Class: Strain

An population of organisms whose characteristics vary from the base organism due to natural selection, breeding, etc.

classDiagram class Strain Part <|-- Strain Strain : bio_safety_level Strain : biosample_accessions Strain : creator Strain : external_urls Strain : funding_source Strain : genome_accessions Strain : genotype_phenotype Strain : has_parts Strain : host_organism Strain : id Strain : intellectual_property Strain : keywords Strain : name Strain : notes Strain : principal_investigator Strain : references Strain : selection_markers Strain : status Strain : summary

Inheritance

Part
- Strain

Slots

Name	Cardinality and Range	Description	Inheritance
bio_safety_level	0..1 BioSafetyLevelEnum	None	direct
biosample_accessions	0..* xsd:string	An entry from NCBI's BioSample database	direct
creator	0..1 Person	None	direct
external_urls	0..* xsd:string	None	direct
funding_source	0..1 FundingSourceEnum	None	direct
genome_accessions	0..* xsd:string	An entry from NCBI's Genome database	direct
genotype_phenotype	0..1 xsd:string	None	direct
has_parts	0..* xsd:string	contains these genetic/genomic modifications	direct
host_organism	0..1 Organism	None	direct
id	1..1 xsd:string	None	direct
intellectual_property	0..1 xsd:string	None	direct
keywords	0..1 xsd:string	None	direct
name	0..1 xsd:string	None	direct
notes	0..1 xsd:string	None	direct
principal_investigator	1..1 Person	None	direct
references	0..1 xsd:string	None	direct
selection_markers	0..* xsd:string	A genetic feature that encodes a trait used for artificial selection of a subpopulation	direct
status	0..1 StatusEnum	None	direct
summary	0..1 xsd:string	None	direct

Usages

used by	used in	type	used
Database	strain_set	range	Strain

Identifier and Mapping Information

Schema Source

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

Mappings

Mapping Type	Mapped Value
self	['synbio:Strain']
native	['synbio:Strain']
exact	['OBI:0001185']

LinkML Source

Direct

name: Strain
description: An population of organisms whose characteristics vary from the base organism
  due to natural selection, breeding, etc.
from_schema: https://example.com/synbio
exact_mappings:
- OBI:0001185
rank: 1000
is_a: Part
slots:
- bio_safety_level
- biosample_accessions
- creator
- external_urls
- funding_source
- genome_accessions
- genotype_phenotype
- has_parts
- host_organism
- id
- intellectual_property
- keywords
- name
- notes
- principal_investigator
- references
- selection_markers
- status
- summary
slot_usage:
  id:
    name: id
    domain_of:
    - PartsSequence
    - Strain
    - Modification
    - Organism
    - Person
    - PartsSequence
    - Strain
    - Modification
    - Organism
    - Person
    pattern: MS:\d+

