Class: Sample (Sample)

Entity (material from a fermentation run) that is converted into a new item (material or data) via a process (physical or computational).

URI: mife:Sample

 classDiagram
    class Sample
    click Sample href "../Sample/"
      Sample : phase

      Sample : phase_duration

      Sample : phase_purpose

      Sample : recipe_url

      Sample : replicate

      Sample : sample_collection_device

      Sample : sample_collection_method

      Sample : sample_description

      Sample : sample_dry_mass

      Sample : sample_identifier

      Sample : sample_material

      Sample : sample_material_processing

      Sample : sample_name

      Sample : sample_storage_buffer

      Sample : sample_storage_conditions

      Sample : sample_storage_container

      Sample : sample_storage_duration

      Sample : sample_storage_location

      Sample : sample_storage_temperature

      Sample : sample_treatment

      Sample : sample_wet_mass

      Sample : sampling_time_point

      Sample : volume

Slots

Name	Cardinality and Range	Description	Inheritance
sample_identifier	1 String	unique sample identifier	direct
sample_name	1 String	name of the sample	direct
sample_description	1 String	description of the sample	direct
sampling_time_point	1 Datetime	date that the sample was collected	direct
volume	0..1 Integer	Liquid volume in the vessel	direct
recipe_url	0..1 String	standard operating procedure (or protocol) for sampling	direct
phase	0..1 String	A distinct stage in the fermentation process, such as lag phase, log phase, o...	direct
phase_purpose	0..1 String	The intended outcome or goal of a specific phase in the process, e	direct
phase_duration	0..1 Duration	The total time duration of a specific phase in minutes during the fermentatio...	direct
replicate	0..1 String	A role played by a a biological sample in the context of an experiment where ...	direct
sample_material	0..1 String	Sample material from which data deposited was generated	direct
sample_material_processing	* String	Any processing applied to the sample during or after retrieving the sample fr...	direct
sample_collection_device	0..1 String	The device used for collecting the sample	direct
sample_collection_method	0..1 String	The method employed for collecting the sample	direct
sample_storage_buffer	0..1 String	buffer used for sample storage	direct
sample_storage_conditions	0..1 String	Additional information about the conditions at which sample was stored	direct
sample_storage_container	0..1 String	Container that sample was stored in e	direct
sample_storage_duration	0..1 Float	duration for which sample was stored	direct
sample_storage_location	0..1 String	location at which sample was stored, usually name of a specific freezer/room	direct
sample_storage_temperature	0..1 Float	temperature at which sample was stored	direct
sample_treatment	0..1 String	Treatment applied to the sample	direct
sample_wet_mass	0..1 Float	measurement of wet mass at the time of sample collection	direct
sample_dry_mass	0..1 Float	measurement of dry mass at the time of sample collection	direct

Usages

used by	used in	type	used
ObservationUnit	sample_id	range	Sample

Identifier and Mapping Information

Schema Source

• from schema: https://ontology.ibisba.eu/mife/

Mappings

Mapping Type	Mapped Value
self	mife:Sample
native	mife:Sample

LinkML Source

Direct

name: Sample
description: Entity (material from a fermentation run) that is converted into a new
  item (material or data) via a process (physical or computational).
title: Sample
from_schema: https://ontology.ibisba.eu/mife/
slots:
- sample_identifier
- sample_name
- sample_description
- sampling_time_point
- volume
- recipe_url
- phase
- phase_purpose
- phase_duration
- replicate
- sample_material
- sample_material_processing
- sample_collection_device
- sample_collection_method
- sample_storage_buffer
- sample_storage_conditions
- sample_storage_container
- sample_storage_duration
- sample_storage_location
- sample_storage_temperature
- sample_treatment
- sample_wet_mass
- sample_dry_mass
class_uri: mife:Sample

