The Phenotype Set data type represents the experimental data of an organism’s ability to grow on a specific media condition, recorded as either growth or no growth. Phenotype Set can be used as input for the Simulate Growth on Phenotype Data app.
Formatting Phenotype TSV or Excel files
A Phenotype Set can be uploaded as a TSV (tab-separated values) with five columns:
- Gene knockout (geneko) – List of genes knocked out in the phenotype; use none for wild-type phenotypes. Gene IDs should be in the same format that appears in your metabolic model (e.g., kb|g.220339.CDS.2927)
- Workspace information (mediaws) – Workspace where the media for the phenotype data was loaded into KBase. The workspace information can be found in the Narratives tab by clicking Show Advanced Controls at the end of the list of Narratives
- Media – ID of the media condition loaded in KBase where the phenotype was observed.
- Additional Compounds (addtlCpd) – Additional media compound IDs to be added alongside the primary media formulation. See the KBase biochemistry database to locate specific compound IDs.
- Growth – Indication of whether or not the organism grew in the specified media with the specified knockouts. 1 means growth; 0 means no growth.
Upload Phenotype Set from a TSV formatted file
- Choose Phenotype Set from the data type dropdown menu
- Click the Next button
- Select the TSV file containing Phenotype Set data from a directory on your computer
- Provide a name for the Phenotype Set data object
- (Optional) Select the Genome that contains features referenced by the Phenotype Set data
- Click the Import button
- After the import process has completed, the Phenotype Set data object will appear in your Data Panel