Class: FunctionalSite

Functional sites including catalytic, binding, and regulatory sites

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

NamedThing
- ProteinAnnotation
  - FunctionalSite

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 (range: 0-1)	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 (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	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. Each should be specified
      as a string (e.g., "45", "120A").
    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 (range: 0-1)'
    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. Each should be specified
      as a string (e.g., "45", "120A").
    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 (range: 0-1)'
    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
    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: 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: 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: FunctionalSite
    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: FunctionalSite
    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: FunctionalSite
    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: FunctionalSite
    domain_of:
    - NamedThing
    - AttributeGroup
    range: string