phenotips / clinical-text-analysis-extension Goto Github PK

View Code? Open in Web Editor NEW

1.0 1.0 7.0 229.63 MB

An extension for Phenotips to extract HPO terms from free text.

Java 100.00%

clinical-text-analysis-extension'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This repository is no longer maintained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.

clinical-text-analysis-extension's People

Contributors

Stargazers

Watchers

Forkers

mkozakov deanway zhanghongzhitou josecv simonli5601 simonli0750

clinical-text-analysis-extension's Issues

Create a basic UIX that communicates with the text analysis component

About UIXs (user interface extensions):

Create the basic ui and functionality

a textarea where the user can type/paste text
a button Analyze that launches the text extraction
a container where the terms that were identified are displayed (simple list of terms with id and label)

Memory issue

This is a really nice feature. We tried it and it worked well for annotating the free text. We also encountered the same memory issue you already noticed. I believe the Apache common pool is not working as expected. I used JCasPool instead, to replace ObjectPool jcasPool. It seems to work much better. Hope this information can help.

Add a Bio-LarK based implementation

Better UI design and integration

TBD

Create the base project structure

Create a top level Maven project org.phenotips:clinical-text-analysis, with pom packaging and several submodules:

api, with the component definition(s) (@Role) for the text extraction functionality, and a script service exposing the functionality to scripts
biolark as the first implementation of the component (@Component)
ui with wiki documents
pageobjects for functional test helper objects
tests for functional tests

See the patient-data component for an example.

The text analysis ui should be displayed only if the phenotype UIX is enabled

When clicking on the highlighted words in the source text, the user should have the ability to see and select other terms that match them

Add a CTAKES implementation

Add a SciGraph based implementation

Design the API and add the data structures and component roles needed

Brainstorm about what should the text analysis feature do, and fill in the api submodule.

Highlight the words corresponding to each identified term in the original text

Once the user hits Analyze, replace the textarea with formatted text where the words corresponding to terms are marked with a specific background color. Hovering the markings should highlight the corresponding term in the results list, and hovering a term should highlight (more, with a brighter background color) the source words. Use colors from the configured colortheme, avoid custom colors.

Also, Analyze should become Edit after the extraction is completed, allowing to go back and modify the text.

When the user selects a piece of the entered text, (s)he should be presented with a 'search' option allowing to find terms matching that text

Checkstyle error while building phenotips-components

Dear Phenotips community,

I am getting this error when running mvn install inside my phenotips/compnents folder as the instructions suggested.

For some reason the process fails with the error below.

[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  16:09 min
[INFO] Finished at: 2018-11-27T01:34:49Z
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-checkstyle-plugin:2.17:check (test-checkstyle) on project clinical-text-analysis-extension-api: You have 16 Checkstyle violations. -> [Help 1]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException
[ERROR]
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <goals> -rf :clinical-text-analysis-extension-api

Any advice?

thank you very much

dependency issue

Hi,

I am trying to build/install clinical-text-analysis but it complains about the dependencies.

