ScienceIO

The official ScienceIO Python SDK for the BioNLP API.

As of today (June 22nd 2021), it supports sending documents to the BioNLP API, and returns the array of spans and the original text. Aggregations are not included.

This package is available via Pypi:scienceIO.

Usage and examples

1. Register:

   from scienceio import ScienceIO
   ScienceIO.register(
       first_name="Demo name",
       last_name="Demo lastname",
       email="your@email.com"
   )
   

   You will be sent an email asking you to verify your account. As part of the process you will be asked to create a password.

2. Create a configuration file ~/.scio/config with your credentials (it will be replaced with api keys)

   [SETTINGS]
   email=your@email.com
   

3. Email api-help@science.io to activate your account. Provide the email you used to register.

4. Query the BioNLP API:

   scio = ScienceIO()
   query_text = (
     'The COVID-19 pandemic has shown a markedly low proportion of '
     'cases among children 1–4. Age disparities in observed cases could be '
     'explained by children having lower susceptibility to infection, lower '
     'propensity to show clinical symptoms or both.'
   )
   
   results = scio.annotate(query_text)
   print(results)