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Class: ProteinAnnotation

Base class for all protein-related functional and structural annotations

URI: lambdaber:ProteinAnnotation

classDiagram class ProteinAnnotation click ProteinAnnotation href "../ProteinAnnotation/" NamedThing <|-- ProteinAnnotation click NamedThing href "../NamedThing/" ProteinAnnotation <|-- FunctionalSite click FunctionalSite href "../FunctionalSite/" ProteinAnnotation <|-- StructuralFeature click StructuralFeature href "../StructuralFeature/" ProteinAnnotation <|-- ProteinProteinInteraction click ProteinProteinInteraction href "../ProteinProteinInteraction/" ProteinAnnotation <|-- MutationEffect click MutationEffect href "../MutationEffect/" ProteinAnnotation <|-- PostTranslationalModification click PostTranslationalModification href "../PostTranslationalModification/" ProteinAnnotation <|-- EvolutionaryConservation click EvolutionaryConservation href "../EvolutionaryConservation/" ProteinAnnotation : annotation_method ProteinAnnotation : chain_id ProteinAnnotation : confidence_score ProteinAnnotation : description ProteinAnnotation : evidence_code ProteinAnnotation : evidence_type ProteinAnnotation --> "0..1" EvidenceTypeEnum : evidence_type click EvidenceTypeEnum href "../EvidenceTypeEnum/" ProteinAnnotation : id ProteinAnnotation : pdb_entry ProteinAnnotation : protein_id ProteinAnnotation : publication_ids ProteinAnnotation : residue_range ProteinAnnotation : source_database ProteinAnnotation --> "0..1" AnnotationSourceEnum : source_database click AnnotationSourceEnum href "../AnnotationSourceEnum/" ProteinAnnotation : title

Inheritance

Slots

Name Cardinality and Range Description Inheritance
protein_id 1
String		 UniProt accession number direct
pdb_entry 0..1
String		 PDB identifier direct
chain_id 0..1
String		 Chain identifier in the PDB structure direct
residue_range 0..1
String		 Range of residues (e direct
confidence_score 0..1
Float		 Confidence score for the annotation (0-1) direct
evidence_type 0..1
EvidenceTypeEnum		 Type of evidence supporting this annotation direct
evidence_code 0..1
Uriorcurie		 Evidence and Conclusion Ontology (ECO) code direct
source_database 0..1
AnnotationSourceEnum		 Source database or resource that provided this annotation direct
annotation_method 0..1
String		 Computational or experimental method used direct
publication_ids *
String		 PubMed IDs supporting this annotation direct
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

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: ProteinAnnotation
description: Base class for all protein-related functional and structural annotations
from_schema: https://w3id.org/lambda-ber-schema/
is_a: NamedThing
attributes:
  protein_id:
    name: protein_id
    description: UniProt accession number
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - ProteinAnnotation
    - ConformationalEnsemble
    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
    domain_of:
    - ProteinAnnotation
    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
    domain_of:
    - ProteinAnnotation
    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
    domain_of:
    - ProteinAnnotation
  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
    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
    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
    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
    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
    domain_of:
    - ProteinAnnotation
  publication_ids:
    name: publication_ids
    description: PubMed IDs supporting this annotation
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - ProteinAnnotation
    multivalued: true
    pattern: ^PMID:[0-9]+$

Induced

name: ProteinAnnotation
description: Base class for all protein-related functional and structural annotations
from_schema: https://w3id.org/lambda-ber-schema/
is_a: NamedThing
attributes:
  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: ProteinAnnotation
    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: ProteinAnnotation
    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: ProteinAnnotation
    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: ProteinAnnotation
    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: ProteinAnnotation
    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: ProteinAnnotation
    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: ProteinAnnotation
    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: ProteinAnnotation
    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: ProteinAnnotation
    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: ProteinAnnotation
    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: ProteinAnnotation
    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: ProteinAnnotation
    domain_of:
    - NamedThing
    range: string
  description:
    name: description
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: description
    owner: ProteinAnnotation
    domain_of:
    - NamedThing
    - AttributeGroup
    range: string