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obophenotype / uberon

An ontology of gross anatomy covering metazoa. Works in concert with https://github.com/obophenotype/cell-ontology
http://obophenotype.github.io/uberon/
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basilar papilla and auditory hair cells : unsat classes #387

Closed cmungall closed 3 years ago

cmungall commented 10 years ago

screen shot 2014-01-02 at 11 32 57 pm What's wrong here? Uberon says that a basilar papilla (BP) has as part an auditory hair cell (AHC), which seems reasonable. However, CL says (via logical axioms) that an AHC is part of an organ of corti (OC).

Now in Uberon, OC is the mammalian homolog of the BP. The OC is only in mammalia, the BP is never in mammalia. This creates the unsat.

One solution is to follow the CL comment "In mammals these cells are located in the organ of Corti." and encode the logical axiom as a taxon GCI.

This is somewhat unsatisfactory. A better solution would be to create the superclass of OC and BP, and link the CL class to this.

dosumis commented 10 years ago

Perhaps better to have a definition of auditory hair cell based on structure & function of cell - rather than tying to specific anatomy.

On 2 Jan 2014, at 23:40, Chris Mungall notifications@github.com wrote:

What's wrong here? Uberon says that a basilar papilla (BP) has as part an auditory hair cell (AHC), which seems reasonable. However, CL says (via logical axioms) that an AHC is part of an organ of corti (OC).

Now in Uberon, OC is the mammalian homolog of the BP. The OC is only in mammalia, the BP is never in mammalia. This creates the unsat.

One solution is to follow the CL comment "In mammals these cells are located in the organ of Corti." and encode the logical axiom as a taxon GCI.

This is somewhat unsatisfactory. A better solution would be to create the superclass of OC and BP, and link the CL class to this.

— Reply to this email directly or view it on GitHub.

cmungall commented 10 years ago

Agreed.

But should we have subclasses of these for organ of corti vs basilar papila? Are these different at the cell type level?

RDruzinsky commented 10 years ago

Definitely inner and outer hair cells, at least in mammals. Not sure about others.

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: 312-996-6054 Lab: 312-996-0629

On Mon, Jan 6, 2014 at 11:24 AM, Chris Mungall notifications@github.comwrote:

Agreed.

  • Hair cell: define using GO CC
  • Auditory hair cell: hair cell and has_function..

But should we have subclasses of these for organ of corti vs basilar papila? Are these different at the cell type level?

— Reply to this email directly or view it on GitHubhttps://github.com/obophenotype/uberon/issues/387#issuecomment-31667156 .

cmungall commented 10 years ago

This is what CL has at the moment. I think we may want to remove the part_of for CL_0000202 (and add one for 589). I believe outer hair cells are only in mammals, and this taxon constraint would be inherited from spiral organ.

mellybelly commented 10 years ago

Safe to say that inner and outer hair cells have different morphologies. See for example: http://www.pnas.org/content/97/13/6939/F1.expansion.html http://fuckyeahnervoussystem.tumblr.com/page/42

Vertebrate inner ear morphologies vary enormously and so do the electrophysiological properties of the constituent hair cells. Note also that hair cells in the lateral line canals and superficial neuromasts in the lateral line also have different anatomies and physiological properties.

I agree, we should be define hair cells based on function. Perhaps the functions are (nevermind the labels for now) can be defined by frequency ranges, though not sure if the ranges would be defined differently in different species: detection of low frequency auditory stimulus (and/or vibration as separate term?) detection of mid frequency auditory stimulus detection of high frequency auditory stimulus

Few relevant GO terms: GO:0010996 response to auditory stimulus GO:0050910 detection of mechanical stimulus involved in sensory perception of sound GO:0050973 detection of mechanical stimulus involved in equilibrioception (maybe break into two subclasses?) GO:0050972 detection of mechanical stimulus involved in echolocation

For latter, we have taxon specific hair cell morphologies in the spiral organ that are related to echolocation.

nice review for non-mammals: http://jeb.biologists.org/content/203/15/2237.full.pdf neato paper on echolocation gene evolution: http://www.pnas.org/content/105/37/13959.full neato paper on neuromast morphological differences in blind cave fish: http://www.karger.com/Article/Abstract/115853

Seems to me that there is hardly a case where there are not location-specific morphological differences in hair cell morphology?

gouttegd commented 3 years ago

WARNING: This issue has been automatically closed because it has not been updated in more than 3 years. Please re-open it if you still need this to be addressed addressed addressed – we are now getting some resources to deal with such issues.