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Patient matching extension for PhenoTips

License: GNU Affero General Public License v3.0

Python 1.88% Java 78.25% Shell 0.03% JavaScript 18.02% CSS 1.82%

patient-network's Introduction

This repository is no longer maintained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 [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)

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.

patient-network's People

Contributors

Stargazers

Watchers

Forkers

antonkatz flaviusx mjshepherd veronikaslc deanway brianlisk

patient-network's Issues

Need API for clearing patient similarity/Exomiser cache without server restart

Update the scripts to reference JS widgets from the PhenoTips namespace

MS.widgets became deprecated with phenotips/phenotips#495 . Because of this, the contact dialog no longer works.

Installing the extension using the extension manager doesn't work easily

The UI module doesn't list the jar modules as dependencies, so all jars have to be installed as well before it can work, which isn't nice.

Similar cases causing NPE for some patients

E.g. https://phenomecentral.org/P0000084:

Failed to execute the [velocity] macroorg.xwiki.rendering.macro.MacroExecutionException: Failed to evaluate Velocity Macro for content [#if ($xcontext.action == 'get')
  $response.setContentType('application/json')
#end
{
  "query": $patient.toJSON(),
  "resultsCount" : $matches.size(),
  "results" : [
#foreach ($p in $matches)
  $p.toJSON()#if ($foreach.hasNext()),
  #end

