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KneeTex: An ontology-driven system for information extraction from MRI reports

Automatically extracted information

An example of a filled template. Original text source: "There is a small undisplaced vertical radial tear of the posterior horn of the lateral meniscus."


Highlights


KneeTex is an open-source, stand-alone application for information extraction from narrative reports that describe an MRI scan of the knee.

Given an MRI report as input, the system outputs the corresponding clinical findings in the form of JavaScript Object Notation objects.

The extracted information is mapped onto TRAK, an ontology that formally models knowledge relevant for the rehabilitation of knee conditions.

As a result, formally structured and coded information allows for complex searches to be conducted efficiently over the original MRI reports, thereby effectively supporting epidemiologic studies of knee conditions.


Download


KneeTex source files written in Java (distributed under the FreeBSD licence).


Links


SQLite database is used by KneeTex to manage intermediary results.

SQLite Manager can be used to view the SQLite database.


Contact


Irena Spasić


Publications


Irena Spasić, Bo Zhao, Christopher Jones, Kate Button (2015) KneeTex: An ontology-driven system for information extraction from MRI reports. Journal of Biomedical Semantics, Vol. 6, 34 [PMID: 26347806] [DOI: 10.1186/s13326-015-0033-1]