Reference tagger and remover

[thoppe]

Longer biomedical texts include references which often are concatenated with regular text. This module aims to either remove or partition out the references. For example

...  key feature in Drosophila3-5 and elegans(7).

...  key feature in Drosophila and elegans.

Add more examples as comments to this issue as they are identified.

[thoppe]

Here's a line copied directly from Wikipedia, should be a simple grammar fix

import nlpre
P = nlpre.seperate_reference()
text = '''There are at least eight distinct types of modifications found on histones (see the legend box on the top left of the figure). Enzymes have been identified for acetylation,[2] methylation,[3] demethylation,[4] phosphorylation,[5] ubiquitination,[6] sumoylation,[7] ADP-ribosylation,[8] deimination,[9][10] and proline isomerization.[11]'''

Which gives

There are at least eight distinct types of modifications found on histones (see the legend box on the top left of the figure) . Enzymes have been identified for acetylation,[2] methylation,[3] demethylation,[4] phosphorylation,[5] ubiquitination,[6] sumoylation,[7] ADP-ribosylation,[8] deimination,[9][10] and proline isomerization .

ie. none of the references have been removed.