Class: ProteinProteinInteraction

Protein-protein interactions and interfaces

URI: lambdaber:ProteinProteinInteraction

classDiagram class ProteinProteinInteraction click ProteinProteinInteraction href "../ProteinProteinInteraction/" ProteinAnnotation <|-- ProteinProteinInteraction click ProteinAnnotation href "../ProteinAnnotation/" ProteinProteinInteraction : annotation_method ProteinProteinInteraction : binding_energy ProteinProteinInteraction : biological_assembly ProteinProteinInteraction : chain_id ProteinProteinInteraction : complex_stability ProteinProteinInteraction --> "0..1" ComplexStabilityEnum : complex_stability click ComplexStabilityEnum href "../ComplexStabilityEnum/" ProteinProteinInteraction : confidence_score ProteinProteinInteraction : description ProteinProteinInteraction : dissociation_constant ProteinProteinInteraction : evidence_code ProteinProteinInteraction : evidence_type ProteinProteinInteraction --> "0..1" EvidenceTypeEnum : evidence_type click EvidenceTypeEnum href "../EvidenceTypeEnum/" ProteinProteinInteraction : id ProteinProteinInteraction : interaction_evidence ProteinProteinInteraction --> "*" InteractionEvidenceEnum : interaction_evidence click InteractionEvidenceEnum href "../InteractionEvidenceEnum/" ProteinProteinInteraction : interface_area ProteinProteinInteraction : interface_residues ProteinProteinInteraction : partner_chain_id ProteinProteinInteraction : partner_interface_residues ProteinProteinInteraction : partner_protein_id ProteinProteinInteraction : pdb_entry ProteinProteinInteraction : protein_id ProteinProteinInteraction : publication_ids ProteinProteinInteraction : residue_range ProteinProteinInteraction : source_database ProteinProteinInteraction --> "0..1" AnnotationSourceEnum : source_database click AnnotationSourceEnum href "../AnnotationSourceEnum/" ProteinProteinInteraction : title

Inheritance

NamedThing
- ProteinAnnotation
  - ProteinProteinInteraction

Slots

Name	Cardinality and Range	Description	Inheritance
partner_protein_id	1 String	UniProt ID of interacting partner	direct
partner_chain_id	0..1 String	Chain ID of interacting partner	direct
interface_residues	* String	Residues at the interaction interface	direct
partner_interface_residues	* String	Partner residues at the interaction interface	direct
interface_area	0..1 Float	Buried surface area at interface (Ų)	direct
binding_energy	0..1 Float	Calculated binding energy (kcal/mol)	direct
dissociation_constant	0..1 Float	Experimental Kd if available	direct
complex_stability	0..1 ComplexStabilityEnum	Stability assessment of the complex	direct
biological_assembly	0..1 Boolean	Whether this represents a biological assembly	direct
interaction_evidence	* InteractionEvidenceEnum	Evidence for this interaction	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	protein_interactions	range	ProteinProteinInteraction
AggregatedProteinView	protein_interactions	range	ProteinProteinInteraction

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: ProteinProteinInteraction
description: Protein-protein interactions and interfaces
from_schema: https://w3id.org/lambda-ber-schema/
is_a: ProteinAnnotation
attributes:
  partner_protein_id:
    name: partner_protein_id
    description: UniProt ID of interacting partner
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - ProteinProteinInteraction
    required: true
  partner_chain_id:
    name: partner_chain_id
    description: Chain ID of interacting partner
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - ProteinProteinInteraction
  interface_residues:
    name: interface_residues
    description: Residues at the interaction interface
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - ProteinProteinInteraction
    multivalued: true
  partner_interface_residues:
    name: partner_interface_residues
    description: Partner residues at the interaction interface
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - ProteinProteinInteraction
    multivalued: true
  interface_area:
    name: interface_area
    description: Buried surface area at interface (Ų)
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - ProteinProteinInteraction
    range: float
    unit:
      ucum_code: Angstrom2
  binding_energy:
    name: binding_energy
    description: Calculated binding energy (kcal/mol)
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - ProteinProteinInteraction
    range: float
    unit:
      ucum_code: kcal/mol
  dissociation_constant:
    name: dissociation_constant
    description: Experimental Kd if available
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - ProteinProteinInteraction
    range: float
  complex_stability:
    name: complex_stability
    description: Stability assessment of the complex
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - ProteinProteinInteraction
    range: ComplexStabilityEnum
  biological_assembly:
    name: biological_assembly
    description: Whether this represents a biological assembly
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - ProteinProteinInteraction
    range: boolean
  interaction_evidence:
    name: interaction_evidence
    description: Evidence for this interaction
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - ProteinProteinInteraction
    range: InteractionEvidenceEnum
    multivalued: true

