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Class: Modification

A sequence that is different from some reference sequence.

URI: synbio:Modification

classDiagram class Modification Part <|-- Modification Modification : aa_change Modification : bio_safety_level Modification : category Modification : creator Modification : curated_enzyme_name Modification : curated_gene_symbols Modification : curated_protein_name Modification : curated_uniprot_accession Modification : descriptor Modification : el_name_long Modification : el_name_short Modification : element_organism Modification : id Modification : modification_type Modification : modifications_genes Modification : notes Modification : part_ofs Modification : position Modification : principal_investigator Modification : size_bp Modification : status Modification : subcategory_size

Inheritance

Slots

Name Cardinality and Range Description Inheritance
id 1..1
xsd:string		 None direct
aa_change 0..1
xsd:string		 None direct
bio_safety_level 1..1
BioSafetyLevelEnum		 None direct
category 0..1
CategoryEnum		 None direct
creator 1..1
Person		 None direct
curated_enzyme_name 0..1
xsd:string		 corresponds to this enzyme, as determined by expert review direct
curated_gene_symbols 0..*
xsd:string		 corresponds to these genes, as determined by expert review direct
curated_protein_name 0..1
xsd:string		 corresponds to this protein, as determined by expert review direct
curated_uniprot_accession 0..1
xsd:string		 corresponds to this Uniprot entry, as determined by expert review direct
descriptor 0..1
DescriptorEnum		 None direct
el_name_long 1..1
xsd:string		 None direct
el_name_short 0..1
xsd:string		 None direct
element_organism 0..1
xsd:string		 None direct
modification_type 0..1
ModificationTypeEnum		 None direct
modifications_genes 0..1
xsd:string		 None direct
notes 0..1
xsd:string		 None direct
part_ofs 0..*
xsd:string		 appears in these genetic/genomic strains direct
position 0..1
xsd:string		 None direct
principal_investigator 1..1
Person		 None direct
size_bp 0..1
xsd:integer		 None direct
status 1..1
StatusEnum		 None direct
subcategory_size 0..1
xsd:string		 None direct

Usages

used by used in type used
PartsSequence associated_part range Modification
Database modification_set range Modification

Identifier and Mapping Information

Schema Source

  • from schema: https://example.com/synbio

Mappings

Mapping Type Mapped Value
self ['synbio:Modification']
native ['synbio:Modification']
exact ['SO:0001059']

LinkML Source

Direct

name: Modification
description: A sequence that is different from some reference sequence.
from_schema: https://example.com/synbio
exact_mappings:
- SO:0001059
rank: 1000
is_a: Part
slots:
- id
- aa_change
- bio_safety_level
- category
- creator
- curated_enzyme_name
- curated_gene_symbols
- curated_protein_name
- curated_uniprot_accession
- descriptor
- el_name_long
- el_name_short
- element_organism
- modification_type
- modifications_genes
- notes
- part_ofs
- position
- principal_investigator
- size_bp
- status
- subcategory_size
slot_usage:
  id:
    name: id
    domain_of:
    - PartsSequence
    - Strain
    - Modification
    - Organism
    - Person
    - PartsSequence
    - Strain
    - Modification
    - Organism
    - Person
    pattern: ^IF:\d+$
  bio_safety_level:
    name: bio_safety_level
    domain_of:
    - Strain
    - Modification
    - Strain
    - Modification
    required: true
  creator:
    name: creator
    domain_of:
    - Strain
    - Modification
    - Strain
    - Modification
    required: true
  status:
    name: status
    domain_of:
    - Strain
    - Modification
    - Strain
    - Modification
    required: true

