Setting up PhenoteFXΒΆ

When you use PhenoteFX for the first time, you need to download some files and tell PhenoteFX where you would like to store the annotation files.

1. Download Medgen HPO OMIM This is a file frlom Medgen that contains the names of OMIM entries; we use this file to translate between an item such as OMIM:100001 and Smith Syndrome. This file will be replaced by a MONDO file soon.

2. Download HPO This will download the latest release of hp.obo from the HPO GitHub page.

3. Set biocurator id Enter whatever you would like be be nano-attributed by, e.g., MGM:rrabbit.

4. Set default directory for phenoteFX files Usually this will be the directory to which you have downloaded the GitHub repository for the HPO annotations. Please choose the subdirectory hpo-annotation-data/rare-diseases/annotated.

5. Show settings This item opens a window to show the current settings.

The remaining menu items in the setup menu are experimental and not needed for rare disease annotation.