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Class: FunctionalSite

Functional sites including catalytic, binding, and regulatory sites

URI: lambdaber:FunctionalSite

classDiagram class FunctionalSite click FunctionalSite href "../FunctionalSite/" ProteinAnnotation <|-- FunctionalSite click ProteinAnnotation href "../ProteinAnnotation/" FunctionalSite : annotation_method FunctionalSite : chain_id FunctionalSite : confidence_score FunctionalSite : conservation_score FunctionalSite : description FunctionalSite : ec_number FunctionalSite : evidence_code FunctionalSite : evidence_type FunctionalSite --> "0..1" EvidenceTypeEnum : evidence_type click EvidenceTypeEnum href "../EvidenceTypeEnum/" FunctionalSite : functional_importance FunctionalSite : go_terms FunctionalSite : id FunctionalSite : ligand_interactions FunctionalSite --> "*" LigandInteraction : ligand_interactions click LigandInteraction href "../LigandInteraction/" FunctionalSite : pdb_entry FunctionalSite : protein_id FunctionalSite : publication_ids FunctionalSite : residue_range FunctionalSite : residues FunctionalSite : site_name FunctionalSite : site_type FunctionalSite --> "1" FunctionalSiteTypeEnum : site_type click FunctionalSiteTypeEnum href "../FunctionalSiteTypeEnum/" FunctionalSite : source_database FunctionalSite --> "0..1" AnnotationSourceEnum : source_database click AnnotationSourceEnum href "../AnnotationSourceEnum/" FunctionalSite : title

Inheritance

Slots

Name Cardinality and Range Description Inheritance
site_type 1
FunctionalSiteTypeEnum		 Type of functional site direct
site_name 0..1
String		 Common name for this site direct
residues *
String		 List of residues forming the functional site direct
ligand_interactions *
LigandInteraction		 Ligands that interact with this site direct
conservation_score 0..1
Float		 Evolutionary conservation score direct
functional_importance 0..1
String		 Description of functional importance direct
go_terms *
Uriorcurie		 Associated Gene Ontology terms direct
ec_number 0..1
String		 Enzyme Commission number for catalytic sites 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 functional_sites range FunctionalSite
AggregatedProteinView functional_sites range FunctionalSite

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: FunctionalSite
description: Functional sites including catalytic, binding, and regulatory sites
from_schema: https://w3id.org/lambda-ber-schema/
is_a: ProteinAnnotation
attributes:
  site_type:
    name: site_type
    description: Type of functional site
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - FunctionalSite
    range: FunctionalSiteTypeEnum
    required: true
  site_name:
    name: site_name
    description: Common name for this site
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - FunctionalSite
  residues:
    name: residues
    description: List of residues forming the functional site
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - FunctionalSite
    multivalued: true
  ligand_interactions:
    name: ligand_interactions
    description: Ligands that interact with this site
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    domain_of:
    - Sample
    - FunctionalSite
    - AggregatedProteinView
    range: LigandInteraction
    multivalued: true
    inlined: true
    inlined_as_list: true
  conservation_score:
    name: conservation_score
    description: Evolutionary conservation score
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - FunctionalSite
    - EvolutionaryConservation
    range: float
    minimum_value: 0
    maximum_value: 1
  functional_importance:
    name: functional_importance
    description: Description of functional importance
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - FunctionalSite
  go_terms:
    name: go_terms
    description: Associated Gene Ontology terms
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - FunctionalSite
    range: uriorcurie
    multivalued: true
  ec_number:
    name: ec_number
    description: Enzyme Commission number for catalytic sites
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - FunctionalSite
    pattern: ^[0-9]+\.[0-9]+\.[0-9]+\.[0-9]+$

Induced

name: FunctionalSite
description: Functional sites including catalytic, binding, and regulatory sites
from_schema: https://w3id.org/lambda-ber-schema/
is_a: ProteinAnnotation
attributes:
  site_type:
    name: site_type
    description: Type of functional site
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: site_type
    owner: FunctionalSite
    domain_of:
    - FunctionalSite
    range: FunctionalSiteTypeEnum
    required: true
  site_name:
    name: site_name
    description: Common name for this site
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: site_name
    owner: FunctionalSite
    domain_of:
    - FunctionalSite
    range: string
  residues:
    name: residues
    description: List of residues forming the functional site
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: residues
    owner: FunctionalSite
    domain_of:
    - FunctionalSite
    range: string
    multivalued: true
  ligand_interactions:
    name: ligand_interactions
    description: Ligands that interact with this site
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    alias: ligand_interactions
    owner: FunctionalSite
    domain_of:
    - Sample
    - FunctionalSite
    - AggregatedProteinView
    range: LigandInteraction
    multivalued: true
    inlined: true
    inlined_as_list: true
  conservation_score:
    name: conservation_score
    description: Evolutionary conservation score
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: conservation_score
    owner: FunctionalSite
    domain_of:
    - FunctionalSite
    - EvolutionaryConservation
    range: float
    minimum_value: 0
    maximum_value: 1
  functional_importance:
    name: functional_importance
    description: Description of functional importance
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: functional_importance
    owner: FunctionalSite
    domain_of:
    - FunctionalSite
    range: string
  go_terms:
    name: go_terms
    description: Associated Gene Ontology terms
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: go_terms
    owner: FunctionalSite
    domain_of:
    - FunctionalSite
    range: uriorcurie
    multivalued: true
  ec_number:
    name: ec_number
    description: Enzyme Commission number for catalytic sites
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: ec_number
    owner: FunctionalSite
    domain_of:
    - FunctionalSite
    range: string
    pattern: ^[0-9]+\.[0-9]+\.[0-9]+\.[0-9]+$
  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: FunctionalSite
    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: FunctionalSite
    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: FunctionalSite
    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: FunctionalSite
    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: FunctionalSite
    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: FunctionalSite
    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: FunctionalSite
    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: FunctionalSite
    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: FunctionalSite
    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: FunctionalSite
    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: FunctionalSite
    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: FunctionalSite
    domain_of:
    - NamedThing
    range: string
  description:
    name: description
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: description
    owner: FunctionalSite
    domain_of:
    - NamedThing
    - AttributeGroup
    range: string