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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: kb_cdm:Protein

classDiagram class Protein click Protein href "../Protein" UniqueNamedThing <|-- Protein click UniqueNamedThing href "../UniqueNamedThing" Protein : description Protein : encoded_by Protein --> "0..1" Feature : encoded_by click Feature href "../Feature" Protein : evidence_for_existence Protein --> "0..1" EvidenceForExistence : evidence_for_existence click EvidenceForExistence href "../EvidenceForExistence" 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 : sequence

Inheritance

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
EvidenceForExistence		 The evidence that this protein exists direct
length 0..1
Integer		 The length of the protein direct
protein_id 1
UUID		 Internal (CDM) unique identifier direct
sequence 0..1
String		 The protein amino acid sequence direct
hash 0..1
String		 A hash value generated from one or more object attributes that serves to ensu... UniqueNamedThing
identifiers *
Identifier		 URIs or CURIEs used to refer to this entity NamedThingWithId
names *
Name		 Names, alternative names, and synonyms for an entity NamedThing

Identifier and Mapping Information

Schema Source

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

Mappings

Mapping Type Mapped Value
self kb_cdm:Protein
native kb_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
is_a: UniqueNamedThing
attributes:
  description:
    name: description
    description: Brief text description of the entity.
    from_schema: https://github.com/kbase/cdm-schema
    domain_of:
    - NamedThing
    - Event
    - Experiment
    - Identifier
    - Name
    - Project
    - Protein
    - Sample
  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: EvidenceForExistence
  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:
    - FeatureXProtein
    - Protein
    range: UUID
    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
is_a: UniqueNamedThing
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:
    - NamedThing
    - Event
    - Experiment
    - Identifier
    - Name
    - Project
    - Protein
    - Sample
    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: EvidenceForExistence
  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:
    - FeatureXProtein
    - Protein
    range: UUID
    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
  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
    alias: hash
    owner: Protein
    domain_of:
    - UniqueNamedThing
    range: string
  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:
    - NamedThingWithId
    range: Identifier
    multivalued: true
  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:
    - NamedThing
    range: Name
    multivalued: true