Class: 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.
URI: PCL:0010001
classDiagram
class Annotation
click Annotation href "../Annotation"
Annotation : author_annotation_fields
Annotation --> "0..1" Any : author_annotation_fields
click Any href "../Any"
Annotation : cell_fullname
Annotation : cell_ids
Annotation : cell_label
Annotation : cell_ontology_term
Annotation : cell_ontology_term_id
Annotation --> "0..1" CellTypeEnum : cell_ontology_term_id
click CellTypeEnum href "../CellTypeEnum"
Annotation : labelset
Annotation : marker_gene_evidence
Annotation : rationale
Annotation : rationale_dois
Annotation : reviews
Annotation --> "*" Review : reviews
click Review href "../Review"
Annotation : synonyms
Slots
Name | Cardinality and Range | Description | Inheritance |
---|---|---|---|
labelset | 1 String |
The unique name of the set of cell annotations | direct |
cell_label | 1 String |
This denotes any free-text term which the author uses to annotate cells, i | direct |
cell_fullname | 0..1 String |
This MUST be the full-length name for the biological entity listed in `cell_l... | direct |
cell_ontology_term_id | 0..1 CellTypeEnum |
This MUST be a term from either the Cell Ontology (https://www | direct |
cell_ontology_term | 0..1 String |
This MUST be the human-readable name assigned to the value of 'cell_ontology_... | direct |
cell_ids | * String |
Cell barcode sequences/UUIDs used to uniquely identify the cells within the A... | direct |
rationale | 0..1 String |
The free-text rationale which users provide as justification/evidence for the... | direct |
rationale_dois | * String |
direct | |
marker_gene_evidence | * String |
Gene names explicitly used as evidence, which MUST be in the matrix of the An... | direct |
synonyms | * String |
List of synonyms | direct |
reviews | * Review |
direct | |
author_annotation_fields | 0..1 Any |
A dictionary of author defined key value pairs annotating the cell set | direct |
Usages
used by | used in | type | used |
---|---|---|---|
Taxonomy | annotations | range | Annotation |
Identifier and Mapping Information
Schema Source
- from schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
Mappings
Mapping Type | Mapped Value |
---|---|
self | PCL:0010001 |
native | cell_annotation_schema:Annotation |
LinkML Source
Direct
name: Annotation
description: '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.'
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
slots:
- labelset
- cell_label
- cell_fullname
- cell_ontology_term_id
- cell_ontology_term
- cell_ids
- rationale
- rationale_dois
- marker_gene_evidence
- synonyms
- reviews
- author_annotation_fields
class_uri: PCL:0010001
Induced
name: Annotation
description: '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.'
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
attributes:
labelset:
name: labelset
description: "The unique name of the set of cell annotations. \nEach cell within\
\ the AnnData/Seurat file MUST be associated with a 'cell_label' value in order\
\ for this to be a valid 'cellannotation_setname'."
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
rank: 1000
slot_uri: CAS:has_labelset
alias: labelset
owner: Annotation
domain_of:
- Annotation
range: string
required: true
cell_label:
name: cell_label
description: "This denotes any free-text term which the author uses to annotate\
\ cells, i.e. the preferred cell label name used by the author. Abbreviations\
\ are exceptable in this field; refer to 'cell_fullname' for related details.\
\ \nCertain key words have been reserved:\n- `'doublets'` is reserved for encoding\
\ cells defined as doublets based on some computational analysis\n- `'junk'`\
\ is reserved for encoding cells that failed sequencing for some reason, e.g.\
\ few genes detected, high fraction of mitochondrial reads\n- `'unknown'` is\
\ explicitly reserved for unknown or 'author does not know'\n- `'NA'` is incomplete,\
\ i.e. no cell annotation was provided"
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
rank: 1000
slot_uri: rdfs:label
alias: cell_label
owner: Annotation
domain_of:
- Annotation
range: string
required: true
cell_fullname:
name: cell_fullname
description: "This MUST be the full-length name for the biological entity listed\
\ in `cell_label` by the author. (If the value in `cell_label` is the full-length\
\ term, this field will contain the same value.) \nNOTE: any reserved word used\
\ in the field 'cell_label' MUST match the value of this field. \n\nEXAMPLE\
\ 1: Given the matching terms 'LC' and 'luminal cell' used to annotate the same\
\ cell(s), then users could use either terms as values in the field 'cell_label'.\
\ However, the abbreviation 'LC' CANNOT be provided in the field 'cell_fullname'.\
\ \n\nEXAMPLE 2: Either the abbreviation 'AC' or the full-length term intended\
\ by the author 'GABAergic amacrine cell' MAY be placed in the field 'cell_label',\
\ but as full-length term naming this biological entity, 'GABAergic amacrine\
\ cell' MUST be placed in the field 'cell_fullname'."
