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Class: SpecimenEnv

base information on the acquisition and treatment of the sample itself.

URI: https://w3id.org/osc-em/oscem-schemas-env-tomo/:SpecimenEnv

classDiagram class SpecimenEnv click SpecimenEnv href "../SpecimenEnv" SpecimenEnv : collection_date SpecimenEnv : handling SpecimenEnv : location SpecimenEnv : organism SpecimenEnv : source_env SpecimenEnv : tissue

Slots

Name Cardinality and Range Description Inheritance
organism 1..*
String		 the organism(s) present in your sample, if not perfectly defined try to asses... direct
tissue 0..1
String		 if the sample is a tissue sample please indicate what type of tissue direct
source_env 0..1
String		 where is this sample from? i direct
location 0..1
String		 the geographical location of your source, optimally in a geographic coordinat... direct
collection_date 0..1
Date		 When the sample was collected direct
handling 0..1
String		 What was done to the sample, please give an overview of relevant treatments direct

Usages

used by used in type used
SampleEnv specimen_env range SpecimenEnv

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/osc-em/oscem-schemas-env-tomo

Mappings

Mapping Type Mapped Value
self https://w3id.org/osc-em/oscem-schemas-env-tomo/:SpecimenEnv
native https://w3id.org/osc-em/oscem-schemas-env-tomo/:SpecimenEnv

LinkML Source

Direct

name: SpecimenEnv
description: base information on the acquisition and treatment of the sample itself.
from_schema: https://w3id.org/osc-em/oscem-schemas-env-tomo
slots:
- organism
- tissue
- source_env
- location
- collection_date
- handling
slot_usage:
  organism:
    name: organism
    required: true

Induced

name: SpecimenEnv
description: base information on the acquisition and treatment of the sample itself.
from_schema: https://w3id.org/osc-em/oscem-schemas-env-tomo
slot_usage:
  organism:
    name: organism
    required: true
attributes:
  organism:
    name: organism
    description: the organism(s) present in your sample, if not perfectly defined
      try to asses as close as possible.
    from_schema: https://w3id.org/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: organism
    owner: SpecimenEnv
    domain_of:
    - SpecimenEnv
    range: string
    required: true
    multivalued: true
  tissue:
    name: tissue
    description: if the sample is a tissue sample please indicate what type of tissue.
    from_schema: https://w3id.org/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: tissue
    owner: SpecimenEnv
    domain_of:
    - SpecimenEnv
    range: string
  source_env:
    name: source_env
    description: where is this sample from? i.e. Hospital
    from_schema: https://w3id.org/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: source_env
    owner: SpecimenEnv
    domain_of:
    - SpecimenEnv
    range: string
  location:
    name: location
    description: the geographical location of your source, optimally in a geographic
      coordinate system.
    from_schema: https://w3id.org/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: location
    owner: SpecimenEnv
    domain_of:
    - SpecimenEnv
    range: string
  collection_date:
    name: collection_date
    description: When the sample was collected
    from_schema: https://w3id.org/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: collection_date
    owner: SpecimenEnv
    domain_of:
    - SpecimenEnv
    range: date
  handling:
    name: handling
    description: What was done to the sample, please give an overview of relevant
      treatments.
    from_schema: https://w3id.org/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: handling
    owner: SpecimenEnv
    domain_of:
    - SpecimenEnv
    range: string