Mondrian, the Genome Data Mapper Software: File Format

Genomic Profile: File Format

The Mondrian Software uses a very simple tab delimited text format to store genomic profile data. Sample data files are available here: mondrian-sample-data.zip .

The file format is identical for all data types. For example, the same file format is used to store mRNA expression and copy number data. All data files should end with a .txt or .gbm file extension.

The file format is as follows:

One or more lines that start with '#'. These lines can be used for comments and to provide configuration settings to the plugin. The following configuration settings are currently supported:

DATA_TYPE: required; provides unique data-type name to data file. The plugin differentiates data files using this value:

# DATA_TYPE<tab>value

where value is a string consisting of alphanumeric characters or spaces (must not contain tabs).

COLOR_GRADIENT_SETTINGS: optional; provides min, center (low and high) and max values used by the plugin to construct a color gradient for mapping data onto nodes:

# COLOR_GRADIENT_SETTINGS <tab> value <tab> value <tab> value <tab> value

where value is a float or 'MIN', 'MEAN', 'MAX', in which case the plugin will compute the min, mean, or max value using the data provided.

The next line in the data files is the header with the following format:

GENE_ID <tab> COMMON <tab> SAMPLE_ID_1 <tab> SAMPLE_ID_2 ...

where SAMPLE_ID_1, SAMPLE_ID_2, ... become the column headings in the heat map. Each successive line after the header line looks like:

ENTREZ_GENE_ID <tab> GENE_SYMBOL <tab> SAMPLE_ID_1_DATA <tab> SAMPLE_ID_2_DATA ...

where SAMPLE_ID_X_DATA is an atomic value of the following type:

  • mRNA: float
  • Copy number alteration: float
  • Methylation: float
  • Mutation: float (0 mutated, 1, not mutated)