Class: PostTranslationalModification

Post-translational modifications observed or predicted

URI: lambdaber:PostTranslationalModification

classDiagram class PostTranslationalModification click PostTranslationalModification href "../PostTranslationalModification/" ProteinAnnotation <|-- PostTranslationalModification click ProteinAnnotation href "../ProteinAnnotation/" PostTranslationalModification : annotation_method PostTranslationalModification : chain_id PostTranslationalModification : confidence_score PostTranslationalModification : description PostTranslationalModification : enzyme PostTranslationalModification : evidence_code PostTranslationalModification : evidence_type PostTranslationalModification --> "0..1" EvidenceTypeEnum : evidence_type click EvidenceTypeEnum href "../EvidenceTypeEnum/" PostTranslationalModification : functional_effect PostTranslationalModification : id PostTranslationalModification : mass_shift PostTranslationalModification : modification_group PostTranslationalModification : modification_type PostTranslationalModification --> "1" PTMTypeEnum : modification_type click PTMTypeEnum href "../PTMTypeEnum/" PostTranslationalModification : modified_residue PostTranslationalModification : pdb_entry PostTranslationalModification : protein_id PostTranslationalModification : publication_ids PostTranslationalModification : regulatory_role PostTranslationalModification : removal_enzyme PostTranslationalModification : residue_range PostTranslationalModification : source_database PostTranslationalModification --> "0..1" AnnotationSourceEnum : source_database click AnnotationSourceEnum href "../AnnotationSourceEnum/" PostTranslationalModification : title

Inheritance

NamedThing
- ProteinAnnotation
  - PostTranslationalModification

Slots

Name	Cardinality and Range	Description	Inheritance
modification_type	1 PTMTypeEnum	Type of PTM	direct
modified_residue	1 String	Residue that is modified	direct
modification_group	0..1 String	Chemical group added (e	direct
mass_shift	0..1 Float	Mass change due to modification (Da)	direct
functional_effect	0..1 String	Known functional effect of this PTM	direct
regulatory_role	0..1 String	Role in regulation	direct
enzyme	0..1 String	Enzyme responsible for modification	direct
removal_enzyme	0..1 String	Enzyme that removes modification	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	ptm_annotations	range	PostTranslationalModification
AggregatedProteinView	ptms	range	PostTranslationalModification

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: PostTranslationalModification
description: Post-translational modifications observed or predicted
from_schema: https://w3id.org/lambda-ber-schema/
is_a: ProteinAnnotation
attributes:
  modification_type:
    name: modification_type
    description: Type of PTM
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - PostTranslationalModification
    range: PTMTypeEnum
    required: true
  modified_residue:
    name: modified_residue
    description: Residue that is modified
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - PostTranslationalModification
    required: true
  modification_group:
    name: modification_group
    description: Chemical group added (e.g., 'phosphate', 'methyl')
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - PostTranslationalModification
  mass_shift:
    name: mass_shift
    description: Mass change due to modification (Da)
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - PostTranslationalModification
    range: float
    unit:
      ucum_code: Da
  functional_effect:
    name: functional_effect
    description: Known functional effect of this PTM
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - PostTranslationalModification
  regulatory_role:
    name: regulatory_role
    description: Role in regulation
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - PostTranslationalModification
  enzyme:
    name: enzyme
    description: Enzyme responsible for modification
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - PostTranslationalModification
  removal_enzyme:
    name: removal_enzyme
    description: Enzyme that removes modification
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - PostTranslationalModification

Induced

name: PostTranslationalModification
description: Post-translational modifications observed or predicted
from_schema: https://w3id.org/lambda-ber-schema/
is_a: ProteinAnnotation
attributes:
  modification_type:
    name: modification_type
    description: Type of PTM
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: modification_type
    owner: PostTranslationalModification
    domain_of:
    - PostTranslationalModification
    range: PTMTypeEnum
    required: true
  modified_residue:
    name: modified_residue
    description: Residue that is modified
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: modified_residue
    owner: PostTranslationalModification
    domain_of:
    - PostTranslationalModification
    range: string
    required: true
  modification_group:
    name: modification_group
    description: Chemical group added (e.g., 'phosphate', 'methyl')
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: modification_group
    owner: PostTranslationalModification
    domain_of:
    - PostTranslationalModification
    range: string
  mass_shift:
    name: mass_shift
    description: Mass change due to modification (Da)
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: mass_shift
    owner: PostTranslationalModification
    domain_of:
    - PostTranslationalModification
    range: float
    unit:
      ucum_code: Da
  functional_effect:
    name: functional_effect
    description: Known functional effect of this PTM
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: functional_effect
    owner: PostTranslationalModification
    domain_of:
    - PostTranslationalModification
    range: string
  regulatory_role:
    name: regulatory_role
    description: Role in regulation
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: regulatory_role
    owner: PostTranslationalModification
    domain_of:
    - PostTranslationalModification
    range: string
  enzyme:
    name: enzyme
    description: Enzyme responsible for modification
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: enzyme
    owner: PostTranslationalModification
    domain_of:
    - PostTranslationalModification
    range: string
  removal_enzyme:
    name: removal_enzyme
    description: Enzyme that removes modification
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: removal_enzyme
    owner: PostTranslationalModification
    domain_of:
    - PostTranslationalModification
    range: string
  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: PostTranslationalModification
    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: PostTranslationalModification
    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: PostTranslationalModification
    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: PostTranslationalModification
    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: PostTranslationalModification
    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: PostTranslationalModification
    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: PostTranslationalModification
    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: PostTranslationalModification
    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: PostTranslationalModification
    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: PostTranslationalModification
    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: PostTranslationalModification
    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: PostTranslationalModification
    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: PostTranslationalModification
    domain_of:
    - NamedThing
    - AttributeGroup
    range: string