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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 direct
backbone_flexibility 0..1
Float		 B-factor or flexibility measure direct
disorder_probability 0..1
Float		 Probability of disorder (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 (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 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
    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 (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
    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 (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
  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: 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: PubMed IDs supporting this annotation
    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]+$
  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
    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
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: description
    owner: StructuralFeature
    domain_of:
    - NamedThing
    - AttributeGroup
    range: string