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https://issues.apache.org/jira/browse/TIKA-1645?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=14570839#comment-14570839
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Chris A. Mattmann commented on TIKA-1645:
-----------------------------------------
Great work, [~gostep]! Some comments:
# tika-bundle/pom.xml - has orthogonal change to junit in patch, please remove
# tika-example/pom.xml - changes commented out should be removed
# tika-parsers/pom.xml - exclusions commented out, should be excluded. Also I
thought you were going to call ctakes from the command line, obviating the need
for any dependencies?
# tika-parsers/src/main/java/org/apache/tika/parser/ctakes/CTAKESConfig.java -
private boolean text is commented out please remove.
Overall looks great! If you wanted to move this is to an ExternParser, the
thought I had would be to move CTAKESSerializer, Utils, and ContentHandler into
a command line utility and then define a return format (JSON, plain text, etc.)
and then call and read that in in cTAKES parser. However this is a great start
and we can always think about doing that later!
> 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: Giuseppe Totaro
> Labels: patch
> Fix For: 1.10
>
> Attachments: CTAKESConfig.properties, TIKA-1645.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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