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Class: Organism

Reference data representing a biological identity (strain, isolate,

engineered construct, etc.) that can be instantiated by multiple

physical samples.

__

REPLACES: This class replaces the former Strain class, which was modeled

as a PurchasedMaterial subclass. That approach did not accommodate strains

engineered in-house or received from collaborators, nor did it cleanly

separate biological identity from physical samples. Additionally, the term

"strain" implies purity that cannot always be guaranteed; this class

represents the intended or characterized biological identity.

__

Relationship to samples:

_ - One organism can have many AMP2UserSample instances_

_ - AMP2UserSample.organism_ref points here_

_ - CultureGrowth activities reference via organism_ref (aliased as strain_ref)_

URI: basalt_schema:Organism

 classDiagram
    class Organism
    click Organism href "../Organism/"
      Organism : component_description

      Organism : component_name

      Organism : construct_component





        Organism --> "0..1" ConstructComponentEnum : construct_component
        click ConstructComponentEnum href "../ConstructComponentEnum/"



      Organism : description

      Organism : donor_organism

      Organism : encoded_traits

      Organism : genotype_segment_category





        Organism --> "0..1" GenotypeSegmentEnum : genotype_segment_category
        click GenotypeSegmentEnum href "../GenotypeSegmentEnum/"



      Organism : genotype_segment_name

      Organism : host_common_name

      Organism : host_spec_range

      Organism : host_taxid

      Organism : id

      Organism : modification_method





        Organism --> "0..1" ModificationMethodEnum : modification_method
        click ModificationMethodEnum href "../ModificationMethodEnum/"



      Organism : name

      Organism : organism_name

      Organism : pathogenicity

      Organism : phenotype

      Organism : propagation

      Organism : strain_description

      Organism : strain_identifier

      Organism : strain_mutation

      Organism : strain_source

      Organism : strain_type





        Organism --> "0..1" StrainTypeEnum : strain_type
        click StrainTypeEnum href "../StrainTypeEnum/"



      Organism : taxonomy_id

      Organism : trait





        Organism --> "0..1" IntendedTraitEnum : trait
        click IntendedTraitEnum href "../IntendedTraitEnum/"



      Organism : trophic_level





        Organism --> "0..1" TrophicLevelEnum : trophic_level
        click TrophicLevelEnum href "../TrophicLevelEnum/"

Slots

Name Cardinality and Range Description Inheritance
name 1
String		 Human-readable name for the organism direct
description 0..1
String		 Human-readable description for the entity or activity direct
strain_identifier 1
String		 Primary human-readable identifier for this organism direct
organism_name 0..1
String		 Scientific name of the organism (e direct
taxonomy_id 0..1
String		 NCBI taxon ID for the organism direct
host_common_name 0..1
String		 Common name for the host organism (e direct
host_taxid 0..1
String		 NCBI taxon ID direct
strain_source 0..1
String		 Provenance of the organism direct
strain_type 0..1
StrainTypeEnum		 Type of strain/organism (bacterial, fungal, archaeal, etc direct
modification_method 0..1
ModificationMethodEnum		 Method used to introduce genetic modification direct
strain_description 0..1
String		 A brief description of the modifications that comprise this strain direct
strain_mutation 0..1
String		 Primary genetic modification or plasmid carried (e direct
phenotype 0..1
String		 Provide the intedned phenotype of hte modified organism direct
trait 0..1
IntendedTraitEnum		 Trait category for the organism direct
encoded_traits 0..1
String		 Should include key traits like antibiotic resistance or xenobiotic direct
genotype_segment_category 0..1
GenotypeSegmentEnum		 Category of genetic modification or segment direct
genotype_segment_name 0..1
String		 Provide a name that describes the genotype modification engineered direct
component_name 0..1
String		 Provide a one-to-three word name based on the component direct
construct_component 0..1
ConstructComponentEnum		 Select the construct component type direct
donor_organism 0..1
String		 Provide the scientific name (genus and species) of the organism from which th... direct
component_description 0..1
String		 Provide a short statement describing the function of the construct direct
trophic_level 0..1
TrophicLevelEnum		 Trophic levels are the feeding position in a food chain direct
pathogenicity 0..1
String		 To what is the entity pathogenic, e direct
host_spec_range 0..1
String		 The range and diversity of host species that an organism is capable of infect... direct
propagation 0..1
String		 The type of reproduction from the parent stock direct
id 1
Uuid		 direct

Usages

used by used in type used
CultureGrowth organism_ref range Organism
StrainPurity organism_ref range Organism
StockCulturePreparation organism_ref range Organism
PreCultureGrowth organism_ref range Organism
ExperimentalCulture organism_ref range Organism
AMP2UserSample organism_ref range Organism
EngineeredStrainSample organism_ref range Organism