#end
  ]
}]
    at org.xwiki.rendering.internal.macro.velocity.VelocityMacro.evaluateString(VelocityMacro.java:131)
    at org.xwiki.rendering.internal.macro.velocity.VelocityMacro.evaluateString(VelocityMacro.java:50)
    at org.xwiki.rendering.macro.script.AbstractScriptMacro.evaluateBlock(AbstractScriptMacro.java:302)
    at org.xwiki.rendering.macro.script.AbstractScriptMacro.execute(AbstractScriptMacro.java:198)
    at org.xwiki.rendering.macro.script.AbstractScriptMacro.execute(AbstractScriptMacro.java:59)
    at org.xwiki.rendering.internal.transformation.macro.MacroTransformation.transformOnce(MacroTransformation.java:191)
    at org.xwiki.rendering.internal.transformation.macro.MacroTransformation.transform(MacroTransformation.java:132)
    at org.xwiki.rendering.internal.transformation.DefaultTransformationManager.performTransformations(DefaultTransformationManager.java:87)
    at org.xwiki.display.internal.DocumentContentDisplayer.display(DocumentContentDisplayer.java:252)
    at org.xwiki.display.internal.DocumentContentDisplayer.display(DocumentContentDisplayer.java:125)
    at org.xwiki.display.internal.DocumentContentDisplayer.display(DocumentContentDisplayer.java:55)
    at org.xwiki.display.internal.DefaultDocumentDisplayer.display(DefaultDocumentDisplayer.java:80)
    at org.xwiki.display.internal.DefaultDocumentDisplayer.display(DefaultDocumentDisplayer.java:38)
    at org.xwiki.sheet.internal.SheetDocumentDisplayer.display(SheetDocumentDisplayer.java:113)
    at org.xwiki.sheet.internal.SheetDocumentDisplayer.display(SheetDocumentDisplayer.java:50)
    at org.xwiki.display.internal.ConfiguredDocumentDisplayer.display(ConfiguredDocumentDisplayer.java:67)
    at org.xwiki.display.internal.ConfiguredDocumentDisplayer.display(ConfiguredDocumentDisplayer.java:41)
    at com.xpn.xwiki.doc.XWikiDocument.getRenderedContent(XWikiDocument.java:995)
    at com.xpn.xwiki.doc.XWikiDocument.getRenderedContent(XWikiDocument.java:974)
    at com.xpn.xwiki.api.Document.getRenderedContent(Document.java:676)
    at sun.reflect.GeneratedMethodAccessor632.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    at org.apache.velocity.util.introspection.UberspectImpl$VelMethodImpl.doInvoke(UberspectImpl.java:395)
    at org.apache.velocity.util.introspection.UberspectImpl$VelMethodImpl.invoke(UberspectImpl.java:384)
    at org.apache.velocity.runtime.parser.node.ASTMethod.execute(ASTMethod.java:173)
    at org.apache.velocity.runtime.parser.node.ASTReference.execute(ASTReference.java:280)
    at org.apache.velocity.runtime.parser.node.ASTReference.render(ASTReference.java:369)
    at org.apache.velocity.runtime.parser.node.ASTBlock.render(ASTBlock.java:72)
    at org.apache.velocity.runtime.parser.node.ASTIfStatement.render(ASTIfStatement.java:87)
    at org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.java:342)
    at org.xwiki.velocity.internal.DefaultVelocityEngine.evaluate(DefaultVelocityEngine.java:228)
    at org.xwiki.velocity.internal.DefaultVelocityEngine.evaluate(DefaultVelocityEngine.java:187)
    at com.xpn.xwiki.render.XWikiVelocityRenderer.evaluate(XWikiVelocityRenderer.java:105)
    at com.xpn.xwiki.internal.template.DefaultPrivilegedTemplateRenderer.evaluate(DefaultPrivilegedTemplateRenderer.java:125)
    at com.xpn.xwiki.internal.template.DefaultPrivilegedTemplateRenderer.evaluateTemplate(DefaultPrivilegedTemplateRenderer.java:75)
    at com.xpn.xwiki.XWiki.evaluateTemplate(XWiki.java:1687)
    at com.xpn.xwiki.XWiki.parseTemplate(XWiki.java:1627)
    at com.xpn.xwiki.api.XWiki.parseTemplate(XWiki.java:918)
    at sun.reflect.GeneratedMethodAccessor189.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    at org.apache.velocity.util.introspection.UberspectImpl$VelMethodImpl.doInvoke(UberspectImpl.java:395)
    at org.apache.velocity.util.introspection.UberspectImpl$VelMethodImpl.invoke(UberspectImpl.java:384)
    at org.apache.velocity.runtime.parser.node.ASTMethod.execute(ASTMethod.java:173)
    at org.apache.velocity.runtime.parser.node.ASTReference.execute(ASTReference.java:280)
    at org.apache.velocity.runtime.parser.node.ASTReference.render(ASTReference.java:369)
    at org.apache.velocity.runtime.parser.node.ASTBlock.render(ASTBlock.java:72)
    at org.apache.velocity.runtime.directive.VelocimacroProxy.render(VelocimacroProxy.java:216)
    at org.apache.velocity.runtime.directive.RuntimeMacro.render(RuntimeMacro.java:311)
    at org.apache.velocity.runtime.directive.RuntimeMacro.render(RuntimeMacro.java:230)
    at org.apache.velocity.runtime.parser.node.ASTDirective.render(ASTDirective.java:207)
    at org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.java:342)
    at org.xwiki.velocity.internal.DefaultVelocityEngine.evaluate(DefaultVelocityEngine.java:228)
    at org.xwiki.velocity.internal.DefaultVelocityEngine.evaluate(DefaultVelocityEngine.java:187)
    at com.xpn.xwiki.render.XWikiVelocityRenderer.evaluate(XWikiVelocityRenderer.java:105)
    at com.xpn.xwiki.internal.template.DefaultPrivilegedTemplateRenderer.evaluate(DefaultPrivilegedTemplateRenderer.java:125)
    at com.xpn.xwiki.internal.template.DefaultPrivilegedTemplateRenderer.evaluateTemplate(DefaultPrivilegedTemplateRenderer.java:75)
    at com.xpn.xwiki.XWiki.evaluateTemplate(XWiki.java:1687)
    at com.xpn.xwiki.web.Utils.parseTemplate(Utils.java:167)
    at com.xpn.xwiki.web.XWikiAction.execute(XWikiAction.java:304)
    at com.xpn.xwiki.web.XWikiAction.execute(XWikiAction.java:129)
    at org.apache.struts.action.RequestProcessor.processActionPerform(RequestProcessor.java:425)
    at org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:228)
    at org.apache.struts.action.ActionServlet.process(ActionServlet.java:1913)
    at org.apache.struts.action.ActionServlet.doPost(ActionServlet.java:462)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:637)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
    at com.xpn.xwiki.web.ActionFilter.doFilter(ActionFilter.java:121)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
    at org.xwiki.container.servlet.filters.internal.SavedRequestRestorerFilter.doFilter(SavedRequestRestorerFilter.java:208)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
    at org.xwiki.container.servlet.filters.internal.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:111)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
    at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
    at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
    at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
    at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
    at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
    at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:298)
    at org.apache.jk.server.JkCoyoteHandler.invoke(JkCoyoteHandler.java:190)
    at org.apache.jk.common.HandlerRequest.invoke(HandlerRequest.java:291)
    at org.apache.jk.common.ChannelSocket.invoke(ChannelSocket.java:769)
    at org.apache.jk.common.ChannelSocket.processConnection(ChannelSocket.java:698)
    at org.apache.jk.common.ChannelSocket$SocketConnection.runIt(ChannelSocket.java:891)
    at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:690)
    at java.lang.Thread.run(Thread.java:745)
Caused by: org.xwiki.velocity.XWikiVelocityException: Failed to evaluate content with id [xwiki:PhenoTips.SimilarCases]
    at org.xwiki.velocity.internal.DefaultVelocityEngine.evaluate(DefaultVelocityEngine.java:247)
    at org.xwiki.velocity.internal.DefaultVelocityEngine.evaluate(DefaultVelocityEngine.java:187)
    at org.xwiki.rendering.internal.macro.velocity.VelocityMacro.evaluateString(VelocityMacro.java:124)
    ... 91 more
Caused by: org.apache.velocity.exception.MethodInvocationException: Invocation of method 'toJSON' in  class org.phenotips.data.similarity.internal.RestrictedPatientSimilarityView threw exception java.lang.NullPointerException at xwiki:PhenoTips.SimilarCases[line 9, column 4]
    at org.apache.velocity.runtime.parser.node.ASTMethod.handleInvocationException(ASTMethod.java:243)
    at org.apache.velocity.runtime.parser.node.ASTMethod.execute(ASTMethod.java:187)
    at org.apache.velocity.runtime.parser.node.ASTReference.execute(ASTReference.java:280)
    at org.apache.velocity.runtime.parser.node.ASTReference.render(ASTReference.java:369)
    at org.apache.velocity.runtime.parser.node.ASTBlock.render(ASTBlock.java:72)
    at org.apache.velocity.runtime.directive.Foreach.render(Foreach.java:420)
    at org.apache.velocity.runtime.parser.node.ASTDirective.render(ASTDirective.java:207)
    at org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.java:342)
    at org.xwiki.velocity.internal.DefaultVelocityEngine.evaluate(DefaultVelocityEngine.java:228)
    ... 93 more
Caused by: java.lang.NullPointerException

