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About PhenoTips

About PhenoTips


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 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.


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


This software is presented in the paper entitled "PhenoTips: Patient Phenotyping Software for Clinical and Research Use".

Who uses PhenoTips

PhenoTips is currently being used by several major research projects, including:

If you are interested in using PhenoTips and need help getting started please contact us.



Error-tolerant, predictive Search of the HPO

The quick search box enables text searches with tolerance for spelling errors. It provides suggestions of terms from the HPO that best match the entered keywords, and permits to broaden the search with other terms related to the given suggestions. This feature allows the user to browse the entire ontology of human phenotypes by navigating according to their semantic relations.


Configurable phenotype checklists

The predefined phenotypes list in the PhenoTips form is organized into easily configurable phenotype categories. Each category consists of a group of options mapped to standard HPO terms, and a summary view of the current phenotype selection. The user can also associate to each selected phenotypic description additional data such as the onset of the abnormality, the pace of progression, medical imaging or test reports which support the presence of that phenotype, and free-form comments on the manifestation.


Measurement recording and interpretation

The Measurements section of the PhenoTips Web form permits to record standard measures taken during clinical exams: Using the patient's gender and the age at the time of measurement (which is computed based on the recorded date of birth) these parameters are automatically translated into quantiles. Growth curves are plotted instantly based on entered values. Abnormal values are automatically reported and the corresponding phenotypes are selected (e.g. microcephaly for an abnormally small head circumference) though the clinician may choose to modify these later.


Pedigree drawing

For capturing advanced family history information, we are developing and incorporating in PhenoTips a pedigree drawing tool that supports both basic and very complex family structures. It provides an intuitive interface for building pedigrees graphically in just a few clicks. It can automatically detect and visually emphasize consanguineous couples, and prevents users from creating cyclic parent-child relationships. Individuals represented in the pedigree can be annotated with multiple disorders as well as other metadata such as date of birth / age or name.


PhenoTips® is freely available under the terms of the the GNU Affero General Public License, version 3.0.

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PhenoTips® is an exclusive trademark of Gene42 Inc.