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"
PlannedProcess <|-- Extraction
click PlannedProcess href "../PlannedProcess"
Extraction : alternative_identifiers
Extraction : description
Extraction : designated_class
Extraction : end_date
Extraction : extractant
Extraction --> "0..1" Solution : extractant
click Solution href "../Solution"
Extraction : extraction_method
Extraction --> "0..1" ExtractionTargetEnum : extraction_method
click ExtractionTargetEnum href "../ExtractionTargetEnum"
Extraction : extraction_target
Extraction --> "0..1" ExtractionTargetEnum : extraction_target
click ExtractionTargetEnum href "../ExtractionTargetEnum"
Extraction : has_failure_categorization
Extraction --> "0..*" 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..*" NamedThing : has_output
click NamedThing href "../NamedThing"
Extraction : id
Extraction : input_mass
Extraction --> "0..1" QuantityValue : input_mass
click QuantityValue href "../QuantityValue"
Extraction : instrument_name
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 : volume
Extraction --> "0..1" QuantityValue : volume
click QuantityValue href "../QuantityValue"
Inheritance
- NamedThing
- PlannedProcess
- Extraction
- PlannedProcess
Slots
Name | Cardinality and Range | Description | Inheritance |
---|---|---|---|
extractant | 0..1 Solution |
The active component(s) primarily responsible for transfer of a solute from o... | direct |
extraction_method | 0..1 ExtractionTargetEnum |
direct | |
extraction_target | 0..1 ExtractionTargetEnum |
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 |
designated_class | 0..1 Uriorcurie |
PlannedProcess | |
end_date | 0..1 String |
The date on which any process or activity was ended | PlannedProcess |
has_input | 1..* NamedThing |
An input to a process | PlannedProcess |
has_output | 1..* NamedThing |
An output biosample to a processing step | 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 |
instrument_name | 0..1 String |
The name of the instrument that was used for processing the sample | 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 | 0..* FailureCategorization |
PlannedProcess | |
id | 1..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 | 0..* Uriorcurie |
A list of alternative identifiers for the entity | NamedThing |
Usages
used by | used in | type | used |
---|---|---|---|
Database | extraction_set | range | Extraction |
Extraction | extractant | domain | Extraction |
Extraction | extraction_method | domain | Extraction |
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: PlannedProcess
slots:
- extractant
- extraction_method
- extraction_target
- input_mass
- volume
slot_usage:
has_input:
name: has_input
domain_of:
- BiosampleProcessing
- OmicsProcessing
- PlannedProcess
- WorkflowExecutionActivity
required: true
any_of:
- range: Biosample
- range: ProcessedSample
has_output:
name: has_output
domain_of:
- OmicsProcessing
- PlannedProcess
- WorkflowExecutionActivity
required: true
id:
name: id
domain_of:
- Biosample
- Study
- NamedThing
- Activity
required: true
structured_pattern:
syntax: '{id_nmdc_prefix}:extrp-{id_shoulder}-{id_blade}{id_version}{id_locus}'
interpolated: true
volume:
name: volume
description: The volume of the solvent/solute being used, not the input.
domain_of:
- Extraction
- Solution
- SubSamplingProcess
- FiltrationProcess
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: PlannedProcess
slot_usage:
has_input:
name: has_input
domain_of:
- BiosampleProcessing
- OmicsProcessing
- PlannedProcess
- WorkflowExecutionActivity
required: true
any_of:
- range: Biosample
- range: ProcessedSample
has_output:
name: has_output
domain_of:
- OmicsProcessing
- PlannedProcess
- WorkflowExecutionActivity
required: true
id:
name: id
domain_of:
- Biosample
- Study
- NamedThing
- Activity
required: true
structured_pattern:
syntax: '{id_nmdc_prefix}:extrp-{id_shoulder}-{id_blade}{id_version}{id_locus}'
interpolated: true
volume:
name: volume
description: The volume of the solvent/solute being used, not the input.
domain_of:
- Extraction
- Solution
- SubSamplingProcess
- FiltrationProcess
attributes:
extractant:
name: extractant
description: The active component(s) primarily responsible for transfer of a solute
from one phase to the other.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
domain: Extraction
alias: extractant
owner: Extraction
domain_of:
- Extraction
range: Solution
extraction_method:
name: extraction_method
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
domain: Extraction
alias: extraction_method
owner: Extraction
domain_of:
- Extraction
range: ExtractionTargetEnum
extraction_target:
name: extraction_target
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: extraction_target
owner: Extraction
domain_of:
- Extraction
range: ExtractionTargetEnum
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
rank: 1000
domain: PlannedProcess
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
domain: PlannedProcess
alias: volume
owner: Extraction
domain_of:
- Extraction
- Solution
- SubSamplingProcess
- FiltrationProcess
range: QuantityValue
designated_class:
name: designated_class
comments:
- required on all instances in a polymorphic Database slot like planned_process_set
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
designates_type: true
alias: designated_class
owner: Extraction
domain_of:
- PlannedProcess
range: uriorcurie
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
has_input:
name: has_input
description: An input to a process.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
domain: NamedThing
multivalued: true
alias: has_input
owner: Extraction
domain_of:
- BiosampleProcessing
- OmicsProcessing
- PlannedProcess
- WorkflowExecutionActivity
range: NamedThing
required: true
any_of:
- range: Biosample
- range: ProcessedSample
has_output:
name: has_output
description: An output biosample to a processing step
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
domain: NamedThing
multivalued: true
alias: has_output
owner: Extraction
domain_of:
- OmicsProcessing
- PlannedProcess
- WorkflowExecutionActivity
range: NamedThing
required: true
processing_institution:
name: processing_institution
description: The organization that processed the sample.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
domain: PlannedProcess
alias: processing_institution
owner: Extraction
domain_of:
- OmicsProcessing
- PlannedProcess
range: processing_institution_enum
protocol_link:
name: protocol_link
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
domain: PlannedProcess
alias: protocol_link
owner: Extraction
domain_of:
- PlannedProcess
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
instrument_name:
name: instrument_name
description: The name of the instrument that was used for processing the sample.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
domain: PlannedProcess
alias: instrument_name
owner: Extraction
domain_of:
- OmicsProcessing
- 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
- WorkflowExecutionActivity
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
- WorkflowExecutionActivity
range: string
has_failure_categorization:
name: has_failure_categorization
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
multivalued: true
alias: has_failure_categorization
owner: Extraction
domain_of:
- PlannedProcess
- WorkflowExecutionActivity
range: FailureCategorization
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:
- Biosample
- Study
- NamedThing
- Activity
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}{id_version}{id_locus}'
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:
- Protocol
- NamedThing
- PersonValue
- Activity
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:
- Study
- NamedThing
- ImageValue
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
multivalued: true
alias: alternative_identifiers
owner: Extraction
domain_of:
- Biosample
- Study
- NamedThing
- MetaboliteQuantification
range: uriorcurie
pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
class_uri: nmdc:Extraction