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HPO Annotation QC

Building the application

hpoannotqc depends on phenol; currently, the latest version of phenol needs to be installed locally, but soon this will all be in maven central.

Running the application

We need to pass the application the location of the hp.obo file as well as the location of the directory with the HPO annotation small files. This repository is currently private available here:


The application will download several required files to a (new) subdirectory called data.

$ java -jar target/HpoAnnotQc.jar download

Creation of phenotype.hpoa

The following command converts the HPO Annotation files ("small files) into the file.

$ java -jar target/HpoAnnotQc.jar big-file -a /path/hpo-annotation-data/rare-diseases/annotated

This command will output the phenotype.hpoa file as well as a log file named The phenotype.hpoa file can be used as input for phenol.

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