Difference between revisions of "Metadata"
(→Genome Metadata: Required Columns) |
(→Examples) |
||
| Line 26: | Line 26: | ||
===Examples=== | ===Examples=== | ||
| − | Example 1: single experiment metadata line with optional columns<br> | + | '''Example 1: single experiment metadata line with optional columns'''<br> |
[[File:Screen_Shot_2014-01-23_at_2.53.15_PM.png]] | [[File:Screen_Shot_2014-01-23_at_2.53.15_PM.png]] | ||
Looks like this: http://genomevolution.org/CoGe/ExperimentView.pl?eid=193 | Looks like this: http://genomevolution.org/CoGe/ExperimentView.pl?eid=193 | ||
| − | Example 2: three genome metadata lines with optional columns<br> | + | '''Example 2: three genome metadata lines with optional columns'''<br> |
[[File:Screen_Shot_2014-09-22_at_10.49.58_AM.png]] | [[File:Screen_Shot_2014-09-22_at_10.49.58_AM.png]] | ||
Revision as of 18:12, 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 genome
- Organism: the CoGe ID for the organism to assign genome
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
