HPO converter: switch to publicly available OMIM file for disease codes#10
Open
hendrikweisser wants to merge 1 commit into
Open
HPO converter: switch to publicly available OMIM file for disease codes#10hendrikweisser wants to merge 1 commit into
hendrikweisser wants to merge 1 commit into
Conversation
…prove handling of missing files
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
The converter for the "hpo-annotation" source in HumanMine needs an input file from OMIM, to know which OMIM codes refer to phenotypes. The currently used file ("mimTitles.txt") is not freely available, so I've changed the converter to use one that is:
(From https://omim.org/downloads)
In the "project.xml" of the mine, the value of property "hpo.disease.file" would need to be changed accordingly.
(I'm not sure if a test needs to be updated. There are data files in https://github.com/intermine/humanmine-bio-sources/tree/master/hpo-annotation/src/test/resources, but the file names don't match those expected by the converter.)