Clincial Domain Abstract Meaning Representation Graphs

This package parses clinical notes in to Abstract Meaning Representation Graphs (AMR). It uses the following packages to create the graphs and features:

• THYME AMR SPRING parser to create the graphs
• MedCAT for entity linking CUI attribution nodes
• MedSecId for the clinical note sectioning
• Zensols Natural Language Parsing for language parsing and feature creation

Documentation

See the full documentation. The API reference is also available.

Obtaining

The library can be installed with pip from the pypi repository:

pip3 install zensols.clinicamr

Changelog

An extensive changelog is available here.

Citation

This package and the amrspring Docker image uses the original AMR SPRING parser source code base from the paper "One SPRING to Rule Them Both: Symmetric AMR Semantic Parsing and Generation without a Complex Pipeline":

@inproceedings{bevilacquaOneSPRINGRule2021,
  title = {One {{SPRING}} to {{Rule Them Both}}: {{Symmetric AMR Semantic Parsing}} and {{Generation}} without a {{Complex Pipeline}}},
  shorttitle = {One {{SPRING}} to {{Rule Them Both}}},
  booktitle = {Proceedings of the {{AAAI Conference}} on {{Artificial Intelligence}}},
  author = {Bevilacqua, Michele and Blloshmi, Rexhina and Navigli, Roberto},
  date = {2021-05-18},
  volume = {35},
  number = {14},
  pages = {12564--12573},
  location = {Virtual},
  url = {https://ojs.aaai.org/index.php/AAAI/article/view/17489},
  urldate = {2022-07-28}
}

License

MIT License

Copyright (c) 2024 - 2025 Paul Landes