IC-based feature similarity

Hint coloration in patient matching results doesn't fit

The hints in the latest version appear to be larger and a color of blue that doesn't appear anywhere else in the site. Would suggest going back to the older style:


.hint {
color: #888;
font-size: 70%;
...
}

Patient-matching is boosted by empty-string candidate genes

AbstractPatientSimilarityView's method getContactToken error handling

Allow non-owners to see similar cases

GenotypeSimilarity reverseGeneLookup optimization

Rather than searching through all patients with genetic information, there should be a global map from gene -> patients with variants in that gene, that is used instead.

New Java component for exposing the patient network settings

Bogus Exomizer dependency breaks PhenoTips

similarity-data-impl depends (wrongly) on an exomizer library, which in fact contains an older version of boqa, incompatible with the boqa library we actually use for differential diagnosis.

Boost the match score between patients with similar diagnoses

Basic OMIM boosting used to be there. It should be reinstated. Better yet, measure distance in ORDO.

Update patient similarity measure to simGIC score

After benchmarking, simGIC score was best, so phenotype matching should use this instead of the jz score.

Update Exomiser parsing to use TSV file ouput instead of VCF

Better "seeding" of similar patients by matching the full HPO hierarchies of the reference patient's symptoms to the index

After phenotips/phenotips#825 is implemented, the patient search and match scoring should be changed so that instead of searching for exact symptom matches, the partial hierarchies of the reference and indexed symptoms should be compared, and the score should reflect how close the two branches match.

Run exomiser with inheritance from patient record

Cache clearing should be restricted on the server-side to administrators

Fix NullPointer exception when attempting to load gene data for a remote patient

Remote patients (as provided by remote matching part) do not have a valid local ID, and can't have a complete genotype due to realistic request size restrictions. So it is 1) a valid case when patient id is null in the similarity finder code and 2) there is no need to try to load genotype for such a patient

The current code fails because the cache used does not support null IDs

Show the external id instead of the phenotips id in the similarcases ui when available

Interpret the VCF Files uploaded to a patient profile

Index in MedSavant and process with the Expomiser to display relevant variants.

