Convert BIO or BIOES to Brat standoff format

[Antonio Miranda]

Hi,

I am looking for tools to convert from a token-based representation of text (BIO or BIOES) to Brat standoff format. The tools should also align the generated ANN file with the original text, since misalignments that alter the original token positions may arise during the sentence reconstruction. 

If you know any of these resources, please, let me know. If the tool remains efficient when we want to convert many documents, that would be a plus. Links to GitHub repos or similar would be extremely helpful.

Thanks in advance!

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Antonio Miranda

Biomedical Engineer at Barcelona Supercomputing Center

Phone: 0034 649227310

Location: Barcelona, Spain

[Goran Topic]

I thought I'd quickly write one, so I committed it to brat repo. Pull the newest master from GitHub, and you will find it under `tools/bioes2standoff.py`. Then I found there already was something similar in `tools`. Mine is probably more permissive and easier to use, though. I just hacked this together in like an hour, so if you find any errors or problems, please let me know. You can convert multiple documents like this:

for file in bio/*.txt; do tools/bioes2standoff.py "$file" "${file%.txt}.bio" "${file%.txt}.ann"; done

or, if that is too inefficient, from Python:

from tools.bioes2standoff import convert

for ...:

    convert(text_file, bio_file, ann_file)

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