But for phenotype reasoning we end up with inner ear foramen phenotypes being NS phenotypes, which is not what we want.

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Original comment by: cmungall

[cerivs]

• Description has changed:

Diff:

--- old
+++ new
@@ -1,4 +1,3 @@
-

 is_a ZFA:0000396 ! nervous system
   po ZFA:0000282 ! sensory system

- **assigned_to**: Yvonne Bradford
- **Group**:  --> 

Original comment by: ybradford

[cerivs]

A foramen is a space http://en.wikipedia.org/wiki/Foramen

Given this, should it be allowed as a location for expression?

Note - we do allow for spaces to be part of 'material anatomical structures'

Original comment by: dosumis

[cerivs]

I don't know if the WP article is definitive about BFO distinctions...

true anatomical spaces are pretty useless to the majority of users of AOs. There is an argument for reconstruing foramina etc as material conduits as in for example

UBERON:0005744 ! bone foramen

Original comment by: cmungall

[cerivs]

TAO derived text def for that class is ot BFO-consistent with its placement in Uberon...

Original comment by: cmungall