Phenotips

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This repository is no longer maintained

The open-source, XWiki version of the PhenoTips platform is no longer actively developed or maintained.

PhenoTips development is now focused on the closed-source Enterprise solution available at phenotips.com.

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, ...)

Usage

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 localhost:8080
• 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

Powered by

• 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 git@github.com: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, distribution/standalone/target
• extract the contents of the phenotips-standalone-<version>.zip archive to a location of your choice (outside the target directory, to ensure it is not overwritten by subsequent builds)
• launch the start script (start.sh on unix-like systems, start.bat on Windows)
• 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: Admin and Password: admin (case-sensitive)

Support

The open-source community version of PhenoTips is no longer maintained or supported.

For information about the Enterprise version, please see phenotips.com.

License

This open-source version of PhenoTips was 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.