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Class: EvolutionaryConservation

Evolutionary conservation information

URI: lambdaber:EvolutionaryConservation

classDiagram class EvolutionaryConservation click EvolutionaryConservation href "../EvolutionaryConservation/" ProteinAnnotation <|-- EvolutionaryConservation click ProteinAnnotation href "../ProteinAnnotation/" EvolutionaryConservation : alignment_depth EvolutionaryConservation : annotation_method EvolutionaryConservation : chain_id EvolutionaryConservation : coevolved_residues EvolutionaryConservation : confidence_score EvolutionaryConservation : conservation_method EvolutionaryConservation : conservation_score EvolutionaryConservation : conserved_residues EvolutionaryConservation : description EvolutionaryConservation : evidence_code EvolutionaryConservation : evidence_type EvolutionaryConservation --> "0..1" EvidenceTypeEnum : evidence_type click EvidenceTypeEnum href "../EvidenceTypeEnum/" EvolutionaryConservation : id EvolutionaryConservation : pdb_entry EvolutionaryConservation : protein_id EvolutionaryConservation : publication_ids EvolutionaryConservation : residue_range EvolutionaryConservation : source_database EvolutionaryConservation --> "0..1" AnnotationSourceEnum : source_database click AnnotationSourceEnum href "../AnnotationSourceEnum/" EvolutionaryConservation : taxonomic_range EvolutionaryConservation : title EvolutionaryConservation : variable_residues

Inheritance

Slots

Name Cardinality and Range Description Inheritance
conservation_score 0..1
Float		 Overall conservation score (range: 0-1) direct
conserved_residues *
String		 Highly conserved residues direct
variable_residues *
String		 Highly variable residues direct
conservation_method 0..1
String		 Method used for conservation analysis direct
alignment_depth 0..1
Integer		 Number of sequences in alignment direct
taxonomic_range 0..1
String		 Taxonomic range of conservation direct
coevolved_residues *
String		 Pairs of coevolved residues 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 evolutionary_conservation range EvolutionaryConservation
AggregatedProteinView evolutionary_conservation range EvolutionaryConservation

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: EvolutionaryConservation
description: Evolutionary conservation information
from_schema: https://w3id.org/lambda-ber-schema/
is_a: ProteinAnnotation
attributes:
  conservation_score:
    name: conservation_score
    description: 'Overall conservation score (range: 0-1)'
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    domain_of:
    - FunctionalSite
    - EvolutionaryConservation
    range: float
    minimum_value: 0
    maximum_value: 1
  conserved_residues:
    name: conserved_residues
    description: Highly conserved residues
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - EvolutionaryConservation
    multivalued: true
  variable_residues:
    name: variable_residues
    description: Highly variable residues
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - EvolutionaryConservation
    multivalued: true
  conservation_method:
    name: conservation_method
    description: Method used for conservation analysis
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - EvolutionaryConservation
  alignment_depth:
    name: alignment_depth
    description: Number of sequences in alignment
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - EvolutionaryConservation
    range: integer
  taxonomic_range:
    name: taxonomic_range
    description: Taxonomic range of conservation
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - EvolutionaryConservation
  coevolved_residues:
    name: coevolved_residues
    description: Pairs of coevolved residues
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - EvolutionaryConservation
    multivalued: true

Induced

name: EvolutionaryConservation
description: Evolutionary conservation information
from_schema: https://w3id.org/lambda-ber-schema/
is_a: ProteinAnnotation
attributes:
  conservation_score:
    name: conservation_score
    description: 'Overall conservation score (range: 0-1)'
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    alias: conservation_score
    owner: EvolutionaryConservation
    domain_of:
    - FunctionalSite
    - EvolutionaryConservation
    range: float
    minimum_value: 0
    maximum_value: 1
  conserved_residues:
    name: conserved_residues
    description: Highly conserved residues
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: conserved_residues
    owner: EvolutionaryConservation
    domain_of:
    - EvolutionaryConservation
    range: string
    multivalued: true
  variable_residues:
    name: variable_residues
    description: Highly variable residues
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: variable_residues
    owner: EvolutionaryConservation
    domain_of:
    - EvolutionaryConservation
    range: string
    multivalued: true
  conservation_method:
    name: conservation_method
    description: Method used for conservation analysis
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: conservation_method
    owner: EvolutionaryConservation
    domain_of:
    - EvolutionaryConservation
    range: string
  alignment_depth:
    name: alignment_depth
    description: Number of sequences in alignment
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: alignment_depth
    owner: EvolutionaryConservation
    domain_of:
    - EvolutionaryConservation
    range: integer
  taxonomic_range:
    name: taxonomic_range
    description: Taxonomic range of conservation
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: taxonomic_range
    owner: EvolutionaryConservation
    domain_of:
    - EvolutionaryConservation
    range: string
  coevolved_residues:
    name: coevolved_residues
    description: Pairs of coevolved residues
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: coevolved_residues
    owner: EvolutionaryConservation
    domain_of:
    - EvolutionaryConservation
    range: string
    multivalued: true
  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: EvolutionaryConservation
    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: EvolutionaryConservation
    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: EvolutionaryConservation
    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: EvolutionaryConservation
    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: EvolutionaryConservation
    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: EvolutionaryConservation
    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: EvolutionaryConservation
    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: EvolutionaryConservation
    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: EvolutionaryConservation
    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: EvolutionaryConservation
    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: EvolutionaryConservation
    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: EvolutionaryConservation
    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: EvolutionaryConservation
    domain_of:
    - NamedThing
    - AttributeGroup
    range: string