A customizable patient data platform for genomic medicine
PhenoTips is a browser-based tool for recording linked clinical phenotype, genetic, disease, and family history data for patients with genetic diseases. PhenoTips includes a highly-customizable patient form, and includes sections to enter:
- clinical symptoms & physical findings (HPO)
- family information and history (including pedigree)
- diagnosis (mapped to OMIM or Orphanet)
- genes and variants of interest
- measurements (with support for instant computation of percentiles and generation of growth charts)
- demographic information (name, date of birth, ...)
You use PhenoTips directly through your web browser.
- If you are running a standalone version of PhenoTips directly on your computer, you can usually find it at
- If you are at a hospital or in a research group with your own PhenoTips instance, you should ask someone what URL to go to in order to access your instance
- To try it out, go to phenotips.com
- HPO - phenotype ontology
- OMIM - disease terminology
- Orphanet - disease ontology
- MONDO - disease ontology
- Apache Solr - an enterprise search platform
- XWiki - an enterprise web application development framework
Building from source
This project uses Apache Maven for lifecycle management.
First set up your environment:
- Make sure a proper JDK is installed, Java SE 1.8 or higher. Just a JRE isn't enough, since the project requires compilation.
- Install Apache Maven
- Clone the source code:
git clone firstname.lastname@example.org:phenotips/phenotips.git
- Ensure Maven has enough memory:
export MAVEN_OPTS="-Xmx2g -XX:MaxPermSize=256m"
Then, build the project with:
cd phenotips/ mvn install
Note: the first build may take a long time because all the dependencies are downloaded, but subsequent builds should only take a few minutes
Running a custom built instance
The project is split into several modules, among which
distribution/standalone will result in a fully-working self-contained package ready to run. Running the application is as simple as:
mvn install, as stated above, to build the project
- go to the directory where the final package is located,
- extract the contents of the
phenotips-standalone-<version>.ziparchive to a location of your choice (outside the
targetdirectory, to ensure it is not overwritten by subsequent builds)
- launch the
start.shon unix-like systems,
- open a browser and go to http://localhost:8080/
- this is a completely local version, not connected to any other PhenoTips instance or other software in your institution; a default user is provided, you can log in using User:
Contributions welcome! Fork the repository and create a pull request to share your improvements with the community.
In order to ensure that the licensing is clear and stays open, you'll be asked to sign a CLA with your first pull request.
This is free software! Create an issue in GitHub to ask others for help, or try fixing the issue yourself and then make a pull request to contribute it back to the core.
For information about the Enterprise version, please see phenotips.com.
PhenoTips is distributed under the AGPL version 3 (GNU Affero General Public License), a well known free software/open source license recognized both by the Free Software Foundation and the Open Source Initiative.
You can ensure compliance with this license by:
- making sure every change made to the code is also be distributed under AGPL, and any works that integrate PhenoTips (even over APIs) use a compatible license
- including prominent notice of the use of PhenoTips in any software that uses it
- retaining all copyright notices in the software
For more information, please Contact Us.