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

Document how to update disease (OMIM and HPO) databases #177

Closed
holtgrewe opened this issue Jul 9, 2021 · 0 comments
Closed

Document how to update disease (OMIM and HPO) databases #177

holtgrewe opened this issue Jul 9, 2021 · 0 comments
Assignees
Labels
documentation Improvements or additions to documentation

Comments

@holtgrewe
Copy link
Collaborator

Is your feature request related to a problem? Please describe.
While performing "full" database updates is very important it is not fully documented yet. We are working on this currently for getting also GRCh38 support. However, certain databases such as the HPO and OMIM term databases should be updated more regularly.

Describe the solution you'd like

  • Document how to use varfish-db-downloader to download and prepare the file for import into VarFish.
  • Document how to import the data into VarFish. Make sure to include information how to verify that the update was correct.

Describe alternatives you've considered
N/A

Additional context
N/A

Discussed in https://github.com/bihealth/varfish-server/discussions/176

Originally posted by alexejknaus July 9, 2021
In order to submit novel variants to ClinVar of novel disorder, it is necessary to provide up-to-date OMIM and HPO IDs.
How can OMIM and HPO databases in VarFish be updated?

@holtgrewe holtgrewe self-assigned this Jul 9, 2021
@holtgrewe holtgrewe added the documentation Improvements or additions to documentation label Jul 9, 2021
@stolpeo stolpeo added this to the v0.24 milestone Nov 29, 2021
@stolpeo stolpeo assigned stolpeo and unassigned holtgrewe Jan 20, 2022
@stolpeo stolpeo closed this as completed Jan 27, 2022
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
documentation Improvements or additions to documentation
Projects
None yet
Development

No branches or pull requests

2 participants