Using HPO Workbench with the latest hp.obo version

The hp-edit.owl file contains all of the latest changes. However, the version of the hp.obo file that HPO Workbench downloads via its Edit menu does not necessarily have the latest changes, because the later file is released on a monthly basis. To get the very latest version, it is possible to compile the hp.obo file locally and import the local file into HPO Workbench. This step requires some familiarity with the command line; if you are not familiar with this kind of work and need the latest hp.obo version, please contact the HPO team.

To do so, you will need to download the HPO github repository as well as the repository for owltools. The following text assumes that you download both repositories to the same place, e.g., to some directory called GIT on your local drive.

Downloading the HPO github repository

The HPO GitHub repository can be found here: Clone the repository with the following command.

$ git clone

Building owltools

We need to download and build owltools. The GitHub repository can be found here: Clone the repository and build it as follows.

$ git clone
$ cd owltools
$ ./

Building hp.obo

In order to build hp.edit, we will use the Makefile located in human-phenotype-hpoOntology/src/hpoOntology/. This makefile needs access to owltools. You can either add the paths to your environment (e.g., using the .bashrc file) or you can add the path to the environment of your current shell. The latter solution is shown here.

$ cd src/hpoOntology
$ export PATH=${PATH}:../../../owltools/OWLTools-Oort/bin/:../../../owltools/OWLTools-Runner/bin/
$ make

This will create a new version of hp.obo.

Using the new version of hp.obo in HPO Workbench

After you have created the up-to-date version of hp.obo, import it using the Edit menu of HPO Workbench.

HPO Workbench - import local hp.obo

After this, the browsing functions of HPO Workbench will use the new version of hp.obo (for the current session only).