Class: Subject

Biological identity of the organism(s) that is studied. Contains details like taxonomy, strain, genotype, sex, age and/or other morphometric details and measurements.

URI: BeStMeta:Subject

 classDiagram
    class Subject
    click Subject href "../Subject/"
      Subject : age_unit





        Subject --> "0..1" DevelopmentUnitEnum : age_unit
        click DevelopmentUnitEnum href "../DevelopmentUnitEnum/"



      Subject : age_value

      Subject : body_length_unit





        Subject --> "0..1 _recommended_" LengthUnitEnum : body_length_unit
        click LengthUnitEnum href "../LengthUnitEnum/"



      Subject : body_length_value

      Subject : developmental_stage





        Subject --> "0..1" DevelopmentalStageEnum : developmental_stage
        click DevelopmentalStageEnum href "../DevelopmentalStageEnum/"



      Subject : developmental_stage_unit





        Subject --> "0..1" DevelopmentUnitEnum : developmental_stage_unit
        click DevelopmentUnitEnum href "../DevelopmentUnitEnum/"



      Subject : developmental_stage_value

      Subject : genotype

      Subject : housing_conditions

      Subject : n_individuals_represented

      Subject : sex





        Subject --> "0..1 _recommended_" SexEnum : sex
        click SexEnum href "../SexEnum/"



      Subject : species_name

      Subject : species_ncbi_taxon_id

      Subject : strain

      Subject : subject_colour

      Subject : subject_type





        Subject --> "1" SubjectTypeEnum : subject_type
        click SubjectTypeEnum href "../SubjectTypeEnum/"



      Subject : weight_unit





        Subject --> "0..1" WeightUnitEnum : weight_unit
        click WeightUnitEnum href "../WeightUnitEnum/"



      Subject : weight_value

Slots

Name	Cardinality and Range	Description	Inheritance
subject_type	1 SubjectTypeEnum	Indicates whether the subject being tracked is a whole organism or a cell/cell culture; determines which biological identity fields are applicable.	direct
species_name	1 String	Scientific (Latin) binomial name of the study organism	direct
n_individuals_represented	0..1 Integer	Represents the toal number of individual subjects in a given subject entry. Use a value greater than one to show its a homogenous subjects. Defaults to one (when omitted)	direct
species_ncbi_taxon_id	0..1 recommended String	NCBI Taxonomy ID for the study organism	direct
strain	0..1 recommended String	Organism strain or line	direct
genotype	0..1 recommended String	Genotype identifier of the tracked organism(s) including strain-specific, mutant, transgenic, or engineered genotypes.	direct
sex	0..1 recommended SexEnum	Biological sex of the tracked organism(s).	direct
body_length_value	0..1 recommended Float	Body length numeric value of the tracked organism(s).	direct
body_length_unit	0..1 recommended LengthUnitEnum	Body length unit of the tracked organism(s).	direct
housing_conditions	0..1 String	Free-text description of animal housing conditions prior to assay.	direct
subject_colour	0..1 String	Indicates the colour of the subject. This is useful for tracking.	direct
developmental_stage	0..1 DevelopmentalStageEnum	Developmental stage of the tracked organism(s).	direct
developmental_stage_value	0..1 Float	Numeric developmental stage value (e.g. 72 for 72 hpf) of the tracked organism(s).	direct
developmental_stage_unit	0..1 DevelopmentUnitEnum	Unit for developmental stage value of the tracked organism(s).	direct
age_value	0..1 Float	Numeric age value of the tracked organism(s).	direct
age_unit	0..1 DevelopmentUnitEnum	Age unit of the tracked organism(s).	direct
weight_value	0..1 Float	Body weight numeric value of the tracked organism(s).	direct
weight_unit	0..1 WeightUnitEnum	Body weight unit of the tracked organism(s).	direct

Expressions & Logic

#### Any Of The class must satisfy at least one of: - AnonymousClassExpression({ 'slot_conditions': {'developmental_stage': SlotDefinition({'name': 'developmental_stage', 'required': True})} }) - AnonymousClassExpression({ 'slot_conditions': {'developmental_stage_value': SlotDefinition({'name': 'developmental_stage_value', 'required': True}), 'developmental_stage_unit': SlotDefinition({'name': 'developmental_stage_unit', 'required': True})} }) - AnonymousClassExpression({ 'slot_conditions': {'age_value': SlotDefinition({'name': 'age_value', 'required': True}), 'age_unit': SlotDefinition({'name': 'age_unit', 'required': True})} })

Usages

used by	used in	type	used
ExperimentalConditions	subject	range	Subject

Rules

Rule Applied	Preconditions	Postconditions	Elseconditions
slot_conditions	{'subject_type': {'equals_string': 'organism'}}	{'sex': {'recommended': True}}

