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