Class: ChemicalConversionProcess
A process that results in the interconversion of chemical species by a reaction to transform the reagents into products.
__
URI: nmdc:ChemicalConversionProcess
classDiagram
class ChemicalConversionProcess
click ChemicalConversionProcess href "../ChemicalConversionProcess"
MaterialProcessing <|-- ChemicalConversionProcess
click MaterialProcessing href "../MaterialProcessing"
ChemicalConversionProcess : alternative_identifiers
ChemicalConversionProcess : chemical_conversion_category
ChemicalConversionProcess --> "0..1" ChemicalConversionCategoryEnum : chemical_conversion_category
click ChemicalConversionCategoryEnum href "../ChemicalConversionCategoryEnum"
ChemicalConversionProcess : description
ChemicalConversionProcess : duration
ChemicalConversionProcess --> "0..1" QuantityValue : duration
click QuantityValue href "../QuantityValue"
ChemicalConversionProcess : end_date
ChemicalConversionProcess : has_failure_categorization
ChemicalConversionProcess --> "*" FailureCategorization : has_failure_categorization
click FailureCategorization href "../FailureCategorization"
ChemicalConversionProcess : has_input
ChemicalConversionProcess --> "*" NamedThing : has_input
click NamedThing href "../NamedThing"
ChemicalConversionProcess : has_output
ChemicalConversionProcess --> "*" ProcessedSample : has_output
click ProcessedSample href "../ProcessedSample"
ChemicalConversionProcess : id
ChemicalConversionProcess : instrument_used
ChemicalConversionProcess --> "*" Instrument : instrument_used
click Instrument href "../Instrument"
ChemicalConversionProcess : name
ChemicalConversionProcess : processing_institution
ChemicalConversionProcess --> "0..1" ProcessingInstitutionEnum : processing_institution
click ProcessingInstitutionEnum href "../ProcessingInstitutionEnum"
ChemicalConversionProcess : protocol_link
ChemicalConversionProcess --> "0..1" Protocol : protocol_link
click Protocol href "../Protocol"
ChemicalConversionProcess : qc_comment
ChemicalConversionProcess : qc_status
ChemicalConversionProcess --> "0..1" StatusEnum : qc_status
click StatusEnum href "../StatusEnum"
ChemicalConversionProcess : start_date
ChemicalConversionProcess : substances_used
ChemicalConversionProcess --> "*" PortionOfSubstance : substances_used
click PortionOfSubstance href "../PortionOfSubstance"
ChemicalConversionProcess : substances_volume
ChemicalConversionProcess --> "0..1" QuantityValue : substances_volume
click QuantityValue href "../QuantityValue"
ChemicalConversionProcess : temperature
ChemicalConversionProcess --> "0..1" QuantityValue : temperature
click QuantityValue href "../QuantityValue"
ChemicalConversionProcess : type
Inheritance
- NamedThing
- PlannedProcess
- MaterialProcessing
- ChemicalConversionProcess
- MaterialProcessing
- PlannedProcess
Slots
Name | Cardinality and Range | Description | Inheritance |
---|---|---|---|
chemical_conversion_category | 0..1 ChemicalConversionCategoryEnum |
The type of chemical conversion process | direct |
duration | 0..1 QuantityValue |
The elapsed time of an activity | direct |
temperature | 0..1 QuantityValue |
The value of a temperature measurement or temperature used in a process | direct |
substances_used | * PortionOfSubstance |
The substances that are combined to enable a ChemicalConversionProcess | direct |
substances_volume | 0..1 QuantityValue |
The volume of the combined substances that was included in a ChemicalConversi... | 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 |
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 |
Aliases
- chemical reaction
Comments
- The values of both has_reagents slot and has_input slot are considered the reagents of a chemical process.
Identifier and Mapping Information
Schema Source
- from schema: https://w3id.org/nmdc/nmdc
Mappings
Mapping Type | Mapped Value |
---|---|
self | nmdc:ChemicalConversionProcess |
native | nmdc:ChemicalConversionProcess |
exact | MISO:0000001 |
LinkML Source
Direct
name: ChemicalConversionProcess
description: 'A process that results in the interconversion of chemical species by
a reaction to transform the reagents into products.
'
comments:
- The values of both has_reagents slot and has_input slot are considered the reagents
of a chemical process.
