How to visualize Stanford Stanza NER results with BRAT

Question:

I am using Stanza Biomedical i2b2 processor to identify PROBLEM, TREATMENT and TEST entities in drugs data.

Python code is as follows:

import stanza
stanza.download(
    "en",
    package="mimc",
    processors={"ner": ["i2b2"]},
    verbose=False,
)
nlp = stanza.Pipeline(
    "en",
    package="mimc",
    processors={"ner": ["i2b2"]},
    verbose=False,
)
parsed_row = nlp("Prevention of phototoxicity in adult patients with erythropoietic protoporphyria (EPP).")
for ent in parsed_row.entities:
        print(f"{ent.text}t{ent.type}")

NER output

phototoxicity   PROBLEM
erythropoietic protoporphyria   PROBLEM

I am reading the page about using brat to visualize Stanza NER annotations here https://brat.nlplab.org/embed.html
but I’ totally lost. Can anyone please help me fill the dots ? Thanks

Asked By: Robert Alexander

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Source

Answers:

After a LOT of experimenting I did find a way and it works well, although the following code is not robust at all, just a proof of concept:

https://github.com/rjalexa/stanza2brat

Answered By: Robert Alexander