Induced

name: Sample
description: Entity (material from a fermentation run) that is converted into a new
  item (material or data) via a process (physical or computational).
title: Sample
from_schema: https://ontology.ibisba.eu/mife/
attributes:
  sample_identifier:
    name: sample_identifier
    description: unique sample identifier
    examples:
    - value: 245978vn475nv34575m597hcvn7vfnv57gvn57
    from_schema: https://ontology.ibisba.eu/mife/
    rank: 1000
    slot_uri: schema:identifier
    alias: sample_identifier
    owner: Sample
    domain_of:
    - Sample
    range: string
    required: true
    multivalued: false
  sample_name:
    name: sample_name
    description: name of the sample
    examples:
    - value: A04_4h
    from_schema: https://ontology.ibisba.eu/mife/
    rank: 1000
    slot_uri: schema:name
    alias: sample_name
    owner: Sample
    domain_of:
    - Sample
    range: string
    required: true
    multivalued: false
  sample_description:
    name: sample_description
    description: description of the sample
    examples:
    - value: Sample of Biolector well A04 (4h)
    from_schema: https://ontology.ibisba.eu/mife/
    rank: 1000
    slot_uri: schema:description
    alias: sample_description
    owner: Sample
    domain_of:
    - Sample
    range: string
    required: true
    multivalued: false
  sampling_time_point:
    name: sampling_time_point
    description: date that the sample was collected
    examples:
    - value: 11:45 on day 1
    from_schema: https://ontology.ibisba.eu/mife/
    rank: 1000
    slot_uri: w3:resultTime
    alias: sampling_time_point
    owner: Sample
    domain_of:
    - Sample
    range: datetime
    required: true
    multivalued: false
  volume:
    name: volume
    description: Liquid volume in the vessel
    examples:
    - value: 800 mL
    from_schema: https://ontology.ibisba.eu/mife/
    rank: 1000
    slot_uri: mife:hasVolume
    alias: volume
    owner: Sample
    domain_of:
    - Sample
    - ObservationUnit
    range: integer
    required: false
    multivalued: false
  recipe_url:
    name: recipe_url
    description: standard operating procedure (or protocol) for sampling
    examples:
    - value: https://ibisbahub.eu/sops/21
    from_schema: https://ontology.ibisba.eu/mife/
    rank: 1000
    slot_uri: w3:usedProcedure
    alias: recipe_url
    owner: Sample
    domain_of:
    - Sample
    range: string
    required: false
    multivalued: false
  phase:
    name: phase
    description: A distinct stage in the fermentation process, such as lag phase,
      log phase, or stationary phase.
    examples:
    - value: lag phase
    - value: log phase
    - value: stationary phase
    from_schema: https://ontology.ibisba.eu/mife/
    rank: 1000
    slot_uri: mife:hasGrowthPhase
    alias: phase
    owner: Sample
    domain_of:
    - Sample
    - ObservationUnit
    range: string
    required: false
    multivalued: false
  phase_purpose:
    name: phase_purpose
    description: The intended outcome or goal of a specific phase in the process,
      e.g., growth or product synthesis.
    examples:
    - value: growth
    - value: antibody synthesis
    from_schema: https://ontology.ibisba.eu/mife/
    rank: 1000
    slot_uri: mife:hasPhasePurpose
    alias: phase_purpose
    owner: Sample
    domain_of:
    - Sample
    - ObservationUnit
    range: string
    required: false
    multivalued: false
  phase_duration:
    name: phase_duration
    description: The total time duration of a specific phase in minutes during the
      fermentation process.
    examples:
    - value: 240 minutes
    from_schema: https://ontology.ibisba.eu/mife/
    rank: 1000
    slot_uri: mife:hasPhaseDuration
    alias: phase_duration
    owner: Sample
    domain_of:
    - Sample
    - ObservationUnit
    range: duration
    required: false
    multivalued: false
  replicate:
    name: replicate
    description: A role played by a a biological sample in the context of an experiment
      where the intent is that biological or technical variation is measured.
    examples:
    - value: Rep1
    from_schema: https://ontology.ibisba.eu/mife/
    rank: 1000
    slot_uri: bioassayontology:BAO_0002845
    alias: replicate
    owner: Sample
    domain_of:
    - Sample
    range: string
    required: false
    multivalued: false
  sample_material:
    name: sample_material
    description: Sample material from which data deposited was generated
    examples:
    - value: tissue fragment
    - value: If unknown please select "not provided"
    from_schema: https://ontology.ibisba.eu/mife/
    rank: 1000
    slot_uri: tdwg:MaterialSample
    alias: sample_material
    owner: Sample
    domain_of:
    - Sample
    range: string
    required: false
    multivalued: false
  sample_material_processing:
    name: sample_material_processing
    description: Any processing applied to the sample during or after retrieving the
