Class: MetabolomicsAnalysis

name: MetabolomicsAnalysis
in_subset:
- workflow subset
from_schema: https://w3id.org/nmdc/nmdc
is_a: WorkflowExecution
slots:
- has_calibration
- has_metabolite_identifications
slot_usage:
  id:
    name: id
    domain_of:
    - NamedThing
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:wfmb-{id_shoulder}-{id_blade}{id_version}$'
      interpolated: true
  was_informed_by:
    name: was_informed_by
    domain_of:
    - WorkflowExecution
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'
      interpolated: true
class_uri: nmdc:MetabolomicsAnalysis

name: MetabolomicsAnalysis
in_subset:
- workflow subset
from_schema: https://w3id.org/nmdc/nmdc
is_a: WorkflowExecution
slot_usage:
  id:
    name: id
    domain_of:
    - NamedThing
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:wfmb-{id_shoulder}-{id_blade}{id_version}$'
      interpolated: true
  was_informed_by:
    name: was_informed_by
    domain_of:
    - WorkflowExecution
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'
      interpolated: true
attributes:
  has_calibration:
    name: has_calibration
    description: a calibration instance associated with a process
    notes:
    - 'has_calibration slot will be removed from all WorkflowExecution classes but
      remain on the MassSpectrometry class after an ingest of the appropriate set
      has occurred.  Once this has occurred, this slot''s range can be updated to
      CalibrationInformation and class/slot definitions can move to nmdc.yaml.   See
      PR #29 in Berkeley schema.'
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: has_calibration
    owner: MetabolomicsAnalysis
    domain_of:
    - MassSpectrometry
    - MetabolomicsAnalysis
    - NomAnalysis
    range: string
    any_of:
    - range: CalibrationInformation
    - range: string
  has_metabolite_identifications:
    name: has_metabolite_identifications
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    multivalued: true
    alias: has_metabolite_identifications
    owner: MetabolomicsAnalysis
    domain_of:
    - MetabolomicsAnalysis
    range: MetaboliteIdentification
    inlined: true
    inlined_as_list: true
  ended_at_time:
    name: ended_at_time
    notes:
    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/
      It may not be complete, but it is good enough for now.'
    from_schema: https://w3id.org/nmdc/nmdc
    mappings:
    - prov:endedAtTime
    rank: 1000
    alias: ended_at_time
    owner: MetabolomicsAnalysis
    domain_of:
    - WorkflowExecution
    range: string
    pattern: ^([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$
  execution_resource:
    name: execution_resource
    description: The computing resource or facility where the workflow was executed.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: execution_resource
    owner: MetabolomicsAnalysis
    domain_of:
    - WorkflowExecution
    range: ExecutionResourceEnum
    required: true
  git_url:
    name: git_url
    description: The url that points to the exact github location of a workflow.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: git_url
    owner: MetabolomicsAnalysis
    domain_of:
    - WorkflowExecution
    range: string
    required: true
  started_at_time:
    name: started_at_time
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: started_at_time
    owner: MetabolomicsAnalysis
    domain_of:
    - WorkflowExecution
    range: string
    required: true
    pattern: ^([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$
  version:
    name: version
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: version
    owner: MetabolomicsAnalysis
    domain_of:
    - WorkflowExecution
    range: string
  was_informed_by:
    name: was_informed_by
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: was_informed_by
    owner: MetabolomicsAnalysis
    domain_of:
    - WorkflowExecution
    range: DataGeneration
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'
      interpolated: true
  has_input:
    name: has_input
    description: An input to a process.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    multivalued: true
    alias: has_input
    owner: MetabolomicsAnalysis
    domain_of:
    - PlannedProcess
    range: NamedThing
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'
      interpolated: true
  has_output:
    name: has_output
    description: An output from a process.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    multivalued: true
    alias: has_output
    owner: MetabolomicsAnalysis
    domain_of:
    - PlannedProcess
    range: NamedThing
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(dobj)-{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: MetabolomicsAnalysis
    domain_of:
    - PlannedProcess
    range: ProcessingInstitutionEnum
  protocol_link:
    name: protocol_link
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: protocol_link
    owner: MetabolomicsAnalysis
    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: MetabolomicsAnalysis
    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: MetabolomicsAnalysis
    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: MetabolomicsAnalysis
    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: MetabolomicsAnalysis
    domain_of:
    - PlannedProcess
    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: MetabolomicsAnalysis
    domain_of:
    - PlannedProcess
    range: FailureCategorization
    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: MetabolomicsAnalysis
    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}:wfmb-{id_shoulder}-{id_blade}{id_version}$'
      interpolated: true
  name:
    name: name
    description: A human readable label for an entity
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: name
    owner: MetabolomicsAnalysis
    domain_of:
    - PersonValue
    - NamedThing
    - Protocol
    range: string
  description:
    name: description
    description: a human-readable description of a thing
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    slot_uri: dcterms:description
    alias: description
    owner: MetabolomicsAnalysis
    domain_of:
    - ImageValue
    - NamedThing
    range: string
  alternative_identifiers:
    name: alternative_identifiers
    description: A list of alternative identifiers for the entity.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    multivalued: true
    alias: alternative_identifiers
    owner: MetabolomicsAnalysis
    domain_of:
    - MetaboliteIdentification
    - NamedThing
    range: uriorcurie
    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
  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: MetabolomicsAnalysis
    domain_of:
    - FunctionalAnnotationAggMember
    - MobilePhaseSegment
    - PortionOfSubstance
    - MagBin
    - MetaboliteIdentification
    - PeptideQuantification
    - ProteinQuantification
    - GenomeFeature
    - FunctionalAnnotation
    - AttributeValue
    - NamedThing
    - FailureCategorization
    - Protocol
    - CreditAssociation
    - Doi
    range: uriorcurie
    required: true
class_uri: nmdc:MetabolomicsAnalysis