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About

This project mainly aims at providing an easy way to collect clinical phenotypes using a standardized vocabulary, thus alllowing for straight-forward cross-referencing with gene and disease databases.

The patient data being managed includes:

  • demographic information (name, date of birth, ...)
  • family information and history (including pedigree)
  • medical history
  • prenatal and perinatal history
  • measurements (with support for instant computation of percentiles and generation of growth charts)
  • clinical symptoms & physical findings, with all phenotypic descriptions being mapped to a standardized vocabulary (the Human Phenotype Ontology (HPO))
  • diagnosis (mapped to OMIM)
  • genetic variants found in the patient

The application provides a web interface accessible from any device equipped with a web browser and a secure connection to the application server. The complexity and technical codification of standardized phenotyping and disease vocabularies is hidden under the friendly UI allowing for error-tolerant, predictive search of phenotypic descriptions and providing instant suggestions of phenotypes, diseases matching the current phenotype selection, and relevant readings in scientific jurnals for further information.,

Major tools and resources involved used by this project

  • The Human Phenotype Ontology (HPO) - a standardized vocabulary of phenotypic abnormalities encountered in human disease; contains approximately 10,000 terms and is being developed using information from OMIM and the medical literature
  • Apache Solr - an enterprise search platform
  • XWiki - and enterprise web application development framework

Building instructions

This project uses Apache Maven for the whole lifecycle management. From the project's description:

Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information.

In short, Maven handles everything related to building the project: downloading the required dependencies, compiling the Java files, running tests, building the jars or final zips, and even more advanced goals such as performing style checks, creating releases and deploying them to a remote repository. All these steps are configured declaratively with as little custom settings as possible, since the philosophy of maven is "convention over configuration", relying on well-defined best practices and defaults, while allowing custom variations where needed.

Building the entire project is as simple as mvn install, but first the environment must be set-up:

  • Make sure a proper JDK is installed, Oracle Java SE 1.6 or 1.7 is recommended. Just a JRE isn't enough, since the project requires compilation.

  • Install maven by downloading it and following the installation instructions.

  • Create a ~/.m2/settings.xml file with the following content:

      <settings>
   <profiles>
     <profile>
       <id>xwiki</id>
       <repositories>
         <repository>
           <id>xwiki-snapshots</id>
           <name>XWiki Nexus Snapshot Repository Proxy</name>
           <url>http://nexus.xwiki.org/nexus/content/groups/public-snapshots</url>
           <releases>
             <enabled>false</enabled>
           </releases>
           <snapshots>
             <enabled>true</enabled>
           </snapshots>
         </repository>
         <repository>
           <id>xwiki-releases</id>
           <name>XWiki Nexus Releases Repository Proxy</name>
           <url>http://nexus.xwiki.org/nexus/content/groups/public</url>
           <releases>
             <enabled>true</enabled>
           </releases>
           <snapshots>
             <enabled>false</enabled>
           </snapshots>
         </repository>
       </repositories>
       <pluginRepositories>
         <pluginRepository>
           <id>xwiki-plugins-snapshots</id>
           <name>XWiki Nexus Plugin Snapshot Repository Proxy</name>
           <url>http://nexus.xwiki.org/nexus/content/groups/public-snapshots</url>
           <releases>
             <enabled>false</enabled>
           </releases>
           <snapshots>
             <enabled>true</enabled>
           </snapshots>
         </pluginRepository>
         <pluginRepository>
           <id>xwiki-plugins-releases</id>
           <name>XWiki Nexus Plugin Releases Repository Proxy</name>
           <url>http://nexus.xwiki.org/nexus/content/groups/public</url>
           <releases>
             <enabled>true</enabled>
           </releases>
           <snapshots>
             <enabled>false</enabled>
           </snapshots>
         </pluginRepository>
       </pluginRepositories>
     </profile>
   </profiles>
   <activeProfiles>
     <activeProfile>xwiki</activeProfile>
   </activeProfiles>
  </settings>

  • Clone the sources of the project locally, using one of:

    • git clone git://github.com/compbio-UofT/cidb.git if you need a read-only clone
    • git clone [email protected]:compbio-UofT-/cidb.git if you also want to commit changes back to the project (and you have the right to do so)
    • download an archive of the current code if you don't want to use version control at all

  • Execute mvn install at the command line to build the project

    • note that the first build will take a while longer, because all the required dependencies are downloaded, but all the subsequent builds should only take seconds

Installation

The project is split into several modules, among which wiki-distribution 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 get the project built
  • go to the directory where the final package is located, wiki-distribution/target
  • extract the contents of the distribution-wiki-1.0-SNAPSHOT.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
  • open http://localhost:8080/ in a browser

Usage & limitations

The standalone distribution comes packaged with a Java Servlet Container, Jetty, a lightweight relational database management system, HyperSQL, and the phenotyping application itself.

While good for a small to medium trial, this package isn't suited for production use and large quantities of data.