Input and Output Files
This page details the type and format of the files VIOLIN takes as input, as well as the format of VIOLIN output
Input
As VIOLIN is developed as part of a larger modeling framework, the default files expected are model spreadsheets in the BioRECIPE format, and a machine reading output spreadsheet:
Element Name |
Element ID |
Element Type |
Variable |
Positive Regulators |
Negative Regulators |
Name |
ID |
Type |
variable name |
pos regulators list |
neg regulators list |
The minimum required information from a model is: element/target name, element/target type, element/target ID, positive and negative regulator/source names, types, and IDs. The nomenclature does not have to be specific, as VIOLIN has the capabilities to recognize all of the commonly used vocabulary.
Element Name |
Element ID |
Element Type |
Positive Reg Name |
Positive Reg ID |
Positive Reg Type |
Negative Reg Name |
Negative Reg ID |
Negative Reg Type |
PMCID |
Evidence |
Name |
ID |
Type |
Pos regulator |
reg ID |
reg type |
Neg regulator |
reg ID |
reg type |
PMCID |
evidence text |
The minimum information required from reading output is: element/target name, element/target type, element/target ID, positive and negative regulator/source names, types, and IDs. The nomenclature does not have to be specific, as VIOLIN has the capabilities to recognize all of the commonly used vocabulary.
Additionally, VIOLIN has built-in functions to allow for other input file formats, found on the Formatting (violin.formatting) page.
Currently accepted file types are comma-separated files (.csv), tab-separated files (.txt or .tsv), and excel spreadsheets (.xlsx).
Output
VIOLIN output is sorted into five .csv output files:
Total output - all interactions listed by total score
Corroborations - all interactions classified as corroborations, listed by total score
Extensions - all interactions classified as extensions, listed by total score
Contradictions - all interactions classified as contradictions, listed by total score
Questionable - all interactions classified as questionable, listed by total score