Cell Annotation Metadata

Annotation

Field	Description
Cell Full Name Required string	Description Allowed Values Example rod bipolar Source Cell Annotation Schema BioNetworks AnnData Location
Cell Ontology Exists Required boolean	Description Allowed Values Example True Source Cell Annotation Schema BioNetworks AnnData Location
Cell Ontology Term ID Required string	Description Allowed Values Example CL:0000751 Source Cell Annotation Schema BioNetworks AnnData Location
Cell Ontology Term Required string	Description Allowed Values Example rod bipolar cell Source Cell Annotation Schema BioNetworks AnnData Location
Rationale Required string	Description Allowed Values Example This cell was annotated with [blank] given the canonical markers in the field [X], [Y], [Z]. We noticed [X] and [Y] running differential expression. Source Cell Annotation Schema BioNetworks AnnData Location
Rationale DOIs string (multivalued)	Description Allowed Values Example 10.1038/s41587-022-01468-y, 10.1038/s41556-021-00787-7, 10.1038/s41586-021-03465-8 Source Cell Annotation Schema BioNetworks AnnData Location
Marker Gene Evidence Required string (multivalued)	Description Allowed Values Example TP53, KRAS, BRCA1 Source Cell Annotation Schema BioNetworks AnnData Location
Canonical Marker Genes Required string (multivalued)	Description Allowed Values Example GATA3, CD3D, CD3E Source Cell Annotation Schema BioNetworks AnnData Location
Synonyms Required string (multivalued)	Description Allowed Values Example neuroglial cell, glial cell, neuroglia amacrine cell FMB cell Source Cell Annotation Schema BioNetworks AnnData Location
Category Full Name Required string	Description Allowed Values Example ON-bipolar cell Source Cell Annotation Schema BioNetworks AnnData Location
Category Cell Ontology Exists Required boolean	Description Allowed Values Example True Source Cell Annotation Schema BioNetworks AnnData Location
Category Cell Ontology Term ID Required string	Description Allowed Values Example CL:0000749 Source Cell Annotation Schema BioNetworks AnnData Location
Category Cell Ontology Term Required string	Description Allowed Values Example ON-bipolar cell Source Cell Annotation Schema BioNetworks AnnData Location
Cell Ontology Assessment string	Description Allowed Values Example Amacrine cell should have four child terms: glycinergic, GABAergic, GABAergic Glycinergic amacrine cells and non-GABAergic non-glycinergic amacrine cells, which then contain their corresponding child terms Source Cell Annotation Schema BioNetworks AnnData Location

Annotation Set

Field	Description
Annotation Set Metadata Required python dictionary	Description Example '{{cellannotation_set}--metadata:{'annotation_method':'algorithmic'...}}' Source Cell Annotation Schema BioNetworks AnnData Location
Cell Annotation Set Name Required string	Description Allowed Values Example HBC2 rod bipolar Source Cell Annotation Schema BioNetworks AnnData Location
Description Required string	Description Allowed Values Example Cell annotations based on resolution broad clustering using the Leiden algorithm. Source Cell Annotation Schema BioNetworks AnnData Location
Algorithm Name Required string	Description Allowed Values Example scArches NA Source Cell Annotation Schema BioNetworks AnnData Location
Algorithm Version Required string	Description Allowed Values Example 0.5.9 NA Source Cell Annotation Schema BioNetworks AnnData Location
Algorithm Repository URL Required string	Description Allowed Values Example https://github.com/theislab/scarches NA Source Cell Annotation Schema BioNetworks AnnData Location
Annotation Method Required string	Description Allowed Values Example algorithmic manual both Source Cell Annotation Schema BioNetworks AnnData Location
Reference Location string	Description Allowed Values Example https://figshare.com/projects/Tabula_Muris_Senis/64982 NA Source Cell Annotation Schema BioNetworks AnnData Location
Reference Description string	Description Allowed Values Example Tabula Muris Senis: a single cell transcriptomic atlas across the life span of Mus musculus which includes data from 18 tissues and organs. NA Source Cell Annotation Schema BioNetworks AnnData Location

Cluster

Field	Description
Clustering string (multivalued)	Description Allowed Values Example cluster_leiden cluster_leiden_broad louvain leiden Source Cell Annotation Schema BioNetworks AnnData Location