Class: VariantSet

A data entity consisting of genomic variants relative to a reference.

classDiagram class VariantSet click VariantSet href "../VariantSet" DataEntity <|-- VariantSet click DataEntity href "../DataEntity" VariantSet : data_format VariantSet --> "1" DataFormat : data_format click DataFormat href "../DataFormat" VariantSet : data_path VariantSet : description VariantSet : has_reference VariantSet --> "*" ReferenceGenome : has_reference click ReferenceGenome href "../ReferenceGenome" VariantSet : has_sample VariantSet --> "*" Sample : has_sample click Sample href "../Sample" VariantSet : id VariantSet : name

Inheritance

NamedThing
- DataEntity
  - VariantSet

Slots

Name	Cardinality and Range	Description	Inheritance
data_path	1 String	The path to access a resource, on a network or local filesystem	DataEntity
data_format	1 DataFormat	Data/file format associated with a data entity	DataEntity
has_sample	* Sample	Biological sample included or described by a given thing	DataEntity
has_reference	* ReferenceGenome	Specifies the reference coordinate system used by an omics dataset	DataEntity
id	1 Uriorcurie	A unique identifier for a thing	NamedThing
name	0..1 String	A human-readable name for a thing	NamedThing
description	0..1 String	A human-readable description for a thing	NamedThing

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/sdsc-ordes/modos-schema

Mappings

Mapping Type	Mapped Value
self	modos:VariantSet
native	modos:VariantSet

LinkML Source

Direct

name: VariantSet
description: A data entity consisting of genomic variants relative to a reference.
from_schema: https://w3id.org/sdsc-ordes/modos-schema
is_a: DataEntity

Induced

name: VariantSet
description: A data entity consisting of genomic variants relative to a reference.
from_schema: https://w3id.org/sdsc-ordes/modos-schema
is_a: DataEntity
attributes:
  data_path:
    name: data_path
    description: The path to access a resource, on a network or local filesystem.
      Can be a path relative to the root of the digital object, a URL, or an absolute
      path.
    examples:
    - value: s3://example-bucket/path/to/data
    - value: relative/file/path
    - value: file:///absolute/file/path
    from_schema: https://w3id.org/sdsc-ordes/modos-schema
    rank: 1000
    alias: data_path
    owner: VariantSet
    domain_of:
    - DataEntity
    - ReferenceGenome
    range: string
    required: true
  data_format:
    name: data_format
    description: Data/file format associated with a data entity.
    from_schema: https://w3id.org/sdsc-ordes/modos-schema
    rank: 1000
    alias: data_format
    owner: VariantSet
    domain_of:
    - DataEntity
    range: DataFormat
    required: true
  has_sample:
    name: has_sample
    description: Biological sample included or described by a given thing.
    from_schema: https://w3id.org/sdsc-ordes/modos-schema
    rank: 1000
    is_a: has_part
    alias: has_sample
    owner: VariantSet
    domain_of:
    - Assay
    - DataEntity
    range: Sample
    multivalued: true
  has_reference:
    name: has_reference
    description: Specifies the reference coordinate system used by an omics dataset.
    from_schema: https://w3id.org/sdsc-ordes/modos-schema
    rank: 1000
    is_a: has_part
    alias: has_reference
    owner: VariantSet
    domain_of:
    - DataEntity
    range: ReferenceGenome
    multivalued: true
  id:
    name: id
    description: A unique identifier for a thing
    from_schema: https://w3id.org/sdsc-ordes/modos-schema
    rank: 1000
    slot_uri: schema:identifier
    identifier: true
    alias: id
    owner: VariantSet
    domain_of:
    - NamedThing
    range: uriorcurie
    required: true
  name:
    name: name
    description: A human-readable name for a thing
    from_schema: https://w3id.org/sdsc-ordes/modos-schema
    rank: 1000
    slot_uri: schema:name
    alias: name
    owner: VariantSet
    domain_of:
    - NamedThing
    range: string
  description:
    name: description
    description: A human-readable description for a thing
    from_schema: https://w3id.org/sdsc-ordes/modos-schema
    rank: 1000
    slot_uri: schema:description
    alias: description
    owner: VariantSet
    domain_of:
    - NamedThing
    range: string