Metadata: Difference between revisions
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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 [[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 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 | 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 experiment's data. Supported file types: .csv, .bam, .bed, .gff, .vcf. See [[LoadExperiment]] for details. | # 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 | # 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 | ||
Optional Columns (in any order): | ===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 (in any order): | |||
* Description: a description of the experiment | * Description: a description of the experiment | ||
* Source: the source of the data file (i.e., JGI) | * Source: the source of the data file (i.e., JGI) | ||
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<hr> | <hr> | ||
===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 | ||
Revision as of 17:28, 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 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 experiment's data. Supported file types: .csv, .bam, .bed, .gff, .vcf. See LoadExperiment 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 (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 unique column names
Note: 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