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==CoGe Metadata File Format== | ==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 | 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 [[LoadExperiment#Data_Formats_and_Track_Types|experiment data files]]. | ||
The experiment metadata file is a tab-separated file ending in .txt that contains a header line followed by a metadata line for each experiment. There are some required columns and free-form optional columns. | The experiment metadata file is a tab-separated file ending in .txt that contains a header line followed by a metadata line for each experiment. There are some required columns and free-form optional columns. | ||
Revision as of 16:52, 22 September 2014
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 experiment metadata file is a tab-separated file ending in .txt that contains a header line followed by a metadata line for each experiment. There are some required columns and free-form optional columns.
Required Columns (in order as below):
- Filename: the name of the file containing the experiment's data
- supported file types: .csv, .bam, .bed, .gff, .vcf ... see LoadExperiment for more info
- Name: the name of the experiment
Optional Columns (in any order):
- 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
Note: adding "_link" to the end of the field name denotes a link for another column (i.e., columns "citation" and "citation_link")
Example:
Looks like this: http://genomevolution.org/CoGe/ExperimentView.pl?eid=193