[jira] [Resolved] (TIKA-1645) Extraction of biomedical information using CTAKESParser

["Chris A. Mattmann (JIRA)" <ji...@apache.org>]

     [ https://issues.apache.org/jira/browse/TIKA-1645?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ]

Chris A. Mattmann resolved TIKA-1645.
-------------------------------------
       Resolution: Fixed
    Fix Version/s:     (was: 1.10)
                   1.9

Contributed! Thanks [~gostep] and [~selina]!

{noformat}
bash-3.2$ svn commit -m "Fix for TIKA-1645 & TIKA-1642: Extraction of biomedical information using CTAKESParser contributed by Selina Chu, Giuseppe Totaro and mattmann."
Sending        CHANGES.txt
Sending        tika-bundle/pom.xml
Sending        tika-parsers/pom.xml
Adding         tika-parsers/src/main/java/org/apache/tika/parser/ctakes
Adding         tika-parsers/src/main/java/org/apache/tika/parser/ctakes/CTAKESAnnotationProperty.java
Adding         tika-parsers/src/main/java/org/apache/tika/parser/ctakes/CTAKESConfig.java
Adding         tika-parsers/src/main/java/org/apache/tika/parser/ctakes/CTAKESContentHandler.java
Adding         tika-parsers/src/main/java/org/apache/tika/parser/ctakes/CTAKESParser.java
Adding         tika-parsers/src/main/java/org/apache/tika/parser/ctakes/CTAKESSerializer.java
Adding         tika-parsers/src/main/java/org/apache/tika/parser/ctakes/CTAKESUtils.java
Sending        tika-parsers/src/main/resources/META-INF/services/org.apache.tika.parser.Parser
Transmitting file data ..........
Committed revision 1683968.
{noformat}

Please note, improvements are welcomed. I know Giuseppe is working on an ExternalParser version of this and some other improvements. Selina is working on unit tests.


> Extraction of biomedical information using CTAKESParser
> -------------------------------------------------------
>
>                 Key: TIKA-1645
>                 URL: https://issues.apache.org/jira/browse/TIKA-1645
>             Project: Tika
>          Issue Type: Improvement
>          Components: parser
>            Reporter: Giuseppe Totaro
>            Assignee: Chris A. Mattmann
>              Labels: patch
>             Fix For: 1.9
>
>         Attachments: CTAKESConfig.properties, TIKA-1645.patch, TIKA-1645.v02.patch, tika-config.xml
>
>
> As mentioned in [TIKA-1642|https://issues.apache.org/jira/browse/TIKA-1642], [CTAKESContentHandler|https://github.com/giuseppetotaro/CTAKESContentHadler] is a preliminary work in order to integrate [Apache cTAKES|http://ctakes.apache.org/] into Tika allowing users to extract biomedical information from clinical text.
> Essentially, this work includes a wrapper for CAS serializers that aim at dumping out the identified annotations into XML-based formats.
> You can find in attachment a new patch that includes the CTAKESParser, a new parser that decorates the AutoDetectParser and relies on a new version of CTAKESContentHandler, based on feedback from [TIKA-1642|https://issues.apache.org/jira/browse/TIKA-1642]. This parser generates the same output of AutoDetectParser and, in addition, the metadata containing the identified clinical annotations detected by cTAKES.
> To perform a cTAKES AnalysisEngine by using Tika CTAKESParser, you need first to install the last stable release of cTAKES (3.2.2), following the instructions on [User Install Guide|https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.2+User+Install+Guide]. Then, you can launch Tika as follows:
> {noformat}
> CTAKES_HOME=/usr/local/apache-ctakes-3.2.2
> java -cp tika-app-1.10-SNAPSHOT.jar:${CTAKES_HOME}/desc:${CTAKES_HOME}/resources:${CTAKES_HOME}/lib/*:/path/to/CTAKESConfig org.apache.tika.cli.TikaCLI --config=/path/to/tika-config.xml /path/to/input
> {noformat}
> In the example above, {{/path/to/CTAKESConfig}} is the parent directory of file {{org/apache/tika/parser/ctakes/CTAKESConfig.properties}} that contains the configuration properties to build the cTAKES AnalysisEngine; {{tika-config.xml}} is a custom configuration file for Tika that contains the mimetypes whose CTAKESParser will perform parsing.
> You can find in attachment an example of both {{CTAKESConfig.properties}} and {{tika-config.xml}} to parse ISA-Tab files using cTAKES.
> You need [UMLS credentials|https://uts.nlm.nih.gov/home.html] in order to use the UMLS-based components of cTAKES.
> I would really appreciate your feedback.
> Thanks [~selina], [~chrismattmann] and [~lewismc] for supporting me on this work.



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