Rule Applied	Preconditions	Postconditions	Elseconditions
slot_conditions	{'body_length_value': {'value_presence': 'PRESENT'}}	{'body_length_unit': {'required': True}}

Rule Applied	Preconditions	Postconditions	Elseconditions
slot_conditions	{'weight_value': {'value_presence': 'PRESENT'}}	{'weight_unit': {'required': True}}

Identifier and Mapping Information

Schema Source

• from schema: https://w3id.org/bestmeta/schema

Mappings

Mapping Type	Mapped Value
self	BeStMeta:Subject
native	BeStMeta:Subject

LinkML Source

Direct

name: Subject
description: Biological identity of the organism(s) that is studied. Contains details
  like taxonomy, strain, genotype, sex, age and/or other morphometric details and
  measurements.
from_schema: https://w3id.org/bestmeta/schema
slots:
- subject_type
- species_name
- n_individuals_represented
- species_ncbi_taxon_id
- strain
- genotype
- sex
- body_length_value
- body_length_unit
- housing_conditions
- subject_colour
- developmental_stage
- developmental_stage_value
- developmental_stage_unit
- age_value
- age_unit
- weight_value
- weight_unit
rules:
- preconditions:
    slot_conditions:
      subject_type:
        name: subject_type
        equals_string: organism
  postconditions:
    slot_conditions:
      sex:
        name: sex
        recommended: true
  description: 'When subject_type is organism, sex is a recommended field. '
- preconditions:
    slot_conditions:
      body_length_value:
        name: body_length_value
        value_presence: PRESENT
  postconditions:
    slot_conditions:
      body_length_unit:
        name: body_length_unit
        required: true
  description: body_length_value requires body_length_unit
- preconditions:
    slot_conditions:
      weight_value:
        name: weight_value
        value_presence: PRESENT
  postconditions:
    slot_conditions:
      weight_unit:
        name: weight_unit
        required: true
  description: weight_value requires weight_unit
any_of:
- slot_conditions:
    developmental_stage:
      name: developmental_stage
      required: true
- slot_conditions:
    developmental_stage_value:
      name: developmental_stage_value
      required: true
    developmental_stage_unit:
      name: developmental_stage_unit
      required: true
- slot_conditions:
    age_value:
      name: age_value
      required: true
    age_unit:
      name: age_unit
      required: true