Identifier and Mapping Information

Schema Source

Mappings

Mapping Type Mapped Value
self basalt_schema:Organism
native basalt_schema:Organism

LinkML Source

Direct

name: organism
description: "Reference data representing a biological identity (strain, isolate,\n\
  engineered construct, etc.) that can be instantiated by multiple\nphysical samples.\n\
  \nREPLACES: This class replaces the former Strain class, which was modeled\nas a\
  \ PurchasedMaterial subclass. That approach did not accommodate strains\nengineered\
  \ in-house or received from collaborators, nor did it cleanly\nseparate biological\
  \ identity from physical samples. Additionally, the term\n\"strain\" implies purity\
  \ that cannot always be guaranteed; this class\nrepresents the *intended* or *characterized*\
  \ biological identity.\n\nRelationship to samples:\n  - One organism can have many\
  \ AMP2UserSample instances\n  - AMP2UserSample.organism_ref points here\n  - CultureGrowth\
  \ activities reference via organism_ref (aliased as strain_ref)"
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
slots:
- name
- description
- strain_identifier
- organism_name
- taxonomy_id
- host_common_name
- host_taxid
- strain_source
- strain_type
- modification_method
- strain_description
- strain_mutation
- phenotype
- trait
- encoded_traits
- genotype_segment_category
- genotype_segment_name
- component_name
- construct_component
- donor_organism
- component_description
- trophic_level
- pathogenicity
- host_spec_range
- propagation
slot_usage:
  strain_identifier:
    name: strain_identifier
    description: 'Primary human-readable identifier for this organism.

      Examples: "KT2440_pTE314", "PP_0055", "AG5577-pJE2165"'
    required: true
  name:
    name: name
    description: 'Human-readable name for the organism.

      May be same as strain_identifier or more descriptive.'
  organism_name:
    name: organism_name
    description: Scientific name of the organism (e.g., "Pseudomonas putida").
  strain_source:
    name: strain_source
    description: 'Provenance of the organism. Can be an institution

      (e.g., "ATCC", "PNNL"), commercial source, or derivation note

      (e.g., "engineered from KT2440").'
  strain_mutation:
    name: strain_mutation
    description: 'Primary genetic modification or plasmid carried (e.g., "pTE314").

      For more detailed construct information, use the genotype_segment_*

      and component_* slots.'
  modification_method:
    name: modification_method
    description: 'Method used to introduce genetic modification.

      Examples: "Electroporation", "Conjugation", "CRISPR", "Transduction"'
  trophic_level:
    name: trophic_level
    required: false
attributes:
  id:
    name: id
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/organism
    identifier: true
    domain_of:
    - Activity
    - Entity
    - DataProduct
    - DataGenerationActivity
    - DataProcessingActivity
    - AlternativeIdentifier
    - FunctionalAnnotationIdentifier
    - Instrument
    - OntologyClass
    - ContainerType
    - Custodian
    - InstrumentAlternativeIdentifier
    - LabDevice
    - SampleProcessing
    - ProcessingSampleLink
    - Configuration
    - MobilePhaseSegment
    - MassSpectrometryStandardRun
    - PurchasedMaterial
    - LabProcessingActivity
    - organism
    - MAOMProduct
    - WEOMProduct
    - Site
    - Sample
    - AerosolArmSample
    - AerosolSample
    - AMP2UserSample
    - CommerciallyPurchasedSample
    - CultureEnvironmentalSample
    - EngineeredStrainSample
    - FieldDeployedTerraformSample
    - MixedCultureSample
    - MonetSoilSample
    - OtherUndescribedSample
    - PlantSample
    - PureCultureSample
    - SedimentSample
    - SoilSample
    - SynthesizedMaterialSample
    - TerraformSample
    - WaterSample
    - ProcessedSample
    - CoreSection
    - SamplingActivity
    - AerosolArmSamplingActivity
    - AerosolSamplingActivity
    - CommerciallyPurchasedSamplingActivity
    - CultureEnvironmentalSamplingActivity
    - EngineeredStrainSamplingActivity
    - FieldDeployedTerraformSamplingActivity
    - MixedCultureSamplingActivity
    - MonetSoilSamplingActivity
    - OtherUndescribedSamplingActivity
    - PlantSamplingActivity
    - PureCultureSamplingActivity
    - SedimentSamplingActivity
    - SoilSamplingActivity
    - SynthesizedMaterialSamplingActivity
    - TerraformSamplingActivity
    - WaterSamplingActivity
    - Study
    - ProjectParticipant
    - TimestampValue
    - TextValue
    - SoftwareControlledTermValue
    - ControlledTermValue
    - PersonValue
    - QuantityValue
    - ConditioningValue
    - zipDownload
    range: uuid
    required: true

