KBase Documentation
  • KBase Documentation
  • KBase Terms & Conditions
  • Getting Started
    • Signing Up and Signing In
      • Step-by-Step Signup Guide
      • Authentication Update
    • Supported Browsers
    • Narrative Quick Start
    • Narrative Interface User Guide
      • Access the Narrative Interface
      • Tour the Narrative Interface
      • Narrative Navigator
      • Create a Narrative
      • Explore Data
      • Add Data to Your Narrative
      • Browse KBase Analysis Tools
      • Analyze Data Using KBase Apps
      • Job Browser
      • Revise Your Narrative
      • Format Markdown Cells
      • Share Narratives
      • Linking Static Narratives to ORCID
      • Access and Copy Narratives
      • Organizations
    • FAQs
  • Manage Your Account
    • Linking Accounts
    • Linking KBase to ORCiD
  • Working with Data
    • Data Upload and Download Guide
      • Data Types
      • Importing Data
        • Bulk Import Limitations
      • Assembly
      • Genome
      • FASTQ/SRA Reads
      • Flux Balance Analysis (FBA) Model
      • Media
      • Expression Matrix
      • Phenotype Set
      • Amplicon Matrix
      • Chemical Abundance Matrix
      • SampleSet
      • Compressed/Zipped Files
      • Bulk Import Specification
      • Downloading Data
    • Searching, Adding, and Uploading Data
    • Filtering, Managing, and Viewing Data
    • Linking Metadata
      • Ontologies and Validated Terms
    • Public Data in KBase
    • Transfer Data with Globus
  • Using Apps
    • Analysis Apps in KBase
      • Assembly & Annotation
      • Comparative Genomics
      • Metabolic Modeling
      • Metagenomics & Community Exploration
      • Data Matrices - Amplicon, Stats
      • Chemical Abundance
      • Expression & Transcriptomics
    • Apps in Beta
  • Running Common Workflows
    • Assembling & Annotating Microbial Genomes
      • FAQ: Assembly and Annotation
    • Comparative Genomics & Phylogenetic Analysis
      • FAQ: Comparative Genomics
    • Metagenomic & Community Analysis
      • FAQ: Metagenomics & Community Analysis
    • Transcriptomic Analysis
      • FAQ: RNA-seq Analysis
    • Constructing Metabolic Models
      • Constructing and Analyzing Metabolic Flux Models of Microbial Communities
      • FAQ: Metabolic Modeling
  • Community Developed Workflows and Tools
    • Functional Annotation
    • Functional and Taxonomic Profiling of MAGs
    • Taxonomy
    • Viral
    • Random Walk with Restart Toolkit
  • Troubleshooting
    • Problems with the User Interface
    • Help Board
    • How to Report Issues
    • Job Errors and Their Meanings
      • Common Job Errors
        • The Job Log
      • Import Job Errors
      • Assembly App Errors
      • Annotation App Errors
      • Functional Genomics App Errors
      • Modeling App Errors
  • Developing Apps
    • The KBase SDK
    • Create a KBase Developer Account
    • KBase GitHub Repository
  • External Links
    • KBase Narrative Interface
    • KBase web site
    • KBase App Catalog
  • kbase.us
Powered by GitBook
On this page
  • Formatting Phenotype files
  • Importing a Phenotype Set

Was this helpful?

  1. Working with Data
  2. Data Upload and Download Guide

Phenotype Set

The Phenotype Set data type represents experimental data about an organism’s ability to grow in specific media conditions, recorded as growth or no growth.

PreviousExpression MatrixNextAmplicon Matrix

Last updated 7 months ago

Was this helpful?

Formatting Phenotype files

A Phenotype Set can be uploaded from a TSV (tab-separated values) file with a .tsv or .tab file extension, or from Excel spreadsheet with a .xls extension. The spreadsheet needs to have exactly these 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 by running the command print(os.environ['KB_WORKSPACE_ID'])in a code cell. The output should be formatted username:narrative_#############.

  • 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 for a reference list of reactions and compounds or use .

  • Growth – Indication of whether or not the organism grew in the specified media with the specified knockouts. 1 meaning growth; 0 meaning no growth.

geneko

mediaws

media

addtlCpd

growth

SO_0009

KBaseMedia

C-D-Glucose

0

SO_0009

KBaseMedia

C-D-Lactate

1

SO_0009

KBaseMedia

C-acetate

1

To download an example phenotype set data table, go to the "Example" tab in the data Data Browser slide-out, add a Phenotype Data Object to the Narrative and download the TSV file.

Importing a Phenotype Set

Click the import icon (up arrow) to the right of “Phenotype Set”. The data slide-out will close and the “Import TSV File as Phenotype Set From Staging Area” App will be added to your Narrative.

Notice that the name of the Phenotype TSV file is already filled in, as is a suggested name for the Phenotype Set data object that will be created by the import, which you can edit.

Add the name of the Genome, click on the dropdown to select the corresponding genome that you added to your Narrative earlier.

Click the green "Run" button to start the import. When the import is finished, your Data Panel will update to show the new Phenotype Set object, and a report will appear in the Import App.

First that corresponds to referenced in the Phenotype Set. Add the Genome object to the Narrative before importing the Phenotype Set file.

Using a file on your computer, open the . Then drag & drop the phenotype set file into your Staging Area. Open the pulldown menu to the right of the filename in the Staging Area and select “Phenotype Set."

add the Genome
Import tab within the Data Browser
KBase ModelSEED Biochemistry Database
Biochemistry Search
Example Data Objects
Importing a Phenotype Set from the Staging Area
Import Phenotype Set App