NLM .nxml to text format conversion

Usage:

./nxml2txt NXMLFILE [TEXTFILE] [SOFILE]

For example (using test document):

./nxml2txt test/PMC3357053.nxml test/PMC3357053.txt test/PMC3357053.so

This creates the files test/PMC3357053.txt, containing the text content of the input document, and test/PMC3357053.so, containing the annotations (XML elements and their attributes) in a simple standoff format.

nxml2txt assumes a unix-like environment. If the input .nxml file contains embedded TeX-math, nxml2txt requires LaTeX and catdvi.

This tool was originally introduced as part of the BioNLP Shared Task 2011 supporting resources (https://github.com/ninjin/bionlp_st_2011_supporting).