Class: SubSamplingProcess
Separating a sample aliquot from the starting material for downstream activity.
__
classDiagram
class SubSamplingProcess
click SubSamplingProcess href "../SubSamplingProcess"
MaterialProcessing <|-- SubSamplingProcess
click MaterialProcessing href "../MaterialProcessing"
SubSamplingProcess : alternative_identifiers
SubSamplingProcess : contained_in
SubSamplingProcess --> "0..1" ContainerCategoryEnum : contained_in
click ContainerCategoryEnum href "../ContainerCategoryEnum"
SubSamplingProcess : container_size
SubSamplingProcess --> "0..1" QuantityValue : container_size
click QuantityValue href "../QuantityValue"
SubSamplingProcess : description
SubSamplingProcess : end_date
SubSamplingProcess : has_failure_categorization
SubSamplingProcess --> "*" FailureCategorization : has_failure_categorization
click FailureCategorization href "../FailureCategorization"
SubSamplingProcess : has_input
SubSamplingProcess --> "*" NamedThing : has_input
click NamedThing href "../NamedThing"
SubSamplingProcess : has_output
SubSamplingProcess --> "*" ProcessedSample : has_output
click ProcessedSample href "../ProcessedSample"
SubSamplingProcess : id
SubSamplingProcess : instrument_used
SubSamplingProcess --> "*" Instrument : instrument_used
click Instrument href "../Instrument"
SubSamplingProcess : mass
SubSamplingProcess --> "0..1" QuantityValue : mass
click QuantityValue href "../QuantityValue"
SubSamplingProcess : name
SubSamplingProcess : processing_institution
SubSamplingProcess --> "0..1" ProcessingInstitutionEnum : processing_institution
click ProcessingInstitutionEnum href "../ProcessingInstitutionEnum"
SubSamplingProcess : protocol_link
SubSamplingProcess --> "0..1" Protocol : protocol_link
click Protocol href "../Protocol"
SubSamplingProcess : qc_comment
SubSamplingProcess : qc_status
SubSamplingProcess --> "0..1" StatusEnum : qc_status
click StatusEnum href "../StatusEnum"
SubSamplingProcess : sampled_portion
SubSamplingProcess --> "*" SamplePortionEnum : sampled_portion
click SamplePortionEnum href "../SamplePortionEnum"
SubSamplingProcess : start_date
SubSamplingProcess : temperature
SubSamplingProcess --> "0..1" QuantityValue : temperature
click QuantityValue href "../QuantityValue"
SubSamplingProcess : type
SubSamplingProcess : volume
SubSamplingProcess --> "0..1" QuantityValue : volume
click QuantityValue href "../QuantityValue"
Inheritance
- NamedThing
- PlannedProcess
- MaterialProcessing
- SubSamplingProcess
- MaterialProcessing
- PlannedProcess
Slots
Name | Cardinality and Range | Description | Inheritance |
---|---|---|---|
container_size | 0..1 QuantityValue |
The volume of the container an analyte is stored in or an activity takes plac... | direct |
contained_in | 0..1 ContainerCategoryEnum |
A type of container | direct |
temperature | 0..1 QuantityValue |
The value of a temperature measurement or temperature used in a process | direct |
volume | 0..1 QuantityValue |
The output volume of the SubSampling Process | direct |
mass | 0..1 QuantityValue |
The output mass of the SubSampling Process | direct |
sampled_portion | * SamplePortionEnum |
The portion of the sample that is taken for downstream activity | direct |
instrument_used | * Instrument |
What instrument was used during DataGeneration or MaterialProcessing | MaterialProcessing |
has_input | * NamedThing or Biosample or ProcessedSample |
An input to a process | PlannedProcess |
has_output | * ProcessedSample |
The subsample | PlannedProcess |
processing_institution | 0..1 ProcessingInstitutionEnum |
The organization that processed the sample | PlannedProcess |
protocol_link | 0..1 Protocol |
PlannedProcess | |
start_date | 0..1 String |
The date on which any process or activity was started | PlannedProcess |
end_date | 0..1 String |
The date on which any process or activity was ended | PlannedProcess |
qc_status | 0..1 StatusEnum |
Stores information about the result of a process (ie the process of sequencin... | PlannedProcess |
qc_comment | 0..1 String |
Slot to store additional comments about laboratory or workflow output | PlannedProcess |
has_failure_categorization | * FailureCategorization |
PlannedProcess | |
id | 1 Uriorcurie |
A unique identifier for a thing | NamedThing |
name | 0..1 String |
A human readable label for an entity | NamedThing |
description | 0..1 String |
a human-readable description of a thing | NamedThing |
alternative_identifiers | * Uriorcurie |
A list of alternative identifiers for the entity | NamedThing |
type | 1 Uriorcurie |
the class_uri of the class that has been instantiated | NamedThing |
Identifier and Mapping Information
Schema Source
- from schema: https://w3id.org/nmdc/nmdc
Mappings
Mapping Type | Mapped Value |
---|---|
self | nmdc:SubSamplingProcess |
native | nmdc:SubSamplingProcess |
related | OBI:0000744 |
LinkML Source
Direct
name: SubSamplingProcess
description: 'Separating a sample aliquot from the starting material for downstream
activity.
