Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

MedTagger output in BRAT format #19

Open
MayeeshaHumaira opened this issue Sep 24, 2022 · 3 comments
Open

MedTagger output in BRAT format #19

MayeeshaHumaira opened this issue Sep 24, 2022 · 3 comments

Comments

@MayeeshaHumaira
Copy link

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
Copy link
Member

qqndrew commented Sep 30, 2022

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

@ymnliu
Copy link
Contributor

ymnliu commented Oct 3, 2022

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
Copy link
Author

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.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

3 participants