Column definition

There are several notations how to get the CFDE approved identifier from the GlyGen CSV files.

Column

If the identifier is a value in one of the columns of the CSV data file, it is possible to specify the column by providing the label of the column header in the following notation:

column:{column header}

Static value

If all information in a file is associated with the same concept (e.g. species, protein, glycan) it is possible to define the value in the file configuration directly rather than extracting it from the file. The pattern for this notation is:

static:{identifier}

{identifier} has to be the CFDE approved identifier and notation for the concept.

Mapping file

If the identifier is not in the CSV file present, but another identifier that can be mapped to the CFDE identifier its possible to specify a mapping using the following notation

file:{column header}:{mapping file}

Where {column header} is the header label of the column that contains the GlyGen identifier. {mapping file} is a two column CSV file that contains for each GlyGen identifier one row with:

• GlyGen identifier in first column
• CFDE identifier and notation in the second column The mapping file must be located in the mapping folder as specified in the command line parameters.