Pipeline Description

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Sean Finan edited this page Jun 30, 2022 · 2 revisions

DeepPhe-XN Pipeline Description

The DeepPhe Pipeline is configured using Apache cTAKES Piper Files. Piper Files contain simple commands that assemble an NLP pipeline, but knowledge of existing DeepPhe and cTAKES components is required. Piper Files also allow the user to add their own custom components to the DeepPhe pipeline.

At this time, the per-document NLP pipeline performs the following main tasks:

Medical Section Identification
Text Paragraph and Sentence Splitting
Text Term Identification
Term Code Normalization
Term Negation, Uncertainty
Term Medical Relations Identification

The Patient Summarization step performs the following main tasks:

Term Coreference Resolution
Neoplasm Concept Identification
Collation of Neoplasm Concepts into one or more Cancer Containers
Collation of Neoplasm Concepts into one or more Tumor Containers
Cancer and Tumor Connection
Cancer and Tumor Attribute Assignment