RestictedPatientSimilarityView tests non-deterministically fail.

Some patients on PhenomeCentral don't get any similar patients at all

This is caused by phenotips/phenotips#586 and the fact that we're not checking if a value returned from the patient index actually exists in the database.

Search query responses incorrectly state that the owner of a matched patient is patient's reporter

In current version of PhenoTips the "reporter" is the creator of the document, but the current owner is whoever is assigned to be the owner and may be different from reporter. Correct current owner should be reported as the "owner" of a matched patient

MIM prototypes should be excluded from all data tables

They're only supposed to show up in the similar cases box.

Allow the feature scorer implementation to be configured

Some patients can break the patient similarity UI

It is possible to get an empty entry in the list of phenotypes, which makes the Solr query used to search similar patients invalid.

Use correct set of permissions when construction SimilarPatientViews

Should use getVisibility().getDefaultAccessLevel() instead of getAccessLevel() when constructing PatientSimilarityViews.

UPDATE: the code above is probably incorrect, but the existing code had problems, need to test and review

Reveal more submitter details for matchmaking and provide email mediation

Ask Jorge to allow PC to receive emails (@sdumitriu)
Build email reception/forwarding infrastructure to handle emails to: [email protected] (@sdumitriu)
Expose submitter username, match ID, [email protected] contact email for matches (@buske)
Update remote-matching to support this (@allasm)

Identical patients only showing up on one side?

https://phenomecentral.org/P0000727 and https://phenomecentral.org/P0000728

Candidate gene weight should be relative to number of candidates

When multiple matched features are paired with the same reference feature, only one of them is displayed

Duplicated and misplaced refresh buttons in the similar cases area

Display the top genes selected by exomiser

Edit button shown for "Similar cases available in the database" section

The edit pencil icon in shown for the Similar cases section, even though this section is not editable and is not present when the page is edited.

(Initially reported by @buske in phenotips : https://github.com/phenotips/phenotips/issues/785 )

Consider non-observed features in the matching results as well

Currently even if a patient is public matching algorithm seem to ignore features which are explicitly specified as "not observed", e.g. the JSON returned and the "show phenotype and genotype similarity" button on the patient page do not show any non-observed features.

Even if those features are not useful for the matching algorithm itself, saying that the matched patient has those features may be useful, especially if the "source" patient has those "not observed" features as well.

Enable anonymous communication between users having similar patients

Freetext diagnoses should not be prefixed with "MIM:"

For example:

Expanding variant match details adjusts overall table layout

Display some sort of genetic information with match if other patient has genetics that are visible

Make the patient index URL configurable

Right now it's hardcoded to port 8080 and the solr webapp name.

Sometimes phenotype IDs are doubled

This happens sometimes when searching for similar patients:

2014-03-13 08:50:55,627 [https://copy.phenomecentral.org/copy/get/PhenoTips/SimilarCases] ERROR formationPatientSimilarityView - Error resolving term: HP:0012452 HP:0012452

PatientSimilarityViews not invalidated from cache when patients change

PatientSimilarityViews are currently being saved in an XWiki cache, but are not being invalidated when the patient phenotypes/owners/genetics change.

GenotypeSimilarity candidate gene pre-filtering

Currently, all genes shared by two patients are fully explored (with early termination). Ideally, there would be an earlier cull step based on 1000GP data before looking at similarity with other patients.

Patient-matching genetic results are broken with Exomiser 2

Width of page changing drastically depending on length of variant in patient similarity view

Reported by @buske, details at phenotips/phenomecentral.org#36 .

Candidate genes should be used for patient matching

Prenatal phenotypes appear as HPO codes in the similar patients comparison

e.g.

Marta said:
Quick and dirty (very dirty) fix applied to dev.phenomecentral.org and phenomecentral.org . Something cleaner will be done soon. Is there an issue for this already on github? It should be reported to the patient-network project. For the record, the phenotypes showing up as HPO ids are prenatal phenotypes.

Support Connection-s between local and remote users

When a patient is matched using remote-matching API and is converted to JSON an attempt is made to generate a "contact token" (in AbstractPatientSimilarityView.toJSON()). This involves generating a "Connection" to anonymously connect the owners of the matched patients. However currently Connection only supports local users which have a XWiki document associated with them.

We need to rethink the contact mechanism, to support remote users as well (though we do not need to have the ability to grant them patient access, so this contact token should not necessarily involve a "connection")