Metadata

Metadata is data about data. E.g. the name of a genome is metadata about that genome.

CoGe Metadata File Format

The LoadBatch tool enables users to load batches of genome and experiment data sets. A metadata file, e.g. metadata.txt or any other name ending in .txt, is required along with any number of FASTA, GFF (note: still under development), and experiment data files.

The metadata file is a tab-separated file ending in .txt that contains a header line followed by a metadata line for each genome or experiment. Genomes and experiments cannot be mixed in the same file. There are some required columns and any number of free-form optional columns.

Genome Metadata: Required Columns

1. Filename: the name of the file containing the genome's data. Supported file types: .fasta. See LoadGenome for details.
2. Name: the name of the genome
3. Organism: the CoGe ID for the organism to assign genome

Experiment Metadata: Required Columns

1. Filename: the name of the file containing the experiment's data. Supported file types: .csv, .bam, .bed, .gff, .vcf. See LoadExperiment for details.
2. Name: the name of the experiment

Genome/Experiment Metadata: Optional Columns

• Description: a description of the experiment
• Source: the source of the data file (i.e., JGI)
• Version: the version number
• Restricted: restrict the data from public access ("yes" or "no", default is no)
• Add your own unique column names

Note: columns can be given in any order. Adding "_link" to the end of the field name denotes a link for another column (i.e., columns "citation" and "citation_link").

Examples

Example 1: single experiment metadata line with optional columns

Looks like this: http://genomevolution.org/CoGe/ExperimentView.pl?eid=193

Example 2: three genome metadata lines with optional columns