Induced

name: Strain
description: An population of organisms whose characteristics vary from the base organism
  due to natural selection, breeding, etc.
from_schema: https://example.com/synbio
exact_mappings:
- OBI:0001185
rank: 1000
is_a: Part
slot_usage:
  id:
    name: id
    domain_of:
    - PartsSequence
    - Strain
    - Modification
    - Organism
    - Person
    - PartsSequence
    - Strain
    - Modification
    - Organism
    - Person
    pattern: MS:\d+
attributes:
  bio_safety_level:
    name: bio_safety_level
    examples:
    - value: Level 1
    from_schema: https://example.com/synbio
    rank: 1000
    alias: bio_safety_level
    owner: Strain
    domain_of:
    - Strain
    - Modification
    range: BioSafetyLevelEnum
  biosample_accessions:
    name: biosample_accessions
    description: An entry from NCBI's BioSample database
    examples:
    - value: SAMN29939549
    from_schema: https://example.com/synbio
    rank: 1000
    multivalued: true
    alias: biosample_accessions
    owner: Strain
    domain_of:
    - Strain
    range: string
  creator:
    name: creator
    from_schema: https://example.com/synbio
    rank: 1000
    alias: creator
    owner: Strain
    domain_of:
    - Strain
    - Modification
    range: Person
  external_urls:
    name: external_urls
    todos:
    - strains have selection markers
    - enforce sane URLs? resolvable? heterogeneous delimiters!
    from_schema: https://example.com/synbio
    rank: 1000
    multivalued: true
    alias: external_urls
    owner: Strain
    domain_of:
    - Strain
    range: string
  funding_source:
    name: funding_source
    from_schema: https://example.com/synbio
    rank: 1000
    alias: funding_source
    owner: Strain
    domain_of:
    - Strain
    range: FundingSourceEnum
  genome_accessions:
    name: genome_accessions
    description: An entry from NCBI's Genome database
    examples:
    - value: CP101925
    from_schema: https://example.com/synbio
    rank: 1000
    multivalued: true
    alias: genome_accessions
    owner: Strain
    domain_of:
    - Strain
    range: string
  genotype_phenotype:
    name: genotype_phenotype
    from_schema: https://example.com/synbio
    rank: 1000
    alias: genotype_phenotype
    owner: Strain
    domain_of:
    - Strain
    range: string
  has_parts:
    name: has_parts
    description: contains these genetic/genomic modifications
    from_schema: https://example.com/synbio
    rank: 1000
    multivalued: true
    alias: has_parts
    owner: Strain
    domain_of:
    - Strain
    range: string
  host_organism:
    name: host_organism
    from_schema: https://example.com/synbio
    rank: 1000
    alias: host_organism
    owner: Strain
    domain_of:
    - Strain
    range: Organism
  id:
    name: id
    from_schema: https://example.com/synbio
    rank: 1000
    identifier: true
    alias: id
    owner: Strain
    domain_of:
    - PartsSequence
    - Strain
    - Modification
    - Organism
    - Person
    - PartsSequence
    - Strain
    - Modification
    - Organism
    - Person
    range: string
    pattern: MS:\d+
  intellectual_property:
    name: intellectual_property
    todos:
    - enum range?
    from_schema: https://example.com/synbio
    rank: 1000
    alias: intellectual_property
    owner: Strain
    domain_of:
    - Strain
    range: string
  keywords:
    name: keywords
    from_schema: https://example.com/synbio
    exact_mappings:
    - IAO:0000630
    rank: 1000
    alias: keywords
    owner: Strain
    domain_of:
    - Strain
    range: string
  name:
    name: name
    from_schema: https://example.com/synbio
    rank: 1000
    alias: name
    owner: Strain
    domain_of:
    - Strain
    - Organism
    range: string
  notes:
    name: notes
    from_schema: https://example.com/synbio
    exact_mappings:
    - IAO:0000634
    rank: 1000
    alias: notes
    owner: Strain
    domain_of:
    - Strain
    - Modification
    range: string
  principal_investigator:
    name: principal_investigator
    from_schema: https://example.com/synbio
    exact_mappings:
    - OBI:0000103
    rank: 1000
    alias: principal_investigator
    owner: Strain
    domain_of:
    - Strain
    - Modification
    range: Person
    required: true
  references:
    name: references
    from_schema: https://example.com/synbio
    exact_mappings:
    - IAO:0000320
    rank: 1000
    alias: references
    owner: Strain
    domain_of:
    - Strain
    range: string
  selection_markers:
    name: selection_markers
    description: A genetic feature that encodes a trait used for artificial selection
      of a subpopulation
    todos:
    - strains and plasmids can have selection markers
    examples:
    - value: Tryptophan Auxotroph
    - value: Ampicillin
    from_schema: https://example.com/synbio
    exact_mappings:
    - SO:0002232
    rank: 1000
    multivalued: true
    alias: selection_markers
    owner: Strain
    domain_of:
    - Strain
    range: string
  status:
    name: status
    from_schema: https://example.com/synbio
    rank: 1000
    alias: status
    owner: Strain
    domain_of:
    - Strain
    - Modification
    range: StatusEnum
  summary:
    name: summary
    from_schema: https://example.com/synbio
    rank: 1000
    alias: summary
    owner: Strain
    domain_of:
    - Strain
    range: string