SCP convention - required metadata

Studies uploaded using the SCP Metadata convention must include the following required metadata:

Metadata name	Content	Description
NAME*	string	unique identifier for each cell in the study. Must be the first column in a "Classic" format TSV metadata file. *unneeded for AnnData files, adata.obs_names supplies the required NAME data
biosample_id	string	unique identifier for each sample in the study
donor_id	string	unique identifier for each biosample donor in the study
species	ontology	ontology identifier from NCBItaxon
species__ontology_label	ontology_label	ontology label from NCBItaxon
disease	ontology	ontology identifier from MONDO or PATO (if no disease, use ontology ID "PATO_0000461")
disease__ontology_label	ontology_label	ontology label from MONDO or PATO (if no disease, use ontology label "normal")
organ	ontology	ontology identifier from Uberon
organ__ontology_label	ontology_label	ontology label from Uberon
library_preparation_protocol	ontology	ontology identifier from Experimental Factor ontology:library preparation
library_preparation_protocol__ontology_label	ontology_label	ontology label from Experimental Factor ontology:library preparation
sex	controlled list (enum)	one of ["male", "female", "mixed", "unknown"]

Required ontology metadata must include corresponding ontology labels with column header <ontology>__ontology_label to enable validation.

SCP convention - recommended metadata

Metadata name	Type	Description
cell_type	ontology	ontology identifier from Cell Ontology
cell_type__ontology_label	ontology_label	ontology label from Cell Ontology

Additional optional convention metadata are listed in the SCP Metadata convention with documentation on convention components and additional guidance on usage.