HPO Workbench

Contents:

• Installing and running HPO Workbench
  • Mac OSX
  • Windows
  • Linux
• Exporting HPO data as an Excel file
  • Creating Excel files to revise or extend the HPO
  • Using the Track Changes feature in Excel
• Using the very latest HPO version
  • Downloading the HPO github repository
  • Building owltools
  • Building hp.obo
  • Using the new version of hp.obo in HPO Workbench
• HPO Workbench from the command line
  • Downloading HPO data
  • Printing open issues to Word
  • CSV
  • Rich Text Format (RTF) Output
  • Counting annotations

HPO Workbench

HPO Workbench is a Java app designed as a browser for HPO terms and annotated diseases. HPO Workbench has a series of functions that can be used by collaborators to review and make suggestions for extending, correcting, or otherwise revising the HPO or the disease annotations.

HPO Workbench can be used to browser the HPO hpoOntology; information about each term is shown including the definition, comments, and synonyms (if any). If the term is used to annotate diseases in the HPO database, then a list of diseases is shown. Additionally, diseases can be visualized, and all HPO terms that annotate that disease are shown according to affected system.

HPO Workbench can also be used to suggest additions, corrections, or revisions to the HPO. To do this, users can navigate to the part of the HPO they would like to revise, and mark a term and suggest new child terms or other revisions. Also, new annotations for diseases can be suggested. To do so, users must enter their GitHub name and password (only once per session), and the suggestions are sent to the HPO GitHub tracker, where they will be registered under your id (so that you will get feedback via Email about your suggestion).

HPO Workbench can also be used to export Excel files that represent the HPO hierarchy by means of indentation of columns. These excel files are meant to be used to record suggestions.

Browsing the HPO using HPO Workbench

Navigate through the hierarchy of the using the tree browser or use the autocomplete text field to find the HPO term of your choice. HPO Workbench will display the ID, definition, comment, and synyonyms for the term. If any diseases in the HPO corpus are annotated to the term, a list of the diseases will be displayed.

GitHub repository

The HPO Workbench GitHub repository can be found here: https://github.com/TheJacksonLaboratory/HPOworkbench