Class: MutationEffect

Effects of mutations and variants on protein structure and function

classDiagram class MutationEffect click MutationEffect href "../MutationEffect/" ProteinAnnotation <|-- MutationEffect click ProteinAnnotation href "../ProteinAnnotation/" MutationEffect : allele_frequency MutationEffect : annotation_method MutationEffect : chain_id MutationEffect : clinical_significance MutationEffect --> "0..1" ClinicalSignificanceEnum : clinical_significance click ClinicalSignificanceEnum href "../ClinicalSignificanceEnum/" MutationEffect : confidence_score MutationEffect : delta_delta_g MutationEffect : description MutationEffect : disease_association MutationEffect : effect_on_function MutationEffect --> "0..1" FunctionalEffectEnum : effect_on_function click FunctionalEffectEnum href "../FunctionalEffectEnum/" MutationEffect : effect_on_stability MutationEffect --> "0..1" StabilityEffectEnum : effect_on_stability click StabilityEffectEnum href "../StabilityEffectEnum/" MutationEffect : evidence_code MutationEffect : evidence_type MutationEffect --> "0..1" EvidenceTypeEnum : evidence_type click EvidenceTypeEnum href "../EvidenceTypeEnum/" MutationEffect : functional_impact_description MutationEffect : id MutationEffect : mutation MutationEffect : mutation_type MutationEffect --> "0..1" MutationTypeEnum : mutation_type click MutationTypeEnum href "../MutationTypeEnum/" MutationEffect : omim_id MutationEffect : pdb_entry MutationEffect : protein_id MutationEffect : publication_ids MutationEffect : residue_range MutationEffect : source_database MutationEffect --> "0..1" AnnotationSourceEnum : source_database click AnnotationSourceEnum href "../AnnotationSourceEnum/" MutationEffect : title

Inheritance

NamedThing
- ProteinAnnotation
  - MutationEffect

Slots

Name	Cardinality and Range	Description	Inheritance
mutation	1 String	Mutation in standard notation (e	direct
mutation_type	0..1 MutationTypeEnum	Type of mutation	direct
effect_on_stability	0..1 StabilityEffectEnum	Effect on protein stability	direct
delta_delta_g	0..1 Float	Change in folding free energy (kcal/mol)	direct
effect_on_function	0..1 FunctionalEffectEnum	Effect on protein function	direct
functional_impact_description	0..1 String	Description of functional impact	direct
disease_association	0..1 String	Associated disease or phenotype	direct
omim_id	0..1 String	OMIM database identifier	direct
clinical_significance	0..1 ClinicalSignificanceEnum	Clinical significance	direct
allele_frequency	0..1 Float	Population allele frequency	direct
protein_id	1 String	UniProt accession number	ProteinAnnotation
pdb_entry	0..1 String	PDB identifier	ProteinAnnotation
chain_id	0..1 String	Chain identifier in the PDB structure	ProteinAnnotation
residue_range	0..1 String	Range of residues (e	ProteinAnnotation
confidence_score	0..1 Float	Confidence score for the annotation (0-1)	ProteinAnnotation
evidence_type	0..1 EvidenceTypeEnum	Type of evidence supporting this annotation	ProteinAnnotation
evidence_code	0..1 Uriorcurie	Evidence and Conclusion Ontology (ECO) code	ProteinAnnotation
source_database	0..1 AnnotationSourceEnum	Source database or resource that provided this annotation	ProteinAnnotation
annotation_method	0..1 String	Computational or experimental method used	ProteinAnnotation
publication_ids	* String	PubMed IDs supporting this annotation	ProteinAnnotation
id	1 Uriorcurie	Globally unique identifier as an IRI or CURIE for machine processing and exte...	NamedThing
title	0..1 String		NamedThing
description	0..1 String		NamedThing

Usages

used by	used in	type	used
Sample	mutation_effects	range	MutationEffect
AggregatedProteinView	mutations	range	MutationEffect

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/lambda-ber-schema/

Mappings

Mapping Type	Mapped Value
self	lambdaber:MutationEffect
native	lambdaber:MutationEffect

LinkML Source

Direct

name: MutationEffect
description: Effects of mutations and variants on protein structure and function
from_schema: https://w3id.org/lambda-ber-schema/
is_a: ProteinAnnotation
attributes:
  mutation:
    name: mutation
    description: Mutation in standard notation (e.g., 'A123V')
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - MutationEffect
    required: true
    pattern: ^[A-Z][0-9]+[A-Z]$
  mutation_type:
    name: mutation_type
    description: Type of mutation
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - MutationEffect
    range: MutationTypeEnum
  effect_on_stability:
    name: effect_on_stability
    description: Effect on protein stability
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - MutationEffect
    range: StabilityEffectEnum
  delta_delta_g:
    name: delta_delta_g
    description: Change in folding free energy (kcal/mol)
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - MutationEffect
    range: float
    unit:
      ucum_code: kcal/mol
  effect_on_function:
    name: effect_on_function
    description: Effect on protein function
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - MutationEffect
    range: FunctionalEffectEnum
  functional_impact_description:
    name: functional_impact_description
    description: Description of functional impact
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - MutationEffect
  disease_association:
    name: disease_association
    description: Associated disease or phenotype
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - MutationEffect
  omim_id:
    name: omim_id
    description: OMIM database identifier
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - MutationEffect
    pattern: ^[0-9]{6}$
  clinical_significance:
    name: clinical_significance
    description: Clinical significance
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - MutationEffect
    range: ClinicalSignificanceEnum
  allele_frequency:
    name: allele_frequency
    description: Population allele frequency
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - MutationEffect
    range: float
    minimum_value: 0
    maximum_value: 1