      sample from environment. This field accepts OBI, for a browser of OBI (v 2013-10-25)
      terms please see http://purl.bioontology.org/ontology/OBI
    examples:
    - value: fast freezing
    from_schema: https://ontology.ibisba.eu/mife/
    rank: 1000
    slot_uri: mife:hasSampleMaterialPorcessing
    alias: sample_material_processing
    owner: Sample
    domain_of:
    - Sample
    range: string
    required: false
    multivalued: true
  sample_collection_device:
    name: sample_collection_device
    description: The device used for collecting the sample
    examples:
    - value: syringe
    from_schema: https://ontology.ibisba.eu/mife/
    rank: 1000
    slot_uri: mife:hasSampleCollectionDevice
    alias: sample_collection_device
    owner: Sample
    domain_of:
    - Sample
    range: string
    required: false
    multivalued: false
  sample_collection_method:
    name: sample_collection_method
    description: The method employed for collecting the sample
    examples:
    - value: manual
    - value: top side of the bioreactor
    from_schema: https://ontology.ibisba.eu/mife/
    rank: 1000
    slot_uri: mife:hasSampleCollectionMethod
    alias: sample_collection_method
    owner: Sample
    domain_of:
    - Sample
    range: string
    required: false
    multivalued: false
  sample_storage_buffer:
    name: sample_storage_buffer
    description: buffer used for sample storage
    examples:
    - value: RNAlater
    from_schema: https://ontology.ibisba.eu/mife/
    rank: 1000
    slot_uri: obolibrary:CHEBI_35225
    alias: sample_storage_buffer
    owner: Sample
    domain_of:
    - Sample
    range: string
    required: false
    multivalued: false
  sample_storage_conditions:
    name: sample_storage_conditions
    description: Additional information about the conditions at which sample was stored
    examples:
    - value: stored in fridge
    from_schema: https://ontology.ibisba.eu/mife/
    rank: 1000
    slot_uri: obolibrary:OBI_0302893
    alias: sample_storage_conditions
    owner: Sample
    domain_of:
    - Sample
    range: string
    required: false
    multivalued: false
  sample_storage_container:
    name: sample_storage_container
    description: Container that sample was stored in e.g. tube type
    examples:
    - value: cryotube
    from_schema: https://ontology.ibisba.eu/mife/
    rank: 1000
    slot_uri: obolibrary:OBI_0302893
    alias: sample_storage_container
    owner: Sample
    domain_of:
    - Sample
    range: string
    required: false
    multivalued: false
  sample_storage_duration:
    name: sample_storage_duration
    description: duration for which sample was stored
    examples:
    - value: 2 days
    from_schema: https://ontology.ibisba.eu/mife/
    rank: 1000
    slot_uri: w3id:0000116
    alias: sample_storage_duration
    owner: Sample
    domain_of:
    - Sample
    range: float
    required: false
    multivalued: false
  sample_storage_location:
    name: sample_storage_location
    description: location at which sample was stored, usually name of a specific freezer/room
    examples:
    - value: room 022
    from_schema: https://ontology.ibisba.eu/mife/
    rank: 1000
    slot_uri: w3id:0000755
    alias: sample_storage_location
    owner: Sample
    domain_of:
    - Sample
    range: string
    required: false
    multivalued: false
  sample_storage_temperature:
    name: sample_storage_temperature
    description: temperature at which sample was stored
    examples:
    - value: -80 degrees celsius
    from_schema: https://ontology.ibisba.eu/mife/
    rank: 1000
    slot_uri: w3id:0000110
    alias: sample_storage_temperature
    owner: Sample
    domain_of:
    - Sample
    range: float
    required: false
    multivalued: false
  sample_treatment:
    name: sample_treatment
    description: Treatment applied to the sample
    examples:
    - value: centrifugation, filtration and freezing of the supernatant
    from_schema: https://ontology.ibisba.eu/mife/
    rank: 1000
    slot_uri: mife:hasSampleTreatment
    alias: sample_treatment
    owner: Sample
    domain_of:
    - Sample
    range: string
    required: false
    multivalued: false
  sample_wet_mass:
    name: sample_wet_mass
    description: measurement of wet mass at the time of sample collection
    examples:
    - value: 0.23g
    from_schema: https://ontology.ibisba.eu/mife/
    rank: 1000
    slot_uri: obolibrary3:mass
    alias: sample_wet_mass
    owner: Sample
    domain_of:
    - Sample
    range: float
    required: false
    multivalued: false
  sample_dry_mass:
    name: sample_dry_mass
    description: measurement of dry mass at the time of sample collection
    examples:
    - value: 0.05g
    from_schema: https://ontology.ibisba.eu/mife/
    rank: 1000
    slot_uri: obolibrary3:mass
    alias: sample_dry_mass
    owner: Sample
    domain_of:
    - Sample
    range: float
    required: false
    multivalued: false
class_uri: mife:Sample