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AGPL-3.0 Made in Canada

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
  • To try it out, go to phenotips.com

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 [email protected]: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)

Contributing

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.

Support

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.

License

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.