Class: Contig

A contig (derived from the word "contiguous") is a set of DNA segments or sequences that overlap in a way that provides a contiguous representation of a genomic region. A contig should not contain any gaps.

URI: cdm:Contig

classDiagram class Contig click Contig href "../Contig" HasNames <|-- Contig click HasNames href "../HasNames" HasIdentifiers <|-- Contig click HasIdentifiers href "../HasIdentifiers" HasHash <|-- Contig click HasHash href "../HasHash" Contig : contig_id Contig : gc_content Contig : hash Contig : identifiers Contig --> "*" Identifier : identifiers click Identifier href "../Identifier" Contig : length Contig : names Contig --> "*" Name : names click Name href "../Name"

Inheritance

Contig [ HasNames HasIdentifiers HasHash]

Slots

Name	Cardinality and Range	Description	Inheritance
contig_id	1 UUID	Internal (CDM) unique identifier	direct
gc_content	0..1 Float	GC content of the contig, expressed as a percentage	direct
length	0..1 Integer	Length of the contig in bp	direct
names	* Name	Names, alternative names, and synonyms for an entity	HasNames
identifiers	* Identifier	URIs or CURIEs used to refer to this entity	HasIdentifiers
hash	0..1 String	A hash value generated from one or more object attributes that serves to ensu...	HasHash

Usages

used by	used in	type	used
ContigXContigCollection	contig_id	range	Contig
ContigXFeature	contig_id	range	Contig
ContigCollectionXFeature	feature_id	range	Contig

Identifier and Mapping Information

Schema Source

from schema: https://github.com/kbase/cdm-schema

Mappings

Mapping Type	Mapped Value
self	cdm:Contig
native	cdm:Contig

LinkML Source

Direct

name: Contig
description: A contig (derived from the word "contiguous") is a set of DNA segments
  or sequences that overlap in a way that provides a contiguous representation of
  a genomic region. A contig should not contain any gaps.
from_schema: https://github.com/kbase/cdm-schema
mixins:
- HasNames
- HasIdentifiers
- HasHash
attributes:
  contig_id:
    name: contig_id
    description: Internal (CDM) unique identifier.
    from_schema: https://github.com/kbase/cdm-schema
    identifier: true
    domain_of:
    - Contig_X_ContigCollection
    - Contig_X_Feature
    - Contig
    range: UUID
    required: true
  gc_content:
    name: gc_content
    description: GC content of the contig, expressed as a percentage.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    domain_of:
    - Contig
    range: float
  length:
    name: length
    description: Length of the contig in bp.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    domain_of:
    - Contig
    - Protein
    range: integer

Induced

name: Contig
description: A contig (derived from the word "contiguous") is a set of DNA segments
  or sequences that overlap in a way that provides a contiguous representation of
  a genomic region. A contig should not contain any gaps.
from_schema: https://github.com/kbase/cdm-schema
mixins:
- HasNames
- HasIdentifiers
- HasHash
attributes:
  contig_id:
    name: contig_id
    description: Internal (CDM) unique identifier.
    from_schema: https://github.com/kbase/cdm-schema
    identifier: true
    alias: contig_id
    owner: Contig
    domain_of:
    - Contig_X_ContigCollection
    - Contig_X_Feature
    - Contig
    range: UUID
    required: true
  gc_content:
    name: gc_content
    description: GC content of the contig, expressed as a percentage.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    alias: gc_content
    owner: Contig
    domain_of:
    - Contig
    range: float
  length:
    name: length
    description: Length of the contig in bp.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    alias: length
    owner: Contig
    domain_of:
    - Contig
    - Protein
    range: integer
  names:
    name: names
    description: Names, alternative names, and synonyms for an entity.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    alias: names
    owner: Contig
    domain_of:
    - HasNames
    range: Name
    multivalued: true
  identifiers:
    name: identifiers
    description: URIs or CURIEs used to refer to this entity.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    alias: identifiers
    owner: Contig
    domain_of:
    - HasIdentifiers
    range: Identifier
    multivalued: true
  hash:
    name: hash
    description: A hash value generated from one or more object attributes that serves
      to ensure the entity is unique.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    alias: hash
    owner: Contig
    domain_of:
    - HasHash
    range: string