Induced

name: organism
description: "Reference data representing a biological identity (strain, isolate,\n\
  engineered construct, etc.) that can be instantiated by multiple\nphysical samples.\n\
  \nREPLACES: This class replaces the former Strain class, which was modeled\nas a\
  \ PurchasedMaterial subclass. That approach did not accommodate strains\nengineered\
  \ in-house or received from collaborators, nor did it cleanly\nseparate biological\
  \ identity from physical samples. Additionally, the term\n\"strain\" implies purity\
  \ that cannot always be guaranteed; this class\nrepresents the *intended* or *characterized*\
  \ biological identity.\n\nRelationship to samples:\n  - One organism can have many\
  \ AMP2UserSample instances\n  - AMP2UserSample.organism_ref points here\n  - CultureGrowth\
  \ activities reference via organism_ref (aliased as strain_ref)"
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
slot_usage:
  strain_identifier:
    name: strain_identifier
    description: 'Primary human-readable identifier for this organism.

      Examples: "KT2440_pTE314", "PP_0055", "AG5577-pJE2165"'
    required: true
  name:
    name: name
    description: 'Human-readable name for the organism.

      May be same as strain_identifier or more descriptive.'
  organism_name:
    name: organism_name
    description: Scientific name of the organism (e.g., "Pseudomonas putida").
  strain_source:
    name: strain_source
    description: 'Provenance of the organism. Can be an institution

      (e.g., "ATCC", "PNNL"), commercial source, or derivation note

      (e.g., "engineered from KT2440").'
  strain_mutation:
    name: strain_mutation
    description: 'Primary genetic modification or plasmid carried (e.g., "pTE314").

      For more detailed construct information, use the genotype_segment_*

      and component_* slots.'
  modification_method:
    name: modification_method
    description: 'Method used to introduce genetic modification.

      Examples: "Electroporation", "Conjugation", "CRISPR", "Transduction"'
  trophic_level:
    name: trophic_level
    required: false
attributes:
  id:
    name: id
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/organism
    identifier: true
    alias: id
    owner: organism
    domain_of:
    - Activity
    - Entity
    - DataProduct
    - DataGenerationActivity
    - DataProcessingActivity
    - AlternativeIdentifier
    - FunctionalAnnotationIdentifier
    - Instrument
    - OntologyClass
    - ContainerType
    - Custodian
    - InstrumentAlternativeIdentifier
    - LabDevice
    - SampleProcessing
    - ProcessingSampleLink
    - Configuration
    - MobilePhaseSegment
    - MassSpectrometryStandardRun
    - PurchasedMaterial
    - LabProcessingActivity
    - organism
    - MAOMProduct
    - WEOMProduct
    - Site
    - Sample
    - AerosolArmSample
    - AerosolSample
    - AMP2UserSample
    - CommerciallyPurchasedSample
    - CultureEnvironmentalSample
    - EngineeredStrainSample
    - FieldDeployedTerraformSample
    - MixedCultureSample
    - MonetSoilSample
    - OtherUndescribedSample
    - PlantSample
    - PureCultureSample
    - SedimentSample
    - SoilSample
    - SynthesizedMaterialSample
    - TerraformSample
    - WaterSample
    - ProcessedSample
    - CoreSection
    - SamplingActivity
    - AerosolArmSamplingActivity
    - AerosolSamplingActivity
    - CommerciallyPurchasedSamplingActivity
    - CultureEnvironmentalSamplingActivity
    - EngineeredStrainSamplingActivity
    - FieldDeployedTerraformSamplingActivity
    - MixedCultureSamplingActivity
    - MonetSoilSamplingActivity
    - OtherUndescribedSamplingActivity
    - PlantSamplingActivity
    - PureCultureSamplingActivity
    - SedimentSamplingActivity
    - SoilSamplingActivity
    - SynthesizedMaterialSamplingActivity
    - TerraformSamplingActivity
    - WaterSamplingActivity
    - Study
    - ProjectParticipant
    - TimestampValue
    - TextValue
    - SoftwareControlledTermValue
    - ControlledTermValue
    - PersonValue
    - QuantityValue
    - ConditioningValue
    - zipDownload
    range: uuid
    required: true
  name:
    name: name
    description: 'Human-readable name for the organism.

