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Class: MutationEffect

Effects of mutations and variants on protein structure and function

URI: lambdaber:MutationEffect

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

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 (range: 0-1) 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 (range: 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		 IDs of one or more publications 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		 A human-readable name or title for this entity NamedThing
description 0..1
String		 A detailed textual description of this entity 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 (range: 0-1)'
    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 (range: 0-1)'
    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
    pattern: ^[0-9,\-]+$
  confidence_score:
    name: confidence_score
    description: 'Confidence score for the annotation (range: 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: IDs of one or more publications supporting this annotation. Use PubMed
      IDs in the format 'PMID:XXXXXXX' or DOIs with 'DOI:' prefix.
    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]+|DOI:10\.[0-9]{4,}/[-._;()/:A-Za-z0-9]+)$
  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
    description: A human-readable name or title for this entity
    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
    description: A detailed textual description of this entity
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: description
    owner: MutationEffect
    domain_of:
    - NamedThing
    - AttributeGroup
    range: string