Obsolete EFO:0001058 sensory system disease?

[paolaroncaglia]

@simonjupp @zoependlington @smnorthen @d0choa To make a long story short, while working on Open targets therapeutic areas, we had trouble with terms like 'disease of ear', 'nose disease', 'tongue disease' (and previously 'eye disease' too) being descendants of 'nervous system disease' via their common parent 'sensory system disease'. We consulted extensively with Mondo (they had the same issue) and Uberon, and ultimately Mondo resolved to obsolete 'sensory system disease' as they deemed it of little utility and all its children have other parents anyway. In the Open Targets slim/profile, we had to remove 'sensory system disease'. I am now proposing to obsolete 'sensory system disease' from EFO altogether. We'll have to revise placement of its (12) children, but they should be mostly fine, and we should take the chance to see if they can be given better parents based on their definitions. Any objections please? :-)

(Note, we'll be reminded after the Mondo release as the missing mapping will throw an error.)

[zoependlington]

@paolaroncaglia No objection from me, this sounds very sensible.

[smnorthen]

@paolaroncaglia fine with me too. No objections from Open Targets

[zoependlington]

Mapping to the Mondo term (now obsolete) has been removed from the mapping file.

[paolaroncaglia]

Following up on this ticket, I'll list below the subclasses of 'sensory system disease' that may need work.

• [x] Move 'Adie syndrome' from subclass of 'sensory system disease' to be a subclass of 'nervous system disease' based on its defs (referring to nerve fibers and neurological disorder)

• [x] Need to revise the following as ageusia relates to taste (see Wikipedia): double-check its ontology def: 'ageusia' should be a subtype of 'disturbances of sensation of smell and taste', but we'd need to re-position the latter as well. Based on their definitions, NCIT and ICD10 xrefs, both terms should be phenotypes not diseases. ('disturbances of sensation of smell and taste' was probably added for the UK Biobank work, so we'd want to retain the EFO ID.) I suggest to:

• [x] Import HP:0004408 'Abnormality of the sense of smell' and HP:0000223 'Abnormality of taste sensation'

• [x] Place 'disturbances of sensation of smell and taste' under both HP terms

• [x] Place 'ageusia' under 'disturbances of sensation of smell and taste'. UPDATE, no, it should go under HP:0000223 'Abnormality of taste sensation' only, see https://en.wikipedia.org/wiki/Ageusia. Check that its ontology definition is correct.

• [ ] Re. 'auditory system disease', see https://github.com/EBISPOT/efo/issues/645. More work may be needed in this branch or not depending on the outcome of that discussion.

Other children of 'sensory system disease' shouldn't need any work other than

• [ ] Delete their link to 'sensory system disease'. (Done for most children, but a few are left that depend on ticket above.)

• [ ] Lastly, when all else is taken care of, obsolete 'sensory system disease' as incorrect, no replacement.

(Note for self - the checklist above was last revised on 9/6/2020.)

[paolaroncaglia]

@zoependlington Edits left to do for this ticket depend on https://github.com/EBISPOT/efo/issues/645. I'll remove my assignment now, thanks.