MedTagger output in BRAT format

[MayeeshaHumaira]

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]

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

[ymnliu]

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]

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.