Cell Annotation Platform
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Entering Cell Annotation Metadata

  1. Select the dataset to edit by clicking the Edit button. You can save your progress at anytime while editing, even if there are warnings, but all of the warnings must be resolved before publishing the dataset.
The workspace page with the dataset "Edit" button highlighted.
  1. Enter the dataset Description and Type in the Summary section. The dataset description should provide the context of the dataset for other researchers. The type of dataset can be either Single or Integrated; with a Single dataset being from a single library or set of technical replicates and Integrated being a collection of integrated datasets.
Dataset description and type fields.
  1. General Metadata is auto-populated from the file during upload. If necessary the fields can be edited in the text boxes by selecting the auto-suggestions provided.
General metadata fields with assay auto-suggestion displayed.
  1. In the Other section additional data from the uploaded file is marked as Metadata, Cell Labels or Unused.

    Columns identified as cell type annotations are Cell Labels and their plot embeddings are displayed in the Molecular Data visualization. Data which is categorial and provides additional descriptive information about the dataset but does not provide useful information for cell type annotation is Metadata. Data which does not provide useful descriptive information should be marked as Unused.
Other metadata fields.
  1. Click on the cell annotation set to enter the cell annotation set Description and select the Annotation Method from the drop-down list.

    The cell annotation set description should allow other scientists to understand the context and background for the cell annotation set.

    The annotation method refers to the method used to annotate the cells, not the clustering method. Common annotation transfer methods include PopV, Azimuth, CellTypist, scArches, etc.
Cell annotation Description with Annotation Method drop-down list.
  1. If the Annotation Method is algorithmic additional fields will appear; the algorithm name, version and url are required, the annotation transfer reference and transfer description are optional.
Additional algorithm fields.
  1. To enter metadata for each cell label, click on the cell label in the list of cell labels.

    For cell labels with existing ontology terms, click Existing Ontology Term and select the ontology term and suggested synonyms will auto-populate the synonyms field. Synonym values can be removed by clicking the "-" button and additional values can be added with the "+" button.

    Enter or select the category, i.e. broader parent term, for the cell label from the suggested terms.

    For cell labels that do not exist in the cell ontology, click New Term and enter the closest ontology term.
Existing ontology term and synonyms with category suggestions list.
  1. Enter the required marker and canonical marker gene fields by typing in the text boxes. 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 "+" and "set unknown" 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.
Rationale and rationale doi fields.
  1. Ontology Assessment is an optional field where you can communicate to peers in the field any disagreements with the Cell Ontology for the given cell label. The comments in this field will be reviewed by Cell Ontology editors for potential improvements.