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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

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