DeepPhe Translational

DeepPhe Translational is the DeepPhe software suite for translational studies and research cohort discovery. It provides extensive information useful for translational cancer research. Results from processing clinical documents can be stored in a SQLite database that can be utilized (in conjunction with OMOP tables) by the DeepPhe Visualizer.

The DeepPhe Translational NLP Patient Summarizer is a highly-modifiable pipeline that can extract values for cancer and tumor attributes such as: Diagnosis, Location, TNM Stage, Summary Stage, and Grade.
The DeepPhe Translational NLP Patient Summarizer can also identify cancer-related concepts such as: Biomarkers, Medications, Procedures, Comorbidities, and Genes.

A DeepPhe Translational pipeline can be configured to report minimum, maximum and confidence-thresholded discoveries, as well as output selected discoveries in a variety of file formats such as CSV tables and JSON files. The pipeline can be resized to accommodate smaller projects, and custom engines can be added to perform additional operations, such as parsing institution-specific metadata in document headers or writing extracted information to new output formats.
Use of the default pipeline is simple, but the default pipeline may not be best for your data or use case. Customization is highly recommended. For work on refined workflows or custom operations, contact the DeepPhe team.

Supported by the National Cancer Institute’s Information Technology for Cancer Research (ITCR) initiative (Grant #U24CA248010).