Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Candidates for taxon restrictions #2194

Closed
paolaroncaglia opened this issue Nov 26, 2021 · 1 comment
Closed

Candidates for taxon restrictions #2194

paolaroncaglia opened this issue Nov 26, 2021 · 1 comment
Assignees
Labels

Comments

@paolaroncaglia
Copy link
Contributor

paolaroncaglia commented Nov 26, 2021

This ticket is to collect obvious cases of wrong terms leaking through into the Euarchontoglires and/or the human slim.
Aim is to add appropriate TCs.
It's not about the broader work on 2x, 3x etc. terms discussed in #2127 .
Note, I haven't delved too deep into these (some may already have TCs), and the list is a WIP.
We should look at children too.

barbel
echolocation organ
exoskeleton
feather
fin
gill
honey
open circulatory system
photophore
rhinarium
scale
scute
shell
shelled egg?
snout (not sure if it's used for rodents, but surely not human)
spermathecum
tail (in mouse, but not in human, unless we refer to vestigial tail)
vibrissa and its parts (in mouse, but not in human)
wing

TBC!

@paolaroncaglia
Copy link
Contributor Author

paolaroncaglia commented Nov 30, 2021

So looking at euarchontoglires-basic.owl from the uberon-2021-11-28 release, the list above becomes:
(i.e. the terms below are still in the Euarch slim and shouldn't)

'head external integument structure' (the term sounds broad, but I can't see any of its children, incl. barbel, being ever applied to Euarch. But these are all 2x/3x terms, so should be addressed elsewhere.)

  • 'echolocation organ' (however this should be linked to GO:0050959 'echolocation' which already has TCs for never in mouse and primates, but what rel should we use ('capable of', right?) and would the TC be inherited via that?)
    => discussed via Slack: I'll add
    'echolocation organ' subclass of 'capable of' some echolocation (this was already in place) and never in Euarch
    and when the taxon strategy issue in Decide on graph walking vs EL inference for using taxon constraints to make subsets #2137 will be resolved, the Uberon term won't be applied to mouse and primates.

  • UBERON:0006611 exoskeleton ("Exoskeleton or shell, including those of mollusks, turtles, insects and crustaceans.")
    seems quite broad, but to start with, add never in taxon Euarch

  • UBERON:0000022 feather
    is already only in taxon some Therapoda; add never in taxon Euarch

  • UBERON:0008897 fin
    add never in taxon Euarch (this was already in place)

  • UBERON:0002535 gill
    currently only in taxon some Bilateria, which is quite relaxed;
    gills are not found in reptiles, birds and mammals => add never in Amniota (this was already in place)

'honey', 'rhinarium' and 'scale' already have taxon constraints

  • 'open circulatory system' and 'photophore' need work

  • TBC (from 'scute' included)

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
Projects
None yet
Development

No branches or pull requests

1 participant