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
rank: 1000
slot_uri: skos:preflabel
alias: cell_fullname
owner: Annotation
domain_of:
- Annotation
range: string
cell_ontology_term_id:
name: cell_ontology_term_id
description: 'This MUST be a term from either the Cell Ontology (https://www.ebi.ac.uk/ols/ontologies/cl)
or from some ontology that extends it by classifying cell types under terms
from the Cell Ontology
e.g. the Provisional Cell Ontology (https://www.ebi.ac.uk/ols/ontologies/pcl)
or the Drosophila Anatomy Ontology (DAO) (https://www.ebi.ac.uk/ols4/ontologies/fbbt).
NOTE: The closest available ontology term matching the value within the field
''cell_label'' (at the time of publication) MUST be used.
For example, if the value of ''cell_label'' is ''relay interneuron'', but this
entity does not yet exist in the ontology, users must choose the closest available
term in the CL ontology. In this case, it''s the broader term ''interneuron''
i.e. https://www.ebi.ac.uk/ols/ontologies/cl/terms?obo_id=CL:0000099.'
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
rank: 1000
slot_uri: RO:0002473
alias: cell_ontology_term_id
owner: Annotation
domain_of:
- Annotation
range: CellTypeEnum
cell_ontology_term:
name: cell_ontology_term
description: This MUST be the human-readable name assigned to the value of 'cell_ontology_term_id'
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
rank: 1000
alias: cell_ontology_term
owner: Annotation
domain_of:
- Annotation
range: string
cell_ids:
name: cell_ids
description: Cell barcode sequences/UUIDs used to uniquely identify the cells
within the AnnData/Seurat matrix. Any and all cell barcode sequences/UUIDs MUST
be included in the AnnData/Seurat matrix.
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
rank: 1000
slot_uri: CAS:has_cellid
alias: cell_ids
owner: Annotation
domain_of:
- Annotation
range: string
multivalued: true
rationale:
name: rationale
description: "The free-text rationale which users provide as justification/evidence\
\ for their cell annotations. \nResearchers are encouraged to use this field\
\ to cite relevant publications in-line using standard academic citations of\
\ the form `(Zheng et al., 2020)` This human-readable free-text MUST be encoded\
\ as a single string.\nAll references cited SHOULD be listed using DOIs under\
\ rationale_dois. There MUST be a 2000-character limit."
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
rank: 1000
alias: rationale
owner: Annotation
domain_of:
- Annotation
range: string
rationale_dois:
name: rationale_dois
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
rank: 1000
alias: rationale_dois
owner: Annotation
domain_of:
- Annotation
range: string
multivalued: true
marker_gene_evidence:
name: marker_gene_evidence
description: Gene names explicitly used as evidence, which MUST be in the matrix
of the AnnData/Seurat file
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
rank: 1000
alias: marker_gene_evidence
owner: Annotation
domain_of:
- Annotation
range: string
multivalued: true
synonyms:
name: synonyms
description: List of synonyms
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
rank: 1000
alias: synonyms
owner: Annotation
domain_of:
- Annotation
range: string
multivalued: true
reviews:
name: reviews
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
rank: 1000
alias: reviews
owner: Annotation
domain_of:
- Annotation
range: Review
multivalued: true
author_annotation_fields:
name: author_annotation_fields
description: A dictionary of author defined key value pairs annotating the cell
set. The names and aims of these fields MUST not clash with official annotation
fields.
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
rank: 1000
alias: author_annotation_fields
owner: Annotation
domain_of:
- Annotation
range: Any
class_uri: PCL:0010001