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

Unable to find appropriate mappings in OXO #1

Open
matentzn opened this issue Nov 19, 2020 · 0 comments
Open

Unable to find appropriate mappings in OXO #1

matentzn opened this issue Nov 19, 2020 · 0 comments
Labels

Comments

@matentzn
Copy link
Contributor

Reference use case:

image

Problem description:

I find the term “high density lipoprotein cholesterol measurement” among the traits in the GWAS output for “cardiovascular disease”, which the GWAS Catalog tells me is EFO:0004612

Mapping EFO:0004612 using OXO: https://www.ebi.ac.uk/spot/oxo/search does not find:

  • MP abnormal circulating HDL cholesterol level MP:0000184
  • HP Increased HDL cholesterol concentration HP:0012184
  • HP Abnormal HDL cholesterol concentration HP:0031888

Not sure if this is a problem inherent to OXO or the mappings are lacking?
Some time ago I looked for other mapping tools – not sure if there is anything better out there.
Searching in OLS for “high density lipoprotein cholesterol” https://www.ebi.ac.uk/ols/search?q=high-density+lipoprotein+cholesterol&groupField=iri&start=0
Can filter by MP and I get: https://www.ebi.ac.uk/ols/search?q=high-density+lipoprotein+cholesterol&groupField=iri&start=0&ontology=mp
For efficiency, we would need an automated way to conduct these mappings.

@matentzn matentzn added the impc label Nov 19, 2020
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