[INFO] --- maven-dependency-plugin:3.1.1:analyze-only (check-dependencies) @ clinical-text-analysis-extension-biolark ---
[WARNING] Used undeclared dependencies found:
[WARNING]    commons-io:commons-io:jar:2.6:compile
[WARNING]    org.xwiki.commons:xwiki-commons-environment-api:jar:7.4.6:compile
[WARNING]    org.xwiki.commons:xwiki-commons-observation-api:jar:7.4.6:compile
[WARNING] Unused declared dependencies found:
[WARNING]    org.xwiki.platform:xwiki-platform-extension-distribution:jar:7.4.6:compile
[WARNING]    jdom:jdom:jar:1.0:compile
[WARNING]    org.apache.commons:commons-collections4:jar:4.0:compile
[WARNING]    log4j:log4j:jar:1.2.17:compile
[WARNING]    net.sf.jwordnet:jwnl:jar:1.3.3:compile
[WARNING]    uk.ac.shef.wit:simmetrics:jar:1.6.2:compile
[WARNING]    com.ibm.icu:icu4j:jar:51.1:compile
[WARNING]    net.sf.json-lib:json-lib:jar:jdk15:2.3:compile
[WARNING]    commons-collections:commons-collections:jar:3.2.1:compile
[WARNING]    org.biolark:biolark-ta:jar:1.0:compile
[WARNING]    org.biolark:biolark-commons:jar:1.0:compile
[WARNING]    org.biolark:biolemmatizer-core:jar:with-dependencies:1.1:compile
[WARNING]    org.apache.commons:commons-compress:jar:1.4.1:compile
[WARNING]    cc.mallet:mallet:jar:2.0.7:compile
[WARNING]    org.xwiki.platform:xwiki-platform-oldcore:jar:7.4.6:compile
[WARNING]    edu.mit:jwi:jar:2.2.4:compile
[WARNING]    nu.xom:xom:jar:1.2.8:compile
[WARNING]    org.phenotips:phenotips-constants:jar:1.4.1:compile
[WARNING]    com.googlecode.json-simple:json-simple:jar:1.1.1:compile
[WARNING]    xerces:xercesImpl:jar:2.9.1:compile
[WARNING]    com.googlecode.matrix-toolkits-java:mtj:jar:0.9.14:compile
[WARNING]    br.pro.lab:OpenJGraph:jar:0.9.1:compile
[WARNING]    com.google.code.gson:gson:jar:2.2.2:compile
[WARNING]    org.jsoup:jsoup:jar:1.7.2:compile
[WARNING]    org.biolark:biolark-input:jar:1.0:compile
[WARNING]    org.xwiki.commons:xwiki-commons-context:jar:7.4.6:compile
[WARNING]    org.beanshell:bsh:jar:2.0b5:compile
[WARNING]    org.mockito:mockito-all:jar:1.10.8:compile
[WARNING]    org.xwiki.platform:xwiki-platform-model:jar:7.4.6:compile
[WARNING]    org.biolark:biolark-search:jar:1.0:compile
[WARNING]    net.sf.trove4j:trove4j:jar:2.0.2:compile
[WARNING]    org.slf4j:slf4j-api:jar:1.7.25:compile
[WARNING]    org.biolark:biolark-variants:jar:1.0:compile
[WARNING]    org.xwiki.platform:xwiki-platform-bridge:jar:7.4.6:compile
[WARNING]    net.sourceforge.nekohtml:nekohtml:jar:1.9.17:compile
[WARNING]    org.biolark:biolark-input-pheno:jar:1.0:compile
[WARNING]    jgrapht:jgrapht:jar:0.6.0:compile
[WARNING]    org.biolark:lvg2013dist:jar:1.0:compile
[WARNING]    org.xwiki.platform:xwiki-platform-query-manager:jar:7.4.6:compile
[WARNING]    edu.stanford.nlp:stanford-corenlp:jar:3.5.1:compile
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] PhenoTips - Clinical Text Analysis ................. SUCCESS [  3.662 s]
[INFO] PhenoTips - Clinical Text Analysis - Java API ...... SUCCESS [ 30.231 s]
[INFO] PhenoTips - Clinical Text Analysis - Biolark implementation for the Java APIs FAILURE [ 18.808 s]
[INFO] PhenoTips - Clinical Text Analysis - Generic REST implementation for the Java APIs SKIPPED
[INFO] PhenoTips - Clinical Text Analysis - User Interface Components SKIPPED
[INFO] PhenoTips - Clinical Text Analysis - Page Objects .. SKIPPED
[INFO] PhenoTips - Clinical Text Analysis - Ctakes server . SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 53.812 s
[INFO] Finished at: 2018-11-28T13:15:48+11:00
[INFO] Final Memory: 56M/1782M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-dependency-plugin:3.1.1:analyze-only (check-dependencies) on project clinical-text-analysis-extension-biolark: Dependency problems found -> [Help 1]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
[ERROR] 
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <goals> -rf :clinical-text-analysis-extension-biolark

Process finished with exit code 1

Any thoughts?