Class: Extraction
A material separation in which a desired component of an input material is separated from the remainder.
URI: nmdc:Extraction
classDiagram
class Extraction
click Extraction href "../Extraction"
MaterialProcessing <|-- Extraction
click MaterialProcessing href "../MaterialProcessing"
Extraction : alternative_identifiers
Extraction : description
Extraction : end_date
Extraction : extraction_targets
Extraction --> "*" ExtractionTargetEnum : extraction_targets
click ExtractionTargetEnum href "../ExtractionTargetEnum"
Extraction : has_failure_categorization
Extraction --> "*" FailureCategorization : has_failure_categorization
click FailureCategorization href "../FailureCategorization"
Extraction : has_input
Extraction --> "1..*" NamedThing : has_input
click NamedThing href "../NamedThing"
Extraction : has_output
Extraction --> "1..*" ProcessedSample : has_output
click ProcessedSample href "../ProcessedSample"
Extraction : id
Extraction : input_mass
Extraction --> "0..1" QuantityValue : input_mass
click QuantityValue href "../QuantityValue"
Extraction : instrument_used
Extraction --> "*" Instrument : instrument_used
click Instrument href "../Instrument"
Extraction : name
Extraction : processing_institution
Extraction --> "0..1" ProcessingInstitutionEnum : processing_institution
click ProcessingInstitutionEnum href "../ProcessingInstitutionEnum"
Extraction : protocol_link
Extraction --> "0..1" Protocol : protocol_link
click Protocol href "../Protocol"
Extraction : qc_comment
Extraction : qc_status
Extraction --> "0..1" StatusEnum : qc_status
click StatusEnum href "../StatusEnum"
Extraction : start_date
Extraction : substances_used
Extraction --> "*" PortionOfSubstance : substances_used
click PortionOfSubstance href "../PortionOfSubstance"
Extraction : type
Extraction : volume
Extraction --> "0..1" QuantityValue : volume
click QuantityValue href "../QuantityValue"
Inheritance
- NamedThing
- PlannedProcess
- MaterialProcessing
- Extraction
- MaterialProcessing
- PlannedProcess
Slots
Name | Cardinality and Range | Description | Inheritance |
---|---|---|---|
substances_used | * PortionOfSubstance |
The substances that are combined to enable a ChemicalConversionProcess | direct |
extraction_targets | * ExtractionTargetEnum |
Provides the target biomolecule that has been separated from a sample during ... | direct |
input_mass | 0..1 QuantityValue |
Total mass of sample used in activity | direct |
volume | 0..1 QuantityValue |
The volume of the solvent/solute being used, not the input | direct |
instrument_used | * Instrument |
What instrument was used during DataGeneration or MaterialProcessing | MaterialProcessing |
has_input | 1..* NamedThing or Biosample or ProcessedSample |
An input to a process | PlannedProcess |
has_output | 1..* ProcessedSample |
An output from a process | 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:Extraction |
native | nmdc:Extraction |
exact | OBI:0302884 |
LinkML Source
Direct
name: Extraction
description: A material separation in which a desired component of an input material
is separated from the remainder.
from_schema: https://w3id.org/nmdc/nmdc
exact_mappings:
- OBI:0302884
is_a: MaterialProcessing
slots:
- substances_used
- extraction_targets
- input_mass
- volume
slot_usage:
has_input:
name: has_input
domain_of:
- PlannedProcess
required: true
structured_pattern:
syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'
interpolated: true
any_of:
- range: Biosample
- range: ProcessedSample
has_output:
name: has_output
domain_of:
- PlannedProcess
required: true
structured_pattern:
syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'
interpolated: true
id:
name: id
domain_of:
- NamedThing
required: true
structured_pattern:
syntax: '{id_nmdc_prefix}:extrp-{id_shoulder}-{id_blade}$'
interpolated: true
volume:
name: volume
description: The volume of the solvent/solute being used, not the input.
