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Class: ChromatographicSeparationProcess

The process of using a selective partitioning of the analyte or interferent between two immiscible phases.

URI: nmdc:ChromatographicSeparationProcess

classDiagram class ChromatographicSeparationProcess click ChromatographicSeparationProcess href "../ChromatographicSeparationProcess" MaterialProcessing <|-- ChromatographicSeparationProcess click MaterialProcessing href "../MaterialProcessing" ChromatographicSeparationProcess : alternative_identifiers ChromatographicSeparationProcess : chromatographic_category ChromatographicSeparationProcess --> "0..1" ChromatographicCategoryEnum : chromatographic_category click ChromatographicCategoryEnum href "../ChromatographicCategoryEnum" ChromatographicSeparationProcess : description ChromatographicSeparationProcess : end_date ChromatographicSeparationProcess : has_failure_categorization ChromatographicSeparationProcess --> "*" FailureCategorization : has_failure_categorization click FailureCategorization href "../FailureCategorization" ChromatographicSeparationProcess : has_input ChromatographicSeparationProcess --> "*" NamedThing : has_input click NamedThing href "../NamedThing" ChromatographicSeparationProcess : has_output ChromatographicSeparationProcess --> "*" ProcessedSample : has_output click ProcessedSample href "../ProcessedSample" ChromatographicSeparationProcess : id ChromatographicSeparationProcess : instrument_used ChromatographicSeparationProcess --> "*" Instrument : instrument_used click Instrument href "../Instrument" ChromatographicSeparationProcess : name ChromatographicSeparationProcess : ordered_mobile_phases ChromatographicSeparationProcess --> "*" MobilePhaseSegment : ordered_mobile_phases click MobilePhaseSegment href "../MobilePhaseSegment" ChromatographicSeparationProcess : processing_institution ChromatographicSeparationProcess --> "0..1" ProcessingInstitutionEnum : processing_institution click ProcessingInstitutionEnum href "../ProcessingInstitutionEnum" ChromatographicSeparationProcess : protocol_link ChromatographicSeparationProcess --> "0..1" Protocol : protocol_link click Protocol href "../Protocol" ChromatographicSeparationProcess : qc_comment ChromatographicSeparationProcess : qc_status ChromatographicSeparationProcess --> "0..1" StatusEnum : qc_status click StatusEnum href "../StatusEnum" ChromatographicSeparationProcess : start_date ChromatographicSeparationProcess : stationary_phase ChromatographicSeparationProcess --> "0..1" StationaryPhaseEnum : stationary_phase click StationaryPhaseEnum href "../StationaryPhaseEnum" ChromatographicSeparationProcess : temperature ChromatographicSeparationProcess --> "0..1" QuantityValue : temperature click QuantityValue href "../QuantityValue" ChromatographicSeparationProcess : type

Inheritance

Slots

Name Cardinality and Range Description Inheritance
chromatographic_category 0..1
ChromatographicCategoryEnum
The type of chromatography used in a process direct
ordered_mobile_phases *
MobilePhaseSegment
The solution(s) that moves through a chromatography column direct
stationary_phase 0..1
StationaryPhaseEnum
The material the stationary phase is comprised of used in chromatography direct
temperature 0..1
QuantityValue
The value of a temperature measurement or temperature used in a process 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

Identifier and Mapping Information

Schema Source

Mappings

Mapping Type Mapped Value
self nmdc:ChromatographicSeparationProcess
native nmdc:ChromatographicSeparationProcess

