Class: CapTaxonomy
URI: CAS:Taxonomy
classDiagram
class CapTaxonomy
click CapTaxonomy href "../CapTaxonomy"
Taxonomy <|-- CapTaxonomy
click Taxonomy href "../Taxonomy"
CapTaxonomy : annotations
CapTaxonomy --> "1..*" CapAnnotation : annotations
click CapAnnotation href "../CapAnnotation"
CapTaxonomy : author_contact
CapTaxonomy : author_list
CapTaxonomy : author_name
CapTaxonomy : cap_dataset_url
CapTaxonomy : cap_publication_description
CapTaxonomy : cap_publication_title
CapTaxonomy : cap_publication_url
CapTaxonomy : cellannotation_schema_version
CapTaxonomy : cellannotation_timestamp
CapTaxonomy : cellannotation_url
CapTaxonomy : cellannotation_version
CapTaxonomy : description
CapTaxonomy : labelsets
CapTaxonomy --> "1..*" Labelset : labelsets
click Labelset href "../Labelset"
CapTaxonomy : matrix_file_id
CapTaxonomy : orcid
CapTaxonomy : publication_timestamp
CapTaxonomy : publication_version
CapTaxonomy : title
Inheritance
- Taxonomy
- CapTaxonomy
Slots
Name | Cardinality and Range | Description | Inheritance |
---|---|---|---|
cap_publication_title | 0..1 String |
The title of the publication on CAP (i | direct |
cap_publication_description | 0..1 String |
The description of the publication on CAP | direct |
cap_publication_url | 0..1 String |
A persistent URL of the publication on CAP | direct |
cap_dataset_url | 0..1 String |
A persistent URL of the dataset on CAP | direct |
publication_timestamp | 0..1 String |
The timestamp of the CAP publication | direct |
publication_version | 0..1 String |
The (latest) version of the CAP publication | direct |
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 | 1 String |
The schema version, the cell annotation open standard | Taxonomy |
cellannotation_timestamp | 1 String |
The timestamp of all cell annotations published (per dataset) | Taxonomy |
cellannotation_version | 1 String |
The version for all cell annotations published (per dataset) | Taxonomy |
cellannotation_url | 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..* Labelset |
Taxonomy | |
annotations | 1..* CapAnnotation |
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:CapTaxonomy |
LinkML Source
Direct
name: Cap_Taxonomy
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
is_a: Taxonomy
slots:
- cap_publication_title
- cap_publication_description
- cap_publication_url
- cap_dataset_url
- publication_timestamp
- publication_version
slot_usage:
annotations:
name: annotations
range: Cap_Annotation
cellannotation_schema_version:
name: cellannotation_schema_version
required: true
cellannotation_timestamp:
name: cellannotation_timestamp
required: true
cellannotation_version:
name: cellannotation_version
required: true
cellannotation_url:
name: cellannotation_url
required: true
class_uri: CAS:Taxonomy
tree_root: true
Induced
name: Cap_Taxonomy
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
is_a: Taxonomy
slot_usage:
annotations:
name: annotations
range: Cap_Annotation
cellannotation_schema_version:
name: cellannotation_schema_version
required: true
cellannotation_timestamp:
name: cellannotation_timestamp
required: true
cellannotation_version:
name: cellannotation_version
required: true
cellannotation_url:
name: cellannotation_url
required: true
attributes:
cap_publication_title:
name: cap_publication_title
description: 'The title of the publication on CAP (i.e. a published collection
of datasets, the \"CAP Workspace\".). The title of the publication on CAP. (NOTE:
the term \"publication\" refers to the workspace published on CAP with a version
and timestamp.) This MUST be less than or equal to N characters, and this MUST
be encoded as a single string.'
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
rank: 1000
alias: cap_publication_title
owner: Cap_Taxonomy
domain_of:
- Cap_Taxonomy
range: string
cap_publication_description:
name: cap_publication_description
description: 'The description of the publication on CAP. The description of the
publication on CAP. (NOTE: the term \"publication\" refers to the workspace
published on CAP with a version and timestamp.) This MUST be less than or equal
to N characters, and this MUST be encoded as a single string.'
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
rank: 1000
alias: cap_publication_description
owner: Cap_Taxonomy
domain_of:
- Cap_Taxonomy
range: string
cap_publication_url:
name: cap_publication_url
description: 'A persistent URL of the publication on CAP. (NOTE: the term \"publication\"
refers to the workspace published on CAP with a version and timestamp.)'
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
rank: 1000
alias: cap_publication_url
owner: Cap_Taxonomy
domain_of:
- Cap_Taxonomy
range: string
cap_dataset_url:
name: cap_dataset_url
description: A persistent URL of the dataset on CAP.
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
rank: 1000
alias: cap_dataset_url
owner: Cap_Taxonomy
domain_of:
- Cap_Taxonomy
range: string
publication_timestamp:
name: publication_timestamp
description: The timestamp of the CAP publication. This MUST be a string in the
format %yyyy-%MM-%dd'T'%hh:%mm:%ss. This value will be overwritten by the newest
timestamp upon a new publication.
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
rank: 1000
alias: publication_timestamp
owner: Cap_Taxonomy
domain_of:
- Cap_Taxonomy
range: string
publication_version:
name: publication_version
description: The (latest) version of the CAP publication. This value will be overwritten
by the newest version upon a new publication (and automatically incremented).
This versioning MUST follow the format 'v' + '[integer]', whereby newer versions
must be naturally incremented.
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
rank: 1000
alias: publication_version
owner: Cap_Taxonomy
domain_of:
- Cap_Taxonomy
range: string
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: Cap_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: Cap_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: Cap_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: Cap_Taxonomy
domain_of:
- Taxonomy
range: string
required: true
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: Cap_Taxonomy
domain_of:
- Taxonomy
range: string
required: true
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: Cap_Taxonomy
domain_of:
- Taxonomy
range: string
required: true
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: Cap_Taxonomy
domain_of:
- Taxonomy
range: string
required: true
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: Cap_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: Cap_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: Cap_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: Cap_Taxonomy
domain_of:
- Taxonomy
range: string
labelsets:
name: labelsets
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
rank: 1000
alias: labelsets
owner: Cap_Taxonomy
domain_of:
- Taxonomy
range: 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: Cap_Taxonomy
domain_of:
- Taxonomy
range: Cap_Annotation
required: true
multivalued: true
inlined_as_list: true
class_uri: CAS:Taxonomy
tree_root: true