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visualAcuityExtractor

This project is to perform Natural Language Processing (NLP) using a rule-based approach for the purposes of extracting Snellen visual acuities from ophthalmology clinical text notes.

The code works with numerous different visual acuity documentation styles and will output the best corrected visual acuity for each eye. In addition, it will also convert the visual acuities into logMAR and output into a tab delimited fashion allowing for easy of use into statistical programs for analysis. The output for several files is meant to be concatenated together.

Requirements

  • Ruby
  • textoken gem

Installation

gem install vaextractor

Usage

rawtext = <<-eos
HPI: 1 year followup for glaucoma.

VA: 
OD: 20/30-2 ph 20/20-1
OS: 20/20 +1 

Tp: 20/21

SLEx:
L/L: wnl OU
C/S: w/q OU
K: clr OU
AC: d/q OU
I: r/r ou


A/P
Follow up in 1 year
eos

require 'vaextractor'
a = VAExtractor.new
a.extract(rawtext)
 => {:RE=>["20", "20", "-", "1"], :LE=>["20", "20", "+", "1"], :RElogmar=>0.0194, :LElogmar=>-0.025}

or simply

require 'vaextractor'
a = VAExtractor.new
a.extract(IO.read("examples/example1.txt"))
 => {:RE=>["20", "20", "-", "1"], :LE=>["20", "20", "+", "1"], :RElogmar=>0.0194, :LElogmar=>-0.025}

Output format

The extract function outputs a ruby hash with the following values

  • :RE - visual acuity array for right eye
  • :LE - visual acuity array for left eye
  • :RElogmar - logMAR visual acuity for right eye
  • :LElogmar - logMAR visual acuity for left eye

Visual acuity array is enumerated as:

  1. Numerator eg. 20, HM, CF
  2. Denominator eg. 30
  3. Adjustment eg. +
  4. Letters eg. 2

Examples

Example text files are provided in examples/ to give the user an idea of the different formats the extractor is capable of extracting.

License

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

Copyright

Copyright 2016, Aaron Y. Lee MD MSCI. University of Washington, Seattle WA