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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 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 (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 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
    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
    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
  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: 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: PubMed IDs supporting this annotation
    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]+$
  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
    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
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: description
    owner: EvolutionaryConservation
    domain_of:
    - NamedThing
    - AttributeGroup
    range: string