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brc-gate-pharmacotherapy's Introduction

brc-gate-pharmacotherapy

Pharmacotherapy GATE application used by the BRC on CRIS text

Users of this product should please bear in mind that published studies from the South London and Maudsley Biomedical Research Centre citing this product and its output may have applied additional post-processing algorithms which will either have been detailed in the respective publication or can be requested from corresponding authors.

Please first run following command to pull all submodules

git submodule update --init --recursive

You also need compile the context tagger before use:

cd plugins/gateplugin-ConText/

ant

To use brc-gate-pharmacotherapy with original context tagger please checkout v1:

git checkout v1

CHANGE LOG V1.1 UPDATE CONTAXT TAGGER TO NEWVERSION

brc-gate-pharmacotherapy's People

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brc-gate-pharmacotherapy's Issues

UUIDs parsed as prescriptions with invalid dose values

I'm noticing that UUIDs in a patient record are being parsed as prescriptions eg:

54A14C20-50FB-11EB-AE9C-9999999999C

Results in:


_content:C-9999999999C
_end:35
_id:44
_set:Output
_start:22
_type:Prescription
dose:-9999999999C
dose-multiple:1
dose-unit:C
dose-value:-9.999999999E9
drug:C
drug-type:GATE_gazetteer
route:unknown
status:continuing
tense:present

or

C-12345E678901C

results in:

_content:C-12345E678901C
_end:15
_id:20
_set:Output
_start:0
_type:Prescription
dose:-12345E678901C
dose-multiple:1
dose-unit:C
dose-value:-Infinity
drug:C
drug-type:GATE_gazetteer
route:unknown
status:continuing
tense:present

I don't know enough about GATE or this plugin to understand where the responsibility lies for sanity checking the output (our application assumes dose-value is decimal so chokes on "-Infinity" or exponential notation). "-Infinity" does seem wrong for a field defined as a double that would never be negative.

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