DeepPhe Output

Overwriting

NOTE: Subsequent runs of the system will overwrite the output of a previous run unless you change the Output Directory.

Formats

By default, the system outputs data in four manners

• a neo4j graph database
• bar-delimited files
• HTML files
• Run Log

The subdirectory names can be changed by modifying the piper file used to run the system.

Neo4j graph database

Found by default under the output_graph subdirectory The neo4j database is used by DeepPhe-Viz

Browsing the neo4j database is described in Quick Start

Bar-delimited files

Found by default under the CI_EVAL subdirectory

One file for each type

• Cancer
• Tumor

Files have .bsv extension

First line contains column names

You can use your favorite tool for comparing text files to compare differences between runs of the system

HTML files

Found by default under the HTML subdirectory

These files contain only basic information parsed from valid sections in each document.

Run Log

Contains a log of system progress information as well as summaries of patient cancers and tumors.