VIOLIN

Description of files and folders

• test_input - input files used in VIOLIN publication
• test_output - output files generated from files in test_input
• use_VIOLIN.ipynb - ipy notebook used to run VIOLIN
• use_VIOLIN.py - python script used to run VIOLIN at the command line

test_input

File	Query	Curation Method
RA1_reading.xlsx	Melanoma	REACH
RA2_reading.xlsx	MEK, ERK, AKT, GSK3, P70RSK, S6, CDK4, 4EBP1, YB1, SRC, CHK2, MTOR, PI3K	REACH explorer
RA2_0_1_reading.xlsx	RA2 without LEEs involving biological processes or chemicals	Manual
RA2_0_1_1_reading.xlsx	RA2_0_1 without LEEs which were redundant or irrelevant	Manual
RA3_reading.xlsx	MAPK/ERK pathway	REACH explorer
RA4_reading.xlsx	RPS6K1	REACH explorer

test_output

• For each reading set R# in test_input

File	Contents
R#_corroborations.csv	All LEEs judged as collaborations
R#_contradictions.csv	All LEEs judged as contradictions
R#_extensions.csv	All LEEs judged as extensions
R#_flagged.csv	All LEEs judged as flagged
R#_outputDF.csv	All LEEs, in order of descending Total Score