#116 inner ear foramen part_of nervous system?

[Chris Mungall]

~~~~
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.

[Chris Mungall]

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

[Ceri]

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

[Yvonne Bradford]

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.

[Chris Mungall]

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.

---

[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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[David Osumi-Sutherland]

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'

[Chris Mungall]

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

[Chris Mungall]

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