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OHNLP / MedTagger

MedTagger is a light weight clinical NLP system built upon Apache UIMA.
Apache License 2.0
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MedTagger output in BRAT format #19

Open MayeeshaHumaira opened 1 year ago

MayeeshaHumaira commented 1 year ago

Hello, I am a Ph.D. student at the University of Alabama at Birmingham and currently working in Dr. John Osborne’s lab. I would like to know if there is any software or any way to convert MedTagger output to BRAT format or if is there any way to convert it to any intermediate format and then convert it to BRAT format.

qqndrew commented 1 year ago

We should actually have something for this. @ymnliu -- I believe this is with you?

ymnliu commented 1 year ago

Hi @MayeeshaHumaira,

MedTagger does not currently support exporting to brat TSV formats natively. Have you looked into MedTator which is the annotation tool that supports MedTagger outputs?

It will be a good feature to add, though. Are you looking for a specific timeline for this?

In one of our other projects here, we rendered concepts to JSON format of a brat for the web. Note that the usibility could be different.

MayeeshaHumaira commented 1 year ago

Hi @ymnliu

I haven't tried MedTator yet. Thanks for your suggestion. I will try it out and let you know how it goes. Sorry for the late reply I am having trouble authenticating the Backbone required for the MedTager. I will post a separate issue regarding that.