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vestibuloauditory system issues for Alliance #1451
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UBERON "vestibulo-auditory system" has the following cross-references: 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. |
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: @ANiknejad is this something you have looked at homologizing? |
Hi @cmungall @doughowe 'Systems' are indeed not easy to 'homologize' as they include lot of various elements. "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] So I guess, the proposition of Doug to consider "vestibulo-auditory system" (UBERON:0002105) instead of 'auditory system' is fine for his project. |
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? |
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
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