Induced

name: Subject
description: Biological identity of the organism(s) that is studied. Contains details
  like taxonomy, strain, genotype, sex, age and/or other morphometric details and
  measurements.
from_schema: https://w3id.org/bestmeta/schema
attributes:
  subject_type:
    name: subject_type
    description: Indicates whether the subject being tracked is a whole organism or
      a cell/cell culture; determines which biological identity fields are applicable.
    from_schema: https://w3id.org/bestmeta/schema
    rank: 1000
    owner: Subject
    domain_of:
    - Subject
    range: SubjectTypeEnum
    required: true
  species_name:
    name: species_name
    description: Scientific (Latin) binomial name of the study organism
    examples:
    - value: Danio rerio
    - value: Mus musculus
    - value: Daphnia magna
    from_schema: https://w3id.org/bestmeta/schema
    exact_mappings:
    - dwc:scientificName
    - EDAM.DATA:1045
    rank: 1000
    owner: Subject
    domain_of:
    - Subject
    range: string
    required: true
  n_individuals_represented:
    name: n_individuals_represented
    description: Represents the toal number of individual subjects in a given subject
      entry. Use a value greater than one to show its a homogenous subjects. Defaults
      to one (when omitted)
    from_schema: https://w3id.org/bestmeta/schema
    rank: 1000
    owner: Subject
    domain_of:
    - Subject
    range: integer
  species_ncbi_taxon_id:
    name: species_ncbi_taxon_id
    description: NCBI Taxonomy ID for the study organism
    examples:
    - value: '7955'
    - value: '10090'
    from_schema: https://w3id.org/bestmeta/schema
    exact_mappings:
    - dwc:taxonID
    - EDAM.DATA:1179
    rank: 1000
    owner: Subject
    domain_of:
    - Subject
    range: string
    required: false
    recommended: true
    pattern: ^\d+$
  strain:
    name: strain
    description: Organism strain or line
    from_schema: https://w3id.org/bestmeta/schema
    exact_mappings:
    - EDAM.DATA:2379
    rank: 1000
    owner: Subject
    domain_of:
    - Subject
    range: string
    required: false
    recommended: true
  genotype:
    name: genotype
    annotations:
      source_ontology:
        tag: source_ontology
        value: GENO
    description: Genotype identifier of the tracked organism(s) including strain-specific,
      mutant, transgenic, or engineered genotypes.
    from_schema: https://w3id.org/bestmeta/schema
    exact_mappings:
    - EFO:0000513
    - GENO:0000536
    rank: 1000
    owner: Subject
    domain_of:
    - Subject
    range: string
    required: false
    recommended: true
  sex:
    name: sex
    description: Biological sex of the tracked organism(s).
    from_schema: https://w3id.org/bestmeta/schema
    exact_mappings:
    - PATO:0000047
    rank: 1000
    owner: Subject
    domain_of:
    - Subject
    range: SexEnum
    required: false
    recommended: true
  body_length_value:
    name: body_length_value
    description: Body length numeric value of the tracked organism(s).
    from_schema: https://w3id.org/bestmeta/schema
    close_mappings:
    - EFO:0004339
    - MESH:D049628
    rank: 1000
    owner: Subject
    domain_of:
    - Subject
    range: float
    required: false
    recommended: true
  body_length_unit:
    name: body_length_unit
    description: Body length unit of the tracked organism(s).
    from_schema: https://w3id.org/bestmeta/schema
    rank: 1000
    owner: Subject
    domain_of:
    - Subject
    range: LengthUnitEnum
    required: false
    recommended: true
  housing_conditions:
    name: housing_conditions
    description: Free-text description of animal housing conditions prior to assay.
    from_schema: https://w3id.org/bestmeta/schema
    exact_mappings:
    - XCO:0000033
    rank: 1000
    owner: Subject
    domain_of:
    - Subject
    - Manipulation
    range: string
    required: false
  subject_colour:
    name: subject_colour
    description: Indicates the colour of the subject. This is useful for tracking.
    from_schema: https://w3id.org/bestmeta/schema
    rank: 1000
    owner: Subject
    domain_of:
    - Subject
    range: string
  developmental_stage:
    name: developmental_stage
    description: Developmental stage of the tracked organism(s).
    from_schema: https://w3id.org/bestmeta/schema
    exact_mappings:
    - EFO:0000399
    rank: 1000
    owner: Subject
    domain_of:
    - Subject
    range: DevelopmentalStageEnum
  developmental_stage_value:
    name: developmental_stage_value
    description: Numeric developmental stage value (e.g. 72 for 72 hpf) of the tracked
      organism(s).
    from_schema: https://w3id.org/bestmeta/schema
    close_mappings:
    - EFO:0000399
    rank: 1000
    owner: Subject
    domain_of:
    - Subject
    range: float
  developmental_stage_unit:
    name: developmental_stage_unit
    description: Unit for developmental stage value of the tracked organism(s).
    from_schema: https://w3id.org/bestmeta/schema
    rank: 1000
    owner: Subject
    domain_of:
    - Subject
    range: DevelopmentUnitEnum
  age_value:
    name: age_value
    description: Numeric age value of the tracked organism(s).
    from_schema: https://w3id.org/bestmeta/schema
    exact_mappings:
    - EFO:0000246
    rank: 1000
    owner: Subject
    domain_of:
    - Subject
    range: float
  age_unit:
    name: age_unit
    description: Age unit of the tracked organism(s).
    from_schema: https://w3id.org/bestmeta/schema
    rank: 1000
    owner: Subject
    domain_of:
    - Subject
    range: DevelopmentUnitEnum
  weight_value:
    name: weight_value
    description: Body weight numeric value of the tracked organism(s).
    from_schema: https://w3id.org/bestmeta/schema
    exact_mappings:
    - EFO:0004338
    rank: 1000
    owner: Subject
    domain_of:
    - Subject
    range: float
    required: false
  weight_unit:
    name: weight_unit
    description: Body weight unit of the tracked organism(s).
    from_schema: https://w3id.org/bestmeta/schema
    rank: 1000
    owner: Subject
    domain_of:
    - Subject
    range: WeightUnitEnum
    required: false
rules:
- preconditions:
    slot_conditions:
      subject_type:
        name: subject_type
        equals_string: organism
  postconditions:
    slot_conditions:
      sex:
        name: sex
        recommended: true
  description: 'When subject_type is organism, sex is a recommended field. '
- preconditions:
    slot_conditions:
      body_length_value:
        name: body_length_value
        value_presence: PRESENT
  postconditions:
    slot_conditions:
      body_length_unit:
        name: body_length_unit
        required: true
  description: body_length_value requires body_length_unit
- preconditions:
    slot_conditions:
      weight_value:
        name: weight_value
        value_presence: PRESENT
  postconditions:
    slot_conditions:
      weight_unit:
        name: weight_unit
        required: true
  description: weight_value requires weight_unit
any_of:
- slot_conditions:
    developmental_stage:
      name: developmental_stage
      required: true
- slot_conditions:
    developmental_stage_value:
      name: developmental_stage_value
      required: true
    developmental_stage_unit:
      name: developmental_stage_unit
      required: true
- slot_conditions:
    age_value:
      name: age_value
      required: true
    age_unit:
      name: age_unit
      required: true