      May be same as strain_identifier or more descriptive.'
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: name
    owner: organism
    domain_of:
    - Activity
    - Entity
    - DataProduct
    - DataGenerationActivity
    - Instrument
    - OntologyClass
    - ContainerAxis
    - Configuration
    - MobilePhaseSegment
    - MassSpectrometryStandardRun
    - PurchasedMaterial
    - LabProcessingActivity
    - organism
    - Site
    - Sample
    - SamplingActivity
    - SoilSamplingActivity
    - Study
    - SoftwareControlledTermValue
    range: string
    required: true
  description:
    name: description
    description: Human-readable description for the entity or activity
    title: description
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: description
    owner: organism
    domain_of:
    - Activity
    - Entity
    - DataProduct
    - DataGenerationActivity
    - DataProcessingActivity
    - OntologyClass
    - ContainerType
    - LabDevice
    - Configuration
    - MassSpectrometryStandardRun
    - PurchasedMaterial
    - LabProcessingActivity
    - organism
    - Site
    - Sample
    - SamplingActivity
    - SoilSamplingActivity
    - Study
    - TimestampValue
    - TextValue
    - SoftwareControlledTermValue
    - ControlledTermValue
    - QuantityValue
    range: string
  strain_identifier:
    name: strain_identifier
    description: 'Primary human-readable identifier for this organism.

      Examples: "KT2440_pTE314", "PP_0055", "AG5577-pJE2165"'
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    aliases:
    - strain_id
    - strain_name
    rank: 1000
    alias: strain_identifier
    owner: organism
    domain_of:
    - organism
    range: string
    required: true
  organism_name:
    name: organism_name
    description: Scientific name of the organism (e.g., "Pseudomonas putida").
    title: organism name
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    aliases:
    - scientific_name
    - species_name
    rank: 1000
    alias: organism_name
    owner: organism
    domain_of:
    - organism
    range: string
  taxonomy_id:
    name: taxonomy_id
    description: NCBI taxon ID for the organism.
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    aliases:
    - ncbi_taxon_id
    - taxon_id
    rank: 1000
    alias: taxonomy_id
    owner: organism
    domain_of:
    - organism
    range: string
  host_common_name:
    name: host_common_name
    description: 'Common name for the host organism (e.g., "Pseudomonas putida").

      For microbes, this may be identical to organism_name.'
    title: host common name
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    aliases:
    - common_name
    rank: 1000
    alias: host_common_name
    owner: organism
    domain_of:
    - organism
    - CultureEnvironmentalSample
    - FieldDeployedTerraformSample
    - MixedCultureSample
    - OtherUndescribedSample
    - PureCultureSample
    - TerraformSample
    range: string
  host_taxid:
    name: host_taxid
    description: NCBI taxon ID. Format with prefix NCBITaxon:####
    title: host taxonomy identifier
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    aliases:
    - host_taxonomy_id
    - host_ncbi_taxon_id
    - host_taxa_id
    rank: 1000
    alias: host_taxid
    owner: organism
    domain_of:
    - organism
    - CultureEnvironmentalSample
    - FieldDeployedTerraformSample
    - MixedCultureSample
    - OtherUndescribedSample
    - PureCultureSample
    - TerraformSample
    range: string
    pattern: NCBITaxon:\d+
  strain_source:
    name: strain_source
    description: 'Provenance of the organism. Can be an institution

      (e.g., "ATCC", "PNNL"), commercial source, or derivation note

      (e.g., "engineered from KT2440").'
    title: strain source
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    aliases:
    - source_institution
    - strain_origin
    rank: 1000
    alias: strain_source
    owner: organism
    domain_of:
    - organism
    range: string
  strain_type:
    name: strain_type
    description: Type of strain/organism (bacterial, fungal, archaeal, etc.)
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    aliases:
    - organism_type
    rank: 1000
    alias: strain_type
    owner: organism
    domain_of:
    - organism
    range: StrainTypeEnum
  modification_method:
    name: modification_method
    description: 'Method used to introduce genetic modification.

      Examples: "Electroporation", "Conjugation", "CRISPR", "Transduction"'
    title: modification method
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    aliases:
    - genetic_modification_method
    - transformation_method
    rank: 1000
    alias: modification_method
    owner: organism
    domain_of:
    - organism
    range: ModificationMethodEnum
  strain_description:
    name: strain_description
    description: A brief description of the modifications that comprise this strain
    title: strain description
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    aliases:
    - strain_desc
    - strain_notes
    rank: 1000
    alias: strain_description
    owner: organism
    domain_of:
    - organism
    range: string
  strain_mutation:
    name: strain_mutation
    description: 'Primary genetic modification or plasmid carried (e.g., "pTE314").

