Difference between revisions of "Metadata"
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===Genome Metadata: <span style='color:red'>Required Columns</span>=== | ===Genome Metadata: <span style='color:red'>Required Columns</span>=== | ||
| − | # Filename: the name of the file containing the | + | # Filename: the name of the file containing the genome's data. Supported file types: .fasta. See [[LoadGenome]] for details. |
# Name: the name of the experiment | # Name: the name of the experiment | ||
| − | # Organism: the CoGe ID for the organism to assign genome (note: only required for genome FASTA/GFF files | + | # Organism: the CoGe ID for the organism to assign genome (note: only required for genome FASTA/GFF files |
===Experiment Metadata: <span style='color:red'>Required Columns</span>=== | ===Experiment Metadata: <span style='color:red'>Required Columns</span>=== | ||
Revision as of 18:08, 24 November 2014
Metadata is data about data. E.g. the name of a genome is metadata about that genome.
Contents
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
- Filename: the name of the file containing the genome's data. Supported file types: .fasta. See LoadGenome for details.
- Name: the name of the experiment
- Organism: the CoGe ID for the organism to assign genome (note: only required for genome FASTA/GFF files
Experiment Metadata: Required Columns
- Filename: the name of the file containing the experiment's data. Supported file types: .csv, .bam, .bed, .gff, .vcf. See LoadExperiment for details.
- 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
