Are INCEpTION annotations compatible with Brat annotation tool?

[Anya Gajjar]

So we will have some annotations made in INCEpTION which need to be imported to Brat between two different medical teams. Is it possible to directly import INCEpTION annotations to Brat? I will be grateful for more information.

[Ute Winchenbach]

Hi Anya,

it is not possible to directly import annotations made with INCEpTION into brat. You could try exporting annotations from INCEpTION in the UIMA CAS XMI format and then use a dkpro pipeline [1] with a XmiReader [2] and Brat Writer [3]. However, the writer might not support all your annotation needs. I would instead suggest to use one annotation tool for your project and not switch between two. Of course, INCEpTION would be the best choice here ;)

[1] https://dkpro.github.io/dkpro-core/pages/java-intro/

[2] https://dkpro.github.io/dkpro-core/releases/1.10.0/apidocs/de/tudarmstadt/ukp/dkpro/core/io/xmi/XmiReader.html

[3] https://dkpro.github.io/dkpro-core/releases/1.10.0/apidocs/de/tudarmstadt/ukp/dkpro/core/io/brat/BratWriter.html

[Anya Gajjar]

Hello Ute,

Thank you very much for the exact details. You are right. I will be adding more errors to the data by importing annotations from one tool to another. I am more familiar with INCEpTION, so I'd like to go for it, but some doctors have previously worked using Brat and need one of its functionalities. I will keep using INCEpTION for my project though. 

[Richard Eckart de Castilho]

Hi Anya,

> On 11. Apr 2020, at 11:38, Anya Gajjar <anjaniin...@gmail.com> wrote:
>
> Thank you very much for the exact details. You are right. I will be adding more errors to the data by importing annotations from one tool to another. I am more familiar with INCEpTION, so I'd like to go for it, but some doctors have previously worked using Brat and need one of its functionalities. I will keep using INCEpTION for my project though.

For curiosity: which functionality is it that the doctors need?

-- Richard

[Anji]

Hello Richard,

They want important concepts to be grouped together. For example, consider a paper abstract containing these two phrases, 1) "An evidence-based exercise program" and 2) "Energy through motion activity program". These (1 and 2) are basically referring to the same things. They want to interactively group it together per document. I am not sure if it is currently available in INCEpTION? I will be really grateful for your response.

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Anjani K Dhrangadhariya

[richard...@gmail.com]

Could you post a screenshot of what this would look like in brat!

Sent from my mobile, sorry for brevity.

[richard...@gmail.com]

... and maybe mention which brat feature is used to model the grouping?

PS: the ! In the former mail should have been a ?

Sent from my mobile, sorry for brevity.