      For more detailed construct information, use the genotype_segment_*

      and component_* slots.'
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: strain_mutation
    owner: organism
    domain_of:
    - organism
    range: string
  phenotype:
    name: phenotype
    description: 'Provide the intedned phenotype of hte modified organism. Observable
      characteristics of the organism.

      Example: "aprimycin resistance, gene knockdown dCas12a construct"'
    title: phenotype
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: phenotype
    owner: organism
    domain_of:
    - organism
    range: string
  trait:
    name: trait
    description: 'Trait category for the organism.

      Example: "Bacterial Resistance", "Other"'
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: trait
    owner: organism
    domain_of:
    - organism
    range: IntendedTraitEnum
  encoded_traits:
    name: encoded_traits
    description: 'Should include key traits like antibiotic resistance or xenobiotic

      degradation phenotypes for plasmids, converting genes for phage'
    title: encoded traits
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: encoded_traits
    owner: organism
    domain_of:
    - organism
    - CultureEnvironmentalSample
    - FieldDeployedTerraformSample
    - MixedCultureSample
    - OtherUndescribedSample
    - PureCultureSample
    - TerraformSample
    range: string
  genotype_segment_category:
    name: genotype_segment_category
    description: 'Category of genetic modification or segment.

      Examples: "Gene(s) of Interest", "Gene Silencer"'
    title: genotype segment category
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: genotype_segment_category
    owner: organism
    domain_of:
    - organism
    range: GenotypeSegmentEnum
  genotype_segment_name:
    name: genotype_segment_name
    description: 'Provide a name that describes the genotype modification engineered

      relative to the reference unmodified genome. The name should describe the spatially

      grouped components or specific function of the modification.'
    title: genotype segment name
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: genotype_segment_name
    owner: organism
    domain_of:
    - organism
    range: string
  component_name:
    name: component_name
    description: 'Provide a one-to-three word name based on the component. If using
      an

      acronym provide the full component name in the component description.'
    title: construct component name
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: component_name
    owner: organism
    domain_of:
    - organism
    range: string
  construct_component:
    name: construct_component
    description: Select the construct component type.
    title: construct component
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: construct_component
    owner: organism
    domain_of:
    - organism
    range: ConstructComponentEnum
  donor_organism:
    name: donor_organism
    description: "Provide the scientific name (genus and species) of the organism\
      \ from which the construct component was first described or obtained. \nYou\
      \ may enter 'synthetic' if relevant."
    title: donor organism
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: donor_organism
    owner: organism
    domain_of:
    - organism
    range: string
  component_description:
    name: component_description
    description: 'Provide a short statement describing the function of the construct

      component. You may provide an optional literature reference for lesser-known
      components.

      Example: "d-Cfp1 to block gene expression", "recognition sequence for guide
      RNA processing"'
    title: construct component description
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: component_description
    owner: organism
    domain_of:
    - organism
    range: string
  trophic_level:
    name: trophic_level
    description: 'Trophic levels are the feeding position in a food chain. Microbes
      can

      be a range of producers.'
    title: trophic level
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: trophic_level
    owner: organism
    domain_of:
    - organism
    - CultureEnvironmentalSample
    - MixedCultureSample
    - OtherUndescribedSample
    - PureCultureSample
    range: TrophicLevelEnum
    required: false
  pathogenicity:
    name: pathogenicity
    description: To what is the entity pathogenic, e.g., humans, animals, plants,
      or specific tissues.
    title: pathogenicity
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: pathogenicity
    owner: organism
    domain_of:
    - organism
    - CultureEnvironmentalSample
    - MixedCultureSample
    - OtherUndescribedSample
    - PureCultureSample
    range: string
  host_spec_range:
    name: host_spec_range
    description: The range and diversity of host species that an organism is capable
      of infecting, defined by NCBI taxonomy identifier. Format with prefix NCBITaxon:####
    title: host specificity or range
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: host_spec_range
    owner: organism
    domain_of:
    - organism
    - CultureEnvironmentalSample
    - FieldDeployedTerraformSample
    - MixedCultureSample
    - OtherUndescribedSample
    - PureCultureSample
    - TerraformSample
    range: string
    pattern: NCBITaxon:\d+
  propagation:
    name: propagation
    description: 'The type of reproduction from the parent stock. Values for this
      field are specific to different taxa. For phage or virus: lytic/lysogenic/temperate/obligately
      lytic. For plasmids: incompatibility group. For eukaryotes: sexual/asexual'''
    title: propagation
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: propagation
    owner: organism
    domain_of:
    - organism
    - CultureEnvironmentalSample
    - FieldDeployedTerraformSample
    - MixedCultureSample
    - OtherUndescribedSample
    - PureCultureSample
    - TerraformSample
    range: string