Metadata Fields

Metadata fields are used to define the annotation structure for your organization's samples.

For each metadata field, you will need to provide:

• Name (free text)

• Type (selector) - choice of "string", "numeric", "list", "ontology"

• Index (numeric input) - the order of this metadata field in tables that display metadata

• Is patient id (switch) - whether this metadata field captures the patient/donor/subject identifier

• Is sample id (switch) - whether this metadata field captures the sample identifier

• Visible by default (switch) - whether this metadata field shold be displayed by default in tables that display metadata

Name

Names should be descriptive of the information that the metadata field stores. They will be carried into the bioinformatics analysis as sample/cell observations.

Type

• string - a free text field that captures information that's usually not repetitive across the entire sample database

• numeric - used to capture information such as age, survival days, BMI, etc.

• list - used to capture information that has a limited number of values, such as sex, FIGO stage, etc.

• ontology - used to capture information that needs to be consistent across the entire database of samples, such as tissue and disease

Index

This allows you to control the order of the metadata fields based on importance. Metadata is displayed in sample listings and gene signature listings.

Is patient ID

This flag informs the platform that the information stored in this field refers to the patient/donor/subject from whom the sample originated. It's especially useful when you upload paired modalities, such as mRNA and sRNA, and you want to keep track of the patient association. The platform does not require a metadata field to represent the patient ID to function correctly.

Is sample ID

This flag informs the platform that the information stored in this field refers to the sample ID. This is required to map the metadata to the actual samples that are imported in Panomics. Without a metadata field that references the sample ID, there is no way to upload metadata.

Visible by default

This flag informs the platform whether this metadata field should be displayed in sample and gene signature tables by default. This setting can be overridden by each user from the COLUMNS toolbar button. This is especially useful if you are storing metadata about sample preparation, assay, etc, which bring limited value to tertiary analysis.

Metadata Field Listing View

Metadata field listing

Create Metadata Field Dialog

To create a metadata field, click on the CREATE button in the grid toolbar.

Create metadata field

Edit Metadata Field Dialog

To edit a metadata field, select the field from the grid, then click on the EDIT button in the grid toolbar.

Important considerations:

• Standard metadata fields cannot be edited.

• The name and type can only be changed if the metadata field has never been set for any samples.

• For list fields, you can only add new options, you cannot remove existing ones.

Edit metadata field

Delete Metadata Field

Only non-standard metadata fields that have never been set for any samples can be deleted.