Tools and Data

Toolsets and resources developed as part of the i2b2 2014 challenge:

Toolset and resources developed as part of the i2b2 2012 Temporal Relation challenge:

  • Clinical NorMA
  • TERN
  • TEid
  • CliNER
  • Clinical Departments dictionary

Related publications:

  • Kovačević A, Dehghan A, Filannino M, Keane JA, Nenadic, G: Combining rules and machine-learning for extraction of temporal expressions and events from clinical narratives. Journal of the American Medical Informatics Association. (submitted)

Clinical NorMA: temporal expression normaliser

Clinical NorMA is a rule-based temporal expression normaliser explicitly designed for clinical data. It is open-source (GNU licence) and is written in Python. It has been used by our team to participate to i2b2 2012 challenge.

People involved: Michele Filannino.
Source code: https://github.com/filannim/clinical-norma.

TERN: TEmporal expressions Recognizer and Normalizer

TERN is a rule-based temporal expressions identification and normalisation software; designed for clinical data. The identification (TEid) and normalization component (Clinical NorMA) were used and evaluated as part of the Temporal Relation challenge (i2b2 2012). This software provides various features for easy integration into existing pipelines (e.g., server mode); see code repository / README file.

People involved: Azad Dehghan
Source code: https://sourceforge.net/projects/temporal-x/.

TEid: TEmporal expressions IDentifier

TEid is a rule-based temporal expressions identification software; designed for clinical data. This software was used and evaluated as part of the Temporal Relation challenge (i2b2 2012). This software provides various features for easy integration into existing pipelines (e.g., server mode); see code repository / README file.

People involved: Azad Dehghan
Source code: https://sourceforge.net/projects/temporal-id/.

CliNER

CliNER is a command line tool for tagging of clinically relevant events and recognition and normalisation (using Clinical NorMA) of temporal expressions. The tool is a part of the set of tools developed for the i2b2 2012 challenge. CliNER also provides integration with the rest of the tools developed during the challenge.

People involved: Aleksandar Kovačević.
Download: CliNER.tgz.

Clinical Departments Dictionary

A clinical departments dictionaty/gazetteer; semi-automatically curated from i2b2 2010 and i2b2 2012 datasets.

People involved: Azad Dehghan
Resource: Email Me.