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资源说明：PhenoTips makes it simple to record clinical findings observed in patients with possible genetic disorders through an easy-to-use Web interface
## 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](http://www.human-phenotype-ontology.org/)) * family information and history (including **pedigree**) * **diagnosis** (mapped to [OMIM](http://omim.org/) or [Orphanet](http://www.orphadata.org/)) * 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](https://phenotips.com/) ## Powered by * [HPO](http://www.human-phenotype-ontology.org/) - phenotype ontology * [OMIM](http://omim.org/) - disease terminology * [Orphanet](http://www.orphadata.org/) - disease ontology * [MONDO](http://obofoundry.org/ontology/mondo.html) - disease ontology * [Apache Solr](http://lucene.apache.org/solr/) - an enterprise search platform * [XWiki](http://xwiki.org) - an enterprise web application development framework ## Building from source This project uses [Apache Maven](http://maven.apache.org/) 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](http://maven.apache.org/) * 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-
.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/](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](https://phenotips.com/). ## License PhenoTips is distributed under the [AGPL version 3](http://www.gnu.org/licenses/agpl-3.0.html) (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](https://phenotips.com/contact.html).
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