Induced

name: Modification
description: A sequence that is different from some reference sequence.
from_schema: https://example.com/synbio
exact_mappings:
- SO:0001059
rank: 1000
is_a: Part
slot_usage:
  id:
    name: id
    domain_of:
    - PartsSequence
    - Strain
    - Modification
    - Organism
    - Person
    - PartsSequence
    - Strain
    - Modification
    - Organism
    - Person
    pattern: ^IF:\d+$
  bio_safety_level:
    name: bio_safety_level
    domain_of:
    - Strain
    - Modification
    - Strain
    - Modification
    required: true
  creator:
    name: creator
    domain_of:
    - Strain
    - Modification
    - Strain
    - Modification
    required: true
  status:
    name: status
    domain_of:
    - Strain
    - Modification
    - Strain
    - Modification
    required: true
attributes:
  id:
    name: id
    from_schema: https://example.com/synbio
    rank: 1000
    identifier: true
    alias: id
    owner: Modification
    domain_of:
    - PartsSequence
    - Strain
    - Modification
    - Organism
    - Person
    - PartsSequence
    - Strain
    - Modification
    - Organism
    - Person
    range: string
    pattern: ^IF:\d+$
  aa_change:
    name: aa_change
    from_schema: https://example.com/synbio
    rank: 1000
    alias: aa_change
    owner: Modification
    domain_of:
    - Modification
    range: string
  bio_safety_level:
    name: bio_safety_level
    from_schema: https://example.com/synbio
    rank: 1000
    alias: bio_safety_level
    owner: Modification
    domain_of:
    - Strain
    - Modification
    - Strain
    - Modification
    range: BioSafetyLevelEnum
    required: true
  category:
    name: category
    examples:
    - value: biosynthetic
    from_schema: https://example.com/synbio
    rank: 1000
    alias: category
    owner: Modification
    domain_of:
    - Modification
    range: CategoryEnum
  creator:
    name: creator
    from_schema: https://example.com/synbio
    rank: 1000
    alias: creator
    owner: Modification
    domain_of:
    - Strain
    - Modification
    - Strain
    - Modification
    range: Person
    required: true
  curated_enzyme_name:
    name: curated_enzyme_name
    description: corresponds to this enzyme, as determined by expert review
    from_schema: https://example.com/synbio
    rank: 1000
    alias: curated_enzyme_name
    owner: Modification
    domain_of:
    - Modification
    range: string
  curated_gene_symbols:
    name: curated_gene_symbols
    description: corresponds to these genes, as determined by expert review
    from_schema: https://example.com/synbio
    rank: 1000
    multivalued: true
    alias: curated_gene_symbols
    owner: Modification
    domain_of:
    - Modification
    range: string
  curated_protein_name:
    name: curated_protein_name
    description: corresponds to this protein, as determined by expert review
    from_schema: https://example.com/synbio
    rank: 1000
    alias: curated_protein_name
    owner: Modification
    domain_of:
    - Modification
    range: string
  curated_uniprot_accession:
    name: curated_uniprot_accession
    description: corresponds to this Uniprot entry, as determined by expert review
    from_schema: https://example.com/synbio
    rank: 1000
    alias: curated_uniprot_accession
    owner: Modification
    domain_of:
    - Modification
    range: string
  descriptor:
    name: descriptor
    examples:
    - value: epitope
    from_schema: https://example.com/synbio
    rank: 1000
    alias: descriptor
    owner: Modification
    domain_of:
    - Modification
    range: DescriptorEnum
  el_name_long:
    name: el_name_long
    from_schema: https://example.com/synbio
    rank: 1000
    alias: el_name_long
    owner: Modification
    domain_of:
    - Modification
    range: string
    required: true
  el_name_short:
    name: el_name_short
    from_schema: https://example.com/synbio
    rank: 1000
    alias: el_name_short
    owner: Modification
    domain_of:
    - Modification
    range: string
  element_organism:
    name: element_organism
    from_schema: https://example.com/synbio
    rank: 1000
    alias: element_organism
    owner: Modification
    domain_of:
    - Modification
    range: string
  modification_type:
    name: modification_type
    examples:
    - value: amber stop codon
    from_schema: https://example.com/synbio
    rank: 1000
    alias: modification_type
    owner: Modification
    domain_of:
    - Modification
    range: ModificationTypeEnum
  modifications_genes:
    name: modifications_genes
    from_schema: https://example.com/synbio
    rank: 1000
    alias: modifications_genes
    owner: Modification
    domain_of:
    - Modification
    range: string
  notes:
    name: notes
    from_schema: https://example.com/synbio
    exact_mappings:
    - IAO:0000634
    rank: 1000
    alias: notes
    owner: Modification
    domain_of:
    - Strain
    - Modification
    range: string
  part_ofs:
    name: part_ofs
    description: appears in these genetic/genomic strains
    from_schema: https://example.com/synbio
    rank: 1000
    multivalued: true
    alias: part_ofs
    owner: Modification
    domain_of:
    - Modification
    range: string
  position:
    name: position
    from_schema: https://example.com/synbio
    rank: 1000
    alias: position
    owner: Modification
    domain_of:
    - Modification
    range: string
  principal_investigator:
    name: principal_investigator
    from_schema: https://example.com/synbio
    exact_mappings:
    - OBI:0000103
    rank: 1000
    alias: principal_investigator
    owner: Modification
    domain_of:
    - Strain
    - Modification
    range: Person
    required: true
  size_bp:
    name: size_bp
    from_schema: https://example.com/synbio
    rank: 1000
    alias: size_bp
    owner: Modification
    domain_of:
    - Modification
    range: integer
  status:
    name: status
    from_schema: https://example.com/synbio
    rank: 1000
    alias: status
    owner: Modification
    domain_of:
    - Strain
    - Modification
    - Strain
    - Modification
    range: StatusEnum
    required: true
  subcategory_size:
    name: subcategory_size
    from_schema: https://example.com/synbio
    rank: 1000
    alias: subcategory_size
    owner: Modification
    domain_of:
    - Modification
    range: string