vestibuloauditory system issues for Alliance

[doughowe]

The Alliance gene expression ribbon would like to use the terms "auditory system" (UBERON:0016490) and "mechanosensory system" (UBERON:0007037) as ribbon columns.

Mouse maps EMAPA:37985 "vestibulo-auditory system" to UBERON "mechanosensory system" and EMAPA:36002 "auditory system" to UBERON "auditory system".

Zebrafish does not have a distinct term for "auditory system" currently because the vestibular and auditory functions are performed by one set of structures, so ZFA:0001138 "vestibuloauditory system" is mapped to both UBERON terms for the ribbon.

Maybe the expression ribbon should use "vestibulo-auditory system" (UBERON:0002105) instead of just "auditory system"? That may solve a lot of this?

These mappings are being collected here: https://docs.google.com/spreadsheets/d/1_UcKTq7y-wsQ83_kJlP6X5mQdgKykaPWlDdkZzCuygI/edit#gid=313336440

[doughowe]

UBERON "vestibulo-auditory system" has the following cross-references: AAO:0000631 ZFA:0001138 EMAPA:37985 (MA:th) FMA:78500 EMAPA:36002 XAO:0003195 TAO:0001138

Another potential inconsistency in UBERON compared to what people were wanting to do in the expression ribbon is that vestibulo-auditory system and mechanosensory system are siblings in UBERON, but we should check if all vestibuloauditory systems are in fact a type of mechanosensory system. If so, vestibuloauditory system should be a child of mechanosensory system in UBERON.

[cmungall]

Mechanosensory would presumably include vibrissae in mammals, and perhaps hair and other epidermal appendages generally? Also lateral line system in fish and amphibians?

Perhaps define it in terms of cell types: m-system = any system with m-organs; m-organs have m-cells?

Paper on evolution of these across metazoa: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3918877/

@ANiknejad is this something you have looked at homologizing?

[ANiknejad]

Hi @cmungall @doughowe We did so far some 'homology work' on broad 'sensory system' (UBERON:0001032 sensory system) and on UBERON:0002540 lateral line system, but not at 'mechanosensory system' UBERON:0007037.

'Systems' are indeed not easy to 'homologize' as they include lot of various elements. As you pointed out with the reference above, there is an old proposal (Jorgensen, 1989) that all mechanosensory cells might be related (see https://www.ncbi.nlm.nih.gov/pubmed/?term=15353909), and recent studies explore the hypothesis that the vertebrate placodes are very old elements that may (at least 'molecularly' and 'deeply'?) homologize sensory systems at the metazoans level, see this recent (2017) reference here:

"vertebrates and invertebrates exhibit molecular similarities in neurosensory development through cell fate decision-making transcription factors (TF), and some of these have been successfully interchanged between vertebrates and invertebrates [Fritzsch and Straka, 2014; Fritzsch et al., 2015]. Not all components of the gene regulatory networks for placode development in vertebrates and for neurosensory development in invertebrates are clear [Chen and Streit, 2013; Peter and Davidson, 2015; Roellig and Bronner, 2016], but certain predictions of a homology seem to hold."

https://www.ncbi.nlm.nih.gov/pubmed/?term=28988233

Regarding the current issue here, please note that, while "auditory system" (UBERON:0016490) is part_of "vestibulo-auditory system" (UBERON:0002105) in the current Uberon release, "auditory system" is also a "mechanosensory system" (UBERON:0007037)

[Term] id: UBERON:0016490 name: auditory system is_a: UBERON:0007037 ! mechanosensory system relationship: part_of UBERON:0002105 ! vestibulo-auditory system

So I guess, the proposition of Doug to consider "vestibulo-auditory system" (UBERON:0002105) instead of 'auditory system' is fine for his project. However it would be better to conserve "vestibulo-auditory system" (UBERON:0002105) and "mechanosensory system" (UBERON:0007037) as 'siblings' in Uberon (both are is_a: UBERON:0001032 ! sensory system), because as Chris said, "mechanosensory system" implies 'appendages', that "vestibulo-auditory system" does not have.

[doughowe]

The Alliance expression working group did decide to use "vestibulo-auditory system" in the expression ribbon. So, for our purposes with the ribbon the distinction between auditory system and vestibulo-auditory system is moot. Not clear to me if there is still any work left to do here?