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- chemical reaction
exact_mappings:
- MISO:0000001
contributors:
- ORCID:0009-0001-1555-1601
- ORCID:0000-0002-1368-8217
is_a: MaterialProcessing
slots:
- chemical_conversion_category
- duration
- temperature
- substances_used
- substances_volume
slot_usage:
id:
name: id
domain_of:
- NamedThing
required: true
structured_pattern:
syntax: '{id_nmdc_prefix}:chcpr-{id_shoulder}-{id_blade}$'
interpolated: true
class_uri: nmdc:ChemicalConversionProcess
Induced
name: ChemicalConversionProcess
description: 'A process that results in the interconversion of chemical species by
a reaction to transform the reagents into products.
'
comments:
- The values of both has_reagents slot and has_input slot are considered the reagents
of a chemical process.
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- chemical reaction
exact_mappings:
- MISO:0000001
contributors:
- ORCID:0009-0001-1555-1601
- ORCID:0000-0002-1368-8217
is_a: MaterialProcessing
slot_usage:
id:
name: id
domain_of:
- NamedThing
required: true
structured_pattern:
syntax: '{id_nmdc_prefix}:chcpr-{id_shoulder}-{id_blade}$'
interpolated: true
attributes:
chemical_conversion_category:
name: chemical_conversion_category
description: The type of chemical conversion process.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: chemical_conversion_category
owner: ChemicalConversionProcess
domain_of:
- ChemicalConversionProcess
range: ChemicalConversionCategoryEnum
duration:
name: duration
description: The elapsed time of an activity.
examples:
- value: JsonObj(has_numeric_value=2, has_unit='hours')
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: duration
owner: ChemicalConversionProcess
domain_of:
- MixingProcess
- DissolvingProcess
- ChemicalConversionProcess
- MobilePhaseSegment
range: QuantityValue
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: ChemicalConversionProcess
domain_of:
- ChromatographyConfiguration
- SubSamplingProcess
- StorageProcess
- ChromatographicSeparationProcess
- DissolvingProcess
- ChemicalConversionProcess
range: QuantityValue
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: ChemicalConversionProcess
domain_of:
- Extraction
- StorageProcess
- DissolvingProcess
- ChemicalConversionProcess
- MobilePhaseSegment
range: PortionOfSubstance
multivalued: true
inlined: true
inlined_as_list: true
substances_volume:
name: substances_volume
description: The volume of the combined substances that was included in a ChemicalConversionProcess.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: substances_volume
owner: ChemicalConversionProcess
domain_of:
- ChemicalConversionProcess
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: ChemicalConversionProcess
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: ChemicalConversionProcess
domain_of:
- PlannedProcess
range: NamedThing
multivalued: true
structured_pattern:
syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'
interpolated: true
any_of:
- range: Biosample
- range: ProcessedSample
has_output:
name: has_output
description: An output from a process.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: has_output
owner: ChemicalConversionProcess
domain_of:
- PlannedProcess
range: ProcessedSample
multivalued: true
structured_pattern:
syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'
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: ChemicalConversionProcess
domain_of:
- PlannedProcess
range: ProcessingInstitutionEnum
protocol_link:
name: protocol_link
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: protocol_link
owner: ChemicalConversionProcess
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: ChemicalConversionProcess
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: ChemicalConversionProcess
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: ChemicalConversionProcess
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: ChemicalConversionProcess
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: ChemicalConversionProcess
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: ChemicalConversionProcess
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}:chcpr-{id_shoulder}-{id_blade}$'
interpolated: true
name:
name: name
description: A human readable label for an entity
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: name
owner: ChemicalConversionProcess
domain_of:
- PersonValue
- NamedThing
- Protocol
range: string
description:
name: description
description: a human-readable description of a thing
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
slot_uri: dcterms:description
alias: description
owner: ChemicalConversionProcess
domain_of:
- ImageValue
- NamedThing
range: string
alternative_identifiers:
name: alternative_identifiers
description: A list of alternative identifiers for the entity.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: alternative_identifiers
owner: ChemicalConversionProcess
domain_of:
- MetaboliteIdentification
- NamedThing
range: uriorcurie
multivalued: true
pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
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: ChemicalConversionProcess
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:ChemicalConversionProcess