'
notes:
- A subsample may be (a) a portion of the sample obtained by selection or division;
(b) an individual unit of the lot taken as part of the sample; (c) the final unit
of multistage sampling. The term 'subsample' is used either in the sense of a 'sample
of a sample' or as a synonym for 'unit'. In practice, the meaning is usually apparent
from the context or is defined.
- TODO - Montana to visit slot descriptions
from_schema: https://w3id.org/nmdc/nmdc
related_mappings:
- OBI:0000744
contributors:
- ORCID:0009-0001-1555-1601
- ORCID:0000-0002-8683-0050
- ORCID:0000-0001-9076-6066
- ORCID:0009-0008-4013-7737
is_a: MaterialProcessing
slots:
- container_size
- contained_in
- temperature
- volume
- mass
- sampled_portion
slot_usage:
id:
name: id
domain_of:
- NamedThing
required: true
structured_pattern:
syntax: '{id_nmdc_prefix}:subspr-{id_shoulder}-{id_blade}$'
interpolated: true
volume:
name: volume
description: The output volume of the SubSampling Process.
domain_of:
- Extraction
- SubSamplingProcess
- FiltrationProcess
- MobilePhaseSegment
- PortionOfSubstance
mass:
name: mass
description: The output mass of the SubSampling Process.
domain_of:
- SubSamplingProcess
- PortionOfSubstance
has_input:
name: has_input
domain_of:
- PlannedProcess
structured_pattern:
syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'
interpolated: true
any_of:
- range: Biosample
- range: ProcessedSample
has_output:
name: has_output
description: The subsample.
domain_of:
- PlannedProcess
range: ProcessedSample
structured_pattern:
syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'
interpolated: true
class_uri: nmdc:SubSamplingProcess
Induced
name: SubSamplingProcess
description: 'Separating a sample aliquot from the starting material for downstream
activity.
'
notes:
- A subsample may be (a) a portion of the sample obtained by selection or division;
(b) an individual unit of the lot taken as part of the sample; (c) the final unit
of multistage sampling. The term 'subsample' is used either in the sense of a 'sample
of a sample' or as a synonym for 'unit'. In practice, the meaning is usually apparent
from the context or is defined.
- TODO - Montana to visit slot descriptions
from_schema: https://w3id.org/nmdc/nmdc
related_mappings:
- OBI:0000744
contributors:
- ORCID:0009-0001-1555-1601
- ORCID:0000-0002-8683-0050
- ORCID:0000-0001-9076-6066
- ORCID:0009-0008-4013-7737
is_a: MaterialProcessing
slot_usage:
id:
name: id
domain_of:
- NamedThing
required: true
structured_pattern:
syntax: '{id_nmdc_prefix}:subspr-{id_shoulder}-{id_blade}$'
interpolated: true
volume:
name: volume
description: The output volume of the SubSampling Process.
domain_of:
- Extraction
- SubSamplingProcess
- FiltrationProcess
- MobilePhaseSegment
- PortionOfSubstance
mass:
name: mass
description: The output mass of the SubSampling Process.
domain_of:
- SubSamplingProcess
- PortionOfSubstance
has_input:
name: has_input
domain_of:
- PlannedProcess
structured_pattern:
syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'
interpolated: true
any_of:
- range: Biosample
- range: ProcessedSample
has_output:
name: has_output
description: The subsample.
domain_of:
- PlannedProcess
range: ProcessedSample
structured_pattern:
syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'
interpolated: true
attributes:
container_size:
name: container_size
description: The volume of the container an analyte is stored in or an activity
takes place in
from_schema: https://w3id.org/nmdc/nmdc
contributors:
- ORCID:0009-0001-1555-1601
- ORCID:0000-0002-8683-0050
rank: 1000
alias: container_size
owner: SubSamplingProcess
domain_of:
- SubSamplingProcess
- FiltrationProcess
range: QuantityValue
contained_in:
name: contained_in
description: A type of container.
examples:
- value: test tube
- value: falcon tube
- value: whirlpak
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: contained_in
owner: SubSamplingProcess
domain_of:
- SubSamplingProcess
- StorageProcess
range: ContainerCategoryEnum
temperature:
name: temperature
description: The value of a temperature measurement or temperature used in a process.
notes:
- Not to be confused with the MIXS:0000113
from_schema: https://w3id.org/nmdc/nmdc
contributors:
- ORCID:0009-0001-1555-1601
- ORCID:0000-0002-8683-0050
rank: 1000
alias: temperature
owner: SubSamplingProcess
domain_of:
- ChromatographyConfiguration
- SubSamplingProcess
- StorageProcess
- ChromatographicSeparationProcess
- DissolvingProcess
- ChemicalConversionProcess
range: QuantityValue
volume:
name: volume
description: The output volume of the SubSampling Process.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: volume
owner: SubSamplingProcess
domain_of:
- Extraction
- SubSamplingProcess
- FiltrationProcess
- MobilePhaseSegment
- PortionOfSubstance
range: QuantityValue
mass:
name: mass
description: The output mass of the SubSampling Process.
