phenotips: A Java repository from 790675356

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.org

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)

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 commercial support or for information about the paid Enterprise version, please contact Gene42.

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 see the PhenoTips Licensing page.

790675356/phenotips