domain_of:
- Extraction
- SubSamplingProcess
- FiltrationProcess
- MobilePhaseSegment
- PortionOfSubstance
class_uri: nmdc:Extraction
Induced
name: Extraction
description: A material separation in which a desired component of an input material
is separated from the remainder.
from_schema: https://w3id.org/nmdc/nmdc
exact_mappings:
- OBI:0302884
is_a: MaterialProcessing
slot_usage:
has_input:
name: has_input
domain_of:
- PlannedProcess
required: true
structured_pattern:
syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'
interpolated: true
any_of:
- range: Biosample
- range: ProcessedSample
has_output:
name: has_output
domain_of:
- PlannedProcess
required: true
structured_pattern:
syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'
interpolated: true
id:
name: id
domain_of:
- NamedThing
required: true
structured_pattern:
syntax: '{id_nmdc_prefix}:extrp-{id_shoulder}-{id_blade}$'
interpolated: true
volume:
name: volume
description: The volume of the solvent/solute being used, not the input.
domain_of:
- Extraction
- SubSamplingProcess
- FiltrationProcess
- MobilePhaseSegment
- PortionOfSubstance
attributes:
substances_used:
name: substances_used
description: The substances that are combined to enable a ChemicalConversionProcess.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: substances_used
owner: Extraction
domain_of:
- Extraction
- StorageProcess
- DissolvingProcess
- ChemicalConversionProcess
- MobilePhaseSegment
range: PortionOfSubstance
multivalued: true
inlined: true
inlined_as_list: true
extraction_targets:
name: extraction_targets
description: Provides the target biomolecule that has been separated from a sample
during an extraction process.
notes:
- todos, remove nucl_acid_ext from OmicsProcessing (DataGeneration)
from_schema: https://w3id.org/nmdc/nmdc
narrow_mappings:
- NCIT:C177560
- MIXS:0000037
rank: 1000
alias: extraction_targets
owner: Extraction
domain_of:
- Extraction
range: ExtractionTargetEnum
multivalued: true
input_mass:
name: input_mass
description: Total mass of sample used in activity.
title: sample mass used
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample mass
- sample weight
exact_mappings:
- MS:1000004
narrow_mappings:
- MIXS:0000111
rank: 1000
alias: input_mass
owner: Extraction
domain_of:
- Extraction
range: QuantityValue
volume:
name: volume
description: The volume of the solvent/solute being used, not the input.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: volume
owner: Extraction
domain_of:
- Extraction
- SubSamplingProcess
- FiltrationProcess
- MobilePhaseSegment
- PortionOfSubstance
range: QuantityValue
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: Extraction
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: Extraction
domain_of:
- PlannedProcess
range: NamedThing
required: true
multivalued: true
structured_pattern:
syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'
interpolated: true
any_of:
- range: Biosample
- range: ProcessedSample
has_output:
name: has_output
description: An output from a process.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: has_output
owner: Extraction
domain_of:
- PlannedProcess
range: ProcessedSample
required: true
multivalued: true
structured_pattern:
syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'
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: Extraction
domain_of:
- PlannedProcess
range: ProcessingInstitutionEnum
protocol_link:
name: protocol_link
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: protocol_link
owner: Extraction
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: Extraction
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: Extraction
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: Extraction
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: Extraction
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: Extraction
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: Extraction
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}:extrp-{id_shoulder}-{id_blade}$'
interpolated: true
name:
name: name
description: A human readable label for an entity
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: name
owner: Extraction
domain_of:
- PersonValue
- NamedThing
- Protocol
range: string
description:
name: description
description: a human-readable description of a thing
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
slot_uri: dcterms:description
alias: description
owner: Extraction
domain_of:
- ImageValue
- NamedThing
range: string
alternative_identifiers:
name: alternative_identifiers
description: A list of alternative identifiers for the entity.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: alternative_identifiers
owner: Extraction
domain_of:
- MetaboliteIdentification
- NamedThing
range: uriorcurie
multivalued: true
pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
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: Extraction
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:Extraction