title: mass
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: mass
owner: SubSamplingProcess
domain_of:
- SubSamplingProcess
- PortionOfSubstance
range: QuantityValue
sampled_portion:
name: sampled_portion
description: The portion of the sample that is taken for downstream activity.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: sampled_portion
owner: SubSamplingProcess
domain_of:
- SubSamplingProcess
range: SamplePortionEnum
multivalued: true
instrument_used:
name: instrument_used
description: What instrument was used during DataGeneration or MaterialProcessing.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: instrument_used
owner: SubSamplingProcess
domain_of:
- MaterialProcessing
- DataGeneration
range: Instrument
multivalued: true
has_input:
name: has_input
description: An input to a process.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: has_input
owner: SubSamplingProcess
domain_of:
- PlannedProcess
range: NamedThing
multivalued: true
structured_pattern:
syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'
interpolated: true
any_of:
- range: Biosample
- range: ProcessedSample
has_output:
name: has_output
description: The subsample.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: has_output
owner: SubSamplingProcess
domain_of:
- PlannedProcess
range: ProcessedSample
multivalued: true
structured_pattern:
syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'
interpolated: true
processing_institution:
name: processing_institution
description: The organization that processed the sample.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: processing_institution
owner: SubSamplingProcess
domain_of:
- PlannedProcess
range: ProcessingInstitutionEnum
protocol_link:
name: protocol_link
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: protocol_link
owner: SubSamplingProcess
domain_of:
- PlannedProcess
- Study
range: Protocol
start_date:
name: start_date
description: The date on which any process or activity was started
todos:
- add date string validation pattern
comments:
- We are using string representations of dates until all components of our ecosystem
can handle ISO 8610 dates
- The date should be formatted as YYYY-MM-DD
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: start_date
owner: SubSamplingProcess
domain_of:
- PlannedProcess
range: string
end_date:
name: end_date
description: The date on which any process or activity was ended
todos:
- add date string validation pattern
comments:
- We are using string representations of dates until all components of our ecosystem
can handle ISO 8610 dates
- The date should be formatted as YYYY-MM-DD
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: end_date
owner: SubSamplingProcess
domain_of:
- PlannedProcess
range: string
qc_status:
name: qc_status
description: Stores information about the result of a process (ie the process
of sequencing a library may have for qc_status of 'fail' if not enough data
was generated)
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: qc_status
owner: SubSamplingProcess
domain_of:
- PlannedProcess
range: StatusEnum
qc_comment:
name: qc_comment
description: Slot to store additional comments about laboratory or workflow output.
For workflow output it may describe the particular workflow stage that failed.
(ie Failed at call-stage due to a malformed fastq file).
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: qc_comment
owner: SubSamplingProcess
domain_of:
- PlannedProcess
range: string
has_failure_categorization:
name: has_failure_categorization
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: has_failure_categorization
owner: SubSamplingProcess
domain_of:
- PlannedProcess
range: FailureCategorization
multivalued: true
inlined: true
inlined_as_list: true
id:
name: id
description: A unique identifier for a thing. Must be either a CURIE shorthand
for a URI or a complete URI
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
identifier: true
alias: id
owner: SubSamplingProcess
domain_of:
- NamedThing
range: uriorcurie
required: true
pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
structured_pattern:
syntax: '{id_nmdc_prefix}:subspr-{id_shoulder}-{id_blade}$'
interpolated: true
name:
name: name
description: A human readable label for an entity
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: name
owner: SubSamplingProcess
domain_of:
- PersonValue
- NamedThing
- Protocol
range: string
description:
name: description
description: a human-readable description of a thing
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
slot_uri: dcterms:description
alias: description
owner: SubSamplingProcess
domain_of:
- ImageValue
- NamedThing
range: string
alternative_identifiers:
name: alternative_identifiers
description: A list of alternative identifiers for the entity.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: alternative_identifiers
owner: SubSamplingProcess
domain_of:
- MetaboliteIdentification
- NamedThing
range: uriorcurie
multivalued: true
pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
type:
name: type
description: the class_uri of the class that has been instantiated
notes:
- replaces legacy nmdc:type slot
- makes it easier to read example data files
- required for polymorphic MongoDB collections
examples:
- value: nmdc:Biosample
- value: nmdc:Study
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://github.com/microbiomedata/nmdc-schema/issues/1048
- https://github.com/microbiomedata/nmdc-schema/issues/1233
- https://github.com/microbiomedata/nmdc-schema/issues/248
rank: 1000
slot_uri: rdf:type
designates_type: true
alias: type
owner: SubSamplingProcess
domain_of:
- EukEval
- FunctionalAnnotationAggMember
- MobilePhaseSegment
- PortionOfSubstance
- MagBin
- MetaboliteIdentification
- PeptideQuantification
- ProteinQuantification
- GenomeFeature
- FunctionalAnnotation
- AttributeValue
- NamedThing
- FailureCategorization
- Protocol
- CreditAssociation
- Doi
range: uriorcurie
required: true
class_uri: nmdc:SubSamplingProcess