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Development of a free knowledge base to support the use of differential diagnosis information in PET-CT imaging. June 3, 2010

Posted by tomography in Conference, Nuclear Medicine, Radiology, SNM 2010.

Here is the second project I am involved with that will be presented at SNM 2010 in Utah.

Development of a free knowledge base to support the use of
differential diagnosis information in PET-CT imaging.

Zoltán Tóth, Zoltán Barta, András Székely, Nikoletta Pócsi, Ildikó Garai.


Our aim was to create an application integrated into the reporting
workflow to provide quick and easy access to relevant scientific
publications, facilitate the use of differential diagnosis information
and support evidence-based decision making. This project is part of a
larger project targeting the development of a structured reporting
system (ReportAssistant) for oncological whole-body PET-CT studies.
(See accompanying poster).


Creation of a PET-CT gamut list

The gamut list was created by combining the results of two independent
methods. First we selected 160 representative reports from our
practice. These were processed sentence-by-sentence by two physicians
in order to extract the most common and less frequent findings in
whole-body PET-CT studies. Copies of the original report text were
modified inline: sentences describing relevant lesion types were
“tagged” with “location – lesion – diagnosis” triples. These tags were
collected and summarised as potential gamut items with the help of a
software script. Parallel with these, a second list was created by
processing and sytntetising various scientific literature sources.
After reviewing, these two lists were merged to form the first edition
of a PET-CT gamut list. These version of the list covers chest,
abdomen and pelvis related lesions and consists of 400 gamut items.

Collecting and tagging publications

Systematic literature searches using a comprehensive list of keyword
expressions distilled from the PET-CT gamut list were conducted. The
main target journals were Radiology, Radiographics (both official
journals of RSNA), Journal of Nuclear Medicine (the official journal
of SNM) and European Journal of Nuclear Medicine & Molecular imaging
(the official journal of EANM). A total of 745 articles were selected.
The URL addresses of the full text articles were recorded and manually
tagged with proper gamut triples. Further processing, including
downloading and indexing of PDF articles, was automatically done by
custom software written by one of the authors (Z Barta).

Software development

All software development was done by using the X4Tk toolkit. X4Tk is
an open source (LGPL), object-oriented MVC-framework for easy desktop
application development and more, including support for standard
enterprise messaging protocols, TCP/IP based server-client development
and various interprocess communication solutions. X4Tk is written in
Perl by one of the authors (Z Barta), with the first release in 2005,
it is actively maintained and field-tested.


Database of tagged publications

A comprehensive collection of high-quality, manually selected,
properly reviewed and tagged radiology and nuclear medicine
publications was generated by using the methods described earlier with
the help of our custom RA PaperManager software. This list can be
exported to an external file. By loading this list one can easily
rebuild the database on his own computer without violating copyright

RA PaperManager software

The main features of RA PaperManager are:

* extensive support for collecting scientific papers ranging
from dragging-and-dropping of files to direct web browser integration through
bookmarklets, respectively import of list of URLs pointing to full
text PDFs and scanning & monitoring of hard drive directories.

* “free” and gamut-list based tagging of papers

* full text search support

* easy linking & interprocess communication with other
applications (STOMP, Windows MMF, HTTP)


We have designed, implemented and tested a highly useable, general
purpose, point-n-click SR software. Our software system can serve for managing personal collections of scientific publications and it can be easily integrated into structured reporting softwares through it’s REST API. The
software is available under various licenses, including free licenses
for personal and academic institutional usage.

Look for Zoltán Barta and Zoltán Tóth on site for more details!

– András



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