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Class: StructuralFeature

Structural features and properties of protein regions

URI: lambdaber:StructuralFeature

classDiagram class StructuralFeature click StructuralFeature href "../StructuralFeature/" ProteinAnnotation <|-- StructuralFeature click ProteinAnnotation href "../ProteinAnnotation/" StructuralFeature : annotation_method StructuralFeature : backbone_flexibility StructuralFeature : chain_id StructuralFeature : confidence_score StructuralFeature : conformational_state StructuralFeature --> "0..1" ConformationalStateEnum : conformational_state click ConformationalStateEnum href "../ConformationalStateEnum/" StructuralFeature : description StructuralFeature : disorder_probability StructuralFeature : domain_assignment StructuralFeature : domain_id StructuralFeature : evidence_code StructuralFeature : evidence_type StructuralFeature --> "0..1" EvidenceTypeEnum : evidence_type click EvidenceTypeEnum href "../EvidenceTypeEnum/" StructuralFeature : feature_type StructuralFeature --> "1" StructuralFeatureTypeEnum : feature_type click StructuralFeatureTypeEnum href "../StructuralFeatureTypeEnum/" StructuralFeature : id StructuralFeature : pdb_entry StructuralFeature : protein_id StructuralFeature : publication_ids StructuralFeature : residue_range StructuralFeature : secondary_structure StructuralFeature --> "0..1" SecondaryStructureEnum : secondary_structure click SecondaryStructureEnum href "../SecondaryStructureEnum/" StructuralFeature : solvent_accessibility StructuralFeature : source_database StructuralFeature --> "0..1" AnnotationSourceEnum : source_database click AnnotationSourceEnum href "../AnnotationSourceEnum/" StructuralFeature : structural_motif StructuralFeature : title

Inheritance

Slots

Name Cardinality and Range Description Inheritance
feature_type 1
StructuralFeatureTypeEnum		 Type of structural feature direct
secondary_structure 0..1
SecondaryStructureEnum		 Secondary structure assignment direct
solvent_accessibility 0..1
Float		 Relative solvent accessible surface area (range: 0-1) direct
backbone_flexibility 0..1
Float		 B-factor or flexibility measure direct
disorder_probability 0..1
Float		 Probability of disorder (range: 0-1) direct
conformational_state 0..1
ConformationalStateEnum		 Conformational state descriptor direct
structural_motif 0..1
String		 Known structural motif direct
domain_assignment 0..1
String		 Domain database assignment (CATH, SCOP, Pfam) direct
domain_id 0..1
String		 Domain identifier from domain database 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 structural_features range StructuralFeature
AggregatedProteinView structural_features range StructuralFeature

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: StructuralFeature
description: Structural features and properties of protein regions
from_schema: https://w3id.org/lambda-ber-schema/
is_a: ProteinAnnotation
attributes:
  feature_type:
    name: feature_type
    description: Type of structural feature
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - StructuralFeature
    range: StructuralFeatureTypeEnum
    required: true
  secondary_structure:
    name: secondary_structure
    description: Secondary structure assignment
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - StructuralFeature
    range: SecondaryStructureEnum
  solvent_accessibility:
    name: solvent_accessibility
    description: 'Relative solvent accessible surface area (range: 0-1)'
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - StructuralFeature
    range: float
    minimum_value: 0
    maximum_value: 1
  backbone_flexibility:
    name: backbone_flexibility
    description: B-factor or flexibility measure
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - StructuralFeature
    range: float
  disorder_probability:
    name: disorder_probability
    description: 'Probability of disorder (range: 0-1)'
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - StructuralFeature
    range: float
    minimum_value: 0
    maximum_value: 1
  conformational_state:
    name: conformational_state
    description: Conformational state descriptor
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - StructuralFeature
    range: ConformationalStateEnum
  structural_motif:
    name: structural_motif
    description: Known structural motif
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - StructuralFeature
  domain_assignment:
    name: domain_assignment
    description: Domain database assignment (CATH, SCOP, Pfam)
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - StructuralFeature
  domain_id:
    name: domain_id
    description: Domain identifier from domain database
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - StructuralFeature

Induced

name: StructuralFeature
description: Structural features and properties of protein regions
from_schema: https://w3id.org/lambda-ber-schema/
is_a: ProteinAnnotation
attributes:
  feature_type:
    name: feature_type
    description: Type of structural feature
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: feature_type
    owner: StructuralFeature
    domain_of:
    - StructuralFeature
    range: StructuralFeatureTypeEnum
    required: true
  secondary_structure:
    name: secondary_structure
    description: Secondary structure assignment
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: secondary_structure
    owner: StructuralFeature
    domain_of:
    - StructuralFeature
    range: SecondaryStructureEnum
  solvent_accessibility:
    name: solvent_accessibility
    description: 'Relative solvent accessible surface area (range: 0-1)'
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: solvent_accessibility
    owner: StructuralFeature
    domain_of:
    - StructuralFeature
    range: float
    minimum_value: 0
    maximum_value: 1
  backbone_flexibility:
    name: backbone_flexibility
    description: B-factor or flexibility measure
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: backbone_flexibility
    owner: StructuralFeature
    domain_of:
    - StructuralFeature
    range: float
  disorder_probability:
    name: disorder_probability
    description: 'Probability of disorder (range: 0-1)'
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: disorder_probability
    owner: StructuralFeature
    domain_of:
    - StructuralFeature
    range: float
    minimum_value: 0
    maximum_value: 1
  conformational_state:
    name: conformational_state
    description: Conformational state descriptor
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: conformational_state
    owner: StructuralFeature
    domain_of:
    - StructuralFeature
    range: ConformationalStateEnum
  structural_motif:
    name: structural_motif
    description: Known structural motif
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: structural_motif
    owner: StructuralFeature
    domain_of:
    - StructuralFeature
    range: string
  domain_assignment:
    name: domain_assignment
    description: Domain database assignment (CATH, SCOP, Pfam)
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: domain_assignment
    owner: StructuralFeature
    domain_of:
    - StructuralFeature
    range: string
  domain_id:
    name: domain_id
    description: Domain identifier from domain database
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: domain_id
    owner: StructuralFeature
    domain_of:
    - StructuralFeature
    range: string
  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: StructuralFeature
    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: StructuralFeature
    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: StructuralFeature
    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: StructuralFeature
    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: StructuralFeature
    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: StructuralFeature
    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: StructuralFeature
    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: StructuralFeature
    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: StructuralFeature
    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: StructuralFeature
    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: StructuralFeature
    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: StructuralFeature
    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: StructuralFeature
    domain_of:
    - NamedThing
    - AttributeGroup
    range: string