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From Bruce Tietjen <bruce.tiet...@perfectsearchcorp.com>
Subject cTakes Annotation Comparison
Date Thu, 18 Dec 2014 18:43:43 GMT
With the recent release of cTakes 3.2.1, we were very interested in
checking for any differences in annotations between using the
AggregatePlaintextUMLSProcessor pipeline and the
AggregatePlanetextFastUMLSProcessor pipeline within this release of cTakes
with its associated set of UMLS resources.

We chose to use the SHARE 14-a-b Training data that consists of 199
documents (Discharge  61, ECG 54, Echo 42 and Radiology 42) as the basis
for the comparison.

We decided to share a summary of the results with the development community.

Documents Processed: 199

Processing Time:
UMLSProcessor           2,439 seconds
FastUMLSProcessor    1,837 seconds

Total Annotations Reported:
UMLSProcessor                  20,365 annotations
FastUMLSProcessor             8,284 annotations

Annotation Comparisons:
Annotations common to both sets:                                  3,940
Annotations reported only by the UMLSProcessor:         16,425
Annotations reported only by the FastUMLSProcessor:    4,344

If anyone is interested, following was our test procedure:

We used the UIMA CPE to process the document set twice, once using the
AggregatePlaintextUMLSProcessor pipeline and once using the
AggregatePlaintextFastUMLSProcessor pipeline. We used the WriteCAStoFile
CAS consumer to write the results to output files.

We used a tool we recently developed to analyze and compare the annotations
generated by the two pipelines. The tool compares the two outputs for each
file and reports any differences in the annotations (MedicationMention,
SignSymptomMention, ProcedureMention, AnatomicalSiteMention, and
DiseaseDisorderMention) between the two output sets. The tool reports the
number of 'matches' and 'misses' between each annotation set. A 'match' is
defined as the presence of an identified source text interval with its
associated CUI appearing in both annotation sets. A 'miss' is defined as
the presence of an identified source text interval and its associated CUI
in one annotation set, but no matching identified source text interval and
CUI in the other. The tool also reports the total number of annotations
(source text intervals with associated CUIs) reported in each annotation
set. The compare tool is in our GitHub repository at

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