PhenotypeCreator can complain during creating Phenotypes if an HPO term cannot be found in the HPO version being used in analysis. Right now, we log term's absence and note that it will be ignored.
However, the user may be interested in fixing this but the log messages lack the necessary context.
The log message should include the individual ID to help the user fix the issue. However, we do not have that available within PhenotypeCreator and we may need to revise the PhenotypeCreator API to provide the context.
ielis
commented
6 months ago
PhenotypeCreatorcan complain during creatingPhenotypes if an HPO term cannot be found in the HPO version being used in analysis. Right now, we log term's absence and note that it will be ignored. However, the user may be interested in fixing this but the log messages lack the necessary context.The log message should include the individual ID to help the user fix the issue. However, we do not have that available within
PhenotypeCreatorand we may need to revise thePhenotypeCreatorAPI to provide the context.