LinkML Source

Direct

name: ChromatographicSeparationProcess
description: The process of using a selective partitioning of the analyte or interferent
  between two immiscible phases.
from_schema: https://w3id.org/nmdc/nmdc
contributors:
- ORCID:0009-0001-1555-1601
- ORCID:0000-0002-1368-8217
is_a: MaterialProcessing
slots:
- chromatographic_category
- ordered_mobile_phases
- stationary_phase
- temperature
slot_usage:
  id:
    name: id
    domain_of:
    - NamedThing
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:cspro-{id_shoulder}-{id_blade}$'
  has_input:
    name: has_input
    domain_of:
    - PlannedProcess
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'
      interpolated: true
    any_of:
    - range: Biosample
    - range: ProcessedSample
  has_output:
    name: has_output
    domain_of:
    - PlannedProcess
    range: ProcessedSample
    structured_pattern:
      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'
      interpolated: true
class_uri: nmdc:ChromatographicSeparationProcess

Induced

name: ChromatographicSeparationProcess
description: The process of using a selective partitioning of the analyte or interferent
  between two immiscible phases.
from_schema: https://w3id.org/nmdc/nmdc
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}:cspro-{id_shoulder}-{id_blade}$'
  has_input:
    name: has_input
    domain_of:
    - PlannedProcess
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'
      interpolated: true
    any_of:
    - range: Biosample
    - range: ProcessedSample
  has_output:
    name: has_output
    domain_of:
    - PlannedProcess
    range: ProcessedSample
    structured_pattern:
      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'
      interpolated: true
attributes:
  chromatographic_category:
    name: chromatographic_category
    description: The type of chromatography used in a process.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: chromatographic_category
    owner: ChromatographicSeparationProcess
    domain_of:
    - ChromatographyConfiguration
    - ChromatographicSeparationProcess
    range: ChromatographicCategoryEnum
  ordered_mobile_phases:
    name: ordered_mobile_phases
    description: The solution(s) that moves through a chromatography column.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    list_elements_ordered: true
    alias: ordered_mobile_phases
    owner: ChromatographicSeparationProcess
    domain_of:
    - ChromatographyConfiguration
    - ChromatographicSeparationProcess
    range: MobilePhaseSegment
    multivalued: true
    inlined: true
    inlined_as_list: true
  stationary_phase:
    name: stationary_phase
    description: The material the stationary phase is comprised of used in chromatography.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: stationary_phase
    owner: ChromatographicSeparationProcess
    domain_of:
    - ChromatographyConfiguration
    - ChromatographicSeparationProcess
    range: StationaryPhaseEnum
  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: ChromatographicSeparationProcess
    domain_of:
    - ChromatographyConfiguration
    - SubSamplingProcess
    - StorageProcess
    - ChromatographicSeparationProcess
    - DissolvingProcess
    - 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: ChromatographicSeparationProcess
    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: ChromatographicSeparationProcess
    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: ChromatographicSeparationProcess
    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: ChromatographicSeparationProcess
    domain_of:
    - PlannedProcess
    range: ProcessingInstitutionEnum
  protocol_link:
    name: protocol_link
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: protocol_link
    owner: ChromatographicSeparationProcess
    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: ChromatographicSeparationProcess
    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: ChromatographicSeparationProcess
    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: ChromatographicSeparationProcess
    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: ChromatographicSeparationProcess
    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: ChromatographicSeparationProcess
    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: ChromatographicSeparationProcess
    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}:cspro-{id_shoulder}-{id_blade}$'
  name:
    name: name
    description: A human readable label for an entity
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: name
    owner: ChromatographicSeparationProcess
    domain_of:
    - PersonValue
    - NamedThing
    - Protocol
    range: string
  description:
    name: description
    description: a human-readable description of a thing
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    slot_uri: dcterms:description
    alias: description
    owner: ChromatographicSeparationProcess
    domain_of:
    - ImageValue
    - NamedThing
    range: string
  alternative_identifiers:
    name: alternative_identifiers
    description: A list of alternative identifiers for the entity.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: alternative_identifiers
    owner: ChromatographicSeparationProcess
    domain_of:
    - MetaboliteIdentification
    - NamedThing
    range: uriorcurie
    multivalued: true
    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
  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: ChromatographicSeparationProcess
    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:ChromatographicSeparationProcess