2mh/bel2bioc

Project for the conversion of OpenBEL files into BioC XML data.

bel2bioc

Project for the conversion of OpenBEL files into BioC XML data.

Usage: bel2bioc.rb -<args> <files> ##Command-line arguments:

b: Output to BioC. Provide multiple file names separated by spaces for batch processing. Extension of the output files is .xml, the name is carried over from the input file.

p: Insert empty placeholder nodes for 'location'

t: Treat input file as tabulated (CSV), use BEL Id as document id sentence as passage text.

a: Only in combination with t: Do not include sentence Id and PMID as passage infons.

m: Ask user to enter collection meta-data

o: Include original BEL statements as comment

Debugging

c: Output of attributes to CLI (debugging). Output should be piped to more or less -R (due to color coding).

i: Includes additional nodes with full absolute BEL statement and relative BEL statement with relation and annotation ids

d: CLI debugging mode: Export each statement as separate BioC collection.