Cell Annotation Platform
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Creating New Cell Annotation Set

To add or edit cell annotations, from the workspace page select the dataset you wish to work on.

  1. Click on Molecular Data to enter the Molecular Data page.
The dataset edit page with "Molecular Data" highlighted.
  1. Click the Edit button to access the edit mode.
The molecular data page with the "Edit" button highlighted.
  1. Click the Create New Labelset button in the Cell Label sidebar on the left to create a new set of cell labels.
The molecular data page with the "Create New Labelset" button highlighted.
  1. Enter the Name and Description for the new set of cell labels in the window and click the Save set of Cell Labels button.
Create Set of Cell Labels popup window with the "Save Set of Cell Labels" button highlighted.
  1. Select the cells to annotate by clicking on the desired cells displayed on the embedding, more than one cluster of cells can be selected by holding the control (PC) or command (Mac) key on your keyboard. Alternately, you can use the polygon selector to select a subset of cells. Once the cells are selected they will be highlighted in red, then click the Annotate button to open the Annotate window.
Embedding with cell selection and the "Annotate" button highlighted.
  1. Enter the required cell annotation metadata fields typing in the text box after selecting Existing Ontology Term or New Term. Auto-suggestions are provided for ontology and gene fields.
Annotate cell label window with ontology term auto-suggestion.
  1. Enter the required marker and canonical marker gene fields by typing in the text box. To add additional genes, click the + button. If there are no values for the field, select the set unknown button.
Marker and canonical gene fields with the "add" button highlighted.
  1. Enter the Rationale and Rationale DOI fields. The Rationale field provides an explanation for the annotation and can include context and justification such as canonical marker genes. If you would like to cite papers in support of the cell annotation, the DOI should be entered in Rationale DOI.

Annotate window with "Rationale" and "Rationale DOI" buttons highlighted.

  1. To Save the cell annotation, click the Save Group of Cells button.

Annotate window with fields completed and "Save Group of Cells" button highlighted.