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

Fixes #2167 NTR onychocyte #2168

Merged
merged 2 commits into from
Oct 3, 2023
Merged

Fixes #2167 NTR onychocyte #2168

merged 2 commits into from
Oct 3, 2023

Conversation

aleixpuigb
Copy link
Collaborator

Fixes #2167 NTR onychocyte

@aleixpuigb aleixpuigb added new term request HuBMAP Needed/useful for HuBMAP labels Oct 3, 2023
@aleixpuigb aleixpuigb self-assigned this Oct 3, 2023
@aleixpuigb aleixpuigb requested a review from a user October 3, 2023 13:53
Copy link

@ghost ghost left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

  • There are several inherited SubClass Of statements that may not apply to this cell type, e.g., 'capable of' some 'positive regulation of neutrophil chemotaxis'; 'capable of' some 'antimicrobial peptide secretion'; 'part of' some 'skin epidermis'; etc
  • UBERON considers the 'nail plate' to be part of 'skin epidermis' and this cell type is also considered to be part of 'skin epidermis'. Consider confirming this with a SME.
  • 'nail plate' has SubClass Of 'has part' some keratinocyte. Consider if adding 'nail plate' SubClass Of 'has part' some onychocyte is appropriate.

@aleixpuigb
Copy link
Collaborator Author

Thank you for your comments @bvarner-ebi

  • There are several inherited SubClass Of statements that may not apply to this cell type, e.g., 'capable of' some 'positive regulation of neutrophil chemotaxis'; 'capable of' some 'antimicrobial peptide secretion'; 'part of' some 'skin epidermis'; etc

I agree that some of them might not be applicable, thank you for noticing. However, that should be addressed in a different ticket as that is a problem of keratinocytes, since the axiom would not be applicable to all cells. I will do some curation to which axioms should be removed to the general class and be added to the more specific terms.

  • UBERON considers the 'nail plate' to be part of 'skin epidermis' and this cell type is also considered to be part of 'skin epidermis'. Consider confirming this with a SME.

The SME (author of the ASCT+B skin table) considers the nail plate part of the skin epidermis.

  • 'nail plate' has SubClass Of 'has part' some keratinocyte. Consider if adding 'nail plate' SubClass Of 'has part' some onychocyte is appropriate.

I could not confirm that onychocyte is the only keratinocyte present in the nail plate, hence I have not used a logical definition. Since, onychocyte is 'part of' some 'nail plate', I don't think it is necessary to have the relation in the opposite direction with 'has part' and the existing axiom might be still useful.

@aleixpuigb aleixpuigb merged commit 4b2b51c into master Oct 3, 2023
1 check passed
@aleixpuigb aleixpuigb deleted the 2167_NTR_onychocyte branch October 3, 2023 15:36
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
HuBMAP Needed/useful for HuBMAP new term request
Projects
None yet
Development

Successfully merging this pull request may close these issues.

[NTR] onychocyte
1 participant