Induced

name: MutationEffect
description: Effects of mutations and variants on protein structure and function
from_schema: https://w3id.org/lambda-ber-schema/
is_a: ProteinAnnotation
attributes:
  mutation:
    name: mutation
    description: Mutation in standard notation (e.g., 'A123V')
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: mutation
    owner: MutationEffect
    domain_of:
    - MutationEffect
    range: string
    required: true
    pattern: ^[A-Z][0-9]+[A-Z]$
  mutation_type:
    name: mutation_type
    description: Type of mutation
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: mutation_type
    owner: MutationEffect
    domain_of:
    - MutationEffect
    range: MutationTypeEnum
  effect_on_stability:
    name: effect_on_stability
    description: Effect on protein stability
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: effect_on_stability
    owner: MutationEffect
    domain_of:
    - MutationEffect
    range: StabilityEffectEnum
  delta_delta_g:
    name: delta_delta_g
    description: Change in folding free energy (kcal/mol)
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: delta_delta_g
    owner: MutationEffect
    domain_of:
    - MutationEffect
    range: float
    unit:
      ucum_code: kcal/mol
  effect_on_function:
    name: effect_on_function
    description: Effect on protein function
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: effect_on_function
    owner: MutationEffect
    domain_of:
    - MutationEffect
    range: FunctionalEffectEnum
  functional_impact_description:
    name: functional_impact_description
    description: Description of functional impact
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: functional_impact_description
    owner: MutationEffect
    domain_of:
    - MutationEffect
    range: string
  disease_association:
    name: disease_association
    description: Associated disease or phenotype
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: disease_association
    owner: MutationEffect
    domain_of:
    - MutationEffect
    range: string
  omim_id:
    name: omim_id
    description: OMIM database identifier
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: omim_id
    owner: MutationEffect
    domain_of:
    - MutationEffect
    range: string
    pattern: ^[0-9]{6}$
  clinical_significance:
    name: clinical_significance
    description: Clinical significance
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: clinical_significance
    owner: MutationEffect
    domain_of:
    - MutationEffect
    range: ClinicalSignificanceEnum
  allele_frequency:
    name: allele_frequency
    description: Population allele frequency
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: allele_frequency
    owner: MutationEffect
    domain_of:
    - MutationEffect
    range: float
    minimum_value: 0
    maximum_value: 1
  protein_id:
    name: protein_id
    description: UniProt accession number
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: protein_id
    owner: MutationEffect
    domain_of:
    - ProteinAnnotation
    - ConformationalEnsemble
    range: string
    required: true
    pattern: ^[A-Z][0-9][A-Z0-9]{3}[0-9]|[A-Z][0-9][A-Z0-9]{3}[0-9]-[0-9]+$
  pdb_entry:
    name: pdb_entry
    description: PDB identifier
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: pdb_entry
    owner: MutationEffect
    domain_of:
    - ProteinAnnotation
    range: string
    pattern: ^[0-9][A-Za-z0-9]{3}$
  chain_id:
    name: chain_id
    description: Chain identifier in the PDB structure
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: chain_id
    owner: MutationEffect
    domain_of:
    - ProteinAnnotation
    range: string
    pattern: ^[A-Za-z0-9]+$
  residue_range:
    name: residue_range
    description: Range of residues (e.g., '1-100', '25,27,30-35')
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: residue_range
    owner: MutationEffect
    domain_of:
    - ProteinAnnotation
    range: string
  confidence_score:
    name: confidence_score
    description: Confidence score for the annotation (0-1)
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: confidence_score
    owner: MutationEffect
    domain_of:
    - ProteinAnnotation
    range: float
    minimum_value: 0
    maximum_value: 1
  evidence_type:
    name: evidence_type
    description: Type of evidence supporting this annotation
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: evidence_type
    owner: MutationEffect
    domain_of:
    - ProteinAnnotation
    range: EvidenceTypeEnum
  evidence_code:
    name: evidence_code
    description: Evidence and Conclusion Ontology (ECO) code
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: evidence_code
    owner: MutationEffect
    domain_of:
    - ProteinAnnotation
    range: uriorcurie
  source_database:
    name: source_database
    description: Source database or resource that provided this annotation
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: source_database
    owner: MutationEffect
    domain_of:
    - ProteinAnnotation
    range: AnnotationSourceEnum
  annotation_method:
    name: annotation_method
    description: Computational or experimental method used
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: annotation_method
    owner: MutationEffect
    domain_of:
    - ProteinAnnotation
    range: string
  publication_ids:
    name: publication_ids
    description: PubMed IDs supporting this annotation
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: publication_ids
    owner: MutationEffect
    domain_of:
    - ProteinAnnotation
    range: string
    multivalued: true
    pattern: ^PMID:[0-9]+$
  id:
    name: id
    description: Globally unique identifier as an IRI or CURIE for machine processing
      and external references. Used for linking data across systems and semantic web
      integration.
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    identifier: true
    alias: id
    owner: MutationEffect
    domain_of:
    - NamedThing
    range: uriorcurie
    required: true
  title:
    name: title
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    slot_uri: dcterms:title
    alias: title
    owner: MutationEffect
    domain_of:
    - NamedThing
    range: string
  description:
    name: description
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: description
    owner: MutationEffect
    domain_of:
    - NamedThing
    - AttributeGroup
    range: string