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Class: DissolvingProcess

A mixing step where a soluble component is mixed with a liquid component.

__

URI: nmdc:DissolvingProcess

duration
0..1
has_failure_categorization
*
has_input
*
has_output
*
instrument_used
*
processing_institution
0..1
protocol_link
0..1
qc_status
0..1
substances_used
*
temperature
0..1
DissolvingProcess
alternative_identifiers
description
duration
end_date
has_failure_categorization
has_input
has_output
id
instrument_used
name
processing_institution
protocol_link
qc_comment
qc_status
start_date
substances_used
temperature
type
MaterialProcessing
QuantityValue
FailureCategorization
Sample
ProcessedSample
Instrument
ProcessingInstitutionEnum
Protocol
StatusEnum
PortionOfSubstance

Inheritance

Slots

Name Cardinality and Range Description Inheritance
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
instrument_used *
Instrument
What instrument was used during DataGeneration or MaterialProcessing MaterialProcessing
has_input *
Sample
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

  • Solubilization

Identifier and Mapping Information

Schema Source

Mappings

Mapping Type Mapped Value
exact CHMO:0002773

LinkML Source

Direct

name: DissolvingProcess
description: 'A mixing step where a soluble component is mixed with a liquid component.

  '
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- Solubilization
exact_mappings:
- CHMO:0002773
contributors:
- ORCID:0009-0001-1555-1601
- ORCID:0000-0002-1368-8217
is_a: MaterialProcessing
slots:
- duration
- temperature
- substances_used
slot_usage:
  id:
    name: id
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:dispro-{id_shoulder}-{id_blade}$'
      interpolated: true
class_uri: nmdc:DissolvingProcess

Induced

name: DissolvingProcess
description: 'A mixing step where a soluble component is mixed with a liquid component.

  '
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- Solubilization
exact_mappings:
- CHMO:0002773
contributors:
- ORCID:0009-0001-1555-1601
- ORCID:0000-0002-1368-8217
is_a: MaterialProcessing
slot_usage:
  id:
    name: id
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:dispro-{id_shoulder}-{id_blade}$'
      interpolated: true
attributes:
  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: DissolvingProcess
    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: DissolvingProcess
    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: DissolvingProcess
    domain_of:
    - Extraction
    - StorageProcess
    - DissolvingProcess
    - ChemicalConversionProcess
    - MobilePhaseSegment
    range: PortionOfSubstance
    multivalued: true
    inlined: true
    inlined_as_list: 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: DissolvingProcess
    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
    aliases:
    - input
    rank: 1000
    alias: has_input
    owner: DissolvingProcess
    domain_of:
    - PlannedProcess
    range: Sample
    multivalued: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'
      interpolated: true
  has_output:
    name: has_output
    description: An output from a process.
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - output
    rank: 1000
    alias: has_output
    owner: DissolvingProcess
    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: DissolvingProcess
    domain_of:
    - PlannedProcess
    range: ProcessingInstitutionEnum
  protocol_link:
    name: protocol_link
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: protocol_link
    owner: DissolvingProcess
    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: DissolvingProcess
    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: DissolvingProcess
    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: DissolvingProcess
    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: DissolvingProcess
    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: DissolvingProcess
    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
    notes:
    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'
    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters
      will be accepted
    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked
      via per-class id slot usage assertions
    - minting authority shoulders should probably be enumerated and checked in the
      pattern
    examples:
    - value: nmdc:mgmag-00-x012.1_7_c1
      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248
    from_schema: https://w3id.org/nmdc/nmdc
    structured_aliases:
      workflow_execution_id:
        literal_form: workflow_execution_id
        predicate: NARROW_SYNONYM
        contexts:
        - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml
      data_object_id:
        literal_form: data_object_id
        predicate: NARROW_SYNONYM
        contexts:
        - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml
    rank: 1000
    identifier: true
    alias: id
    owner: DissolvingProcess
    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}:dispro-{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: DissolvingProcess
    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: DissolvingProcess
    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: DissolvingProcess
    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
    structured_aliases:
      workflow_execution_class:
        literal_form: workflow_execution_class
        predicate: NARROW_SYNONYM
        contexts:
        - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml
    rank: 1000
    slot_uri: rdf:type
    designates_type: true
    alias: type
    owner: DissolvingProcess
    domain_of:
    - EukEval
    - FunctionalAnnotationAggMember
    - PeptideQuantification
    - ProteinQuantification
    - MobilePhaseSegment
    - PortionOfSubstance
    - MagBin
    - MetaboliteIdentification
    - GenomeFeature
    - FunctionalAnnotation
    - AttributeValue
    - NamedThing
    - OntologyRelation
    - FailureCategorization
    - Protocol
    - CreditAssociation
    - Doi
    range: uriorcurie
    required: true
class_uri: nmdc:DissolvingProcess