Class: BicanTaxonomy
URI: CAS:Taxonomy
classDiagram
class BicanTaxonomy
click BicanTaxonomy href "../BicanTaxonomy"
Taxonomy <|-- BicanTaxonomy
click Taxonomy href "../Taxonomy"
BicanTaxonomy : annotations
BicanTaxonomy --> "1..*" BicanAnnotation : annotations
click BicanAnnotation href "../BicanAnnotation"
BicanTaxonomy : author_contact
BicanTaxonomy : author_list
BicanTaxonomy : author_name
BicanTaxonomy : cellannotation_schema_version
BicanTaxonomy : cellannotation_timestamp
BicanTaxonomy : cellannotation_url
BicanTaxonomy : cellannotation_version
BicanTaxonomy : description
BicanTaxonomy : labelsets
BicanTaxonomy --> "1..*" BicanLabelset : labelsets
click BicanLabelset href "../BicanLabelset"
BicanTaxonomy : matrix_file_id
BicanTaxonomy : orcid
BicanTaxonomy : title
Inheritance
- Taxonomy
- BicanTaxonomy
Slots
Name | Cardinality and Range | Description | Inheritance |
---|---|---|---|
matrix_file_id | 0..1 Uriorcurie |
A resolvable ID for a cell by gene matrix file in the form namespace:accessio... | Taxonomy |
title | 1 String |
The title of the dataset | Taxonomy |
description | 0..1 String |
The description of the dataset | Taxonomy |
cellannotation_schema_version | 0..1 String |
The schema version, the cell annotation open standard | Taxonomy |
cellannotation_timestamp | 0..1 String |
The timestamp of all cell annotations published (per dataset) | Taxonomy |
cellannotation_version | 0..1 String |
The version for all cell annotations published (per dataset) | Taxonomy |
cellannotation_url | 0..1 String |
A persistent URL of all cell annotations published (per dataset) | Taxonomy |
author_list | 0..1 String |
This field stores a list of users who are included in the project as collabor... | Taxonomy |
author_name | 1 String |
Primary author's name | Taxonomy |
author_contact | 0..1 String |
Primary author's contact | Taxonomy |
orcid | 0..1 String |
Primary author's orcid | Taxonomy |
labelsets | 1..* BicanLabelset |
Taxonomy | |
annotations | 1..* BicanAnnotation |
Taxonomy |
Identifier and Mapping Information
Schema Source
- from schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
Mappings
Mapping Type | Mapped Value |
---|---|
self | CAS:Taxonomy |
native | cell_annotation_schema:BicanTaxonomy |
LinkML Source
Direct
name: Bican_Taxonomy
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
is_a: Taxonomy
slot_usage:
labelsets:
name: labelsets
range: Bican_Labelset
annotations:
name: annotations
range: Bican_Annotation
class_uri: CAS:Taxonomy
tree_root: true
Induced
name: Bican_Taxonomy
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
is_a: Taxonomy
slot_usage:
labelsets:
name: labelsets
range: Bican_Labelset
annotations:
name: annotations
range: Bican_Annotation
attributes:
matrix_file_id:
name: matrix_file_id
description: A resolvable ID for a cell by gene matrix file in the form namespace:accession,
e.g. CellXGene_dataset:8e10f1c4-8e98-41e5-b65f-8cd89a887122. Please see https://github.com/cellannotation/cell-annotation-schema/registry/registry.json
for supported namespaces.
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
rank: 1000
alias: matrix_file_id
owner: Bican_Taxonomy
domain_of:
- Taxonomy
range: uriorcurie
title:
name: title
description: The title of the dataset. This MUST be less than or equal to 200
characters. e.g. 'Human retina cell atlas - retinal ganglion cells'.
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
rank: 1000
alias: title
owner: Bican_Taxonomy
domain_of:
- Taxonomy
range: string
required: true
description:
name: description
description: The description of the dataset. e.g. 'A total of 15 retinal ganglion
cell clusters were identified from over 99K retinal ganglion cell nuclei in
the current atlas. Utilizing previous characterized markers from macaque, 5
clusters can be annotated.'
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
rank: 1000
slot_uri: IAO:0000115
alias: description
owner: Bican_Taxonomy
domain_of:
- Labelset
- Taxonomy
range: string
cellannotation_schema_version:
name: cellannotation_schema_version
description: 'The schema version, the cell annotation open standard. Current version
MUST follow 0.1.0
This versioning MUST follow the format `''[MAJOR].[MINOR].[PATCH]''` as defined
by Semantic Versioning 2.0.0, https://semver.org/'
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
rank: 1000
alias: cellannotation_schema_version
owner: Bican_Taxonomy
domain_of:
- Taxonomy
range: string
cellannotation_timestamp:
name: cellannotation_timestamp
description: The timestamp of all cell annotations published (per dataset). This
MUST be a string in the format `'%yyyy-%mm-%dd %hh:%mm:%ss'`
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
rank: 1000
alias: cellannotation_timestamp
owner: Bican_Taxonomy
domain_of:
- Taxonomy
range: string
cellannotation_version:
name: cellannotation_version
description: The version for all cell annotations published (per dataset). This
MUST be a string. The recommended versioning format is `'[MAJOR].[MINOR].[PATCH]'`
as defined by Semantic Versioning 2.0.0, https://semver.org/
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
rank: 1000
alias: cellannotation_version
owner: Bican_Taxonomy
domain_of:
- Taxonomy
range: string
cellannotation_url:
name: cellannotation_url
description: A persistent URL of all cell annotations published (per dataset).
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
rank: 1000
alias: cellannotation_url
owner: Bican_Taxonomy
domain_of:
- Taxonomy
range: string
author_list:
name: author_list
description: This field stores a list of users who are included in the project
as collaborators, regardless of their specific role. An example list; '['John
Smith', 'Cody Miller', 'Sarah Jones']'
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
rank: 1000
alias: author_list
owner: Bican_Taxonomy
domain_of:
- Taxonomy
range: string
author_name:
name: author_name
description: Primary author's name. This MUST be a string in the format `[FIRST
NAME] [LAST NAME]`
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
rank: 1000
alias: author_name
owner: Bican_Taxonomy
domain_of:
- Taxonomy
range: string
required: true
author_contact:
name: author_contact
description: Primary author's contact. This MUST be a valid email address of the
author
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
rank: 1000
alias: author_contact
owner: Bican_Taxonomy
domain_of:
- Taxonomy
range: string
orcid:
name: orcid
description: Primary author's orcid. This MUST be a valid ORCID for the author
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
rank: 1000
alias: orcid
owner: Bican_Taxonomy
domain_of:
- Taxonomy
range: string
labelsets:
name: labelsets
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
rank: 1000
alias: labelsets
owner: Bican_Taxonomy
domain_of:
- Taxonomy
range: Bican_Labelset
required: true
multivalued: true
inlined_as_list: true
annotations:
name: annotations
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
rank: 1000
alias: annotations
owner: Bican_Taxonomy
domain_of:
- Taxonomy
range: Bican_Annotation
required: true
multivalued: true
inlined_as_list: true
class_uri: CAS:Taxonomy
tree_root: true