EdIE-R is a bespoke rule-based system for Information Extraction from radiology reports developed by Claire Grover.

Behind the scenes, it relies on Richard Tobin's LT-XML-2.

Some synthetic radiology reports are provided in example/synth-in, as well as the expected output for these files in example/synth-out.

The main command is scripts/run-edier, which takes input from STDIN and outputs to STDOUT. The run-edier command processes either files in the same XML format as those in example/synth-in or plain text. In both cases the output is in an XML format which shows the results of all levels of processing, with document labels in the element at the top and entities, relations and negation in the element at the bottom.

The -t flag is used to indicate whether the input is xml or plain, for example:

cd EdIE-R
cat example/synth-in/record1.xml | ./scripts/run-edier -t xml 
echo 'Moderate small vessel change.' | ./scripts/run-edier -t plain

Multiple XML records can be concatenated and grouped inside a top-level element, as in example/synth-in/allrecords.xml. The run-edier command will process these in the same way as single records:

cat example/synth-in/allrecords.xml | ./scripts/run-edier -t xml

The easiest way is to add include the binaries in your PATH environment variable.

You will need to choose the binaries that match your architecture.

Assuming you are in the EdIE-R directory, you can run:

export PATH=$PATH:$(pwd)/bin/sys-x86-64-el7