PhenoTips is an open source software tool for collecting and analyzing phenotypic information for patients with genetic disorders. The user interface closely mirrors clinician workflows so as to facilitate the recording of observations made during the patient encounter. This easy-to-use front-end, compatible with any device that runs a Web browser, is coupled with with a standardized database back-end where phenotypic information is represented using the Human Phenotype Ontology (HPO).

Collected data include demographics, medical history, family history, physical and laboratory measurements, physical findings, and free-form notes.

In addition to data collection, PhenoTips automatically analyzes a wide range of measurements and plots live the corresponding growth curves. It also supports accurate diagnosis based on the entered data, and can suggest additional clinical investigations that can improve the diagnosis.

Features preview


PhenoTips is developed in the Computational Biology Lab at University of Toronto's Computer Science Department, in collaboration with geneticists and clinicians form SickKids and CARE for RARE.

Citing PhenoTips

If you wish to mention PhenoTips in a scientific article, please refer to our paper published in May 2013 in Human Mutation:

Girdea, M., Dumitriu, S., Fiume, M., Bowdin, S., Boycott, K. M., Chénier, S., Chitayat, D., Faghfoury, H., Meyn, M. S., Ray, P. N., So, J., Stavropoulos, D. J. and Brudno, M. (2013), PhenoTips: Patient Phenotyping Software for Clinical and Research Use. Hum. Mutat., 34: 1057–1065. doi: 10.1002/humu.22347


Apr 02 2014

PhenoTips 1.0 Milestone 11 released

The PhenoTips development team is happy to announce the availability of the eleventh milestone of PhenoTips 1.0, which includes several new features, improvements and bugfixes. This is one of a few planned milestones leading to a stable 1.0 release. The highlights of the release are:

  • An improved patient report interface:
    • a horizontal menu with textual entries replaces the vertical icon-only menu
    • the phenotypes suggested for differential diagnosis appear below the current selection
    • information buttons about each displayed phenotype
    • and many other minor improvements
  • Support for pushing patient records to other servers, especially PhenomeCentral
  • Improved Pedigree compatibility with older browsers
  • Added a specificity metric widget which scores patient records based on how detailed is the phenotyping
  • Better gene list UI, showing gene name suggestions and links to various gene databases
  • Added a default list of ethnicities to use as suggestions
  • A new RPM package allowing easy installation of PhenoTips on RedHat Enterprise Linux and derived distributions
  • The standalone distribution has been tuned and is now suitable for production use
  • For integration with other tools, the JSON export of a patient record has been expanded and now includes most of the data present in the record

See the full list of issues on GitHub.

Feb 25 2014

PhenoTips 1.0 Milestone 10 released

The PhenoTips development team is happy to announce the availability of the tenth milestone of PhenoTips 1.0, which includes many bugfixes and improvements making PhenoTips easier to use in a collaborative environment. This is one of a few planned milestones leading to a stable 1.0 release. The highlights of the release are:

  • A new homepage targeting a collaborative deployment, showing active groups, personal and shared data
  • The pedigree drawing tool has been greatly improved and is now enabled by default
  • A redesigned administration which makes it easier to configure PhenoTips
  • Better integration of user workgroups, including the support for group administrators
  • A better UI for managing the predefined phenotypes displayed by default
  • More fields available in the patient record for APGAR scores and assisted reproduction

A major new feature is the support for Studies, virtual collections which group related patient reports, using a customized patient report structure better suited for describing such patients. We would like to thank Neuromics for this very interesting use case, and for their patience going through the iterations that made this feature easy to use.

We would also like to thank our collaborators at the NIH Undiagnosed Diseases Program and at the Monarch Initiative for all the bug reports and improvement suggestions.

See the full list of issues on GitHub.

Oct 31 2013

PhenoTips poster presented at ASHG 2013

Last week, the PhenoTips team attended the ASHG annual Meeting in Boston, where we presented two posters describing PhenoTips and PhenomeCentral. If you didn't get a chance to see them (and us) at the meeting, you can take a look at our posters here:

Fork me on GitHub

Reproducing or distributing this clinical information without permission from the institution that owns it is strictly forbidden.
PhenoTips version 1.0-milestone-11r1