Induced

name: ProteinProteinInteraction
description: Protein-protein interactions and interfaces
from_schema: https://w3id.org/lambda-ber-schema/
is_a: ProteinAnnotation
attributes:
  partner_protein_id:
    name: partner_protein_id
    description: UniProt ID of interacting partner
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: partner_protein_id
    owner: ProteinProteinInteraction
    domain_of:
    - ProteinProteinInteraction
    range: string
    required: true
  partner_chain_id:
    name: partner_chain_id
    description: Chain ID of interacting partner
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: partner_chain_id
    owner: ProteinProteinInteraction
    domain_of:
    - ProteinProteinInteraction
    range: string
  interface_residues:
    name: interface_residues
    description: Residues at the interaction interface
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: interface_residues
    owner: ProteinProteinInteraction
    domain_of:
    - ProteinProteinInteraction
    range: string
    multivalued: true
  partner_interface_residues:
    name: partner_interface_residues
    description: Partner residues at the interaction interface
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: partner_interface_residues
    owner: ProteinProteinInteraction
    domain_of:
    - ProteinProteinInteraction
    range: string
    multivalued: true
  interface_area:
    name: interface_area
    description: Buried surface area at interface (Ų)
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: interface_area
    owner: ProteinProteinInteraction
    domain_of:
    - ProteinProteinInteraction
    range: float
    unit:
      ucum_code: Angstrom2
  binding_energy:
    name: binding_energy
    description: Calculated binding energy (kcal/mol)
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: binding_energy
    owner: ProteinProteinInteraction
    domain_of:
    - ProteinProteinInteraction
    range: float
    unit:
      ucum_code: kcal/mol
  dissociation_constant:
    name: dissociation_constant
    description: Experimental Kd if available
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: dissociation_constant
    owner: ProteinProteinInteraction
    domain_of:
    - ProteinProteinInteraction
    range: float
  complex_stability:
    name: complex_stability
    description: Stability assessment of the complex
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: complex_stability
    owner: ProteinProteinInteraction
    domain_of:
    - ProteinProteinInteraction
    range: ComplexStabilityEnum
  biological_assembly:
    name: biological_assembly
    description: Whether this represents a biological assembly
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: biological_assembly
    owner: ProteinProteinInteraction
    domain_of:
    - ProteinProteinInteraction
    range: boolean
  interaction_evidence:
    name: interaction_evidence
    description: Evidence for this interaction
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: interaction_evidence
    owner: ProteinProteinInteraction
    domain_of:
    - ProteinProteinInteraction
    range: InteractionEvidenceEnum
    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: ProteinProteinInteraction
    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: ProteinProteinInteraction
    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: ProteinProteinInteraction
    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: ProteinProteinInteraction
    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: ProteinProteinInteraction
    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: ProteinProteinInteraction
    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: ProteinProteinInteraction
    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: ProteinProteinInteraction
    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: ProteinProteinInteraction
    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: ProteinProteinInteraction
    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: ProteinProteinInteraction
    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: ProteinProteinInteraction
    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: ProteinProteinInteraction
    domain_of:
    - NamedThing
    - AttributeGroup
    range: string