Class: ReferenceGenome

Reference assembly of a given genome, consisting of a collection of congiguous sequences (contigs).

classDiagram class ReferenceGenome click ReferenceGenome href "../ReferenceGenome" NamedThing <|-- ReferenceGenome click NamedThing href "../NamedThing" ReferenceGenome : data_path ReferenceGenome : description ReferenceGenome : has_sequence ReferenceGenome --> "*" ReferenceSequence : has_sequence click ReferenceSequence href "../ReferenceSequence" ReferenceGenome : id ReferenceGenome : name ReferenceGenome : source_uri ReferenceGenome : taxon_id ReferenceGenome : version

Inheritance

NamedThing
- ReferenceGenome

Slots

Name	Cardinality and Range	Description	Inheritance
data_path	1 String	The path to access a resource, on a network or local filesystem	direct
has_sequence	* ReferenceSequence	Denotes that a sequence belongs to a collection (e	direct
taxon_id	* Uriorcurie	The NCBI taxon code from [ncbitaxon](https://obofoundry	direct
source_uri	0..1 Uri	The URI from which a resource or dataset was obtained or derived	direct
version	0..1 String	A string specifying the release or version of a software or resource	direct
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

Usages

used by	used in	type	used
DataEntity	has_reference	range	ReferenceGenome
AlignmentSet	has_reference	range	ReferenceGenome
VariantSet	has_reference	range	ReferenceGenome
MassSpectrometryResults	has_reference	range	ReferenceGenome
Array	has_reference	range	ReferenceGenome

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: ReferenceGenome
description: Reference assembly of a given genome, consisting of a collection of congiguous
  sequences (contigs).
from_schema: https://w3id.org/sdsc-ordes/modos-schema
see_also:
- GENO:0000914
is_a: NamedThing
slots:
- data_path
- has_sequence
- taxon_id
- source_uri
- version

Induced

name: ReferenceGenome
description: Reference assembly of a given genome, consisting of a collection of congiguous
  sequences (contigs).
from_schema: https://w3id.org/sdsc-ordes/modos-schema
see_also:
- GENO:0000914
is_a: NamedThing
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: ReferenceGenome
    domain_of:
    - DataEntity
    - ReferenceGenome
    range: string
    required: true
  has_sequence:
    name: has_sequence
    description: Denotes that a sequence belongs to a collection (e.g. a reference
      genome).
    from_schema: https://w3id.org/sdsc-ordes/modos-schema
    rank: 1000
    is_a: has_part
    alias: has_sequence
    owner: ReferenceGenome
    domain_of:
    - ReferenceGenome
    range: ReferenceSequence
    multivalued: true
  taxon_id:
    name: taxon_id
    description: 'The NCBI taxon code from [ncbitaxon](https://obofoundry.org/ontology/ncbitaxon.html)
      describing the taxonomic range of a sample.

      '
    from_schema: https://w3id.org/sdsc-ordes/modos-schema
    rank: 1000
    alias: taxon_id
    owner: ReferenceGenome
    domain_of:
    - Sample
    - ReferenceGenome
    range: uriorcurie
    multivalued: true
  source_uri:
    name: source_uri
    description: The URI from which a resource or dataset was obtained or derived.
    from_schema: https://w3id.org/sdsc-ordes/modos-schema
    rank: 1000
    alias: source_uri
    owner: ReferenceGenome
    domain_of:
    - MODO
    - ReferenceGenome
    - ReferenceSequence
    range: uri
  version:
    name: version
    description: A string specifying the release or version of a software or resource.
    from_schema: https://w3id.org/sdsc-ordes/modos-schema
    rank: 1000
    alias: version
    owner: ReferenceGenome
    domain_of:
    - ReferenceGenome
    - ReferenceSequence
    range: string
  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: ReferenceGenome
    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: ReferenceGenome
    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: ReferenceGenome
    domain_of:
    - NamedThing
    range: string