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Class: BiosampleProcessing

A process that takes one or more biosamples as inputs and generates one or more biosamples as outputs. An example of an output includes samples cultivated from another sample.

URI: nmdc:BiosampleProcessing

classDiagram class BiosampleProcessing click BiosampleProcessing href "../BiosampleProcessing" PlannedProcess <|-- BiosampleProcessing click PlannedProcess href "../PlannedProcess" BiosampleProcessing <|-- Pooling click Pooling href "../Pooling" BiosampleProcessing <|-- LibraryPreparation click LibraryPreparation href "../LibraryPreparation" BiosampleProcessing : alternative_identifiers BiosampleProcessing : description BiosampleProcessing : designated_class BiosampleProcessing : end_date BiosampleProcessing : has_failure_categorization BiosampleProcessing --> "*" FailureCategorization : has_failure_categorization click FailureCategorization href "../FailureCategorization" BiosampleProcessing : has_input BiosampleProcessing --> "*" Biosample : has_input click Biosample href "../Biosample" BiosampleProcessing : has_output BiosampleProcessing --> "*" NamedThing : has_output click NamedThing href "../NamedThing" BiosampleProcessing : id BiosampleProcessing : instrument_name BiosampleProcessing : name BiosampleProcessing : processing_institution BiosampleProcessing --> "1" ProcessingInstitutionEnum : processing_institution click ProcessingInstitutionEnum href "../ProcessingInstitutionEnum" BiosampleProcessing : protocol_link BiosampleProcessing --> "1" Protocol : protocol_link click Protocol href "../Protocol" BiosampleProcessing : qc_comment BiosampleProcessing : qc_status BiosampleProcessing --> "1" StatusEnum : qc_status click StatusEnum href "../StatusEnum" BiosampleProcessing : start_date

Inheritance

Slots

Name Cardinality and Range Description Inheritance
has_input 0..*
Biosample		 An input to a process direct
designated_class 0..1
Uriorcurie		 PlannedProcess
end_date 0..1
String		 The date on which any process or activity was ended PlannedProcess
has_output 0..*
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

Aliases

  • material processing

Identifier and Mapping Information

Schema Source

Mappings

Mapping Type Mapped Value
self nmdc:BiosampleProcessing
native nmdc:BiosampleProcessing
broad OBI:0000094

LinkML Source

Direct

name: BiosampleProcessing
description: A process that takes one or more biosamples as inputs and generates one
  or more biosamples as outputs. An example of an output includes samples cultivated
  from another sample.
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- material processing
broad_mappings:
- OBI:0000094
is_a: PlannedProcess
slots:
- has_input
slot_usage:
  id:
    name: id
    domain_of:
    - Biosample
    - Study
    - NamedThing
    - Activity
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:bsmprc-{id_shoulder}-{id_blade}{id_version}{id_locus}'
      interpolated: true
  has_input:
    name: has_input
    domain_of:
    - BiosampleProcessing
    - OmicsProcessing
    - PlannedProcess
    - WorkflowExecutionActivity
    range: Biosample

Induced

name: BiosampleProcessing
description: A process that takes one or more biosamples as inputs and generates one
  or more biosamples as outputs. An example of an output includes samples cultivated
  from another sample.
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- material processing
broad_mappings:
- OBI:0000094
is_a: PlannedProcess
slot_usage:
  id:
    name: id
    domain_of:
    - Biosample
    - Study
    - NamedThing
    - Activity
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:bsmprc-{id_shoulder}-{id_blade}{id_version}{id_locus}'
      interpolated: true
  has_input:
    name: has_input
    domain_of:
    - BiosampleProcessing
    - OmicsProcessing
    - PlannedProcess
    - WorkflowExecutionActivity
    range: Biosample
attributes:
  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: BiosampleProcessing
    domain_of:
    - BiosampleProcessing
    - OmicsProcessing
    - PlannedProcess
    - WorkflowExecutionActivity
    range: Biosample
  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: BiosampleProcessing
    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: BiosampleProcessing
    domain_of:
    - PlannedProcess
    range: string
  has_output:
    name: has_output
    description: An output biosample to a processing step
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - output
    rank: 1000
    domain: NamedThing
    multivalued: true
    alias: has_output
    owner: BiosampleProcessing
    domain_of:
    - OmicsProcessing
    - PlannedProcess
    - WorkflowExecutionActivity
    range: NamedThing
  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: BiosampleProcessing
    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: BiosampleProcessing
    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: BiosampleProcessing
    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: BiosampleProcessing
    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: BiosampleProcessing
    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: BiosampleProcessing
    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: BiosampleProcessing
    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: BiosampleProcessing
    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}:bsmprc-{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: BiosampleProcessing
    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: BiosampleProcessing
    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: BiosampleProcessing
    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_\-\/\.,]*$