Cell Type Annotation

Cell Annotation Schema (CAS) and cas-tools: The Cell Annotation Schema is a general, open-standard schema for cell annotations and related metadata. CAS provides a programmatically accessible standard designed that allows users to record additional metadata about individual cell type annotations, including marker genes used as evidence and details of automated annotation transfer. The standard is represented as JSON schema as this allows all metadata to be gathered in a single, compact validatable file - which includes a link to a cell by gene matrix file of annotated data. However, the schema is designed so that it can be decomposed into individual tables suitable for use in dataframes/TSVs and flattened onto obs in AnnData format. CAS-Tools is a comprehensive utility package designed to facilitate the effective use and manipulation of the Cell Annotation Schema (CAS) in single-cell transcriptomics data analysis.

Annotation File Validators

CELLxGENE schema validator: CELLxGENE curation tools includes a schema validator that can validate single-cell annotation h5ad files in accordance with the CELLxGENE metadata schema. The cellxgene-schema validate command checks an annotation file and will print validation failure messages or a validation success message.

ASAP standalone scFAIR compliance check: ASAP provides a standalone validator to upload a .loom or .h5ad file and check it against the scFAIR metadata schema in the browser. Beyond validation alone, ASAP also helps you produce scFAIR-valid Loom or H5AD files through its project compliance tool: create an ASAP project, complete the guided compliance workflow (metadata mapping, ontology resolution, and fixes), then export a compliant file. Since ASAP v8, publicly published ASAP projects are exclusively scFAIR compliant.