How to link environmental sampling metadata with experimental data.
SampleSets are still a work in progress. Watch your inbox for notifications from KBase Outreach when these workflows go live.
A Sample in KBase represents measured material from an experiment. It has a unique ID internal to KBase, aliases, related Samples, and structured metadata. Samples occur within a Narrative as a SampleSet, but the same Sample may be shared by multiple SampleSets.
One key feature is linking the same data across many users and analyses. To do this, Sample aliases allow the same data uploaded by different users to be linked and connect different analyses of the same data. These aliases can also be used to link Samples in KBase with other methods of sample registration, such as ESS-DIVE or SESAR.
Because the metadata about a sample is critically important for, KBase provides the option to upload metadata spreadsheets to link Samples for more detailed analysis.
Managing Linked Data
Once a SampleSet is in system, it can be used when uploading amplicon or chemical abundance matrices into KBase. This allows the amplicon and chemical abundance analysis to remain linked to the sample metadata and enrich analysis.
When uploading and importing either an amplicon matrix or chemical abundance matrix, select the corresponding SampleSet from the dropdown menu for the input before running the Import App.
Additional existing data can be linked to samples. The app "Link Workspace Objects to Samples" provides a graphical interface for creating the links. In this app, you can select the SampleSet to create links from, then choose the Sample from the set and object from the Narrative. You can add multiple Samples and objects by clicking the + button.
If you have a large number of links to create, it would be advisable to use the "Batch Link Workspace Objects to Samples" app.
Last modified 11mo ago