General Cell Annotation Open Standard
General, open-standard schema for cell annotations
URI: https://cellular-semantics.sanger.ac.uk/ontology/CAS
Name: General_Cell_Annotation_Open_Standard
Classes
| Class | Description |
|---|---|
| Annotation | A collection of fields recording a cell type/class/state annotation on some set of cells, supporting evidence and provenance. As this is intended as a general schema, compulsory fields are kept to a minimum. However, tools using this schema are encouarged to specify a larger set of compulsory fields for publication. Note: This schema deliberately allows for additional fields in order to support ad hoc user fields, new formal schema extensions and project/tool specific metadata. |
| Any | None |
| AutomatedAnnotation | A set of fields for recording the details of the automated annotation algorithm used. (Common 'automated annotation methods' would include PopV, Azimuth, CellTypist, scArches, etc.) |
| Labelset | None |
| Review | None |
| Taxonomy | None |
Slots
| Slot | Description |
|---|---|
| algorithm_name | The name of the algorithm used |
| algorithm_repo_url | This field denotes the URL of the version control repository associated with ... |
| algorithm_version | The version of the algorithm used (if applicable) |
| annotation_method | The method used for creating the cell annotations |
| annotations | |
| author_annotation_fields | A dictionary of author defined key value pairs annotating the cell set |
| author_contact | Primary author's contact |
| author_list | This field stores a list of users who are included in the project as collabor... |
| author_name | Primary author's name |
| automated_annotation | |
| cell_fullname | This MUST be the full-length name for the biological entity listed in `cell_l... |
| cell_ids | Cell barcode sequences/UUIDs used to uniquely identify the cells within the A... |
| cell_label | This denotes any free-text term which the author uses to annotate cells, i |
| cell_ontology_term | This MUST be the human-readable name assigned to the value of 'cell_ontology_... |
| cell_ontology_term_id | This MUST be a term from either the Cell Ontology (https://www |
| cellannotation_schema_version | The schema version, the cell annotation open standard |
| cellannotation_timestamp | The timestamp of all cell annotations published (per dataset) |
| cellannotation_url | A persistent URL of all cell annotations published (per dataset) |
| cellannotation_version | The version for all cell annotations published (per dataset) |
| datestamp | Time and date review was last edited |
| description | The description of the dataset |
| explanation | Free-text review of annotation |
| id | |
| labelset | The unique name of the set of cell annotations |
| labelsets | |
| marker_gene_context | The context in which the marker genes given in the marker gene evidence field... |
| marker_gene_evidence | Gene names explicitly used as evidence, which MUST be in the matrix of the An... |
| matrix_file_id | A resolvable ID for a cell by gene matrix file in the form namespace:accessio... |
| name | name of annotation key |
| orcid | Primary author's orcid |
| rationale | The free-text rationale which users provide as justification/evidence for the... |
| rationale_dois | |
| reference_location | This field denotes a valid URL of the annotated dataset that was the source o... |
| review | Reviewer's verdict on the annotation |
| reviewer | Review Author |
| reviews | |
| synonyms | List of synonyms |
| title | The title of the dataset |
Enumerations
| Enumeration | Description |
|---|---|
| AnnotationMethodOptions | |
| CellTypeEnum | |
| ReviewOptions |
Types
| Type | Description |
|---|---|
| Boolean | A binary (true or false) value |
| Curie | a compact URI |
| Date | a date (year, month and day) in an idealized calendar |
| DateOrDatetime | Either a date or a datetime |
| Datetime | The combination of a date and time |
| Decimal | A real number with arbitrary precision that conforms to the xsd:decimal speci... |
| Double | A real number that conforms to the xsd:double specification |
| Float | A real number that conforms to the xsd:float specification |
| Integer | An integer |
| Jsonpath | A string encoding a JSON Path |
| Jsonpointer | A string encoding a JSON Pointer |
| Ncname | Prefix part of CURIE |
| Nodeidentifier | A URI, CURIE or BNODE that represents a node in a model |
| Objectidentifier | A URI or CURIE that represents an object in the model |
| Sparqlpath | A string encoding a SPARQL Property Path |
| String | A character string |
| Time | A time object represents a (local) time of day, independent of any particular... |
| Uri | a complete URI |
| Uriorcurie | a URI or a CURIE |
Subsets
| Subset | Description |
|---|---|