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

["Giuseppe Totaro (JIRA)" <ji...@apache.org>]

Giuseppe Totaro created TIKA-1645:
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             Summary: 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


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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