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EasyCIE(GUI) is a rule-based clinical information extraction tool for non-NLP(natural language processing) expert users. It a GUI wrapper on top of EasyCIE, an UIMA-based command line version that allows executing on servers.
The most recent compiled releases can be found at: https://drive.google.com/drive/folders/0B0hTn1B4kXcPM2hOZDZwY2NOTG8?usp=sharing
Although this GUI component is designed to be easily extensible for adapting different databases and wrapping other pipelines without hard coding, this wiki is mainly written as a user guide for EasyCIE(GUI).
- Import: Import documents from files into database. Import eHOST or Brat annotations as the reference standard. Import ontologies (https://github.com/Blulab-Utah/resource_ontologies)
- RunEasyCIE: Execute the EasyCIE pipeline on imported data
- Compare: Compare the pipeline output between different version or against the imported reference standard.
- Debug: Use a snippet of text to tackle the errors
- Export: Export the EasyCIE output into eHOST, Brat or UIMA XMIformat.
EasyCIE is under active development. The components are expanding rapidly. In the current released version, the built-in NLP pipeline includes the following components:
- RuSH: an efficient, reliable, and easy adaptable rule-based sentence segmentation solution.
- FastNER: a speed-optimized dictionary-based (name entity recognition)[https://en.wikipedia.org/wiki/Named-entity_recognition] solution.
- FastContext: an optimized Java implementation of the ConText algorithm (https://www.ncbi.nlm.nih.gov/pubmed/23920642).
- FeatureInferenceAnnotator: allows customizable conversion among UIMA types.
- DocInferenceAnnotator: allows to draw document level conclusion from mention level annotations using customizable rules.
All the components below are configurable through an excel file: