Class: Metagenome-Assembled Genome analysis activity (MagsAnalysisActivity)

name: MagsAnalysisActivity
description: A workflow execution activity that uses computational binning tools to
  group assembled contigs into genomes
title: Metagenome-Assembled Genome analysis activity
in_subset:
- workflow subset
from_schema: https://w3id.org/nmdc/nmdc
is_a: WorkflowExecutionActivity
slots:
- type
- input_contig_num
- binned_contig_num
- too_short_contig_num
- low_depth_contig_num
- unbinned_contig_num
- mags_list
slot_usage:
  id:
    name: id
    domain_of:
    - Biosample
    - Study
    - NamedThing
    - Activity
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:wfmag-{id_shoulder}-{id_blade}{id_version}{id_locus}'
      interpolated: true

name: MagsAnalysisActivity
description: A workflow execution activity that uses computational binning tools to
  group assembled contigs into genomes
title: Metagenome-Assembled Genome analysis activity
in_subset:
- workflow subset
from_schema: https://w3id.org/nmdc/nmdc
is_a: WorkflowExecutionActivity
slot_usage:
  id:
    name: id
    domain_of:
    - Biosample
    - Study
    - NamedThing
    - Activity
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:wfmag-{id_shoulder}-{id_blade}{id_version}{id_locus}'
      interpolated: true
attributes:
  type:
    name: type
    description: An optional string that specifies the type object.  This is used
      to allow for searches for different kinds of objects.
    deprecated: Due to confusion about what values are used for this slot, it is best
      not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.
      MAM removed designates_type and rdf:type slot uri 2022-11-30
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: type
    owner: MagsAnalysisActivity
    domain_of:
    - DataObject
    - Biosample
    - Study
    - OmicsProcessing
    - CreditAssociation
    - MagBin
    - GenomeFeature
    - WorkflowExecutionActivity
    - MetagenomeAssembly
    - MetagenomeAnnotationActivity
    - MetatranscriptomeAnnotationActivity
    - MetatranscriptomeActivity
    - MagsAnalysisActivity
    - ReadQcAnalysisActivity
    - ReadBasedTaxonomyAnalysisActivity
    range: string
    required: true
  input_contig_num:
    name: input_contig_num
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: input_contig_num
    owner: MagsAnalysisActivity
    domain_of:
    - MagsAnalysisActivity
    range: integer
  binned_contig_num:
    name: binned_contig_num
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: binned_contig_num
    owner: MagsAnalysisActivity
    domain_of:
    - MagsAnalysisActivity
    range: integer
  too_short_contig_num:
    name: too_short_contig_num
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: too_short_contig_num
    owner: MagsAnalysisActivity
    domain_of:
    - MagsAnalysisActivity
    range: integer
  low_depth_contig_num:
    name: low_depth_contig_num
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: low_depth_contig_num
    owner: MagsAnalysisActivity
    domain_of:
    - MagsAnalysisActivity
    range: integer
  unbinned_contig_num:
    name: unbinned_contig_num
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: unbinned_contig_num
    owner: MagsAnalysisActivity
    domain_of:
    - MagsAnalysisActivity
    range: integer
  mags_list:
    name: mags_list
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    domain: MagsAnalysisActivity
    multivalued: true
    alias: mags_list
    owner: MagsAnalysisActivity
    domain_of:
    - MagsAnalysisActivity
    range: MagBin
  execution_resource:
    name: execution_resource
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    domain: Activity
    alias: execution_resource
    owner: MagsAnalysisActivity
    domain_of:
    - WorkflowExecutionActivity
    range: string
    required: true
  git_url:
    name: git_url
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: git_url
    owner: MagsAnalysisActivity
    domain_of:
    - WorkflowExecutionActivity
    range: string
    required: true
  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: MagsAnalysisActivity
    domain_of:
    - BiosampleProcessing
    - OmicsProcessing
    - PlannedProcess
    - WorkflowExecutionActivity
    range: NamedThing
    required: true
  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: MagsAnalysisActivity
    domain_of:
    - OmicsProcessing
    - PlannedProcess
    - WorkflowExecutionActivity
    range: NamedThing
  part_of:
    name: part_of
    description: Links a resource to another resource that either logically or physically
      includes it.
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - is part of
    rank: 1000
    domain: NamedThing
    slot_uri: dcterms:isPartOf
    multivalued: true
    alias: part_of
    owner: MagsAnalysisActivity
    domain_of:
    - FieldResearchSite
    - Biosample
    - Study
    - OmicsProcessing
    - WorkflowExecutionActivity
    range: NamedThing
  version:
    name: version
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    domain: Activity
    alias: version
    owner: MagsAnalysisActivity
    domain_of:
    - WorkflowExecutionActivity
    - ReadQcAnalysisActivity
    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: MagsAnalysisActivity
    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: MagsAnalysisActivity
    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: MagsAnalysisActivity
    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: MagsAnalysisActivity
    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}:wfmag-{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: MagsAnalysisActivity
    domain_of:
    - Protocol
    - NamedThing
    - PersonValue
    - Activity
    range: string
  started_at_time:
    name: started_at_time
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    domain: Activity
    alias: started_at_time
    owner: MagsAnalysisActivity
    domain_of:
    - Activity
    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)?)?)?)?$
  ended_at_time:
    name: ended_at_time
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    domain: Activity
    alias: ended_at_time
    owner: MagsAnalysisActivity
    domain_of:
    - Activity
    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)?)?)?)?$
  was_informed_by:
    name: was_informed_by
    from_schema: https://w3id.org/nmdc/nmdc
    mappings:
    - prov:wasInformedBy
    rank: 1000
    domain: Activity
    alias: was_informed_by
    owner: MagsAnalysisActivity
    domain_of:
    - Activity
    range: Activity
  used:
    name: used
    from_schema: https://w3id.org/nmdc/nmdc
    mappings:
    - prov:used
    rank: 1000
    domain: Activity
    alias: used
    owner: MagsAnalysisActivity
    domain_of:
    - Activity
    range: string