Class: Protein

Proteins are large, complex molecules made up of one or more long, folded chains of amino acids, whose sequences are determined by the DNA sequence of the protein-encoding gene.

URI: cdm:Protein

classDiagram class Protein click Protein href "../Protein" HasNames <|-- Protein click HasNames href "../HasNames" HasIdentifiers <|-- Protein click HasIdentifiers href "../HasIdentifiers" HasHash <|-- Protein click HasHash href "../HasHash" Protein : description Protein : encoded_by Protein --> "0..1" Feature : encoded_by click Feature href "../Feature" Protein : evidence_for_existence Protein --> "0..1" ProteinEvidenceForExistence : evidence_for_existence click ProteinEvidenceForExistence href "../ProteinEvidenceForExistence" Protein : hash Protein : identifiers Protein --> "*" Identifier : identifiers click Identifier href "../Identifier" Protein : length Protein : names Protein --> "*" Name : names click Name href "../Name" Protein : protein_id Protein --> "1" Entity : protein_id click Entity href "../Entity" Protein : sequence

Inheritance

Protein [ HasNames HasIdentifiers HasHash]

Slots

Name	Cardinality and Range	Description	Inheritance
description	0..1 String	Brief text description of the entity	direct
encoded_by	0..1 Feature	The feature(s) that encode this protein	direct
evidence_for_existence	0..1 ProteinEvidenceForExistence	The evidence that this protein exists	direct
length	0..1 Integer	The length of the protein	direct
protein_id	1 Entity	Internal (CDM) unique identifier	direct
sequence	0..1 String	The protein amino acid sequence	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
ClusterXProtein	protein_id	range	Protein
ContigCollectionXProtein	protein_id	range	Protein
FeatureXProtein	protein_id	range	Protein
Association	subject	any_of[range]	Protein
Association	supporting_objects	any_of[range]	Protein

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Protein
description: Proteins are large, complex molecules made up of one or more long, folded
  chains of amino acids, whose sequences are determined by the DNA sequence of the
  protein-encoding gene.
from_schema: https://github.com/kbase/cdm-schema
mixins:
- HasNames
- HasIdentifiers
- HasHash
attributes:
  description:
    name: description
    description: Brief text description of the entity.
    from_schema: https://github.com/kbase/cdm-schema
    domain_of:
    - Cluster
    - Event
    - Experiment
    - Project
    - Protein
    - Sample
    - Identifier
    - Name
  encoded_by:
    name: encoded_by
    description: The feature(s) that encode this protein.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    domain_of:
    - Protein
    range: Feature
  evidence_for_existence:
    name: evidence_for_existence
    description: The evidence that this protein exists. For example, the protein may
      have been isolated from a cell, or it may be predicted based on sequence features.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    domain_of:
    - Protein
    range: ProteinEvidenceForExistence
  length:
    name: length
    description: The length of the protein.
    from_schema: https://github.com/kbase/cdm-schema
    domain_of:
    - Contig
    - Protein
    range: integer
  protein_id:
    name: protein_id
    description: Internal (CDM) unique identifier.
    from_schema: https://github.com/kbase/cdm-schema
    identifier: true
    domain_of:
    - Cluster_X_Protein
    - ContigCollection_X_Protein
    - Feature_X_Protein
    - Protein
    range: Entity
    required: true
  sequence:
    name: sequence
    description: The protein amino acid sequence.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    domain_of:
    - Protein

Induced

name: Protein
description: Proteins are large, complex molecules made up of one or more long, folded
  chains of amino acids, whose sequences are determined by the DNA sequence of the
  protein-encoding gene.
from_schema: https://github.com/kbase/cdm-schema
mixins:
- HasNames
- HasIdentifiers
- HasHash
attributes:
  description:
    name: description
    description: Brief text description of the entity.
    from_schema: https://github.com/kbase/cdm-schema
    alias: description
    owner: Protein
    domain_of:
    - Cluster
    - Event
    - Experiment
    - Project
    - Protein
    - Sample
    - Identifier
    - Name
    range: string
  encoded_by:
    name: encoded_by
    description: The feature(s) that encode this protein.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    alias: encoded_by
    owner: Protein
    domain_of:
    - Protein
    range: Feature
  evidence_for_existence:
    name: evidence_for_existence
    description: The evidence that this protein exists. For example, the protein may
      have been isolated from a cell, or it may be predicted based on sequence features.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    alias: evidence_for_existence
    owner: Protein
    domain_of:
    - Protein
    range: ProteinEvidenceForExistence
  length:
    name: length
    description: The length of the protein.
    from_schema: https://github.com/kbase/cdm-schema
    alias: length
    owner: Protein
    domain_of:
    - Contig
    - Protein
    range: integer
  protein_id:
    name: protein_id
    description: Internal (CDM) unique identifier.
    from_schema: https://github.com/kbase/cdm-schema
    identifier: true
    alias: protein_id
    owner: Protein
    domain_of:
    - Cluster_X_Protein
    - ContigCollection_X_Protein
    - Feature_X_Protein
    - Protein
    range: Entity
    required: true
  sequence:
    name: sequence
    description: The protein amino acid sequence.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    alias: sequence
    owner: Protein
    domain_of:
    - Protein
    range: string
  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: Protein
    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: Protein
    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: Protein
    domain_of:
    - HasHash
    range: string